diff --git a/.gitignore b/.gitignore index abd2c763..97b02af0 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,13 @@ target/ src/test/resources/biocreative_chemprot/ src/test/resources/concepts+assertions/ /src/test/resources/biocreative_chemprot_small/ +/.clj-kondo/ +/node_modules/ +/.shadow-cljs/ +/resources/public/ +/.lein-failures +/.dir-locals.el +/.nrepl-port +/.idea/libraries/ +/.idea/knowtator.iml +/.attach_pid272926 diff --git a/.idea/encodings.xml b/.idea/encodings.xml index b26911bd..af673e73 100644 --- a/.idea/encodings.xml +++ b/.idea/encodings.xml @@ -2,5 +2,7 @@ + + \ No newline at end of file diff --git a/.idea/jarRepositories.xml b/.idea/jarRepositories.xml new file mode 100644 index 00000000..947ef884 --- /dev/null +++ b/.idea/jarRepositories.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/libraries/Maven__com_jgoodies_jgoodies_common_1_6_0.xml b/.idea/libraries/Maven__com_jgoodies_jgoodies_common_1_6_0.xml deleted file mode 100644 index 1183961c..00000000 --- a/.idea/libraries/Maven__com_jgoodies_jgoodies_common_1_6_0.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__com_jgoodies_jgoodies_looks_2_5_3.xml b/.idea/libraries/Maven__com_jgoodies_jgoodies_looks_2_5_3.xml deleted file mode 100644 index 94d282e3..00000000 --- a/.idea/libraries/Maven__com_jgoodies_jgoodies_looks_2_5_3.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__edu_stanford_protege_org_protege_common_5_0_0_beta_17.xml b/.idea/libraries/Maven__edu_stanford_protege_org_protege_common_5_0_0_beta_17.xml deleted file mode 100644 index 7cc1cffb..00000000 --- a/.idea/libraries/Maven__edu_stanford_protege_org_protege_common_5_0_0_beta_17.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__edu_stanford_protege_org_protege_editor_core_application_5_0_0_beta_17.xml b/.idea/libraries/Maven__edu_stanford_protege_org_protege_editor_core_application_5_0_0_beta_17.xml deleted file mode 100644 index d8fc52be..00000000 --- a/.idea/libraries/Maven__edu_stanford_protege_org_protege_editor_core_application_5_0_0_beta_17.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__edu_stanford_protege_org_protege_editor_owl_5_0_0_beta_17.xml b/.idea/libraries/Maven__edu_stanford_protege_org_protege_editor_owl_5_0_0_beta_17.xml deleted file mode 100644 index f621f006..00000000 --- a/.idea/libraries/Maven__edu_stanford_protege_org_protege_editor_owl_5_0_0_beta_17.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__edu_stanford_protege_org_protege_xmlcatalog_1_0_5.xml b/.idea/libraries/Maven__edu_stanford_protege_org_protege_xmlcatalog_1_0_5.xml deleted file mode 100644 index 602cd043..00000000 --- a/.idea/libraries/Maven__edu_stanford_protege_org_protege_xmlcatalog_1_0_5.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__edu_stanford_protege_protege_common_5_0_0_RC1.xml b/.idea/libraries/Maven__edu_stanford_protege_protege_common_5_0_0_RC1.xml deleted file mode 100644 index 847bd125..00000000 --- a/.idea/libraries/Maven__edu_stanford_protege_protege_common_5_0_0_RC1.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__edu_stanford_protege_protege_editor_core_5_0_0_RC1.xml b/.idea/libraries/Maven__edu_stanford_protege_protege_editor_core_5_0_0_RC1.xml deleted file mode 100644 index 143b30f9..00000000 --- a/.idea/libraries/Maven__edu_stanford_protege_protege_editor_core_5_0_0_RC1.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__edu_stanford_protege_protege_editor_owl_5_0_0_RC1.xml b/.idea/libraries/Maven__edu_stanford_protege_protege_editor_owl_5_0_0_RC1.xml deleted file mode 100644 index 0f420972..00000000 --- a/.idea/libraries/Maven__edu_stanford_protege_protege_editor_owl_5_0_0_RC1.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__edu_stanford_protege_protege_owlapi_extensions_3_2_6.xml b/.idea/libraries/Maven__edu_stanford_protege_protege_owlapi_extensions_3_2_6.xml deleted file mode 100644 index 893047d7..00000000 --- a/.idea/libraries/Maven__edu_stanford_protege_protege_owlapi_extensions_3_2_6.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__log4j_log4j_1_2_17.xml b/.idea/libraries/Maven__log4j_log4j_1_2_17.xml deleted file mode 100644 index e383c1bf..00000000 --- a/.idea/libraries/Maven__log4j_log4j_1_2_17.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__net_sourceforge_owlapi_jfact_1_0_0.xml b/.idea/libraries/Maven__net_sourceforge_owlapi_jfact_1_0_0.xml deleted file mode 100644 index a98c30bf..00000000 --- a/.idea/libraries/Maven__net_sourceforge_owlapi_jfact_1_0_0.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__org_apache_felix_org_apache_felix_framework_4_4_1.xml b/.idea/libraries/Maven__org_apache_felix_org_apache_felix_framework_4_4_1.xml deleted file mode 100644 index 568d2ce8..00000000 --- a/.idea/libraries/Maven__org_apache_felix_org_apache_felix_framework_4_4_1.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__org_apache_felix_org_apache_felix_main_4_4_1.xml b/.idea/libraries/Maven__org_apache_felix_org_apache_felix_main_4_4_1.xml deleted file mode 100644 index 045e14f3..00000000 --- a/.idea/libraries/Maven__org_apache_felix_org_apache_felix_main_4_4_1.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/libraries/Maven__xml_resolver_xml_resolver_1_2.xml b/.idea/libraries/Maven__xml_resolver_xml_resolver_1_2.xml deleted file mode 100644 index 3c94b040..00000000 --- a/.idea/libraries/Maven__xml_resolver_xml_resolver_1_2.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/uiDesigner.xml b/.idea/uiDesigner.xml index a6eb9493..d4c1b7df 100644 --- a/.idea/uiDesigner.xml +++ b/.idea/uiDesigner.xml @@ -152,6 +152,9 @@ + + + diff --git a/.idea/vcs.xml b/.idea/vcs.xml index 1d53947a..35eb1ddf 100644 --- a/.idea/vcs.xml +++ b/.idea/vcs.xml @@ -2,7 +2,5 @@ - - \ No newline at end of file diff --git a/.idea/workspace.xml b/.idea/workspace.xml index a2d7cdb0..416bb6f2 100644 --- a/.idea/workspace.xml +++ b/.idea/workspace.xml @@ -1,13 +1,39 @@ + + + + + + + + + + + + + + + + + + + + + + - - - - - - - \ No newline at end of file diff --git a/Knowtator-2.0.iml b/Knowtator-2.0.iml index c4c84312..2166d006 100644 --- a/Knowtator-2.0.iml +++ b/Knowtator-2.0.iml @@ -1,5 +1,25 @@ + + + + + + + + + + + + + + + + + + + + @@ -8,11 +28,15 @@ + + + + @@ -71,31 +95,27 @@ - + + + + - - - + + + + - - - - - - + + + - - - - - diff --git a/pom.xml b/pom.xml index aff3b57d..3ed3c4ab 100644 --- a/pom.xml +++ b/pom.xml @@ -53,28 +53,23 @@ edu.stanford.protege protege-common - 5.0.0-RC1 + 5.5.0 edu.stanford.protege protege-editor-core - 5.0.0-RC1 + 5.5.0 edu.stanford.protege protege-editor-owl - 5.0.0-RC1 + 5.5.0 org.slf4j slf4j-api 1.7.10 - - edu.stanford.protege - org.protege.editor.owl - 5.0.0-beta-17 - com.github.vlsi.mxgraph jgraphx diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/KnowtatorStandalone.java b/src/main/java/edu/ucdenver/ccp/knowtator/KnowtatorStandalone.java index f6d64545..2085d59e 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/KnowtatorStandalone.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/KnowtatorStandalone.java @@ -29,9 +29,7 @@ import java.awt.event.WindowEvent; import java.io.File; import java.io.IOException; -import javax.swing.JButton; import javax.swing.JFrame; -import javax.swing.JLabel; import javax.swing.UIManager; import javax.swing.UnsupportedLookAndFeelException; import org.apache.commons.cli.CommandLine; diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/iaa/Iaa.java b/src/main/java/edu/ucdenver/ccp/knowtator/iaa/Iaa.java index 4da384e6..ea71a509 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/iaa/Iaa.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/iaa/Iaa.java @@ -274,7 +274,7 @@ void setConceptAnnotations(Set conceptAnnotations) { for (ConceptAnnotation conceptAnnotation : conceptAnnotations) { String setName = conceptAnnotation.getAnnotator().getId(); - String annotationClass = conceptAnnotation.getOwlClassLabel(); + String annotationClass = conceptAnnotation.getOwlClassRendering(); annotationClasses.add(annotationClass); // throw exception here if there is a setName in the conceptAnnotations // that was not passed in. @@ -290,7 +290,7 @@ void setConceptAnnotations(Set conceptAnnotations) { class2AnnotationsMap.put(setName, classAnnotations); for (ConceptAnnotation setConceptAnnotation : setConceptAnnotations) { - String annotationClass = setConceptAnnotation.getOwlClassLabel(); + String annotationClass = setConceptAnnotation.getOwlClassRendering(); if (!classAnnotations.containsKey(annotationClass)) { classAnnotations.put(annotationClass, new HashSet<>()); } @@ -506,7 +506,7 @@ private Set match( */ public Set getAnnotationsOfSameType( ConceptAnnotation conceptAnnotation, String compareSetName) { - String annotationClass = conceptAnnotation.getOwlClassLabel(); + String annotationClass = conceptAnnotation.getOwlClassRendering(); return safeReturn(class2AnnotationsMap.get(compareSetName).get(annotationClass)); } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/iaa/KnowtatorIaa.java b/src/main/java/edu/ucdenver/ccp/knowtator/iaa/KnowtatorIaa.java index 0705a025..14a223be 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/iaa/KnowtatorIaa.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/iaa/KnowtatorIaa.java @@ -31,30 +31,30 @@ import edu.ucdenver.ccp.knowtator.iaa.matcher.Matcher; import edu.ucdenver.ccp.knowtator.iaa.matcher.SpanMatcher; import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; -import edu.ucdenver.ccp.knowtator.model.collection.ConceptAnnotationCollection; -import edu.ucdenver.ccp.knowtator.model.collection.TextSourceCollection; import edu.ucdenver.ccp.knowtator.model.object.ConceptAnnotation; -import edu.ucdenver.ccp.knowtator.model.object.Profile; import edu.ucdenver.ccp.knowtator.model.object.TextSource; import java.io.File; import java.io.IOException; import java.io.PrintStream; +import java.util.Collection; import java.util.HashMap; +import java.util.HashSet; import java.util.Map; +import java.util.Optional; import java.util.Set; import java.util.stream.Collectors; -/** The type Knowtator iaa. */ +/** + * The type Knowtator iaa. + */ public class KnowtatorIaa { private final File outputDirectory; // KnowtatorFilter filter; - private final TextSourceCollection textSources; - // Project project; - private final KnowtatorModel controller; + private final KnowtatorModel model; // KnowtatorProjectUtil kpu; @@ -66,7 +66,7 @@ public class KnowtatorIaa { private final Map annotationTextNames; - private Map textSourceAnnotationsMap; + private Map> textSourceAnnotationsMap; private PrintStream html; @@ -76,28 +76,42 @@ public class KnowtatorIaa { * Instantiates a new Knowtator iaa. * * @param outputDirectory the output directory - * @param controller the controller + * @param model the model * @throws IaaException the iaa exception */ @SuppressWarnings("unused") - public KnowtatorIaa(File outputDirectory, KnowtatorModel controller) throws IaaException { + public KnowtatorIaa(File outputDirectory, KnowtatorModel model, + Collection textSources, + Collection profiles, + Collection owlClasses) throws IaaException { this.outputDirectory = outputDirectory; // this.filter = filter; - this.textSources = controller.getTextSources(); - this.controller = controller; + HashSet owlClasses1 = new HashSet<>(owlClasses); + this.model = model; annotationTexts = new HashMap<>(); annotationTextNames = new HashMap<>(); - initSetNames(); - initTextSourceAnnotations(); + setNames = new HashSet<>(profiles); + textSourceAnnotationsMap = new HashMap<>(); + textSources.stream() + .map(id -> model.getTextSources().get(id)) + .filter(Optional::isPresent) + .map(Optional::get) + .forEach(textSource -> { + + Collection conceptAnnotations = textSource.getConceptAnnotations().stream() + .filter(conceptAnnotation -> owlClasses1.contains(conceptAnnotation.getOwlClass())) + .collect(Collectors.toList()); + + textSourceAnnotationsMap.put(textSource, conceptAnnotations); + }); initHtml(); } private void initSetNames() { - setNames = controller.getProfiles().stream().map(Profile::getId).collect(Collectors.toSet()); - setNames.remove("Default"); + } private void initHtml() throws IaaException { @@ -110,7 +124,9 @@ private void initHtml() throws IaaException { } } - /** Close html. */ + /** + * Close html. + */ public void closeHtml() { html.println(""); html.println(""); @@ -118,13 +134,6 @@ public void closeHtml() { html.close(); } - private void initTextSourceAnnotations() { - textSourceAnnotationsMap = new HashMap<>(); - for (TextSource textSource : textSources) { - textSourceAnnotationsMap.put(textSource, textSource.getConceptAnnotations()); - } - } - /** * Run class iaa. * @@ -141,21 +150,20 @@ public void runClassIaa() throws IaaException { classIaa, classMatcher, outputDirectory, - textSources.size(), + textSourceAnnotationsMap.size(), annotationTexts, annotationTextNames); html.printf( "
  • %s
    • %n", classMatcher.getName(), classMatcher.getName()); - closeHtml(); } catch (Exception e) { throw new IaaException(e); } } private void runIaaWithMatcher(Matcher matcher, Iaa iaa) throws IaaException { - for (ConceptAnnotationCollection conceptAnnotationCollection : + for (Collection conceptAnnotationCollection : textSourceAnnotationsMap.values()) { - Set conceptAnnotations = conceptAnnotationCollection.getCollection(); + Set conceptAnnotations = new HashSet<>(conceptAnnotationCollection); iaa.setConceptAnnotations(conceptAnnotations); iaa.allwayIaa(matcher); iaa.pairwiseIaa(matcher); @@ -168,24 +176,26 @@ private void runIaaWithMatcher(Matcher matcher, Iaa iaa) throws IaaException { * @throws IaaException the iaa exception */ public void runSpanIaa() throws IaaException { - try { - SpanMatcher spanMatcher = new SpanMatcher(); - Iaa spanIaa = new Iaa(setNames); - runIaaWithMatcher(spanMatcher, spanIaa); + SpanMatcher spanMatcher = new SpanMatcher(); + Iaa spanIaa = new Iaa(setNames); + + runIaaWithMatcher(spanMatcher, spanIaa); + try { SpanMatcherHtml.printIaa( spanIaa, spanMatcher, outputDirectory, - textSources.size(), + textSourceAnnotationsMap.size(), annotationTexts, annotationTextNames); - html.printf( - "
  • %s
    • %n", spanMatcher.getName(), spanMatcher.getName()); - closeHtml(); - } catch (Exception e) { - throw new IaaException(e); + } catch (IOException e) { + e.printStackTrace(); } + html.printf( + "
  • %s
    • %n", + spanMatcher.getName(), + spanMatcher.getName()); } /** @@ -204,13 +214,12 @@ public void runClassAndSpanIaa() throws IaaException { classAndSpanIaa, classAndSpanMatcher, outputDirectory, - textSources.size(), + textSourceAnnotationsMap.size(), annotationTexts, annotationTextNames); html.printf( "
  • %s
    • %n", classAndSpanMatcher.getName(), classAndSpanMatcher.getName()); - closeHtml(); } catch (Exception e) { throw new IaaException(e); } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/iaa/html/Iaa2Html.java b/src/main/java/edu/ucdenver/ccp/knowtator/iaa/html/Iaa2Html.java index 9b5e9cf4..1e936047 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/iaa/html/Iaa2Html.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/iaa/html/Iaa2Html.java @@ -86,7 +86,7 @@ public static void printIaa( "This file is provided to facilitate cut-n-paste into a spreadsheet.%n" + "If you cannot directly copy the data below into a spreadsheet " + "without it all going into a single cell,%n" - + "then try copying to a text editor firstConceptAnnotation " + + "then try copying to a text editor first " + "and then copy it from there. " + "There is typically a 'paste special'%noption under the Edit menu that will " + "allow you to paste the copied data as text. This will also work.%n%n%n%n"); @@ -205,6 +205,9 @@ public static void printIaa( (double) classNontrivialMatches / ((double) classNontrivialMatches + (double) classNontrivialNonmatches); + if (type.startsWith("<") && type.endsWith(">")) { + type = type.substring(1, type.length()- 2); + } if (matcher.returnsTrivials()) { html.printf( "%s%s%s%s%s%d%d%d%d%d%d%n", @@ -231,8 +234,15 @@ public static void printIaa( } else { html.printf( "%s%s%d%d%n", - type, percentageFormat.format(iaaScore), classMatches, classNonmatches); - tabular.printf("%s\t%d\t%d%n", type, classMatches, classNonmatches); + type, + percentageFormat.format(iaaScore), + classMatches, + classNonmatches); + tabular.printf( + "%s\t%d\t%d%n", + type, + classMatches, + classNonmatches); } } html.println(""); @@ -576,7 +586,7 @@ static Map> sortByType( sortedAnnotations.put(type, new HashSet<>()); } for (ConceptAnnotation conceptAnnotation : conceptAnnotations) { - String type = conceptAnnotation.getOwlClassLabel(); + String type = conceptAnnotation.getOwlClassRendering(); sortedAnnotations.get(type).add(conceptAnnotation); } return sortedAnnotations; diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/iaa/html/SpanMatcherHtml.java b/src/main/java/edu/ucdenver/ccp/knowtator/iaa/html/SpanMatcherHtml.java index ab31ccb1..6ab4b1b9 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/iaa/html/SpanMatcherHtml.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/iaa/html/SpanMatcherHtml.java @@ -29,6 +29,7 @@ import edu.ucdenver.ccp.knowtator.iaa.matcher.Matcher; import edu.ucdenver.ccp.knowtator.model.object.ConceptAnnotation; import java.io.File; +import java.io.IOException; import java.io.PrintStream; import java.text.NumberFormat; import java.util.ArrayList; @@ -50,7 +51,6 @@ public class SpanMatcherHtml { * @param numberOfDocs the number of docs * @param annotationTexts the annotation texts * @param annotationTextNames the annotation text names - * @throws Exception the exception */ public static void printIaa( Iaa iaa, @@ -58,8 +58,7 @@ public static void printIaa( File directory, int numberOfDocs, Map annotationTexts, - Map annotationTextNames) - throws Exception { + Map annotationTextNames) throws IOException { NumberFormat percentageFormat = NumberFormat.getPercentInstance(); percentageFormat.setMinimumFractionDigits(2); @@ -114,14 +113,22 @@ public static void printIaa( int classNonmatches = sortedAllwayNonmatches.get(type).size(); iaaScore = (double) classMatches / ((double) classMatches + (double) classNonmatches); + Map confusionCounts = errorMatrix(sortedAllwayMatches.get(type), matchSets); + if (type.startsWith("<") && type.endsWith(">")) { + type = type.substring(1, type.length()- 2); + } html.printf( "%s%s%d%d%n", type, percentageFormat.format(iaaScore), classMatches, classNonmatches); - Map confusionCounts = errorMatrix(sortedAllwayMatches.get(type), matchSets); + html.println(""); for (Map.Entry confusedClass : confusionCounts.entrySet()) { - html.printf(" %s=%d%n", confusedClass.getKey(), confusedClass.getValue()[0]); + String confusedType = confusedClass.getKey(); + if (confusedType.startsWith("<") && confusedType.endsWith(">")) { + confusedType = confusedType.substring(1, confusedType.length()- 2); + } + html.printf(" %s=%d%n", confusedType, confusedClass.getValue()[0]); } html.println(""); } @@ -172,7 +179,7 @@ private static Map errorMatrix( Set matchedConceptAnnotations = matchSets.get(match); for (ConceptAnnotation matchedConceptAnnotation : matchedConceptAnnotations) { if (!matchedConceptAnnotation.equals(match)) { - String annotationClass = matchedConceptAnnotation.getOwlClassLabel(); + String annotationClass = matchedConceptAnnotation.getOwlClassRendering(); if (!counts.containsKey(annotationClass)) { counts.put(annotationClass, new int[1]); } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/iaa/matcher/ClassAndSpanMatcher.java b/src/main/java/edu/ucdenver/ccp/knowtator/iaa/matcher/ClassAndSpanMatcher.java index 86225cc0..9db92b05 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/iaa/matcher/ClassAndSpanMatcher.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/iaa/matcher/ClassAndSpanMatcher.java @@ -95,7 +95,7 @@ private static Set matches( String compareSetName, Iaa iaa, Set excludeConceptAnnotations) { - String type = conceptAnnotation.getOwlClassLabel(); + String type = conceptAnnotation.getOwlClassRendering(); Set candidateConceptAnnotations = new HashSet<>(iaa.getExactlyOverlappingAnnotations(conceptAnnotation, compareSetName)); candidateConceptAnnotations.removeAll(excludeConceptAnnotations); @@ -106,7 +106,7 @@ private static Set matches( Set returnValues = new HashSet<>(); for (ConceptAnnotation candidateConceptAnnotation : candidateConceptAnnotations) { if (!excludeConceptAnnotations.contains(candidateConceptAnnotation) - && candidateConceptAnnotation.getOwlClassLabel().equals(type)) { + && candidateConceptAnnotation.getOwlClassRendering().equals(type)) { returnValues.add(candidateConceptAnnotation); return returnValues; } @@ -115,7 +115,7 @@ private static Set matches( } public String getName() { - return "Class and Span matcher"; + return "Class and span matcher"; } public String getDescription() { diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/io/brat/BratStandoffUtil.java b/src/main/java/edu/ucdenver/ccp/knowtator/io/brat/BratStandoffUtil.java index b6b5ddec..93843b1c 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/io/brat/BratStandoffUtil.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/io/brat/BratStandoffUtil.java @@ -24,6 +24,7 @@ package edu.ucdenver.ccp.knowtator.io.brat; +import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; import edu.ucdenver.ccp.knowtator.model.collection.ConceptAnnotationCollection; import edu.ucdenver.ccp.knowtator.model.object.AnnotationNode; @@ -245,7 +246,13 @@ private void readToConceptAnnotationCollection( annotation[1].split(StandoffTags.textBoundAnnotationTripleDelimiter)[0]; ConceptAnnotation newConceptAnnotation = new ConceptAnnotation( - textSource, annotation[0], owlClassID, profile, "identity", ""); + textSource, + annotation[0], + owlClassID, + profile, + "identity", + "", + BaseModel.DEFAULT_LAYERS); conceptAnnotationCollection.add(newConceptAnnotation); Map> map = new HashMap<>(); List list = new ArrayList<>(); @@ -407,7 +414,7 @@ private void writeFromConceptAnnotation( writer.append(String.format("%s\t%s ", conceptAnnotation.getBratID(), renderedOwlClassID)); - visualConfig.get("labels").put(renderedOwlClassID, conceptAnnotation.getOwlClassLabel()); + visualConfig.get("labels").put(renderedOwlClassID, conceptAnnotation.getOwlClassRendering()); visualConfig .get("drawing") .put( diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUField.java b/src/main/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUField.java index 2d3e958d..a39bf461 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUField.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUField.java @@ -25,5 +25,5 @@ package edu.ucdenver.ccp.knowtator.io.conll; public enum ConllUField { - ID, FORM, LEMMA, UPOS, XPOS, FEATS, HEAD, DEPREL, DEPS, MISC; + ID, FORM, LEMMA, UPOS, XPOS, FEATS, HEAD, DEPREL, DEPS, MISC } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUtil.java b/src/main/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUtil.java index 91e3b1eb..0f4ccd02 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUtil.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUtil.java @@ -36,16 +36,19 @@ import java.io.FileReader; import java.io.IOException; import java.util.ArrayList; +import java.util.Collections; import java.util.HashMap; +import java.util.HashSet; import java.util.List; import java.util.Map; +import java.util.Objects; import java.util.stream.Collectors; import org.apache.log4j.Logger; public class ConllUtil { private static final Logger log = Logger.getLogger(KnowtatorModel.class); - public void readToStructureAnnotations(KnowtatorModel model, File file) { + void readToStructureAnnotations(KnowtatorModel model, File file) { model .getTextSources() @@ -127,7 +130,7 @@ public void readToStructureAnnotations(KnowtatorModel model, File file) { GraphSpace graphSpace = new GraphSpace( textSource, String.format("%s-Sentence %d", textSource.getId(), i1)); - textSource.getStructureGraphSpaces().add(graphSpace); + textSource.add(graphSpace); List nodes = sentence1.stream() .map( @@ -139,16 +142,17 @@ public void readToStructureAnnotations(KnowtatorModel model, File file) { fields.get(ConllUField.DEPREL), model.getDefaultProfile(), null, - ""); + "", + new HashSet<>(Collections.singletonList("Structures"))); int[] range = findEnd.apply(fields.get(ConllUField.FORM)); - Span span = new Span(conceptAnnotation, null, range[0], range[1]); + Span span = new Span(conceptAnnotation, null, Objects.requireNonNull(range)[0], range[1]); conceptAnnotation.add(span); return conceptAnnotation; }) .peek( conceptAnnotation -> - textSource.getStructureAnnotations().add(conceptAnnotation)) + textSource.getConceptAnnotations().add(conceptAnnotation)) .map( conceptAnnotation -> new AnnotationNode(null, conceptAnnotation, 0, 0, graphSpace)) @@ -183,22 +187,23 @@ public void readToStructureAnnotations(KnowtatorModel model, File file) { }); } - private int checkRealText( - TextSource textSource, int[] start, String text, int start1, int end) { + private int checkRealText(TextSource textSource, int[] start, String text, int start1, int end) { String realText; realText = textSource.getContent(); if (end <= realText.length()) { realText = realText.substring(start1, end); end += realText.split("·").length - 1; - realText = textSource.getContent().substring(start1, end) + realText = + textSource + .getContent() + .substring(start1, end) .replace("(", "[") .replace(")", "]") .replace("}", "]") .replace("{", "[") .replace("″", "\""); - if (realText.replace("·", "").equals(text)) { start[0] = end + 1; return end; diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/KnowtatorXmlAttributes.java b/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/KnowtatorXmlAttributes.java index 4159c558..ff1c2fb2 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/KnowtatorXmlAttributes.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/KnowtatorXmlAttributes.java @@ -28,6 +28,7 @@ class KnowtatorXmlAttributes { /** The constant ID. */ public static final String ID = "id"; + static final String LAYER = "layer"; /** The Annotator. */ static final String ANNOTATOR = "annotator"; // also in OLD diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/KnowtatorXmlUtil.java b/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/KnowtatorXmlUtil.java index d5e22859..080117a4 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/KnowtatorXmlUtil.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/KnowtatorXmlUtil.java @@ -26,6 +26,7 @@ import com.mxgraph.model.mxGraphModel; import edu.ucdenver.ccp.knowtator.io.XmlUtil; +import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; import edu.ucdenver.ccp.knowtator.model.collection.ConceptAnnotationCollection; import edu.ucdenver.ccp.knowtator.model.collection.GraphSpaceCollection; @@ -42,6 +43,8 @@ import java.util.Arrays; import java.util.List; import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; import org.semanticweb.owlapi.model.OWLClass; import org.semanticweb.owlapi.model.OWLObjectProperty; import org.slf4j.Logger; @@ -91,22 +94,6 @@ public void readToTextSource(TextSource textSource, File file) { }); } - public void readStructuresToTextSource(TextSource textSource, File file) { - Optional parentOptional = getRootElement(file); - parentOptional.ifPresent( - parent -> { - for (Node documentNode : - KnowtatorXmlUtil.asList(parent.getElementsByTagName(KnowtatorXmlTags.DOCUMENT))) { - Element documentElement = (Element) documentNode; - readToTextSource( - textSource, - textSource.structureAnnotations, - textSource.structureGraphSpaces, - documentElement); - } - }); - } - private void readToTextSource( TextSource textSource, ConceptAnnotationCollection annotations, @@ -125,7 +112,7 @@ private void readToTextSource( * @param model the model * @param file the file */ - public void readToTextSourceCollection(KnowtatorModel model, File file, boolean isStructures) { + public void readToTextSourceCollection(KnowtatorModel model, File file) { Optional parentOptional = getRootElement(file); parentOptional.ifPresent( parent -> { @@ -141,19 +128,12 @@ public void readToTextSourceCollection(KnowtatorModel model, File file, boolean TextSource newTextSource = textSource.orElse(new TextSource(model, file, textFileName)); model.getTextSources().add(newTextSource); - if (isStructures) { - readToTextSource( - newTextSource, - newTextSource.structureAnnotations, - newTextSource.structureGraphSpaces, - documentElement); - } else { - readToTextSource( - newTextSource, - newTextSource.getConceptAnnotations(), - newTextSource.getGraphSpaces(), - documentElement); - } + + readToTextSource( + newTextSource, + newTextSource.getConceptAnnotations(), + newTextSource.getGraphSpaces(), + documentElement); } }); } @@ -180,13 +160,32 @@ private void readToConceptAnnotationCollection( Optional owlClass = model.getOwlClassById(owlClassID); + Set layers = + KnowtatorXmlUtil.asList( + annotationElement.getElementsByTagName(KnowtatorXmlAttributes.LAYER)) + .stream() + .map(node -> (Element) node) + .map(Node::getTextContent) + .collect(Collectors.toSet()); + if (owlClass.isPresent()) { owlClassID = owlClass.get().toStringID(); + } else { + log.warn( + String.format( + "OWL Class: %s not found for concept: %s", owlClassID, annotationID)); + model.addOWLClassNotFoundAnnotations(annotationID, owlClassID); } ConceptAnnotation newConceptAnnotation = new ConceptAnnotation( - textSource, annotationID, owlClassID, profile, type, motivation); + textSource, + annotationID, + owlClassID, + profile, + type, + motivation, + layers.size() == 0 ? BaseModel.DEFAULT_LAYERS : layers); readToConceptAnnotation(newConceptAnnotation, annotationElement); if (newConceptAnnotation.size() == 0) { return Optional.empty(); @@ -255,9 +254,7 @@ private void readToGraphSpace(GraphSpace graphSpace, Element parent) { Optional conceptAnnotation = graphSpace.getTextSource().getAnnotation(annotationID); if (conceptAnnotation.isPresent()) { - AnnotationNode newVertex = - new AnnotationNode(id, conceptAnnotation.get(), x, y, graphSpace); - graphSpace.addCellToGraph(newVertex); + graphSpace.addAnnotationNode(id, conceptAnnotation.get(), x, y); } else { log.info(String.format("Annotation could not be found %s", annotationID)); } @@ -388,7 +385,6 @@ public void writeFromTextSource(TextSource textSource) { File file = textSource.getSaveLocation(); Optional domOptional = startWrite(file); - File finalFile = file; domOptional.ifPresent( dom -> { Element root = dom.createElement(KnowtatorXmlTags.KNOWTATOR_PROJECT); @@ -403,31 +399,7 @@ public void writeFromTextSource(TextSource textSource) { writeFromGraphSpaceCollection(textSource.getGraphSpaces(), dom, textSourceElement); root.appendChild(textSourceElement); } finally { - XmlUtil.finishWritingXml(dom, finalFile); - } - }); - file = - new File( - textSource.getKnowtatorModel().getStructuresLocation(), - textSource.getSaveLocation().getName()); - Optional domOptional2 = startWrite(file); - File finalFile1 = file; - domOptional2.ifPresent( - dom -> { - Element root = dom.createElement(KnowtatorXmlTags.KNOWTATOR_PROJECT); - dom.appendChild(root); - try { - Element textSourceElement = dom.createElement(KnowtatorXmlTags.DOCUMENT); - textSourceElement.setAttribute(KnowtatorXmlAttributes.ID, textSource.getId()); - textSourceElement.setAttribute( - KnowtatorXmlAttributes.FILE, textSource.getTextFile().getName()); - writeFromConceptAnnotationCollection( - textSource.getStructureAnnotations(), dom, textSourceElement); - writeFromGraphSpaceCollection( - textSource.getStructureGraphSpaces(), dom, textSourceElement); - root.appendChild(textSourceElement); - } finally { - XmlUtil.finishWritingXml(dom, finalFile1); + XmlUtil.finishWritingXml(dom, file); } }); } @@ -521,7 +493,7 @@ private void writeFromConceptAnnotation( Element classElement = dom.createElement(KnowtatorXmlTags.CLASS); classElement.setAttribute(KnowtatorXmlAttributes.ID, conceptAnnotation.getOwlClass()); - classElement.setAttribute(KnowtatorXmlAttributes.LABEL, conceptAnnotation.getOwlClassLabel()); + classElement.setAttribute(KnowtatorXmlAttributes.LABEL, conceptAnnotation.getOwlClassRendering()); annotationElem.appendChild(classElement); conceptAnnotation.forEach(span -> writeFromSpan(span, dom, annotationElem)); diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/OldKnowtatorXmlUtil.java b/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/OldKnowtatorXmlUtil.java index c6f097b2..e57566d6 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/OldKnowtatorXmlUtil.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/io/knowtator/OldKnowtatorXmlUtil.java @@ -25,6 +25,7 @@ package edu.ucdenver.ccp.knowtator.io.knowtator; import edu.ucdenver.ccp.knowtator.io.XmlUtil; +import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; import edu.ucdenver.ccp.knowtator.model.collection.ConceptAnnotationCollection; import edu.ucdenver.ccp.knowtator.model.object.AnnotationNode; @@ -178,44 +179,48 @@ private void readToConceptAnnotationCollection( Profile profile = model.getProfile(profileID).orElse(model.getDefaultProfile()); Optional owlClass = model.getOwlClassById(owlClassID); - if (owlClass.isPresent()) { - ConceptAnnotation newConceptAnnotation = - new ConceptAnnotation( - textSource, - annotationID, - owlClass.get().toStringID(), - profile, - "identity", - ""); - if (conceptAnnotationCollection.containsID(annotationID)) { - newConceptAnnotation.setId(model.verifyId(null, newConceptAnnotation, false)); - } - readToConceptAnnotation(newConceptAnnotation, annotationElement); - // No need to keep annotations with no allSpanCollection - if (newConceptAnnotation.size() == 0) { - return Optional.empty(); - } else { - KnowtatorXmlUtil.asList( - classElement.getElementsByTagName(OldKnowtatorXmlTags.HAS_SLOT_MENTION)) - .stream() - .map(node -> (Element) node) - .forEach( - slotMentionElement -> { - String slotMentionID = - slotMentionElement.getAttribute(OldKnowtatorXmlAttributes.ID); - Element slotElement = slotToClassIdMap.get(slotMentionID); - if (slotElement != null) { - annotationToSlotMap.put(newConceptAnnotation, slotElement); - } - }); - return Optional.of(newConceptAnnotation); - } + if (owlClass.isPresent()) { + owlClassID = owlClass.get().toStringID(); } else { log.warn( String.format( "OWL Class: %s not found for concept: %s", owlClassID, annotationID)); + model.addOWLClassNotFoundAnnotations(annotationID, owlClassID); + } + + ConceptAnnotation newConceptAnnotation = + new ConceptAnnotation( + textSource, + annotationID, + owlClassID, + profile, + "identity", + "", + BaseModel.DEFAULT_LAYERS); + if (conceptAnnotationCollection.containsID(annotationID)) { + newConceptAnnotation.setId(model.verifyId(null, newConceptAnnotation, false)); + } + readToConceptAnnotation(newConceptAnnotation, annotationElement); + + // No need to keep annotations with no allSpanCollection + if (newConceptAnnotation.size() == 0) { return Optional.empty(); + } else { + KnowtatorXmlUtil.asList( + classElement.getElementsByTagName(OldKnowtatorXmlTags.HAS_SLOT_MENTION)) + .stream() + .map(node -> (Element) node) + .forEach( + slotMentionElement -> { + String slotMentionID = + slotMentionElement.getAttribute(OldKnowtatorXmlAttributes.ID); + Element slotElement = slotToClassIdMap.get(slotMentionID); + if (slotElement != null) { + annotationToSlotMap.put(newConceptAnnotation, slotElement); + } + }); + return Optional.of(newConceptAnnotation); } }) .forEach( diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/model/BaseModel.java b/src/main/java/edu/ucdenver/ccp/knowtator/model/BaseModel.java index d43e4578..7cd9b550 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/model/BaseModel.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/model/BaseModel.java @@ -38,6 +38,7 @@ import java.io.File; import java.io.IOException; import java.nio.file.Files; +import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.Map; @@ -52,14 +53,9 @@ /** The type Base model. */ public abstract class BaseModel extends UndoManager implements CaretListener, Savable { + public static final HashSet DEFAULT_LAYERS = + new HashSet<>(Collections.singletonList("Default")); private final File projectLocation; - private final File annotationsLocation; - private final File articlesLocation; - private final File profilesLocation; - final File structuresLocation; - - /** The Ontologies location. */ - final File ontologiesLocation; private final Set modelListeners; private final Map filters; @@ -76,8 +72,8 @@ public abstract class BaseModel extends UndoManager implements CaretListener, Sa /** The Loading. */ boolean loading; - private Boolean isStructureMode; private Set structureModeListeners; + private Set activeLayers; /** * Instantiates a new Base model. @@ -94,39 +90,43 @@ public abstract class BaseModel extends UndoManager implements CaretListener, Sa filters.put(FilterType.PROFILE, false); filters.put(FilterType.OWLCLASS, false); loading = false; - isStructureMode = false; + activeLayers = new HashSet<>(); + activeLayers.addAll(DEFAULT_LAYERS); selection = new Selection(0, 0); + this.projectLocation = validateProjectLocation(projectLocation); + + if (!this.projectLocation.exists()) { + Files.createDirectories(projectLocation.toPath()); + } + if (Files.list(this.projectLocation.toPath()) + .noneMatch(path -> path.toString().endsWith(".knowtator"))) { + Files.createFile( + new File(this.projectLocation, String.format("%s.knowtator", projectLocation.getName())) + .toPath()); + } + + Files.createDirectories(getArticlesLocation(this.projectLocation).toPath()); + Files.createDirectories(getAnnotationsLocation(this.projectLocation).toPath()); + Files.createDirectories(getProfilesLocation(this.projectLocation).toPath()); + Files.createDirectories(getOntologiesLocation(this.projectLocation).toPath()); + } + + public static File validateProjectLocation(File projectLocation) throws IOException { if (projectLocation.isFile()) { if (projectLocation.getName().endsWith(".knowtator")) { - projectLocation = new File(projectLocation.getParent()); + return new File(projectLocation.getParent()); } else { throw new IOException(); } + } else { + return projectLocation; } + } - - Files.createDirectories(projectLocation.toPath()); - - if (Files.list(projectLocation.toPath()) - .noneMatch(path -> path.toString().endsWith(".knowtator"))) { - Files.createFile( - new File(projectLocation, String.format("%s.knowtator", projectLocation.getName())) - .toPath()); - } - - this.projectLocation = projectLocation; - articlesLocation = new File(projectLocation, "Articles"); - annotationsLocation = new File(projectLocation, "Annotations"); - profilesLocation = (new File(projectLocation, "Profiles")); - ontologiesLocation = new File(projectLocation, "Ontologies"); - structuresLocation = new File(projectLocation, "Structures"); - Files.createDirectories(articlesLocation.toPath()); - Files.createDirectories(annotationsLocation.toPath()); - Files.createDirectories(profilesLocation.toPath()); - Files.createDirectories(ontologiesLocation.toPath()); - Files.createDirectories(structuresLocation.toPath()); + public static File getOntologiesLocation(File projectLocation) { + return new File(projectLocation, "Ontologies"); } @Override @@ -174,8 +174,9 @@ public int getNumberOfProfiles() { * * @return the annotations location */ - public File getAnnotationsLocation() { - return annotationsLocation; + public static File getAnnotationsLocation(File projectLocation) { + return new File(projectLocation, "Annotations"); + } /** @@ -230,7 +231,7 @@ public Profile getDefaultProfile() { public String verifyId(String id, ModelObject modelObject, boolean hasPriority) { String verifiedId = id; - if (hasPriority && idRegistry.keySet().contains(id)) { + if (hasPriority && idRegistry.containsKey(id)) { ModelObject mo = idRegistry.get(id); modelObject.setId(verifyId(id, mo, false)); } else { @@ -238,7 +239,7 @@ public String verifyId(String id, ModelObject modelObject, boolean hasPriority) while (verifiedId == null || verifiedId.equals("") - || idRegistry.keySet().contains(verifiedId)) { + || idRegistry.containsKey(verifiedId)) { if (modelObject instanceof TextBoundModelObject) { verifiedId = String.format( @@ -295,9 +296,10 @@ public void addProfile(Profile profile) { * Gets articles location. * * @return the articles location + * @param projectLocation project location */ - public File getArticlesLocation() { - return articlesLocation; + public static File getArticlesLocation(File projectLocation) { + return new File(projectLocation, "Articles"); } /** @@ -314,20 +316,17 @@ public Optional getSelectedConceptAnnotation() { } public Optional getSelectedGraphSpace() { - if (isStructureMode) { - return getSelectedTextSource().flatMap(TextSource::getSelectedStructureGraphSpace); - } else { - return getSelectedTextSource().flatMap(TextSource::getSelectedGraphSpace); - } + return getSelectedTextSource().flatMap(TextSource::getSelectedGraphSpace); } /** * Gets profiles location. * * @return the profiles location + * @param projectLocation project location */ - File getProfilesLocation() { - return profilesLocation; + public static File getProfilesLocation(File projectLocation) { + return new File(projectLocation, "Profiles"); } /** Dispose. */ @@ -383,8 +382,8 @@ public void setFilter(FilterType filterType, boolean isFilter) { modelListeners.forEach(ModelListener::filterChangedEvent); } - public void setStructureMode(Boolean isStructureMode) { - this.isStructureMode = isStructureMode; + public void addActiveLayer(String layer) { + activeLayers.add(layer); fireStructureModeChangedEvent(); } @@ -430,7 +429,16 @@ public void addStructureModeListener(StructureModeListener listener) { structureModeListeners.add(listener); } - public File getStructuresLocation() { - return structuresLocation; + public Set getActiveLayers() { + return activeLayers; + } + + public static File getArticlesLocation(File annotationFileLocation, File projectLocation) { + File file = new File(annotationFileLocation.getParentFile(), "Articles"); + if (file.exists()) { + return file; + } else { + return getArticlesLocation(projectLocation); + } } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/model/KnowtatorModel.java b/src/main/java/edu/ucdenver/ccp/knowtator/model/KnowtatorModel.java index bd720bdf..aeb15ad8 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/model/KnowtatorModel.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/model/KnowtatorModel.java @@ -36,6 +36,10 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.util.ArrayList; +import java.util.HashSet; +import java.util.List; +import java.util.Set; import org.apache.log4j.Logger; import org.protege.editor.owl.model.OWLWorkspace; @@ -49,6 +53,12 @@ public class KnowtatorModel extends OwlModel { private static final Logger log = Logger.getLogger(KnowtatorModel.class); + public List getOWLClassNotFoundAnnotations() { + return OWLClassNotFoundAnnotations; + } + + private List OWLClassNotFoundAnnotations; + /** * The constructor initializes all of the models and managers @param projectLocation the project * location. @@ -80,8 +90,13 @@ public void save() { } @Override - public void load() { - super.load(); + public void load(File projectLocation) { + try { + projectLocation = validateProjectLocation(projectLocation); + } catch (IOException e) { + e.printStackTrace(); + } + super.load(projectLocation); setLoading(true); @@ -91,43 +106,44 @@ public void load() { OldKnowtatorXmlUtil oldXmlUtil = new OldKnowtatorXmlUtil(); try { - Files.list(getProfilesLocation().toPath()) + Files.list(getProfilesLocation(projectLocation).toPath()) .filter(path -> path.toString().endsWith(".xml")) .map(Path::toFile) .forEach(file -> xmlUtil.readToProfileCollection(this, file)); - - Files.list(getArticlesLocation().toPath()) + } catch (IOException e) { + e.printStackTrace(); + } + try { + Files.list(getArticlesLocation(projectLocation).toPath()) .filter(path -> path.toString().endsWith(".txt")) .map(Path::toFile) .forEach( file -> { - TextSource newTextSource = new TextSource(this, null, file.getName()); + TextSource newTextSource = new TextSource(this, file, null); textSources.add(newTextSource); }); + } catch (IOException e) { + e.printStackTrace(); + } + try { log.info("Loading annotations"); - Files.list(getAnnotationsLocation().toPath()) + OWLClassNotFoundAnnotations = new ArrayList<>(); + Files.list(getAnnotationsLocation(projectLocation).toPath()) .filter(path -> path.toString().endsWith(".xml")) .map(Path::toFile) - .peek(file -> xmlUtil.readToTextSourceCollection(this, file, false)) + .peek(file -> xmlUtil.readToTextSourceCollection(this, file)) .forEach(file -> oldXmlUtil.readToTextSourceCollection(this, file)); - - log.info("Loading structures"); - Files.list(structuresLocation.toPath()) - .filter(path -> path.toString().endsWith(".xml")) - .map(Path::toFile) - .forEach(file -> xmlUtil.readToTextSourceCollection(this, file, true)); - Files.list(structuresLocation.toPath()) - .filter(path -> path.toString().endsWith(".conllu") || path.toString().endsWith(".conll")) - .map(Path::toFile) - .forEach(file -> conllUtil.readToStructureAnnotations(this, file)); - - profiles.first().ifPresent(profiles::setSelection); - textSources.first().ifPresent(textSources::setSelection); - } catch (IOException e) { e.printStackTrace(); } + profiles.first().ifPresent(profiles::setSelection); + textSources.first().ifPresent(textSources::setSelection); + + Set owlClasses = new HashSet<>(); + textSources.forEach(textSource -> textSource.getConceptAnnotations().forEach(conceptAnnotation -> owlClasses.add(conceptAnnotation.getOwlClass()))); + profiles.verifyHighlighters(owlClasses); + setLoading(false); } @@ -145,7 +161,7 @@ public void loadWithAppropriateFormat(File file) { switch (extension) { case "xml": KnowtatorXmlUtil xmlUtil = new KnowtatorXmlUtil(); - xmlUtil.readToTextSourceCollection(this, file, false); + xmlUtil.readToTextSourceCollection(this, file); break; case "ann": BratStandoffUtil standoffUtil = new BratStandoffUtil(); @@ -168,4 +184,8 @@ public void loadWithAppropriateFormat(File file) { public static void main(String[] args) { log.info("Knowtator"); } + + public void addOWLClassNotFoundAnnotations(String annotationID, String owlClassID) { + OWLClassNotFoundAnnotations.add(new String[]{annotationID, owlClassID}); + } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/model/OwlModel.java b/src/main/java/edu/ucdenver/ccp/knowtator/model/OwlModel.java index 82aa0824..e575bc83 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/model/OwlModel.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/model/OwlModel.java @@ -34,6 +34,7 @@ import java.nio.file.Files; import java.util.Arrays; import java.util.HashSet; +import java.util.List; import java.util.Optional; import java.util.Set; import java.util.stream.Collectors; @@ -45,14 +46,21 @@ import org.protege.editor.owl.model.OWLWorkspace; import org.protege.editor.owl.model.event.OWLModelManagerListener; import org.protege.editor.owl.model.selection.OWLSelectionModel; +import org.protege.editor.owl.model.selection.OWLSelectionModelListener; +import org.protege.editor.owl.ui.prefix.OWLEntityPrefixedNameRenderer; +import org.protege.editor.owl.ui.renderer.OWLEntityRendererImpl; +import org.protege.editor.owl.ui.renderer.OWLRendererPreferences; +import org.protege.editor.owl.ui.renderer.plugin.RendererPlugin; import org.protege.editor.owl.ui.search.SearchDialogPanel; import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.model.HasAnnotationPropertiesInSignature; import org.semanticweb.owlapi.model.IRI; import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom; import org.semanticweb.owlapi.model.OWLClass; import org.semanticweb.owlapi.model.OWLDataFactory; import org.semanticweb.owlapi.model.OWLEntity; import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLNamedObject; import org.semanticweb.owlapi.model.OWLObjectProperty; import org.semanticweb.owlapi.model.OWLOntology; import org.semanticweb.owlapi.model.OWLOntologyChangeListener; @@ -60,21 +68,24 @@ import org.semanticweb.owlapi.model.OWLOntologyManager; import org.semanticweb.owlapi.model.OWLOntologyStorageException; -/** The type Owl model. */ +/** + * The type Owl model. + */ public abstract class OwlModel extends BaseModel implements Serializable { @SuppressWarnings("unused") private static final Logger log = LogManager.getLogger(OwlModel.class); - private OWLOntologyManager owlOntologyManager; + private final OWLOntologyManager owlOntologyManager; @SuppressWarnings("OptionalUsedAsFieldOrParameterType") - private Optional owlWorkSpace; + private final Optional owlWorkSpace; + private List iris; /** * Instantiates a new Owl model. * * @param projectLocation the project location - * @param owlWorkspace the owl workspace + * @param owlWorkspace the owl workspace * @throws IOException the io exception */ OwlModel(File projectLocation, OWLWorkspace owlWorkspace) throws IOException { @@ -92,22 +103,26 @@ public abstract class OwlModel extends BaseModel implements Serializable { */ public Optional getOwlClassById(@Nonnull String classID) { if (owlWorkSpace.isPresent()) { - return owlWorkSpace.map( + return owlWorkSpace.flatMap( owlWorkspace -> - owlWorkspace.getOWLModelManager().getOWLEntityFinder().getOWLClass(classID)); + owlWorkspace.getOWLModelManager().getOWLEntityFinder().getEntities(IRI.create(classID)).stream() + .filter(owlEntity -> owlEntity instanceof OWLClass) + .map(owlEntity -> (OWLClass) owlEntity) + .findAny()); } else { for (OWLOntology ontology : owlOntologyManager.getOntologies()) { Optional owlClassOptional = ontology.getClassesInSignature().stream() .filter( owlClass -> - owlClass.getIRI().getShortForm().equals(classID) + owlClass.getIRI().toString().equals(classID) + || owlClass.getIRI().getShortForm().equals(classID) || ontology.getAnnotationAssertionAxioms(owlClass.getIRI()).stream() - .anyMatch( - owlAnnotationAssertionAxiom -> - getAnnotationLiteral(owlAnnotationAssertionAxiom) - .map(label -> label.equals(classID)) - .orElse(false))) + .anyMatch( + owlAnnotationAssertionAxiom -> + getAnnotationLiteral(owlAnnotationAssertionAxiom) + .map(label -> label.equals(classID)) + .orElse(false))) .findFirst(); if (owlClassOptional.isPresent()) { return owlClassOptional; @@ -269,11 +284,13 @@ public void searchForString(String stringToSearch) { }); } - /** Load. */ - public void load() { + /** + * Load. + */ + public void load(File projectLocation) { log.info("Loading ontologies"); try { - Files.list(ontologiesLocation.toPath()) + Files.list(getOntologiesLocation(projectLocation).toPath()) .filter(path -> path.toString().endsWith(".owl")) .map(path -> path.toFile().toURI().toString()) .forEach( @@ -377,6 +394,15 @@ public void addOwlModelManagerListener(OWLModelManagerListener listener) { owlWorkSpace.ifPresent(owlWorkSpace -> owlWorkSpace.getOWLModelManager().addListener(listener)); } + /** + * Add owl model manager listener. + * + * @param listener the listener + */ + public void addOwlSelectionModelListener(OWLSelectionModelListener listener) { + owlWorkSpace.ifPresent(owlWorkSpace -> owlWorkSpace.getOWLSelectionModel().addListener(listener)); + } + public void setSelectedOwlClass(String owlClass) { setSelectedOwlEntity(owlOntologyManager.getOWLDataFactory().getOWLClass(IRI.create(owlClass))); } @@ -411,4 +437,50 @@ private OWLDataFactory getOwlDataFactory() { public void setSelectedOwlObjectProperty(String property) { setSelectedOwlEntity(getOwlDataFactory().getOWLObjectProperty(IRI.create(property))); } + + public IRI[] getOWLAnnotationProperties() { + return owlWorkSpace + .map(owlWorkspace -> owlWorkspace.getOWLModelManager().getOntologies().stream() + .map(HasAnnotationPropertiesInSignature::getAnnotationPropertiesInSignature) + .flatMap(Set::stream) + .map(OWLNamedObject::getIRI) + .toArray(IRI[]::new)) + .orElseGet(() -> owlOntologyManager.getOntologies().stream() + .map(HasAnnotationPropertiesInSignature::getAnnotationPropertiesInSignature) + .flatMap(Set::stream) + .map(OWLNamedObject::getIRI) + .toArray(IRI[]::new)); + } + + protected boolean isMyRendererPlugin(RendererPlugin plugin) { + return plugin.getRendererClassName().equals("org.protege.editor.owl.ui.prefix.OWLEntityPrefixedNameRenderer"); + } + + void setRendering() { + + owlWorkSpace.ifPresent(owlWorkspace -> { + OWLRendererPreferences preferences = OWLRendererPreferences.getInstance(); + preferences.setRendererPlugin(preferences.getRendererPluginByClassName(OWLEntityPrefixedNameRenderer.class.getName())); + for (RendererPlugin plugin : preferences.getRendererPlugins()) { + log.warn(plugin.getRendererClassName()); + if (isMyRendererPlugin(plugin)) { + preferences.setRendererPlugin(plugin); + owlWorkspace.getOWLModelManager().refreshRenderer(); + break; + } + } + }); + } + + void resetRendering() { + owlWorkSpace.ifPresent(owlWorkspace -> { + OWLRendererPreferences preferences = OWLRendererPreferences.getInstance(); + preferences.setRendererPlugin(preferences.getRendererPluginByClassName(OWLEntityRendererImpl.class.getName())); + owlWorkspace.getOWLModelManager().refreshRenderer(); + }); + } + + public void removeOwlSelectionModelListener(OWLSelectionModelListener listener) { + owlWorkSpace.ifPresent(owlWorkSpace -> owlWorkSpace.getOWLSelectionModel().removeListener(listener)); + } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/ConceptAnnotationCollection.java b/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/ConceptAnnotationCollection.java index 99b4b2fe..9f52f82b 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/ConceptAnnotationCollection.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/ConceptAnnotationCollection.java @@ -152,32 +152,22 @@ public Iterator iterator() { /** Select next span. */ public void selectNextSpan() { - getSelection() - .ifPresent( - conceptAnnotation -> - conceptAnnotation - .getSelection() - .map(span -> getSpans(null).getNext(span)) - .ifPresent( - nextSpan -> { - setSelection(nextSpan.getConceptAnnotation()); - nextSpan.getConceptAnnotation().setSelection(nextSpan); - })); + getSelection().flatMap(conceptAnnotation -> conceptAnnotation + .getSelection() + .map(span -> getSpans(null).getNext(span))).ifPresent(nextSpan -> { + setSelection(nextSpan.getConceptAnnotation()); + nextSpan.getConceptAnnotation().setSelection(nextSpan); + }); } /** Select previous span. */ public void selectPreviousSpan() { - getSelection() - .ifPresent( - conceptAnnotation -> - conceptAnnotation - .getSelection() - .map(span -> getSpans(null).getPrevious(span)) - .ifPresent( - nextSpan -> { - setSelection(nextSpan.getConceptAnnotation()); - nextSpan.getConceptAnnotation().setSelection(nextSpan); - })); + getSelection().flatMap(conceptAnnotation -> conceptAnnotation + .getSelection() + .map(span -> getSpans(null).getPrevious(span))).ifPresent(nextSpan -> { + setSelection(nextSpan.getConceptAnnotation()); + nextSpan.getConceptAnnotation().setSelection(nextSpan); + }); } /* @@ -218,6 +208,7 @@ public void add(ConceptAnnotation conceptAnnotation) { @Override public void dispose() { model.removeOntologyChangeListener(this); + model.removeModelListener(this); super.dispose(); } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/ProfileCollection.java b/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/ProfileCollection.java index c79720f1..aecfd94b 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/ProfileCollection.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/ProfileCollection.java @@ -27,6 +27,7 @@ import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; import edu.ucdenver.ccp.knowtator.model.object.Profile; import java.util.Optional; +import java.util.Set; /** The type Profile collection. */ public class ProfileCollection extends KnowtatorCollection { @@ -79,4 +80,8 @@ public void remove(Profile profile) { super.remove(profile); selectNext(); } + + public void verifyHighlighters(Set owlClasses) { + forEach(profile -> profile.verifyHighLighters(owlClasses)); + } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/SpanCollection.java b/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/SpanCollection.java index 2e1579c1..c1b7b6da 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/SpanCollection.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/model/collection/SpanCollection.java @@ -50,18 +50,22 @@ public SpanCollection(KnowtatorModel model) { @Override public Stream stream() { - boolean filterByProfile = model.isFilter(PROFILE); + if (model != null) { + boolean filterByProfile = model.isFilter(PROFILE); - return model - .getSelectedProfile() - .map( - profile -> - super.stream() - .filter( - span -> - !filterByProfile - || span.getConceptAnnotation().getAnnotator().equals(profile))) - .orElse(super.stream()); + return model + .getSelectedProfile() + .map( + profile -> + super.stream() + .filter( + span -> + !filterByProfile + || span.getConceptAnnotation().getAnnotator().equals(profile))) + .orElse(super.stream()); + } else { + return super.stream(); + } } @Override diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/model/object/ConceptAnnotation.java b/src/main/java/edu/ucdenver/ccp/knowtator/model/object/ConceptAnnotation.java index 67099660..8c558589 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/model/object/ConceptAnnotation.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/model/object/ConceptAnnotation.java @@ -34,7 +34,6 @@ import java.util.stream.Collectors; import javax.annotation.Nonnull; import org.apache.log4j.Logger; -import org.semanticweb.owlapi.model.IRI; /** The type Concept annotation. */ public class ConceptAnnotation extends SpanCollection @@ -51,6 +50,7 @@ public class ConceptAnnotation extends SpanCollection private String bratID; private String motivation; private String id; + private final Set layers; /** * Instantiates a new Concept annotation. @@ -68,7 +68,8 @@ public ConceptAnnotation( String owlClass, @Nonnull Profile annotator, String annotationType, - String motivation) { + String motivation, + Set layers) { super(textSource.getKnowtatorModel()); this.annotator = annotator; @@ -76,6 +77,8 @@ public ConceptAnnotation( this.motivation = motivation; this.owlClass = owlClass; this.textSource = textSource; + this.layers = new HashSet<>(); + this.layers.addAll(layers); this.id = model.verifyId(annotationID, this, false); @@ -183,15 +186,6 @@ public void setBratID(String bratID) { this.bratID = bratID; } - /** - * Gets owl class label. - * - * @return the owl class label - */ - public String getOwlClassLabel() { - return IRI.create(owlClass).getShortForm(); - } - /** * This needs to be moved out of this class. * @@ -329,6 +323,10 @@ public String getAnnotationType() { * @return the owl class rendering */ public String getOwlClassRendering() { - return model.getOwlEntityRendering(owlClass); + return model.getOwlEntityRendering(owlClass); + } + + public Set getLayers() { + return layers; } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/model/object/GraphSpace.java b/src/main/java/edu/ucdenver/ccp/knowtator/model/object/GraphSpace.java index e2b1ef8b..413c1dbd 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/model/object/GraphSpace.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/model/object/GraphSpace.java @@ -279,10 +279,13 @@ public AnnotationNode getAnnotationNodeForConceptAnnotation(ConceptAnnotation co * @return the annotation node */ public AnnotationNode makeAnnotationNode(ConceptAnnotation conceptAnnotation) { - // String nodeId = textSource.getGraphSpaces().verifyID(null, "node"); - AnnotationNode newVertex = new AnnotationNode(null, conceptAnnotation, 20, 20, this); + return addAnnotationNode(null, conceptAnnotation, 20, 20); + } + + public AnnotationNode addAnnotationNode(String id, ConceptAnnotation conceptAnnotation, double x, double y) { + AnnotationNode newVertex = new AnnotationNode(id, conceptAnnotation, x, y, this); addCellToGraph(newVertex); - return newVertex; // (AnnotationNode) ((mxGraphModel) getModel()).getCells().get(nodeId); + return newVertex; } @Override @@ -406,7 +409,7 @@ public void ontologiesChanged(@Nonnull List changes @Override public void handleChange(OWLModelManagerChangeEvent event) { - if (event.isType(EventType.ENTITY_RENDERING_CHANGED)) { + if (event.isType(EventType.ENTITY_RENDERER_CHANGED)) { try { Arrays.asList(getChildCells(getDefaultParent())) .forEach( @@ -414,8 +417,7 @@ public void handleChange(OWLModelManagerChangeEvent event) { if (o instanceof RelationAnnotation) { ((RelationAnnotation) o).setLabel(); } else if (o instanceof AnnotationNode) { - ((AnnotationNode) o) - .setValue(((AnnotationNode) o).getConceptAnnotation().toMultilineString()); + ((AnnotationNode) o).setValue(((AnnotationNode) o).getConceptAnnotation().toMultilineString()); } }); refresh(); diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/model/object/Profile.java b/src/main/java/edu/ucdenver/ccp/knowtator/model/object/Profile.java index 351fb95a..44c444eb 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/model/object/Profile.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/model/object/Profile.java @@ -34,6 +34,7 @@ import java.io.File; import java.util.HashMap; import java.util.Map; +import java.util.Set; import org.apache.log4j.LogManager; import org.apache.log4j.Logger; @@ -43,7 +44,7 @@ public class Profile implements ModelObject, Savable, ModelListener { private static Logger log = LogManager.getLogger(Profile.class); private String id; - private final HashMap colors; // + private HashMap colors; // private final KnowtatorModel model; /** @@ -160,4 +161,12 @@ public void colorChangedEvent(Profile profile) { @Override public void modelChangeEvent(ChangeEvent event) {} + + public void verifyHighLighters(Set owlClasses) { + HashMap verifiedColors = new HashMap<>(); + colors.entrySet().stream() + .filter(entry -> model.getOwlClassById(entry.getKey()).isPresent()) + .forEach(entry -> verifiedColors.put(entry.getKey(), entry.getValue())); + colors = verifiedColors; + } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/model/object/Span.java b/src/main/java/edu/ucdenver/ccp/knowtator/model/object/Span.java index 0405a05d..704576b3 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/model/object/Span.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/model/object/Span.java @@ -251,8 +251,9 @@ public void modify(int startModification, int endModification) { model.fireModelEvent(new ChangeEvent<>(model, null, this)); } + @Override public String toString() { - return String.format("%s [%d, %d]", getSpannedText(), start, end); + return getSpannedText(); } public ConceptAnnotation getConceptAnnotation() { diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/model/object/TextSource.java b/src/main/java/edu/ucdenver/ccp/knowtator/model/object/TextSource.java index 418b309b..a66c7ece 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/model/object/TextSource.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/model/object/TextSource.java @@ -25,6 +25,7 @@ package edu.ucdenver.ccp.knowtator.model.object; import edu.ucdenver.ccp.knowtator.io.knowtator.KnowtatorXmlUtil; +import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; import edu.ucdenver.ccp.knowtator.model.ModelListener; import edu.ucdenver.ccp.knowtator.model.Savable; @@ -52,40 +53,42 @@ public class TextSource implements ModelObject, Savable, ModelListen private final KnowtatorModel model; private final File saveFile; private final ConceptAnnotationCollection conceptAnnotations; - public ConceptAnnotationCollection structureAnnotations; private File textFile; private String content; private final GraphSpaceCollection graphSpaces; - public final GraphSpaceCollection structureGraphSpaces; private String id; /** * Instantiates a new Text source. * * @param model the model - * @param saveFile the save file - * @param textFileName the text file name + * @param file save file or source text file */ - public TextSource(KnowtatorModel model, File saveFile, String textFileName) { + public TextSource(KnowtatorModel model, File file, String textSourceName) { this.model = model; - this.saveFile = - saveFile == null - ? new File( - model.getAnnotationsLocation().getAbsolutePath(), - textFileName.replace(".txt", ".xml")) - : saveFile; + if (file.getName().endsWith(".txt")) { + this.saveFile = new File(BaseModel.getAnnotationsLocation(model.getProjectLocation()).getAbsolutePath(), + file.getName().replace(".txt", ".xml")); + this.textFile = file; + } else if (file.getName().endsWith(".xml")) { + this.saveFile = file; + String textFileName = textSourceName == null ? file.getName().replace(".xml", ".txt") : textSourceName.endsWith(".txt") ? textSourceName : textSourceName.concat(".txt"); + this.textFile = new File(BaseModel.getArticlesLocation(file.getParentFile().getParentFile()).getAbsolutePath(), textFileName); + if (!this.textFile.exists()) { + this.textFile = new File(BaseModel.getArticlesLocation(model.getProjectLocation()).getAbsolutePath(), textFileName); + } + + } else { + this.saveFile = new File(BaseModel.getArticlesLocation(model.getProjectLocation()).getAbsolutePath(), + file.getName().concat(".xml")); + this.textFile = new File(BaseModel.getArticlesLocation(model.getProjectLocation()).getAbsolutePath(), + file.getName().concat(".txt")); + } this.conceptAnnotations = new ConceptAnnotationCollection(model, this); this.graphSpaces = new GraphSpaceCollection(model); - this.structureAnnotations = new ConceptAnnotationCollection(model, this); - this.structureGraphSpaces = new GraphSpaceCollection(model); model.addModelListener(this); - this.id = model.verifyId(FilenameUtils.getBaseName(textFileName), this, true); - - textFile = - new File( - model.getArticlesLocation(), - textFileName.endsWith(".txt") ? textFileName : String.format("%s.txt", textFileName)); + this.id = model.verifyId(FilenameUtils.getBaseName(this.textFile.getName().replace(".txt", "")), this, true); if (!textFile.exists()) { JFileChooser fileChooser = new JFileChooser(); @@ -93,12 +96,12 @@ public TextSource(KnowtatorModel model, File saveFile, String textFileName) { String.format("Could not find file for %s. Choose file location", id)); if (fileChooser.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) { - File file = fileChooser.getSelectedFile(); + File file1 = fileChooser.getSelectedFile(); try { textFile = Files.copy( Paths.get(file.toURI()), - Paths.get(model.getArticlesLocation().toURI().resolve(file.getName()))) + Paths.get(BaseModel.getArticlesLocation(model.getProjectLocation()).toURI().resolve(file1.getName()))) .toFile(); } catch (IOException e) { e.printStackTrace(); @@ -163,7 +166,7 @@ public String getContent() { content = FileUtils.readFileToString(textFile, "UTF-8"); return content; } catch (IOException e) { - textFile = new File(model.getArticlesLocation(), String.format("%s.txt", id)); + textFile = new File(BaseModel.getArticlesLocation(model.getProjectLocation()), String.format("%s.txt", id)); while (!textFile.exists()) { JFileChooser fileChooser = new JFileChooser(); if (fileChooser.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) { @@ -198,7 +201,7 @@ public void save() { * @return the save location */ public File getSaveLocation() { - return new File(model.getAnnotationsLocation().getAbsolutePath(), saveFile.getName()); + return new File(BaseModel.getAnnotationsLocation(model.getProjectLocation()).getAbsolutePath(), saveFile.getName()); } @Override @@ -263,11 +266,8 @@ public void selectPreviousSpan() { * @return the annotation */ public Optional getAnnotation(String annotationID) { - Optional conceptAnnotation = conceptAnnotations.get(annotationID); - if (conceptAnnotation.isPresent()) { - return conceptAnnotation; - } - return structureAnnotations.get(annotationID); + return conceptAnnotations.get(annotationID); + } /** @@ -357,24 +357,4 @@ public void setSelectedGraphSpace(GraphSpace graphSpace) { public void selectNextConceptAnnotation() { conceptAnnotations.selectNext(); } - - public ConceptAnnotationCollection getStructureAnnotations() { - return structureAnnotations; - } - - public GraphSpaceCollection getStructureGraphSpaces() { - return structureGraphSpaces; - } - - public int getNumberOfStructureAnnotations() { - return structureAnnotations.size(); - } - - public int getNumberOfStructureGraphSpaces() { - return structureGraphSpaces.size(); - } - - public Optional getSelectedStructureGraphSpace() { - return structureGraphSpaces.getSelection(); - } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/AnnotationNotes.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/AnnotationNotes.java index 991e294e..0da84eeb 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/AnnotationNotes.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/AnnotationNotes.java @@ -45,7 +45,8 @@ public class AnnotationNotes extends JTextArea implements KnowtatorComponent, Mo * Instantiates a new Annotation notes. * */ - AnnotationNotes() { + AnnotationNotes(KnowtatorView view) { + this.view = view; addKeyListener( new KeyListener() { @Override @@ -78,11 +79,6 @@ public void changedUpdate(DocumentEvent e) { }); } - @Override - public void setView(KnowtatorView view) { - this.view = view; - } - @Override public void reset() { view.getModel().ifPresent(model -> model.addModelListener(this)); diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorColorPalette.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorColorPalette.java index 658ffa8f..965a71e8 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorColorPalette.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorColorPalette.java @@ -185,7 +185,7 @@ public Icon getLargeDisplayIcon() { * Reimplementation of the SwatchPanel class used to make the default swatch panel because it * wasn't public. */ - class SwatchPanel extends JPanel { + static class SwatchPanel extends JPanel { /** The Colors. */ List colors; diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorComponent.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorComponent.java index bf62685b..c0ee4bc7 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorComponent.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorComponent.java @@ -31,6 +31,4 @@ public interface KnowtatorComponent { /** Dispose. */ void dispose(); - - void setView(KnowtatorView view); } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorView.form b/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorView.form index 3f4861e0..97fd627a 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorView.form +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorView.form @@ -2,7 +2,7 @@
    - + @@ -31,1120 +31,1002 @@ - + - - + - - - + - + - - + - - - + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + - + - - + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - + - - - + - + - + - - + + + + + + + - + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - + - + - + - - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + - + - + - - - - - + + - - - - - - - + + - - + + + + + + + + + + + + + + + + + - - - - + + - - - - - - - - - - - - - - - - - - - - - + + - - + + + - - - - - + + + + + + + + + + + + + + + + + + - - - + - + - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + - - - - + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + - + - - + + - - - + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - + + - + - - - - + + + - + - - - - + + + - + - - - - + + - - + + + + + + + + + + + + - - - - + + - + - + + + + - - - - - - - - - - - - + + + + + + - - + + - - + + + - + - - + + - - - + - - - - - + + - + + + + + + + + + + + + + + + + + + - + - - + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - + + - + + + - - - - - - - + + - + + + @@ -1152,36 +1034,63 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - - - - - - - - - - - - - + @@ -1199,15 +1108,25 @@ - - - - - - - - - + + + + + + + + + + + + + + + + + + + diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorView.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorView.java index 92551914..7e5c341e 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorView.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/KnowtatorView.java @@ -29,18 +29,13 @@ import static edu.ucdenver.ccp.knowtator.view.actions.collection.CollectionActionType.REMOVE; import static edu.ucdenver.ccp.knowtator.view.actions.collection.KnowtatorCollectionType.ANNOTATION; import static edu.ucdenver.ccp.knowtator.view.actions.collection.KnowtatorCollectionType.DOCUMENT; -import static edu.ucdenver.ccp.knowtator.view.actions.collection.KnowtatorCollectionType.PROFILE; import static edu.ucdenver.ccp.knowtator.view.actions.collection.KnowtatorCollectionType.SPAN; -import static edu.ucdenver.ccp.knowtator.view.actions.modelactions.ProfileAction.assignColorToClass; import com.mxgraph.swing.util.mxGraphTransferable; -import edu.ucdenver.ccp.knowtator.iaa.IaaException; -import edu.ucdenver.ccp.knowtator.iaa.KnowtatorIaa; import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.FilterType; import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; import edu.ucdenver.ccp.knowtator.model.ModelListener; -import edu.ucdenver.ccp.knowtator.model.OwlModel; import edu.ucdenver.ccp.knowtator.model.collection.SelectableCollection; import edu.ucdenver.ccp.knowtator.model.collection.event.ChangeEvent; import edu.ucdenver.ccp.knowtator.model.object.GraphSpace; @@ -50,27 +45,29 @@ import edu.ucdenver.ccp.knowtator.view.actions.ActionUnperformable; import edu.ucdenver.ccp.knowtator.view.actions.collection.ActionParameters; import edu.ucdenver.ccp.knowtator.view.actions.modelactions.FilterAction; +import edu.ucdenver.ccp.knowtator.view.actions.modelactions.ReassignOwlClassAction; import edu.ucdenver.ccp.knowtator.view.actions.modelactions.SpanActions; import edu.ucdenver.ccp.knowtator.view.chooser.TextSourceChooser; import edu.ucdenver.ccp.knowtator.view.graph.GraphViewDialog; import edu.ucdenver.ccp.knowtator.view.label.AnnotationAnnotatorLabel; import edu.ucdenver.ccp.knowtator.view.label.AnnotationClassLabel; import edu.ucdenver.ccp.knowtator.view.label.AnnotationIdLabel; -import edu.ucdenver.ccp.knowtator.view.list.ColorList; +import edu.ucdenver.ccp.knowtator.view.label.AnnotatorLabel; import edu.ucdenver.ccp.knowtator.view.list.GraphSpaceList; -import edu.ucdenver.ccp.knowtator.view.list.ProfileList; -import edu.ucdenver.ccp.knowtator.view.list.SpanList; +import edu.ucdenver.ccp.knowtator.view.profile.ProfileDialog; import edu.ucdenver.ccp.knowtator.view.table.AnnotationTable; import edu.ucdenver.ccp.knowtator.view.table.AnnotationTableForOwlClass; import edu.ucdenver.ccp.knowtator.view.table.AnnotationTableForSpannedText; import edu.ucdenver.ccp.knowtator.view.table.KnowtatorTable; import edu.ucdenver.ccp.knowtator.view.table.RelationTable; +import edu.ucdenver.ccp.knowtator.view.table.SpanTable; import edu.ucdenver.ccp.knowtator.view.textpane.KnowtatorTextPane; import java.awt.BorderLayout; import java.awt.CardLayout; import java.awt.Component; import java.awt.Container; import java.awt.Dimension; +import java.awt.FlowLayout; import java.awt.Font; import java.awt.GridBagConstraints; import java.awt.GridBagLayout; @@ -87,6 +84,7 @@ import java.awt.image.BufferedImage; import java.io.File; import java.io.IOException; +import java.lang.reflect.Method; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; @@ -127,13 +125,12 @@ public class KnowtatorView extends AbstractOWLClassViewComponent private JComponent cardPanel; private KnowtatorTextPane textPane; - private JTabbedPane header; private GraphSpaceList graphSpaceList; private AnnotationIdLabel annotationIdLabel; private AnnotationAnnotatorLabel annotationAnnotatorLabel; private AnnotationClassLabel annotationClassLabel; private AnnotationNotes annotationNotes; - private SpanList spanList; + private SpanTable spanTable; private JButton shrinkEndButton; private JButton growEndButton; private JButton growStartButton; @@ -153,13 +150,8 @@ public class KnowtatorView extends AbstractOWLClassViewComponent private JSlider fontSizeSlider; private JButton undoButton; private JButton redoButton; - private JButton assignColorToClassButton; private JProgressBar progressBar; private JList fileList; - private JButton removeProfileButton; - private ProfileList profileList; - private JButton addProfileButton; - private ColorList colorList; private JTextField annotationsContainingTextTextField; private JCheckBox exactMatchCheckBox; private JLabel owlClassLabel; @@ -185,17 +177,8 @@ public class KnowtatorView extends AbstractOWLClassViewComponent private JSplitPane body; private JPanel infoPane; private JPanel spanPane; - private JPanel annotationPaneButtons; private JPanel graphSpacePane; - private JPanel undoPane; - private JPanel filterPane; private JComponent rootPane; - private JPanel textSourcePane; - private JPanel iaaPane; - private JButton runIaaButton; - private JCheckBox iaaSpanCheckBox; - private JCheckBox iaaClassAndSpanCheckBox; - private JCheckBox iaaClassCheckBox; private JButton captureImageButton; private JCheckBox oneClickGraphsCheckBox; private JTable conceptAnnotationsForTextTable; @@ -206,10 +189,14 @@ public class KnowtatorView extends AbstractOWLClassViewComponent private JButton nextRelationReviewButton; private JButton refreshRelationReviewButton; private JCheckBox snapToWordsCheckBox; - private JRadioButton structuresRadioButton; - private JRadioButton conceptsRadioButton; + private JTabbedPane header; + private JButton reassignButton; + private JCheckBox reviewRegexCheckBox; + private AnnotatorLabel activeProfileLabel; + private JButton fileButton; + private JButton profileButton; - private final List knowtatorComponents; + public final List knowtatorComponents; private final HashMap spanSizeButtons; private final HashMap selectionSizeButtons; @@ -240,19 +227,18 @@ public KnowtatorView() { } catch (ClassNotFoundException e) { e.printStackTrace(); } - header.setSelectedIndex(1); makeButtons(); + header.setSelectedIndex(0); knowtatorComponents.addAll( Arrays.asList( - profileList, - colorList, textPane, graphViewDialog, annotationNotes, annotationIdLabel, annotationAnnotatorLabel, + activeProfileLabel, annotationClassLabel, - spanList, + spanTable, graphSpaceList, textSourceChooser, (KnowtatorComponent) conceptAnnotationsForTextTable, @@ -260,11 +246,6 @@ public KnowtatorView() { relationsForPropertyList)); } - @Override - public void setView(KnowtatorView view) { - knowtatorComponents.forEach(component -> component.setView(this)); - } - private static void changeFont(Component component, Font font) { component.setFont(font); if (component instanceof Container) { @@ -306,34 +287,34 @@ private void createUIComponents() { includeClassDescendantsCheckBox = new JCheckBox(); includePropertyDescendantsCheckBox = new JCheckBox(); exactMatchCheckBox = new JCheckBox(); + reviewRegexCheckBox = new JCheckBox(); owlClassLabel = new JLabel(); owlPropertyLabel = new JLabel(); textPane = - new KnowtatorTextPane( + new KnowtatorTextPane(this, searchTextField, onlyAnnotationsCheckBox, regexCheckBox, caseSensitiveCheckBox); - graphViewDialog = new GraphViewDialog(); + graphViewDialog = new GraphViewDialog(this); - annotationAnnotatorLabel = new AnnotationAnnotatorLabel(); - annotationClassLabel = new AnnotationClassLabel(); - annotationIdLabel = new AnnotationIdLabel(); - annotationNotes = new AnnotationNotes(); + annotationAnnotatorLabel = new AnnotationAnnotatorLabel(this); + activeProfileLabel = new AnnotatorLabel(this); + annotationClassLabel = new AnnotationClassLabel(this); + annotationIdLabel = new AnnotationIdLabel(this); + annotationNotes = new AnnotationNotes(this); - textSourceChooser = new TextSourceChooser(); + textSourceChooser = new TextSourceChooser(this); - graphSpaceList = new GraphSpaceList(); - spanList = new SpanList(); - profileList = new ProfileList(); - colorList = new ColorList(); + graphSpaceList = new GraphSpaceList(this); + spanTable = new SpanTable(this); annotationsContainingTextTextField = new JTextField(); annotationsForClassTable = - new AnnotationTableForOwlClass(includeClassDescendantsCheckBox, owlClassLabel); + new AnnotationTableForOwlClass(this, includeClassDescendantsCheckBox, owlClassLabel); conceptAnnotationsForTextTable = - new AnnotationTableForSpannedText(exactMatchCheckBox, annotationsContainingTextTextField); + new AnnotationTableForSpannedText(this, exactMatchCheckBox, reviewRegexCheckBox, annotationsContainingTextTextField); relationsForPropertyList = - new RelationTable(includePropertyDescendantsCheckBox, owlPropertyLabel); + new RelationTable(this, includePropertyDescendantsCheckBox, owlPropertyLabel); // The following methods keep the graph view dialog on top only when the view is active. KnowtatorView view = this; @@ -373,10 +354,6 @@ public void ancestorMoved(AncestorEvent event) { * Makes the buttons in the main display pane. */ private void makeButtons() { - structuresRadioButton.addChangeListener( - e -> - getModel() - .ifPresent(model -> model.setStructureMode(structuresRadioButton.isSelected()))); captureImageButton.addActionListener( e -> @@ -415,22 +392,20 @@ private void makeButtons() { if (model1.isNotLoading()) { CardLayout cl = (CardLayout) cardPanel.getLayout(); cl.show(cardPanel, "Main"); - header.setSelectedIndex(1); + header.setSelectedIndex(0); } }); } else { CardLayout cl = (CardLayout) cardPanel.getLayout(); cl.show(cardPanel, "Main"); - header.setSelectedIndex(1); + header.setSelectedIndex(0); } }); - header.addChangeListener( + fileButton.addActionListener( e -> { - if (header.getTitleAt(header.getSelectedIndex()).equals("File")) { - CardLayout cl = (CardLayout) cardPanel.getLayout(); - cl.show(cardPanel, "File"); - } + CardLayout cl = (CardLayout) cardPanel.getLayout(); + cl.show(cardPanel, "File"); }); findTextInOntologyButton.addActionListener( @@ -439,22 +414,16 @@ private void makeButtons() { previousMatchButton.addActionListener(e -> textPane.searchPrevious()); searchTextField.addActionListener(e -> textPane.searchForward()); - makeReviewPane(); + profileButton.addActionListener( + e -> { + ProfileDialog dialog = new ProfileDialog(JOptionPane.getFrameForComponent(this), this); + dialog.pack(); + dialog.colorList.selectionChanged(); + dialog.setVisible(true); + } + ); - addProfileButton.addActionListener( - e -> - Optional.ofNullable(JOptionPane.showInputDialog(this, "Enter a name for the profile")) - .ifPresent( - profileName -> - pickAction(this, profileName, null, new ActionParameters(ADD, PROFILE)))); - removeProfileButton.addActionListener( - e -> - Optional.of( - JOptionPane.showConfirmDialog( - this, "Are you sure you wish to remove this profile?")) - .filter(result -> JOptionPane.OK_OPTION == result) - .ifPresent( - result -> pickAction(this, null, null, new ActionParameters(REMOVE, PROFILE)))); + makeReviewPane(); addAnnotationButton.addActionListener( e -> @@ -473,6 +442,27 @@ private void makeButtons() { new ActionParameters(REMOVE, ANNOTATION), new ActionParameters(REMOVE, SPAN))); + reassignButton.addActionListener(e -> getModel() + .ifPresent( + model -> { + Optional selectedOwlClass = model.getSelectedOwlClass(); + selectedOwlClass.ifPresent( + owlClass -> + model + .getSelectedTextSource().flatMap(TextSource::getSelectedAnnotation).ifPresent(conceptAnnotation -> { + try { + model.registerAction( + new ReassignOwlClassAction( + model, + conceptAnnotation, + owlClass)); + } catch (ActionUnperformable e1) { + JOptionPane.showMessageDialog( + this, e1.getMessage()); + } + })); + })); + makeSpanButtons(); fontSizeSlider.setValue(textPane.getFont().getSize()); @@ -525,7 +515,7 @@ private void makeButtons() { getModel() .ifPresent( model1 -> { - fileChooser.setCurrentDirectory(model1.getArticlesLocation()); + fileChooser.setCurrentDirectory(BaseModel.getArticlesLocation(model.getProjectLocation())); if (fileChooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION) { pickAction( @@ -540,13 +530,6 @@ private void makeButtons() { removeTextSourceButton.addActionListener( e -> pickAction(this, null, null, new ActionParameters(REMOVE, DOCUMENT))); - assignColorToClassButton.addActionListener( - e -> - // TODO: This could be removed if class selection were reflected in color list - getModel() - .flatMap(OwlModel::getSelectedOwlClass) - .ifPresent(owlClass -> assignColorToClass(this, owlClass))); - undoButton.addActionListener( e -> getModel().filter(UndoManager::canUndo).ifPresent(UndoManager::undo)); redoButton.addActionListener( @@ -639,40 +622,7 @@ private void makeButtons() { fileChooser.showOpenDialog(KnowtatorView.this); }); - runIaaButton.addActionListener( - e -> - getModel() - .ifPresent( - model -> { - JFileChooser fileChooser = new JFileChooser(); - fileChooser.setCurrentDirectory(model.getSaveLocation()); - fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); - // - // disable the "All files" option. - // - fileChooser.setAcceptAllFileFilterUsed(false); - if (fileChooser.showSaveDialog(this) == JFileChooser.APPROVE_OPTION) { - File outputDirectory = fileChooser.getSelectedFile(); - - try { - KnowtatorIaa knowtatorIaa = new KnowtatorIaa(outputDirectory, model); - - if (iaaClassCheckBox.isSelected()) { - knowtatorIaa.runClassIaa(); - } - if (iaaSpanCheckBox.isSelected()) { - knowtatorIaa.runSpanIaa(); - } - if (iaaClassAndSpanCheckBox.isSelected()) { - knowtatorIaa.runClassAndSpanIaa(); - } - knowtatorIaa.closeHtml(); - } catch (IaaException e1) { - e1.printStackTrace(); - } - } - })); } private void open(JFileChooser fileChooser) { @@ -723,25 +673,19 @@ private void makeSpanButtons() { .ifPresent( model1 -> model1 - .getSelectedConceptAnnotation() - .ifPresent( - conceptAnnotation -> - conceptAnnotation - .getSelection() - .ifPresent( - span -> { - try { - model1.registerAction( - new SpanActions.ModifySpanAction( - model1, - SpanActions.END, - SpanActions.SHRINK, - span)); - } catch (ActionUnperformable e1) { - JOptionPane.showMessageDialog( - this, e1.getMessage()); - } - })))); + .getSelectedConceptAnnotation().flatMap(SelectableCollection::getSelection).ifPresent(span -> { + try { + model1.registerAction( + new SpanActions.ModifySpanAction( + model1, + SpanActions.END, + SpanActions.SHRINK, + span)); + } catch (ActionUnperformable e1) { + JOptionPane.showMessageDialog( + this, e1.getMessage()); + } + }))); spanSizeButtons.put( shrinkStartButton, @@ -750,25 +694,19 @@ private void makeSpanButtons() { .ifPresent( model1 -> model1 - .getSelectedConceptAnnotation() - .ifPresent( - conceptAnnotation -> - conceptAnnotation - .getSelection() - .ifPresent( - span -> { - try { - model1.registerAction( - new SpanActions.ModifySpanAction( - model1, - SpanActions.START, - SpanActions.SHRINK, - span)); - } catch (ActionUnperformable e1) { - JOptionPane.showMessageDialog( - this, e1.getMessage()); - } - })))); + .getSelectedConceptAnnotation().flatMap(SelectableCollection::getSelection).ifPresent(span -> { + try { + model1.registerAction( + new SpanActions.ModifySpanAction( + model1, + SpanActions.START, + SpanActions.SHRINK, + span)); + } catch (ActionUnperformable e1) { + JOptionPane.showMessageDialog( + this, e1.getMessage()); + } + }))); spanSizeButtons.put( growEndButton, e -> @@ -776,25 +714,19 @@ private void makeSpanButtons() { .ifPresent( model1 -> model1 - .getSelectedConceptAnnotation() - .ifPresent( - conceptAnnotation -> - conceptAnnotation - .getSelection() - .ifPresent( - span -> { - try { - model1.registerAction( - new SpanActions.ModifySpanAction( - model1, - SpanActions.END, - SpanActions.GROW, - span)); - } catch (ActionUnperformable e1) { - JOptionPane.showMessageDialog( - this, e1.getMessage()); - } - })))); + .getSelectedConceptAnnotation().flatMap(SelectableCollection::getSelection).ifPresent(span -> { + try { + model1.registerAction( + new SpanActions.ModifySpanAction( + model1, + SpanActions.END, + SpanActions.GROW, + span)); + } catch (ActionUnperformable e1) { + JOptionPane.showMessageDialog( + this, e1.getMessage()); + } + }))); spanSizeButtons.put( growStartButton, e -> @@ -802,25 +734,19 @@ private void makeSpanButtons() { .ifPresent( model1 -> model1 - .getSelectedConceptAnnotation() - .ifPresent( - conceptAnnotation -> - conceptAnnotation - .getSelection() - .ifPresent( - span -> { - try { - model1.registerAction( - new SpanActions.ModifySpanAction( - model1, - SpanActions.START, - SpanActions.GROW, - span)); - } catch (ActionUnperformable e1) { - JOptionPane.showMessageDialog( - this, e1.getMessage()); - } - })))); + .getSelectedConceptAnnotation().flatMap(SelectableCollection::getSelection).ifPresent(span -> { + try { + model1.registerAction( + new SpanActions.ModifySpanAction( + model1, + SpanActions.START, + SpanActions.GROW, + span)); + } catch (ActionUnperformable e1) { + JOptionPane.showMessageDialog( + this, e1.getMessage()); + } + }))); selectionSizeButtons.put( shrinkEndButton, @@ -959,7 +885,6 @@ public void dragOver(DropTargetDragEvent e) { * @throws IOException the io exception */ public void loadProject(File file, ModelListener progressListener) throws IOException { - setView(this); if (!getModel().isPresent() || getModel().get().isNotLoading()) { getModel().ifPresent(BaseModel::dispose); if (getOWLWorkspace() != null) { @@ -971,7 +896,7 @@ public void loadProject(File file, ModelListener progressListener) throws IOExce getModel().ifPresent(model1 -> model1.addModelListener(progressListener)); } log.info(String.format("Opening from %s", file.getAbsolutePath())); - getModel().ifPresent(OwlModel::load); + getModel().ifPresent(owlModel -> owlModel.load(owlModel.getProjectLocation())); if (progressListener != null) { getModel().ifPresent(model1 -> model1.removeModelListener(progressListener)); } @@ -1004,17 +929,12 @@ public void filterChangedEvent() { @Override public void modelChangeEvent(ChangeEvent event) { - getModel() - .ifPresent( - model1 -> - event - .getNew() - .ifPresent( - o -> { - if (o instanceof GraphSpace && isVisible()) { - graphViewDialog.setVisible(true); - } - })); + getModel().flatMap(model1 -> event + .getNew()).ifPresent(o -> { + if (o instanceof GraphSpace && isVisible()) { + graphViewDialog.setVisible(true); + } + }); getModel() .ifPresent( @@ -1085,23 +1005,128 @@ public boolean isSnapToWords() { final JPanel panel1 = new JPanel(); panel1.setLayout(new BorderLayout(0, 0)); body.setRightComponent(panel1); + header = new JTabbedPane(); + Font headerFont = this.$$$getFont$$$(null, -1, 14, header.getFont()); + if (headerFont != null) { + header.setFont(headerFont); + } + panel1.add(header, BorderLayout.CENTER); + final JPanel panel2 = new JPanel(); + panel2.setLayout(new BorderLayout(0, 0)); + header.addTab("Annotation", panel2); infoPane = new JPanel(); infoPane.setLayout(new GridBagLayout()); infoPane.setMaximumSize(new Dimension(200, 2147483647)); infoPane.setMinimumSize(new Dimension(200, 158)); - panel1.add(infoPane, BorderLayout.CENTER); - infoPane.setBorder(BorderFactory.createTitledBorder(null, "Info", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 18, infoPane.getFont()))); - spanPane = new JPanel(); - spanPane.setLayout(new GridBagLayout()); + panel2.add(infoPane, BorderLayout.CENTER); + final JPanel panel3 = new JPanel(); + panel3.setLayout(new FlowLayout(FlowLayout.LEFT, 5, 5)); GridBagConstraints gbc; gbc = new GridBagConstraints(); gbc.gridx = 0; - gbc.gridy = 8; - gbc.gridwidth = 2; + gbc.gridy = 0; + gbc.fill = GridBagConstraints.BOTH; + infoPane.add(panel3, gbc); + previousSpanButton = new JButton(); + previousSpanButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24 (reversed).png"))); + previousSpanButton.setText(""); + previousSpanButton.setToolTipText("Previous annotation or span"); + panel3.add(previousSpanButton); + nextSpanButton = new JButton(); + nextSpanButton.setHorizontalAlignment(0); + nextSpanButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24.png"))); + nextSpanButton.setText(""); + nextSpanButton.setToolTipText("Next annotation or span"); + panel3.add(nextSpanButton); + final JPanel panel4 = new JPanel(); + panel4.setLayout(new GridBagLayout()); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 1; + gbc.weightx = 1.0; + gbc.fill = GridBagConstraints.BOTH; + infoPane.add(panel4, gbc); + final JPanel panel5 = new JPanel(); + panel5.setLayout(new FlowLayout(FlowLayout.LEFT, 5, 5)); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 0; + gbc.weightx = 1.0; + gbc.fill = GridBagConstraints.BOTH; + panel4.add(panel5, gbc); + panel5.setBorder(BorderFactory.createTitledBorder(null, "", TitledBorder.LEFT, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel5.getFont()), null)); + final JLabel label1 = new JLabel(); + Font label1Font = this.$$$getFont$$$(null, Font.BOLD, 12, label1.getFont()); + if (label1Font != null) { + label1.setFont(label1Font); + } + label1.setText("ID:"); + panel5.add(label1); + Font annotationIdLabelFont = this.$$$getFont$$$("Verdana", -1, -1, annotationIdLabel.getFont()); + if (annotationIdLabelFont != null) { + annotationIdLabel.setFont(annotationIdLabelFont); + } + annotationIdLabel.setText(""); + panel5.add(annotationIdLabel); + final JPanel panel6 = new JPanel(); + panel6.setLayout(new FlowLayout(FlowLayout.LEFT, 5, 5)); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 2; + gbc.weightx = 1.0; + gbc.fill = GridBagConstraints.BOTH; + infoPane.add(panel6, gbc); + panel6.setBorder(BorderFactory.createTitledBorder(null, "", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel6.getFont()), null)); + final JLabel label2 = new JLabel(); + Font label2Font = this.$$$getFont$$$(null, Font.BOLD, 12, label2.getFont()); + if (label2Font != null) { + label2.setFont(label2Font); + } + label2.setText("Annotator:"); + panel6.add(label2); + Font annotationAnnotatorLabelFont = this.$$$getFont$$$("Verdana", -1, -1, annotationAnnotatorLabel.getFont()); + if (annotationAnnotatorLabelFont != null) { + annotationAnnotatorLabel.setFont(annotationAnnotatorLabelFont); + } + panel6.add(annotationAnnotatorLabel); + final JPanel panel7 = new JPanel(); + panel7.setLayout(new FlowLayout(FlowLayout.LEFT, 5, 5)); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 3; + gbc.weightx = 1.0; + gbc.fill = GridBagConstraints.BOTH; + infoPane.add(panel7, gbc); + panel7.setBorder(BorderFactory.createTitledBorder(null, "", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel7.getFont()), null)); + final JLabel label3 = new JLabel(); + Font label3Font = this.$$$getFont$$$(null, Font.BOLD, 12, label3.getFont()); + if (label3Font != null) { + label3.setFont(label3Font); + } + label3.setText("OWL Class:"); + panel7.add(label3); + Font annotationClassLabelFont = this.$$$getFont$$$("Verdana", -1, -1, annotationClassLabel.getFont()); + if (annotationClassLabelFont != null) { + annotationClassLabel.setFont(annotationClassLabelFont); + } + annotationClassLabel.setText(""); + panel7.add(annotationClassLabel); + reassignButton = new JButton(); + reassignButton.setText("Reassign"); + reassignButton.setToolTipText("Reassign to currently selected OWL class"); + panel7.add(reassignButton); + final JTabbedPane tabbedPane1 = new JTabbedPane(); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 4; gbc.weightx = 1.0; + gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; - infoPane.add(spanPane, gbc); - spanPane.setBorder(BorderFactory.createTitledBorder(null, "Spans", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, spanPane.getFont()))); + infoPane.add(tabbedPane1, gbc); + spanPane = new JPanel(); + spanPane.setLayout(new GridBagLayout()); + tabbedPane1.addTab("Spans", spanPane); + spanPane.setBorder(BorderFactory.createTitledBorder(null, "", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, spanPane.getFont()), null)); final JScrollPane scrollPane1 = new JScrollPane(); gbc = new GridBagConstraints(); gbc.gridx = 0; @@ -1110,74 +1135,55 @@ public boolean isSnapToWords() { gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; spanPane.add(scrollPane1, gbc); - Font spanListFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, spanList.getFont()); - if (spanListFont != null) { - spanList.setFont(spanListFont); + Font spanTableFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, spanTable.getFont()); + if (spanTableFont != null) { + spanTable.setFont(spanTableFont); } - scrollPane1.setViewportView(spanList); - final JPanel panel2 = new JPanel(); - panel2.setLayout(new GridBagLayout()); + scrollPane1.setViewportView(spanTable); + final JPanel panel8 = new JPanel(); + panel8.setLayout(new FlowLayout(FlowLayout.LEFT, 5, 5)); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; gbc.weightx = 1.0; gbc.fill = GridBagConstraints.BOTH; - spanPane.add(panel2, gbc); + spanPane.add(panel8, gbc); growStartButton = new JButton(); Font growStartButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, growStartButton.getFont()); if (growStartButtonFont != null) { growStartButton.setFont(growStartButtonFont); } growStartButton.setText("Grow Start"); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weighty = 1.0; - panel2.add(growStartButton, gbc); + growStartButton.setToolTipText("Decrease the selected span's start index"); + panel8.add(growStartButton); shrinkStartButton = new JButton(); Font shrinkStartButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, shrinkStartButton.getFont()); if (shrinkStartButtonFont != null) { shrinkStartButton.setFont(shrinkStartButtonFont); } shrinkStartButton.setText("Shrink Start"); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 0; - gbc.weighty = 1.0; - panel2.add(shrinkStartButton, gbc); + shrinkStartButton.setToolTipText("Increase the selected span's start index"); + panel8.add(shrinkStartButton); shrinkEndButton = new JButton(); Font shrinkEndButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, shrinkEndButton.getFont()); if (shrinkEndButtonFont != null) { shrinkEndButton.setFont(shrinkEndButtonFont); } shrinkEndButton.setText("Shrink End"); - gbc = new GridBagConstraints(); - gbc.gridx = 2; - gbc.gridy = 0; - gbc.weighty = 1.0; - panel2.add(shrinkEndButton, gbc); + shrinkEndButton.setToolTipText("Decrease the selected span's end index"); + panel8.add(shrinkEndButton); growEndButton = new JButton(); Font growEndButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, growEndButton.getFont()); if (growEndButtonFont != null) { growEndButton.setFont(growEndButtonFont); } growEndButton.setText("Grow End"); - gbc = new GridBagConstraints(); - gbc.gridx = 3; - gbc.gridy = 0; - gbc.weighty = 1.0; - panel2.add(growEndButton, gbc); + growEndButton.setToolTipText("Increase the selected span's end index"); + panel8.add(growEndButton); graphSpacePane = new JPanel(); graphSpacePane.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 9; - gbc.gridwidth = 2; - gbc.gridheight = 2; - gbc.weightx = 1.0; - gbc.fill = GridBagConstraints.BOTH; - infoPane.add(graphSpacePane, gbc); - graphSpacePane.setBorder(BorderFactory.createTitledBorder(null, "Graph Spaces", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, graphSpacePane.getFont()))); + tabbedPane1.addTab("Graph Spaces", graphSpacePane); + graphSpacePane.setBorder(BorderFactory.createTitledBorder(null, "", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, graphSpacePane.getFont()), null)); final JScrollPane scrollPane2 = new JScrollPane(); gbc = new GridBagConstraints(); gbc.gridx = 0; @@ -1191,922 +1197,600 @@ public boolean isSnapToWords() { graphSpaceList.setFont(graphSpaceListFont); } scrollPane2.setViewportView(graphSpaceList); + final JPanel panel9 = new JPanel(); + panel9.setLayout(new GridBagLayout()); + tabbedPane1.addTab("Notes", panel9); final JScrollPane scrollPane3 = new JScrollPane(); gbc = new GridBagConstraints(); gbc.gridx = 0; - gbc.gridy = 3; - gbc.gridheight = 5; + gbc.gridy = 0; gbc.weightx = 1.0; gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; - infoPane.add(scrollPane3, gbc); - scrollPane3.setBorder(BorderFactory.createTitledBorder(null, "Notes", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, scrollPane3.getFont()))); + panel9.add(scrollPane3, gbc); + scrollPane3.setBorder(BorderFactory.createTitledBorder(null, "", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, scrollPane3.getFont()), null)); Font annotationNotesFont = this.$$$getFont$$$("Verdana", -1, 12, annotationNotes.getFont()); if (annotationNotesFont != null) { annotationNotes.setFont(annotationNotesFont); } + annotationNotes.setText(""); scrollPane3.setViewportView(annotationNotes); - final JPanel panel3 = new JPanel(); - panel3.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.fill = GridBagConstraints.BOTH; - infoPane.add(panel3, gbc); - panel3.setBorder(BorderFactory.createTitledBorder(null, "ID", TitledBorder.LEFT, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel3.getFont()))); - Font annotationIdLabelFont = this.$$$getFont$$$("Verdana", -1, -1, annotationIdLabel.getFont()); - if (annotationIdLabelFont != null) { - annotationIdLabel.setFont(annotationIdLabelFont); - } - annotationIdLabel.setText(""); + final JPanel panel10 = new JPanel(); + panel10.setLayout(new GridBagLayout()); + header.addTab("Review", panel10); + final JPanel panel11 = new JPanel(); + panel11.setLayout(new GridBagLayout()); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; + gbc.gridwidth = 2; gbc.weightx = 1.0; gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel3.add(annotationIdLabel, gbc); - final JPanel panel4 = new JPanel(); - panel4.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 1; - gbc.weightx = 1.0; gbc.fill = GridBagConstraints.BOTH; - infoPane.add(panel4, gbc); - panel4.setBorder(BorderFactory.createTitledBorder(null, "Annotator", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel4.getFont()))); - Font annotationAnnotatorLabelFont = this.$$$getFont$$$("Verdana", -1, -1, annotationAnnotatorLabel.getFont()); - if (annotationAnnotatorLabelFont != null) { - annotationAnnotatorLabel.setFont(annotationAnnotatorLabelFont); + panel10.add(panel11, gbc); + reviewTabbedPane = new JTabbedPane(); + Font reviewTabbedPaneFont = this.$$$getFont$$$("Verdana", -1, 14, reviewTabbedPane.getFont()); + if (reviewTabbedPaneFont != null) { + reviewTabbedPane.setFont(reviewTabbedPaneFont); } + reviewTabbedPane.setTabPlacement(2); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; gbc.weightx = 1.0; gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel4.add(annotationAnnotatorLabel, gbc); - final JPanel panel5 = new JPanel(); - panel5.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 2; - gbc.weightx = 1.0; gbc.fill = GridBagConstraints.BOTH; - infoPane.add(panel5, gbc); - panel5.setBorder(BorderFactory.createTitledBorder(null, "OWL CLass", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel5.getFont()))); - Font annotationClassLabelFont = this.$$$getFont$$$("Verdana", -1, -1, annotationClassLabel.getFont()); - if (annotationClassLabelFont != null) { - annotationClassLabel.setFont(annotationClassLabelFont); - } - annotationClassLabel.setText(""); + panel11.add(reviewTabbedPane, gbc); + final JPanel panel12 = new JPanel(); + panel12.setLayout(new BorderLayout(0, 0)); + reviewTabbedPane.addTab("Text", panel12); + final JPanel panel13 = new JPanel(); + panel13.setLayout(new GridBagLayout()); + panel12.add(panel13, BorderLayout.NORTH); + panel13.setBorder(BorderFactory.createTitledBorder(null, "Text", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$(null, -1, 14, panel13.getFont()), null)); gbc = new GridBagConstraints(); - gbc.gridx = 0; + gbc.gridx = 1; gbc.gridy = 0; gbc.weightx = 1.0; gbc.weighty = 1.0; gbc.anchor = GridBagConstraints.WEST; - panel5.add(annotationClassLabel, gbc); - final JScrollPane scrollPane4 = new JScrollPane(); - body.setLeftComponent(scrollPane4); - textPane.setMinimumSize(new Dimension(200, 22)); - textPane.setPreferredSize(new Dimension(500, 500)); - scrollPane4.setViewportView(textPane); - header = new JTabbedPane(); - Font headerFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 14, header.getFont()); - if (headerFont != null) { - header.setFont(headerFont); - } - header.setPreferredSize(new Dimension(788, 200)); - header.setTabLayoutPolicy(0); - header.setTabPlacement(1); - mainPanel.add(header, BorderLayout.NORTH); - final JPanel panel6 = new JPanel(); - panel6.setLayout(new GridBagLayout()); - header.addTab("File", panel6); - final JPanel panel7 = new JPanel(); - panel7.setLayout(new GridBagLayout()); - header.addTab("Home", panel7); - textSourcePane = new JPanel(); - textSourcePane.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.gridheight = 3; - gbc.weightx = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel7.add(textSourcePane, gbc); - textSourcePane.setBorder(BorderFactory.createTitledBorder(null, "Document", TitledBorder.CENTER, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, textSourcePane.getFont()))); - final JPanel panel8 = new JPanel(); - panel8.setLayout(new GridBagLayout()); + gbc.fill = GridBagConstraints.HORIZONTAL; + panel13.add(annotationsContainingTextTextField, gbc); + final JLabel label4 = new JLabel(); + label4.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-search-52.png"))); + label4.setText(""); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; - gbc.gridwidth = 2; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - textSourcePane.add(panel8, gbc); - previousTextSourceButton = new JButton(); - previousTextSourceButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24 (reversed).png"))); - previousTextSourceButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 1; - gbc.weightx = 1.0; - panel8.add(previousTextSourceButton, gbc); - nextTextSourceButton = new JButton(); - nextTextSourceButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24.png"))); - nextTextSourceButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 1; - gbc.weightx = 1.0; - panel8.add(nextTextSourceButton, gbc); - addTextSourceButton = new JButton(); - addTextSourceButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-plus-24.png"))); - addTextSourceButton.setText(""); + gbc.anchor = GridBagConstraints.WEST; + panel13.add(label4, gbc); + previousTextReviewButton = new JButton(); + previousTextReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-sort-up-24.png"))); + previousTextReviewButton.setText(""); + previousTextReviewButton.setToolTipText("Previous match"); gbc = new GridBagConstraints(); - gbc.gridx = 0; + gbc.gridx = 2; gbc.gridy = 0; - gbc.weightx = 1.0; gbc.weighty = 1.0; gbc.fill = GridBagConstraints.HORIZONTAL; - panel8.add(addTextSourceButton, gbc); - removeTextSourceButton = new JButton(); - removeTextSourceButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-delete-24.png"))); - removeTextSourceButton.setText(""); + panel13.add(previousTextReviewButton, gbc); + nextTextReviewButton = new JButton(); + nextTextReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-sort-down-24.png"))); + nextTextReviewButton.setText(""); + nextTextReviewButton.setToolTipText("Next match"); gbc = new GridBagConstraints(); - gbc.gridx = 1; + gbc.gridx = 3; gbc.gridy = 0; - gbc.weightx = 1.0; gbc.weighty = 1.0; gbc.fill = GridBagConstraints.HORIZONTAL; - panel8.add(removeTextSourceButton, gbc); - textSourceChooser.setPreferredSize(new Dimension(150, 24)); + panel13.add(nextTextReviewButton, gbc); + refreshTextReviewButton = new JButton(); + refreshTextReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-synchronize-32.png"))); + refreshTextReviewButton.setText(""); + refreshTextReviewButton.setToolTipText("Refresh"); gbc = new GridBagConstraints(); gbc.gridx = 2; gbc.gridy = 1; - panel8.add(textSourceChooser, gbc); - final JPanel panel9 = new JPanel(); - panel9.setLayout(new GridBagLayout()); + gbc.gridwidth = 2; + gbc.weighty = 1.0; + gbc.fill = GridBagConstraints.HORIZONTAL; + panel13.add(refreshTextReviewButton, gbc); + final JPanel panel14 = new JPanel(); + panel14.setLayout(new FlowLayout(FlowLayout.LEFT, 5, 5)); gbc = new GridBagConstraints(); gbc.gridx = 1; gbc.gridy = 1; - gbc.weightx = 1.0; gbc.fill = GridBagConstraints.BOTH; - textSourcePane.add(panel9, gbc); - panel9.setBorder(BorderFactory.createTitledBorder("Font Size")); - fontSizeSlider = new JSlider(); - fontSizeSlider.setInverted(false); - fontSizeSlider.setMajorTickSpacing(8); - fontSizeSlider.setMaximum(28); - fontSizeSlider.setMinimum(8); - fontSizeSlider.setMinorTickSpacing(1); - fontSizeSlider.setSnapToTicks(true); - fontSizeSlider.setValue(16); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel9.add(fontSizeSlider, gbc); - captureImageButton = new JButton(); - captureImageButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-unsplash-32.png"))); - captureImageButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 1; - gbc.weightx = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - textSourcePane.add(captureImageButton, gbc); - undoPane = new JPanel(); - undoPane.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 2; - gbc.gridy = 0; - gbc.gridheight = 4; - gbc.weightx = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel7.add(undoPane, gbc); - undoButton = new JButton(); - undoButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-undo-32.png"))); - undoButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - undoPane.add(undoButton, gbc); - showGraphViewerButton = new JButton(); - Font showGraphViewerButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, showGraphViewerButton.getFont()); - if (showGraphViewerButtonFont != null) { - showGraphViewerButton.setFont(showGraphViewerButtonFont); - } - showGraphViewerButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-tree-structure-32.png"))); - showGraphViewerButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 1; - gbc.weightx = 1.0; - gbc.fill = GridBagConstraints.BOTH; - undoPane.add(showGraphViewerButton, gbc); - filterPane = new JPanel(); - filterPane.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 2; - gbc.gridwidth = 2; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - undoPane.add(filterPane, gbc); - owlClassFilterCheckBox = new JCheckBox(); - Font owlClassFilterCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, owlClassFilterCheckBox.getFont()); - if (owlClassFilterCheckBoxFont != null) { - owlClassFilterCheckBox.setFont(owlClassFilterCheckBoxFont); - } - owlClassFilterCheckBox.setText("OWL Class"); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - filterPane.add(owlClassFilterCheckBox, gbc); - profileFilterCheckBox = new JCheckBox(); - Font profileFilterCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, profileFilterCheckBox.getFont()); - if (profileFilterCheckBoxFont != null) { - profileFilterCheckBox.setFont(profileFilterCheckBoxFont); + panel13.add(panel14, gbc); + Font exactMatchCheckBoxFont = this.$$$getFont$$$(null, -1, 14, exactMatchCheckBox.getFont()); + if (exactMatchCheckBoxFont != null) { + exactMatchCheckBox.setFont(exactMatchCheckBoxFont); } - profileFilterCheckBox.setText("Profile"); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - filterPane.add(profileFilterCheckBox, gbc); - redoButton = new JButton(); - redoButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-redo-32.png"))); - redoButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - undoPane.add(redoButton, gbc); - assignColorToClassButton = new JButton(); - assignColorToClassButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-color-dropper-filled-50 (Custom).png"))); - assignColorToClassButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 1; - gbc.weightx = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - undoPane.add(assignColorToClassButton, gbc); - annotationPaneButtons = new JPanel(); - annotationPaneButtons.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 0; - gbc.gridheight = 3; - gbc.weightx = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel7.add(annotationPaneButtons, gbc); - annotationPaneButtons.setBorder(BorderFactory.createTitledBorder(null, "Annotation", TitledBorder.CENTER, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, annotationPaneButtons.getFont()))); - final JPanel panel10 = new JPanel(); - panel10.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 1; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - annotationPaneButtons.add(panel10, gbc); - previousSpanButton = new JButton(); - previousSpanButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24 (reversed).png"))); - previousSpanButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel10.add(previousSpanButton, gbc); - nextSpanButton = new JButton(); - nextSpanButton.setHorizontalAlignment(0); - nextSpanButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24.png"))); - nextSpanButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel10.add(nextSpanButton, gbc); - final JPanel panel11 = new JPanel(); - panel11.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - annotationPaneButtons.add(panel11, gbc); - addAnnotationButton = new JButton(); - Font addAnnotationButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, addAnnotationButton.getFont()); - if (addAnnotationButtonFont != null) { - addAnnotationButton.setFont(addAnnotationButtonFont); + exactMatchCheckBox.setText("Exact"); + panel14.add(exactMatchCheckBox); + Font reviewRegexCheckBoxFont = this.$$$getFont$$$(null, Font.BOLD, 14, reviewRegexCheckBox.getFont()); + if (reviewRegexCheckBoxFont != null) { + reviewRegexCheckBox.setFont(reviewRegexCheckBoxFont); } - addAnnotationButton.setHorizontalTextPosition(0); - addAnnotationButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-plus-24.png"))); - addAnnotationButton.setText(""); - addAnnotationButton.setVerticalAlignment(0); - addAnnotationButton.setVerticalTextPosition(3); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - panel11.add(addAnnotationButton, gbc); - removeAnnotationButton = new JButton(); - Font removeAnnotationButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, removeAnnotationButton.getFont()); - if (removeAnnotationButtonFont != null) { - removeAnnotationButton.setFont(removeAnnotationButtonFont); + reviewRegexCheckBox.setText(".*"); + panel14.add(reviewRegexCheckBox); + final JScrollPane scrollPane4 = new JScrollPane(); + panel12.add(scrollPane4, BorderLayout.CENTER); + Font conceptAnnotationsForTextTableFont = this.$$$getFont$$$("Verdana", -1, 12, conceptAnnotationsForTextTable.getFont()); + if (conceptAnnotationsForTextTableFont != null) { + conceptAnnotationsForTextTable.setFont(conceptAnnotationsForTextTableFont); } - removeAnnotationButton.setHorizontalTextPosition(0); - removeAnnotationButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-delete-24.png"))); - removeAnnotationButton.setText(""); - removeAnnotationButton.setVerticalTextPosition(3); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - panel11.add(removeAnnotationButton, gbc); - oneClickGraphsCheckBox = new JCheckBox(); - oneClickGraphsCheckBox.setText("One Click Graphs"); - gbc = new GridBagConstraints(); - gbc.gridx = 3; - gbc.gridy = 0; - gbc.gridheight = 2; - gbc.weightx = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel7.add(oneClickGraphsCheckBox, gbc); - snapToWordsCheckBox = new JCheckBox(); - snapToWordsCheckBox.setSelected(true); - snapToWordsCheckBox.setText("Snap to words"); - gbc = new GridBagConstraints(); - gbc.gridx = 3; - gbc.gridy = 2; - gbc.gridwidth = 2; - gbc.weightx = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel7.add(snapToWordsCheckBox, gbc); - structuresRadioButton = new JRadioButton(); - structuresRadioButton.setText("Structures"); - gbc = new GridBagConstraints(); - gbc.gridx = 4; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel7.add(structuresRadioButton, gbc); - conceptsRadioButton = new JRadioButton(); - conceptsRadioButton.setText("Concepts"); - gbc = new GridBagConstraints(); - gbc.gridx = 4; - gbc.gridy = 1; - gbc.weightx = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel7.add(conceptsRadioButton, gbc); - final JPanel panel12 = new JPanel(); - panel12.setLayout(new GridBagLayout()); - header.addTab("Profile", panel12); + scrollPane4.setViewportView(conceptAnnotationsForTextTable); + final JPanel panel15 = new JPanel(); + panel15.setLayout(new GridBagLayout()); + reviewTabbedPane.addTab("Concept", panel15); final JScrollPane scrollPane5 = new JScrollPane(); gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel12.add(scrollPane5, gbc); - scrollPane5.setBorder(BorderFactory.createTitledBorder(null, "Colors", TitledBorder.CENTER, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, scrollPane5.getFont()))); - Font colorListFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, colorList.getFont()); - if (colorListFont != null) { - colorList.setFont(colorListFont); - } - scrollPane5.setViewportView(colorList); - final JPanel panel13 = new JPanel(); - panel13.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel12.add(panel13, gbc); - panel13.setBorder(BorderFactory.createTitledBorder(null, "Profiles", TitledBorder.CENTER, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel13.getFont()))); - final JScrollPane scrollPane6 = new JScrollPane(); - gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 1; + gbc.gridwidth = 2; gbc.weightx = 1.0; gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; - panel13.add(scrollPane6, gbc); - Font profileListFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 12, profileList.getFont()); - if (profileListFont != null) { - profileList.setFont(profileListFont); - } - scrollPane6.setViewportView(profileList); - final JPanel panel14 = new JPanel(); - panel14.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel13.add(panel14, gbc); - addProfileButton = new JButton(); - Font addProfileButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, addProfileButton.getFont()); - if (addProfileButtonFont != null) { - addProfileButton.setFont(addProfileButtonFont); - } - addProfileButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-plus-24.png"))); - addProfileButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - panel14.add(addProfileButton, gbc); - removeProfileButton = new JButton(); - removeProfileButton.setEnabled(true); - Font removeProfileButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, removeProfileButton.getFont()); - if (removeProfileButtonFont != null) { - removeProfileButton.setFont(removeProfileButtonFont); - } - removeProfileButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-delete-24.png"))); - removeProfileButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - panel14.add(removeProfileButton, gbc); - iaaPane = new JPanel(); - iaaPane.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 2; - gbc.gridy = 0; - gbc.weighty = 1.0; - panel12.add(iaaPane, gbc); - iaaPane.setBorder(BorderFactory.createTitledBorder(null, "IAA", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, iaaPane.getFont()))); - runIaaButton = new JButton(); - Font runIaaButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, runIaaButton.getFont()); - if (runIaaButtonFont != null) { - runIaaButton.setFont(runIaaButtonFont); - } - this.$$$loadButtonText$$$(runIaaButton, ResourceBundle.getBundle("log4j").getString("run.iaa")); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 3; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - iaaPane.add(runIaaButton, gbc); - iaaSpanCheckBox = new JCheckBox(); - Font iaaSpanCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, iaaSpanCheckBox.getFont()); - if (iaaSpanCheckBoxFont != null) { - iaaSpanCheckBox.setFont(iaaSpanCheckBoxFont); - } - this.$$$loadButtonText$$$(iaaSpanCheckBox, ResourceBundle.getBundle("ui").getString("span1")); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 1; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - iaaPane.add(iaaSpanCheckBox, gbc); - iaaClassAndSpanCheckBox = new JCheckBox(); - Font iaaClassAndSpanCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, iaaClassAndSpanCheckBox.getFont()); - if (iaaClassAndSpanCheckBoxFont != null) { - iaaClassAndSpanCheckBox.setFont(iaaClassAndSpanCheckBoxFont); - } - this.$$$loadButtonText$$$(iaaClassAndSpanCheckBox, ResourceBundle.getBundle("ui").getString("class.and.span")); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 2; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - iaaPane.add(iaaClassAndSpanCheckBox, gbc); - iaaClassCheckBox = new JCheckBox(); - Font iaaClassCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, iaaClassCheckBox.getFont()); - if (iaaClassCheckBoxFont != null) { - iaaClassCheckBox.setFont(iaaClassCheckBoxFont); - } - this.$$$loadButtonText$$$(iaaClassCheckBox, ResourceBundle.getBundle("log4j").getString("class1")); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - iaaPane.add(iaaClassCheckBox, gbc); - final JPanel panel15 = new JPanel(); - panel15.setLayout(new GridBagLayout()); - header.addTab("Search", panel15); - Font searchTextFieldFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, searchTextField.getFont()); - if (searchTextFieldFont != null) { - searchTextField.setFont(searchTextFieldFont); + panel15.add(scrollPane5, gbc); + Font annotationsForClassTableFont = this.$$$getFont$$$("Verdana", -1, 12, annotationsForClassTable.getFont()); + if (annotationsForClassTableFont != null) { + annotationsForClassTable.setFont(annotationsForClassTableFont); } - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 0; - gbc.gridwidth = 3; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel15.add(searchTextField, gbc); + scrollPane5.setViewportView(annotationsForClassTable); final JPanel panel16 = new JPanel(); panel16.setLayout(new GridBagLayout()); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; gbc.weightx = 1.0; - gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; panel15.add(panel16, gbc); - nextMatchButton = new JButton(); - Font nextMatchButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, nextMatchButton.getFont()); - if (nextMatchButtonFont != null) { - nextMatchButton.setFont(nextMatchButtonFont); - } - nextMatchButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24.png"))); - nextMatchButton.setText(""); + panel16.setBorder(BorderFactory.createTitledBorder(null, "OWL Class", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel16.getFont()), null)); + previousConceptReviewButton = new JButton(); + previousConceptReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-sort-up-24.png"))); + previousConceptReviewButton.setText(""); + previousConceptReviewButton.setToolTipText("Previous match"); gbc = new GridBagConstraints(); gbc.gridx = 1; gbc.gridy = 0; - gbc.weightx = 1.0; gbc.weighty = 1.0; gbc.fill = GridBagConstraints.HORIZONTAL; - panel16.add(nextMatchButton, gbc); - previousMatchButton = new JButton(); - Font previousMatchButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, previousMatchButton.getFont()); - if (previousMatchButtonFont != null) { - previousMatchButton.setFont(previousMatchButtonFont); - } - previousMatchButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24 (reversed).png"))); - previousMatchButton.setText(""); + panel16.add(previousConceptReviewButton, gbc); + nextConceptReviewButton = new JButton(); + nextConceptReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-sort-down-24.png"))); + nextConceptReviewButton.setText(""); + nextConceptReviewButton.setToolTipText("Next match"); gbc = new GridBagConstraints(); - gbc.gridx = 0; + gbc.gridx = 2; gbc.gridy = 0; - gbc.weightx = 1.0; gbc.weighty = 1.0; gbc.fill = GridBagConstraints.HORIZONTAL; - panel16.add(previousMatchButton, gbc); - findTextInOntologyButton = new JButton(); - Font findTextInOntologyButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, findTextInOntologyButton.getFont()); - if (findTextInOntologyButtonFont != null) { - findTextInOntologyButton.setFont(findTextInOntologyButtonFont); + panel16.add(nextConceptReviewButton, gbc); + Font owlClassLabelFont = this.$$$getFont$$$(null, -1, 12, owlClassLabel.getFont()); + if (owlClassLabelFont != null) { + owlClassLabel.setFont(owlClassLabelFont); } - this.$$$loadButtonText$$$(findTextInOntologyButton, ResourceBundle.getBundle("log4j").getString("find.in.ontology1")); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 1; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - panel15.add(findTextInOntologyButton, gbc); - Font onlyAnnotationsCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, onlyAnnotationsCheckBox.getFont()); - if (onlyAnnotationsCheckBoxFont != null) { - onlyAnnotationsCheckBox.setFont(onlyAnnotationsCheckBoxFont); - } - onlyAnnotationsCheckBox.setText("Only in Annotations"); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 1; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - panel15.add(onlyAnnotationsCheckBox, gbc); - Font regexCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, regexCheckBox.getFont()); - if (regexCheckBoxFont != null) { - regexCheckBox.setFont(regexCheckBoxFont); - } - regexCheckBox.setText("Regex"); - gbc = new GridBagConstraints(); - gbc.gridx = 2; - gbc.gridy = 1; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel15.add(regexCheckBox, gbc); - Font caseSensitiveCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, caseSensitiveCheckBox.getFont()); - if (caseSensitiveCheckBoxFont != null) { - caseSensitiveCheckBox.setFont(caseSensitiveCheckBoxFont); - } - caseSensitiveCheckBox.setText("Case Sensitive"); - gbc = new GridBagConstraints(); - gbc.gridx = 3; - gbc.gridy = 1; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel15.add(caseSensitiveCheckBox, gbc); - final JPanel panel17 = new JPanel(); - panel17.setLayout(new GridBagLayout()); - header.addTab("Review", panel17); - final JPanel panel18 = new JPanel(); - panel18.setLayout(new GridBagLayout()); + owlClassLabel.setText("Select a class and click refresh."); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; - gbc.gridwidth = 2; gbc.weightx = 1.0; gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel17.add(panel18, gbc); - reviewTabbedPane = new JTabbedPane(); - Font reviewTabbedPaneFont = this.$$$getFont$$$("Verdana", -1, 14, reviewTabbedPane.getFont()); - if (reviewTabbedPaneFont != null) { - reviewTabbedPane.setFont(reviewTabbedPaneFont); + gbc.anchor = GridBagConstraints.WEST; + panel16.add(owlClassLabel, gbc); + Font includeClassDescendantsCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 12, includeClassDescendantsCheckBox.getFont()); + if (includeClassDescendantsCheckBoxFont != null) { + includeClassDescendantsCheckBox.setFont(includeClassDescendantsCheckBoxFont); } - reviewTabbedPane.setTabPlacement(2); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel18.add(reviewTabbedPane, gbc); - final JPanel panel19 = new JPanel(); - panel19.setLayout(new GridBagLayout()); - reviewTabbedPane.addTab("Text", panel19); - final JScrollPane scrollPane7 = new JScrollPane(); + this.$$$loadButtonText$$$(includeClassDescendantsCheckBox, this.$$$getMessageFromBundle$$$("log4j", "include.descendants")); + includeClassDescendantsCheckBox.setToolTipText("Toggle include descendants of currently selected OWL class"); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 1; - gbc.gridwidth = 5; gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel19.add(scrollPane7, gbc); - Font conceptAnnotationsForTextTableFont = this.$$$getFont$$$("Verdana", -1, 12, conceptAnnotationsForTextTable.getFont()); - if (conceptAnnotationsForTextTableFont != null) { - conceptAnnotationsForTextTable.setFont(conceptAnnotationsForTextTableFont); - } - scrollPane7.setViewportView(conceptAnnotationsForTextTable); - Font exactMatchCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 12, exactMatchCheckBox.getFont()); - if (exactMatchCheckBoxFont != null) { - exactMatchCheckBox.setFont(exactMatchCheckBoxFont); - } - this.$$$loadButtonText$$$(exactMatchCheckBox, ResourceBundle.getBundle("log4j").getString("exact.match")); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel19.add(exactMatchCheckBox, gbc); - final JPanel panel20 = new JPanel(); - panel20.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel19.add(panel20, gbc); - panel20.setBorder(BorderFactory.createTitledBorder(null, "Text", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel20.getFont()))); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.weighty = 1.0; gbc.anchor = GridBagConstraints.WEST; - gbc.fill = GridBagConstraints.HORIZONTAL; - panel20.add(annotationsContainingTextTextField, gbc); - final JPanel panel21 = new JPanel(); - panel21.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 2; - gbc.gridy = 0; - gbc.gridwidth = 3; - gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel19.add(panel21, gbc); - previousTextReviewButton = new JButton(); - previousTextReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24 (reversed).png"))); - previousTextReviewButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - panel21.add(previousTextReviewButton, gbc); - nextTextReviewButton = new JButton(); - nextTextReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24.png"))); - nextTextReviewButton.setText(""); + panel16.add(includeClassDescendantsCheckBox, gbc); + refreshConceptReviewButton = new JButton(); + refreshConceptReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-synchronize-32.png"))); + refreshConceptReviewButton.setText(""); + refreshConceptReviewButton.setToolTipText("Refresh with currently selected OWL class"); gbc = new GridBagConstraints(); gbc.gridx = 1; - gbc.gridy = 0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - panel21.add(nextTextReviewButton, gbc); - refreshTextReviewButton = new JButton(); - refreshTextReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-synchronize-32.png"))); - refreshTextReviewButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 2; - gbc.gridy = 0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - panel21.add(refreshTextReviewButton, gbc); - final JPanel panel22 = new JPanel(); - panel22.setLayout(new GridBagLayout()); - reviewTabbedPane.addTab("Concept", panel22); - final JScrollPane scrollPane8 = new JScrollPane(); - gbc = new GridBagConstraints(); - gbc.gridx = 0; gbc.gridy = 1; - gbc.gridwidth = 3; - gbc.weightx = 1.0; + gbc.gridwidth = 2; gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel22.add(scrollPane8, gbc); - Font annotationsForClassTableFont = this.$$$getFont$$$("Verdana", -1, 12, annotationsForClassTable.getFont()); - if (annotationsForClassTableFont != null) { - annotationsForClassTable.setFont(annotationsForClassTableFont); - } - scrollPane8.setViewportView(annotationsForClassTable); - Font includeClassDescendantsCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 12, includeClassDescendantsCheckBox.getFont()); - if (includeClassDescendantsCheckBoxFont != null) { - includeClassDescendantsCheckBox.setFont(includeClassDescendantsCheckBoxFont); - } - this.$$$loadButtonText$$$(includeClassDescendantsCheckBox, ResourceBundle.getBundle("log4j").getString("include.descendants")); - gbc = new GridBagConstraints(); - gbc.gridx = 1; - gbc.gridy = 0; - gbc.weightx = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel22.add(includeClassDescendantsCheckBox, gbc); - final JPanel panel23 = new JPanel(); - panel23.setLayout(new GridBagLayout()); + gbc.fill = GridBagConstraints.HORIZONTAL; + panel16.add(refreshConceptReviewButton, gbc); + final JPanel panel17 = new JPanel(); + panel17.setLayout(new GridBagLayout()); + reviewTabbedPane.addTab("Relation", panel17); + final JScrollPane scrollPane6 = new JScrollPane(); gbc = new GridBagConstraints(); gbc.gridx = 0; - gbc.gridy = 0; + gbc.gridy = 1; + gbc.gridwidth = 2; gbc.weightx = 1.0; + gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; - panel22.add(panel23, gbc); - panel23.setBorder(BorderFactory.createTitledBorder(null, "OWL Class", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel23.getFont()))); - owlClassLabel.setText(""); + panel17.add(scrollPane6, gbc); + Font relationsForPropertyListFont = this.$$$getFont$$$("Verdana", -1, 12, relationsForPropertyList.getFont()); + if (relationsForPropertyListFont != null) { + relationsForPropertyList.setFont(relationsForPropertyListFont); + } + scrollPane6.setViewportView(relationsForPropertyList); + final JPanel panel18 = new JPanel(); + panel18.setLayout(new GridBagLayout()); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; gbc.weightx = 1.0; - gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel23.add(owlClassLabel, gbc); - final JPanel panel24 = new JPanel(); - panel24.setLayout(new GridBagLayout()); - gbc = new GridBagConstraints(); - gbc.gridx = 2; - gbc.gridy = 0; - gbc.weightx = 1.0; gbc.fill = GridBagConstraints.BOTH; - panel22.add(panel24, gbc); - previousConceptReviewButton = new JButton(); - previousConceptReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24 (reversed).png"))); - previousConceptReviewButton.setText(""); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - panel24.add(previousConceptReviewButton, gbc); - nextConceptReviewButton = new JButton(); - nextConceptReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24.png"))); - nextConceptReviewButton.setText(""); + panel17.add(panel18, gbc); + panel18.setBorder(BorderFactory.createTitledBorder(null, "OWL Object Property", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel18.getFont()), null)); + previousRelationReviewButton = new JButton(); + previousRelationReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-sort-up-24.png"))); + previousRelationReviewButton.setText(""); + previousRelationReviewButton.setToolTipText("Previous match"); gbc = new GridBagConstraints(); gbc.gridx = 1; gbc.gridy = 0; gbc.weighty = 1.0; gbc.fill = GridBagConstraints.HORIZONTAL; - panel24.add(nextConceptReviewButton, gbc); - refreshConceptReviewButton = new JButton(); - refreshConceptReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-synchronize-32.png"))); - refreshConceptReviewButton.setText(""); + panel18.add(previousRelationReviewButton, gbc); + nextRelationReviewButton = new JButton(); + nextRelationReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-sort-down-24.png"))); + nextRelationReviewButton.setText(""); + nextRelationReviewButton.setToolTipText("Next match"); gbc = new GridBagConstraints(); gbc.gridx = 2; gbc.gridy = 0; gbc.weighty = 1.0; gbc.fill = GridBagConstraints.HORIZONTAL; - panel24.add(refreshConceptReviewButton, gbc); - final JPanel panel25 = new JPanel(); - panel25.setLayout(new GridBagLayout()); - reviewTabbedPane.addTab("Relation", panel25); - final JScrollPane scrollPane9 = new JScrollPane(); + panel18.add(nextRelationReviewButton, gbc); + Font owlPropertyLabelFont = this.$$$getFont$$$(null, -1, 12, owlPropertyLabel.getFont()); + if (owlPropertyLabelFont != null) { + owlPropertyLabel.setFont(owlPropertyLabelFont); + } + owlPropertyLabel.setText("Select an object property and click refresh."); gbc = new GridBagConstraints(); gbc.gridx = 0; - gbc.gridy = 1; - gbc.gridwidth = 3; + gbc.gridy = 0; gbc.weightx = 1.0; gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.BOTH; - panel25.add(scrollPane9, gbc); - Font relationsForPropertyListFont = this.$$$getFont$$$("Verdana", -1, 12, relationsForPropertyList.getFont()); - if (relationsForPropertyListFont != null) { - relationsForPropertyList.setFont(relationsForPropertyListFont); - } - scrollPane9.setViewportView(relationsForPropertyList); + gbc.anchor = GridBagConstraints.WEST; + panel18.add(owlPropertyLabel, gbc); Font includePropertyDescendantsCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 12, includePropertyDescendantsCheckBox.getFont()); if (includePropertyDescendantsCheckBoxFont != null) { includePropertyDescendantsCheckBox.setFont(includePropertyDescendantsCheckBoxFont); } - this.$$$loadButtonText$$$(includePropertyDescendantsCheckBox, ResourceBundle.getBundle("log4j").getString("include.descendants1")); + this.$$$loadButtonText$$$(includePropertyDescendantsCheckBox, this.$$$getMessageFromBundle$$$("log4j", "include.descendants1")); + includePropertyDescendantsCheckBox.setToolTipText("Toggle include descendants of currently selected OWL object property"); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 1; + gbc.weightx = 1.0; + gbc.anchor = GridBagConstraints.WEST; + panel18.add(includePropertyDescendantsCheckBox, gbc); + refreshRelationReviewButton = new JButton(); + refreshRelationReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-synchronize-32.png"))); + refreshRelationReviewButton.setText(""); + refreshRelationReviewButton.setToolTipText("Refresh with currently selected OWL object property"); gbc = new GridBagConstraints(); gbc.gridx = 1; + gbc.gridy = 1; + gbc.gridwidth = 2; + gbc.weighty = 1.0; + gbc.fill = GridBagConstraints.HORIZONTAL; + panel18.add(refreshRelationReviewButton, gbc); + final JPanel panel19 = new JPanel(); + panel19.setLayout(new GridBagLayout()); + header.addTab("Settings", panel19); + oneClickGraphsCheckBox = new JCheckBox(); + oneClickGraphsCheckBox.setText("One Click Graphs"); + gbc = new GridBagConstraints(); + gbc.gridx = 0; gbc.gridy = 0; gbc.weightx = 1.0; gbc.anchor = GridBagConstraints.WEST; - panel25.add(includePropertyDescendantsCheckBox, gbc); - final JPanel panel26 = new JPanel(); - panel26.setLayout(new GridBagLayout()); + panel19.add(oneClickGraphsCheckBox, gbc); + snapToWordsCheckBox = new JCheckBox(); + snapToWordsCheckBox.setSelected(true); + snapToWordsCheckBox.setText("Snap to words"); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 1; + gbc.weightx = 1.0; + gbc.anchor = GridBagConstraints.WEST; + panel19.add(snapToWordsCheckBox, gbc); + final JPanel panel20 = new JPanel(); + panel20.setLayout(new BorderLayout(0, 0)); + body.setLeftComponent(panel20); + final JScrollPane scrollPane7 = new JScrollPane(); + panel20.add(scrollPane7, BorderLayout.CENTER); + textPane.setMinimumSize(new Dimension(200, 22)); + textPane.setPreferredSize(new Dimension(500, 500)); + textPane.setText(""); + scrollPane7.setViewportView(textPane); + final JPanel panel21 = new JPanel(); + panel21.setLayout(new GridBagLayout()); + panel20.add(panel21, BorderLayout.SOUTH); + final JPanel panel22 = new JPanel(); + panel22.setLayout(new BorderLayout(0, 0)); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; gbc.weightx = 1.0; gbc.fill = GridBagConstraints.BOTH; - panel25.add(panel26, gbc); - panel26.setBorder(BorderFactory.createTitledBorder(null, "OWL Object Property", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel26.getFont()))); - Font owlPropertyLabelFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, owlPropertyLabel.getFont()); - if (owlPropertyLabelFont != null) { - owlPropertyLabel.setFont(owlPropertyLabelFont); + panel21.add(panel22, gbc); + final JPanel panel23 = new JPanel(); + panel23.setLayout(new FlowLayout(FlowLayout.RIGHT, 5, 5)); + panel22.add(panel23, BorderLayout.EAST); + profileFilterCheckBox = new JCheckBox(); + Font profileFilterCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, profileFilterCheckBox.getFont()); + if (profileFilterCheckBoxFont != null) { + profileFilterCheckBox.setFont(profileFilterCheckBoxFont); + } + profileFilterCheckBox.setText("Current Profile"); + profileFilterCheckBox.setToolTipText("Toggle filter annotations by current profile"); + panel23.add(profileFilterCheckBox); + owlClassFilterCheckBox = new JCheckBox(); + Font owlClassFilterCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, owlClassFilterCheckBox.getFont()); + if (owlClassFilterCheckBoxFont != null) { + owlClassFilterCheckBox.setFont(owlClassFilterCheckBoxFont); } - owlPropertyLabel.setText(""); + owlClassFilterCheckBox.setText("Current OWL Class"); + owlClassFilterCheckBox.setToolTipText("Toggle filter annotations by current OWL class"); + panel23.add(owlClassFilterCheckBox); + captureImageButton = new JButton(); + captureImageButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-unsplash-32.png"))); + captureImageButton.setText(""); + captureImageButton.setToolTipText("Capture document"); + panel23.add(captureImageButton); + final JPanel panel24 = new JPanel(); + panel24.setLayout(new GridBagLayout()); + panel23.add(panel24); + panel24.setBorder(BorderFactory.createTitledBorder(null, "Font Size", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, null, null)); + fontSizeSlider = new JSlider(); + fontSizeSlider.setInverted(false); + fontSizeSlider.setMajorTickSpacing(8); + fontSizeSlider.setMaximum(28); + fontSizeSlider.setMinimum(8); + fontSizeSlider.setMinorTickSpacing(1); + fontSizeSlider.setSnapToTicks(true); + fontSizeSlider.setValue(16); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; gbc.weightx = 1.0; gbc.weighty = 1.0; - gbc.anchor = GridBagConstraints.WEST; - panel26.add(owlPropertyLabel, gbc); + gbc.fill = GridBagConstraints.BOTH; + panel24.add(fontSizeSlider, gbc); + final JPanel panel25 = new JPanel(); + panel25.setLayout(new FlowLayout(FlowLayout.CENTER, 5, 5)); + panel22.add(panel25, BorderLayout.WEST); + addTextSourceButton = new JButton(); + addTextSourceButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-plus-24.png"))); + addTextSourceButton.setText(""); + addTextSourceButton.setToolTipText("Add a document"); + panel25.add(addTextSourceButton); + removeTextSourceButton = new JButton(); + removeTextSourceButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-delete-24.png"))); + removeTextSourceButton.setText(""); + removeTextSourceButton.setToolTipText("Remove current document from display"); + panel25.add(removeTextSourceButton); + final JPanel panel26 = new JPanel(); + panel26.setLayout(new BorderLayout(0, 0)); + panel20.add(panel26, BorderLayout.NORTH); final JPanel panel27 = new JPanel(); - panel27.setLayout(new GridBagLayout()); + panel27.setLayout(new BorderLayout(0, 0)); + panel26.add(panel27, BorderLayout.CENTER); + final JPanel panel28 = new JPanel(); + panel28.setLayout(new GridBagLayout()); + panel27.add(panel28, BorderLayout.WEST); + panel28.setBorder(BorderFactory.createTitledBorder(null, "", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$(null, -1, 14, panel28.getFont()), null)); + profileButton = new JButton(); + Font profileButtonFont = this.$$$getFont$$$(null, Font.BOLD, 12, profileButton.getFont()); + if (profileButtonFont != null) { + profileButton.setFont(profileButtonFont); + } + profileButton.setText("Active Profile:"); gbc = new GridBagConstraints(); - gbc.gridx = 2; + gbc.gridx = 0; gbc.gridy = 0; - gbc.weightx = 1.0; + panel28.add(profileButton, gbc); + final JPanel panel29 = new JPanel(); + panel29.setLayout(new FlowLayout(FlowLayout.CENTER, 5, 5)); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 1; + gbc.gridwidth = 2; gbc.fill = GridBagConstraints.BOTH; - panel25.add(panel27, gbc); - previousRelationReviewButton = new JButton(); - previousRelationReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24 (reversed).png"))); - previousRelationReviewButton.setText(""); + panel28.add(panel29, gbc); + addAnnotationButton = new JButton(); + Font addAnnotationButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, addAnnotationButton.getFont()); + if (addAnnotationButtonFont != null) { + addAnnotationButton.setFont(addAnnotationButtonFont); + } + addAnnotationButton.setHorizontalTextPosition(0); + addAnnotationButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-plus-24.png"))); + addAnnotationButton.setText(""); + addAnnotationButton.setToolTipText("Add annotation or span"); + addAnnotationButton.setVerticalAlignment(0); + addAnnotationButton.setVerticalTextPosition(3); + panel29.add(addAnnotationButton); + removeAnnotationButton = new JButton(); + Font removeAnnotationButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, removeAnnotationButton.getFont()); + if (removeAnnotationButtonFont != null) { + removeAnnotationButton.setFont(removeAnnotationButtonFont); + } + removeAnnotationButton.setHorizontalTextPosition(0); + removeAnnotationButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-delete-24.png"))); + removeAnnotationButton.setText(""); + removeAnnotationButton.setToolTipText("Remove annotation or span"); + removeAnnotationButton.setVerticalTextPosition(3); + panel29.add(removeAnnotationButton); + showGraphViewerButton = new JButton(); + Font showGraphViewerButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, showGraphViewerButton.getFont()); + if (showGraphViewerButtonFont != null) { + showGraphViewerButton.setFont(showGraphViewerButtonFont); + } + showGraphViewerButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-tree-structure-32.png"))); + showGraphViewerButton.setText(""); + showGraphViewerButton.setToolTipText("Open graph space viewer for document"); + panel29.add(showGraphViewerButton); + final JPanel panel30 = new JPanel(); + panel30.setLayout(new GridBagLayout()); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 2; + gbc.gridwidth = 2; + gbc.fill = GridBagConstraints.BOTH; + panel28.add(panel30, gbc); + previousTextSourceButton = new JButton(); + previousTextSourceButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24 (reversed).png"))); + previousTextSourceButton.setText(""); + previousTextSourceButton.setToolTipText("Next document"); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - panel27.add(previousRelationReviewButton, gbc); - nextRelationReviewButton = new JButton(); - nextRelationReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24.png"))); - nextRelationReviewButton.setText(""); + panel30.add(previousTextSourceButton, gbc); + nextTextSourceButton = new JButton(); + nextTextSourceButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-advance-24.png"))); + nextTextSourceButton.setText(""); + nextTextSourceButton.setToolTipText("Previous document"); gbc = new GridBagConstraints(); gbc.gridx = 1; gbc.gridy = 0; - gbc.weighty = 1.0; - gbc.fill = GridBagConstraints.HORIZONTAL; - panel27.add(nextRelationReviewButton, gbc); - refreshRelationReviewButton = new JButton(); - refreshRelationReviewButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-synchronize-32.png"))); - refreshRelationReviewButton.setText(""); + panel30.add(nextTextSourceButton, gbc); + textSourceChooser.setPreferredSize(new Dimension(150, 24)); + textSourceChooser.setToolTipText("Choose a document to view"); gbc = new GridBagConstraints(); gbc.gridx = 2; gbc.gridy = 0; + panel30.add(textSourceChooser, gbc); + Font activeProfileLabelFont = this.$$$getFont$$$(null, -1, -1, activeProfileLabel.getFont()); + if (activeProfileLabelFont != null) { + activeProfileLabel.setFont(activeProfileLabelFont); + } + activeProfileLabel.setText(""); + gbc = new GridBagConstraints(); + gbc.gridx = 1; + gbc.gridy = 0; + panel28.add(activeProfileLabel, gbc); + final JPanel panel31 = new JPanel(); + panel31.setLayout(new GridBagLayout()); + panel27.add(panel31, BorderLayout.CENTER); + Font searchTextFieldFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, searchTextField.getFont()); + if (searchTextFieldFont != null) { + searchTextField.setFont(searchTextFieldFont); + } + searchTextField.setToolTipText("Find in document"); + gbc = new GridBagConstraints(); + gbc.gridx = 1; + gbc.gridy = 0; + gbc.gridwidth = 2; + gbc.weightx = 1.0; gbc.weighty = 1.0; gbc.fill = GridBagConstraints.HORIZONTAL; - panel27.add(refreshRelationReviewButton, gbc); - filePanel = new JPanel(); - filePanel.setLayout(new GridBagLayout()); - cardPanel.add(filePanel, "File"); - progressBar = new JProgressBar(); - progressBar.setStringPainted(true); + panel31.add(searchTextField, gbc); + final JLabel label5 = new JLabel(); + label5.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-search-52.png"))); + label5.setText(""); gbc = new GridBagConstraints(); gbc.gridx = 0; - gbc.gridy = 2; - gbc.gridwidth = 5; - gbc.fill = GridBagConstraints.HORIZONTAL; - filePanel.add(progressBar, gbc); - final JScrollPane scrollPane10 = new JScrollPane(); + gbc.gridy = 0; + gbc.anchor = GridBagConstraints.WEST; + panel31.add(label5, gbc); + final JPanel panel32 = new JPanel(); + panel32.setLayout(new FlowLayout(FlowLayout.RIGHT, 5, 5)); gbc = new GridBagConstraints(); - gbc.gridx = 0; + gbc.gridx = 2; gbc.gridy = 1; - gbc.gridwidth = 2; - gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; - filePanel.add(scrollPane10, gbc); + panel31.add(panel32, gbc); + Font onlyAnnotationsCheckBoxFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, onlyAnnotationsCheckBox.getFont()); + if (onlyAnnotationsCheckBoxFont != null) { + onlyAnnotationsCheckBox.setFont(onlyAnnotationsCheckBoxFont); + } + onlyAnnotationsCheckBox.setText("Only in Annotations"); + onlyAnnotationsCheckBox.setToolTipText("Toggle search for text contained only in annotations"); + panel32.add(onlyAnnotationsCheckBox); + Font regexCheckBoxFont = this.$$$getFont$$$(null, Font.BOLD, 14, regexCheckBox.getFont()); + if (regexCheckBoxFont != null) { + regexCheckBox.setFont(regexCheckBoxFont); + } + regexCheckBox.setText(".*"); + regexCheckBox.setToolTipText("Toggle regex search"); + panel32.add(regexCheckBox); + Font caseSensitiveCheckBoxFont = this.$$$getFont$$$(null, Font.BOLD, 12, caseSensitiveCheckBox.getFont()); + if (caseSensitiveCheckBoxFont != null) { + caseSensitiveCheckBox.setFont(caseSensitiveCheckBoxFont); + } + caseSensitiveCheckBox.setText("Aa"); + caseSensitiveCheckBox.setToolTipText("Toggle case sensitive search"); + panel32.add(caseSensitiveCheckBox); + findTextInOntologyButton = new JButton(); + Font findTextInOntologyButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, findTextInOntologyButton.getFont()); + if (findTextInOntologyButtonFont != null) { + findTextInOntologyButton.setFont(findTextInOntologyButtonFont); + } + this.$$$loadButtonText$$$(findTextInOntologyButton, this.$$$getMessageFromBundle$$$("log4j", "find.in.ontology1")); + findTextInOntologyButton.setToolTipText("Search for match using Protege"); + gbc = new GridBagConstraints(); + gbc.gridx = 3; + gbc.gridy = 1; + panel31.add(findTextInOntologyButton, gbc); + final JPanel panel33 = new JPanel(); + panel33.setLayout(new FlowLayout(FlowLayout.LEFT, 5, 5)); + gbc = new GridBagConstraints(); + gbc.gridx = 3; + gbc.gridy = 0; + gbc.fill = GridBagConstraints.BOTH; + panel31.add(panel33, gbc); + previousMatchButton = new JButton(); + Font previousMatchButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, previousMatchButton.getFont()); + if (previousMatchButtonFont != null) { + previousMatchButton.setFont(previousMatchButtonFont); + } + previousMatchButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-sort-up-24.png"))); + previousMatchButton.setText(""); + previousMatchButton.setToolTipText("Previous match"); + panel33.add(previousMatchButton); + nextMatchButton = new JButton(); + Font nextMatchButtonFont = this.$$$getFont$$$("Verdana", Font.PLAIN, 10, nextMatchButton.getFont()); + if (nextMatchButtonFont != null) { + nextMatchButton.setFont(nextMatchButtonFont); + } + nextMatchButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-sort-down-24.png"))); + nextMatchButton.setText(""); + nextMatchButton.setToolTipText("Next match"); + panel33.add(nextMatchButton); + final JPanel panel34 = new JPanel(); + panel34.setLayout(new FlowLayout(FlowLayout.LEFT, 5, 5)); + panel26.add(panel34, BorderLayout.NORTH); + final JToolBar toolBar1 = new JToolBar(); + toolBar1.setFloatable(false); + panel34.add(toolBar1); + fileButton = new JButton(); + fileButton.setText("File"); + toolBar1.add(fileButton); + undoButton = new JButton(); + undoButton.setHorizontalAlignment(0); + undoButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-undo-52.png"))); + undoButton.setText(""); + undoButton.setToolTipText("Undo"); + toolBar1.add(undoButton); + redoButton = new JButton(); + redoButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-redo-52.png"))); + redoButton.setText(""); + redoButton.setToolTipText("Redo"); + toolBar1.add(redoButton); + filePanel = new JPanel(); + filePanel.setLayout(new BorderLayout(0, 0)); + cardPanel.add(filePanel, "File"); + final JScrollPane scrollPane8 = new JScrollPane(); + filePanel.add(scrollPane8, BorderLayout.CENTER); fileList = new JList(); Font fileListFont = this.$$$getFont$$$("Verdana", Font.BOLD, 14, fileList.getFont()); if (fileListFont != null) { @@ -2118,18 +1802,17 @@ public boolean isSnapToWords() { defaultListModel1.addElement("Import"); defaultListModel1.addElement("Export"); fileList.setModel(defaultListModel1); - scrollPane10.setViewportView(fileList); + scrollPane8.setViewportView(fileList); + final JPanel panel35 = new JPanel(); + panel35.setLayout(new BorderLayout(0, 0)); + filePanel.add(panel35, BorderLayout.NORTH); + progressBar = new JProgressBar(); + progressBar.setStringPainted(true); + panel35.add(progressBar, BorderLayout.CENTER); backButton = new JButton(); backButton.setText("Back"); - gbc = new GridBagConstraints(); - gbc.gridx = 0; - gbc.gridy = 0; - gbc.fill = GridBagConstraints.HORIZONTAL; - filePanel.add(backButton, gbc); - ButtonGroup buttonGroup; - buttonGroup = new ButtonGroup(); - buttonGroup.add(structuresRadioButton); - buttonGroup.add(conceptsRadioButton); + panel35.add(backButton, BorderLayout.WEST); + label5.setLabelFor(searchTextField); } /** @@ -2153,6 +1836,23 @@ public boolean isSnapToWords() { return new Font(resultName, style >= 0 ? style : currentFont.getStyle(), size >= 0 ? size : currentFont.getSize()); } + private static Method $$$cachedGetBundleMethod$$$ = null; + + private String $$$getMessageFromBundle$$$(String path, String key) { + ResourceBundle bundle; + try { + Class thisClass = this.getClass(); + if ($$$cachedGetBundleMethod$$$ == null) { + Class dynamicBundleClass = thisClass.getClassLoader().loadClass("com.intellij.DynamicBundle"); + $$$cachedGetBundleMethod$$$ = dynamicBundleClass.getMethod("getBundle", String.class, Class.class); + } + bundle = (ResourceBundle) $$$cachedGetBundleMethod$$$.invoke(null, path, thisClass); + } catch (Exception e) { + bundle = ResourceBundle.getBundle(path); + } + return bundle.getString(key); + } + /** * @noinspection ALL */ diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/Loader.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/Loader.java index ecfd79fb..a52cd6a5 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/Loader.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/Loader.java @@ -34,9 +34,13 @@ import java.io.File; import java.util.Objects; import javax.swing.JComponent; +import javax.swing.JOptionPane; import javax.swing.JProgressBar; +import javax.swing.JScrollPane; import javax.swing.JTabbedPane; +import javax.swing.JTable; import javax.swing.SwingWorker; +import javax.swing.table.DefaultTableModel; /** The type Loader. */ public class Loader extends SwingWorker implements ModelListener { @@ -100,6 +104,27 @@ protected Object doInBackground() throws Exception { progressBar1.setValue(0); view.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); view.loadProject(file, this); + + view.getModel().ifPresent(model -> { + if (!model.getOWLClassNotFoundAnnotations().isEmpty()) { + JTable message = new JTable(); + message.setAutoCreateRowSorter(true); + message.setModel( + new DefaultTableModel( + new Object[][] {}, new String[] {"Annotation ID", "OWL class not found"}) { + @Override + public boolean isCellEditable(int row, int col) { + return false; + } + }); + for (String[] item : model.getOWLClassNotFoundAnnotations()) { + ((DefaultTableModel) message.getModel()) + .addRow(item); + } + JOptionPane.showMessageDialog(view, new JScrollPane(message)); + } + }); + return null; } @@ -110,18 +135,13 @@ public void filterChangedEvent() {} public void modelChangeEvent(ChangeEvent event) { event .getNew() - .filter(modelObject -> modelObject instanceof TextSource || modelObject instanceof Profile) - .ifPresent( - textSource -> - view.getModel() - .ifPresent( - model -> { - float x = - (model.getNumberOfTextSources() + model.getNumberOfProfiles()) - / maxVal - * 100; - setProgress(Math.min(100, (int) x)); - })); + .filter(modelObject -> modelObject instanceof TextSource || modelObject instanceof Profile).flatMap(textSource -> view.getModel()).ifPresent(model -> { + float x = + (model.getNumberOfTextSources() + model.getNumberOfProfiles()) + / maxVal + * 100; + setProgress(Math.min(100, (int) x)); + }); } @Override diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/collection/AbstractKnowtatorCollectionAction.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/collection/AbstractKnowtatorCollectionAction.java index 42be3cb7..308c43a6 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/collection/AbstractKnowtatorCollectionAction.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/collection/AbstractKnowtatorCollectionAction.java @@ -24,9 +24,11 @@ package edu.ucdenver.ccp.knowtator.view.actions.collection; +import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; import edu.ucdenver.ccp.knowtator.model.collection.KnowtatorCollection; import edu.ucdenver.ccp.knowtator.model.object.ModelObject; +import edu.ucdenver.ccp.knowtator.model.object.TextSource; import edu.ucdenver.ccp.knowtator.view.KnowtatorView; import edu.ucdenver.ccp.knowtator.view.actions.AbstractKnowtatorAction; import edu.ucdenver.ccp.knowtator.view.actions.ActionUnperformable; @@ -50,20 +52,24 @@ public abstract class AbstractKnowtatorCollectionAction extends AbstractKnowtatorAction { - /** The Action type. */ + /** + * The Action type. + */ protected final CollectionActionType actionType; private final KnowtatorCollection collection; - /** The Object. */ + /** + * The Object. + */ protected K object; /** * Instantiates a new Abstract knowtator collection action. * - * @param model the model - * @param actionType the action type + * @param model the model + * @param actionType the action type * @param presentationName the presentation name - * @param collection the collection + * @param collection the collection */ protected AbstractKnowtatorCollectionAction( KnowtatorModel model, @@ -189,7 +195,9 @@ public void prepareRemove() throws ActionUnperformable { } } - /** Prepare add. */ + /** + * Prepare add. + */ protected abstract void prepareAdd(); /** @@ -199,7 +207,9 @@ public void prepareRemove() throws ActionUnperformable { */ protected abstract void cleanUpRemove() throws ActionUnperformable; - /** Clean up add. */ + /** + * Clean up add. + */ @SuppressWarnings("EmptyMethod") protected abstract void cleanUpAdd(); @@ -215,9 +225,9 @@ public void setObject(K object) { /** * Way to choose which action should occur. * - * @param view The Knowtator view - * @param id The profile id - * @param file The document file + * @param view The Knowtator view + * @param id The profile id + * @param file The document file * @param actionParametersList Additional parameters for actions */ public static void pickAction( @@ -245,33 +255,38 @@ public static void pickAction( break; case SPAN: model - .getSelectedTextSource() - .ifPresent( - textSource -> - textSource - .getSelectedAnnotation() - .ifPresent( - conceptAnnotation -> - actions.add( - new SpanAction( - model, - actionType, - conceptAnnotation)))); + .getSelectedTextSource().flatMap(TextSource::getSelectedAnnotation).ifPresent(conceptAnnotation -> + actions.add( + new SpanAction( + model, + actionType, + conceptAnnotation))); break; case PROFILE: actions.add(new ProfileAction(model, actionType, id)); break; case DOCUMENT: - JOptionPane.showMessageDialog(view, "Select annotation file"); - JFileChooser fileChooser = new JFileChooser(); - fileChooser.setCurrentDirectory(model.getAnnotationsLocation()); - File annotationFile = null; - if (fileChooser.showOpenDialog(view) == JFileChooser.APPROVE_OPTION) { - annotationFile = fileChooser.getSelectedFile(); + if (actionType.equals(CollectionActionType.ADD)) { + int choice = JOptionPane.showConfirmDialog(view, "Select annotation file?", "Annotation file", JOptionPane.YES_NO_OPTION); + if (choice == JOptionPane.YES_OPTION) { + JFileChooser fileChooser = new JFileChooser(); + fileChooser.setCurrentDirectory(BaseModel.getAnnotationsLocation(model.getProjectLocation())); + if (fileChooser.showOpenDialog(view) == JFileChooser.APPROVE_OPTION) { + annotationFile = fileChooser.getSelectedFile(); + } + } + + actions.add(new TextSourceAction(model, actionType, file, annotationFile)); + + } else { + int response = JOptionPane.showConfirmDialog(view, "Remove document from project? (document and annotations will NOT be deleted)", null, JOptionPane.YES_NO_OPTION); + if (response == JOptionPane.YES_OPTION) { + actions.add( + new TextSourceAction(model, actionType, file, annotationFile)); + } } - actions.add( - new TextSourceAction(model, actionType, file, annotationFile)); + break; default: break; diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/ConceptAnnotationAction.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/ConceptAnnotationAction.java index e9965f2f..0dfcca11 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/ConceptAnnotationAction.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/ConceptAnnotationAction.java @@ -79,7 +79,8 @@ protected void prepareAdd() { if (owlClassOptional.isPresent()) { ConceptAnnotation newConceptAnnotation = new ConceptAnnotation( - textSource, null, owlClassOptional.get(), profileOptional.get(), "identity", ""); + textSource, null, owlClassOptional.get(), profileOptional.get(), "identity", "", + model.getActiveLayers()); newConceptAnnotation.add( new Span( newConceptAnnotation, diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/ProfileAction.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/ProfileAction.java index f20fc2d3..e2945eaa 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/ProfileAction.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/ProfileAction.java @@ -42,7 +42,6 @@ import javax.swing.JColorChooser; import javax.swing.JDialog; import javax.swing.JOptionPane; -import org.semanticweb.owlapi.model.OWLClass; /** The type Profile action. */ public class ProfileAction extends AbstractKnowtatorCollectionAction { diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/TextSourceAction.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/TextSourceAction.java index 75c53134..56ce81e3 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/TextSourceAction.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/actions/modelactions/TextSourceAction.java @@ -25,6 +25,7 @@ package edu.ucdenver.ccp.knowtator.view.actions.modelactions; import edu.ucdenver.ccp.knowtator.io.knowtator.KnowtatorXmlUtil; +import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; import edu.ucdenver.ccp.knowtator.model.object.TextSource; import edu.ucdenver.ccp.knowtator.view.actions.collection.AbstractKnowtatorCollectionAction; @@ -55,14 +56,14 @@ public TextSourceAction( @Override protected void prepareAdd() { - if (!file.getParentFile().equals(model.getArticlesLocation())) { + if (!file.getParentFile().equals(BaseModel.getArticlesLocation(model.getProjectLocation()))) { try { - FileUtils.copyFile(file, new File(model.getArticlesLocation(), file.getName())); + FileUtils.copyFile(file, new File(BaseModel.getArticlesLocation(model.getProjectLocation()), file.getName())); } catch (IOException e) { e.printStackTrace(); } } - setObject(new TextSource(model, file, file.getName())); + setObject(new TextSource(model, file, null)); } @Override diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/GraphSpaceChooser.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/GraphSpaceChooser.java index d08127d4..937bb0b3 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/GraphSpaceChooser.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/GraphSpaceChooser.java @@ -24,7 +24,9 @@ package edu.ucdenver.ccp.knowtator.view.chooser; +import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.object.GraphSpace; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; /** The type Graph space chooser. */ public class GraphSpaceChooser extends KnowtatorChooser { @@ -33,19 +35,15 @@ public class GraphSpaceChooser extends KnowtatorChooser { * Instantiates a new Graph space chooser. * */ - public GraphSpaceChooser() { + public GraphSpaceChooser(KnowtatorView view) { + super(view); } /** * React to click. * */ public void react() { - view.getModel() - .ifPresent( - model -> - model - .getSelectedTextSource() - .ifPresent(textSource -> setCollection(textSource.getGraphSpaces()))); + view.getModel().flatMap(BaseModel::getSelectedTextSource).ifPresent(textSource -> setCollection(textSource.getGraphSpaces())); setSelected(); } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/KnowtatorChooser.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/KnowtatorChooser.java index 7ebf660b..82a7de2c 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/KnowtatorChooser.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/KnowtatorChooser.java @@ -48,11 +48,9 @@ public abstract class KnowtatorChooser extends JComboBox< /** The View. */ KnowtatorView view; - /** - * Instantiates a new Knowtator chooser. - * - */ - KnowtatorChooser() { + /** Instantiates a new Knowtator chooser. */ + KnowtatorChooser(KnowtatorView view) { + this.view = view; al = e -> { JComboBox comboBox = (JComboBox) e.getSource(); @@ -122,9 +120,4 @@ public void filterChangedEvent() { public void colorChangedEvent(Profile profile) { react(); } - - @Override - public void setView(KnowtatorView view) { - this.view = view; - } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/TextSourceChooser.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/TextSourceChooser.java index 0413b28d..59b5fc6c 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/TextSourceChooser.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/chooser/TextSourceChooser.java @@ -25,10 +25,20 @@ package edu.ucdenver.ccp.knowtator.view.chooser; import edu.ucdenver.ccp.knowtator.model.object.TextSource; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; /** The type Text source chooser. */ public class TextSourceChooser extends KnowtatorChooser { + /** + * Instantiates a new Knowtator chooser. + * + * @param view The Knowtator view + */ + public TextSourceChooser(KnowtatorView view) { + super(view); + } + @Override protected void react() { view.getModel().ifPresent(model -> setCollection(model.getTextSources())); diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/GraphView.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/GraphView.java index 6c010950..53e97c9f 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/GraphView.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/GraphView.java @@ -117,8 +117,9 @@ public class GraphView extends JPanel * * @param dialog the dialog */ - GraphView(JDialog dialog) { + GraphView(KnowtatorView view, JDialog dialog) { + this.view = view; this.dialog = dialog; $$$setupUI$$$(); setVisible(false); @@ -312,7 +313,7 @@ private void showGraph(GraphSpace graphSpace) { private void createUIComponents() { JScrollPane scrollPane = new JScrollPane(); scrollPane.getVerticalScrollBar().setUnitIncrement(20); - graphSpaceChooser = new GraphSpaceChooser(); + graphSpaceChooser = new GraphSpaceChooser(view); mxGraph testGraph = new mxGraph(); graphComponent = new mxGraphComponent(testGraph); } @@ -432,12 +433,6 @@ public void dispose() { graphSpaceChooser.dispose(); } - @Override - public void setView(KnowtatorView view) { - this.view = view; - graphSpaceChooser.setView(view); - } - /** * Gets graph component. * @@ -477,13 +472,9 @@ public void modelChangeEvent(ChangeEvent event) { event .getNew() .filter(modelObject -> modelObject instanceof TextSource) - .map(modelObject -> (TextSource) modelObject) - .ifPresent( - textSource -> - textSource - .getKnowtatorModel() - .getSelectedGraphSpace() - .ifPresent(GraphView.this::showGraph)); + .map(modelObject -> (TextSource) modelObject).flatMap(textSource -> textSource + .getKnowtatorModel() + .getSelectedGraphSpace()).ifPresent(GraphView.this::showGraph); event .getNew() .filter(modelObject -> modelObject instanceof AnnotationNode) @@ -605,7 +596,7 @@ public KnowtatorView getView() { final JPanel panel2 = new JPanel(); panel2.setLayout(new GridBagLayout()); panel1.add(panel2, BorderLayout.WEST); - panel2.setBorder(BorderFactory.createTitledBorder(null, "Nodes and Edges", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel2.getFont()))); + panel2.setBorder(BorderFactory.createTitledBorder(null, "Nodes and Edges", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel2.getFont()), null)); addAnnotationNodeButton = new JButton(); addAnnotationNodeButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-plus-24.png"))); addAnnotationNodeButton.setText(""); @@ -654,7 +645,7 @@ public KnowtatorView getView() { final JPanel panel3 = new JPanel(); panel3.setLayout(new GridBagLayout()); panel1.add(panel3, BorderLayout.EAST); - panel3.setBorder(BorderFactory.createTitledBorder(null, "Graph Spaces", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel3.getFont()))); + panel3.setBorder(BorderFactory.createTitledBorder(null, "Graph Spaces", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 14, panel3.getFont()), null)); final JPanel panel4 = new JPanel(); panel4.setLayout(new GridBagLayout()); gbc = new GridBagConstraints(); @@ -782,7 +773,7 @@ public KnowtatorView getView() { gbc.weightx = 1.0; gbc.fill = GridBagConstraints.BOTH; panel9.add(panel10, gbc); - panel10.setBorder(BorderFactory.createTitledBorder(null, "Node ID", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel10.getFont()))); + panel10.setBorder(BorderFactory.createTitledBorder(null, "Node ID", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel10.getFont()), null)); final JLabel label1 = new JLabel(); Font label1Font = this.$$$getFont$$$("Verdana", -1, -1, label1.getFont()); if (label1Font != null) { @@ -804,7 +795,7 @@ public KnowtatorView getView() { gbc.weightx = 1.0; gbc.fill = GridBagConstraints.BOTH; panel9.add(panel11, gbc); - panel11.setBorder(BorderFactory.createTitledBorder(null, "Concept Annotation", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel11.getFont()))); + panel11.setBorder(BorderFactory.createTitledBorder(null, "Concept Annotation", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel11.getFont()), null)); final JLabel label2 = new JLabel(); Font label2Font = this.$$$getFont$$$("Verdana", -1, -1, label2.getFont()); if (label2Font != null) { @@ -831,7 +822,7 @@ public KnowtatorView getView() { gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; panel12.add(panel13, gbc); - panel13.setBorder(BorderFactory.createTitledBorder(null, "Relation ID", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel13.getFont()))); + panel13.setBorder(BorderFactory.createTitledBorder(null, "Relation ID", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel13.getFont()), null)); final JLabel label3 = new JLabel(); label3.setEnabled(false); Font label3Font = this.$$$getFont$$$("Verdana", -1, -1, label3.getFont()); @@ -860,7 +851,7 @@ public KnowtatorView getView() { gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; panel12.add(panel14, gbc); - panel14.setBorder(BorderFactory.createTitledBorder(null, "OWL Object Property", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel14.getFont()))); + panel14.setBorder(BorderFactory.createTitledBorder(null, "OWL Object Property", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel14.getFont()), null)); final JLabel label4 = new JLabel(); Font label4Font = this.$$$getFont$$$("Verdana", -1, -1, label4.getFont()); if (label4Font != null) { @@ -884,7 +875,7 @@ public KnowtatorView getView() { gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; panel12.add(panel15, gbc); - panel15.setBorder(BorderFactory.createTitledBorder(null, "Quantifier", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel15.getFont()))); + panel15.setBorder(BorderFactory.createTitledBorder(null, "Quantifier", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel15.getFont()), null)); final JComboBox comboBox1 = new JComboBox(); comboBox1.setEnabled(false); Font comboBox1Font = this.$$$getFont$$$("Verdana", -1, -1, comboBox1.getFont()); @@ -916,7 +907,7 @@ public KnowtatorView getView() { gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; panel12.add(panel16, gbc); - panel16.setBorder(BorderFactory.createTitledBorder(null, "Quantifier Value", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel16.getFont()))); + panel16.setBorder(BorderFactory.createTitledBorder(null, "Quantifier Value", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel16.getFont()), null)); final JFormattedTextField formattedTextField1 = new JFormattedTextField(); Font formattedTextField1Font = this.$$$getFont$$$("Verdana", -1, -1, formattedTextField1.getFont()); if (formattedTextField1Font != null) { @@ -953,7 +944,7 @@ public KnowtatorView getView() { gbc.weighty = 1.0; gbc.fill = GridBagConstraints.BOTH; panel12.add(panel17, gbc); - panel17.setBorder(BorderFactory.createTitledBorder(null, "Notes", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel17.getFont()))); + panel17.setBorder(BorderFactory.createTitledBorder(null, "Notes", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, this.$$$getFont$$$("Verdana", -1, 16, panel17.getFont()), null)); final JScrollPane scrollPane1 = new JScrollPane(); gbc = new GridBagConstraints(); gbc.gridx = 0; diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/GraphViewDialog.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/GraphViewDialog.java index 2fc43748..f2faff36 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/GraphViewDialog.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/GraphViewDialog.java @@ -49,8 +49,8 @@ public class GraphViewDialog extends JDialog implements KnowtatorComponent { /** * Instantiates a new Graph view dialog. */ - public GraphViewDialog() { -// $$$setupUI$$$(); + public GraphViewDialog(KnowtatorView view) { + this.view = view; $$$setupUI$$$(); setSize(new Dimension(800, 800)); @@ -100,7 +100,7 @@ private void onCancel() { } private void createUIComponents() { - graphView = new GraphView(this); + graphView = new GraphView(this.view, this); } @Override @@ -115,12 +115,6 @@ public void dispose() { setVisible(false); } - @Override - public void setView(KnowtatorView view) { - this.view = view; - graphView.setView(view); - } - @Override public void setVisible(boolean visible) { super.setVisible(visible); diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/RelationOptionsDialog.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/RelationOptionsDialog.java index f2a7d4e4..65d2d524 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/RelationOptionsDialog.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/graph/RelationOptionsDialog.java @@ -34,6 +34,7 @@ import java.awt.event.KeyEvent; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; +import java.lang.reflect.Method; import java.util.ResourceBundle; import javax.swing.AbstractButton; import javax.swing.DefaultComboBoxModel; @@ -311,7 +312,7 @@ String getMotivation() { if (label2Font != null) { label2.setFont(label2Font); } - this.$$$loadLabelText$$$(label2, ResourceBundle.getBundle("log4j").getString("value2")); + this.$$$loadLabelText$$$(label2, this.$$$getMessageFromBundle$$$("log4j", "value2")); gbc = new GridBagConstraints(); gbc.gridx = 1; gbc.gridy = 0; @@ -371,7 +372,7 @@ String getMotivation() { if (negateCheckBoxFont != null) { negateCheckBox.setFont(negateCheckBoxFont); } - this.$$$loadButtonText$$$(negateCheckBox, ResourceBundle.getBundle("log4j").getString("negate1")); + this.$$$loadButtonText$$$(negateCheckBox, this.$$$getMessageFromBundle$$$("log4j", "negate1")); gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 1; @@ -427,6 +428,23 @@ String getMotivation() { return new Font(resultName, style >= 0 ? style : currentFont.getStyle(), size >= 0 ? size : currentFont.getSize()); } + private static Method $$$cachedGetBundleMethod$$$ = null; + + private String $$$getMessageFromBundle$$$(String path, String key) { + ResourceBundle bundle; + try { + Class thisClass = this.getClass(); + if ($$$cachedGetBundleMethod$$$ == null) { + Class dynamicBundleClass = thisClass.getClassLoader().loadClass("com.intellij.DynamicBundle"); + $$$cachedGetBundleMethod$$$ = dynamicBundleClass.getMethod("getBundle", String.class, Class.class); + } + bundle = (ResourceBundle) $$$cachedGetBundleMethod$$$.invoke(null, path, thisClass); + } catch (Exception e) { + bundle = ResourceBundle.getBundle(path); + } + return bundle.getString(key); + } + /** * @noinspection ALL */ @@ -491,4 +509,5 @@ String getMotivation() { public JComponent $$$getRootComponent$$$() { return contentPane; } + } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/iaa/IAAOptionsDialog.form b/src/main/java/edu/ucdenver/ccp/knowtator/view/iaa/IAAOptionsDialog.form new file mode 100644 index 00000000..69206673 --- /dev/null +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/iaa/IAAOptionsDialog.form @@ -0,0 +1,259 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/iaa/IAAOptionsDialog.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/iaa/IAAOptionsDialog.java new file mode 100644 index 00000000..a7fe3e9f --- /dev/null +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/iaa/IAAOptionsDialog.java @@ -0,0 +1,594 @@ +/* + * MIT License + * + * Copyright (c) 2018 Harrison Pielke-Lombardo + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + * SOFTWARE. + */ + +package edu.ucdenver.ccp.knowtator.view.iaa; + +import edu.ucdenver.ccp.knowtator.iaa.IaaException; +import edu.ucdenver.ccp.knowtator.iaa.KnowtatorIaa; +import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; +import edu.ucdenver.ccp.knowtator.model.object.ConceptAnnotation; +import edu.ucdenver.ccp.knowtator.model.object.ModelObject; +import edu.ucdenver.ccp.knowtator.model.object.Profile; +import edu.ucdenver.ccp.knowtator.view.KnowtatorComponent; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; +import java.awt.BorderLayout; +import java.awt.GridBagConstraints; +import java.awt.GridBagLayout; +import java.awt.Window; +import java.awt.event.KeyEvent; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.io.File; +import java.io.IOException; +import java.lang.reflect.Method; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashSet; +import java.util.List; +import java.util.Optional; +import java.util.ResourceBundle; +import java.util.Set; +import java.util.stream.Collectors; +import java.util.stream.IntStream; +import javax.swing.AbstractButton; +import javax.swing.BorderFactory; +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JComponent; +import javax.swing.JDialog; +import javax.swing.JFileChooser; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JSplitPane; +import javax.swing.JTable; +import javax.swing.KeyStroke; +import javax.swing.ListSelectionModel; +import javax.swing.border.TitledBorder; +import javax.swing.filechooser.FileFilter; +import javax.swing.filechooser.FileNameExtensionFilter; +import javax.swing.table.DefaultTableModel; +import org.apache.log4j.Logger; +import org.protege.editor.owl.model.OWLWorkspace; +import org.protege.editor.owl.model.selection.OWLSelectionModelListener; + +public class IAAOptionsDialog extends JDialog implements KnowtatorComponent { + private final KnowtatorView view; + private KnowtatorModel iaaModel; + private KnowtatorModel model; + private JPanel contentPane; + private JButton buttonOK; + private JButton buttonCancel; + private JButton documentsSelectAllButton; + private JPanel profilesPanel; + private JPanel documentsPanel; + private final File outputDirectory; + private JCheckBox iaaClassCheckBox; + private JCheckBox iaaSpanCheckBox; + private JCheckBox iaaClassAndSpanCheckBox; + private JButton profilesSelectAllButton; + private JTable profilesTable; + private JTable documentsTable; + private JButton owlClassesSelectAllButton; + private OWLClassesTable owlClassesTable; + private JButton compareAcrossProjectsButton; + private JCheckBox includeSubclassesCheckBox; + IAATableModel profilesTableModel; + IAATableModel documentsTableModel; + IAATableModel owlClassesTableModel; + + private static final Logger log = Logger.getLogger(IAAOptionsDialog.class); + + public IAAOptionsDialog(Window parent, KnowtatorModel model, KnowtatorView view, File outputDirectory) { + super(parent); + this.outputDirectory = outputDirectory; + this.model = model; + this.iaaModel = model; + this.view = view; + $$$setupUI$$$(); + + setContentPane(contentPane); + setModal(false); + getRootPane().setDefaultButton(buttonOK); + + buttonOK.addActionListener(e -> onOK()); + + buttonCancel.addActionListener(e -> onCancel()); + + // call onCancel() when cross is clicked + setDefaultCloseOperation(DO_NOTHING_ON_CLOSE); + addWindowListener(new WindowAdapter() { + public void windowClosing(WindowEvent e) { + onCancel(); + } + }); + + // call onCancel() on ESCAPE + contentPane.registerKeyboardAction(e -> onCancel(), + KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), + JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); + + setModels(model); + documentsTable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); + owlClassesTable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); + profilesTable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); + owlClassesSelectAllButton.addActionListener(e -> owlClassesTableModel.toggleAll()); + documentsSelectAllButton.addActionListener(e -> documentsTableModel.toggleAll()); + profilesSelectAllButton.addActionListener(e -> profilesTableModel.toggleAll()); + + compareAcrossProjectsButton.addActionListener(e -> { + JFileChooser fileChooser = new JFileChooser(); + Optional.ofNullable(KnowtatorView.PREFERENCES.get("Last Project", null)) + .map(File::new) + .filter(File::exists) + .map( + file -> { + fileChooser.setCurrentDirectory(file); + return file; + }) + .map(File::listFiles) + .flatMap( + files -> + Arrays.stream(files) + .filter(file1 -> file1.getName().endsWith(".knowtator")) + .findAny()) + .ifPresent(fileChooser::setSelectedFile); + fileChooser.addActionListener( + e1 -> + Optional.ofNullable(e1) + .filter( + event -> event.getActionCommand().equals(JFileChooser.APPROVE_SELECTION)) + .ifPresent(event -> { + try { + File projectLocation1 = fileChooser.getSelectedFile(); + KnowtatorModel newModel = mergeProjects(projectLocation1, this.model, view.getOWLWorkspace(), false, this); + + setModels(newModel); + + } catch (IOException ioException) { + ioException.printStackTrace(); + } + })); + + FileFilter fileFilter = new FileNameExtensionFilter("Knowtator", "knowtator"); + fileChooser.setFileFilter(fileFilter); + fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY); + + fileChooser.showOpenDialog(view); + }); + + reset(); + } + + public static KnowtatorModel mergeProjects(File projectLocation1, KnowtatorModel model2, OWLWorkspace owlWorkspace, boolean mergeProfiles, JDialog component) throws IOException { + KnowtatorModel newModel = new KnowtatorModel(projectLocation1, owlWorkspace); + newModel.load(projectLocation1); + Set profilesInCommon = newModel.getProfiles().stream() + .filter(profile -> model2.getProfiles().contains(profile)) + .collect(Collectors.toSet()); + + for (Profile profile : profilesInCommon) { + if (mergeProfiles || JOptionPane.showConfirmDialog(component, + String.format("Merge %s between projects for IAA?", profile), + "Profile merge?", + JOptionPane.YES_NO_OPTION) == JOptionPane.NO_OPTION) { + profile.setId(String.format("%s - %s", + profile.getId(), + projectLocation1 + .getName() + .replace(".knowtator", ""))); + } + } + + newModel.load(model2.getProjectLocation()); + return newModel; + } + + private void setModels(KnowtatorModel model) { + this.iaaModel = model; + documentsTableModel = new IAATableModel( + new Object[][] {}, + "Document", + model.getTextSources().stream() + .map(ModelObject::getId) + .collect(Collectors.toList())); + documentsTable.setModel(documentsTableModel); + + profilesTableModel = new IAATableModel( + new Object[][] {}, + "Profile", + model.getProfiles().stream() + .map(ModelObject::getId) + .collect(Collectors.toList())); + profilesTable.setModel(profilesTableModel); + + + owlClassesTableModel = new IAATableModel( + new Object[][] {}, + "OWL Classes", + new ArrayList<>(new HashSet<>(model.getTextSources().stream() + .flatMap(textSource -> textSource.getConceptAnnotations().stream() + .map(ConceptAnnotation::getOwlClass)) + .collect(Collectors.toSet())))); + owlClassesTable.setModel(owlClassesTableModel); + } + + private void createUIComponents() { + includeSubclassesCheckBox = new JCheckBox(); + owlClassesTable = new OWLClassesTable(view, includeSubclassesCheckBox); + } + + private static class OWLClassesTable extends JTable implements KnowtatorComponent, OWLSelectionModelListener { + + private final KnowtatorView view; + private final JCheckBox includeSubclassesCheckBox; + + public OWLClassesTable(KnowtatorView view, JCheckBox includeSubclassesCheckBox) { + super(); + this.view = view; + this.includeSubclassesCheckBox = includeSubclassesCheckBox; + } + + @Override + public void selectionChanged() throws Exception { + view.getModel().ifPresent(model -> { + Optional owlClassOptional = model.getSelectedOwlClass(); + + owlClassOptional.ifPresent(owlClass -> { + int i = selectOwlClass(owlClass); + if (includeSubclassesCheckBox.isSelected()) { + for (String d : model.getOwlClassDescendants(owlClass)) { + selectOwlClass(d); + } + } + + if (-1 < i && i < getModel().getRowCount()) { + scrollRectToVisible(getCellRect(i, 0, true)); + } + }); + + }); + + } + + private int selectOwlClass(String owlClass) { + int i = getModel().getRowCount() == 0 ? -1 : 0; + while (i < getModel().getRowCount() && (i != -1 && !getValueAt(i, 0).equals(owlClass))) { + i++; + } + + if (-1 < i && i < getModel().getRowCount()) { + setValueAt(Boolean.TRUE, i, 1); + } + return i; + } + + @Override + public void reset() { + view.getModel().ifPresent(model -> model.addOwlSelectionModelListener(this)); + } + + @Override + public void dispose() { + view.getModel().ifPresent(model -> model.removeOwlSelectionModelListener(this)); + } + } + + private static class IAATableModel extends DefaultTableModel { + private final int checkCol = 1; + + IAATableModel(Object[][] data, String col, List collection) { + super(data, new String[] {col, "Checkbox"}); + + setCollection(collection); + } + + private void setCollection(List collection) { + for (int i = 0; i < this.getRowCount(); i++) { + removeRow(i); + } + for (String item : collection) { + addRow(new Object[] {item, Boolean.FALSE}); + } + } + + @Override + public Class getColumnClass(int columnIndex) { + if (columnIndex == 1) { + return getValueAt(0, checkCol).getClass(); + } else { + return super.getColumnClass(columnIndex); + } + } + + Set getSelectedItems() { + return IntStream.range(0, getRowCount()) + .filter(i -> (Boolean) getValueAt(i, 1)) + .mapToObj(i -> (String) getValueAt(i, 0)) + .collect(Collectors.toSet()); + } + + boolean allSelected() { + return IntStream.range(0, getRowCount()) + .allMatch(i -> (Boolean) getValueAt(i, 1)); + } + + void toggleAll() { + if (allSelected()) { + IntStream.range(0, getRowCount()) + .forEach(i -> setValueAt(Boolean.FALSE, i, checkCol)); + } else { + IntStream.range(0, getRowCount()) + .forEach(i -> setValueAt(Boolean.TRUE, i, checkCol)); + } + } + + } + + private void onOK() { + Set profiles = profilesTableModel.getSelectedItems(); + Set owlClasses = owlClassesTableModel.getSelectedItems(); + + Set textSources = documentsTableModel.getSelectedItems(); + if (profiles.size() <= 2 && !textSources.isEmpty() && + (iaaClassCheckBox.isSelected() || iaaSpanCheckBox.isSelected() || iaaClassAndSpanCheckBox.isSelected())) { + try { + KnowtatorIaa knowtatorIaa = new KnowtatorIaa(outputDirectory, iaaModel, textSources, profiles, owlClasses); + + if (iaaClassCheckBox.isSelected()) { + knowtatorIaa.runClassIaa(); + } + if (iaaSpanCheckBox.isSelected()) { + knowtatorIaa.runSpanIaa(); + } + if (iaaClassAndSpanCheckBox.isSelected()) { + knowtatorIaa.runClassAndSpanIaa(); + } + + knowtatorIaa.closeHtml(); + } catch (IaaException e1) { + e1.printStackTrace(); + } + dispose(); + } + } + + private void onCancel() { + // add your code here if necessary + dispose(); + } + + @Override + public void reset() { + view.knowtatorComponents.add(owlClassesTable); + owlClassesTable.reset(); + } + + @Override + public void dispose() { + view.knowtatorComponents.remove(owlClassesTable); + super.dispose(); + } + + /** + * Method generated by IntelliJ IDEA GUI Designer + * >>> IMPORTANT!! <<< + * DO NOT edit this method OR call it in your code! + * + * @noinspection ALL + */ + private void $$$setupUI$$$() { + createUIComponents(); + contentPane = new JPanel(); + contentPane.setLayout(new GridBagLayout()); + final JSplitPane splitPane1 = new JSplitPane(); + GridBagConstraints gbc; + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 0; + gbc.fill = GridBagConstraints.BOTH; + contentPane.add(splitPane1, gbc); + final JSplitPane splitPane2 = new JSplitPane(); + splitPane1.setLeftComponent(splitPane2); + final JPanel panel1 = new JPanel(); + panel1.setLayout(new GridBagLayout()); + splitPane2.setLeftComponent(panel1); + panel1.setBorder(BorderFactory.createTitledBorder(null, "Mode", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, null, null)); + iaaClassCheckBox = new JCheckBox(); + this.$$$loadButtonText$$$(iaaClassCheckBox, this.$$$getMessageFromBundle$$$("log4j", "class.iaa")); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 0; + gbc.anchor = GridBagConstraints.WEST; + panel1.add(iaaClassCheckBox, gbc); + iaaSpanCheckBox = new JCheckBox(); + this.$$$loadButtonText$$$(iaaSpanCheckBox, this.$$$getMessageFromBundle$$$("log4j", "span.iaa")); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 1; + gbc.anchor = GridBagConstraints.WEST; + panel1.add(iaaSpanCheckBox, gbc); + iaaClassAndSpanCheckBox = new JCheckBox(); + this.$$$loadButtonText$$$(iaaClassAndSpanCheckBox, this.$$$getMessageFromBundle$$$("log4j", "class.and.span.iaa")); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 2; + gbc.anchor = GridBagConstraints.WEST; + panel1.add(iaaClassAndSpanCheckBox, gbc); + final JPanel panel2 = new JPanel(); + panel2.setLayout(new BorderLayout(0, 0)); + splitPane2.setRightComponent(panel2); + panel2.setBorder(BorderFactory.createTitledBorder(null, this.$$$getMessageFromBundle$$$("ui", "profiles"), TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, null, null)); + profilesPanel = new JPanel(); + profilesPanel.setLayout(new BorderLayout(0, 0)); + panel2.add(profilesPanel, BorderLayout.NORTH); + final JScrollPane scrollPane1 = new JScrollPane(); + profilesPanel.add(scrollPane1, BorderLayout.CENTER); + profilesTable = new JTable(); + profilesTable.setAutoCreateRowSorter(true); + scrollPane1.setViewportView(profilesTable); + final JPanel panel3 = new JPanel(); + panel3.setLayout(new BorderLayout(0, 0)); + profilesPanel.add(panel3, BorderLayout.NORTH); + profilesSelectAllButton = new JButton(); + this.$$$loadButtonText$$$(profilesSelectAllButton, this.$$$getMessageFromBundle$$$("log4j", "select.all")); + panel3.add(profilesSelectAllButton, BorderLayout.EAST); + final JSplitPane splitPane3 = new JSplitPane(); + splitPane1.setRightComponent(splitPane3); + final JPanel panel4 = new JPanel(); + panel4.setLayout(new BorderLayout(0, 0)); + splitPane3.setLeftComponent(panel4); + panel4.setBorder(BorderFactory.createTitledBorder(null, this.$$$getMessageFromBundle$$$("log4j", "documents"), TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, null, null)); + documentsPanel = new JPanel(); + documentsPanel.setLayout(new BorderLayout(0, 0)); + panel4.add(documentsPanel, BorderLayout.NORTH); + final JScrollPane scrollPane2 = new JScrollPane(); + documentsPanel.add(scrollPane2, BorderLayout.CENTER); + documentsTable = new JTable(); + scrollPane2.setViewportView(documentsTable); + final JPanel panel5 = new JPanel(); + panel5.setLayout(new BorderLayout(0, 0)); + documentsPanel.add(panel5, BorderLayout.NORTH); + documentsSelectAllButton = new JButton(); + this.$$$loadButtonText$$$(documentsSelectAllButton, this.$$$getMessageFromBundle$$$("log4j", "select.all")); + panel5.add(documentsSelectAllButton, BorderLayout.EAST); + final JPanel panel6 = new JPanel(); + panel6.setLayout(new BorderLayout(0, 0)); + splitPane3.setRightComponent(panel6); + panel6.setBorder(BorderFactory.createTitledBorder(null, "OWL Classes", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, null, null)); + final JPanel panel7 = new JPanel(); + panel7.setLayout(new BorderLayout(0, 0)); + panel6.add(panel7, BorderLayout.CENTER); + final JScrollPane scrollPane3 = new JScrollPane(); + panel7.add(scrollPane3, BorderLayout.CENTER); + scrollPane3.setViewportView(owlClassesTable); + final JPanel panel8 = new JPanel(); + panel8.setLayout(new BorderLayout(0, 0)); + panel7.add(panel8, BorderLayout.NORTH); + owlClassesSelectAllButton = new JButton(); + owlClassesSelectAllButton.setText("Select all"); + panel8.add(owlClassesSelectAllButton, BorderLayout.EAST); + final JPanel panel9 = new JPanel(); + panel9.setLayout(new GridBagLayout()); + panel6.add(panel9, BorderLayout.SOUTH); + includeSubclassesCheckBox.setText("Include subclasses"); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 0; + gbc.anchor = GridBagConstraints.WEST; + panel9.add(includeSubclassesCheckBox, gbc); + final JPanel panel10 = new JPanel(); + panel10.setLayout(new GridBagLayout()); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 1; + gbc.fill = GridBagConstraints.BOTH; + contentPane.add(panel10, gbc); + compareAcrossProjectsButton = new JButton(); + compareAcrossProjectsButton.setText("Compare across projects"); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 0; + gbc.fill = GridBagConstraints.HORIZONTAL; + panel10.add(compareAcrossProjectsButton, gbc); + buttonCancel = new JButton(); + this.$$$loadButtonText$$$(buttonCancel, this.$$$getMessageFromBundle$$$("log4j", "cancel")); + gbc = new GridBagConstraints(); + gbc.gridx = 3; + gbc.gridy = 0; + gbc.weightx = 1.0; + gbc.weighty = 1.0; + gbc.fill = GridBagConstraints.HORIZONTAL; + panel10.add(buttonCancel, gbc); + buttonOK = new JButton(); + buttonOK.setText("Run"); + gbc = new GridBagConstraints(); + gbc.gridx = 2; + gbc.gridy = 0; + gbc.weightx = 1.0; + gbc.weighty = 1.0; + gbc.fill = GridBagConstraints.HORIZONTAL; + panel10.add(buttonOK, gbc); + final JPanel spacer1 = new JPanel(); + gbc = new GridBagConstraints(); + gbc.gridx = 1; + gbc.gridy = 0; + gbc.fill = GridBagConstraints.HORIZONTAL; + panel10.add(spacer1, gbc); + } + + private static Method $$$cachedGetBundleMethod$$$ = null; + + private String $$$getMessageFromBundle$$$(String path, String key) { + ResourceBundle bundle; + try { + Class thisClass = this.getClass(); + if ($$$cachedGetBundleMethod$$$ == null) { + Class dynamicBundleClass = thisClass.getClassLoader().loadClass("com.intellij.DynamicBundle"); + $$$cachedGetBundleMethod$$$ = dynamicBundleClass.getMethod("getBundle", String.class, Class.class); + } + bundle = (ResourceBundle) $$$cachedGetBundleMethod$$$.invoke(null, path, thisClass); + } catch (Exception e) { + bundle = ResourceBundle.getBundle(path); + } + return bundle.getString(key); + } + + /** + * @noinspection ALL + */ + private void $$$loadButtonText$$$(AbstractButton component, String text) { + StringBuffer result = new StringBuffer(); + boolean haveMnemonic = false; + char mnemonic = '\0'; + int mnemonicIndex = -1; + for (int i = 0; i < text.length(); i++) { + if (text.charAt(i) == '&') { + i++; + if (i == text.length()) { + break; + } + if (!haveMnemonic && text.charAt(i) != '&') { + haveMnemonic = true; + mnemonic = text.charAt(i); + mnemonicIndex = result.length(); + } + } + result.append(text.charAt(i)); + } + component.setText(result.toString()); + if (haveMnemonic) { + component.setMnemonic(mnemonic); + component.setDisplayedMnemonicIndex(mnemonicIndex); + } + } + + /** + * @noinspection ALL + */ + public JComponent $$$getRootComponent$$$() { + return contentPane; + } + +} diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AbstractConceptAnnotationLabel.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AbstractConceptAnnotationLabel.java index 051d08b6..4314c693 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AbstractConceptAnnotationLabel.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AbstractConceptAnnotationLabel.java @@ -26,6 +26,7 @@ import edu.ucdenver.ccp.knowtator.model.object.ConceptAnnotation; import edu.ucdenver.ccp.knowtator.model.object.TextSource; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; import java.util.Optional; /** Abstract label for concept annotations. */ @@ -35,7 +36,8 @@ public abstract class AbstractConceptAnnotationLabel extends KnowtatorLabel { * Instantiates a new Abstract concept annotation label. * */ - AbstractConceptAnnotationLabel() { + AbstractConceptAnnotationLabel(KnowtatorView view) { + super(view); } @Override diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationAnnotatorLabel.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationAnnotatorLabel.java index fc22b350..1ef65b2e 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationAnnotatorLabel.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationAnnotatorLabel.java @@ -26,6 +26,7 @@ import edu.ucdenver.ccp.knowtator.model.object.ConceptAnnotation; import edu.ucdenver.ccp.knowtator.view.KnowtatorComponent; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; /** The type Annotation annotator label. */ public class AnnotationAnnotatorLabel extends AbstractConceptAnnotationLabel @@ -35,7 +36,8 @@ public class AnnotationAnnotatorLabel extends AbstractConceptAnnotationLabel * Instantiates a new Annotation annotator label. * */ - public AnnotationAnnotatorLabel() { + public AnnotationAnnotatorLabel(KnowtatorView view) { + super(view); } @Override diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationClassLabel.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationClassLabel.java index c2a12a5c..125cd1b4 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationClassLabel.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationClassLabel.java @@ -25,6 +25,7 @@ package edu.ucdenver.ccp.knowtator.view.label; import edu.ucdenver.ccp.knowtator.model.object.ConceptAnnotation; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; import org.protege.editor.owl.model.event.EventType; import org.protege.editor.owl.model.event.OWLModelManagerChangeEvent; import org.protege.editor.owl.model.event.OWLModelManagerListener; @@ -33,6 +34,15 @@ public class AnnotationClassLabel extends AbstractConceptAnnotationLabel implements OWLModelManagerListener { + /** + * Instantiates a new Abstract concept annotation label. + * + * @param view The view + */ + public AnnotationClassLabel(KnowtatorView view) { + super(view); + } + @Override public void displayConceptAnnotation(ConceptAnnotation conceptAnnotation) { view.getModel() diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationIdLabel.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationIdLabel.java index 9365a70c..609fe06d 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationIdLabel.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotationIdLabel.java @@ -25,11 +25,21 @@ package edu.ucdenver.ccp.knowtator.view.label; import edu.ucdenver.ccp.knowtator.model.object.ConceptAnnotation; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; /** The type Annotation id label. */ public class AnnotationIdLabel extends AbstractConceptAnnotationLabel { + /** + * Instantiates a new Abstract concept annotation label. + * + * @param view The view + */ + public AnnotationIdLabel(KnowtatorView view) { + super(view); + } + @Override public void displayConceptAnnotation(ConceptAnnotation conceptAnnotation) { setText(conceptAnnotation.getId()); diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotatorLabel.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotatorLabel.java new file mode 100644 index 00000000..ab4b0e8c --- /dev/null +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/AnnotatorLabel.java @@ -0,0 +1,45 @@ +/* + * MIT License + * + * Copyright (c) 2018 Harrison Pielke-Lombardo + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + * SOFTWARE. + */ + +package edu.ucdenver.ccp.knowtator.view.label; + +import edu.ucdenver.ccp.knowtator.model.BaseModel; +import edu.ucdenver.ccp.knowtator.view.KnowtatorComponent; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; + +public class AnnotatorLabel extends KnowtatorLabel implements KnowtatorComponent { + /** + * Instantiates a new Knowtator label. + * + * @param view The Knowtator view + */ + public AnnotatorLabel(KnowtatorView view) { + super(view); + } + + @Override + protected void react() { + view.getModel().flatMap(BaseModel::getSelectedProfile).ifPresent(profile -> setText(profile.getId())); + } +} diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/label/KnowtatorLabel.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/KnowtatorLabel.java index d5ca1574..1ccb3ed3 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/label/KnowtatorLabel.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/label/KnowtatorLabel.java @@ -42,7 +42,8 @@ public abstract class KnowtatorLabel extends JLabel implements KnowtatorComponen * Instantiates a new Knowtator label. * */ - KnowtatorLabel() { + KnowtatorLabel(KnowtatorView view) { + this.view = view; } /** React. */ @@ -73,9 +74,4 @@ public void modelChangeEvent(ChangeEvent event) { public void colorChangedEvent(Profile profile) { react(); } - - @Override - public void setView(KnowtatorView view) { - this.view = view; - } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/list/ColorList.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/list/ColorList.java index 309c3b01..23d6972f 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/list/ColorList.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/list/ColorList.java @@ -27,71 +27,72 @@ import static edu.ucdenver.ccp.knowtator.view.actions.modelactions.ProfileAction.assignColorToClass; import edu.ucdenver.ccp.knowtator.model.ModelListener; +import edu.ucdenver.ccp.knowtator.model.OwlModel; import edu.ucdenver.ccp.knowtator.model.collection.event.ChangeEvent; import edu.ucdenver.ccp.knowtator.model.object.ModelObject; import edu.ucdenver.ccp.knowtator.model.object.Profile; import edu.ucdenver.ccp.knowtator.view.KnowtatorComponent; import edu.ucdenver.ccp.knowtator.view.KnowtatorView; +import java.awt.BasicStroke; import java.awt.Component; +import java.util.Enumeration; +import java.util.Optional; +import javax.swing.BorderFactory; import javax.swing.DefaultListModel; import javax.swing.JLabel; import javax.swing.JList; import javax.swing.ListCellRenderer; import javax.swing.event.ListSelectionListener; +import org.apache.log4j.Logger; +import org.protege.editor.owl.model.selection.OWLSelectionModelListener; -/** The type Color list. */ -public class ColorList extends JList implements KnowtatorComponent, ModelListener { +/** + * The type Color list. + */ +public class ColorList extends JList implements KnowtatorComponent, ModelListener, OWLSelectionModelListener { private final ListSelectionListener lsl; - private KnowtatorView view; + private final KnowtatorView view; + private static final Logger log = Logger.getLogger(ColorList.class); /** * Instantiates a new Color list. - * */ - public ColorList() { + public ColorList(KnowtatorView view) { + this.view = view; setModel(new DefaultListModel<>()); setCellRenderer(new ColorListRenderer<>()); - lsl = e -> assignColorToClass(view, getSelectedValue()); + lsl = e -> assignColorToClass(view, getSelectedValue()[0]); } private void setCollection() { removeListSelectionListener(lsl); setModel(new DefaultListModel<>()); - view.getModel() - .ifPresent( - model -> - model - .getSelectedProfile() - .ifPresent( - profile -> - profile.getColors().keySet().stream() - .sorted() - .forEach( - o -> ((DefaultListModel) getModel()).addElement(o)))); - + view.getModel().ifPresent(model -> model.getSelectedProfile().ifPresent(profile -> + profile.getColors().keySet().stream() + .sorted() + .forEach(o -> + ((DefaultListModel) getModel()).addElement(new String[] {o, model.getOwlEntityRendering(o)})))); addListSelectionListener(lsl); } - @Override - public void setView(KnowtatorView view) { - this.view = view; - } - @Override public void reset() { view.getModel().ifPresent(model -> model.addModelListener(this)); + view.getModel().ifPresent(model -> model.addOwlSelectionModelListener(this)); setCollection(); } @Override public void dispose() { view.getModel().ifPresent(model -> model.removeModelListener(this)); + view.getModel().ifPresent(model -> model.removeOwlSelectionModelListener(this)); setModel(new DefaultListModel<>()); } @Override - public void filterChangedEvent() {} + public void filterChangedEvent() { + } @Override public void modelChangeEvent(ChangeEvent event) { @@ -106,6 +107,27 @@ public void colorChangedEvent(Profile profile) { setCollection(); } + @Override + public void selectionChanged() { + Optional owlClassOptional = view.getModel().flatMap(OwlModel::getSelectedOwlClass); + + owlClassOptional.ifPresent(owlClass -> { + setCollection(); + int i = -1; + Enumeration e = ((DefaultListModel) getModel()).elements(); + while(e.hasMoreElements()) { + i++; + if(owlClass.equals(e.nextElement()[0])) { + break; + } + } + + if (-1 < i) { + scrollRectToVisible(getCellBounds(i, i)); + } + }); + } + /** * The type Color list renderer. * @@ -113,7 +135,9 @@ public void colorChangedEvent(Profile profile) { */ class ColorListRenderer extends JLabel implements ListCellRenderer { - /** Instantiates a new Color list renderer. */ + /** + * Instantiates a new Color list renderer. + */ ColorListRenderer() { setOpaque(true); } @@ -122,13 +146,20 @@ class ColorListRenderer extends JLabel implements ListCellRenderer { public Component getListCellRendererComponent( JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) { view.getModel() - .filter(model -> value instanceof String) + .filter(model -> value instanceof String[]) .ifPresent( model -> { + String[] val = (String[]) value; + Optional owlClass = model.getSelectedOwlClass(); + if (owlClass.isPresent() && val[0].equals(owlClass.get())) { + setBorder(BorderFactory.createStrokeBorder(new BasicStroke(2))); + } else { + setBorder(null); + } model .getSelectedProfile() - .ifPresent(profile -> setBackground(profile.getColors().get(value))); - setText(value.toString()); + .ifPresent(profile -> setBackground(profile.getColors().get(val[0]))); + setText(val[1]); }); return this; } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/list/GraphSpaceList.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/list/GraphSpaceList.java index d25bb084..d07493fe 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/list/GraphSpaceList.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/list/GraphSpaceList.java @@ -27,6 +27,7 @@ import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.object.GraphSpace; import edu.ucdenver.ccp.knowtator.model.object.TextSource; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; import java.util.Optional; /** The type Graph space list. */ @@ -35,7 +36,8 @@ public class GraphSpaceList extends KnowtatorList { * Instantiates a new Graph space list. * */ - public GraphSpaceList() { + public GraphSpaceList(KnowtatorView view) { + super(view); } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/list/KnowtatorList.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/list/KnowtatorList.java index de377cad..7201ef60 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/list/KnowtatorList.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/list/KnowtatorList.java @@ -48,11 +48,9 @@ public abstract class KnowtatorList extends JList /** The View. */ KnowtatorView view; - /** - * Instantiates a new Knowtator list. - * - */ - KnowtatorList() { + /** Instantiates a new Knowtator list. */ + KnowtatorList(KnowtatorView view) { + this.view = view; setModel(new DefaultListModel<>()); KnowtatorList list = this; @@ -122,7 +120,7 @@ public void dispose() { } /** React to model event. */ - void reactToModelEvent() { + private void reactToModelEvent() { ((DefaultListModel) getModel()).clear(); addElementsFromModel(); setSelected(); @@ -142,9 +140,4 @@ public void modelChangeEvent(ChangeEvent event) { public void colorChangedEvent(Profile profile) { reactToModelEvent(); } - - @Override - public void setView(KnowtatorView view) { - this.view = view; - } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/list/ProfileList.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/list/ProfileList.java index efb7a0c5..0f3f6913 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/list/ProfileList.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/list/ProfileList.java @@ -26,11 +26,21 @@ import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.object.Profile; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; import java.util.Optional; /** The type Profile list. */ public class ProfileList extends KnowtatorList { + /** + * Instantiates a new Knowtator list. + * + * @param view The view + */ + public ProfileList(KnowtatorView view) { + super(view); + } + @Override public void reactToClick() { // TODO: Something is going wrong when double clicking a profile with no colors. diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/profile/ProfileDialog.form b/src/main/java/edu/ucdenver/ccp/knowtator/view/profile/ProfileDialog.form new file mode 100644 index 00000000..3d840701 --- /dev/null +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/profile/ProfileDialog.form @@ -0,0 +1,156 @@ + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/profile/ProfileDialog.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/profile/ProfileDialog.java new file mode 100644 index 00000000..b6399b23 --- /dev/null +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/profile/ProfileDialog.java @@ -0,0 +1,286 @@ +/* + * MIT License + * + * Copyright (c) 2018 Harrison Pielke-Lombardo + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + * SOFTWARE. + */ + +package edu.ucdenver.ccp.knowtator.view.profile; + +import static edu.ucdenver.ccp.knowtator.view.actions.collection.AbstractKnowtatorCollectionAction.pickAction; +import static edu.ucdenver.ccp.knowtator.view.actions.collection.CollectionActionType.ADD; +import static edu.ucdenver.ccp.knowtator.view.actions.collection.CollectionActionType.REMOVE; +import static edu.ucdenver.ccp.knowtator.view.actions.collection.KnowtatorCollectionType.PROFILE; +import static edu.ucdenver.ccp.knowtator.view.actions.modelactions.ProfileAction.assignColorToClass; + +import edu.ucdenver.ccp.knowtator.model.OwlModel; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; +import edu.ucdenver.ccp.knowtator.view.actions.collection.ActionParameters; +import edu.ucdenver.ccp.knowtator.view.iaa.IAAOptionsDialog; +import edu.ucdenver.ccp.knowtator.view.list.ColorList; +import edu.ucdenver.ccp.knowtator.view.list.ProfileList; +import java.awt.BorderLayout; +import java.awt.FlowLayout; +import java.awt.GridBagConstraints; +import java.awt.GridBagLayout; +import java.awt.Window; +import java.awt.event.KeyEvent; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.util.Arrays; +import java.util.Optional; +import javax.swing.BorderFactory; +import javax.swing.DefaultListModel; +import javax.swing.ImageIcon; +import javax.swing.JButton; +import javax.swing.JComponent; +import javax.swing.JDialog; +import javax.swing.JFileChooser; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JSplitPane; +import javax.swing.KeyStroke; +import javax.swing.border.TitledBorder; + +public class ProfileDialog extends JDialog { + private JPanel contentPane; + private JButton buttonOK; + ProfileList profileList; + public ColorList colorList; + private JButton addProfileButton; + private JButton removeProfileButton; + private JButton addColorButton; + private JButton runIaaButton; + private final KnowtatorView view; + + public ProfileDialog(Window parent, KnowtatorView view) { + super(parent); + this.view = view; + $$$setupUI$$$(); + setContentPane(contentPane); + setModal(true); + getRootPane().setDefaultButton(buttonOK); + + view.knowtatorComponents.addAll( + Arrays.asList( + profileList, + colorList)); + + addProfileButton.addActionListener( + e -> + Optional.ofNullable(JOptionPane.showInputDialog(this, "Enter a name for the profile")) + .ifPresent( + profileName -> + pickAction(this.view, profileName, null, new ActionParameters(ADD, PROFILE)))); + removeProfileButton.addActionListener( + e -> + Optional.of( + JOptionPane.showConfirmDialog( + this, "Are you sure you wish to remove this profile?")) + .filter(result -> JOptionPane.OK_OPTION == result) + .ifPresent( + result -> pickAction(this.view, null, null, new ActionParameters(REMOVE, PROFILE)))); + + addColorButton.addActionListener( + e -> + // TODO: This could be removed if class selection were reflected in color list + this.view.getModel() + .flatMap(OwlModel::getSelectedOwlClass) + .ifPresent(owlClass -> assignColorToClass(this.view, owlClass))); + runIaaButton.addActionListener( + e -> + this.view.getModel() + .ifPresent( + model -> { + JFileChooser fileChooser = new JFileChooser(); + fileChooser.setCurrentDirectory(model.getSaveLocation()); + fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); + // + // disable the "All files" option. + // + fileChooser.setAcceptAllFileFilterUsed(false); + if (fileChooser.showSaveDialog(this) == JFileChooser.APPROVE_OPTION) { + File outputDirectory = new File(fileChooser.getSelectedFile(), "IAA_results"); + try { + Files.createDirectories(outputDirectory.toPath()); + } catch (IOException ioException) { + ioException.printStackTrace(); + } + this.onCancel(); + JDialog iaaDialog = new IAAOptionsDialog(JOptionPane.getFrameForComponent(this), model, view, outputDirectory); + iaaDialog.pack(); + iaaDialog.setVisible(true); + } + })); + + buttonOK.addActionListener(e -> onOK()); + + // call onCancel() when cross is clicked + setDefaultCloseOperation(DO_NOTHING_ON_CLOSE); + addWindowListener(new WindowAdapter() { + public void windowClosing(WindowEvent e) { + onCancel(); + } + }); + + // call onCancel() on ESCAPE + contentPane.registerKeyboardAction(e -> onCancel(), KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), + JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); + + + profileList.reset(); + colorList.reset(); + } + + private void onOK() { + // add your code here + this.view.knowtatorComponents.remove(profileList); + this.view.knowtatorComponents.remove(colorList); + dispose(); + } + + void onCancel() { + // add your code here if necessary + this.view.knowtatorComponents.remove(profileList); + this.view.knowtatorComponents.remove(colorList); + dispose(); + } + + private void createUIComponents() { + profileList = new ProfileList(this.view); + colorList = new ColorList(this.view); + } + + /** + * Method generated by IntelliJ IDEA GUI Designer + * >>> IMPORTANT!! <<< + * DO NOT edit this method OR call it in your code! + * + * @noinspection ALL + */ + private void $$$setupUI$$$() { + createUIComponents(); + contentPane = new JPanel(); + contentPane.setLayout(new GridBagLayout()); + final JPanel panel1 = new JPanel(); + panel1.setLayout(new GridBagLayout()); + GridBagConstraints gbc; + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 1; + gbc.weightx = 1.0; + gbc.fill = GridBagConstraints.BOTH; + contentPane.add(panel1, gbc); + final JPanel panel2 = new JPanel(); + panel2.setLayout(new GridBagLayout()); + gbc = new GridBagConstraints(); + gbc.gridx = 2; + gbc.gridy = 0; + gbc.weighty = 1.0; + gbc.fill = GridBagConstraints.BOTH; + panel1.add(panel2, gbc); + buttonOK = new JButton(); + buttonOK.setText("OK"); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 0; + gbc.weightx = 1.0; + gbc.weighty = 1.0; + gbc.fill = GridBagConstraints.HORIZONTAL; + panel2.add(buttonOK, gbc); + runIaaButton = new JButton(); + runIaaButton.setText("Run IAA"); + runIaaButton.setToolTipText("Run inter-annotator agreement calculation"); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 0; + gbc.weighty = 1.0; + gbc.fill = GridBagConstraints.HORIZONTAL; + panel1.add(runIaaButton, gbc); + final JPanel panel3 = new JPanel(); + panel3.setLayout(new GridBagLayout()); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 0; + gbc.weightx = 1.0; + gbc.weighty = 1.0; + gbc.fill = GridBagConstraints.BOTH; + contentPane.add(panel3, gbc); + final JSplitPane splitPane1 = new JSplitPane(); + gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 0; + gbc.weightx = 1.0; + gbc.weighty = 1.0; + gbc.fill = GridBagConstraints.BOTH; + panel3.add(splitPane1, gbc); + final JPanel panel4 = new JPanel(); + panel4.setLayout(new BorderLayout(0, 0)); + splitPane1.setLeftComponent(panel4); + panel4.setBorder(BorderFactory.createTitledBorder(null, "Profiles", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, null, null)); + final JPanel panel5 = new JPanel(); + panel5.setLayout(new FlowLayout(FlowLayout.CENTER, 5, 5)); + panel4.add(panel5, BorderLayout.NORTH); + addProfileButton = new JButton(); + addProfileButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-plus-24.png"))); + addProfileButton.setText(""); + addProfileButton.setToolTipText("Add a profile"); + panel5.add(addProfileButton); + removeProfileButton = new JButton(); + removeProfileButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-delete-24.png"))); + removeProfileButton.setText(""); + removeProfileButton.setToolTipText("Delete a profile"); + panel5.add(removeProfileButton); + final JScrollPane scrollPane1 = new JScrollPane(); + panel4.add(scrollPane1, BorderLayout.CENTER); + final DefaultListModel defaultListModel1 = new DefaultListModel(); + profileList.setModel(defaultListModel1); + profileList.setToolTipText("Click to activate a profile."); + scrollPane1.setViewportView(profileList); + final JPanel panel6 = new JPanel(); + panel6.setLayout(new BorderLayout(0, 0)); + splitPane1.setRightComponent(panel6); + panel6.setBorder(BorderFactory.createTitledBorder(null, "Colors", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, null, null)); + final JScrollPane scrollPane2 = new JScrollPane(); + panel6.add(scrollPane2, BorderLayout.CENTER); + colorList.setToolTipText("Click to select color for OWL class."); + scrollPane2.setViewportView(colorList); + final JPanel panel7 = new JPanel(); + panel7.setLayout(new FlowLayout(FlowLayout.CENTER, 5, 5)); + panel6.add(panel7, BorderLayout.NORTH); + addColorButton = new JButton(); + addColorButton.setIcon(new ImageIcon(getClass().getResource("/icon/icons8-plus-24.png"))); + addColorButton.setText(""); + addColorButton.setToolTipText("Add color for current OWL class"); + panel7.add(addColorButton); + } + + /** + * @noinspection ALL + */ + public JComponent $$$getRootComponent$$$() { + return contentPane; + } + +} diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTable.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTable.java index 48e57f46..15e2d10a 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTable.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTable.java @@ -27,6 +27,7 @@ import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.object.ConceptAnnotation; import edu.ucdenver.ccp.knowtator.model.object.TextSource; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; import java.util.Optional; import javax.swing.table.DefaultTableModel; @@ -37,8 +38,8 @@ public class AnnotationTable extends KnowtatorTable { * Instantiates a new Annotation table. * */ - AnnotationTable() { - super(); + AnnotationTable(KnowtatorView view) { + super(view); setModel( new DefaultTableModel( new Object[][] {}, new String[] {"Spanned Text", "OWL Entity", "Text Source"}) { diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTableForOwlClass.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTableForOwlClass.java index 7c403c6a..c80d7867 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTableForOwlClass.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTableForOwlClass.java @@ -24,6 +24,7 @@ package edu.ucdenver.ccp.knowtator.view.table; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; import java.util.HashSet; import java.util.Set; import javax.swing.JCheckBox; @@ -42,7 +43,8 @@ public class AnnotationTableForOwlClass extends AnnotationTable { * @param owlClassLabel the owl class label */ public AnnotationTableForOwlClass( - JCheckBox includeClassDescendantsCheckBox, JLabel owlClassLabel) { + KnowtatorView view, JCheckBox includeClassDescendantsCheckBox, JLabel owlClassLabel) { + super(view); this.includeClassDescendantsCheckBox = includeClassDescendantsCheckBox; this.owlClassLabel = owlClassLabel; this.activeOwlClassDescendants = new HashSet<>(); diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTableForSpannedText.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTableForSpannedText.java index 19ff4b96..c6e47219 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTableForSpannedText.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/AnnotationTableForSpannedText.java @@ -24,52 +24,76 @@ package edu.ucdenver.ccp.knowtator.view.table; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; +import java.util.regex.Pattern; import javax.swing.JCheckBox; import javax.swing.JTextField; -/** The type Annotation table for spanned text. */ +/** + * The type Annotation table for spanned text. + */ public class AnnotationTableForSpannedText extends AnnotationTable { private final JCheckBox exactMatchCheckBox; + private final JCheckBox regexCheckBox; private final JTextField annotationsContainingTextTextField; /** * Instantiates a new Annotation table for spanned text. * - * @param exactMatchCheckBox the exact match check box + * @param exactMatchCheckBox the exact match check box * @param annotationsContainingTextTextField the annotations containing text text field */ - public AnnotationTableForSpannedText( - JCheckBox exactMatchCheckBox, - JTextField annotationsContainingTextTextField) { + public AnnotationTableForSpannedText(KnowtatorView view, + JCheckBox exactMatchCheckBox, + JCheckBox regexCheckBox, + JTextField annotationsContainingTextTextField) { + super(view); this.exactMatchCheckBox = exactMatchCheckBox; + this.regexCheckBox = regexCheckBox; this.annotationsContainingTextTextField = annotationsContainingTextTextField; } @Override public void addElementsFromModel() { - view.getModel() - .ifPresent( - model -> - model - .getTextSources() - .forEach( - textSource -> - textSource.getConceptAnnotations().stream() - .filter( - conceptAnnotation -> - (exactMatchCheckBox.isSelected() - && conceptAnnotation - .getSpannedText() - .equals( - annotationsContainingTextTextField - .getText())) - || (!exactMatchCheckBox.isSelected() - && conceptAnnotation - .getSpannedText() - .contains( - annotationsContainingTextTextField - .getText()))) - .forEach(this::addValue))); + String text = annotationsContainingTextTextField.getText(); + + if (regexCheckBox.isSelected()) { + final Pattern pattern = Pattern.compile(text); + view.getModel() + .ifPresent( + model -> + model + .getTextSources() + .forEach( + textSource -> + textSource.getConceptAnnotations().stream() + .filter( + conceptAnnotation -> pattern + .matcher(conceptAnnotation.getSpannedText()) + .find() + ) + .forEach(this::addValue))); + } else { + view.getModel() + .ifPresent( + model -> + model + .getTextSources() + .forEach( + textSource -> + textSource.getConceptAnnotations().stream() + .filter( + conceptAnnotation -> (exactMatchCheckBox.isSelected() + && conceptAnnotation + .getSpannedText() + .equals(text)) + || (!exactMatchCheckBox.isSelected() + && conceptAnnotation + .getSpannedText() + .contains(text)) + ) + .forEach(this::addValue))); + } } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/table/KnowtatorTable.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/KnowtatorTable.java index 749d5684..fc2373c4 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/table/KnowtatorTable.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/KnowtatorTable.java @@ -33,7 +33,6 @@ import java.awt.Font; import java.awt.event.MouseEvent; import java.util.Optional; -import javax.swing.DefaultListModel; import javax.swing.JTable; import javax.swing.SwingUtilities; import javax.swing.event.MouseInputAdapter; @@ -50,7 +49,8 @@ public abstract class KnowtatorTable extends JTable KnowtatorView view; /** Instantiates a new Knowtator table. */ - KnowtatorTable() { + KnowtatorTable(KnowtatorView view) { + this.view = view; getTableHeader().setFont(new Font(getFont().getName(), Font.BOLD, 16)); setAutoCreateRowSorter(true); @@ -129,7 +129,7 @@ public void dispose() { /** React to model event. */ public void reactToModelEvent() { - ((DefaultListModel) getModel()).clear(); + ((DefaultTableModel) getModel()).setRowCount(0); addElementsFromModel(); setSelected(); } @@ -148,9 +148,4 @@ public void modelChangeEvent(ChangeEvent event) { public void colorChangedEvent(Profile profile) { reactToModelEvent(); } - - @Override - public void setView(KnowtatorView view) { - this.view = view; - } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/table/RelationTable.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/RelationTable.java index 4f35d425..1ed42582 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/table/RelationTable.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/RelationTable.java @@ -29,6 +29,7 @@ import edu.ucdenver.ccp.knowtator.model.object.AnnotationNode; import edu.ucdenver.ccp.knowtator.model.object.RelationAnnotation; import edu.ucdenver.ccp.knowtator.model.object.TextSource; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; import java.util.HashSet; import java.util.Optional; import java.util.Set; @@ -49,8 +50,8 @@ public class RelationTable extends KnowtatorTable { * @param owlPropertyLabel the owl property label */ public RelationTable( - JCheckBox includePropertyDescendantsCheckBox, JLabel owlPropertyLabel) { - super(); + KnowtatorView view, JCheckBox includePropertyDescendantsCheckBox, JLabel owlPropertyLabel) { + super(view); setModel( new DefaultTableModel( new Object[][] {}, diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/list/SpanList.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/SpanTable.java similarity index 63% rename from src/main/java/edu/ucdenver/ccp/knowtator/view/list/SpanList.java rename to src/main/java/edu/ucdenver/ccp/knowtator/view/table/SpanTable.java index fb5a755c..dc757217 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/list/SpanList.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/table/SpanTable.java @@ -22,21 +22,39 @@ * SOFTWARE. */ -package edu.ucdenver.ccp.knowtator.view.list; +package edu.ucdenver.ccp.knowtator.view.table; import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.object.ConceptAnnotation; import edu.ucdenver.ccp.knowtator.model.object.Span; import edu.ucdenver.ccp.knowtator.model.object.TextSource; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; import java.util.Optional; +import javax.swing.table.DefaultTableModel; /** The type Span list. */ -public class SpanList extends KnowtatorList { +public class SpanTable extends KnowtatorTable { + /** + * Instantiates a new Knowtator list. + * + * @param view The Knowtator view + */ + public SpanTable(KnowtatorView view) { + super(view); + setModel( + new DefaultTableModel( + new Object[][] {}, new String[] {"Spanned Text", "Start", "End"}) { + @Override + public boolean isCellEditable(int row, int col) { + return false; + } + }); + } @Override public void reactToClick() { - Optional spanOptional = Optional.ofNullable(getSelectedValue()); + Optional spanOptional = getSelectedValue(); spanOptional.ifPresent( span -> { view.getModel() @@ -47,20 +65,33 @@ public void reactToClick() { } @Override - protected void addElementsFromModel() { + public void addElementsFromModel() { view.getModel() .flatMap(BaseModel::getSelectedTextSource) .flatMap(TextSource::getSelectedAnnotation) - .ifPresent( - conceptAnnotation -> - conceptAnnotation.forEach(span -> getDefaultListModel().addElement(span))); + .ifPresent(conceptAnnotation -> conceptAnnotation.forEach(this::addValue)); } @Override - protected Optional getSelectedFromModel() { + protected Optional getSelectedFromModel() { return view.getModel() .flatMap(BaseModel::getSelectedTextSource) .flatMap(TextSource::getSelectedAnnotation) - .flatMap(ConceptAnnotation::getSelection); + .flatMap(ConceptAnnotation::getSelection) + .map(span -> span); + } + + @Override + Optional getSelectedValue() { + return Optional.empty(); + } + + @Override + void addValue(Span modelObject) { + ((DefaultTableModel) getModel()) + .addRow( + new Object[] { + modelObject, modelObject.getStart(), modelObject.getEnd() + }); } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/AnnotatableTextPane.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/AnnotatableTextPane.java index 7a563f71..c86451b8 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/AnnotatableTextPane.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/AnnotatableTextPane.java @@ -44,9 +44,8 @@ import edu.ucdenver.ccp.knowtator.model.object.TextSource; import edu.ucdenver.ccp.knowtator.view.KnowtatorComponent; import edu.ucdenver.ccp.knowtator.view.KnowtatorDefaultSettings; -import edu.ucdenver.ccp.knowtator.view.actions.ActionUnperformable; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; import edu.ucdenver.ccp.knowtator.view.actions.collection.ActionParameters; -import edu.ucdenver.ccp.knowtator.view.actions.modelactions.ReassignOwlClassAction; import java.awt.BasicStroke; import java.awt.Color; import java.awt.Font; @@ -59,7 +58,6 @@ import java.util.Optional; import java.util.Set; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPopupMenu; import javax.swing.JTextField; import javax.swing.SwingUtilities; @@ -77,7 +75,7 @@ public abstract class AnnotatableTextPane extends SearchableTextPane implements KnowtatorComponent, ModelListener { @SuppressWarnings("unused") - private Logger log = LogManager.getLogger(AnnotatableTextPane.class.getName()); + private final Logger log = LogManager.getLogger(AnnotatableTextPane.class.getName()); private final DefaultHighlighter.DefaultHighlightPainter overlapHighlighter = new DefaultHighlighter.DefaultHighlightPainter(Color.LIGHT_GRAY); @@ -87,8 +85,8 @@ public abstract class AnnotatableTextPane extends SearchableTextPane * * @param searchTextField the search text field */ - AnnotatableTextPane(JTextField searchTextField) { - super(searchTextField); + AnnotatableTextPane(KnowtatorView view, JTextField searchTextField) { + super(view, searchTextField); setEditable(false); setFont(KnowtatorDefaultSettings.FONT); @@ -109,6 +107,12 @@ public abstract class AnnotatableTextPane extends SearchableTextPane public void mouseDragged(MouseEvent e) { super.mouseDragged(e); refreshHighlights(); + highlightRegion(pressOffset, pressOffset, new RectanglePainter(Color.BLACK)); + + view.getModel() + .flatMap(BaseModel::getSelectedTextSource) + .flatMap(TextSource::getSelectedAnnotation) + .ifPresent(annotation -> annotation.setSelection(null)); } @Override @@ -120,14 +124,7 @@ public void mouseMoved(MouseEvent e) { public void mousePressed(MouseEvent e) { super.mousePressed(e); pressOffset = viewToModel(e.getPoint()); - highlightRegion(pressOffset, pressOffset, new RectanglePainter(Color.BLACK)); - view.getModel() - .flatMap(BaseModel::getSelectedTextSource) - .ifPresent( - textSource -> { - // TODO: I may want to make this set the selected span to null instead - textSource.setSelectedConceptAnnotation(null); - }); + } @Override @@ -214,6 +211,7 @@ protected void refreshHighlights() { if (view.getModel() .flatMap(BaseModel::getSelectedTextSource) .flatMap(TextSource::getSelectedAnnotation) + .flatMap(ConceptAnnotation::getSelection) .isPresent()) { highlightSelectedAnnotation(); } else { @@ -300,7 +298,7 @@ private void highlightOverlaps(Set spans) { Iterator spanIterator = spans.iterator(); if (spanIterator.hasNext()) { Span lastSpan = spanIterator.next(); - for (; spanIterator.hasNext(); ) { + while (spanIterator.hasNext()) { Span span = spanIterator.next(); if (span.intersects(lastSpan)) { highlightRegion( @@ -420,7 +418,7 @@ public void dispose() { } /** The type Rectangle painter. */ - class RectanglePainter extends DefaultHighlighter.DefaultHighlightPainter { + static class RectanglePainter extends DefaultHighlighter.DefaultHighlightPainter { /** * Instantiates a new Rectangle painter. @@ -514,40 +512,6 @@ class AnnotationPopupMenu extends JPopupMenu { this.mouseEvent = mouseEvent; } - private JMenuItem reassignOwlClassCommand() { - JMenuItem menuItem = new JMenuItem("Reassign OWL class"); - menuItem.addActionListener( - e -> - view.getModel() - .ifPresent( - model -> { - Optional selectedOwlClass = model.getSelectedOwlClass(); - selectedOwlClass.ifPresent( - owlClass -> - model - .getSelectedTextSource() - .ifPresent( - textSource1 -> - textSource1 - .getSelectedAnnotation() - .ifPresent( - conceptAnnotation -> { - try { - model.registerAction( - new ReassignOwlClassAction( - model, - conceptAnnotation, - owlClass)); - } catch (ActionUnperformable e1) { - JOptionPane.showMessageDialog( - view, e1.getMessage()); - } - }))); - })); - - return menuItem; - } - private JMenuItem addAnnotationCommand() { JMenuItem menuItem = new JMenuItem("Add concept"); menuItem.addActionListener( @@ -628,20 +592,14 @@ && getSelectionStart() != getSelectionEnd()) { show(mouseEvent.getComponent(), mouseEvent.getX(), mouseEvent.getY()); } else { view.getModel() - .flatMap(BaseModel::getSelectedTextSource) - .ifPresent( - textSource -> - textSource - .getSelectedAnnotation() - .ifPresent( - conceptAnnotation -> - conceptAnnotation - .getSelection() - .filter( - span -> - span.getStart() <= releaseOffset - && releaseOffset <= span.getEnd()) - .ifPresent(span -> clickedInsideSpan(conceptAnnotation)))); + .flatMap(BaseModel::getSelectedTextSource).flatMap(TextSource::getSelectedAnnotation).ifPresent(conceptAnnotation -> + conceptAnnotation + .getSelection() + .filter( + span -> + span.getStart() <= releaseOffset + && releaseOffset <= span.getEnd()) + .ifPresent(span -> clickedInsideSpan(conceptAnnotation))); } } @@ -650,7 +608,6 @@ private void clickedInsideSpan(ConceptAnnotation conceptAnnotation) { if (conceptAnnotation.size() > 1) { add(removeSpanFromAnnotationCommand(conceptAnnotation)); } - add(reassignOwlClassCommand()); show(mouseEvent.getComponent(), mouseEvent.getX(), mouseEvent.getY()); } } diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/KnowtatorTextPane.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/KnowtatorTextPane.java index 67f2a069..9956699b 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/KnowtatorTextPane.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/KnowtatorTextPane.java @@ -27,6 +27,7 @@ import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.ModelListener; import edu.ucdenver.ccp.knowtator.view.KnowtatorComponent; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; import java.awt.image.BufferedImage; import java.util.regex.Matcher; import java.util.regex.Pattern; @@ -55,11 +56,12 @@ public class KnowtatorTextPane extends AnnotatableTextPane * @param caseSensitiveCheckBox A check box specifying if the search should be case sensitive */ public KnowtatorTextPane( + KnowtatorView view, JTextField searchTextField, JCheckBox onlyInAnnotationsCheckBox, JCheckBox regexCheckBox, JCheckBox caseSensitiveCheckBox) { - super(searchTextField); + super(view, searchTextField); this.onlyInAnnotationsCheckBox = onlyInAnnotationsCheckBox; this.regexCheckBox = regexCheckBox; this.caseSensitiveCheckBox = caseSensitiveCheckBox; diff --git a/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/SearchableTextPane.java b/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/SearchableTextPane.java index 75ceaf55..3de2f2ba 100644 --- a/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/SearchableTextPane.java +++ b/src/main/java/edu/ucdenver/ccp/knowtator/view/textpane/SearchableTextPane.java @@ -26,6 +26,7 @@ import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.ModelListener; +import edu.ucdenver.ccp.knowtator.model.collection.SelectableCollection; import edu.ucdenver.ccp.knowtator.model.collection.event.ChangeEvent; import edu.ucdenver.ccp.knowtator.model.object.ModelObject; import edu.ucdenver.ccp.knowtator.model.object.TextSource; @@ -48,18 +49,14 @@ public abstract class SearchableTextPane extends JTextPane /** The View. */ KnowtatorView view; - @Override - public void setView(KnowtatorView view) { - this.view = view; - } - /** * Instantiates a new Searchable text pane. * * @param searchTextField A text field used to search the text pane */ - SearchableTextPane(JTextField searchTextField) { + SearchableTextPane(KnowtatorView view, JTextField searchTextField) { super(); + this.view = view; this.searchTextField = searchTextField; this.isSearching = false; addCaretListener( @@ -126,12 +123,7 @@ public void searchForward() { } } } - view.getModel() - .ifPresent( - model -> - model - .getSelectedTextSource() - .ifPresent(textSource -> textSource.setSelectedConceptAnnotation(null))); + view.getModel().flatMap(BaseModel::getSelectedTextSource).ifPresent(textSource -> textSource.setSelectedConceptAnnotation(null)); select(matchStart, matchEnd); refreshHighlights(); isSearching = false; @@ -191,16 +183,11 @@ void makePattern() { public void modelChangeEvent(ChangeEvent event) { view.getModel() .flatMap(BaseModel::getSelectedTextSource) - .ifPresent( - textSource -> - textSource - .getSelectedAnnotation() - .ifPresent( - conceptAnnotation -> - conceptAnnotation - .getSelection() - .ifPresent( - span -> searchTextField.setText(span.getSpannedText())))); + .flatMap(textSource -> textSource + .getSelectedAnnotation() + .flatMap(SelectableCollection::getSelection)) + .filter(span -> shouldUpdateSearchTextFieldCondition()) + .ifPresent(span -> searchTextField.setText(span.getSpannedText())); event .getNew() .ifPresent( diff --git a/src/main/resources/icon/icons8-redo-52.png b/src/main/resources/icon/icons8-redo-52.png new file mode 100644 index 00000000..6cb7475f Binary files /dev/null and b/src/main/resources/icon/icons8-redo-52.png differ diff --git a/src/main/resources/icon/icons8-search-52.png b/src/main/resources/icon/icons8-search-52.png new file mode 100644 index 00000000..f7678a38 Binary files /dev/null and b/src/main/resources/icon/icons8-search-52.png differ diff --git a/src/main/resources/icon/icons8-synchronize-32.png b/src/main/resources/icon/icons8-synchronize-32.png index 06046b08..f383a335 100644 Binary files a/src/main/resources/icon/icons8-synchronize-32.png and b/src/main/resources/icon/icons8-synchronize-32.png differ diff --git a/src/main/resources/icon/icons8-undo-52.png b/src/main/resources/icon/icons8-undo-52.png new file mode 100644 index 00000000..6a49f55f Binary files /dev/null and b/src/main/resources/icon/icons8-undo-52.png differ diff --git a/src/main/resources/log4j.properties b/src/main/resources/log4j.properties index fbef1c70..9616ed9c 100644 --- a/src/main/resources/log4j.properties +++ b/src/main/resources/log4j.properties @@ -89,4 +89,12 @@ exact.match=&Exact Match include.descendants1=Include &descendants relation.annotations.for.owl.objectproperty=Relation Annotations for OWL ObjectProperty: new=New -new1=&New \ No newline at end of file +new1=&New +select.all=Select all +span.iaa=Span IAA +class.iaa=Class IAA +class.and.span.iaa=Class and Span IAA +ok=OK +cancel=Cancel +mode=Mode +documents=Documents \ No newline at end of file diff --git a/src/test/java/edu/ucdenver/ccp/knowtator/KnowtatorIaaTest.java b/src/test/java/edu/ucdenver/ccp/knowtator/KnowtatorIaaTest.java index d569e3d1..17df605f 100644 --- a/src/test/java/edu/ucdenver/ccp/knowtator/KnowtatorIaaTest.java +++ b/src/test/java/edu/ucdenver/ccp/knowtator/KnowtatorIaaTest.java @@ -28,15 +28,27 @@ import edu.ucdenver.ccp.knowtator.iaa.IaaException; import edu.ucdenver.ccp.knowtator.iaa.KnowtatorIaa; import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; +import edu.ucdenver.ccp.knowtator.model.collection.ProfileCollection; +import edu.ucdenver.ccp.knowtator.model.object.ConceptAnnotation; +import edu.ucdenver.ccp.knowtator.model.object.Profile; +import edu.ucdenver.ccp.knowtator.model.object.TextSource; import java.io.File; import java.io.IOException; +import java.util.ArrayList; +import java.util.HashSet; +import java.util.stream.Collectors; import org.apache.commons.io.FileUtils; +import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; class KnowtatorIaaTest { private static KnowtatorIaa knowtatorIAA; + private static File outputDir; + private static File goldStandardDir; + private static KnowtatorModel model; + private static final TestingHelpers.ProjectCounts counts = new TestingHelpers.ProjectCounts(4, 456, 456, 4, 3, 0, 0, 0, 0); @BeforeAll static void makeProjectTest() throws IaaException, IOException { @@ -44,39 +56,95 @@ static void makeProjectTest() throws IaaException, IOException { File projectDirectory = TestingHelpers.getProjectFile(projectFileName).getParentFile(); File tempProjectDir = Files.createTempDir(); FileUtils.copyDirectory(projectDirectory, tempProjectDir); - KnowtatorModel controller = new KnowtatorModel(tempProjectDir, null); - controller.load(); - // File goldStandardDir = new File(model.getProjectLocation(), "iaa"); - File outputDir = new File(controller.getProjectLocation(), "iaa_results"); - //noinspection ResultOfMethodCallIgnored + model = new KnowtatorModel(tempProjectDir, null); + model.load(model.getProjectLocation()); + + goldStandardDir = new File(model.getProjectLocation(), "iaa"); + + outputDir = new File(model.getProjectLocation(), "iaa_results"); + boolean created = outputDir.mkdir(); if (created) { - knowtatorIAA = new KnowtatorIaa(outputDir, controller); + ProfileCollection profiles = new ProfileCollection(model); + profiles.remove(profiles.getDefaultProfile()); + HashSet myProfiles = new HashSet<>(); + myProfiles.add("Kristin Garcia"); + myProfiles.add("Mike Bada"); + + model.getProfile("Kristin Garcia").ifPresent(profiles::add); + model.getProfile("Mike Bada").ifPresent(profiles::add); + knowtatorIAA = new KnowtatorIaa(outputDir, + model, + model.getTextSources().stream().map(TextSource::getId).collect(Collectors.toSet()), + model.getProfiles().stream() + .map(Profile::getId) + .filter(myProfiles::contains) + .collect(Collectors.toSet()), + new ArrayList<>(new HashSet<>(model.getTextSources().stream() + .flatMap(textSource -> textSource.getConceptAnnotations().stream() + .map(ConceptAnnotation::getOwlClass)) + .collect(Collectors.toSet())))); } } @Test - void runClassIaaTest() throws IaaException { + void runClassIaaTest() throws IOException, IaaException { + TestingHelpers.countCollections(model, counts); knowtatorIAA.runClassIaa(); // TODO: Rerun test data because concept annotations no longer store owl class label - // assert FileUtils.contentEqualsIgnoreEOL(new File(outputDir, "Class matcher.dat"), new - // File(goldStandardDir, "Class matcher.dat"), "utf-8"); + try { + assert FileUtils.contentEqualsIgnoreEOL( + new File(outputDir, "Class matcher.dat"), + new File(goldStandardDir, "Class matcher.dat"), + "utf-8"); + } catch (AssertionError e) { + System.out.println(String.format("Gold: %s\nThis: %s\n", + new File(goldStandardDir, "index.html").getAbsolutePath(), + new File(outputDir, "index.html").getAbsolutePath())); + throw e; + } } @Test - void runSpanIaaTest() throws IaaException { + void runSpanIaaTest() throws IOException, IaaException { + TestingHelpers.countCollections(model, counts); knowtatorIAA.runSpanIaa(); - // assert FileUtils.contentEqualsIgnoreEOL(new File(outputDir, "Span matcher.dat"), new - // File(goldStandardDir, "Span matcher.dat"), "utf-8"); + + try { + assert FileUtils.contentEqualsIgnoreEOL( + new File(outputDir, "Span matcher.html"), + new File(goldStandardDir, "Span matcher.html"), + "utf-8"); + } catch (AssertionError e) { + System.out.println(String.format("Gold: %s\nThis: %s\n", + new File(goldStandardDir, "index.html").getAbsolutePath(), + new File(outputDir, "index.html").getAbsolutePath())); + throw e; + } } @Test - void runClassAndSpanIaaTest() throws IaaException { + void runClassAndSpanIaaTest() throws IaaException, IOException { + TestingHelpers.countCollections(model, counts); knowtatorIAA.runClassAndSpanIaa(); - // assert FileUtils.contentEqualsIgnoreEOL(new File(outputDir, "Class and span - // matcher.dat"), new File(goldStandardDir, "Class and span matcher.dat"), "utf-8"); + try { + assert FileUtils.contentEqualsIgnoreEOL( + new File(outputDir, "Class and span matcher.dat"), + new File(goldStandardDir, "Class and span matcher.dat"), + "utf-8"); + } catch (AssertionError e) { + System.out.println(String.format("Gold: %s\nThis: %s\n", + new File(goldStandardDir, "index.html").getAbsolutePath(), + new File(outputDir, "index.html").getAbsolutePath())); + throw e; + } + } + + @AfterAll + static void cleanUp() { + knowtatorIAA.closeHtml(); } } diff --git a/src/test/java/edu/ucdenver/ccp/knowtator/ProjectManagerTest.java b/src/test/java/edu/ucdenver/ccp/knowtator/ProjectManagerTest.java index e3eb0035..1c508490 100644 --- a/src/test/java/edu/ucdenver/ccp/knowtator/ProjectManagerTest.java +++ b/src/test/java/edu/ucdenver/ccp/knowtator/ProjectManagerTest.java @@ -27,6 +27,7 @@ import difflib.Delta; import difflib.DiffUtils; import difflib.Patch; +import edu.ucdenver.ccp.knowtator.model.BaseModel; import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; import java.io.BufferedReader; import java.io.File; @@ -34,6 +35,7 @@ import java.io.IOException; import java.util.LinkedList; import java.util.List; +import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; @SuppressWarnings("EmptyMethod") @@ -41,18 +43,15 @@ class ProjectManagerTest { private static KnowtatorModel model; - static { - try { - model = TestingHelpers.getLoadedModel(); - } catch (IOException e) { - e.printStackTrace(); - } + @BeforeEach + void setup() throws IOException { + model = TestingHelpers.getLoadedModel(); } @Test void loadProjectTest() { TestingHelpers.checkDefaultCollectionValues(model); - model.load(); + model.load(model.getProjectLocation()); } private static List fileToLines(File file) { @@ -74,7 +73,7 @@ void saveProjectTest() { TestingHelpers.checkDefaultCollectionValues(model); model.save(); TestingHelpers.checkDefaultCollectionValues(model); - File file1 = new File(model.getAnnotationsLocation(), "document1.xml"); + File file1 = new File(BaseModel.getAnnotationsLocation(model.getProjectLocation()), "document1.xml"); File referenceFile = new File( TestingHelpers.class @@ -103,7 +102,20 @@ void newProjectTest() {} void importToManagerTest() {} @Test - void importProjectTest() {} + void importProjectTest() throws IOException { + TestingHelpers.checkDefaultCollectionValues(model); + String projectName = "iaa_test_project"; + File projectFile = new File( + TestingHelpers.class + .getResource(String.format("/%s/%s.knowtator", projectName, projectName)) + .getFile()); + projectFile = BaseModel.validateProjectLocation(projectFile); + model.load(projectFile); + + TestingHelpers.ProjectCounts counts = TestingHelpers.defaultCounts.copy(4, 456, 456, 4, 2, 0, 0, 0, 0); + TestingHelpers.countCollections(model, counts); + + } @SuppressWarnings("EmptyMethod") @Test diff --git a/src/test/java/edu/ucdenver/ccp/knowtator/TestingHelpers.java b/src/test/java/edu/ucdenver/ccp/knowtator/TestingHelpers.java index 287f5cf0..8a83173a 100644 --- a/src/test/java/edu/ucdenver/ccp/knowtator/TestingHelpers.java +++ b/src/test/java/edu/ucdenver/ccp/knowtator/TestingHelpers.java @@ -41,6 +41,8 @@ public class TestingHelpers { /** The constant projectFileName. */ private static final String projectFileName = "test_project_using_uris"; + public static final ProjectCounts defaultCounts = new ProjectCounts(5, 6, 7, 3, 2, 3, 7, 4, 0); + /** The constant defaultExpectedTextSources. */ public static final int defaultExpectedTextSources = 5; @@ -55,8 +57,6 @@ public class TestingHelpers { /** The constant defaultExpectedGraphSpaces. */ public static final int defaultExpectedGraphSpaces = 3; - public static final int defaultExpectedStructureGraphSpaces = 0; - /** The constant defaultExpectedProfiles. */ public static final int defaultExpectedProfiles = 2; @@ -66,12 +66,10 @@ public class TestingHelpers { /** The constant defaultExpectedAnnotationNodes. */ public static final int defaultExpectedAnnotationNodes = 7; - public static final int defaultExpectedStructureAnnotationNodes = 0; - /** The constant defaultExpectedTriples. */ public static final int defaultExpectedTriples = 4; - public static final int defaultExpectedStructureTriples = 0; + public static int defaultAnnotationLayers = 1; /** * Gets project file. @@ -111,7 +109,7 @@ public static KnowtatorModel getLoadedModel() throws IOException { File tempProjectDir = Files.createTempDir(); FileUtils.copyDirectory(projectDirectory, tempProjectDir); KnowtatorModel model = new KnowtatorModel(tempProjectDir, null); - model.load(); + model.load(model.getProjectLocation()); return model; } @@ -127,7 +125,7 @@ public static KnowtatorModel getLoadedModel(String projectFileName) throws IOExc File tempProjectDir = Files.createTempDir(); FileUtils.copyDirectory(projectDirectory, tempProjectDir); KnowtatorModel model = new KnowtatorModel(tempProjectDir, null); - model.load(); + model.load(model.getProjectLocation()); return model; } @@ -138,45 +136,42 @@ public static KnowtatorModel getLoadedModel(String projectFileName) throws IOExc * @param model the model */ public static void checkDefaultCollectionValues(KnowtatorModel model) { - TestingHelpers.countCollections( - model, - defaultExpectedTextSources, - defaultExpectedConceptAnnotations, - defaultExpectedSpans, - defaultExpectedGraphSpaces, - defaultExpectedProfiles, - defaultExpectedHighlighters, - defaultExpectedAnnotationNodes, - defaultExpectedTriples, - defaultExpectedStructureAnnotations, - defaultExpectedStructureGraphSpaces, - defaultExpectedStructureAnnotationNodes, - defaultExpectedStructureTriples); + TestingHelpers.countCollections(model, defaultCounts); } - public static void countCollections( - KnowtatorModel model, - int expectedTextSources, - int expectedConceptAnnotations, - int expectedSpans, - int expectedGraphSpaces, - int expectedProfiles, - int expectedHighlighters, - int expectedAnnotationNodes, - int expectedTriples, - int expectedStructureAnnotations, - int expectedStructureGraphSpaces, - int expectedStructureAnnotationNodes, - int expectedStructureTriples) { + public static void countCollections(KnowtatorModel model, ProjectCounts counts) { int actualTextSources = model.getNumberOfTextSources(); int actualConceptAnnotations = - model.getTextSources().stream().mapToInt(TextSource::getNumberOfConceptAnnotations).sum(); + model.getTextSources().stream() + .mapToInt( + textSource -> + Math.toIntExact( + textSource.getConceptAnnotations().stream() + .filter( + conceptAnnotation -> + !conceptAnnotation.getLayers().contains("Structures")) + .count())) + .sum(); int actualStructureAnnotations = - model.getTextSources().stream().mapToInt(TextSource::getNumberOfStructureAnnotations).sum(); + model.getTextSources().stream() + .mapToInt( + textSource -> + Math.toIntExact( + textSource.getConceptAnnotations().stream() + .filter( + conceptAnnotation -> + conceptAnnotation.getLayers().contains("Structures")) + .count())) + .sum(); int actualSpans = model.getTextSources().stream() - .mapToInt(textSource -> textSource.getSpans(null).size()) + .mapToInt( + textSource -> + Math.toIntExact(textSource.getSpans(null).stream() + .filter( + span -> !span.getConceptAnnotation().getLayers().contains("Structures")) + .count())) .sum(); int actualProfiles = model.getNumberOfProfiles(); int actualHighlighters = @@ -193,6 +188,7 @@ public static void countCollections( graphSpace1.getChildVertices(graphSpace1.getDefaultParent()).length) .sum()) .sum(); + int actualTriples = model.getTextSources().stream() .mapToInt( @@ -203,122 +199,81 @@ public static void countCollections( graphSpace1.getChildEdges(graphSpace1.getDefaultParent()).length) .sum()) .sum(); - int actualStructureGraphSpaces = - model.getTextSources().stream().mapToInt(TextSource::getNumberOfStructureGraphSpaces).sum(); - int actualStructureAnnotationNodes = - model.getTextSources().stream() - .mapToInt( - textSource -> - textSource.getStructureGraphSpaces().stream() - .mapToInt( - graphSpace1 -> - graphSpace1.getChildVertices(graphSpace1.getDefaultParent()).length) - .sum()) - .sum(); - int actualStructureTriples = - model.getTextSources().stream() - .mapToInt( - textSource -> - textSource.getStructureGraphSpaces().stream() - .mapToInt( - graphSpace1 -> - graphSpace1.getChildEdges(graphSpace1.getDefaultParent()).length) - .sum()) - .sum(); - assert actualTextSources == expectedTextSources - : String.format( - "There were %d text sources instead of %d", actualTextSources, expectedTextSources); - assert actualConceptAnnotations == expectedConceptAnnotations - : String.format( - "There were %d concept annotations instead of %d", - actualConceptAnnotations, expectedConceptAnnotations); - assert actualStructureAnnotations == expectedStructureAnnotations - : String.format( - "There were %d structure annotations instead of %d", - actualStructureAnnotations, expectedStructureAnnotations); - assert actualSpans == expectedSpans - : String.format("There were %d spans instead of %d", actualSpans, expectedSpans); - - assert actualProfiles == expectedProfiles - : String.format("There were %d profiles instead of %d", actualProfiles, expectedProfiles); - - assert actualHighlighters == expectedHighlighters - : String.format( - "There were %d highlighters instead of %d", actualHighlighters, expectedHighlighters); - - assert actualGraphSpaces == expectedGraphSpaces - : String.format( - "There were %d graph spaces instead of %d", actualGraphSpaces, expectedGraphSpaces); - - assert actualAnnotationNodes == expectedAnnotationNodes - : String.format( - "There were %d vertices instead of %d", actualAnnotationNodes, expectedAnnotationNodes); - - assert actualTriples == expectedTriples - : String.format("There were %d triples instead of %d", actualTriples, expectedTriples); - - assert actualStructureGraphSpaces == expectedStructureGraphSpaces - : String.format( - "There were %d structure graph spaces instead of %d", - actualStructureGraphSpaces, expectedStructureGraphSpaces); - - assert actualStructureAnnotationNodes == expectedStructureAnnotationNodes - : String.format( - "There were %d structure vertices instead of %d", - actualStructureAnnotationNodes, expectedStructureAnnotationNodes); - - assert actualStructureTriples == expectedStructureTriples - : String.format( - "There were %d structure triples instead of %d", - actualStructureTriples, expectedStructureTriples); + String error = ""; + + try { + assert actualTextSources == counts.ets; + } catch (AssertionError e) { + error = error.concat(String.format("\nThere were %d text sources instead of %d", actualTextSources, counts.ets)); + } + + try { + assert actualConceptAnnotations == counts.eca; + } catch (AssertionError e) { + error = error.concat(String.format("\nThere were %d concept annotations instead of %d", actualConceptAnnotations, counts.eca)); + } + + try { + assert actualStructureAnnotations == counts.esa; + } catch (AssertionError e) { + error = error.concat(String.format("\nThere were %d structure annotations instead of %d", actualStructureAnnotations, counts.esa)); + } + + try { + assert actualSpans == counts.es; + } catch (AssertionError e) { + error = error.concat(String.format("\nThere were %d spans instead of %d", actualSpans, counts.es)); + } + + try { + assert actualProfiles == counts.ep; + } catch (AssertionError e) { + error = error.concat(String.format("\nThere were %d profiles instead of %d", actualProfiles, counts.ep)); + } + + try { + assert actualHighlighters == counts.eh; + } catch (AssertionError e) { + error = error.concat(String.format("\nThere were %d highlighters instead of %d", actualHighlighters, counts.eh)); + } + + try { + assert actualGraphSpaces == counts.egs; + } catch (AssertionError e) { + error = error.concat(String.format("\nThere were %d graph spaces instead of %d", actualGraphSpaces, counts.egs)); + } + + try { + assert actualAnnotationNodes == counts.ean; + } catch (AssertionError e) { + error = error.concat(String.format("\nThere were %d annotation nodes instead of %d", actualAnnotationNodes, counts.ean)); + } + + try { + assert actualTriples == counts.et; + } catch (AssertionError e) { + error = error.concat(String.format("\nThere were %d triples instead of %d", actualTriples, counts.et)); + } + + if (!error.equals("")) { + throw new AssertionError(error); + } } + /** * Test owl action. * * @param controller the controller * @param changes the changes - * @param expectedTextSources the expected text sources - * @param expectedConceptAnnotations the expected concept annotations - * @param expectedSpans the expected spans - * @param expectedGraphSpaces the expected graph spaces - * @param expectedProfiles the expected profiles - * @param expectedHighlighters the expected highlighters - * @param expectedAnnotationNodes the expected annotation nodes - * @param expectedTriples the expected triples */ public static void testOwlAction( KnowtatorModel controller, - List changes, - int expectedTextSources, - int expectedConceptAnnotations, - int expectedStructureAnnotations, - int expectedSpans, - int expectedGraphSpaces, - int expectedStructureGraphSpaces, - int expectedProfiles, - int expectedHighlighters, - int expectedAnnotationNodes, - int expectedStructureAnnotationNodes, - int expectedTriples, - int expectedStructureTriples) { + List changes, ProjectCounts counts) { TestingHelpers.checkDefaultCollectionValues(controller); controller.getOwlOntologyManager().applyChanges(changes); - TestingHelpers.countCollections( - controller, - expectedTextSources, - expectedConceptAnnotations, - expectedSpans, - expectedGraphSpaces, - expectedProfiles, - expectedHighlighters, - expectedAnnotationNodes, - expectedTriples, - expectedStructureAnnotations, - expectedStructureGraphSpaces, - expectedStructureAnnotationNodes, - expectedStructureTriples); + TestingHelpers.countCollections(controller, counts); } /** @@ -326,65 +281,83 @@ public static void testOwlAction( * * @param controller the controller * @param action the action - * @param expectedTextSources the expected text sources - * @param expectedConceptAnnotations the expected concept annotations - * @param expectedSpans the expected spans - * @param expectedGraphSpaces the expected graph spaces - * @param expectedProfiles the expected profiles - * @param expectedHighlighters the expected highlighters - * @param expectedAnnotationNodes the expected annotation nodes - * @param expectedTriples the expected triples * @throws ActionUnperformable the action unperformable exception */ public static void testKnowtatorAction( KnowtatorModel controller, AbstractKnowtatorAction action, - int expectedTextSources, - int expectedConceptAnnotations, - int expectedSpans, - int expectedGraphSpaces, - int expectedProfiles, - int expectedHighlighters, - int expectedAnnotationNodes, - int expectedTriples, - int expectedStructureAnnotations, - int expectedStructureGraphSpaces, - int expectedStructureAnnotationNodes, - int expectedStructureTriples) + ProjectCounts counts) throws ActionUnperformable { TestingHelpers.checkDefaultCollectionValues(controller); controller.registerAction(action); - TestingHelpers.countCollections( - controller, - expectedTextSources, - expectedConceptAnnotations, - expectedSpans, - expectedGraphSpaces, - expectedProfiles, - expectedHighlighters, - expectedAnnotationNodes, - expectedTriples, - expectedStructureAnnotations, - expectedStructureGraphSpaces, - expectedStructureAnnotationNodes, - expectedStructureTriples); + TestingHelpers.countCollections(controller, counts); controller.undo(); TestingHelpers.checkDefaultCollectionValues(controller); controller.redo(); - TestingHelpers.countCollections( - controller, - expectedTextSources, - expectedConceptAnnotations, - expectedSpans, - expectedGraphSpaces, - expectedProfiles, - expectedHighlighters, - expectedAnnotationNodes, - expectedTriples, - expectedStructureAnnotations, - expectedStructureGraphSpaces, - expectedStructureAnnotationNodes, - expectedStructureTriples); + TestingHelpers.countCollections(controller, counts); controller.undo(); } + + public static class ProjectCounts { + private final int ets; + private final int eca; + private final int es; + private final int egs; + private final int ep; + private final int eh; + private final int ean; + private final int et; + private final int esa; + + public ProjectCounts(int ets, int eca, int es, int egs, int ep, int eh, int ean, int et, int esa) { + this.ets = ets; + this.eca = eca; + this.es = es; + this.egs = egs; + this.ep = ep; + this.eh = eh; + this.ean = ean; + this.et = et; + this.esa = esa; + } + + public ProjectCounts copy(int etsC, int ecaC, int esC, int egsC, int epC, int ehC, int eanC, int etC, int esaC) { + return new ProjectCounts( + this.ets + etsC, + this.eca + ecaC, + this.es + esC, + this.egs + egsC, + this.ep + epC, + this.eh + ehC, + this.ean + eanC, + this.et + etC, + this.esa + esaC); + } + + public ProjectCounts copy() { + return new ProjectCounts( + this.ets, + this.eca, + this.es, + this.egs, + this.ep, + this.eh, + this.ean, + this.et, + this.esa); + } + + public ProjectCounts add(ProjectCounts counts2, ProjectCounts overlaps) { + return new ProjectCounts( + this.ets + counts2.ets - overlaps.ets, + this.eca + counts2.eca - overlaps.eca, + this.es + counts2.es - overlaps.es, + this.egs + counts2.egs - overlaps.egs, + this.ep + counts2.ep - overlaps.ep, + this.eh + counts2.eh - overlaps.eh, + this.ean + counts2.ean - overlaps.ean, + this.et + counts2.et - overlaps.et, + this.esa + counts2.esa - overlaps.esa); + } + } } diff --git a/src/test/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUtilTest.java b/src/test/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUtilTest.java index 6e12e5c3..236f0dc7 100644 --- a/src/test/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUtilTest.java +++ b/src/test/java/edu/ucdenver/ccp/knowtator/io/conll/ConllUtilTest.java @@ -26,7 +26,9 @@ import edu.ucdenver.ccp.knowtator.TestingHelpers; import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; +import java.io.File; import java.io.IOException; +import java.nio.file.Files; import org.junit.jupiter.api.Test; class ConllUtilTest { @@ -34,19 +36,13 @@ class ConllUtilTest { @Test void readToStructureAnnotations() throws IOException { KnowtatorModel model = TestingHelpers.getLoadedModel("structure_test_project"); - TestingHelpers.countCollections(model, - 1, - 0, - 0, - 0, - 1, - 0, - 0, - 0, - 8072, - 361, - 8072, - 7711); + ConllUtil util = new ConllUtil(); + Files.list(new File(model.getProjectLocation(), "Structures").toPath()) + .forEach(file -> util.readToStructureAnnotations(model, file.toFile())); + + TestingHelpers.ProjectCounts counts = new TestingHelpers.ProjectCounts(1, 0, 0, 361, 1, 0, 8072, 7711, 8072); + + TestingHelpers.countCollections(model, counts); } // @Test @@ -66,40 +62,4 @@ void readToStructureAnnotations() throws IOException { // 8072, // 7711); // } - -// @Test -// void readBioCreativeProject() throws IOException { -// KnowtatorModel model = TestingHelpers.getLoadedModel("biocreative_chemprot"); -// TestingHelpers.countCollections(model, -// 1020, -// 25752, -// 25752, -// 6437, -// 1, -// 0, -// 12874, -// 6437, -// 271288, -// 10365, -// 271288, -// 260923); -// } - - @Test - void readBioCreativeProject() throws IOException { - KnowtatorModel model = TestingHelpers.getLoadedModel("biocreative_chemprot_small"); - TestingHelpers.countCollections(model, - 1, - 0, - 0, - 0, - 1, - 0, - 0, - 0, - 281, - 11, - 281, - 270); - } } diff --git a/src/test/java/edu/ucdenver/ccp/knowtator/model/OwlModelTest.java b/src/test/java/edu/ucdenver/ccp/knowtator/model/OwlModelTest.java index 488afd10..8d6c386a 100644 --- a/src/test/java/edu/ucdenver/ccp/knowtator/model/OwlModelTest.java +++ b/src/test/java/edu/ucdenver/ccp/knowtator/model/OwlModelTest.java @@ -104,21 +104,7 @@ void changeOwlClassIriTest() { Map entityToIriMap = new HashMap<>(); entityToIriMap.put(class2, IRI.create(class2.getIRI().getNamespace(), "BetterPizza")); - TestingHelpers.testOwlAction( - model, - renamer.changeIRI(entityToIriMap), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.testOwlAction(model, renamer.changeIRI(entityToIriMap), TestingHelpers.defaultCounts); ConceptAnnotation conceptAnnotation = model.getSelectedTextSource().get().getSelectedAnnotation().get(); @@ -140,21 +126,7 @@ void changeOwlObjectPropertyIriTest() { Map entityToIriMap = new HashMap<>(); entityToIriMap.put(property, IRI.create(property.getIRI().getNamespace(), "betterHasBass")); - TestingHelpers.testOwlAction( - model, - renamer.changeIRI(entityToIriMap), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.testOwlAction(model, renamer.changeIRI(entityToIriMap), TestingHelpers.defaultCounts); GraphSpace graphSpace = model.getSelectedTextSource().get().getSelectedGraphSpace().get(); RelationAnnotation relationAnnotation = @@ -176,18 +148,7 @@ void removeOwlClassTest() { TestingHelpers.testOwlAction( model, remover.getChanges(), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations - 2, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedSpans - 2, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes - 3, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedTriples - 2, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, -2, -2, 0, 0, 0, -3, -2,0)); assert !ontology.containsClassInSignature(class2.getIRI()); } @@ -197,21 +158,8 @@ void removeObjectPropertyTest() { assert ontology.containsObjectPropertyInSignature(owlObjectProperty.getIRI()); OWLEntityRemover remover = new OWLEntityRemover(Collections.singleton(ontology)); owlObjectProperty.accept(remover); - TestingHelpers.testOwlAction( - model, - remover.getChanges(), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedTriples - 2, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.testOwlAction(model, remover.getChanges(), + TestingHelpers.defaultCounts.copy(0, 0, 0, 0, 0, 0, 0, -2, 0)); assert !ontology.containsObjectPropertyInSignature(owlObjectProperty.getIRI()); } @@ -231,21 +179,7 @@ void moveOwlClassTest() { owlSubClassOfAxiom -> changes.add(new RemoveAxiom(ontology, owlSubClassOfAxiom))); changes.add(new AddAxiom(ontology, axiom2)); - TestingHelpers.testOwlAction( - model, - changes, - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.testOwlAction(model, changes, TestingHelpers.defaultCounts); assert !isSubClassTest(class1, class2); assert isSubClassTest(class3, class2); @@ -291,21 +225,7 @@ void moveOwlObjectPropertyTest() { owlSubClassOfAxiom -> changes.add(new RemoveAxiom(ontology, owlSubClassOfAxiom))); changes.add(new AddAxiom(ontology, axiom2)); - TestingHelpers.testOwlAction( - model, - changes, - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.testOwlAction(model, changes, TestingHelpers.defaultCounts); assert isSubObjectPropertyTest(property1, property2); assert isSubObjectPropertyTest(property3, property2); diff --git a/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/FilterActionsTest.java b/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/FilterActionsTest.java index 16360c95..885cc56b 100644 --- a/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/FilterActionsTest.java +++ b/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/FilterActionsTest.java @@ -40,9 +40,6 @@ class FilterActionsTest { private static KnowtatorModel model; - static { - } - @BeforeAll static void setup() { try { @@ -55,24 +52,10 @@ static void setup() { @Test void filterActionTest() throws ActionUnperformable { TestingHelpers.checkDefaultCollectionValues(model); - TestingHelpers.testKnowtatorAction( - model, - new FilterAction(model, PROFILE, true), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans - 3, TestingHelpers.defaultExpectedGraphSpaces, TestingHelpers.defaultExpectedProfiles, TestingHelpers.defaultExpectedHighlighters, TestingHelpers.defaultExpectedAnnotationNodes, TestingHelpers.defaultExpectedTriples, TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); - TestingHelpers.testKnowtatorAction( - model, - new FilterAction(model, PROFILE, false), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans, TestingHelpers.defaultExpectedGraphSpaces, TestingHelpers.defaultExpectedProfiles, TestingHelpers.defaultExpectedHighlighters, TestingHelpers.defaultExpectedAnnotationNodes, TestingHelpers.defaultExpectedTriples, TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.testKnowtatorAction(model, new FilterAction(model, PROFILE, true), + TestingHelpers.defaultCounts.copy(0, -2, -3, 0, 0, 0, 0, 0, 0)); + TestingHelpers.testKnowtatorAction(model, new FilterAction(model, PROFILE, false), + TestingHelpers.defaultCounts); model.getTextSources().setSelection(model.getTextSources().get("document1").get()); TextSource textSource = model.getSelectedTextSource().get(); @@ -84,20 +67,10 @@ void filterActionTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new FilterAction(model, OWLCLASS, true), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans - 5, TestingHelpers.defaultExpectedGraphSpaces, TestingHelpers.defaultExpectedProfiles, TestingHelpers.defaultExpectedHighlighters, TestingHelpers.defaultExpectedAnnotationNodes, TestingHelpers.defaultExpectedTriples, TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, -4, -5, 0, 0, 0, 0, 0, 0)); TestingHelpers.testKnowtatorAction( model, new FilterAction(model, OWLCLASS, false), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans, TestingHelpers.defaultExpectedGraphSpaces, TestingHelpers.defaultExpectedProfiles, TestingHelpers.defaultExpectedHighlighters, TestingHelpers.defaultExpectedAnnotationNodes, TestingHelpers.defaultExpectedTriples, TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts); } } diff --git a/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/GraphActionsTest.java b/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/GraphActionsTest.java index 16c566a8..9ca885d5 100644 --- a/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/GraphActionsTest.java +++ b/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/GraphActionsTest.java @@ -59,18 +59,7 @@ void removeSelectedAnnotationNodeTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new GraphActions.RemoveCellsAction(model, graphSpace), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes - 1, - TestingHelpers.defaultExpectedTriples - 1, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, 0, 0, 0, 0, 0, -1, -1, 0)); } @Test @@ -83,18 +72,7 @@ void removeSelectedTripleTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new GraphActions.RemoveCellsAction(model, graphSpace), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedTriples - 1, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0,0, 0, 0, 0, 0, 0, -1, 0)); } @Test @@ -107,18 +85,7 @@ void addAnnotationNodeTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new GraphActions.AddAnnotationNodeAction(null, model, graphSpace, conceptAnnotation), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes + 1, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, 0, 0, 0, 0, 0, 1, 0, 0)); } @Test @@ -136,18 +103,7 @@ void addTripleTest() throws ActionUnperformable { model, new GraphActions.AddTripleAction( model, source, target, property, Quantifier.some, null, false, "", graphSpace), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedTriples + 1, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, 0, 0, 0, 0, 0, 0, 1, 0)); } @Test @@ -160,17 +116,6 @@ void applyLayoutTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new GraphActions.ApplyLayoutAction(null, model, graphSpace, false), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts); } } diff --git a/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/KnowtatorCollectionActionsTest.java b/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/KnowtatorCollectionActionsTest.java index b95781f0..9a0cfb9d 100644 --- a/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/KnowtatorCollectionActionsTest.java +++ b/src/test/java/edu/ucdenver/ccp/knowtator/view/actions/KnowtatorCollectionActionsTest.java @@ -55,22 +55,8 @@ public void addTextSourceActionTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new TextSourceAction( - model, - ADD, - TestingHelpers.getArticleFile("structure_test_project", "11532192"), - null), - TestingHelpers.defaultExpectedTextSources + 1, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + model, ADD, TestingHelpers.getArticleFile("structure_test_project", "11532192"), null), + TestingHelpers.defaultCounts.copy(1, 0, 0, 0, 0, 0, 0, 0, 0)); } @Test @@ -79,18 +65,7 @@ public void removeTextSourceActionTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new TextSourceAction(model, REMOVE, null, null), - TestingHelpers.defaultExpectedTextSources - 1, - TestingHelpers.defaultExpectedConceptAnnotations - 2, - TestingHelpers.defaultExpectedSpans - 3, - TestingHelpers.defaultExpectedGraphSpaces - 1, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes - 2, - TestingHelpers.defaultExpectedTriples - 1, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(-1, -2, -3, -1, 0, 0, -2, -1, 0)); } @Test @@ -99,18 +74,7 @@ public void addConceptAnnotationActionTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new ConceptAnnotationAction(model, ADD, model.getSelectedTextSource().get()), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations + 1, - TestingHelpers.defaultExpectedSpans + 1, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, 1, 1, 0, 0, 0,0, 0, 0)); } @Test @@ -121,18 +85,7 @@ public void removeConceptAnnotationActionTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new ConceptAnnotationAction(model, REMOVE, model.getSelectedTextSource().get()), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations - 1, - TestingHelpers.defaultExpectedSpans - 1, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes - 1, - TestingHelpers.defaultExpectedTriples - 1, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, -1, -1, 0,0, 0, -1, -1, 0)); } @Test @@ -144,18 +97,7 @@ public void addSpanActionTest() throws ActionUnperformable { model, new SpanAction( model, ADD, model.getSelectedTextSource().get().getSelectedAnnotation().get()), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans + 1, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, 0, 1, 0, 0, 0, 0, 0, 0)); } @Test @@ -171,18 +113,7 @@ public void removeSpanActionTest() throws ActionUnperformable { model, new SpanAction( model, REMOVE, model.getSelectedTextSource().get().getSelectedAnnotation().get()), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations - 1, - TestingHelpers.defaultExpectedSpans - 1, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes - 1, - TestingHelpers.defaultExpectedTriples - 1, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, -1, -1, 0, 0, 0, -1, -1, 0)); // Next test remove span if there are multiple spans. This should only remove the span. conceptAnnotation.setSelection(conceptAnnotation.first().get()); @@ -193,18 +124,7 @@ public void removeSpanActionTest() throws ActionUnperformable { model, new SpanAction( model, REMOVE, model.getSelectedTextSource().get().getSelectedAnnotation().get()), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans - 1, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, 0, -1, 0, 0, 0, 0, 0, 0)); } @Test @@ -212,18 +132,7 @@ public void addProfileActionTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new ProfileAction(model, ADD, "I'm new here"), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles + 1, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, 0, 0, 0, 1, 0, 0, 0, 0)); } @Test @@ -232,18 +141,7 @@ public void removeProfileActionTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new ProfileAction(model, REMOVE, null), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations - 2, - TestingHelpers.defaultExpectedSpans - 3, - TestingHelpers.defaultExpectedGraphSpaces, - TestingHelpers.defaultExpectedProfiles - 1, - TestingHelpers.defaultExpectedHighlighters - 2, - TestingHelpers.defaultExpectedAnnotationNodes - 2, - TestingHelpers.defaultExpectedTriples - 2, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, -2, -3, 0, -1, -2, -2, -2, 0)); assertThrows(ActionUnperformable.class, this::removeDefaultProfileActionTest); } @@ -260,18 +158,8 @@ public void addGraphSpaceActionTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new GraphSpaceAction(model, ADD, "new_graph_space", model.getSelectedTextSource().get()), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces + 1, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes, - TestingHelpers.defaultExpectedTriples, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, 0, 0, 1, 0, 0, 0, 0, 0) + ); } @Test @@ -282,18 +170,7 @@ public void removeGraphSpaceActionTest() throws ActionUnperformable { TestingHelpers.testKnowtatorAction( model, new GraphSpaceAction(model, REMOVE, null, model.getSelectedTextSource().get()), - TestingHelpers.defaultExpectedTextSources, - TestingHelpers.defaultExpectedConceptAnnotations, - TestingHelpers.defaultExpectedSpans, - TestingHelpers.defaultExpectedGraphSpaces - 1, - TestingHelpers.defaultExpectedProfiles, - TestingHelpers.defaultExpectedHighlighters, - TestingHelpers.defaultExpectedAnnotationNodes - 2, - TestingHelpers.defaultExpectedTriples - 1, - TestingHelpers.defaultExpectedStructureAnnotations, - TestingHelpers.defaultExpectedStructureGraphSpaces, - TestingHelpers.defaultExpectedStructureAnnotationNodes, - TestingHelpers.defaultExpectedStructureTriples); + TestingHelpers.defaultCounts.copy(0, 0, 0, -1, 0, 0, -2, -1, 0)); } public void setModel(KnowtatorModel model) { diff --git a/src/test/java/edu/ucdenver/ccp/knowtator/view/iaa/IAAOptionsDialogTest.java b/src/test/java/edu/ucdenver/ccp/knowtator/view/iaa/IAAOptionsDialogTest.java new file mode 100644 index 00000000..484e5702 --- /dev/null +++ b/src/test/java/edu/ucdenver/ccp/knowtator/view/iaa/IAAOptionsDialogTest.java @@ -0,0 +1,60 @@ +/* + * MIT License + * + * Copyright (c) 2018 Harrison Pielke-Lombardo + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + * SOFTWARE. + */ + +package edu.ucdenver.ccp.knowtator.view.iaa; + +import edu.ucdenver.ccp.knowtator.TestingHelpers; +import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; +import edu.ucdenver.ccp.knowtator.view.actions.ActionUnperformable; +import java.io.IOException; +import org.junit.jupiter.api.Test; + +class IAAOptionsDialogTest { + + private void checkMerge(String projectName1, TestingHelpers.ProjectCounts project1Counts, String projectName2, TestingHelpers.ProjectCounts project2Counts, TestingHelpers.ProjectCounts overlapCounts) throws IOException { + KnowtatorModel model1 = TestingHelpers.getLoadedModel(projectName1); + TestingHelpers.countCollections(model1, project1Counts); + + KnowtatorModel model2 = TestingHelpers.getLoadedModel(projectName2); + TestingHelpers.countCollections(model2, project2Counts); + + model2.load(model1.getProjectLocation()); + TestingHelpers.ProjectCounts mergeCounts = project2Counts.add(project1Counts, overlapCounts); + TestingHelpers.countCollections(model2, mergeCounts); + + } + + @Test + public void mergeProjectsTest() throws ActionUnperformable, IOException { + String projectName1 = "import_test_project1"; + + TestingHelpers.ProjectCounts model1Counts = new TestingHelpers.ProjectCounts(1, 1, 1, 0 , 1, 0 , 0, 0, 0); + + String projectName2 = "import_test_project2"; + TestingHelpers.ProjectCounts model2Counts = new TestingHelpers.ProjectCounts(1, 2, 1, 0, 1, 0, 0, 0, 0); + + TestingHelpers.ProjectCounts overlaps = new TestingHelpers.ProjectCounts(1,1,1,0,1,0,0,0,0); + checkMerge(projectName1, model1Counts, projectName2, model2Counts, overlaps); + } +} \ No newline at end of file diff --git a/src/test/java/edu/ucdenver/ccp/knowtator/view/profile/ProfileDialogTest.java b/src/test/java/edu/ucdenver/ccp/knowtator/view/profile/ProfileDialogTest.java new file mode 100644 index 00000000..15865a04 --- /dev/null +++ b/src/test/java/edu/ucdenver/ccp/knowtator/view/profile/ProfileDialogTest.java @@ -0,0 +1,130 @@ +/* + * MIT License + * + * Copyright (c) 2018 Harrison Pielke-Lombardo + * + * Permission is hereby granted, free of charge, to any person obtaining a copy + * of this software and associated documentation files (the "Software"), to deal + * in the Software without restriction, including without limitation the rights + * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the Software is + * furnished to do so, subject to the following conditions: + * + * The above copyright notice and this permission notice shall be included in + * all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + * SOFTWARE. + */ + +package edu.ucdenver.ccp.knowtator.view.profile; + +import static edu.ucdenver.ccp.knowtator.view.actions.collection.CollectionActionType.ADD; + +import edu.ucdenver.ccp.knowtator.TestingHelpers; +import edu.ucdenver.ccp.knowtator.model.KnowtatorModel; +import edu.ucdenver.ccp.knowtator.view.KnowtatorView; +import edu.ucdenver.ccp.knowtator.view.actions.AbstractKnowtatorAction; +import edu.ucdenver.ccp.knowtator.view.actions.ActionUnperformable; +import edu.ucdenver.ccp.knowtator.view.actions.modelactions.ProfileAction; +import java.io.IOException; +import javax.swing.JOptionPane; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +class ProfileDialogTest { + private static KnowtatorView view; + private static final int defaultExpectedHighlighters = 1; + + @BeforeAll + static void setUp() { + view = new KnowtatorView(); + } + + @Test + void cancelProfileDialogTest() throws IOException { + KnowtatorModel model = TestingHelpers.getLoadedModel(); + TestingHelpers.checkDefaultCollectionValues(model); + view.loadProject(model.getProjectLocation(), null); + TestingHelpers.checkDefaultCollectionValues(view.getModel().get()); + + ProfileDialog dialog = new ProfileDialog(JOptionPane.getFrameForComponent(view), view); + dialog.pack(); + dialog.onCancel(); + TestingHelpers.checkDefaultCollectionValues(model); + } + + @Test + void okProfileDialogTest() throws IOException { + KnowtatorModel model = TestingHelpers.getLoadedModel(); + TestingHelpers.checkDefaultCollectionValues(model); + view.loadProject(model.getProjectLocation(), null); + TestingHelpers.checkDefaultCollectionValues(view.getModel().get()); + + ProfileDialog dialog = new ProfileDialog(JOptionPane.getFrameForComponent(view), view); + dialog.pack(); + dialog.onCancel(); + TestingHelpers.checkDefaultCollectionValues(model); + } + + public static void testKnowtatorAction( + ProfileDialog dialog, + KnowtatorModel controller, + AbstractKnowtatorAction action, + int expectedProfiles, + int expectedHighlighters) + throws ActionUnperformable { + checkDefaultCollectionValues(dialog); + controller.registerAction(action); + countCollections( + dialog, + expectedProfiles, + expectedHighlighters); + controller.undo(); + controller.getProfiles().setSelection(controller.getDefaultProfile()); + checkDefaultCollectionValues(dialog); + controller.redo(); + countCollections( + dialog, + expectedProfiles, + expectedHighlighters); + controller.undo(); + } + + private static void countCollections(ProfileDialog dialog, int expectedProfiles, int expectedHighlighters) { + assert dialog.profileList.getModel().getSize() == expectedProfiles; + assert dialog.colorList.getModel().getSize() == expectedHighlighters; + } + + private static void checkDefaultCollectionValues(ProfileDialog dialog) { + assert dialog.profileList.getModel().getSize() == TestingHelpers.defaultExpectedProfiles; + assert dialog.colorList.getModel().getSize() == defaultExpectedHighlighters; + } + + @Test + void addProfileDialogTest() throws IOException, ActionUnperformable { + KnowtatorModel model = TestingHelpers.getLoadedModel(); + TestingHelpers.checkDefaultCollectionValues(model); + view.loadProject(model.getProjectLocation(), null); + TestingHelpers.checkDefaultCollectionValues(view.getModel().get()); + + ProfileDialog dialog = new ProfileDialog(JOptionPane.getFrameForComponent(view), view); + dialog.pack(); + + model = view.getModel().get(); + + testKnowtatorAction(dialog, model, + new ProfileAction(model, ADD, "I'm new here"), + TestingHelpers.defaultExpectedProfiles + 1, + 0); + + dialog.onCancel(); + TestingHelpers.checkDefaultCollectionValues(model); + } + +} \ No newline at end of file diff --git a/src/test/resources/iaa_test_project/Ontologies/CRAFT_aggregate_OWL_ontology.owl b/src/test/resources/iaa_test_project/Ontologies/CRAFT_aggregate_OWL_ontology.owl new file mode 100755 index 00000000..0f8f9a8a --- /dev/null +++ b/src/test/resources/iaa_test_project/Ontologies/CRAFT_aggregate_OWL_ontology.owl @@ -0,0 +1,226976 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + exact synonyms + + + + + + + + + + + + + + + + + + + + + + + + + + + related synonyms + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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[] + CN(C)C(=O)Cc1c(nc2ccc(C)cn12)-c1ccc(C)cc1 + CHEBI:zolpidem + C19H21N3O + InChI=1S/C19H21N3O/c1-13-5-8-15(9-6-13)19-16(11-18(23)21(3)4)22-12-14(2)7-10-17(22)20-19/h5-10,12H,11H2,1-4H3 + + + beta-particle + CHEBI:electron + e + e(-) + [*-] + negatron + . + e- + beta(-) + "Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV." [] + beta + electron + CHEBI:10545 + electron + + + CHEBI:beta-carboline + InChIKey=AIFRHYZBTHREPW-UHFFFAOYSA-N + Carbazoline + "The parent compound of the beta-carbolines, a tricyclic structure comprising an indole ring system ortho- fused to C-3 and C-4 of a pyridine ring." [] + 2,9-Diazafluorene + 9H-Pyrido(3,4-B)indole + Norharmane + 2-Azacarbazole + 9H-beta-Carboline + C11H8N2 + InChI=1S/C11H8N2/c1-2-4-10-8(3-1)9-5-6-12-7-11(9)13-10/h1-7,13H + beta-carboline + CHEBI:109895 + beta-carboline + Norharman + 9H-beta-carboline + c1ccc2c(c1)[nH]c1cnccc21 + 9H-pyrido[3,4-b]indole + + + (4-carboxy-3-hydroxy-3-methylbutanoyl)-CoA + 3'-phosphoadenosine 5'-{3-[(3R)-4-{[3-({2-[(4-carboxy-3-hydroxy-3-methylbutanoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl] dihydrogen diphosphate} + 3-hydroxy-3-methylglutaryl-coenzyme A + CHEBI:3-hydroxy-3-methylglutaryl-CoA + "An alpha,omega dicarboxyacyl-CoA that results from the formal condensation of the thiol group of coenzyme A with one of the carboxy groups of 3-hydroxy-3-methylglutaric acid." [] + 3-hydroxy-3-methylglutaryl-CoA + InChIKey=CABVTRNMFUVUDM-SJBCKIPMSA-N + C27H44N7O20P3S + CC(O)(CC(O)=O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12 + InChI=1S/C27H44N7O20P3S/c1-26(2,21(40)24(41)30-5-4-15(35)29-6-7-58-17(38)9-27(3,42)8-16(36)37)11-51-57(48,49)54-56(46,47)50-10-14-20(53-55(43,44)45)19(39)25(52-14)34-13-33-18-22(28)31-12-32-23(18)34/h12-14,19-21,25,39-40,42H,4-11H2,1-3H3,(H,29,35)(H,30,41)(H,36,37)(H,46,47)(H,48,49)(H2,28,31,32)(H2,43,44,45)/t14-,19-,20-,21+,25-,27?/m1/s1 + (4-carboxy-3-hydroxy-3-methylbutanoyl)-coenzyme A + CHEBI:11814 + + + "The carboxamide resulting from the formal condensation of the aryl amino group of N-phenyl-1-(2-phenylethyl)piperidin-4-amine with propanoic acid." [] + N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide + N-(1-phenethylpiperidin-4-yl)-N-phenylpropionamide + CHEBI:fentanyl + InChIKey=PJMPHNIQZUBGLI-UHFFFAOYSA-N + fentanila + InChI=1S/C22H28N2O/c1-2-22(25)24(20-11-7-4-8-12-20)21-14-17-23(18-15-21)16-13-19-9-5-3-6-10-19/h3-12,21H,2,13-18H2,1H3 + N-(1-phenethyl-4-piperidyl)propionanilide + N-(1-Phenethyl-piperidin-4-yl)-N-phenyl-propionamide + CHEBI:119915 + N-phenethyl-4-(N-propionylanilino)piperidine + 1-phenethyl-4-N-propionylanilinopiperidine + fentanyl + N-phenyl-N-(1-(2-phenylethyl)-4-piperidinyl)propanamide + FENTANYL + CCC(=O)N(C1CCN(CC1)CCc1ccccc1)c1ccccc1 + fentanylum + 1-phenethyl-4-(N-phenylpropionamido)piperidine + C22H28N2O + N-(1-phenethyl-4-piperidinyl)-N-phenylpropionamide + fentanyl + + + InChI=1S/C20H23N7O6/c21-20-24-16-15(18(31)25-20)27-9-26(8-12(27)7-22-16)11-3-1-10(2-4-11)17(30)23-13(19(32)33)5-6-14(28)29/h1-4,12-13H,5-9H2,(H,23,30)(H,28,29)(H,32,33)(H4,21,22,24,25,31)/p-2/t12?,13-/m0/s1 + Nc1nc2NCC3CN(CN3c2c(=O)[nH]1)c1ccc(cc1)C(=O)N[C@@H](CCC([O-])=O)C([O-])=O + CHEBI:12071 + CHEBI:5,10-methylenetetrahydrofolate(2-) + C20H21N7O6 + N-{4-[3-amino-1-oxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]benzoyl}-L-glutamate + "A tetrahydrofolate that has formula C20H21N7O6." [] + InChIKey=QYNUQALWYRSVHF-ABLWVSNPSA-L + 5,10-methylenetetrahydrofolate + 5,10-methylenetetrahydrofolate(2-) + + + CHEBI:anilide + [*]C(=O)Nc1ccccc1 + an anilide + "Any aromatic amide obtained by acylation of aniline." [] + CHEBI:13248 + C7H6NOR + anilide + N-phenyl amides + N-phenyl amide + + + nicotinamide-adenine dinucleotide + CHEBI:13389 + CHEBI:NAD + NAD + NAD + "Abbreviation for nicotinamide-adenine dinucleotide when its oxidation state is unknown or unspecified. It is used in metabolic pathways like glycolysis and citric acid cycle." [] + . + + + CHEBI:NAD(P)(+) + NAD(P)(+) + . + CHEBI:13390 + "A coenzyme that may be NAD(+) or NADP(+)." [] + + + glycols + glycol + CHEBI:13643 + a glycol + CHEBI:glycol + "A diol in which the two hydroxy groups are on different carbon atoms, usually but not necessarily adjacent." [] + Glykol + + + apoprotein + "An apoprotein is a protein devoid of its characteristic prosthetic group or metal." [] + CHEBI:13850 + apoprotein + CHEBI:apoprotein + apoproteins + N[*] + . + + + InChIKey=UMCMPZBLKLEWAF-BCTGSCMUSA-N + "A 1,1-diunsubstituted alkanesulfonate that has formula C32H58N2O7S." [] + C32H58N2O7S + CHEBI:3-[(3-cholamidopropyl)dimethylammonio]propane-1-sulfonate + CHAPS + CHEBI:1418 + InChI=1S/C32H58N2O7S/c1-21(8-11-29(38)33-14-6-15-34(4,5)16-7-17-42(39,40)41)24-9-10-25-30-26(20-28(37)32(24,25)3)31(2)13-12-23(35)18-22(31)19-27(30)36/h21-28,30,35-37H,6-20H2,1-5H3,(H-,33,38,39,40,41)/t21-,22+,23-,24-,25+,26+,27-,28+,30+,31+,32-/m1/s1 + 3-[(3-cholamidopropyl)dimethylammonio]propane-1-sulfonate + 3-((3-Cholamidopropyl)dimethylammonium)-1-propanesulfonate + C[C@H](CCC(=O)NCCC[N+](C)(C)CCCS([O-])(=O)=O)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@]12C + + + D-glucose 6-phosphate + CHEBI:14314 + "A D-glucose monophosphate in which the phosphate group is attached to position 6." [] + D-glucose 6-(dihydrogen phosphate) + CHEBI:D-glucose 6-phosphate + C6H13O9P + 6-O-phosphono-D-glucose + + + CHEBI:14434 + imidazole + CHEBI:imidazole + imidazole + C3H4N2 + + + InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3 + "An enal that consists of 3,7-dimethyl-9-nona-2,4,6,8-tetraenal (double bond geometry unspecified) carrying a 2,6,6-trimethylcyclohex-1-en-1-yl group at the 9-position." [] + CHEBI:15035 + C20H28O + 3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal + InChIKey=NCYCYZXNIZJOKI-UHFFFAOYSA-N + CHEBI:retinal + [H]C(=O)C=C(C)C=CC=C(C)C=CC1=C(C)CCCC1(C)C + retinal + retinal + + + InChI=1S/C4H6O3/c1-3(5)2-4(6)7/h2H2,1H3,(H,6,7) + 3-ketobutanoic acid + acetoacetic acid + CHEBI:acetoacetic acid + CC(=O)CC(O)=O + CHEBI:15344 + C4H6O3 + InChIKey=WDJHALXBUFZDSR-UHFFFAOYSA-N + Acetoacetic acid + ACETOACETIC ACID + "A 3-oxo monocarboxylic acid that is butyric acid bearing a 3-oxo substituent." [] + 3-oxobutanoic acid + 3-Ketobutyric acid + beta-Ketobutyric acid + 3-Oxobutyric acid + 3-Oxobutanoic acid + + + CHEBI:coenzyme A + InChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1 + C21H36N7O16P3S + [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl dihydrogen diphosphate (non-preferred name) + [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate + [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3S)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl dihydrogen diphosphate (non-preferred name) + CoA-SH + CoASH + HSCoA + Coenzyme A + COENZYME A + "A thiol comprising a panthothenate unit in phosphoric anhydride linkage with a 3',5'-adenosine diphosphate unit; and an aminoethanethiol unit." [] + 3'-phosphoadenosine-(5')diphospho(4')pantatheine + Koenzym A + coenzyme A + 3'-phosphoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl] dihydrogen diphosphate} + Coenzym A + CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCS + CHEBI:15346 + InChIKey=RGJOEKWQDUBAIZ-IBOSZNHHSA-N + CoA + + + Dimethylketon + propanone + Pyroacetic ether + dimethylcetone + CHEBI:acetone + 2-Propanone + propan-2-one + CC(C)=O + beta-Ketopropane + Azeton + Dimethyl ketone + "A methyl ketone that consists of propane bearing an oxo group at C2." [] + InChIKey=CSCPPACGZOOCGX-UHFFFAOYSA-N + Acetone + ACETONE + acetone + methyl ketone + Propanon + acetone + Aceton + dimethylketone + C3H6O + CHEBI:15347 + InChI=1S/C3H6O/c1-3(2)4/h1-2H3 + + + InChI=1S/C7H16NO2/c1-7(9)10-6-5-8(2,3)4/h5-6H2,1-4H3/q+1 + choline acetate + CHEBI:15355 + CC(=O)OCC[N+](C)(C)C + 2-acetoxyethyl(trimethyl)ammonium + O-Acetylcholine + 2-(acetyloxy)-N,N,N-trimethylethanaminium + ACETYLCHOLINE + Acetylcholine + acetylcholine + C7H16NO2 + InChIKey=OIPILFWXSMYKGL-UHFFFAOYSA-N + acetylcholine + 2-acetyloxy-N,N,N-trimethylethanaminium + 2-acetyloxyethyl(trimethyl)azanium + 2-acetyloxyethyl(trimethyl)ammonium + ACh + CHEBI:acetylcholine + "Actylcholine is an ester of acetic acid and choline, which acts as a neurotransmitter." [] + Azetylcholin + + + Histone + [histone] + CHEBI:15358 + CHEBI:histone + . + histone + + + InChIKey=LCTONWCANYUPML-UHFFFAOYSA-M + pyruvate + 2-oxopropanoic acid, ion(1-) + CHEBI:15361 + 2-oxopropanoate + C3H3O3 + InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)/p-1 + pyruvate + CHEBI:pyruvate + CC(=O)C([O-])=O + "A 2-oxo monocarboxylic acid anion that is the conjugate base of pyruvic acid, arising from deprotonation of the carboxy group." [] + 2-oxopropanoate + + + CHEBI:acetic acid + ethoic acid + Methanecarboxylic acid + CH3CO2H + HOAc + InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4) + E260 + E-260 + MeCOOH + ACETIC ACID + Ethanoic acid + acetic acid + "A simple monocarboxylic acid containing two carbons." [] + Ethylic acid + acetic acid + INS No. 260 + acide acetique + CH3-COOH + C2H4O2 + InChIKey=QTBSBXVTEAMEQO-UHFFFAOYSA-N + Acetic acid + MeCO2H + AcOH + E 260 + Essigsaeure + CC(O)=O + CHEBI:15366 + + + CHEBI:15369 + actinomycin + Actinomycin + CHEBI:actinomycin + actinomycin + . + "A large group of antibiotics isolated from various species of Streptomyces and characterised by having a substituted phenoxazine ring linked to two cyclic heterodetic peptides." [] + actinomycins + + + Wasser + oxidane + WATER + Water + BOUND WATER + [H]O[H] + H2O + CHEBI:water + [OH2] + HOH + aqua + acqua + eau + water + dihydridooxygen + GLUCOSE 4-O4 GROUP + CHEBI:15377 + agua + OXYGEN ATOM + water + InChI=1S/H2O/h1H2 + "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms." [] + InChIKey=XLYOFNOQVPJJNP-UHFFFAOYSA-N + DISORDERED SOLVENT + dihydrogen oxide + hydrogen hydroxide + BOUND OXYGEN + + + Disauerstoff + CHEBI:15379 + InChIKey=MYMOFIZGZYHOMD-UHFFFAOYSA-N + E948 + CHEBI:dioxygen + E-948 + molecular oxygen + InChI=1S/O2/c1-2 + "An elemental molecule that has formula O2." [] + OXYGEN MOLECULE + dioxygen + O2 + E 948 + [OO] + dioxygen + O=O + Oxygen + dioxygene + + + Supraene + "A triterpene consisting of 2,6,10,15,19,23-hexamethyltetracosane having six double bonds at the 2-, 6-, 10-, 14-, 18- and 22-positions with (all-E)-configuration." [] + CHEBI:squalene + C30H50 + (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene + InChIKey=YYGNTYWPHWGJRM-AAJYLUCBSA-N + Spinacene + InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3/b27-17+,28-18+,29-23+,30-24+ + (all-E)-2,6,10,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaene + squalene + squalene + Squalene + CC(C)=CCC\\C(C)=C\\CC\\C(C)=C\\CC\\C=C(/C)CC\\C=C(/C)CCC=C(C)C + CHEBI:15440 + (14E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene + + + CHEBI:15525 + C37H66N7O17P3S + Palmitoyl coenzyme A + palmitoyl-CoA + 3'-phosphoadenosine 5'-(3-{(3R)-4-[(3-{[2-(hexadecanoylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl} dihydrogen diphosphate) + CHEBI:palmitoyl-CoA + CCCCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12 + Coenzyme A, S-hexadecanoate + InChI=1S/C37H66N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-28(46)65-21-20-39-27(45)18-19-40-35(49)32(48)37(2,3)23-58-64(55,56)61-63(53,54)57-22-26-31(60-62(50,51)52)30(47)36(59-26)44-25-43-29-33(38)41-24-42-34(29)44/h24-26,30-32,36,47-48H,4-23H2,1-3H3,(H,39,45)(H,40,49)(H,53,54)(H,55,56)(H2,38,41,42)(H2,50,51,52)/t26-,30-,31-,32+,36-/m1/s1 + "A palmitoyl bioconjugate that has formula C37H66N7O17P3S." [] + InChIKey=MNBKLUUYKPBKDU-BBECNAHFSA-N + S-Palmitoylcoenzyme A + Palmitoyl-CoA + Hexadecanoyl-CoA + + + octylyl-CoA + Octanoyl-coa + Octanoyl-CoA + capryloyl-coenzyme A + octanoyl-CoA + InChI=1S/C29H50N7O17P3S/c1-4-5-6-7-8-9-20(38)57-13-12-31-19(37)10-11-32-27(41)24(40)29(2,3)15-50-56(47,48)53-55(45,46)49-14-18-23(52-54(42,43)44)22(39)28(51-18)36-17-35-21-25(30)33-16-34-26(21)36/h16-18,22-24,28,39-40H,4-15H2,1-3H3,(H,31,37)(H,32,41)(H,45,46)(H,47,48)(H2,30,33,34)(H2,42,43,44)/t18-,22-,23-,24+,28-/m1/s1 + OCTANOYL-COENZYME A + Octanoyl-coenzyme A + octanoylcoenzyme A + InChIKey=KQMZYOXOBSXMII-CECATXLMSA-N + C29H50N7O17P3S + "A medium-chain fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of octanoic acid." [] + CHEBI:octanoyl-CoA + CHEBI:15533 + capryloyl-CoA + 8:0-CoA + Coenzyme A, S-octanoate + S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-9,13,15-trihydroxy-10,10-dimethyl-13,15-dioxido-4,8-dioxo-12,14,16-trioxa-3,7-diaza-13,15-diphosphaheptadec-1-yl} octanethioate (non-preferred name) + octylyl-coenzyme A + C8:0-CoA + CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12 + 3'-phosphoadenosine 5'-(3-{(3R)-3-hydroxy-2,2-dimethyl-4-[(3-{[2-(octanoylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-4-oxobutyl} dihydrogen diphosphate) + + + InChI=1S/C24H40N7O17P3S/c1-4-15(33)52-8-7-26-14(32)5-6-27-22(36)19(35)24(2,3)10-45-51(42,43)48-50(40,41)44-9-13-18(47-49(37,38)39)17(34)23(46-13)31-12-30-16-20(25)28-11-29-21(16)31/h11-13,17-19,23,34-35H,4-10H2,1-3H3,(H,26,32)(H,27,36)(H,40,41)(H,42,43)(H2,25,28,29)(H2,37,38,39)/t13-,17-,18-,19+,23-/m1/s1 + InChIKey=QAQREVBBADEHPA-IEXPHMLFSA-N + CCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12 + Propionyl coenzyme A + S-Propionyl-coenzym-A + Propionyl-CoA + S-propanoyl-CoA + Propanoyl-CoA + propionyl-CoA + 3'-phosphoadenosine 5'-(3-{(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-[(3-oxo-3-{[2-(propanoylsulfanyl)ethyl]amino}propyl)amino]butyl} dihydrogen diphosphate) + CHEBI:15539 + propanoyl-coenzyme A + "An acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of propionic acid." [] + C24H40N7O17P3S + S-propanoyl-coenzyme A + Propionyl-coenzyme A + CHEBI:propionyl-CoA + S-Propionylcoenzyme A + + + CHEBI:stearoyl-CoA + C18:0-coenzyme A + S-stearoylcoenzyme A + CCCCCCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12 + Stearyl-CoA + CHEBI:15541 + Stearoyl-CoA + 3'-phosphoadenosine 5'-(3-{(3R)-3-hydroxy-2,2-dimethyl-4-[(3-{[2-(octadecanoylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-4-oxobutyl} dihydrogen diphosphate) + stearoyl-coenzyme A + stearoyl-CoA + S-stearoyl-CoA + InChIKey=SIARJEKBADXQJG-LFZQUHGESA-N + C18:0-CoA + Stearyl coenzyme A + octadecanoyl-coenzyme A + InChI=1S/C39H70N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-30(48)67-23-22-41-29(47)20-21-42-37(51)34(50)39(2,3)25-60-66(57,58)63-65(55,56)59-24-28-33(62-64(52,53)54)32(49)38(61-28)46-27-45-31-35(40)43-26-44-36(31)46/h26-28,32-34,38,49-50H,4-25H2,1-3H3,(H,41,47)(H,42,51)(H,55,56)(H,57,58)(H2,40,43,44)(H2,52,53,54)/t28-,32-,33-,34+,38-/m1/s1 + "A long-chain fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of stearic acid." [] + C39H70N7O17P3S + octadecanoyl-CoA + + + Propess + CHEBI:prostaglandin E2 + Dinoproston + dinoprostona + "Prostaglandin F2alpha in which the hydroxy group at position 9 has been oxidised to the corresponding ketone. Prostaglandin E2 is the most common and most biologically potent of mammalian prostaglandins." [] + dinoprostonum + dinoprostone + (5Z,11alpha,13E,15S)-11,15-dihydroxy-9-oxoprosta-5,13-dien-1-oic acid + (15S)-prostaglandin E2 + InChI=1S/C20H32O5/c1-2-3-6-9-15(21)12-13-17-16(18(22)14-19(17)23)10-7-4-5-8-11-20(24)25/h4,7,12-13,15-17,19,21,23H,2-3,5-6,8-11,14H2,1H3,(H,24,25)/b7-4-,13-12+/t15-,16+,17+,19+/m0/s1 + CHEBI:15551 + C20H32O5 + (E,Z)-(1R,2R,3R)-7-(3-Hydroxy-2-((3S)-(3-hydroxy-1-octenyl))-5-oxocyclopentyl)-5-heptenoic acid + (5Z,13E)-(15S)-11alpha,15-Dihydroxy-9-oxoprost-13-enoate + PGE2 + (5Z,13E,15S)-11alpha,15-dihydroxy-9-oxoprosta-5,13-dien-1-oic acid + prostaglandin E2 + CCCCC[C@H](O)\\C=C\\[C@H]1[C@H](O)CC(=O)[C@@H]1C\\C=C/CCCC(O)=O + Prostin E2 + Prostaglandin E2 + Dinoprostone + (5Z,13E)-(15S)-11alpha,15-Dihydroxy-9-oxoprosta-5,13-dienoate + (Z)-7-((1R,2R,3R)-3-hydroxy-2-((S,E)-3-hydroxyoct-1-enyl)-5-oxocyclopentyl)hept-5-enoic acid + Prepidil + InChIKey=XEYBRNLFEZDVAW-ARSRFYASSA-N + + + aldose + C2H4O2(CH2O)n + CHEBI:aldose + an aldose + aldoses + "Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals." [] + CHEBI:15693 + Aldose + + + L-alpha-amino acids + L-alpha-amino acids + CHEBI:15705 + "Any alpha-amino acid having L-configuration at the alpha-carbon." [] + L-Amino acid + L-alpha-amino acid + L-2-Amino acid + C2H4NO2R + CHEBI:L-alpha-amino acid + N[C@@H]([*])C(O)=O + L-alpha-amino acid + + + primary alcohol + [H]C([H])(O)[*] + "A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it." [] + primary alcohols + CHEBI:15734 + a primary alcohol + CH3OR + 1-Alcohol + Primary alcohol + CHEBI:primary alcohol + + + CHEBI:15738 + InChI=1S/C28H26N4O3/c1-28-26(34-3)17(29-2)12-20(35-28)31-18-10-6-4-8-14(18)22-23-16(13-30-27(23)33)21-15-9-5-7-11-19(15)32(28)25(21)24(22)31/h4-11,17,20,26,29H,12-13H2,1-3H3,(H,30,33)/t17-,20-,26-,28+/m1/s1 + InChIKey=HKSZLNNOFSGOKW-FYTWVXJKSA-N + CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n1c3ccccc3c3c4CNC(=O)c4c4c5ccccc5n2c4c13 + (+)-Staurosporine + staurosporine + "An indolocarbazole alkaloid that has formula C28H26N4O3." [] + STAUROSPORINE + Staurosporine + STS + C28H26N4O3 + (5S,6R,7R,9R)-6-methoxy-5-methyl-7-methylamino-6,7,8,9,15,16-hexahydro-5H,14H-5,9-epoxy-4b,9a,15-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-14-one + Staurosporin + (5S,6R,7R,9R)-6-methoxy-5-methyl-7-(methylamino)-6,7,8,9,15,16-hexahydro-5H,14H-5,9-epoxy-4b,9a,15-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-14-one + CHEBI:staurosporine + + + [H]C([O-])=O + aminate + CHEBI:15740 + formic acid, ion(1-) + CHEBI:formate + "A monocarboxylic acid anion that is the conjugate base of formic acid. Induces severe metabolic acidosis and ocular injury in human subjects." [] + HCO2 anion + methanoate + formylate + formiate + InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)/p-1 + formate + formate + InChIKey=BDAGIHXWWSANSR-UHFFFAOYSA-M + hydrogen carboxylate + CHO2 + + + 1-Pentadecanecarboxylic acid + Palmitic acid + Hexaectylic acid + palmitic acid + Palmitinic acid + cetylic acid + C16H32O2 + CH3-[CH2]14-COOH + InChIKey=IPCSVZSSVZVIGE-UHFFFAOYSA-N + CHEBI:palmitic acid + hexadecoic acid + n-hexadecoic acid + hexadecanoic acid + CCCCCCCCCCCCCCCC(O)=O + Hexadecylic acid + 16:00 + Palmitate + C16 fatty acid + hexadecanoic acid + PALMITIC ACID + Pentadecanecarboxylic acid + n-hexadecanoic acid + C16:0 + "A straight-chain, sixteen-carbon, saturated long-chain fatty acid." [] + C16 + CHEBI:15756 + Hexadecanoate + 1-hexyldecanoic acid + InChI=1S/C16H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h2-15H2,1H3,(H,17,18) + Palmitinsaeure + + + (2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid + CHEBI:L-dopa + L-Dopa + levodopa + (2S)-2-amino-3-(3,4-dihydroxyphenyl)propionic acid + Dihydroxy-L-phenylalanine + InChIKey=WTDRDQBEARUVNC-LURJTMIESA-N + L-dopa + (-)-3-(3,4-dihydroxyphenyl)-L-alanine + "An optically active form of dopa having L-configuration. Used to treat the stiffness, tremors, spasms, and poor muscle control of Parkinson's disease" [] + beta-(3,4-dihydroxyphenyl)-L-alanine + InChI=1S/C9H11NO4/c10-6(9(13)14)3-5-1-2-7(11)8(12)4-5/h1-2,4,6,11-12H,3,10H2,(H,13,14)/t6-/m0/s1 + L-beta-(3,4-Dihydroxyphenyl)alanine + beta-(3,4-dihydroxyphenyl)alanine + (-)-dopa + 3-HYDROXY-L-TYROSINE + CHEBI:15765 + 3-Hydroxy-L-tyrosine + levodopum + L-DOPA + L-dopa + Dopar + (2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid + 3,4-DIHYDROXYPHENYLALANINE + N[C@@H](Cc1ccc(O)c(O)c1)C(O)=O + 3,4-Dihydroxy-L-phenylalanine + C9H11NO4 + + + polypeptides + polypeptide + CHEBI:polypeptide + CHEBI:15841 + Polypeptid + polipeptido + "A peptide containing ten or more amino acid residues." [] + Polypeptide + polypeptide + C4H6N2O3R2(C2H2NOR)n + + + DPN + Diphosphopyridine nucleotide + C21H28N7O14P2 + InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/p+1/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 + InChIKey=BAWFJGJZGIEFAR-NNYOXOHSSA-O + adenosine 5'-{3-[1-(3-carbamoylpyridinio)-1,4-anhydro-D-ribitol-5-yl] dihydrogen diphosphate} + "The oxidised form of nicotinamide adenine dinucleotide found in all living cells. In metabolism, NAD(+) is involved in redox reactions, carrying electrons from one reaction to another." [] + NAD + beta-NAD + CHEBI:NAD(+) + NAD(+) + Nadide + NAD+ + Nicotinamide adenine dinucleotide + CHEBI:15846 + NC(=O)c1ccc[n+](c1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n2cnc3c(N)ncnc23)[C@@H](O)[C@H]1O + + + [H][C@]1(C[C@@H]2CC[N@]1C[C@@H]2C=C)[C@H](O)c1ccnc2ccc(OC)cc12 + Chinin + Quinine + (R)-(6-methoxyquinolin-4-yl)((2S,4S,8R)-8-vinylquinuclidin-2-yl)methanol + (-)-Quinine + InChI=1S/C20H24N2O2/c1-3-13-12-22-9-7-14(13)10-19(22)20(23)16-6-8-21-18-5-4-15(24-2)11-17(16)18/h3-6,8,11,13-14,19-20,23H,1,7,9-10,12H2,2H3/t13-,14-,19-,20+/m0/s1 + (-)-quinine + quinine + quinine + (8S,9R)-quinine + C20H24N2O2 + CHEBI:15854 + CHEBI:quinine + quinina + (R)-(6-Methoxy-quinolin-4-yl)-((2S,5S)-5-vinyl-1-aza-bicyclo[2.2.2]oct-2-yl)-methanol + (R)-(6-methoxy-quinolin-4-yl)-((2S,5S)-5-vinyl-1-aza-bicyclo[2.2.2]oct-2-yl)-methanol + chinine + (9R)-6'-methoxy-8alpha-cinchonan-9-ol + 6'-methoxycinchonidine + (R)-(-)-quinine + InChIKey=LOUPRKONTZGTKE-WZBLMQSHSA-N + "A cinchona alkaloid that is cinchonidine in which the hydrogen at the 6-position of the quinoline ring is substituted by methoxy." [] + chininum + + + Phenylic acid + InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H + PhOH + acide phenique + Oc1ccccc1 + "An organic hydroxy compound that consists of benzene bearing a single hydroxy substituent. The parent of the class of phenols." [] + C6H6O + CHEBI:15882 + Phenic acid + CHEBI:phenol + acide carbolique + Carbolsaeure + Phenylic alcohol + Hydroxybenzene + InChIKey=ISWSIDIOOBJBQZ-UHFFFAOYSA-N + Oxybenzene + phenol + carbolic acid + Karbolsaeure + Phenol + PHENOL + phenol + Benzenol + + + InChI=1S/C17H28O/c18-13-6-9-15-12(10-13)5-8-16-14-3-1-2-11(14)4-7-17(15)16/h11-18H,1-10H2 + sterols + CHEBI:sterol + 3-hydroxysteroids + . + CHEBI:15889 + InChIKey=FPXSXMFOYWRHDX-UHFFFAOYSA-N + "A 3-hydroxy steroid closely related to cholestan-3-ol." [] + sterol + OC1CCC2C(CCC3C4CCCC4CCC23)C1 + Sterol + sterol + + + CHEBI:15891 + Aminoethylsulfonic acid + C2H7NO3S + 2-aminoethyl sulfonate + beta-aminoethylsulfonic acid + 2-aminoethanesulfonic acid + NCCS(O)(=O)=O + CHEBI:taurine + "An amino sulfonic acid that is the 2-amino derivative of ethanesulfonic acid. It is a naturally occurring amino acid derived from methionine and cysteine metabolism." [] + taurine + InChIKey=XOAAWQZATWQOTB-UHFFFAOYSA-N + Taurine + InChI=1S/C2H7NO3S/c3-1-2-7(4,5)6/h1-3H2,(H,4,5,6) + 2-aminoethanesulfonic acid + 2-Aminoethanesulfonic acid + + + Long-chain fatty acid + CHEBI:long-chain fatty acid + CHO2R + "A fatty acid with a chain length ranging from C13 to C22." [] + long-chain fatty acid + CHEBI:15904 + long-chain fatty acids + LCFA + LCFAs + OC([*])=O + Higher fatty acid + + + 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid + cis-Tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid + Biotin + biotin + biotine + CHEBI:biotin + biotina + Coenzyme R + 5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoic acid + cis-Hexahydro-2-oxo-1H-thieno(3,4)imidazole-4-valeric acid + CHEBI:15956 + [H][C@]12CS[C@@H](CCCCC(O)=O)[C@@]1([H])NC(=O)N2 + Vitamin H + C10H16N2O3S + D-(+)-biotin + vitamin B7 + (+)-cis-Hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-valeric acid + biotinum + BIOTIN + InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-/m0/s1 + (3aS,4S,6aR)-Hexahydro-2-oxo-1H-thieno[3,4-d]imidazole-4-valeric acid + 5-[(1R,5S,6S)-3-oxo-7-thia-2,4-diazabicyclo[3.3.0]oct-6-yl]pentanoic acid + "An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins." [] + cis-(+)-Tetrahydro-2-oxothieno[3,4]imidazoline-4-valeric acid + D-Biotin + InChIKey=YBJHBAHKTGYVGT-ZKWXMUAHSA-N + + + CHEBI:D-hexose phosphate + "Any mono-phosphorylated D-hexose having a chain of six carbon atoms in the molecule." [] + . + D-Hexose phosphate + D-hexose phosphate + D-hexose phosphate + CHEBI:15965 + + + Polynucleotide + C10H17O10PR2(C5H8O6PR)n + "A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues." [] + CHEBI:15986 + polynucleotides + polynucleotide + CHEBI:polynucleotide + + + phosphatidylethanolamines + C7H12NO8PR2 + (3-Phosphatidyl)-ethanolamine + O-(1-beta-Acyl-2-acyl-sn-glycero-3-phospho)ethanolamine + Cephalin + 1-Acyl-2-acyl-sn-glycero-3-phosphoethanolamine + PHOSPHATIDYLETHANOLAMINE + Phosphatidylethanolamine + 1,2-diacyl-sn-glycero-3-phosphoethanolamine + (3-Phosphatidyl)ethanolamine + "A class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxy group of ethanolamine." [] + PtdEtn + phosphatidylethanolamine + phosphatidyl(amino)ethanols + phosphatidylethanolamines + CHEBI:16038 + PE + NCCOP(O)(=O)OCC(COC([*])=O)OC([*])=O + CHEBI:phosphatidylethanolamine + + + HX + CHEBI:halide anion + halogen anion + CHEBI:16042 + halide anion + X + halide + Hydrogen halide + Halide + halide anions + Halo acid + halide(1-) + halide ions + halides + "A monoatomic monoanion resulting from the addition of an electron to any halogen atom." [] + + + 11-cis-Retinal + (2E,4Z,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenal + CC(/C=C\\C=C(C)\\C=C\\C1=C(C)CCCC1(C)C)=C\\C=O + 11-cis-retinal + 11-cis-vitamin A aldehyde + 11-cis-Vitamin A aldehyde + InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3/b9-6-,12-11+,16-8+,17-13+ + InChIKey=NCYCYZXNIZJOKI-IOUUIBBYSA-N + CHEBI:11-cis-retinal + CHEBI:16066 + C20H28O + "A retinal having 2E,4Z,6E,8E-double bond geometry." [] + 11-cis-Retinene + 11-cis-retinene + 11-cis-retinal + + + CHEBI:16113 + "A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group." [] + CHEBI:cholesterol + Cholesterin + InChIKey=HVYWMOMLDIMFJA-DPAQBDIFSA-N + InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1 + [H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCCC(C)C + cholest-5-en-3beta-ol + Cholest-5-en-3beta-ol + C27H46O + Cholesterol + cholesterol + (3beta,14beta,17alpha)-cholest-5-en-3-ol + CHOLESTEROL + cholesterol + + + CHEBI:16134 + NITROGEN + spirit of hartshorn + [NH3] + AMINO SUBSTITUTION GROUP + InChIKey=QGZKDVFQNNGYKY-UHFFFAOYSA-N + Ammoniak + NH3 + azane + [H]N([H])[H] + ammoniac + ammonia + "An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms." [] + amoniaco + InChI=1S/H3N/h1H3 + Ammonia + AMMONIA + ammonia + CHEBI:ammonia + H3N + R-717 + + + Phenylcarboxylate + benzoate anion + InChI=1S/C7H6O2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H,8,9)/p-1 + CHEBI:benzoate + Phenylformate + Benzenecarboxylate + benzoic acid, ion(1-) + InChIKey=WPYMKLBDIGXBTP-UHFFFAOYSA-M + benzoate + Benzeneformate + C7H5O2 + [O-]C(=O)c1ccccc1 + "The simplest member of the class of benzoates that is the conjugate base of benzoic acid, comprising a benzoic acid core with a proton missing to give a charge of -1." [] + Benzenemethanoate + benzoate + CHEBI:16150 + + + CHEBI:N-acylglycine + "An N-acyl-amino acid in which amino acid specified is glycine." [] + N-acylglycine + C3H4NO3R + OC(=O)CNC([*])=O + CHEBI:16180 + N-Acylglycine + + + urea + H2NC(O)NH2 + CHEBI:16199 + E927b + carbamide + urea + Urea + Carbamide + UREA + Karbamid + "A carbonyl group with two C-bound amine groups." [] + InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4) + CHEBI:urea + CH4N2O + carbonyldiamide + Harnstoff + InChIKey=XSQUKJJJFZCRTK-UHFFFAOYSA-N + NC(N)=O + uree + ur + + + InChIKey=OGGXGZAMXPVRFZ-UHFFFAOYSA-M + [As(CH3)2O2](-) + CHEBI:16223 + InChI=1S/C2H7AsO2/c1-3(2,4)5/h1-2H3,(H,4,5)/p-1 + CHEBI:dimethylarsinate + Me2AsO2(-) + DMA + "The arsenic oxoanion that is the conjugate base of dimethylarsinic acid." [] + C2H6AsO2 + CACODYLATE ION + Dimethylarsinate + dimethylarsinate + Kakodylat + dimethylarsinate + C[As](C)([O-])=O + + + InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 + hydroxyethane + alcohol etilico + alcohol + CCO + [CH2Me(OH)] + Aethylalkohol + CHEBI:ethanol + Aethanol + spiritus vini + ethanol + Ethyl alcohol + ethanol + [OEtH] + alcool ethylique + Alkohol + 1-hydroxyethane + Dehydrated ethanol + C2H5OH + C2H6O + InChIKey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N + Methylcarbinol + EtOH + OXYDIMETHYLENE GROUP + CHEBI:16236 + Ethanol + "A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group." [] + ETHANOL + etanol + + + CHEBI:16240 + hydrogen peroxide + dioxidane + dihydrogen dioxide + [OH(OH)] + dihydrogen(peroxide) + HOOH + [H]OO[H] + "An inorganic peroxide that has formula H2O2." [] + Hydrogen peroxide + hydrogen peroxide + HYDROGEN PEROXIDE + dihydrogen peroxide + Oxydol + InChI=1S/H2O2/c1-2/h1-2H + InChIKey=MHAJPDPJQMAIIY-UHFFFAOYSA-N + bis(hydridooxygen)(O--O) + H2O2 + CHEBI:hydrogen peroxide + + + Phospholipid + phospholipid derivative + "A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides." [] + phospholipids + CHEBI:phospholipid + phospholipid + CHEBI:16247 + C5H6O8PR3 + + + protein disulfides + [*]NC(=O)[C@H]1CSSC[C@@H](NC([*])=O)C(=O)N1 + CHEBI:protein disulfide + C7H9N3O3S2R2 + [protein]-disulfide + Protein disulfide + protein disulfide + CHEBI:16249 + + + Hyaluronic acid + [beta-N-Acetyl-D-glucosaminyl(1,4)beta-D-glucuronosyl(1,3)]n + Hyaluronsaeure + acide hyaluronique + [beta-D-glucopyranuronosyl-(1->3)-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->4)]n + "A mucopolysaccharide composed of N-acetylglucosamine and glucuronic acid subunits. It is found in the connective tissues of vertebrates." [] + hyaluronan + CHEBI:16336 + hyaluronic acid + CHEBI:hyaluronic acid + (C14H21NO12)n + acido hialuronico + + + InChI=1S/HI/h1H/p-1 + iodide + I- + "A monoatomic iodine that has formula I." [] + iodide(1-) + I + CHEBI:16382 + Iodide + iodide + IODIDE ION + InChIKey=XMBWDFGMSWQBCA-UHFFFAOYSA-M + CHEBI:iodide + iodine anion + [I-] + I(-) + + + Thioether + thioether + Sulfide + RSR + "Compounds having the structure RSR (R =/= H). Such compounds were once called thioethers." [] + thioethers + [*]S[*] + CHEBI:16385 + SR2 + CHEBI:organic sulfide + organic sulfide + sulfides + organic sulfides + + + CHEBI:16397 + formimidic acid + Methanamid + InChIKey=ZHNUHDYFZUAESO-UHFFFAOYSA-N + CHEBI:formamide + InChI=1S/CH3NO/c2-1-3/h1H,(H2,2,3) + "The simplest monocarboxylic acid amide, obtained by formal condensation of formic acid with ammonia. The parent of the class of formaldehydes." [] + formamide + carbamaldehyde + FORMAMIDE + Formamide + formamide + Formamid + CH3NO + Ameisensaeureamid + Methanamide + [H]C(N)=O + + + lipopolysaccharide + . + LPS + Lipopolysaccharide + lipopolysaccharide + lipopolysaccharides + "Liposaccharide natural compounds consisting of a trisaccharide repeating unit (two heptose units and octulosonic acid) with oligosaccharide side chains and 3-hydroxytetradecanoic acid units (they are a major constituent of the cell walls of Gram-negative bacteria)." [] + CHEBI:lipopolysaccharide + CHEBI:16412 + + + 17beta-estra-1,3,5(10)-triene-3,17-diol + 17beta-estradiol + 17beta oestradiol + (9beta,13alpha,14beta,17alpha)-estra-1,3,5(10)-triene-3,17-diol + estra-1,3,5(10)-triene-3,17beta-diol + cis-estradiol + InChI=1S/C18H24O2/c1-18-9-8-14-13-5-3-12(19)10-11(13)2-4-15(14)16(18)6-7-17(18)20/h3,5,10,14-17,19-20H,2,4,6-9H2,1H3/t14-,15-,16+,17+,18+/m1/s1 + Estradiol + ESTRADIOL + [H][C@]12CC[C@]3(C)[C@@H](O)CC[C@@]3([H])[C@]1([H])CCc1cc(O)ccc21 + (17beta)-estra-1,3,5(10)-triene-3,17-diol + "The 17beta-isomer of estradiol." [] + 17beta-estradiol + beta-Estradiol + 17beta-oestradiol + CHEBI:16469 + C18H24O2 + (8R,9S,13S,14S,17S)-13-methyl-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthrene-3,17-diol + InChIKey=VOXZDWNPVJITMN-ZBRFXRBCSA-N + CHEBI:17beta-estradiol + Estradiol-17beta + + + Nitrogen monoxide + CHEBI:16480 + mononitrogen monoxide + nitrogen monooxide + NO(.) + "A nitrogen oxide which is a free radical, each molecule of which consists of one nitrogen and one oxygen atom." [] + CHEBI:nitric oxide + oxyde nitrique + endothelium-derived relaxing factor + oxoazanyl + oxido nitrico + InChI=1S/NO/c1-2 + Stickstoff(II)-oxid + Nitric oxide + NITRIC OXIDE + EDRF + nitrosyl + [N]=O + nitrogen monoxide + monoxido de nitrogeno + NO + [NO] + (.)NO + (NO)(.) + monoxyde d'azote + oxido de nitrogeno(II) + oxyde azotique + oxidonitrogen(.) + Stickstoffmonoxid + InChIKey=MWUXSHHQAYIFBG-UHFFFAOYSA-N + nitric oxide + nitric oxide + + + dioxomethane + E 290 + [CO2] + CHEBI:16526 + "A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food." [] + InChI=1S/CO2/c2-1-3 + CHEBI:carbon dioxide + InChIKey=CURLTUGMZLYLDI-UHFFFAOYSA-N + Carbon dioxide + CARBON DIOXIDE + carbon dioxide + R-744 + dioxidocarbon + carbon dioxide + E-290 + CO2 + O=C=O + E290 + carbonic anhydride + + + 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + 1-Phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + C11H20O22P4R2 + PtsIns(3,4,5)P3 + PIP3 + 1-O-(3-sn-phosphatidyl)-1D-myo-inositol 3,4,5-tris(dihydrogen phosphate) + PtsIns-3,4,5-P3 + Phosphatidylinositol-3,4,5-trisphosphate + [H][C@@](COC([*])=O)(COP(O)(=O)O[C@@H]1[C@H](O)[C@H](OP(O)(O)=O)[C@@H](OP(O)(O)=O)[C@H](OP(O)(O)=O)[C@H]1O)OC([*])=O + CHEBI:16618 + 1,2-Diacyl-sn-glycero-3-phospho-(1'-myo-inositol-3',4',5'-bisphosphate) + CHEBI:1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + + + C25H40N7O19P3S + CC(C(O)=O)C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12 + InChIKey=MZFOKIKEPGUZEN-FBMOWMAESA-N + Methylmalonyl coemzyme A + Methylmalonyl coenzyme A + methylmalonyl coenzyme A + Methylmalonyl-CoA + CHEBI:methylmalonyl-CoA + InChI=1S/C25H40N7O19P3S/c1-12(23(37)38)24(39)55-7-6-27-14(33)4-5-28-21(36)18(35)25(2,3)9-48-54(45,46)51-53(43,44)47-8-13-17(50-52(40,41)42)16(34)22(49-13)32-11-31-15-19(26)29-10-30-20(15)32/h10-13,16-18,22,34-35H,4-9H2,1-3H3,(H,27,33)(H,28,36)(H,37,38)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/t12?,13-,16-,17-,18+,22-/m1/s1 + "A member of the class of malonyl-CoAs that is malonyl-CoA carrying a methyl group on the malony side chain." [] + 3'-phosphoadenosine 5'-[3-(3-hydroxy-2,2-dimethyl-4-{[3-({2-[(2-methyl-3-oxopropanoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-4-oxobutyl) dihydrogen diphosphate] + methylmalonyl-CoA + 2-methyl-3-oxopropanoyl-CoAs + 2-Methylmalonyl-CoA + 2-methylmalonyl-CoA + CHEBI:16625 + + + hydrates de carbone + glucides + saccharidum + CHEBI:carbohydrate + saccharide + "Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates." [] + Kohlenhydrate + glucido + carbohydrate + Kohlenhydrat + carbohidratos + carbohydrate + carbohidrato + . + glucidos + saccharides + carbohydrates + CHEBI:16646 + glucide + + + CHEBI:16670 + peptido + peptide + Peptide + peptides + (C2H2NOR)nC2H3NOR + "Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc." [] + Peptid + CHEBI:peptide + peptidos + + + corticosterone + 11beta,21-dihydroxyprogesterone + C21H30O4 + (8S,9S,10R,11S,13S,14S,17S)-11-hydroxy-17-(2-hydroxy-1-oxoethyl)-10,13-dimethyl-1,2,6,7,8,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-3-one + "A 21-hydroxy steroid that is consists of pregn-4-ene substituted by hydroxy groups at positions 11 and 21 and oxo groups at positions 3 and 20. Corticosterone is a 21-carbon steroid hormone of the corticosteroid type produced in the cortex of the adrenal glands." [] + Reichstein's substance H + Kendall's compound B + InChI=1S/C21H30O4/c1-20-8-7-13(23)9-12(20)3-4-14-15-5-6-16(18(25)11-22)21(15,2)10-17(24)19(14)20/h9,14-17,19,22,24H,3-8,10-11H2,1-2H3/t14-,15-,16+,17-,19+,20-,21-/m0/s1 + [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4=CC(=O)CC[C@]4(C)[C@@]3([H])[C@@H](O)C[C@]12C)C(=O)CO + 17-deoxycortisol + InChIKey=OMFXVFTZEKFJBZ-HJTSIMOOSA-N + 11beta,21-dihydroxypregn-4-ene-3,20-dione + 11beta,21-Dihydroxy-4-pregnene-3,20-dione + (8S,9S,10R,11S,13S,14S,17S)-17-glycoloyl-11-hydroxy-10,13-dimethyl-1,2,6,7,8,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-3-one + corticosterone + CORTICOSTERONE + (8S,9S,10R,11S,13S,14S,17S)-11-hydroxy-17-(2-hydroxyethanoyl)-10,13-dimethyl-1,2,6,7,8,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-3-one + Corticosterone + (11beta)-11,21-dihydroxypregn-4-ene-3,20-dione + CHEBI:corticosterone + CHEBI:16827 + (8S,9S,10R,11S,13S,14S,17S)-11-hydroxy-17-(2-hydroxyacetyl)-10,13-dimethyl-1,2,6,7,8,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-3-one + + + [H]C([H])=O + InChIKey=WSFSSNUMVMOOMR-UHFFFAOYSA-N + "The simplest aldehyde." [] + Methylene oxide + CHEBI:16842 + Oxomethylene + Formalin + FORMALIN + CHEBI:formaldehyde + InChI=1S/CH2O/c1-2/h1H2 + formaldehyde + Formaldehyde + FORMALDEHYDE + Oxomethane + formaldehyde + Methanal + Formaldehyd + CH2O + + + Glutathione-SH + N-(N-gamma-L-Glutamyl-L-cysteinyl)glycine + InChI=1S/C10H17N3O6S/c11-5(10(18)19)1-2-7(14)13-6(4-20)9(17)12-3-8(15)16/h5-6,20H,1-4,11H2,(H,12,17)(H,13,14)(H,15,16)(H,18,19)/t5-,6-/m0/s1 + C10H17N3O6S + GSH + 5-L-Glutamyl-L-cysteinylglycine + "A tripeptide compound consisting of glutamic acid attached via its side chain to the N-terminus of cysteinylglycine." [] + CHEBI:16856 + glutathione + InChIKey=RWSXRVCMGQZWBV-WDSKDSINSA-N + Glutathione + gamma-L-Glutamyl-L-cysteinyl-glycine + L-gamma-glutamyl-L-cysteinylglycine + Reduced glutathione + CHEBI:glutathione + N[C@@H](CCC(=O)N[C@@H](CS)C(=O)NCC(O)=O)C(O)=O + N-[(4S)-4-ammonio-4-carboxybutanoyl]-L-cysteinylglycine + L-gamma-glutamyl-L-cysteinylglycine + + + piperidinic acid + "A gamma-amino acid that is butanoic acid with the amino substituent located at C-4." [] + 4Abu + piperidic acid + CHEBI:gamma-aminobutyric acid + NCCCC(O)=O + InChI=1S/C4H9NO2/c5-3-1-2-4(6)7/h1-3,5H2,(H,6,7) + CHEBI:16865 + gamma-Aminobuttersaeure + gamma-aminobutanoic acid + GAMMA-AMINO-BUTANOIC ACID + 4-aminobutyric acid + 4-Aminobutyric acid + C4H9NO2 + gamma-aminobutyric acid + gamma-Aminobutyric acid + InChIKey=BTCSSZJGUNDROE-UHFFFAOYSA-N + 4-aminobutanoic acid + GABA + omega-aminobutyric acid + gamma-aminobutyric acid + 4-Aminobutanoic acid + gamma-amino-n-butyric acid + 4-aminobutanoic acid + + + Turkey Red + Alizarin + alizarin + Dihydroxyanthraquinone + "A dihydroxyanthraquinone in which the hydroxy groups are at C-1 and C-2 and whch has oxo groups at C-9 and C-10." [] + Alizarin Red + CHEBI:16866 + Oc1ccc2C(=O)c3ccccc3C(=O)c2c1O + InChI=1S/C14H8O4/c15-10-6-5-9-11(14(10)18)13(17)8-4-2-1-3-7(8)12(9)16/h1-6,15,18H + 1,2-dihydroxyanthra-9,10-quinone + 1,2-dihydroxy-9,10-anthraquinone + 1,2-dihydroxyanthracene-9,10-dione + alizarin + InChIKey=RGCKGOZRHPZPFP-UHFFFAOYSA-N + Alizarin B + 1,2-Dihydroxyanthraquinone + 1,2-Anthraquinonediol + Az + CHEBI:alizarin + Mordant Red 11 + C14H8O4 + Dihydroxy-9,10-anthracenedione + + + CHEBI:creatine + N-amidinosarcosine + N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE + alpha-Methylguanidino acetic acid + Methylglycocyamine + InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9) + creatine + (N-methylcarbamimidamido)acetic acid + InChIKey=CVSVTCORWBXHQV-UHFFFAOYSA-N + N-carbamimidoyl-N-methylglycine + N-Methyl-N-guanylglycine + N-methyl-N-guanylglycine + Kreatin + C4H9N3O2 + N-[amino(imino)methyl]-N-methylglycine + ((amino(imino)methyl)(methyl)amino)acetic acid + CHEBI:16919 + Creatine + Creatin + (alpha-methylguanido)acetic acid + N-(aminoiminomethyl)-N-methylglycine + CN(CC(O)=O)C(N)=N + "A glycine derivative having methyl and amidino groups attached to the nitrogen." [] + + + Provitamin D2 + (3S,9S,10R,13R,14R,17R)-17-[(E,2R,5R)-5,6-dimethylhept-3-en-2-yl]-10,13-dimethyl-2,3,4,9,11,12,14,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-3-ol + InChI=1S/C28H44O/c1-18(2)19(3)7-8-20(4)24-11-12-25-23-10-9-21-17-22(29)13-15-27(21,5)26(23)14-16-28(24,25)6/h7-10,18-20,22,24-26,29H,11-17H2,1-6H3/b8-7+/t19-,20+,22-,24+,25-,26-,27-,28+/m0/s1 + C28H44O + [H][C@@]1(CC[C@@]2([H])C3=CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)\\C=C\\[C@H](C)C(C)C + CHEBI:16933 + ergosterol + ERGOSTEROL + Ergosterol + (22E,24S)-24-methylcholesta-5,7,22-trien-3beta-ol + (22E)-ergosta-5,7,22-trien-3beta-ol + Ergosta-5,7,22-trien-3-ol, (3beta,22E)- + ergosterol + (3S,9S,10R,13R,14R,17R)-10,13-dimethyl-17-[(E,1R,4R)-1,4,5-trimethylhex-2-enyl]-2,3,4,9,11,12,14,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-3-ol + 24R-Methylcholesta-5,7,2E-trien-3beta-ol + InChIKey=DNVPQKQSNYMLRS-APGDWVJJSA-N + Ergosta-5,7,22-trien-3beta-ol + CHEBI:ergosterol + "A phytosterol consiting of ergostane having double bonds at the 5,6-, 7,8- and 22,23-positions as well as a 3beta-hydroxy group." [] + 24alpha-Methyl-22E-dehydrocholesterol + (3beta,14beta,17alpha,22E)-ergosta-5,7,22-trien-3-ol + Ergosterin + + + CHEBI:16976 + hygromycin B + (1R,2S,3R,5S,6R)-3-amino-2,6-dihydroxy-5-(methylamino)cyclohexyl O-6-amino-6-deoxy-L-glycero-D-galacto-heptopyranosylidene-(1->2-3)-beta-D-talopyranoside + O-6-amino-6-deoxy-L-glycero-D-galacto-heptopyranosylidene-(1->2-3)-O-beta-D-talopyranosyl-(1->5)-2-deoxy-N(3)-methyl-D-streptamine + CN[C@H]1C[C@@H](N)[C@H](O)[C@@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@@H]3O[C@@]4(O[C@H](C(N)CO)[C@H](O)[C@H](O)[C@H]4O)O[C@H]23)[C@@H]1O + InChIKey=GRRNUXAQVGOGFE-NZSRVPFOSA-N + "A hygromycin that has formula C20H37N3O13." [] + InChI=1S/C20H37N3O13/c1-23-7-2-5(21)9(26)15(10(7)27)33-19-17-16(11(28)8(4-25)32-19)35-20(36-17)18(31)13(30)12(29)14(34-20)6(22)3-24/h5-19,23-31H,2-4,21-22H2,1H3/t5-,6?,7+,8-,9+,10-,11+,12-,13+,14-,15-,16+,17+,18-,19+,20-/m1/s1 + CHEBI:hygromycin B + HYGROMYCIN B + Hygromycin B + C20H37N3O13 + Antibiotic A-396-II + + + Ethandisaeure + ethane-1,2-dioic acid + InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6) + CHEBI:16995 + Ethanedioic acid + ethanedioic acid + OXALIC ACID + Oxalic acid + oxalic acid + OC(=O)C(O)=O + H2ox + InChIKey=MUBZPKHOEPUJKR-UHFFFAOYSA-N + CHEBI:oxalic acid + "An alpha,omega-dicarboxylic acid that is ethane substituted by carboxyl groups at positions 1 and 2." [] + oxalic acid + Oxalsaeure + HOOCCOOH + C2H2O4 + + + a cholesterol ester + cholesterol esters + [H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@H](CC[C@]4(C)[C@@]3([H])CC[C@]12C)OC([*])=O)[C@H](C)CCCC(C)C + Cholesterol ester + CHEBI:cholesterol ester + cholesterol ester + CHEBI:17002 + "Cholesterol esterified at the 3-hydroxy group." [] + C28H45O2R + + + CHEBI:streptomycin + streomycin + streptomycin + Kantrex + InChIKey=UCSJYZPVAKXKNQ-HZYVHMACSA-N + N,N'''-[(1R,2R,3S,4R,5R,6S)-4-{5-deoxy-2-O-[2-deoxy-2-(methylamino)-alpha-L-glucopyranosyl]-3-C-formyl-alpha-L-lyxofuranosyloxy}-2,5,6-trihydroxycyclohexane-1,3-diyl]diguanidine + streptomycin + 2,4-Diguanidino-3,5,6-trihydroxycyclohexyl 5-deoxy-2-O-(2-deoxy-2-methylamino-alpha-L-glucopyranosyl)-3-C-formyl-beta-L-lyxopentanofuranoside + InChI=1S/C21H39N7O12/c1-5-21(36,4-30)16(40-17-9(26-2)13(34)10(31)6(3-29)38-17)18(37-5)39-15-8(28-20(24)25)11(32)7(27-19(22)23)12(33)14(15)35/h4-18,26,29,31-36H,3H2,1-2H3,(H4,22,23,27)(H4,24,25,28)/t5-,6-,7+,8-,9-,10-,11+,12-,13-,14+,15+,16-,17-,18-,21+/m0/s1 + CHEBI:17076 + STREPTOMYCIN + C21H39N7O12 + "A amino cyclitol glycoside that consists of streptidine having a disaccharyl moiety attached at the 4-position. The parent of the streptomycin class" [] + SM + CN[C@H]1[C@H](O)[C@@H](O)[C@H](CO)O[C@H]1O[C@H]1[C@@H](O[C@@H](C)[C@]1(O)C=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](NC(N)=N)[C@@H](O)[C@@H]1NC(N)=N + [2-deoxy-2-(dimethylamino)-alpha-L-glucopyranosyl]-(1->2)-[5-deoxy-3-C-formyl-alpha-L-lyxofuranosyl]-(1->4)-{N',N'''-[(1,3,5/2,4,6)-2,4,5,6-tetrahydroxycyclohexane-1,3-diyl]diguanidine} + + + ketones + CHEBI:ketone + COR2 + a ketone + CHEBI:17087 + Keton + cetone + "A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H)." [] + ketone + [*]C([*])=O + R-CO-R' + ketones + Ketone + + + Glykoproteine + Glycoprotein + CHEBI:17089 + glicoproteina + glycoproteines + CHEBI:glycoprotein + glicoproteinas + Glykoprotein + glycoprotein + glycoproteins + [glycoprotein] + "A compound in which a carbohydrate component is covalently bound to a protein component." [] + glycoproteine + + + C7H15NO3 + carnitine + CHEBI:carnitine + C[N+](C)(C)CC(O)CC([O-])=O + 3-hydroxy-4-(trimethylammonio)butanoate + InChIKey=PHIQHXFUZVPYII-UHFFFAOYSA-N + carnitine + CHEBI:17126 + D,L-carnitine + "An amino-acid betaine that is butanoate substituted with a hydroxy group at position C-3 and a trimethylammonium group at C-4." [] + InChI=1S/C7H15NO3/c1-8(2,3)5-6(9)4-7(10)11/h6,9H,4-5H2,1-3H3 + + + Glycerinaldehyd-3-phosphat + 2-hydroxy-3-oxopropyl dihydrogen phosphate + Glyceraldehyde 3-phosphate + CHEBI:17138 + glyceraldehyde 3-(dihydrogen phosphate) + Glyzerinaldehyd-3-phosphat + gliceraldehido-3-fosfato + 3-phosphoglyceraldehyde + 2-hydroxy-3-(phosphonooxy)propanal + glyceraldehyde 3-phosphate + [H]C(=O)C(O)COP(O)(O)=O + CHEBI:glyceraldehyde 3-phosphate + glyceraldehyde-3-phosphate + InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h1,3,5H,2H2,(H2,6,7,8) + "An aldotriose phosphate that is the 3-phospho derivative of glyceraldehyde. It is an important metabolic intermediate in several central metabolic pathways in all organisms." [] + InChIKey=LXJXRIRHZLFYRP-UHFFFAOYSA-N + C3H7O6P + + + vitamin B3 + Nikotinamid + niacin + NICOTINAMIDE + nicotinamide + Nicotinamide + Nicotinamid + "A pyridinecarboxamide that is pyridine in which the hydrogen at position 3 is replaced by a carboxamide group." [] + pyridine-3-carboxamide + Niacinamide + beta-pyridinecarboxamide + Vitamin PP + CHEBI:nicotinamide + Nicotinic acid amide + 3-pyridinecarboxamide + Nikotinsaeureamid + pyridine-3-carboxamide + nicotinamide + Nicotinsaeureamid + C6H6N2O + CHEBI:17154 + InChIKey=DFPAKSUCGFBDDF-UHFFFAOYSA-N + InChI=1S/C6H6N2O/c7-6(9)5-2-1-3-8-4-5/h1-4H,(H2,7,9) + NC(=O)c1cccnc1 + + + 1,2-propanedione + methylglyoxal + CHEBI:17158 + [H]C(=O)C(C)=O + CHEBI:methylglyoxal + C3H4O2 + alpha-ketopropionaldehyde + Pyruvic aldehyde + acetylformyl + 2-oxopropionaldehyde + 2-Ketopropionaldehyde + 2-oxopropanal + methylglyoxal + CH3COCHO + Methylglyoxal + InChI=1S/C3H4O2/c1-3(5)2-4/h2H,1H3 + "A 2-oxo aldehyde derived from propanal." [] + 2-Oxopropanal + acetylformaldehyde + InChIKey=AIJULSRZWUXGPQ-UHFFFAOYSA-N + Pyruvaldehyde + + + gluco-hexose + Glukose + CHEBI:glucose + glucose + DL-glucose + "An aldohexose used as a source of energy and metabolic intermediate." [] + Glc + glucose + C6H12O6 + Glucose + CHEBI:17234 + + + N-Phosphorylcreatine + CHEBI:17287 + phosphorylcreatine + InChI=1S/C4H10N3O5P/c1-7(2-3(8)9)4(5)6-13(10,11)12/h2H2,1H3,(H,8,9)(H4,5,6,10,11,12) + N-(Phosphonoamidino)sarcosine + CN(CC(O)=O)C(=N)NP(O)(O)=O + Creatine phosphate + {[imino(phosphonoamino)methyl](methyl)amino}acetic acid + 2-[methyl-(N'-phosphonocarbamimidoyl)amino]ethanoic acid + "A phosphoamino acid consisting of creatine having a phospho group attached at the primary nitrogen of the guanidino group." [] + CHEBI:N-phosphocreatine + N-phosphocreatine + C4H10N3O5P + InChIKey=DRBBFCLWYRJSJZ-UHFFFAOYSA-N + N-[imino(phosphonoamino)methyl]-N-methylglycine + Phosphocreatine + 2-[methyl-(N'-phosphonocarbamimidoyl)amino]acetic acid + 2-[(amino-phosphonoimino-methyl)-methyl-amino]acetic acid + Creatine phosphic acid + N(omega)-phosphonocreatine + N-(N-phosphonoamido)sarcosine + N-Phosphocreatine + N-phosphocreatine + + + CHEBI:17334 + CHEBI:penicillin + C9H11N2O4SR + penicillins + penicillins + "Any member of the group of substituted penams containing two methyl substituents at position 2, a carboxylate substituent at position 3 and a carboxamido group at position 6." [] + [H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC([*])=O)C(O)=O + Penicillin + penicillin + + + CHEBI:17348 + C6H13O9P + 6-O-phosphono-D-glycero-hexose + D-aldohexose 6-phosphate + CHEBI:D-aldohexose 6-phosphate + "Any D-aldose having a six-carbon chain with a phosphate group at C-6." [] + D-glycero-hexose 6-(dihydrogen phosphate) + + + 1,7-dihydro-6H-purin-6-one + CHEBI:hypoxanthine + InChIKey=FDGQSTZJBFJUBT-UHFFFAOYSA-N + CHEBI:17368 + hypoxanthine + hypoxanthine + Hypoxanthine + HYPOXANTHINE + Purine-6-ol + InChI=1S/C5H4N4O/c10-5-3-4(7-1-6-3)8-2-9-5/h1-2H,(H2,6,7,8,9,10) + C5H4N4O + O=c1[nH]cnc2nc[nH]c12 + 6-oxopurine + "A purine nucleobase that consists of purine bearing an oxo substituent at position 6." [] + Hyp + purin-6(1H)-one + 6(1H)-purinone + 9H-purin-6(1H)-one + + + 6-O-phosphono-D-mannose + D-Mannose 6-phosphate + CHEBI:17369 + D-mannose 6-(dihydrogen phosphate) + "A mannose phosphate in which the phosphate group is attached to position 6." [] + D-mannose 6-phosphate + Mannose 6-phosphate + CHEBI:D-mannose 6-phosphate + C6H13O9P + + + CHEBI:O-acylcarnitine + O-acylcarnitine + CHEBI:17387 + O-acylcarnitines + "Any carboxylic ester obtained by the O-acylation of carnitine." [] + + + valeric acid, normal + pentoic acid + InChIKey=NQPDZGIKBAWPEJ-UHFFFAOYSA-N + n-Valeric acid + valeric acid + CCCCC(O)=O + C5H10O2 + n-BuCOOH + pentanoic acid + propylacetic acid + CHEBI:17418 + Valerate + CHEBI:valeric acid + Valeric acid + Pentanoate + LEVULINIC ACID + n-valeric acid + pentanoic acid + "A straight-chain saturated fatty acid containing five carbon atoms." [] + InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7) + PENTANOIC ACID + Pentanoic acid + Valerianic acid + n-pentanoic acid + Valeriansaeure + 1-butanecarboxylic acid + CH3-[CH2]3-COOH + n-Pentanoate + + + aldehydum + aldehydes + CHEBI:aldehyde + aldehidos + "A compound RC(=O)H, in which a carbonyl group is bonded to one hydrogen atom and to one R group." [] + aldehyde + aldehydes + aldehido + RCHO + an aldehyde + CHEBI:17478 + Aldehyde + aldehyde + CHOR + RC(=O)H + Aldehyd + [H]C([*])=O + + + Nc1ncnc2n(cnc12)[C@@H]1O[C@@H]2COP(O)(=O)O[C@H]2[C@H]1O + 3',5'-Cyclic AMP + "A 3',5'-cyclic purine nucleotide having having adenine as the nucleobase." [] + Adenosine 3',5'-phosphate + Adenosine 3',5'-cyclic phosphate + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE + adenosine 3',5'-cyclic monophosphate + cAMP + InChI=1S/C10H12N5O6P/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7-4(20-10)1-19-22(17,18)21-7/h2-4,6-7,10,16H,1H2,(H,17,18)(H2,11,12,13)/t4-,6-,7-,10-/m1/s1 + Cyclic AMP + Cyclic adenylic acid + 3',5'-cyclic AMP + C10H12N5O6P + CHEBI:3',5'-cyclic AMP + InChIKey=IVOMOUWHDPKRLL-KQYNXXCUSA-N + adenosine 3',5'-(hydrogen phosphate) + (1R,6R,7R,8R)-8-(6-aminopurin-9-yl)-4-hydroxy-4-oxo-3,5,9-trioxa-4$l^{5}-phosphabicyclo[4.3.0]nonan-7-ol + CHEBI:17489 + + + Cholest-5-ene-3beta,7alpha-diol + 7alpha-hydroxy-cholesterol + InChI=1S/C27H46O2/c1-17(2)7-6-8-18(3)21-9-10-22-25-23(12-14-27(21,22)5)26(4)13-11-20(28)15-19(26)16-24(25)29/h16-18,20-25,28-29H,6-15H2,1-5H3/t18-,20+,21-,22+,23+,24-,25+,26+,27-/m1/s1 + [H][C@@]1(CC[C@@]2([H])[C@]3([H])[C@H](O)C=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCCC(C)C + 7alpha-hydroxycholesterol + 7alpha-Hydroxycholesterol + C27H46O2 + cholest-5-ene-3beta,7alpha-diol + InChIKey=OYXZMSRRJOYLLO-RVOWOUOISA-N + 7alpha-hydroxycholesterol + CHEBI:7alpha-hydroxycholesterol + "The 7alpha-hydroxy derivative of cholesterol." [] + CHEBI:17500 + + + alditol + "A carbohydrate that is an acyclic polyol having the general formula HOCH2[CH(OH)]nCH2OH (formally derivable from an aldose by reduction of the carbonyl group)." [] + CHEBI:alditol + Glycitol + alditols + Alditol + Sugar alcohol + CHEBI:17522 + (CH2O)nC2H6O2 + + + BICARBONATE ION + CHO3 + OC([O-])=O + Acid carbonate + HCO3(-) + hydrogen carbonate + bicarbonate + Bicarbonate + hydrogentrioxocarbonate(IV) + hydrogencarbonate + [CO2(OH)](-) + hydrogencarbonate + Hydrogencarbonate + InChIKey=BVKZGUZCCUSVTD-UHFFFAOYSA-M + InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1 + "The carbon oxoanion resulting from the removal of a proton from carbonic acid." [] + hydrogencarbonate(1-) + hydrogentrioxocarbonate(1-) + CHEBI:17544 + HCO3- + hydrogen(trioxidocarbonate)(1-) + hydroxidodioxidocarbonate(1-) + CHEBI:hydrogencarbonate + + + CHEBI:toluene + toluene + methylbenzene + Toluen + "The simplest member of the class toluenes consisting of a benzene core which bears a single methyl substituent." [] + C7H8 + InChIKey=YXFVVABEGXRONW-UHFFFAOYSA-N + Toluol + Cc1ccccc1 + Toluene + toluene + TOLUENE + phenylmethane + CHEBI:17578 + InChI=1S/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3 + + + D-aldohexoses + D-aldohexose + C6H12O6 + "Any D-aldose having a chain of six carbon atoms in the molecule." [] + CHEBI:17608 + D-aldohexose + CHEBI:D-aldohexose + + + D-gluco-hexose + CHEBI:D-glucose + D-(+)-glucose + CHEBI:17634 + C6H12O6 + dextrose + "A glucose with D-configuration." [] + Traubenzucker + D-glucose + D(+)-glucose + D-glucose + grape sugar + + + Sificetina + Fenicol + Chloromycetin + chloramphenicolum + CHEBI:chloramphenicol + levomicetina + D-(-)-threo-1-p-nitrophenyl-2-dichloroacetylamino-1,3-propanediol + "An organochlorine compound that is dichloro-substituted acetamide containing a nitrobenzene ring, an amide bond and two alcohol functions." [] + chlornitromycin + Halomycetin + chloramphenicol + cloramfenicol + chloramphenicol + chloramphenicol + Oleomycetin + chloramphenicols + CHEBI:17698 + InChI=1S/C11H12Cl2N2O5/c12-10(13)11(18)14-8(5-16)9(17)6-1-3-7(4-2-6)15(19)20/h1-4,8-10,16-17H,5H2,(H,14,18)/t8-,9-/m1/s1 + Chlorocol + Globenicol + laevomycetinum + Chlorocid + levomycetin + OC[C@@H](NC(=O)C(Cl)Cl)[C@H](O)c1ccc(cc1)[N+]([O-])=O + 2,2-dichloro-N-[(1R,2R)-2-hydroxy-1-(hydroxymethyl)-2-(4-nitrophenyl)ethyl]acetamide + C11H12Cl2N2O5 + CHLORAMPHENICOL + Chloramphenicol + InChIKey=WIIZWVCIJKGZOK-RKDXNWHRSA-N + D-(-)-2,2-dichloro-N-(beta-hydroxy-alpha-(hydroxymethyl)-p-nitrophenylethyl)acetamide + Chloramex + + + 24-Dehydrocholesterol + 3beta-cholesta-5,24-dien-3-ol + InChIKey=AVSXSVCZWQODGV-DPAQBDIFSA-N + CHEBI:17737 + cholesta-5,24-dien-3beta-ol + Desmosterol + C27H44O + "A cholestanoid that is cholesta-5,24-diene substituted by a beta-hydroxy group at position 3. It is an intermediate metabolite obtained during the synthesis of cholesterol." [] + CHEBI:desmosterol + InChI=1S/C27H44O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h7,9,19,21-25,28H,6,8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1 + desmosterol + Cholesta-5,24-dien-3beta-ol + [H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC=C(C)C + cholesta-5,24-dien-3beta-ol + + + 1,2,3-Trihydroxypropane + Glycerin + Glyzerin + Glycerol + glycyl alcohol + glycerolum + propane-1,2,3-triol + Trihydroxypropane + CHEBI:glycerol + 1,2,3-Propanetriol + CHEBI:17754 + propane-1,2,3-triol + OCC(O)CO + InChIKey=PEDCQBHIVMGVHV-UHFFFAOYSA-N + glycerol + glycerol + GLYCEROL + glycerol + Propanetriol + InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2 + Oelsuess + C3H8O3 + "A triol with a structure of propane substituted at positions 1, 2 and 3 by hydroxy groups." [] + glycerine + Glyceritol + Gro + + + CHEBI:cholesta-5,7-dien-3beta-ol + 5,7-cholestadien-3-beta-ol + Provitamin D3 + CHEBI:17759 + C27H44O + "A 3beta-sterol that has formula C27H44O." [] + 7-Dehydrocholesterol + [H][C@@]1(CC[C@@]2([H])C3=CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCCC(C)C + InChIKey=UCTLRSWJYQTBFZ-DDPQNLDTSA-N + (3beta)-cholesta-5,7-dien-3-ol + InChI=1S/C27H44O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9-10,18-19,21,23-25,28H,6-8,11-17H2,1-5H3/t19-,21+,23-,24+,25+,26+,27-/m1/s1 + 5,7-cholestadien-3beta-ol + cholesta-5,7-dien-3beta-ol + Cholesta-5,7-dien-3beta-ol + cholesta-5,7-dien-3beta-ol + + + N-acylated sphingoid + ceramide + a ceramide + "Ceramides (N-acyl-sphingoid bases) are a major subclass of sphingoid base derivatives with an amide-linked fatty acid. The fatty acids are typically saturated or monounsaturated with chain lengths from 14 to 26 carbon atoms; the presence of a hydroxyl group on carbon 2 is fairly common. Ceramides are generally precursors of more complex sphingolipids. In the illustrated generalised structure, R(1) = OH, OX (where X = acyl, glycosyl, phosphate, phosphonate, etc.), or H." [] + CHEBI:ceramide + Cer + CHEBI:17761 + ceramides + Ceramide + O[C@H]([*])[C@H](C[*])NC([*])=O + C4H6NO2R3 + + + methanol + wood naphtha + CO + Methyl alcohol + Methylalkohol + CHEBI:17790 + METHANOL + Methanol + methanol + InChI=1S/CH4O/c1-2/h2H,1H3 + carbinol + MeOH + "The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group." [] + wood alcohol + OXYMETHYLENE BRIDGING GROUP + CH3OH + wood spirit + InChIKey=OKKJLVBELUTLKV-UHFFFAOYSA-N + CHEBI:methanol + CH4O + + + propan-2-ol + C3H8O + Isopropanol + i-propanol + InChI=1S/C3H8O/c1-3(2)4/h3-4H,1-2H3 + "A secondary alcohol that is propane in which one of the hydrogens attached to the central carbon is substituted by a hydroxy group." [] + IPA + Isopropylalkohol + CHEBI:propan-2-ol + CHEBI:17824 + 1-methylethyl alcohol + 2-hydroxypropane + i-Propylalkohol + InChIKey=KFZMGEQAYNKOFK-UHFFFAOYSA-N + CC(C)O + propan-2-ol + Propan-2-ol + 2-Propanol + 1-methylethanol + Isopropyl alcohol + isopropyl alcohol + sec-propanol + ISOPROPYL ALCOHOL + + + Triglyzerid + Triacylglycerol + a triacylglycerol + triacylglycerols + triglyceride + triglycerides + Triglycerid + C6H5O6R3 + CHEBI:triglyceride + triglycerides + Triglyceride + [*]C(=O)OCC(COC([*])=O)OC([*])=O + CHEBI:17855 + + + oxidised glutathione + (2S)-2-amino-4-[[(1R)-2-[(2R)-2-[[(4S)-4-amino-4-carboxy-butanoyl]amino]-2-(carboxymethylcarbamoyl)ethyl]disulfanyl-1-(carboxymethylcarbamoyl)ethyl]carbamoyl]butanoic acid + glutathione disulphide + InChIKey=YPZRWBKMTBYPTK-BJDJZHNGSA-N + (2S,2'S)-5,5'-[disulfanediylbis({(2R)-3-[(carboxymethyl)amino]-3-oxopropane-1,2-diyl}imino)]bis(2-amino-5-oxopentanoic acid) (non-preferred name) + (2S)-2-amino-4-[[[(1R)-2-[(2R)-2-[[(4S)-4-amino-4-carboxy-1-oxo-butyl]amino]-2-[(carboxymethylamino)-oxo-methyl]ethyl]disulfanyl-1-[(carboxymethylamino)-oxo-methyl]ethyl]amino]-oxo-methyl]butanoic acid + CHEBI:glutathione disulfide + Oxidized glutathione + C20H32N6O12S2 + GSSG + N[C@@H](CCC(=O)N[C@@H](CSSC[C@H](NC(=O)CC[C@H](N)C(O)=O)C(=O)NCC(O)=O)C(=O)NCC(O)=O)C(O)=O + OXIDIZED GLUTATHIONE DISULFIDE + (2S,2'S)-5,5'-[disulfanediylbis({(2R)-3-[(carboxymethyl)amino]-3-oxopropane-1,2-diyl}imino)]bis(2-amino-5-oxopentanoic acid) + "A glutathione derivative that has formula C20H32N6O12S2." [] + InChI=1S/C20H32N6O12S2/c21-9(19(35)36)1-3-13(27)25-11(17(33)23-5-15(29)30)7-39-40-8-12(18(34)24-6-16(31)32)26-14(28)4-2-10(22)20(37)38/h9-12H,1-8,21-22H2,(H,23,33)(H,24,34)(H,25,27)(H,26,28)(H,29,30)(H,31,32)(H,35,36)(H,37,38)/t9-,10-,11-,12-/m0/s1 + Glutathione disulfide + CHEBI:17858 + glutathione disulfide + Oxiglutatione + + + alpha-ketoisocaproate + "A 2-oxo monocarboxylic acid anion that is the conjugate base of 4-methyl-2-oxopentanoic acid." [] + InChI=1S/C6H10O3/c1-4(2)3-5(7)6(8)9/h4H,3H2,1-2H3,(H,8,9)/p-1 + 4-methyl-2-oxopentanoate + CHEBI:4-methyl-2-oxopentanoate + 2-Oxoisocaproate + InChIKey=BKAJNAXTPSGJCU-UHFFFAOYSA-M + 4-methyl-2-oxopentanoate + C6H9O3 + CC(C)CC(=O)C([O-])=O + CHEBI:17865 + + + "A mononuclear parent hydride consisting of covalently bonded hydrogen and chlorine atoms." [] + CHEBI:hydrogen chloride + cloruro de hidrogeno + chloridohydrogen + CHEBI:17883 + ClH + hydrogen chloride + HCl + Hydrochloride + Hydrogen chloride + hydrogen chloride + InChIKey=VEXZGXHMUGYJMC-UHFFFAOYSA-N + hydrochloric acid + Wasserstoffchlorid + Chlorwasserstoff + InChI=1S/ClH/h1H + chlorure d'hydrogene + Cl[H] + [HCl] + chlorane + Hydrogenchlorid + + + puromicina + "An aminonucleoside antibiotic, derived from the Streptomyces alboniger bacterium, that causes premature chain termination during translation taking place in the ribosome." [] + 3'-deoxy-N,N-dimethyl-3'-(O-methyl-L-tyrosinamido)adenosine + puromycinum + CHEBI:puromycin + puromycin + C22H29N7O5 + 3'-(L-alpha-Amino-p-methoxyhydrocinnamamido)-3'-deoxy-N,N-dimethyladenosine + puromycin + Achromycin + (S)-3'-((2-Amino-3-(4-methoxyphenyl)-1-oxopropyl)amino)-3'-deoxy-N,N-dimethyladenosine + COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@H]([C@@H]2O)n2cnc3c(ncnc23)N(C)C)cc1 + 3'-[[(2S)-2-amino-3-(4-methoxyphenyl)-1-oxopropyl]amino]-3'-deoxy-N,N-diemthyladenosine + CHEBI:17939 + 9-{3-deoxy-3-[(O-methyl-L-tyrosyl)amino]-beta-D-xylofuranosyl}-N,N-dimethyl-9H-purin-6-amine + InChI=1S/C22H29N7O5/c1-28(2)19-17-20(25-10-24-19)29(11-26-17)22-18(31)16(15(9-30)34-22)27-21(32)14(23)8-12-4-6-13(33-3)7-5-12/h4-7,10-11,14-16,18,22,30-31H,8-9,23H2,1-3H3,(H,27,32)/t14-,15+,16+,18+,22+/m0/s1 + PUROMYCIN + Puromycin + InChIKey=RXWNCPJZOCPEPQ-NVWDDTSBSA-N + puromycine + + + InChIKey=FERIUCNNQQJTOY-UHFFFAOYSA-M + butanate + C4H7O2 + CHEBI:butyrate + CH3-[CH2]2-COO(-) + butanoate + "A short-chain fatty acid anion that is the conjugate base of butyric acid, obtained by deprotonation of the carboxy group." [] + butyrate + InChI=1S/C4H8O2/c1-2-3-4(5)6/h2-3H2,1H3,(H,5,6)/p-1 + n-butanoate + butanoate + 1-propanecarboxylate + butyrate + CCCC([O-])=O + 1-butanoate + CHEBI:17968 + 1-butyrate + propanecarboxylate + propylformate + butanoic acid, ion(1-) + n-butyrate + + + CHEBI:17984 + "A thioester that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any carboxylic acid." [] + Acyl-CoA + C22H35N7O17P3SR + CHEBI:acyl-CoA + CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCSC([*])=O + Acyl coenzyme A + acyl-CoA + + + alpha-toluenol + CHEBI:benzyl alcohol + Benzyl alcohol + Benzenemethanol + alcool benzylique + "An aromatic alcohol that consists of benzene bearing a single hydroxymethyl substituent." [] + benzyl alcohol + (hydroxymethyl)benzene + alcoholum benzylicum + Benzylalkohol + CHEBI:17987 + phenylmethanol + Hydroxymethylbenzene + benzenecarbinol + benzyl alcohol + phenylmethyl alcohol + Phenylcarbinol + Aromatic alcohol + Phenylmethanol + benzylic alcohol + C7H8O + OCc1ccccc1 + InChIKey=WVDDGKGOMKODPV-UHFFFAOYSA-N + InChI=1S/C7H8O/c8-6-7-4-2-1-3-5-7/h1-5,8H,6H2 + alpha-Hydroxytoluene + + + Sacharose + (2R,3R,4S,5R,6R)-2-[(2S,3S,4R,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol + (2R,3R,4S,5R,6R)-2-[(2S,3S,4R,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)tetrahydrofuran-2-yl]oxy-6-(hydroxymethyl)tetrahydropyran-3,4,5-triol + White sugar + CHEBI:17992 + (2R,3R,4S,5R,6R)-2-[(2S,3S,4R,5R)-3,4-dihydroxy-2,5-dimethylol-tetrahydrofuran-2-yl]oxy-6-methylol-tetrahydropyran-3,4,5-triol + Saccharose + "Sucrose is a disaccharide formed by glucose and fructose units joined by an acetal oxygen bridge from hemiacetal of glucose to the hemiketal of the fructose." [] + sacarosa + beta-D-fructofuranosyl alpha-D-glucopyranoside + CHEBI:sucrose + 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside + Cane sugar + C12H22O11 + beta-D-Fruf-(2<->1)-alpha-D-Glcp + InChIKey=CZMRCDWAGMRECN-UGDNZRGBSA-N + InChI=1S/C12H22O11/c13-1-4-6(16)8(18)9(19)11(21-4)23-12(3-15)10(20)7(17)5(2-14)22-12/h4-11,13-20H,1-3H2/t4-,5-,6-,7-,8+,9-,10+,11-,12+/m1/s1 + table sugar + sucrose + OC[C@H]1O[C@H](O[C@]2(CO)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O + SUCROSE + Sucrose + sucrose + + + CHEBI:chloride + Cl- + Cl(-) + chloride + "A halide anion formed when chlorine picks up an electron to form an an anion." [] + chloride + CHEBI:17996 + Chloride + InChIKey=VEXZGXHMUGYJMC-UHFFFAOYSA-M + [Cl-] + Chlorine anion + chloride(1-) + Cl + CHLORIDE ION + Chloride ion + Chloride(1-) + InChI=1S/ClH/h1H/p-1 + + + N2 + CHEBI:dinitrogen + nitrogen + Nitrogen + N#N + dinitrogen + "An elemental molecule consisting of two trivalently-bonded nitrogen atoms." [] + CHEBI:17997 + dinitrogen + InChI=1S/N2/c1-2 + NITROGEN MOLECULE + molecular nitrogen + InChIKey=IJGRMHOSHXDMSA-UHFFFAOYSA-N + + + TPN + InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/p+1/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 + Nicotinamide adenine dinucleotide phosphate + oxidized nicotinamide-adenine dinucleotide phosphate + beta-Nicotinamide adenine dinucleotide phosphate + beta-nicotinamide adenine dinucleotide phosphate + 2'-O-phosphonoadenosine 5'-{3-[1-(3-carbamoylpyridinio)-1,4-anhydro-D-ribitol-5-yl] dihydrogen diphosphate} + "A NAD(P)(+) that has formula C21H29N7O17P3." [] + NADP + NADP(+) + InChIKey=XJLXINKUBYWONI-NNYOXOHSSA-O + CHEBI:18009 + C21H29N7O17P3 + NC(=O)c1ccc[n+](c1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](OP(O)(O)=O)[C@@H]2O)n2cnc3c(N)ncnc23)[C@@H](O)[C@H]1O + Triphosphopyridine nucleotide + CHEBI:NADP(+) + NADP+ + + + O-phosphono-enol-pyruvate + 2-hydroxy-2-propenoate phosphate (ester) + PEP + 2-hydroxy-2-propenoate (dihydrogen phosphate) (ester) + PHOSPHOENOLPYRUVATE + Phosphoenolpyruvate + 2-(phosphonooxy)prop-2-enoate + "A monocarboxylic acid anion resuting from selective deprotonation of the carboxy group of phosphoenolpyruvic acid." [] + phosphoenolpyruvate + phosphoenolpyruvate(1-) + 2-(phosphonooxy)-2-propenoate + InChI=1S/C3H5O6P/c1-2(3(4)5)9-10(6,7)8/h1H2,(H,4,5)(H2,6,7,8)/p-1 + C3H4O6P + CHEBI:18021 + InChIKey=DTBNBXWJWCWCIK-UHFFFAOYSA-M + CHEBI:phosphoenolpyruvate + 2-(phosphonooxy)acrylate + OP(O)(=O)OC(=C)C([O-])=O + + + InChI=1S/CHNS/c2-1-3/h3H/p-1 + [S-C#N](-) + nitridothiocarbonate(1-) + thiocyanate + THIOCYANATE ION + "A pseudohalide anion obtained by deprotonation of the thiol group of thiocyanic acid." [] + InChIKey=ZMZDMBWJUHKJPS-UHFFFAOYSA-M + CNS + thiocyanate ion (1-) + [S-]C#N + SCN(-) + nitridosulfidocarbonate(1-) + rhodanide + N#C-S(-) + NCS- + nitridothiocarbonate(IV) + CHEBI:thiocyanate + CHEBI:18022 + Thiozyanat + thiocyanate + Rhodanid + + + Diacylglycerol + a diacylglycerol + CHEBI:18035 + diglycerides + [*]OCC(CO[*])O[*] + "A glyceride in which any two of the R groups (positions not specified) are acyl groups while the remaining R group can be either H or an alkyl group." [] + CHEBI:diglyceride + diglyceride + C5H6O5R2 + di-O-acylglycerols + diglycerides + diacylglycerols + Diglyceride + + + lipid + "'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids." [] + lipid + Lipid + CHEBI:lipid + CHEBI:18059 + . + lipids + + + CHEBI:cytochrome c + Cytochrome C + cytochrome c + CHEBI:18070 + c-type cytochrome + Holocytochrome c + CC(SC[C@H](NC([*])=O)C(=O)N[*])C1=C(C)/C2=C/c3c(C(C)SC[C@H](NC([*])=O)C(=O)N[*])c(C)c4\\C=C5/N=C(C=c6c(CCC(O)=O)c(C)c(=CC1=N\\2)n6[Fe]n34)C(CCC(O)=O)=C/5C + . + + + CHEBI:glycosaminoglycan + CHEBI:18085 + Glycosaminoglycan + Glykosaminoglykan + glycosaminoglycan + glicosaminoglicano + glycosaminoglycan + . + glycosaminoglycane + "Any polysaccharide containing a substantial proportion of aminomonosaccharide residues." [] + glycosaminoglycans + + + CHEBI:18087 + myo-inositol polyphosphates + myo-inositol polyphosphate + myo-Inositol polyphosphate + myo-inositol polyphosphate + CHEBI:myo-inositol polyphosphate + . + + + CHEBI:hexose + CHEBI:18133 + hexose + Hexose + hexoses + hexose + . + "Any six-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldohexose) or a ketone group at position 2 (ketohexose)." [] + + + HX + Halo acid + hydrogen halide + CHEBI:hydrogen halide + hydrogen halides + [F,Cl,Br,I] + hydrogen halide + CHEBI:18140 + hydrogen halides + + + Glykane + polysaccharide + Glycan + "A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues." [] + polisacarido + Glycane + polisacaridos + polysaccharides + Glykan + polysaccharide + Polysaccharide + CHEBI:18154 + glycans + CHEBI:polysaccharide + + + phosphoinositide + CHEBI:phosphoinositide + Phosphatidylinositol + phosphatidylinositol + CHEBI:18179 + "Any phosphatidylinositol that is phosphorylated at one or more of the hydroxy groups of inositol." [] + C11H17O13PR2 + + + InChI=1S/C16H18N2O4S/c1-16(2)12(15(21)22)18-13(20)11(14(18)23-16)17-10(19)8-9-6-4-3-5-7-9/h3-7,11-12,14H,8H2,1-2H3,(H,17,19)(H,21,22)/t11-,12+,14-/m1/s1 + benzylpenicillin + Penicillin G + PENICILLIN G + bencilpenicilina + C16H18N2O4S + benzylpenicillinic acid + InChIKey=JGSARLDLIJGVTE-MBNYWOFBSA-N + benzylpenicilline + CHEBI:benzylpenicillin + 2,2-dimethyl-6beta-(phenylacetamido)penam-3alpha-carboxylic acid + "A penicillin in which the substituent at position 6 of the penam ring is a phenylacetamido group." [] + Benzylpenicillin + 6-(2-phenylacetamido)penicillanic acid + [H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC(=O)Cc1ccccc1)C(O)=O + (2S,5R,6R)-3,3-dimethyl-7-oxo-6-(phenylacetamido)-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid + free penicillin II + CHEBI:18208 + bensylpenicillin + benzylpenicillinum + PG + benzylpenicillin + + + hidroxido de amonio + ammonia water + H5NO + CHEBI:ammonium hydroxide + H4N.HO + Ammonium hydroxide + ammonium hydroxide + CHEBI:18219 + NH4OH + hydroxyde d'ammonium + E527 + InChI=1S/H3N.H2O/h1H3;1H2 + ammonium hydroxide + ammonia solution + agua de amoniaco + ammonia aqueous + Ammoniumhydroxid + [NH4+].[OH-] + ammoniaque + InChIKey=VHUUQVKOLVNVRT-UHFFFAOYSA-N + "A solution of ammonia in water." [] + + + 4-(2-Aminoethyl)benzene-1,2-diol + Hydroxytyramin + InChI=1S/C8H11NO2/c9-4-3-6-1-2-7(10)8(11)5-6/h1-2,5,10-11H,3-4,9H2 + 2-(3,4-dihydroxyphenyl)ethylamine + 4-(2-aminoethyl)catechol + 4-(2-aminoethyl)pyrocatechol + CHEBI:18243 + 4-(2-aminoethyl)-1,2-benzenediol + 3-Hydroxytyramine + C8H11NO2 + CHEBI:dopamine + dopamine + dopamina + Deoxyepinephrine + dopaminum + dopamine + L-DOPAMINE + 2-(3,4-Dihydroxyphenyl)ethylamine + 3,4-Dihydroxyphenethylamine + Dopamine + NCCc1ccc(O)c(O)c1 + InChIKey=VYFYYTLLBUKUHU-UHFFFAOYSA-N + 4-(2-Aminoethyl)-1,2-benzenediol + 4-(2-aminoethyl)benzene-1,2-diol + "Catechol in which the hydrogen at position 4 is substituted by a 2-aminoethyl group." [] + 4-(2-azanylethyl)benzene-1,2-diol + + + CHEBI:ribonucleoside + ribonucleosides + CHEBI:18254 + OC[C@H]1O[C@@H]([*])[C@H](O)[C@@H]1O + a ribonucleoside + C5H9O4R + D-Ribosyl-base1 + Ribonucleoside + D-Ribosyl-base2 + ribonucleoside + D-ribosyl-base + D-Ribosyl-base + "Any nucleoside where the sugar component is D-ribose." [] + + + (C6H10O5)nH2O + "An alpha-D-glucan in which the glucose units are connected by (1->6) linkages." [] + 1,6-alpha-D-Glucan + CHEBI:(1->6)-alpha-D-glucan + (1,6-alpha-D-Glucosyl)n + (1,6-alpha-D-glucosyl)n + CHEBI:18269 + (1->6)-alpha-D-glucan + + + Deoxynucleoside + 2-Deoxy-D-ribosyl-base + OC[C@H]1O[C@@H]([*])C[C@@H]1O + CHEBI:18274 + C5H9O3R + a 2'-deoxyribonucleoside + 2'-Deoxynucleoside + CHEBI:2'-deoxyribonucleoside + 2'-deoxyribonucleoside + 2'-deoxyribonucleosides + + + CHEBI:nucleobase + a nucleobase + Base1 + "That part of DNA or RNA that may be involved in pairing." [] + nucleobase + Base2 + CHEBI:18282 + Base + nucleobases + + + CHEBI:histamine + histamine + NCCc1c[nH]cn1 + 2-(1H-imidazol-5-yl)ethylamine + InChI=1S/C5H9N3/c6-2-1-5-3-7-4-8-5/h3-4H,1-2,6H2,(H,7,8) + 2-(1H-imidazol-4-yl)ethanamine + 2-(1H-imidazol-5-yl)ethanamine + HISTAMINE + 1H-Imidazole-4-ethanamine + Histamine + CHEBI:18295 + InChIKey=NTYJJOPFIAHURM-UHFFFAOYSA-N + C5H9N3 + "A 1H-imidazol-4-yl group substituted at position C-4 by a 2-aminoethyl group." [] + 2-(4-Imidazolyl)ethylamine + + + phosphatidyl-L-serines + C8H12NO10PR2 + PS + "A class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxy group of serine." [] + Ptd-L-Ser + Phosphatidylserine + phosphatidyl-L-serine + CHEBI:18303 + N[C@@H](COP(O)(=O)OCC(COC([*])=O)OC([*])=O)C(O)=O + CHEBI:phosphatidyl-L-serine + + + alcanes + RH + an alkane + CHEBI:18310 + C[*] + alcano + alkanes + Alkan + alkane + Alkane + alkane + "An acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, and therefore consisting entirely of hydrogen atoms and saturated carbon atoms." [] + CH3R + alcanos + CHEBI:alkane + alcane + + + "The threo-diastereomer of 1,4-dimercaptobutane-2,3-diol." [] + DL-threo-1,4-Dimercapto-2,3-butanediol + DTT + Cleland's reagent + (R*,R*)-1,4-dimercapto-2,3-butanediol + rac-Dithiothreitol + C4H10O2S2 + 1,4-dithiothreitol + DTL + InChIKey=VHJLVAABSRFDPM-UHFFFAOYSA-N + Dithiotreitol + 1,4-dithiothreitol + 1,4-Dithiothreitol + OC(CS)C(O)CS + InChI=1S/C4H10O2S2/c5-3(1-7)4(6)2-8/h3-8H,1-2H2 + threo-1,4-Dimercapto-2,3-butanediol + rel-(2R,3R)-1,4-disulfanylbutane-2,3-diol + CHEBI:1,4-dithiothreitol + Dithiothreitol + CHEBI:18320 + + + C5H7O5PR2 + CHEBI:18375 + nucleoside 3',5'-cyclic phosphates + CHEBI:nucleoside 3',5'-cyclic phosphate + 3',5'-cyclic nucleotides + nucleoside 3',5'-cyclic phosphate + Nucleoside 3',5'-cyclic phosphate + nucleoside 3',5'-cyclic phosphate + OP1(=O)OC[C@H]2O[C@@H]([*])[C@H]([*])[C@@H]2O1 + 3',5'-Cyclic nucleotide + "A ribosyl or deoxyribosyl derivative of a pyrimidine or purine base in which C-3 and C-5 of the ribose ring are engaged in formation of a cyclic mono-, di-, tri- or tetra-phosphate." [] + + + "A compound having the structure RC#N; thus a C-substituted derivative of hydrocyanic acid, HC#N. In systematic nomenclature, the suffix nitrile denotes the triply bound #N atom, not the carbon atom attached to it." [] + CNR + Nitrile + nitrile + nitriles + a nitrile + nitrile + R-CN + nitrilos + [*]C#N + CHEBI:18379 + Nitril + CHEBI:nitrile + + + magnesium + magnesium(2+) ion + Mg + magnesium(2+) + CHEBI:18420 + magnesium(2+) + InChI=1S/Mg/q+2 + InChIKey=JLVVSXFLKOJNIY-UHFFFAOYSA-N + magnesium cation + Mg2+ + [Mg++] + magnesium(II) cation + "A magnesium cation that has formula Mg." [] + MAGNESIUM ION + CHEBI:magnesium(2+) + magnesium, doubly charged positive ion + Mg(2+) + magnesium, ion (Mg(2+)) + + + superoxide + superoxyde + "An oxygen radical that has formula O2." [] + dioxidanidyl + superoxide anion radical + superoxide radical anion + InChI=1S/HO2/c1-2/h1H/p-1 + Hyperoxid + InChIKey=OUUQCZGPVNCOIJ-UHFFFAOYSA-M + CHEBI:18421 + hyperoxide + CHEBI:superoxide + [O][O-] + O2- + (O2)(.-) + superoxide radical + O2(-) + superoxide + Superoxide anion + dioxide(1-) + O2(.-) + O2.- + dioxide(.1-) + O2 + + + pyrimidine 2'-deoxyribonucleosides + CHEBI:pyrimidine 2'-deoxyribonucleoside + 2'-deoxypyrimidine nucleosides + CHEBI:19255 + pyrimidine 2'-deoxyribonucleoside + + + 3',5'-cyclic purine nucleotide + 3',5'-cyclic purine nucleotides + CHEBI:3',5'-cyclic purine nucleotide + CHEBI:19834 + + + 3-hydroxy fatty acyl coenzyme A + CHEBI:3-hydroxy fatty acyl-CoA + beta-hydroxy fatty acyl-CoA + beta-hydroxyacyl-coenzyme A + beta-hydroxyacyl-CoA + beta-hydroxyacyl-CoAs + beta-hydroxyacyl-coenzyme As + 3-hydroxy fatty acyl-CoA + beta-hydroxy fatty acyl-CoAs + C24H39N7O18P3SR + 3-hydroxy fatty acyl coenzyme As + CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)CC(O)[*] + CHEBI:20060 + beta-hydroxy fatty acyl-coenzyme As + 3-hydroxy fatty acyl CoAs + 3-hydroxyacyl-CoAs + "A hydroxy fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any 3-hydroxy fatty acid." [] + 3-hydroxy fatty acyl CoA + beta-hydroxy fatty acyl-coenzyme A + + + InChI=1S/C4H8O3/c1-3(5)2-4(6)7/h3,5H,2H2,1H3,(H,6,7) + 3 HBA + 3-hydroxybutyric acid + "A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics." [] + beta-hydroxybutyric acid + CHEBI:3-hydroxybutyric acid + DL-beta-Hydroxybutyric acid + beta-Hydroxy-n-butyric acid + beta-hydroxy-n-butyric acid + 3-OH-butyric acid + 3-hydroxybutanoic acid + beta-Hydroxybuttersaeure + C4H8O3 + BHBA + 3-Hydroxybuttersaeure + CHEBI:20067 + 3-hydroxybutanoic acid + beta-hydroxybutanoic acid + 3-hydroxybutyric acid + CC(O)CC(O)=O + InChIKey=WHBMMWSBFZVSSR-UHFFFAOYSA-N + (1)-3-Hydroxybutyric acid + + + CHEBI:20702 + "Any aminopurine having the amino substituent at the 2-position." [] + CHEBI:2-aminopurines + 2-aminopurines + 2-aminopurines + + + galactose phosphate + . + D-galactose phosphates + galactose phosphates + CHEBI:galactose phosphate + galactose phosphate + CHEBI:20960 + + + . + OC[C@H]1O[C@@H](O[*])[C@H](O)[C@@H](O)[C@H]1O + CHEBI:D-galactoside + D-Galactoside + D-galactoside + CHEBI:20961 + D-galactoside + D-galactosides + C6H11O6R + + + CHEBI:D-glucose monophosphate + D-glucose monophosphate + CHEBI:21006 + D-glucose monophosphate + D-glucose monophosphates + C6H13O9P + + + . + glucose phosphate + glucose phosphates + CHEBI:glucose phosphate + CHEBI:21008 + D-glucose phosphates + + + CHEBI:21037 + aldohexose phosphate + CHEBI:aldohexose phosphate + aldohexose phosphate + aldohexose phosphates + . + + + D-mannose phosphates + mannose phosphate + mannose phosphates + CHEBI:mannose phosphate + CHEBI:21060 + . + + + glycosylamines + N-glycosyl compound + "A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond." [] + N-glycosyl compounds + glycosylamine + . + N-glycoside + CHEBI:N-glycosyl compound + CHEBI:21731 + N-glycosides + + + acridines + CHEBI:22213 + acridines + CHEBI:acridines + + + CHEBI:22216 + acrylamides + acrylamides + "An enamide which is acrylamide or a derivative of acrylamide obtained by replacement of one or more of its hydrogens." [] + CHEBI:acrylamides + + + acyl groups + . + CHEBI:22221 + groupe acyle + "An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids." [] + alkanoyl + acyl group + alkanoyl group + acyl group + CHEBI:acyl group + + + CHEBI:22251 + adenosine bisphosphates + CHEBI:adenosine bisphosphate + adenosine bisphosphate + + + CHEBI:adenosine phosphate + adenosine phosphates + adenosine phosphate + CHEBI:22256 + + + adenosines + CHEBI:22260 + CHEBI:adenosines + adenosines + + + aldonates + aldonate + . + CHEBI:22299 + CHEBI:aldonate + aldonate + + + . + Alkaloid + alcaloide + CHEBI:alkaloid + "Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids." [] + alkaloid + CHEBI:22315 + alkaloids + alcaloides + Alkaloide + + + alkanesulfonates + O3RS + alkanesulfonate + CHEBI:22318 + an alkanesulfonate + CHEBI:alkanesulfonate + OS(=O)(=O)C[*] + + + "A univalent group -CnH2n+1 derived from an alkane by removal of a hydrogen atom from any carbon atom." [] + grupo alquilo + grupos alquilo + groupe alkyle + CHEBI:22323 + alkyl group + alkyl group + alkyl groups + CHEBI:alkyl group + . + + + (C6H10O5)n + alpha-D-Glucan + CHEBI:22385 + CHEBI:alpha-D-glucan + alpha-D-glucan + alpha-D-glucans + + + CHEBI:22478 + CHEBI:amino alcohol + aminoalcohols + "An alcohol containing an amino functional group in addition to the alcohol-defining hydroxy group." [] + amino alcohol + amino alcohols + . + aminoalcohol + + + CHEBI:22479 + amino cyclitols + aminoglycosides + amino cyclitol glycoside + amino cyclitol glycoside + amino cyclitol glycosides + CHEBI:amino cyclitol glycoside + . + + + CHEBI:22506 + aminoglycan + CHEBI:aminoglycan + aminoglycans + + + . + CHEBI:aminoglycoside antibiotic + CHEBI:22507 + aminoglycoside antibiotics + aminoglycoside antibiotic + + + CHEBI:22527 + aminopurine + aminopurines + CHEBI:aminopurine + "Any purine having at least one amino substituent." [] + + + CHEBI:anion + anions + aniones + Anion + anion + . + Anionen + anion + "A monoatomic or polyatomic species having one or more elementary charges of the electron." [] + CHEBI:22563 + + + ansamycin + CHEBI:22565 + ansamycins + CHEBI:ansamycin + + + CHEBI:22580 + anthracenequinones + anthraquinone + CHEBI:anthraquinone + anthraquinones + + + . + arabinoside + CHEBI:arabinoside + arabinoside + CHEBI:22601 + arabinosides + + + CHEBI:22632 + arsenic molecular entity + arsenic molecular entity + arsenic compounds + arsenic molecular entities + CHEBI:arsenic molecular entity + . + + + arenecarboxamide + "A monocarboxylic acid amide in which the amide linkage is bonded directly to an arene ring system." [] + arenecarboxamides + CHEBI:arenecarboxamide + CHEBI:22645 + + + CHEBI:barbiturate anion + . + CHEBI:22691 + barbiturate anion + barbiturate anions + barbiturates + + + "Members of the class of pyrimidones consisting of pyrimidine-2,4,6(1H,3H,5H)-trione (barbituric acid) and its derivatives. Largest group of the synthetic sedative/hypnotics, sharing a characteristic six-membered ring structure." [] + barbiturates + barbiturates + . + CHEBI:22693 + CHEBI:barbiturates + barbituric acids + + + benzamides + CHEBI:benzamides + CHEBI:22702 + benzamides + + + trihydroxybenzenes + "A triol in which three hydroxy groups are substituted onto a benzene ring." [] + benzene triols + CHEBI:benzenetriol + benzenetriols + benzenetriol + CHEBI:22707 + + + benzenes + benzenes + CHEBI:22712 + CHEBI:benzenes + "Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives." [] + + + CHEBI:benzimidazoles + "An organic heterocyclic compound containing a benzene ring fused to an imidazole ring." [] + benzimidazoles + CHEBI:22715 + benzimidazoles + . + + + benzoates + CHEBI:benzoates + "A monocarboxylic acid anion obtained by deprotonation of the carboxy group of any benzoic acid." [] + benzoates + benzoate anion + CHEBI:22718 + + + "A group of heterocyclic compounds consisting of a benzene ring fused to a diazepine ring." [] + . + benzodiazepines + CHEBI:22720 + benzodiazepine + CHEBI:benzodiazepine + + + benzoic acids + CHEBI:benzoic acids + benzoic acids + "Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group." [] + CHEBI:22723 + + + benzopyrans + CHEBI:benzopyran + benzopyran + CHEBI:22727 + + + benzopyrrole + benzopyrroles + CHEBI:22728 + CHEBI:benzopyrrole + + + benzylic alcohols + benzylic alcohol + CHEBI:22743 + CHEBI:benzyl alcohols + benzyl alcohols + "Compounds containing a phenylmethanol skeleton." [] + benzyl alcohols + + + OC[C@H]1O[C@@H](O[*])[C@H](O)[C@@H](O)[C@@H]1O + . + beta-D-glucoside + beta-D-Glucoside + beta-D-glucosides + beta-D-glucoside + C6H11O6R + CHEBI:22798 + CHEBI:beta-D-glucoside + + + amino-acid betaine + amino-acid betaines + . + "Any amino acid-derived zwitterion - such as glycine betaine (N,N,N-trimethylammonioacetate) - in which the ammonium nitrogen carries three methyl substituents." [] + CHEBI:amino-acid betaine + CHEBI:22860 + betaines + amino acid betaines + + + "A sodium salt of the conjugate of any bile acid with either glycine or taurine." [] + CHEBI:bile salt + InChI=1S/C24H40O5/c1-13(4-7-21(28)29)16-5-6-17-22-18(12-20(27)24(16,17)3)23(2)9-8-15(25)10-14(23)11-19(22)26/h13-20,22,25-27H,4-12H2,1-3H3,(H,28,29)/t13?,14-,15+,16?,17?,18?,19+,20-,22?,23?,24?/m0/s1 + InChIKey=BHQCQFFYRZLCQQ-UMZBRFQRSA-N + CC(CCC(O)=O)C1CCC2C3[C@H](O)C[C@@H]4C[C@H](O)CCC4(C)C3C[C@H](O)C12C + Bile acid + bile salts + CHEBI:22868 + bile salt + . + + + CHEBI:22885 + biotinyl + biotinyl group + C10H15N2O2S + biotinoyl + biotinyl group + CHEBI:biotinyl group + + + biphenyls + "Benzenoid aromatic compounds containing two phenyl or substituted-phenyl groups which are joined together by a single bond." [] + biphenyls + CHEBI:22888 + CHEBI:biphenyls + + + CHEBI:bleomycin + "A glycopeptide produced by the bacterium Streptomyces verticillus. The term, 'bleomycin' refers to a family of structurally related compounds. When used as an anti-cancer agent, the chemotherapeutical forms are primarily bleomycin A2 and B2." [] + bleomycin + CHEBI:22907 + bleomycins + + + "Salts and esters of boric acid." [] + Borat + borates + borates + . + CHEBI:borates + CHEBI:22910 + + + CHEBI:boron molecular entity + . + CHEBI:22916 + boron compounds + boron molecular entities + boron molecular entity + boron molecular entity + + + branched chain amino acids + branched-chain amino acid + "Any amino acid in which the parent hydrocarbon chain has one or more alkyl substituents" [] + CHEBI:branched-chain amino acid + CHEBI:22918 + + + . + CHEBI:bromide salt + CHEBI:22925 + bromides + bromide salt + bromide salts + + + bromine molecular entity + CHEBI:bromine molecular entity + CHEBI:22928 + . + bromine molecular entities + bromine molecular entity + bromine compounds + + + "A diol that is a butanediol or a derivative of a butanediol." [] + CHEBI:butanediols + CHEBI:22944 + butanediols + butanediols + + + cadmium molecular entities + CHEBI:cadmium molecular entity + CHEBI:22978 + . + cadmium molecular entity + cadmium compounds + + + . + CHEBI:22985 + calcium compounds + calcium molecular entities + calcium molecular entity + calcium molecular entity + CHEBI:calcium molecular entity + + + CHEBI:23003 + carbamate ester + carbamate esters + carbamates + "Any ester of carbamic acid or its N-substituted derivatives." [] + . + CHEBI:carbamate ester + + + carbohydrate-containing antibiotic + CHEBI:23007 + carbohydrate-containing antibiotics + "Any carbohydrate derivative that exhibits antibiotic activity." [] + CHEBI:carbohydrate-containing antibiotic + + + CHEBI:carbon oxide + carbon oxides + CHEBI:23014 + oxides of carbon + carbon oxide + . + + + chelate-forming peptide + CHEBI:chelate-forming peptide + chelate-forming peptides + CHEBI:23089 + + + CHEBI:23114 + CHEBI:chloride salt + chloride salts + chloride salt + . + chlorides + + + "A compound derived from a hydrocarbon by replacing a hydrogen atom with a chlorine atom." [] + chlorinated hydrocarbons + CHEBI:chlorohydrocarbon + chlorohydrocarbons + CHEBI:23115 + chlorohydrocarbon + + + CHEBI:chlorine molecular entity + chlorine molecular entities + CHEBI:23117 + chlorine molecular entity + "A halogen molecular entity containing one or more atoms of chlorine." [] + . + chlorine compounds + + + CHEBI:23128 + chloroalkane + alkyl chlorides + chloroalkanes + chloroalkane + CHEBI:chloroalkane + "Any haloalkane that consists of an alkane substituted by at least one chloro group." [] + alkyl chloride + . + + + CHEBI:chlorobenzenes + . + "Any organochlorine compound containing a benzene ring which is substituted by one or more chlorines." [] + chlorobenzenes + CHEBI:23132 + + + CHEBI:23148 + CHEBI:chloromethanes + chloromethanes + chloromethanes + . + + + choline ester + C[N+](C)(C)CCOC([*])=O + choline esters + Choline ester + C6H13NO2R + CHEBI:23213 + CHEBI:choline ester + + + cholines + CHEBI:cholines + CHEBI:23217 + "A quaternary ammonium ion based on the choline ion and its substituted derivatives thereof." [] + + + bile acid taurine conjugate + . + CHEBI:23219 + "Amide of a bile acid with taurine." [] + bile acid taurine conjugates + CHEBI:bile acid taurine conjugate + + + chromenes + chromenes + CHEBI:chromenes + CHEBI:23232 + + + CHEBI:23239 + chromopeptide + chromopeptides + CHEBI:chromopeptide + + + CHEBI:cineole + cineoles + cineole + CHEBI:23243 + + + cobalamins + CHEBI:cobalamins + CHEBI:23334 + cobalamins + + + cobalt cation + Co + cobalt cation + CHEBI:23336 + cobalt cations + CHEBI:cobalt cation + + + cobamides + CHEBI:23341 + cobamides + CHEBI:cobamides + + + entidad molecular + CHEBI:molecular entity + entite moleculaire + "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity." [] + molecular entity + molecular entity + molekulare Entitaet + . + molecular entities + CHEBI:23367 + entidades moleculares + + + copper molecular entity + CHEBI:23377 + CHEBI:copper molecular entity + copper molecular entities + . + copper molecular entity + copper compounds + + + CHEBI:copper cation + CHEBI:23378 + copper cations + Cu cation + copper cation + Cu + copper cation + + + corrinoid hexaamides + CHEBI:23390 + cobalt-corrinoid hexaamides + cobalt-corrinoid hexaamide + CHEBI:cobalt-corrinoid hexaamide + + + "A metal sulfate compound having copper(2+) as the metal ion." [] + InChIKey=ARUVKPQLZAKDPS-UHFFFAOYSA-L + CuO4S + CHEBI:copper(II) sulfate + InChI=1S/Cu.H2O4S/c;1-5(2,3)4/h;(H2,1,2,3,4)/q+2;/p-2 + copper(II) sulfate + CHEBI:23414 + Cupric sulfate + cupric sulfate anhydrous + CuSO4 + copper(II) sulfate + Copper(II) sulfate + copper sulfate + [Cu++].[O-]S([O-])(=O)=O + copper(2+) sulfate + + + cyanides + CHEBI:23424 + cyanides + CHEBI:cyanides + "Salts and C-organyl derivatives of hydrogen cyanide, HC#N." [] + . + + + . + CHEBI:cyclic amide + cyclic amide + CHEBI:23443 + Cyclic amide + cyclic amide + cyclic amides + + + CHEBI:cyclic nucleotide + nucleoside cyclic phosphate + cyclic nucleotide + cyclic nucleotides + CHEBI:23447 + + + cyclic oligosaccharide + cyclic oligosaccharides + CHEBI:23448 + CHEBI:cyclic oligosaccharide + + + peptide cyclique + CHEBI:23449 + Cyclopeptid + cyclic peptide + Zyklopeptid + peptido ciclico + CHEBI:cyclic peptide + cyclic peptides + + + CHEBI:cyclitol phosphate + . + CHEBI:23450 + cyclitol phosphate + cyclitol phosphates + + + cyclitols + "A polyol consisting of a cycloalkane containing at least three hydroxy groups, each attached to a different ring carbon atom." [] + CHEBI:cyclitol + CHEBI:23451 + . + cyclitol + + + CHEBI:cyclodextrin + cyclodextrin + "A macrocycle composed of five or more D-glucopyranose units bonded via (1->4)-linkages." [] + CHEBI:23456 + cyclodextrins + + + cyclohexanones + CHEBI:cyclohexanones + "Any alicyclic ketone based on a cyclohexane skeleton and its substituted derivatives thereof." [] + CHEBI:23482 + cyclohexanones + + + "An amino acid derivative resulting from reaction of cysteine at the amino group, carboxy group, or thiol group, or from the replacement of any hydrogen of cysteine by a heteroatom. The definition normally excludes peptides containing cysteine residues." [] + cysteine derivative + cysteine derivatives + CHEBI:cysteine derivative + CHEBI:23509 + cysteine derivative + + + CHEBI:deoxyribonucleoside + deoxyribonucleosides + deoxyribonucleoside + CHEBI:23636 + + + CHEBI:23677 + CHEBI:diazole + diazoles + diazole + "An azole that is either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring." [] + + + "A compound that contains two hydroxy groups, generally assumed to be, but not necessarily, alcoholic. Aliphatic diols are also called glycols." [] + CHEBI:diol + diols + diols + CHEBI:23824 + diol + + + . + diterpenoides + CHEBI:diterpenoid + CHEBI:23849 + "Any terpenoid derived from a diterpene. The term includes compounds in which the C20 skeleton of the parent diterpene has been rearranged or modified by the removal of one or more skeletal atoms (generally methyl groups)." [] + diterpenoids + C20 isoprenoids + diterpenoid + + + CHEBI:dithiol + dithiols + CHEBI:23853 + dithiol + + + . + icosanoid + eicosanoid + eicosanoids + CHEBI:23899 + icosanoid + "Any member of the group of signalling molecules arising from oxidation of the three C20 essential fatty acids (EFAs) icosapentaenoic acid (EPA), arachidonic acid (AA) and dihomo-gamma-linolenic acid (DGLA)." [] + CHEBI:icosanoid + icosanoids + + + CHEBI:monoatomic anion + monoatomic anions + monoatomic anion + . + CHEBI:23905 + + + CHEBI:monoatomic cation + . + CHEBI:23906 + monoatomic cation + monoatomic cations + + + CHEBI:23965 + ESTRADIOL + oestradiol + C18H24O2 + estradiol + [H][C@]12CC[C@]3(C)C(O)CC[C@@]3([H])[C@]1([H])CCc1cc(O)ccc21 + InChI=1S/C18H24O2/c1-18-9-8-14-13-5-3-12(19)10-11(13)2-4-15(14)16(18)6-7-17(18)20/h3,5,10,14-17,19-20H,2,4,6-9H2,1H3/t14-,15-,16+,17?,18+/m1/s1 + estra-1,3,5(10)-triene-3,17-diol + InChIKey=VOXZDWNPVJITMN-WKUFJEKOSA-N + CHEBI:estradiol + (5beta,9beta,10alpha,13alpha,14beta)-estrane-3,17-dione + "A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17." [] + estradiols + + + "Any diol that is ethane or substituted ethane carrying two hydroxy groups." [] + CHEBI:ethanediol + ethanediols + ethanediol + CHEBI:23976 + + + CHEBI:ethanolamines + CHEBI:23981 + ethanolamine + . + ethanolamines + + + ethanols + "Any primary alcohol based on an ethanol skeleton." [] + CHEBI:23982 + ethanols + CHEBI:ethanols + + + ethyl ester + carboxylic acid ethyl ester + CHEBI:ethyl ester + C3H5O2R + "Any carboxylic ester resulting from the formal condensation of the carboxy group of a carboxylic acid with ethanol." [] + ethyl esters + ethyl carboxylate + CHEBI:23990 + ethyl carboxylates + CCOC([*])=O + carboxylic acid ethyl esters + + + InChI=1S/C3H7N3O2/c1-2-6(5-8)3(4)7/h2H2,1H3,(H2,4,7) + ENU + 1-Ethyl-1-nitrosourea + N-Ethyl-N-nitroso-urea + Aethylnitroso-harnstoff + CHEBI:N-ethyl-N-nitrosourea + 1-(Aminocarbonyl)-1-ethyl-2-oxohydrazine + Ethyl nitrosourea + CCN(N=O)C(N)=O + CHEBI:23995 + InChIKey=FUSGACRLAFQQRL-UHFFFAOYSA-N + N-Ethylnitrosourea + NEU + N-Ethyl-N-nitroso carbamide + C3H7N3O2 + N-ethyl-N-nitrosourea + "A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups." [] + 1-ethyl-1-nitrosourea + + + eumelanin + eumelanin + CHEBI:eumelanin + CHEBI:24009 + + + . + fluorides + CHEBI:24060 + fluoride salt + fluoride salts + CHEBI:fluoride salt + + + fluorine molecular entities + fluorine molecular entity + fluorine compounds + CHEBI:fluorine molecular entity + fluorine molecular entity + CHEBI:24062 + . + + + "Amides with the general formula R(1)R(2)NCHO (R(1) and R(2) can be H)." [] + CHEBI:24079 + CHEBI:formamides + formamides + . + + + CHEBI:24163 + galactoside + galactosides + . + galactoside + CHEBI:galactoside + + + O[C@@H]1[C@@H](COC(=O)c2cc(O)c(O)c(O)c2)O[C@@H](OC(=O)c2cc(O)c(O)c(O)c2)[C@H](O)[C@H]1OC(=O)c1cc(O)c(O)c(O)c1 + CHEBI:gallotannin + CHEBI:24182 + InChIKey=RNKMOGIPOMVCHO-SJMVAQJGSA-N + "A class of hydrolysable tannins obtained by condensation of the carboxy group of gallic acid (and its polymeric derivatives) with the hydroxy groups of a monosaccharide (most commonly glucose)." [] + gallotannins + InChI=1S/C27H24O18/c28-11-1-8(2-12(29)18(11)34)24(39)42-7-17-21(37)23(44-25(40)9-3-13(30)19(35)14(31)4-9)22(38)27(43-17)45-26(41)10-5-15(32)20(36)16(33)6-10/h1-6,17,21-23,27-38H,7H2/t17-,21-,22-,23+,27+/m1/s1 + 1,3,6-Tri-o-galloyl-beta-D-glucose + gallotannin + + + gamma-glutamylcysteine + gamma-glutamylcysteines + CHEBI:gamma-glutamylcysteine + CHEBI:24195 + + + . + "Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood." [] + glucocorticoid + glucocorticoids + CHEBI:24261 + CHEBI:glucocorticoid + + + glucosides + glucoside + . + CHEBI:glucoside + CHEBI:24278 + + + CHEBI:24323 + glutamyl-L-amino acid + "A dipeptide in which one of the amino acid residues is glutamine." [] + glutamyl-L-amino acids + CHEBI:glutamyl-L-amino acid + + + CHEBI:24337 + "Any organonitrogen compound derived from the Glu-Cys-Gly tripeptide glutathione." [] + glutathione derivative + CHEBI:glutathione derivative + glutathione derivatives + + + CHEBI:24347 + CHEBI:glycerates + glycerates + glycerates + 2,3-dihydroxypropanoate + . + + + CHEBI:glycine derivative + "A proteinogenic amino acid derivative resulting from reaction of glycine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom." [] + CHEBI:24373 + glycine derivative + glycine derivatives + + + glycogens + CHEBI:24384 + glycogens + CHEBI:glycogens + + + "Any carbohydrate derivative that consists of glycan moieties covalently attached to the side chains of the amino acid residues that constitute the peptide." [] + CHEBI:glycopeptide + CHEBI:24396 + glycopeptide + glycopeptides + + + O-glycoside + O-glycosides + glycosides + glycosides + . + glycoside + CHEBI:24400 + CHEBI:glycoside + "A glycosyl compound resulting from the attachment of a glycosyl group to a non-acyl group RO-, RS-, RSe-, etc. The bond between the glycosyl group and the non-acyl group is called a glycosidic bond. By extension, the terms N-glycosides and C-glycosides are used as class names for glycosylamines and for compounds having a glycosyl group attached to a hydrocarbyl group respectively. These terms are misnomers and should not be used. The preferred terms are glycosylamines and C-glycosyl compounds, respectively." [] + + + glycosyl glycoside + CHEBI:glycosyl glycoside + . + CHEBI:24407 + "Any disaccharide in which the two monosaccharide components are connected by a glycosidic linkage between their anomeric centres." [] + glycosyl glycosides + glycosyl glycoside + + + "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances." [] + chemical entity + . + grouped_by_chemistry + chemical entity + CHEBI:chemical entity + CHEBI:24431 + + + "A defined linked collection of atoms or a single atom within a molecular entity." [] + groupe + grupo + grupos + group + Gruppe + . + group + CHEBI:24433 + CHEBI:group + Rest + + + guanidines + CHEBI:guanidines + "Any organonitrogen compound containing a carbamimidamido (guanidino) group. Guanidines have the general structure (R(1)R(2)N)(R(3)R(4)N)C=N-R(5) and are related structurally to amidines and ureas." [] + CHEBI:24436 + guanidines + + + CHEBI:24469 + alkyl halide + CHEBI:haloalkane + haloalkane + "A compound derived from an alkane by replacing a hydrogen atom with a halogen atom." [] + alkyl halides + haloalkanes + . + + + CHEBI:halogen molecular entity + halogen molecular entity + halogen molecular entity + . + halogen compounds + halogen molecular entities + CHEBI:24471 + + + halohydrocarbon + CHEBI:halohydrocarbon + halogenated hydrocarbons + "A compound derived from a hydrocarbon by replacing a hydrogen atom with a halogen atom." [] + halohydrocarbons + CHEBI:24472 + + + CHEBI:24505 + heparins + heparins + CHEBI:heparins + + + heterocyclic antibiotic + CHEBI:heterocyclic antibiotic + heterocyclic antibiotics + CHEBI:24531 + + + organic heterocyclic compound + . + organic heterocyclic compounds + CHEBI:24532 + "A cyclic compound having as ring members atoms of carbon and at least of one other element." [] + organic heterocycle + CHEBI:organic heterocyclic compound + + + heterodetic cyclic peptides + CHEBI:heterodetic cyclic peptide + peptido ciclico heterodetico + . + heterodetic cyclic peptide + CHEBI:24533 + heterodetic cyclic peptide + "A heterodetic cyclic peptide is a peptide consisting only of amino-acid residues, but in which the linkages forming the ring are not solely peptide bonds; one or more is an isopeptide, disulfide, ester, or other bond." [] + peptide cyclique heterodetique + + + hexitol + . + CHEBI:hexitol + hexitol + hexitols + CHEBI:24583 + + + homocysteines + CHEBI:24610 + homocysteine derivatives + homocysteine derivative + CHEBI:homocysteines + homocysteines + + + CHEBI:24613 + peptide cyclique homodetique + CHEBI:homodetic cyclic peptide + peptido ciclico homodetico + homodetic cyclic peptide + "A homodetic cyclic peptide is a cyclic peptide in which the ring consists solely of amino-acid residues in peptide linkages." [] + homodetic cyclic peptides + . + homodetic cyclic peptide + + + Kohlenwasserstoffe + hidrocarburos + . + CHEBI:24632 + CHEBI:hydrocarbon + hidrocarburo + hydrocarbon + Kohlenwasserstoff + hydrocarbon + "A compound consisting of carbon and hydrogen only." [] + hydrocarbure + hydrocarbons + + + CHEBI:hydroquinones + "Benzenediol compounds having the hydroxy substituents in the 1- and 4-positions." [] + hydroquinones + CHEBI:24646 + + + . + N-hydroxy-amides + N-hydroxy amide + N-hydroxyamide + N-hydroxyamides + hydroxamic acid + N-hydroxy-amide + N-hydroxy amides + CHEBI:hydroxamic acid + "A compound, RkE(=O)lNHOH, derived from an oxoacid RkE(=O)l(OH) (l =/= 0) by replacing -OH with -NHOH, and derivatives thereof. Specific examples of hydroxamic acids are preferably named as N-hydroxy amides." [] + hydroxamic acids + CHEBI:24650 + hydroxamic acids + + + CHEBI:24651 + hydroxides + . + CHEBI:hydroxides + "Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-))." [] + hydroxides + + + . + CHEBI:24654 + hydroxy fatty acids + CHEBI:hydroxy fatty acid + hydroxy fatty acid + "Any fatty acid carrying one or more hydroxy substituents." [] + + + hydroxy-amino acids + "A non-proteinogenic alpha-amino acid bearing one or more hydroxy groups at unspecified positions." [] + hydroxy-amino acid + CHEBI:hydroxy-amino acid + CHEBI:24662 + + + hydroxy-5beta-cholanic acid + hydroxy-5beta-cholanic acids + . + "Any member of the class of 5beta-cholanic acids carrying at least one hydroxy group at unspecified position." [] + CHEBI:24663 + CHEBI:hydroxy-5beta-cholanic acid + + + "Any carboxylic acid with at least one hydroxy group." [] + hydroxy carboxylic acids + CHEBI:hydroxy carboxylic acid + CHEBI:24669 + hydroxyacids + hydroxy carboxylic acid + + + "Any compound comprising a butyric acid core carrying at least one hydroxy substituent." [] + C4H8O3 + hydroxybutyric acid + hydroxybutanoic acids + CHEBI:hydroxybutyric acid + CHEBI:24684 + hydroxybutanoic acid + hydroxybutyric acids + + + CHEBI:24734 + hydroxyphenylalanines + hydroxyphenylalanine + CHEBI:hydroxyphenylalanine + + + hydroxytoluenes + hydroxytoluene + CHEBI:24751 + CHEBI:hydroxytoluene + "Any member of the class of toluenes carrying one or more hydroxy substituents." [] + hydroxytoluene + + + hygromycin + CHEBI:24753 + CHEBI:hygromycin + hygromycins + + + imidazoles + CHEBI:imidazoles + "A five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton." [] + imidazoles + CHEBI:24780 + + + imide + CHEBI:24782 + imide + CHEBI:imide + imides + + + indolyl carbohydrates + indolyl carbohydrate + CHEBI:indolyl carbohydrate + CHEBI:24821 + indole-carbohydrate conjugates + + + CHEBI:indoles + "Any compound containing an indole skeleton." [] + indoles + CHEBI:24828 + indoles + + + oxacids + . + oxoacid + CHEBI:24833 + oxiacids + oxo acid + inorganic acids + oxoacid + oxoacids + CHEBI:oxoacid + oxy-acids + oxyacids + "A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons)." [] + + + . + CHEBI:inorganic anion + inorganic anion + CHEBI:24834 + inorganic anions + + + CHEBI:inorganic molecular entity + inorganics + inorganic entity + . + inorganic compounds + inorganic molecular entities + CHEBI:24835 + inorganic molecular entity + anorganische Verbindungen + "A molecular entity that contains no carbon." [] + + + CHEBI:inorganic oxide + inorganic oxides + CHEBI:24836 + inorganic oxide + + + inorganic peroxides + inorganic peroxide + CHEBI:inorganic peroxide + "Compounds of structure ROOR' in which R and R' are inorganic groups." [] + CHEBI:24837 + inorganic peroxide + + + "Any phosphate that contains no carbon atom." [] + CHEBI:inorganic phosphate + inorganic phosphate + CHEBI:24838 + inorganic phosphates + + + inorganic salts + CHEBI:inorganic salt + inorganic salt + . + anorganisches Salz + CHEBI:24839 + + + inorganic sulfates + inorganic sulfate salts + CHEBI:inorganic sulfate salt + CHEBI:24840 + inorganic sulfate salt + + + . + CHEBI:inositol phosphate + inositol phosphate + inositol phosphates + CHEBI:24846 + + + . + iodide salt + iodide salts + iodides + CHEBI:iodide salt + CHEBI:24858 + + + iodine molecular entities + CHEBI:24860 + iodine molecular entity + CHEBI:iodine molecular entity + . + iodine molecular entity + iodine compounds + + + CHEBI:salt + sels + sel + Salz + salts + sal + Salze + "A salt is an assembly of cations and anions." [] + ionic compound + ionic compounds + CHEBI:24866 + salt + sales + salt + . + + + CHEBI:24867 + CHEBI:monoatomic ion + ionic elements + monoatomic ions + monoatomic ion + . + + + organic salts + CHEBI:organic salt + organic salt + CHEBI:24868 + . + organisches Salz + + + ions + . + "A molecular entity having a net electric charge." [] + CHEBI:ion + iones + ion + CHEBI:24870 + ion + Ion + Ionen + + + CHEBI:24873 + iron molecular entity + iron molecular entities + iron molecular entity + . + CHEBI:iron molecular entity + iron compounds + + + isoprenoids + CHEBI:24913 + isoprenoid + . + isoprenoid + CHEBI:isoprenoid + "Any lipid formally derived from isoprene (2-methylbuta-1,3-diene), the skeleton of which can generally be discerned in repeated occurrence in the molecule. The skeleton of isoprenoids may differ from strict additivity of isoprene units by loss or shift of a fragment, commonly a methyl group. The class includes both hydrocarbons and oxygenated derivatives." [] + isoprenoids + + + kanamycins + . + CHEBI:kanamycins + CHEBI:24951 + kanamycins + + + CHEBI:ketoaldehyde + ketoaldehydes + ketoaldehyde + "Any compound that has an aldehydic and ketonic group in the same molecule." [] + CHEBI:24960 + + + ketohexose biphosphates + ketohexose bisphosphate + . + ketohexose bisphosphate + ketohexose bisphosphates + CHEBI:ketohexose bisphosphate + CHEBI:24970 + + + ketohexose phosphate + ketohexose phosphates + . + CHEBI:24972 + CHEBI:ketohexose phosphate + ketohexose phosphate + + + CHEBI:24995 + CHEBI:lactam + Laktam + lactam + "Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring." [] + lactams + Laktame + . + lactam + lactams + + + lactate + MeCH(OH)CO2 anion + C3H5O3 + b-lactate + 2-hydroxypropanoic acid, ion(1-) + 2-hydroxypropanoate + lactate + InChIKey=JVTAAEKCZFNVCJ-UHFFFAOYSA-M + 2-hydroxypropionate + "A hydroxy monocarboxylic acid anion that is the conjugate base of lactic acid, arising from deprotonation of the carboxy group." [] + InChI=1S/C3H6O3/c1-2(4)3(5)6/h2,4H,1H3,(H,5,6)/p-1 + CHEBI:24996 + CHEBI:lactate + beta-lactate + CC(O)C([O-])=O + + + "Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring." [] + lactonas + lactone + Lacton + CHEBI:lactone + lactones + Laktone + lactone + . + Lakton + lactona + CHEBI:25000 + + + CHEBI:25105 + "A macrocyclic lactone with a ring of twelve or more members which exhibits antibiotic activity." [] + macrolide antibiotics + CHEBI:macrolide antibiotic + macrolide antibiotic + . + Makrolidantibiotika + + + CHEBI:macrolide + "A macrocyclic lactone with a ring of twelve or more members derived from a polyketide." [] + macrolide + CHEBI:25106 + macrolides + . + macrolide + Makrolid + macrolides + + + magnesium molecular entities + magnesium molecular entity + magnesium molecular entity + CHEBI:25108 + CHEBI:magnesium molecular entity + . + magnesium compounds + + + Agarose + CHEBI:2511 + CHEBI:agarose + agarose + "A linear polysaccharide made up from alternating D-galactose and 3,6-anhydro-alpha-L-galactopyranose residues joined by alpha-(1->3)- and beta-(1->4)-linkages." [] + [4)-3,6-An-alpha-L-Galp-(1->3)-beta-D-Galp-(1->]n + (1->4)-3,6-anhydro-alpha-L-galactopyranosyl-(1->3)-beta-D-galactopyranan + Sepharose + C12H20O10(C12H18O9)n + + + CHEBI:25136 + "Any short-chain fatty acyl-CoA in which the the fatty acid specified is malonic acid or its derivatives." [] + malonyl-CoAs + CHEBI:malonyl-CoAs + + + Melanin + melanin + CHEBI:25179 + melanins + CHEBI:melanin + + + CHEBI:p-menthane monoterpenoid + p-menthane monoterpenoid + CHEBI:25186 + menthanes + p-menthane monoterpenoids + + + InChI=1S/C4H10O2S2/c5-3(1-7)4(6)2-8/h3-8H,1-2H2 + OC(CS)C(O)CS + 1,4-disulfanylbutane-2,3-diol + CHEBI:25189 + 1,4-dimercapto-2,3-butanediol + CHEBI:1,4-dimercaptobutane-2,3-diol + 1,4-dimercaptobutane-2,3-diol + InChIKey=VHJLVAABSRFDPM-UHFFFAOYSA-N + "A glycol that is butane-2,3-diol in which a hydrogen from each of the methyl groups is replaced by a thiol group." [] + 1,4-dimercaptobutane-2,3-diol + C4H10O2S2 + + + . + CHEBI:metal cation + a metal cation + metal cations + CHEBI:25213 + metal cation + + + 2-methyl-2-propenoate + CHEBI:methacrylate + "A monocarboxylic acid anion that is obtained by removal of a proton from the carboxylic acid group of methacrylic acid." [] + methacrylate(1-) + C4H5O2 + InChI=1S/C4H6O2/c1-3(2)4(5)6/h1H2,2H3,(H,5,6)/p-1 + CHEBI:25218 + 2-methyl-2-propenoic acid, ion(1-) + methacrylate + methacrylate anion + 2-methylprop-2-enoate + CC(=C)C([O-])=O + InChIKey=CERQOIWHTDAKMF-UHFFFAOYSA-M + methacrylate + + + CHEBI:25235 + . + monomethoxybenzene + CHEBI:monomethoxybenzene + methoxybenzenes + monomethoxybenzenes + "Compounds containing a benzene skeleton substituted with one methoxy group." [] + + + CHEBI:25248 + CHEBI:methyl ester + C2H3O2R + carboxylic acid methyl ester + "Any carboxylic ester resulting from the formal condensation of a carboxy group with methanol." [] + methyl ester + carboxylic acid methyl esters + COC([*])=O + + + CHEBI:methylxanthine + methylxanthines + methylxanthine + CHEBI:25348 + + + CHEBI:25357 + CHEBI:mitomycin + "A family of aziridine-containing natural products isolated from Streptomyces caespitosus or Streptomyces lavendulae." [] + mitomycins + mitomycin + + + CHEBI:25362 + "A molecule all atoms of which have the same atomic number." [] + elemental molecule + . + homoatomic molecule + CHEBI:elemental molecule + homoatomic molecules + + + CHEBI:25367 + neutral molecular compounds + . + molecules + molecule + "Any polyatomic entity that is an electrically neutral entity consisting of more than one atom." [] + Molekuel + molecule + molecula + CHEBI:molecule + + + . + monoamine molecular messenger + CHEBI:monoamine molecular messenger + monamines + "A group of neurotransmitters and neuromodulators that contain one amino group that is connected to an aromatic ring by ethylene group (-CH2-CH2-). Monoamines are derived from the aromatic amino acids phenylalanine, tyrosine, histidine and tryptophan." [] + monoamine + CHEBI:25375 + monoamines + + + monocarboxylic acid + CHEBI:monocarboxylic acid + monocarboxylic acid + monocarboxylic acids + . + CHEBI:25384 + "An oxoacid containing a single carboxy group." [] + + + CHEBI:monoterpenoid + . + CHEBI:25409 + monoterpenoids + "Any terpenoid derived from a monoterpene. The term includes compounds in which the C10 skeleton of the parent monoterpene has been rearranged or modified by the removal of one or more skeletal atoms (generally methyl groups)." [] + monoterpenoid + + + [*+] + monoatomic monocation + CHEBI:25414 + monovalent cation + monovalent inorganic cations + . + CHEBI:monoatomic monocation + monoatomic monocations + + + . + myo-inositol phosphate + "An inositol phosphate in which the inositol component has myo-configuration." [] + myo-inositol phosphate + myo inositol phosphates + myo-inositol phosphates + CHEBI:myo-inositol phosphate + CHEBI:25448 + + + . + CHEBI:25450 + myo-inositol trisphosphates + CHEBI:myo-inositol trisphosphate + myo-inositol trisphosphate + + + CHEBI:25480 + naphthohydroquinone antibiotic + CHEBI:naphthohydroquinone antibiotic + naphthohydroquinone antibiotics + + + CHEBI:25523 + CHEBI:NADP + NADP + "Abbreviation for nicotinamide-adenine dinucleotide phosphate when its oxidation state is unknown or unspecified." [] + nicotinamide-adenine dinucleotide phosphate + + + CHEBI:25524 + CHEBI:NAD(P) + NAD(P) + "A coenzyme that may be NAD or NADP." [] + nicotinamide adenine dinucleotides + . + + + CHEBI:25527 + CHEBI:nicotinamide nucleotide + nicotinamide nucleotide + nicotinamide nucleotides + + + CHEBI:pyridinecarboxamide + pyridinecarboxamides + pyridinecarboxamide + "A member of the class of pyridines that is a substituted pyridine in which at least one of the substituents is a carboxamide or N-substituted caraboxamide group." [] + CHEBI:25529 + + + nitrobenzoic acids + CHEBI:25553 + nitrobenzoic acid + CHEBI:nitrobenzoic acid + "Any member of the class of benzoic acids with at least one nitro substituent attached to the benzene ring." [] + + + organonitrogen heterocyclic antibiotic + organonitrogen heterocyclic antibiotics + CHEBI:25558 + CHEBI:organonitrogen heterocyclic antibiotic + nitrogenous heterocyclic antibiotics + + + no metales + CHEBI:nonmetal atom + nonmetal atom + Nichtmetalle + . + no metal + non-metaux + non-metal + CHEBI:25585 + nonmetal + nonmetal + nonmetals + Nichtmetall + + + aldohexose 6-phosphate + Aldohexose 6-phosphate + C6H13O9P + CHEBI:2559 + CHEBI:aldohexose 6-phosphate + + + O[C@H]1[C@H]([*])O[C@H](COP(O)(O)=O)[C@H]1O + nucleoside phosphate + Nucleoside monophosphate + CHEBI:nucleoside phosphate + CHEBI:25608 + "A nucleobase-containing molecular entity that is a nucleoside in which one or more of the sugar hydroxy groups has been converted into a mono- or poly-phosphate. The term includes both nucleotides and non-nucleotide nucleoside phosphates." [] + NMP + nucleoside phosphates + + + nucleotidyl groups + CHEBI:nucleotidyl group + CHEBI:25613 + nucleotidyl group + + + nylons + nylons + CHEBI:nylons + CHEBI:25614 + + + oligomycins + oligomycin + CHEBI:25675 + CHEBI:oligomycin + "Any of the 26-membered ring macrolides produced by Streptomyces species that can be toxic to other organisms through their ability to inhibit mitochondrial membrane-bound ATP synthases." [] + + + C2H4NO2R(C2H2NOR)n + CHEBI:oligopeptide + Oligopeptide + CHEBI:25676 + oligopeptides + oligopeptido + Oligopeptid + oligopeptide + oligopeptides + + + organic heteromonocyclic compounds + organic heteromonocyclic compound + CHEBI:organic heteromonocyclic compound + one-ring heterocyclic compounds + CHEBI:25693 + . + + + CHEBI:25696 + organic anion + organic anions + . + CHEBI:organic anion + + + "Any organic ion with a net positive charge." [] + organic cation + CHEBI:organic cation + CHEBI:25697 + . + organic cations + + + ethers + ethers + [*]O[*] + . + OR2 + ether + CHEBI:ether + ether + CHEBI:25698 + "An organooxygen compound with formula ROR, where R is not hydrogen." [] + + + organic ion + . + organic ions + CHEBI:25699 + CHEBI:organic ion + + + organic oxide + CHEBI:organic oxide + organic oxides + CHEBI:25701 + "An oxide in which the oxygen atom is bonded to a carbon atom." [] + + + organophosphate ester + CHEBI:organic phosphate + organophosphate esters + organic phosphate + organic phosphate + organic phosphate ester + . + organic phosphate esters + CHEBI:25703 + organic phosphates + + + CHEBI:25704 + organic sulfates + "Compounds of the general formula SO3HOR where R is an organyl group" [] + . + CHEBI:organic sulfate + organic sulfate + + + aliphatic alcohol + CHEBI:aliphatic alcohol + HOR + Aliphatic alcohol + O[*] + CHEBI:2571 + "An alcohol derived from an aliphatic compound." [] + an aliphatic alcohol + aliphatic alcohols + + + . + organophosphorus compound + "An organophosphorus compound is formally a compound containing at least one carbon-phosphorus bond, but the term is often extended to include esters and thioesters." [] + organophosphorus compound + CHEBI:25710 + CHEBI:organophosphorus compound + organophosphorus compounds + + + oxide + oxides + . + "An oxide is a chemical compound of oxygen with other chemical elements." [] + oxide + CHEBI:25741 + CHEBI:oxide + + + oxo carboxylic acid + oxo carboxylic acids + oxo acids + . + "Any compound that has an aldehydic or ketonic group as well as a carboxylic acid group in the same molecule." [] + CHEBI:oxo carboxylic acid + CHEBI:25754 + oxo carboxylic acids + + + an unsaturated fatty acid + unsaturated fatty acid anion + "Any fatty acid anion containing at least one C-C unsaturated bond; formed by deprotonation of the carboxylic acid moiety." [] + CHEBI:unsaturated fatty acid anion + . + CHEBI:2580 + + + . + CHEBI:oxygen molecular entity + oxygen molecular entities + oxygen compounds + oxygen molecular entity + CHEBI:25806 + oxygen molecular entity + + + oxopurine + CHEBI:25810 + oxopurines + oxypurines + CHEBI:oxopurine + + + CHEBI:ozone + trioxygen + ozone + InChI=1S/O3/c1-3-2 + "An elemental molecule with formula O3. An explosive, pale blue gas (b.p. -112degreeC) that has a characteristic, pleasant odour, it is continuously produced in the upper atmosphere by the action of solar ultraviolet radiation on atmospheric oxygen. It is an antimicrobial agent used in the production of bottled water, as well as in the treatment of meat, poultry and other foodstuffs." [] + trioxygene + [O-][O+]=O + CHEBI:25812 + [OO2] + ozone + O3 + ozono + Trisauerstoff + InChIKey=CBENFWSGALASAD-UHFFFAOYSA-N + Ozon + + + penicillanic acids + CHEBI:penicillanic acids + CHEBI:25865 + penicillanic acids + + + aldopentose phosphate + . + pentose phosphates + aldopentose phosphate + CHEBI:25900 + aldopentose phosphates + CHEBI:aldopentose phosphate + + + . + peptide antibiotics + CHEBI:peptide antibiotic + CHEBI:25903 + peptide antibiotic + + + CHEBI:peptide hormone + polypeptide hormone + CHEBI:25905 + peptide hormones + . + peptide hormone + "Any peptide with hormonal activity in animals, whether endocrine, neuroendocrine, or paracrine." [] + + + [*]OO[*] + "Compounds of structure ROOR'." [] + a peroxide + O2R2 + CHEBI:peroxides + peroxides + CHEBI:25940 + peroxides + + + phenylalanine derivative + phenylalanine derivatives + CHEBI:25985 + CHEBI:phenylalanine derivative + "An amino acid derivative resulting from reaction of alanine at the amino group or the carboxy group, or from the replacement of any hydrogen of phenylalanine by a heteroatom. The definition normally excludes peptides containing phenylalanine residues." [] + + + CHEBI:phenylpropanoid + . + phenylpropanoid + "Any organic aromatic compound with a structure based on a phenylpropane skeleton. The class includes naturally occurring phenylpropanoid esters, flavonoids, anthocyanins, coumarins and many small phenolic molecules as well as their semi-synthetic and synthetic analogues. Phenylpropanoids are also precursors of lignin." [] + phenylpropanoids + CHEBI:26004 + + + phosphate + "Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom." [] + phosphates + CHEBI:26020 + . + CHEBI:phosphate + phosphates + + + phosphoamino acids + CHEBI:phosphoamino acid + CHEBI:26051 + phosphoamino acid + + + phosphoric acids + phosphoric acid derivatives + phosphoric acid derivative + CHEBI:phosphoric acid derivative + . + CHEBI:26079 + + + phosphorus molecular entity + CHEBI:phosphorus molecular entity + CHEBI:26082 + phosphorus molecular entities + phosphorus compounds + . + + + CHEBI:phytosteroid + phytosteroids + CHEBI:26124 + phytosteroid + + + "Sterols similar to cholesterol which occur in plants and vary only in carbon side chains and/or presence or absence of a double bond." [] + CHEBI:26125 + CHEBI:phytosterols + phytosterols + + + CHEBI:piperazines + CHEBI:26144 + piperazines + piperazines + + + CHEBI:26151 + piperidines + CHEBI:piperidines + piperidines + + + CHEBI:polyene antibiotic + "A family of antibiotics containing a conjugated polyene moiety, usuallly isolated from some species of Streptomyces." [] + polyene antibiotics + polyene antibiotic + . + CHEBI:26177 + + + polyketides + "Natural and synthetic compounds containing alternating carbonyl and methylene groups ('beta-polyketones'), biogenetically derived from repeated condensation of acetyl coenzyme A (via malonyl coenzyme A), and usually the compounds derived from them by further condensations. Considered by many to be synonymous with the less frequently used terms acetogenins and ketides." [] + polyketide + CHEBI:polyketide + . + polyketide + CHEBI:26188 + + + polyols + CHEBI:polyol + "A compound that contains two or more hydroxy groups." [] + . + CHEBI:26191 + polyol + + + . + polyphenol + CHEBI:polyphenol + polyphenols + CHEBI:26195 + "Members of the class of phenols that contain 2 or more benzene rings each of which is substituted by at least one hydroxy group." [] + + + polyunsaturated fatty acids + PUFA + PUFAs + polyunsaturated fatty acid + CHEBI:26208 + CHEBI:polyunsaturated fatty acid + "Any fatty acid containing more than one double bond. Acids in this group are reported to have cardioprotective effects; and levels are lowered in chronic fatigue syndrome." [] + + + potassium compounds + potassium molecular entity + . + potassium molecular entity + potassium molecular entities + CHEBI:26217 + CHEBI:potassium molecular entity + + + CHEBI:potassium salt + . + Kaliumsalze + potassium salts + potassium salt + Kaliumsalz + CHEBI:26218 + "Any alkali metal salt having potassium(1+) as the cation." [] + + + CHEBI:propanals + "An aldehyde based on a propanal skeleton and its derivatives." [] + propanals + propanals + CHEBI:26282 + + + propane-1,2-diols + CHEBI:26284 + propane-1,2-diols + CHEBI:propane-1,2-diols + + + propanediols + CHEBI:propanediol + propanediol + CHEBI:26288 + + + CHEBI:propanone + propanone + propanones + CHEBI:26292 + "A ketone that is propane carrying at least one oxo substituent." [] + + + "Naturally occurring compounds derived from the parent C20 acid, prostanoic acid." [] + prostaglandins + prostaglandin + CHEBI:prostaglandin + CHEBI:26333 + . + prostaglandin + prostaglandins + + + CHEBI:26338 + O[C@@H]1CC(=O)[C@H]([*])[C@H]1[*] + C5H6O2R2 + CHEBI:prostaglandins E + prostaglandins E + PGE + + + . + prostanoid + "The family of natural prostaglandins and prostaglandin-like compounds." [] + prostanoids + CHEBI:26347 + prostanoid + prostanoids + CHEBI:prostanoid + + + CHEBI:26385 + CHEBI:purine alkaloid + purine alkaloid + purine alkaloids + + + . + purine nucleobase + CHEBI:purine nucleobase + CHEBI:26386 + purine nucleobase + purine bases + purine nucleobases + + + CHEBI:26394 + CHEBI:purine nucleoside + . + purine nucleosides + purine nucleoside + purine nucleoside + + + CHEBI:26395 + CHEBI:purine nucleotide + purine nucleoside phosphate + "Any nucleotide that has a purine nucleobase." [] + purine nucleotides + purine nucleotide + + + purine ribonucleosides + CHEBI:26399 + purine ribonucleoside + CHEBI:purine ribonucleoside + + + purine ribonucleotides + "Any ribonucleotide that has a purine nucleobase." [] + purine ribonucleotide + CHEBI:26400 + CHEBI:purine ribonucleotide + + + a purine + purines + . + CHEBI:26401 + "A class of imidazopyrimidines that consists of purine and its substituted derivatives." [] + CHEBI:purines + + + puromycins + puromycins + CHEBI:26404 + CHEBI:puromycins + + + pyridine alkaloid + CHEBI:26416 + CHEBI:pyridine alkaloid + pyridine alkaloids + + + pyridines + CHEBI:26421 + "Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives." [] + CHEBI:pyridines + pyridines + + + CHEBI:pyrimidine nucleoside + pyrimidine nucleosides + CHEBI:26440 + N-D-Ribosylpyrimidine + pyrimidine nucleoside + + + pyrimidinecarboxylic acids + pyrimidinemonocarboxylic acid + pyrimidinemonocarboxylic acids + CHEBI:26447 + CHEBI:pyrimidinemonocarboxylic acid + + + . + "A nitrogen molecular entity that is electronically neutral but which contains a quaternary nitrogen." [] + CHEBI:26469 + quaternary nitrogen compounds + quaternary nitrogen compound + CHEBI:quaternary nitrogen compound + + + CHEBI:quinoline alkaloid + CHEBI:26509 + quinoline alkaloids + quinoline alkaloid + + + CHEBI:quinolines + "A class of aromatic heterocyclic compounds each of which contains a benzene ring ortho fused to carbons 2 and 3 of a pyridine ring." [] + quinolines + CHEBI:26513 + quinolines + + + Radikale + Radikal + "A molecular entity possessing an unpaired electron." [] + freies Radikal + CHEBI:26519 + free radical + radicales libres + radical libre + CHEBI:radical + . + radical + radicals + radical + + + "Molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers." [] + reactive oxygen species + . + CHEBI:reactive oxygen species + ROS + CHEBI:26523 + + + retinals + CHEBI:retinals + retinals + CHEBI:26534 + + + "A retinoid consisting of 3,7-dimethylnona-2,4,6,8-tetraenoic acid substituted at position 9 by a 2,6,6-trimethylcyclohex-1-en-1-yl group (geometry of the four exocyclic double bonds is not specified)." [] + CHEBI:retinoic acid + InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22) + CC(C=CC1=C(C)CCCC1(C)C)=CC=CC(C)=CC(O)=O + InChIKey=SHGAZHPCJJPHSC-UHFFFAOYSA-N + 3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid + C20H28O2 + CHEBI:26536 + retinoic acid + + + retinoid + retinoids + . + retinoid + CHEBI:26537 + CHEBI:retinoid + retinoids + "Oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof." [] + + + CHEBI:26561 + CHEBI:ribonucleotide + ribonucleotides + ribonucleotide + + + CHEBI:26562 + ribose phosphate + ribose phosphates + ribose phosphate + CHEBI:ribose phosphate + + + rifamycin + CHEBI:26580 + rifamycins + CHEBI:rifamycin + + + CHEBI:salicylates + "Any salt or ester arising from reaction of the carboxy group of salicylic acid, or any ester resulting from the condensation of the phenolic hydroxy group of salicylic acid with an organic acid." [] + salicylates + CHEBI:26596 + + + CHEBI:26605 + sapogenin glycosides + saponin + sapogenin glycoside + . + saponins + CHEBI:saponin + "A glycoside that is a compound containing one or more hydrophilic glycoside moieties combined with a lipophilic triterpenoid or steroid derivative. Found in particular abundance in plant species." [] + + + CHEBI:26606 + sapogenin + sapogenin + "Any organic polycyclic compound that is the aglycon moiety of a saponin; sapogenins may be steroids or triterpenoids." [] + CHEBI:sapogenin + sapogenins + + + saturated fatty acid + saturated fatty acids + CHEBI:26607 + "Any fatty acid containing no carbon to carbon multiple bonds. Known to produce adverse biological effects when ingested to excess." [] + CHEBI:saturated fatty acid + SFAs + saturated fatty acid + . + SFA + + + serine derivative + serine derivatives + CHEBI:serine derivative + CHEBI:26649 + "An amino acid derivative resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of serine by a heteroatom. The definition normally excludes peptides containing serine residues." [] + + + SCFAs + "An aliphatic monocarboxylic acid with a chain length of less than C6. If any non-hydrocarbon substituent is present, the compound is not normally regarded as a short-chain fatty acid." [] + short-chain fatty acid + SCFA + CH2OR + CHEBI:short-chain fatty acid + OC([*])=O + short-chain fatty acids + CHEBI:26666 + + + silicon compounds + CHEBI:silicon molecular entity + silicon molecular entity + . + silicon molecular entity + silicon molecular entities + CHEBI:26677 + + + CHEBI:26710 + CHEBI:sodium chloride + Kochsalz + [Na+].[Cl-] + cloruro sodico + halite + table salt + InChI=1S/ClH.Na/h1H;/q;+1/p-1 + common salt + natrii chloridum + rock salt + Natriumchlorid + salt + chlorure de sodium + ClNa + NaCl + sodium chloride + "An inorganic chloride salt having sodium(1+) as the counterion." [] + sodium chloride + InChIKey=FAPWRFPIFSIZLT-UHFFFAOYSA-M + + + sodium molecular entity + CHEBI:26712 + sodium molecular entities + . + sodium compounds + CHEBI:sodium molecular entity + + + "Any alkali metal salt having sodium(1+) as the cation." [] + Natriumsalze + CHEBI:26714 + CHEBI:sodium salt + sodium salts + sodium salt + Natriumsalz + . + + + CHEBI:26739 + sphingolipid + CHEBI:sphingolipid + sphingolipids + "Sphingolipids are a complex family of compounds that share a common structural feature, a sphingoid base backbone." [] + + + hormones steroides + Steroidhormone + CHEBI:steroid hormone + hormone steroide + hormonas esteroideas + steroid hormones + CHEBI:26764 + . + hormona esteroide + Steroidhormon + "Any steroid that acts as hormone." [] + steroid hormone + + + stilbenoid + CHEBI:stilbenoid + . + stilbenoids + CHEBI:26776 + "Any olefinic compound characterised by a 1,2-diphenylethylene backbone." [] + stilbenes + + + CHEBI:streptomycins + . + streptomycins + streptomycins + CHEBI:26788 + + + CHEBI:carbohydrate phosphate + sugar phosphates + CHEBI:26816 + carbohydrate phosphate + carbohydrate phosphates + + + "An ester of an alcohol and sulfuric acid." [] + sulfuric acid esters + sulfate ester + sulfate esters + sulfuric esters + sulfuric acid ester + O4SR2 + . + CHEBI:sulfuric ester + [*]OS(=O)(=O)O[*] + CHEBI:26819 + sulfuric ester + + + amphotericinum B + amphotericin B + InChIKey=APKFDSVGJQXUKY-INPOYWNPSA-N + CHEBI:2682 + CHEBI:amphotericin B + C47H73NO17 + amphotericin B + (1R,3S,5R,6R,9R,11R,15S,16R,17R,18S,19E,21E,23E,25E,27E,29E,31E,33R,35S,36R,37S)-33-[(3-amino-3,6-dideoxy-beta-D-mannopyranosyl)oxy]-1,3,5,6,9,11,17,37-octahydroxy-15,16,18-trimethyl-13-oxo-14,39-dioxabicyclo[33.3.1]nonatriaconta-19,21,23,25,27,29,31-heptaene-36-carboxylic acid + Liposomal Amphotericin B + amfotericina B + AMPH-B + Amphotericine B + amphotericine B + InChI=1S/C47H73NO17/c1-27-17-15-13-11-9-7-5-6-8-10-12-14-16-18-34(64-46-44(58)41(48)43(57)30(4)63-46)24-38-40(45(59)60)37(54)26-47(61,65-38)25-33(51)22-36(53)35(52)20-19-31(49)21-32(50)23-39(55)62-29(3)28(2)42(27)56/h5-18,27-38,40-44,46,49-54,56-58,61H,19-26,48H2,1-4H3,(H,59,60)/b6-5+,9-7+,10-8+,13-11+,14-12+,17-15+,18-16+/t27-,28-,29-,30+,31+,32+,33-,34-,35+,36+,37-,38-,40+,41-,42+,43+,44-,46-,47+/m0/s1 + "A macrolide antibiotic used to treat potentially life-threatening fungal infections." [] + [H][C@]12C[C@@H](O[C@@H]3O[C@H](C)[C@@H](O)[C@H](N)[C@@H]3O)\\C=C\\C=C\\C=C\\C=C\\C=C\\C=C\\C=C\\[C@H](C)[C@@H](O)[C@@H](C)[C@H](C)OC(=O)C[C@H](O)C[C@H](O)CC[C@@H](O)[C@H](O)C[C@H](O)C[C@](O)(C[C@H](O)[C@H]1C(O)=O)O2 + + + sulfates + sulfuric acid derivative + . + CHEBI:sulfates + "Salts and esters of sulfuric acid" [] + CHEBI:26820 + sulphates + sulfates + + + sulfide + CHEBI:26822 + "Any sulfur molecular entity that involves either covalently bonded or anionic sulfur." [] + sulphides + . + sulfides + CHEBI:sulfide + + + theion + "A chalcogen that has formula S." [] + InChIKey=NINIDFKCEFEMDL-UHFFFAOYSA-N + CHEBI:sulfur atom + sulfur + sulphur + soufre + azufre + InChI=1S/S + Schwefel + [S] + CHEBI:26833 + 16S + S + sulfur + sulfur atom + Elemental sulfur + + + sulfur molecular entity + CHEBI:26835 + sulfur molecular entities + sulfur molecular entity + CHEBI:sulfur molecular entity + . + sulfur compounds + + + tannin + tannins + CHEBI:26848 + . + CHEBI:tannin + "Any of a group of astringent polyphenolic vegetable principles or compounds, chiefly complex glucosides of catechol and pyrogallol." [] + + + terpenoid + CHEBI:26873 + CHEBI:terpenoid + terpenoids + "Any isoprenoid that is a natural product or related compound formally derived from isoprene units. Terpenoids may contain oxygen in various functional groups. This class is subdivided according to the number of carbon atoms in the parent terpene. The skeleton of terpenoids may differ from strict additivity of isoprene units by the loss or shift of a fragment, generally a methyl group." [] + terpenoide + Terpenoid + terpenoides + . + + + CHEBI:tertiary alcohol + "A tertiary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has three other carbon atoms attached to it." [] + C4H7OR3 + tertiary alcohol + tertiary alcohols + . + CHEBI:26878 + tertiary alcohol + OC(C[*])(C[*])C[*] + + + "A subclass of polyketides having an octahydrotetracene-2-carboxamide skeleton, substituted with many hydroxy and other groups." [] + CHEBI:tetracyclines + CHEBI:26895 + . + tetracyclines + tetracyclines + + + tetrahydrofurans + CHEBI:oxolanes + "Any oxacycle having an oxolane (tetrahydrofuran) skeleton." [] + oxolanes + CHEBI:26912 + + + tetrapyrrole + "A natural pigment containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next." [] + tetrapyrroles + . + CHEBI:26932 + CHEBI:tetrapyrrole + tetrapyrrole + + + CHEBI:thiamine + thiamins + thiamine + CHEBI:26948 + thiamines + + + . + thioesters + "An ester in which one or both oxygens of an ester group have been replaced by divalent sulfur." [] + thiocarboxylic ester + CHEBI:26959 + CHEBI:thiocarboxylic ester + thiocarboxylic esters + thiolester + + + "Compounds containing at least one thiophene ring." [] + thiofurans + . + thiophenes + CHEBI:thiophenes + thiophenes + CHEBI:26961 + + + organic heterotricyclic compounds + CHEBI:organic heterotricyclic compound + CHEBI:26979 + heterotricyclic compounds + organic heterotricyclic compound + "An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms." [] + . + + + toluenes + CHEBI:27024 + "Any member of the class of benzenes that is a substituted benzene in which the substituents include one (and only one) methyl group." [] + toluenes + CHEBI:toluenes + + + metal de transicion + transition element + . + transition metals + metaux de transition + CHEBI:transition element atom + transition metal + metales de transicion + metal de transition + transition element atom + Uebergangselement + Uebergangsmetalle + CHEBI:27081 + transition elements + transition element + "An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell." [] + + + Tricarbonsaeure + CHEBI:tricarboxylic acid + C3H3O6R + "An oxoacid containing three carboxy groups." [] + Trikarbonsaeure + CHEBI:27093 + tricarboxylic acid + tricarboxylic acids + + + trimethylxanthines + CHEBI:27134 + CHEBI:trimethylxanthine + trimethylxanthine + + + CHEBI:27136 + triol + "A chemical compound containing three hydroxy groups." [] + triols + CHEBI:triol + + + tryptamines + CHEBI:tryptamines + . + CHEBI:27162 + "Tryptamine and its substitution derivatives." [] + + + CHEBI:27171 + organic heterobicyclic compound + organic heterobicyclic compounds + CHEBI:organic heterobicyclic compound + heterobicyclic compounds + . + two-ring heterocyclic compounds + + + L-tyrosine derivatives + L-tyrosine derivative + CHEBI:27177 + CHEBI:L-tyrosine derivative + "A proteinogenic amino acid derivative resulting from reaction of L-tyrosine at the amino group or the carboxy group, or from the replacement of any hydrogen of L-tyrosine by a heteroatom." [] + + + univalent carboacyl group + univalent carboxylic acyl groups + CHEBI:27207 + univalent acyl group + . + univalent carboacyl groups + CHEBI:univalent carboacyl group + "A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid." [] + + + unsaturated fatty acid + CHEBI:27208 + alkene acid + unsaturated fatty acids + olefinic acid + . + CHEBI:unsaturated fatty acid + "Any fatty acid containing at least one C=C or C#C bond." [] + + + VLCFAs + VLCFA + CHEBI:very long-chain fatty acid + CH2OR + higher fatty acid + "A fatty acid which has a chain length greater than C22." [] + OC([*])=O + very long-chain fatty acids + very long-chain fatty acid + CHEBI:27283 + + + CHEBI:vitamin D + vitamin D + "Vitamin D is a group of fat-soluble prohormones, which can be obtained from sun exposure, food and supplements. Vitamin D is biologically inactive and converted to the biologically active calcitriol via double hydroxylation in the body." [] + CHEBI:27300 + vitamin Ds + D vitamins + + + methyl toluene + methyltoluene + CHEBI:xylene + Xylole + xylene + xylenes + Xylol + xilenos + CHEBI:27338 + xylene + dimethylbenzene + xileno + Dimethylbenzol + C8H10 + + + CHEBI:yohimban alkaloid + CHEBI:27358 + yohimban alkaloids + yohimban alkaloid + + + zinc molecular entity + zinc compounds + zinc molecular entities + . + CHEBI:zinc molecular entity + CHEBI:27364 + + + zinc ions + zinc ion + CHEBI:zinc ion + . + CHEBI:27365 + zinc ion + + + zwitterion + . + CHEBI:zwitterion + zwitteriones + CHEBI:27369 + compuestos zwitterionicos + zwitterion + compose zwitterionique + zwitterions + zwitterionic compounds + "A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer)." [] + + + InChIKey=NWIBSHFKIJFRCO-WUDYKRTCSA-N + C15H18N4O5 + 7-Amino-9alpha-methoxymitosane + "A mitomycin that has formula C15H18N4O5." [] + Ametycine + mitomycin C + [(1aS,8S,8aR,8bS)-6-amino-8a-methoxy-5-methyl-4,7-dioxo-1,1a,2,4,7,8,8a,8b-octahydroazirino[2',3':3,4]pyrrolo[1,2-a]indol-8-yl]methyl carbamate + Mitomycin C + CHEBI:mitomycin C + Mitomycin + InChI=1S/C15H18N4O5/c1-5-9(16)12(21)8-6(4-24-14(17)22)15(23-2)13-7(18-13)3-19(15)10(8)11(5)20/h6-7,13,18H,3-4,16H2,1-2H3,(H2,17,22)/t6-,7+,13+,15-/m1/s1 + MMC + [H][C@]12CN3C4=C([C@@H](COC(N)=O)[C@@]3(OC)[C@@]1([H])N2)C(=O)C(N)=C(C)C4=O + Mitocin-C + Mutamycin + CHEBI:27504 + + + C10H16N5O12P3S + gamma-Thio-ATP + PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER + Adenosine 5-O-(3-thiotriphophate) + InChIKey=NLTUCYMLOPLUHL-KQYNXXCUSA-N + Adenosine 5'-(3-thio)triphosphate + CHEBI:adenosine 5'-[gamma-thio]triphosphate + 5'-O-(hydroxy{[hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl)adenosine + 5'-O-[(S)-hydroxy{[(S)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]adenosine + InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1 + Adenosine 5'-O-(3-thiotriphosphate) + CHEBI:27575 + Adenosine 5'-(gamma-thio)triphosphate + Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=S)[C@@H](O)[C@H]1O + "A nucleoside triphosphate analogue that is ATP in which one of the oxygens attached to 3-phosphate group is replaced by sulfur." [] + adenosine 5'-[gamma-thio]triphosphate + ATP-gammaS + ATP-gamma-S + (gamma-S)ATP + + + Carbon + 6C + carbon + C + carbono + CHEBI:carbon atom + CHEBI:27594 + "A carbon group element atom that has formula C." [] + carbon + Kohlenstoff + carbon atom + InChIKey=OKTJSMMVPCPJKN-UHFFFAOYSA-N + [C] + carbonium + InChI=1S/C + carbone + + + Cycloheximide + naramycin A + "A dicarboximide that is 4-(2-hydroxyethyl)piperidine-2,6-dione in which one of the hydrogens attached to the carbon bearing the hydroxy group is replaced by a 3,5-dimethyl-2-oxocyclohexyl group. It is an antibiotic produced by the bacterium Streptomyces griseus." [] + C[C@H]1C[C@H](C)C(=O)[C@@H](C1)[C@H](O)CC1CC(=O)NC(=O)C1 + naramycin + 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione + InChIKey=YPHMISFOHDHNIV-FSZOTQKASA-N + C15H23NO4 + CHEBI:cicloheximide + cicloheximidum + CHEBI:27641 + cicloheximide + Zykloheximid + 3-((R)-2-((1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl)-2-hydroxyethyl)glutarimide + cicloheximida + Cycloheximid + cicloheximide + InChI=1S/C15H23NO4/c1-8-3-9(2)15(20)11(4-8)12(17)5-10-6-13(18)16-14(19)7-10/h8-12,17H,3-7H2,1-2H3,(H,16,18,19)/t8-,9-,11-,12+/m0/s1 + + + CHEBI:27659 + CHEBI:2-oxo aldehyde + 2-oxo aldehydes + C2HO2R + 2-oxo aldehyde + 2-oxoaldehyde + 2-Oxoaldehyde + [H]C(=O)C(C)=O + "Any aldehyde having an oxo substituent at the 2-position." [] + + + 2-amino-N,N'-bis(hexadecahydro-2,5,9-trimethyl-6,13-bis(1-methylethyl)-1,4,7,11,14-pentaoxo-1H-pyrrolo(2,1-i)(1,4,7,10,13)oxatetra-azacyclohexadecin-10-yl)-4,6-dimethyl-3-oxo-3H-phenoxazine-1,9-dicarboxamide + actinomycin D + CHEBI:27666 + CHEBI:actinomycin D + ActD + [H][C@@]12CCCN1C(=O)[C@H](NC(=O)[C@@H](NC(=O)c1ccc(C)c3oc4c(C)c(=O)c(N)c(C(=O)N[C@H]5[C@@H](C)OC(=O)[C@H](C(C)C)N(C)C(=O)CN(C)C(=O)[C@]6([H])CCCN6C(=O)[C@H](NC5=O)C(C)C)c4nc13)[C@@H](C)OC(=O)[C@H](C(C)C)N(C)C(=O)CN(C)C2=O)C(C)C + 2-amino-4,6-dimethyl-3-oxo-1-N,9-N-bis-[(18aS)-10c,14,17-trimethyl-5,8,12,15,18-pentaoxo-6c,13t-di(propan-2-yl)-18ar-hexadecahydro-1H-pyrrolo[2,1-i][1,4,7,10,13]oxatetraazacyclohexadecin-9c-yl]-3H-phenoxazine-1,9-dicarboxamide + InChI=1S/C62H86N12O16/c1-27(2)42-59(84)73-23-17-19-36(73)57(82)69(13)25-38(75)71(15)48(29(5)6)61(86)88-33(11)44(55(80)65-42)67-53(78)35-22-21-31(9)51-46(35)64-47-40(41(63)50(77)32(10)52(47)90-51)54(79)68-45-34(12)89-62(87)49(30(7)8)72(16)39(76)26-70(14)58(83)37-20-18-24-74(37)60(85)43(28(3)4)66-56(45)81/h21-22,27-30,33-34,36-37,42-45,48-49H,17-20,23-26,63H2,1-16H3,(H,65,80)(H,66,81)(H,67,78)(H,68,79)/t33-,34-,36+,37+,42-,43-,44+,45+,48+,49+/m1/s1 + C62H86N12O16 + actinomycin C1 + actinomycin IV + "An actinomycin that has formula C62H86N12O16." [] + Dactinomycin + InChIKey=RJURFGZVJUQBHK-IIXSONLDSA-N + Actinomycin D + + + Harzol + beta-Sitosterin + Triastonal + beta-Sitosterol + sitosterol + InChIKey=KZJWDPNRJALLNS-VJSFXXLFSA-N + (3S,8S,9S,10R,13R,14S,17R)-17-[(1R,4R)-4-ethyl-1,5-dimethyl-hexyl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol + Cupreol + (3S,8S,9S,10R,13R,14S,17R)-17-[(1R,4R)-4-ethyl-1,5-dimethylhexyl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol + 24alpha-Ethylcholesterol + stigmast-5-en-3beta-ol + "A phytosterols that is stigmast-5-ene substituted by a beta-hydroxy group at position 3." [] + InChI=1S/C29H50O/c1-7-21(19(2)3)9-8-20(4)25-12-13-26-24-11-10-22-18-23(30)14-16-28(22,5)27(24)15-17-29(25,26)6/h10,19-21,23-27,30H,7-9,11-18H2,1-6H3/t20-,21-,23+,24+,25-,26+,27+,28+,29-/m1/s1 + Phytosterol + (24R)-Stigmast-5-en-3beta-ol + 22,23-Dihydrostigmasterol + Rhamnol + Prostasal + Nimbosterol + (24R)-ethylcholest-5-en-3beta-ol + Cinchol + Stigmast-5-en-3-beta-ol + [H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CC[C@@H](CC)C(C)C + Sito-Lande + Angelicin + CHEBI:sitosterol + alpha-Dihydrofucosterol + Azuprostat + C29H50O + (3S,8S,9S,10R,13R,14S,17R)-17-[(2R,5R)-5-ethyl-6-methyl-heptan-2-yl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol + 24beta-Ethylcholesterol + Sobatum + (-)-beta-Sitosterol + (3S,8S,9S,10R,13R,14S,17R)-17-[(2R,5R)-5-ethyl-6-methylheptan-2-yl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol + Quebrachol + Sitosterol + (3beta)-Stigmast-5-en-3-ol + CHEBI:27693 + (24R)-Ethylcholest-5-en-3beta-ol + + + Digitin + Digitonin + [H][C@@]12CC[C@]3([H])[C@]([H])(CC[C@@]4(C)[C@@]3([H])[C@H](O)[C@]3([H])O[C@]5(CC[C@@H](C)CO5)[C@@H](C)[C@]43[H])[C@@]1(C)C[C@@H](O)[C@@H](C2)O[C@@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O[C@@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@H]2O)[C@H](O)[C@H]1O + InChI=1S/C56H92O29/c1-19-7-10-56(75-17-19)20(2)31-45(85-56)37(67)32-22-6-5-21-11-26(24(61)12-55(21,4)23(22)8-9-54(31,32)3)76-50-42(72)39(69)44(30(16-60)80-50)81-53-48(47(36(66)29(15-59)79-53)83-49-40(70)33(63)25(62)18-74-49)84-52-43(73)46(35(65)28(14-58)78-52)82-51-41(71)38(68)34(64)27(13-57)77-51/h19-53,57-73H,5-18H2,1-4H3/t19-,20+,21+,22-,23+,24-,25-,26-,27-,28-,29-,30-,31+,32-,33+,34-,35-,36-,37+,38+,39-,40-,41-,42-,43-,44+,45-,46+,47+,48-,49+,50-,51+,52+,53+,54-,55+,56-/m1/s1 + digitonin + C56H92O29 + CHEBI:27729 + (25R)-2alpha,15beta-dihydroxy-5alpha-spirostan-3beta-yl beta-D-glucopyranosyl-(1->3)-beta-D-galactopyranosyl-(1->2)-[beta-D-xylopyranosyl-(1->3)]-beta-D-glucopyranosyl-(1->4)-beta-D-galactopyranoside + InChIKey=UVYVLBIGDKGWPX-XJVHMSFUSA-N + "A spirostanyl glycoside that has formula C56H92O29." [] + CHEBI:digitonin + + + Cn1cnc2n(C)c(=O)n(C)c(=O)c12 + CAFFEINE + caffeine + 1-methyltheobromine + mateina + 1,3,7-trimethyl-2,6-dioxopurine + 1,3,7-trimethylpurine-2,6-dione + guaranine + 7-methyltheophylline + 1,3,7-trimethylpurine-2,6-quinone + "A trimethylxanthine in which the three methyl groups are located at positions 1, 3, and 7. A purine alkaloid that occurs naturally in tea and coffee." [] + InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 + 1,3,7-trimethylxanthine + Koffein + 1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione + InChIKey=RYYVLZVUVIJVGH-UHFFFAOYSA-N + cafeine + Caffeine + cafeina + Coffein + C8H10N4O2 + CHEBI:27732 + anhydrous caffeine + caffeine + Thein + methyltheobromine + theine + teina + 3,7-Dihydro-1,3,7-trimethyl-1H-purin-2,6-dion + 1,3,7-Trimethylxanthine + CHEBI:caffeine + + + Ethyl acetate + CHEBI:27750 + acetic ester + ethyl acetic ester + Acetyl ester + ethyl ethanoate + CCOC(C)=O + vinegar naphtha + EtOAc + InChIKey=XEKOWRVHYACXOJ-UHFFFAOYSA-N + ethyl acetate + AcOEt + ETHYL ACETATE + Essigsaeureethylester + acetic acid, ethyl ester + acetoxyethane + acetic acid ethyl ester + CHEBI:ethyl acetate + "The acetate ester formed between acetic acid and ethanol." [] + Essigester + Ethylacetat + CH3-CO-O-CH3 + C4H8O2 + InChI=1S/C4H8O2/c1-3-6-4(2)5/h3H2,1-2H3 + ethyl acetate + 1-acetoxyethane + Ethylazetat + + + Deschlorobiomycin + Abramycin + InChIKey=OFVLGDICTFRJMM-WESIUVDSSA-N + CHEBI:27902 + [H][C@@]12C[C@@]3([H])C(C(=O)c4c(O)cccc4[C@@]3(C)O)=C(O)[C@]1(O)C(=O)C(C(N)=O)=C(O)[C@H]2N(C)C + tetracycline + (4S,4aS,5aS,12aS)-4-(Dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-2-naphthacenecarboxamide + Anhydrotetracycline + C22H24N2O8 + (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide + tetracyclinum + tetracycline + Achromycin + Liquamycin + Tetracyclin + Tetracycline + TETRACYCLINE + tetracycline + "A broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria." [] + Tetrazyklin + CHEBI:tetracycline + Tsiklomitsin + InChI=1S/C22H24N2O8/c1-21(31)8-5-4-6-11(25)12(8)16(26)13-9(21)7-10-15(24(2)3)17(27)14(20(23)30)19(29)22(10,32)18(13)28/h4-6,9-10,15,25,27-28,31-32H,7H2,1-3H3,(H2,23,30)/t9-,10-,15-,21+,22-/m0/s1 + + + "An organonitrogen heterocyclic antibiotic that contains a beta-lactam ring." [] + beta-lactam antibiotic + CHEBI:27933 + CHEBI:beta-lactam antibiotic + beta-lactam antibiotics + beta-Lactam antibiotics + C6H3NO3SR2 + + + Cocaina + C17H21NO4 + CHEBI:cocaine + Cocain + methyl (1R,2R,3S,5S)-8-methyl-3-[(phenylcarbonyl)oxy]-8-azabicyclo[3.2.1]octane-2-carboxylate + InChI=1S/C17H21NO4/c1-18-12-8-9-13(18)15(17(20)21-2)14(10-12)22-16(19)11-6-4-3-5-7-11/h3-7,12-15H,8-10H2,1-2H3/t12-,13+,14-,15+/m0/s1 + methyl benzoylecgonine + Benzoylmethylecgonine + beta-Cocain + methyl (1R,2R,3S,5S)-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate + Neurocaine + [1R-(exo,exo)]-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylic acid, methyl ester + (1R,2R,3S,5S)-2-(methoxycarbonyl)tropan-3-yl benzoate + methyl [1R-(exo,exo)]-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate + l-cocaine + [H][C@]12CC[C@]([H])([C@H]([C@H](C1)OC(=O)c1ccccc1)C(=O)OC)N2C + InChIKey=ZPUCINDJVBIVPJ-LJISPDSOSA-N + l-Cocain + cocaine + CHEBI:27958 + COCAINE + Cocaine + 2-methyl-3beta-hydroxy-1alphaH,5alphaH-tropane-2beta-carboxylate benzoate (ester) + Kokain + "A tropane alkaloid obtained from leaves of the South American shrub Erythroxylon coca." [] + (-)-cocaine + cocainum + + + CCCCNC(=O)NS(=O)(=O)c1ccc(C)cc1 + tolbutamidum + 1-p-Toluenesulfonyl-3-butylurea + N-(p-Methylbenzenesulfonyl)-N'-butylurea + CHEBI:tolbutamide + N-Butyl-N'-(p-tolylsulfonyl)urea + N-(4-Methylbenzenesulfonyl)-N'-butylurea + Tolylsulfonylbutylurea + InChI=1S/C12H18N2O3S/c1-3-4-9-13-12(15)14-18(16,17)11-7-5-10(2)6-8-11/h5-8H,3-4,9H2,1-2H3,(H2,13,14,15) + N-(4-Methylphenylsulfonyl)-N'-butylurea + N-[(butylamino)carbonyl]-4-methylbenzenesulfonamide + N-Butyl-N'-p-toluenesulfonylurea + tolbutamida + N-n-Butyl-N'-tosylurea + tolbutamide + tolbutamide + "An N-sulfonylurea that consists of 1-butylurea having a tosyl group attached at the 3-position." [] + 1-Butyl-3-(p-methylphenylsulfonyl)urea + 3-(p-Tolyl-4-sulfonyl)-1-butylurea + CHEBI:27999 + 1-Butyl-3-tosylurea + N-(Sulfonyl-p-methylbenzene)-N'-N-butylurea + N-Butyl-N'-(4-methylphenylsulfonyl)urea + Orinase (TN) + C12H18N2O3S + Tolbutamide + 1-Butyl-3-(p-tolylsulfonyl)urea + InChIKey=JLRGJRBPOGGCBT-UHFFFAOYSA-N + + + beta-D-galactosides + C6H11O6R + CHEBI:beta-D-galactoside + beta-D-galactoside + beta-D-Galactoside + beta-D-galactopyranoside + CHEBI:28034 + a beta-D-galactoside + OC[C@H]1O[C@@H](O[*])[C@H](O)[C@@H](O)[C@H]1O + + + rifampicin + rifampicina + InChIKey=JQXXHWHPUNPDRT-WLSIYKJHSA-N + rifamcin + "A rifamycin that is a a semisynthetic antibiotic derived from Amycolatopsis rifamycinica (previously known as Amycolatopsis mediterranei and Streptomyces mediterranei)" [] + CO[C@H]1\\C=C\\O[C@@]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)\\C(C)=C/C=C/[C@H](C)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]1C)c(\\C=N\\N1CCN(C)CC1)c(O)c4c3C2=O + rifampicin + 3-(((4-Methyl-1-piperazinyl)imino)methyl)rifamycin SV + CHEBI:28077 + Rifampicin + rifampicinum + C43H58N4O12 + InChI=1S/C43H58N4O12/c1-21-12-11-13-22(2)42(55)45-33-28(20-44-47-17-15-46(9)16-18-47)37(52)30-31(38(33)53)36(51)26(6)40-32(30)41(54)43(8,59-40)57-19-14-29(56-10)23(3)39(58-27(7)48)25(5)35(50)24(4)34(21)49/h11-14,19-21,23-25,29,34-35,39,49-53H,15-18H2,1-10H3,(H,45,55)/b12-11+,19-14+,22-13-,44-20+/t21-,23+,24+,25+,29-,34-,35+,39+,43-/m0/s1 + CHEBI:rifampicin + (7S,9E,11S,12R,13S,14R,15R,16R,17S,18S,19E,21Z)-2,15,17,27,29-pentahydroxy-11-methoxy-3,7,12,14,16,18,22-heptamethyl-26-{(E)-[(4-methylpiperazin-1-yl)imino]methyl}-6,23-dioxo-8,30-dioxa-24-azatetracyclo[23.3.1.1(4,7).0(5,28)]triaconta-1(28),1(29),2,4,9,19,21,25,27-nonaen-13-yl acetate + Rifampin + RFP + + + C2H3Cl3O2 + trichloroacetaldehyde hydrate + Noctec + Chloral hydrate + OC(O)C(Cl)(Cl)Cl + CHEBI:28142 + 2,2,2-trichloroethane-1,1-diol + InChI=1S/C2H3Cl3O2/c3-2(4,5)1(6)7/h1,6-7H + CHEBI:chloral hydrate + 2,2,2-trichloro-1,1-ethanediol + Somnote + InChIKey=RNFNDJAIBTYOQL-UHFFFAOYSA-N + knockout drops + Aquachloral Supprettes + Trichloracetaldehyd-hydrat + 1,1,1-trichloro-2,2-dihydroxyethane + Chloralhydrat + chloral hydrate + 1,1,1-trichloro-2,2-ethanediol + chloral monohydrate + "An organochlorine compound that is the hydrate of trichloroacetaldehyde." [] + + + paraderil + Deril + [2R-(2alpha,6aalpha,12aalpha)]-1,2,12,12a-tetrahydro-8,9-dimethoxy-2-(1-methylethenyl)[1]benzopyrano[3,4-b]furo[2,3-H][1]benzopyran-6(6aH)-one + "A member of the class of rotenones that consists of 1,2,12,12a-tetrahydrochromeno[3,4-b]furo[2,3-h]chromen-6(6aH)-one substituted at position 2 by a prop-1-en-2-yl group and at positions 8 and 9 by methoxy groups (the 2R,6aS,12aS-isomer). A non-systemic insecticide, it is the principal insecticidal constituent of derris (the dried rhizome and root of Derris elliptica)." [] + (2R,6aS,12aS)-8,9-dimethoxy-2-(prop-1-en-2-yl)-1,2,12,12a-tetrahydrochromeno[3,4-b]furo[2,3-h]chromen-6(6aH)-one + (12aS,6aS,2R)-8,9-dimethoxy-2-(1-methylvinyl)-1,2-dihydrochromano[3,4-b]furano [2,3-h]chroman-6-one + tubatoxin + CHEBI:rotenone + Derrin + [H][C@@]1(Cc2c(O1)ccc1C(=O)[C@@]3([H])c4cc(OC)c(OC)cc4OC[C@@]3([H])Oc21)C(C)=C + (2R,6aS,12aS)-1,2,6,6a,12,12a-hexahydro-2-isopropenyl-8,9-dimethoxychromeno(3,4-b)furo(2,3-h)chromen-6-one + Rotenone + Synpren + 5'beta-rotenone + Ronone + Derris + C23H22O6 + CHEBI:28201 + dactinol + (-)-rotenone + (-)-cis-rotenone + InChI=1S/C23H22O6/c1-11(2)16-8-14-15(28-16)6-5-12-22(24)21-13-7-18(25-3)19(26-4)9-17(13)27-10-20(21)29-23(12)14/h5-7,9,16,20-21H,1,8,10H2,2-4H3/t16-,20-,21+/m1/s1 + barbasco + noxfire + canex + InChIKey=JUVIOZPCNVVQFO-HBGVWJBISA-N + rotenone + Rotocide + + + Gal + galacto-hexose + C6H12O6 + Galaktose + "An aldohexose that is the C-4 epimer of glucose." [] + galactose + CHEBI:galactose + CHEBI:28260 + Galactose + galactose + + + DMSO + dmso + InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 + C2H6OS + S(O)Me2 + DIMETHYL SULFOXIDE + CHEBI:28262 + Dimethyl sulfoxide + CS(C)=O + InChIKey=IAZDPXIOMUYVGZ-UHFFFAOYSA-N + CHEBI:dimethyl sulfoxide + dimethyl sulphoxide + dimethyl sulfur oxide + Dimethylsulfoxid + dimethyl sulfoxide + sulfinylbis(methane) + (CH3)2SO + dimetil sulfoxido + dimethyl sulfoxide + dimethyli sulfoxidum + dimethyl sulfoxide + dimethylsulfoxyde + (methanesulfinyl)methane + methylsulfinylmethane + "A 2-carbon sulfoxide in which the sulfur atom has two methyl substituents." [] + + + Cy 222 + Bemiparin + Fluxum + heparinum + Heparin + Reviparin + heparin + "A highly sulfated linear glycosaminoglycan comprising complex patterns of uronic acid-(1->4)-D-glucosamine repeating subunits. Used as an injectable anticoagulant, it has the highest negative charge density of any known biological molecule." [] + heparine + heparin + Sandoparin + Certoparin + Heparinic acid + CHEBI:28304 + heparina + Enoxaparin + Parnaparin + (C26H40N2O36S5)n + CHEBI:heparin + + + 2-Hydroxypropionic acid + (+-)-2-hydroxypropanoic acid + CHEBI:rac-lactic acid + Milchsaeure + E270 + alpha-hydroxypropanoic acid + C3H6O3 + alpha-hydroxypropionic acid + "A racemate comprising equimolar amounts of (R)- and (S)-lactic acid." [] + rac-lactic acid + CHEBI:28358 + Lactic acid + 2-Hydroxypropanoic acid + rac-2-hydroxypropanoic acid + + + CHEBI:28383 + alpha,omega-dicarboxylic acid + alpha,omega-Dicarboxylic acid + CHEBI:alpha,omega-dicarboxylic acid + . + alphaomega-dicarboxylic acid + alpha,omega-dicarboxylic acids + alpha(omega)-Dicarboxylic acid + + + InChIKey=QEVHRUUCFGRFIF-MDEJGZGSSA-N + C33H40N2O9 + (-)-reserpine + Reserpine + (3beta,16beta,17alpha,18beta,20alpha)-11,17-dimethoxy-18-[(3,4,5-trimethoxybenzoyl)oxy]yohimban-16-carboxylic acid methyl ester + CHEBI:reserpine + Reserpin + Serpalan + [H][C@]12C[C@@H](OC(=O)c3cc(OC)c(OC)c(OC)c3)[C@H](OC)[C@@H](C(=O)OC)[C@@]1([H])C[C@@]1([H])N(CCc3c1[nH]c1cc(OC)ccc31)C2 + methyl (3beta,16beta,17alpha,18beta,20alpha)-11,17-dimethoxy-18-[(3,4,5-trimethoxybenzoyl)oxy]yohimban-16-carboxylate + CHEBI:28487 + "An alkaloid found in the roots of Rauwolfia serpentina and R. vomitoria." [] + 3,4,5-trimethoxybenzoyl methyl reserpate + reserpine + InChI=1S/C33H40N2O9/c1-38-19-7-8-20-21-9-10-35-16-18-13-27(44-32(36)17-11-25(39-2)30(41-4)26(12-17)40-3)31(42-5)28(33(37)43-6)22(18)15-24(35)29(21)34-23(20)14-19/h7-8,11-12,14,18,22,24,27-28,31,34H,9-10,13,15-16H2,1-6H3/t18-,22+,24-,27-,28+,31+/m1/s1 + Apoplon + + + InChIKey=HRPVXLWXLXDGHG-UHFFFAOYSA-N + NC(=O)C=C + Akrylamid + CHEBI:28619 + InChI=1S/C3H5NO/c1-2-3(4)5/h2H,1H2,(H2,4,5) + C3H5NO + CHEBI:acrylamide + prop-2-enamide + acrylamide + prop-2-enamide + "A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia." [] + acrylamide + Acrylamide + 2-Propenamide + ethylenecarboxamide + + + H3tea + tris(2-hydroxyethyl)amine + Triethanolamine + triethanolamine + tris(beta-hydroxyethyl)amine + CHEBI:28621 + N(CH2CH2OH)3 + Trolamine + C6H15NO3 + nitrilo-2,2',2''-triethanol + triethanolamine + "A tertiary amino compound that is ammonia in which each of the hydrogens is substituted by a 2-hydroxyethyl group." [] + 2,2',2''-NITRILOTRIETHANOL + 2,2',2''-nitrilotriethanol + CHEBI:triethanolamine + 2-(bis(2-hydroxyethyl)amino)ethanol + TEA + InChI=1S/C6H15NO3/c8-4-1-7(2-5-9)3-6-10/h8-10H,1-6H2 + InChIKey=GSEJCLTVZPLZKY-UHFFFAOYSA-N + OCCN(CCO)CCO + nitrilotriethanol + 2,2',2''-nitrilotriethanol + 2,2',2''-nitrilotris(ethanol) + + + CHEBI:campesterol + campest-5-en-3beta-ol + [H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CC[C@@H](C)C(C)C + "A phytosterol that has formula C28H48O." [] + Campesterol + CHEBI:28623 + (24R)ergost-5-en-3beta-ol + InChIKey=SGNBVLSWZMBQTH-PODYLUTMSA-N + C28H48O + campesterol + InChI=1S/C28H48O/c1-18(2)19(3)7-8-20(4)24-11-12-25-23-10-9-21-17-22(29)13-15-27(21,5)26(23)14-16-28(24,25)6/h9,18-20,22-26,29H,7-8,10-17H2,1-6H3/t19-,20-,22+,23+,24-,25+,26+,27+,28-/m1/s1 + + + CHEBI:phosphorus atom + Phosphor + InChI=1S/P + InChIKey=OAICVXFJPJFONN-UHFFFAOYSA-N + [P] + phosphorus + phosphore + 15P + P + fosforo + CHEBI:28659 + phosphorus + phosphorus atom + Phosphorus + "A pnictogen that has formula P." [] + + + CHEBI:cytarabine + Cytosine-1-beta-D-arabinofuranoside + 4-amino-1-beta-D-arabinofuranosylpyrimidin-2(1H)-one + InChIKey=UHDGCWIWMRVCDJ-CCXZUQQUSA-N + CHEBI:28680 + Cytosine arabinoside + Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=O)n1 + 1-beta-D-Arabinofuranosylcytosine + cytosine-beta-D-arabinofuranoside + "A pyrimidine nucleoside in which cytosine is attached to D-arabinofuranose via a beta-N(1)-glycosidic bond." [] + C9H13N3O5 + cytarabine + InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7+,8-/m1/s1 + CYTARABINE + Cytarabine + 4-Amino-1-beta-D-arabinofuranosyl-2(1H)-pyrimidinone + + + C8H18N2O3S + Buthionine sulfoximine + CHEBI:S-butyl-DL-homocysteine (S,R)-sulfoximine + buthionine sulfoximine + 2-amino-4-(S-butylsulfonimidoyl)butanoic acid + "A sulfoximide that is the sulfoximine derivative of an analogue of DL-methionine in which the S-methyl group is replaced by S-butyl." [] + 2-amino-4-(S-butylsulfonimidoyl)butyric acid + CCCCS(=N)(=O)CCC(N)C(O)=O + CHEBI:28714 + InChIKey=KJQFBVYMGADDTQ-UHFFFAOYSA-N + DL-butathionine-(S,R)-sulfoximine + InChI=1S/C8H18N2O3S/c1-2-3-5-14(10,13)6-4-7(9)8(11)12/h7,10H,2-6,9H2,1H3,(H,11,12) + 2-amino-4-(S-butylsulfonimidoyl)butanoic acid + S-Butyl-DL-homocysteine-[S,R]-sulfoximine + S-butyl-DL-homocysteine-[S,R]-sulfoximine + S-butyl-DL-homocysteine (S,R)-sulfoximine + + + sodium fluoride + InChI=1S/FH.Na/h1H;/q;+1/p-1 + "A metal fluoride salt with a Na(+) counterion." [] + FNa + NaF + CHEBI:sodium fluoride + InChIKey=PUZPDOWCWNUUKD-UHFFFAOYSA-M + CHEBI:28741 + Sodium fluoride + sodium fluoride + Na.F + [F-].[Na+] + + + InChI=1S/C27H29NO11/c1-10-22(31)13(28)6-17(38-10)39-15-8-27(36,16(30)9-29)7-12-19(15)26(35)21-20(24(12)33)23(32)11-4-3-5-14(37-2)18(11)25(21)34/h3-5,10,13,15,17,22,29,31,33,35-36H,6-9,28H2,1-2H3/t10-,13-,15-,17-,22+,27-/m0/s1 + InChIKey=AOJJSUZBOXZQNB-TZSSRYMLSA-N + CHEBI:doxorubicin + COc1cccc2C(=O)c3c(O)c4C[C@](O)(C[C@H](O[C@H]5C[C@H](N)[C@H](O)[C@H](C)O5)c4c(O)c3C(=O)c12)C(=O)CO + C27H29NO11 + "An anthracycline antibiotic that has formula C27H29NO11." [] + (1S,3S)-3-glycoloyl-3,5,12-trihydroxy-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside + 14-hydroxydaunomycin + doxorubicine + doxorubicinum + DOXORUBICIN + Doxorubicin + (1S,3S)-3,5,12-trihydroxy-3-(hydroxyacetyl)-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside + (8S-cis)-10-((3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranosyl)oxy)-7,8,9,10-tetrahydro-6,8,11-trihydroxy-8-(hydroxyacetyl)-1-methoxy-5,12-naphthacenedione + Adriamycin + doxorubicin + doxorubicin + 14-hydroxydaunorubicine + CHEBI:28748 + + + CHEBI:phosphatidylinositol phosphate + phosphatidylinositol phosphates + phosphatidylinositol phosphate + CHEBI:28765 + "Any member of the phosphoinositide family of compounds, of which seven occur naturally." [] + + + CHEBI:28790 + InChIKey=QZAYGJVTTNCVMB-UHFFFAOYSA-N + "A primary amino compound that is the 5-hydroxy derivative of tryptamine." [] + SEROTONIN + Serotonin + NCCc1c[nH]c2ccc(O)cc12 + InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2 + Enteramine + serotonine + Antemoqua + thrombocytin + 3-(2-aminoethyl)-1H-indol-5-ol + CHEBI:serotonin + C10H12N2O + 5-HT + Hippophaine + serotonin + Antemovis + 3-(2-Aminoethyl)-1H-indol-5-ol + 3-(2-azanylethyl)-1H-indol-5-ol + 5-Hydroxytryptamine + thrombotonin + 5-hydroxy-tryptamine + + + beta-Glucan + beta-D-Glucan + beta-D-glucan + beta-D-glucans + CHEBI:28793 + C12H22O11(C6H10O5)n + CHEBI:beta-D-glucan + + + (3S,8S,9S,10R,13R,14S,17R)-17-[(E,1R,4R)-4-ethyl-1,5-dimethylhex-2-enyl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol + beta-stigmasterol + InChI=1S/C29H48O/c1-7-21(19(2)3)9-8-20(4)25-12-13-26-24-11-10-22-18-23(30)14-16-28(22,5)27(24)15-17-29(25,26)6/h8-10,19-21,23-27,30H,7,11-18H2,1-6H3/b9-8+/t20-,21-,23+,24+,25-,26+,27+,28+,29-/m1/s1 + (3beta,22E)-stigmasta-5,22-dien-3-ol + (3S,8S,9S,10R,13R,14S,17R)-17-[(E,2R,5R)-5-ethyl-6-methyl-hept-3-en-2-yl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol + (24S)-5,22-Stigmastadien-3beta-ol + Stigmasterin + 5,22-Cholestadien-24-ethyl-3beta-ol + CHEBI:28824 + "A 3beta-sterol that consists of 3beta-hydroxystigmastane having double bonds at the 5,6- and 22,23-positions." [] + stigmasterol + poriferasterol + Stigmasta-5,22-dien-3-ol, (3beta,22E)- + C29H48O + stigmasta-5,22-dien-3beta-ol + (3S,8S,9S,10R,13R,14S,17R)-17-[(E,2R,5R)-5-ethyl-6-methylhept-3-en-2-yl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol + Stigmasta-5,22-dien-3-beta-ol + stigmasterol + InChIKey=HCXVJBMSMIARIN-PHZDYDNGSA-N + phytosterol + (3S,8S,9S,10R,13R,14S,17R)-17-[(E,1R,4R)-4-ethyl-1,5-dimethyl-hex-2-enyl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol + CHEBI:stigmasterol + (22E)-stigmasta-5,22-dien-3beta-ol + Stigmasterol + [H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)\\C=C\\[C@@H](CC)C(C)C + + + "The conjugate base of a fatty acid, arising from deprotonation of the carboxylic acid group of the corresponding fatty acid." [] + Fettsaeureanionen + fatty acid anion + Fatty acid anion + acidos grasos anionicos + fatty acid anions + acido graso anionico + [O-]C([*])=O + CHEBI:28868 + a fatty acid + CHEBI:fatty acid anion + Alkanate + CO2R + anion de l'acide gras + Fettsaeureanion + + + CHEBI:phosphatidylinositol + PI + "Any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol." [] + 1,2-Diacyl-sn-glycero-3-phosphoinositol + 1,2-diacyl-sn-glycero-3-phosphoinositol + CHEBI:28874 + phosphatidylinositol + PtdIns + C11H17O13PR2 + phosphatidylinositols + + + [O-]C(=O)[*]C([O-])=O + CHEBI:28965 + dicarboxylate + a dicarboxylate + dicarboxylic acid dianion + dicarboxylic acid dianions + dicarboxylic acid dianion + C2O4R + "A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid." [] + CHEBI:dicarboxylic acid dianion + dicarboxylates + + + nonanoic acid + 1-octanecarboxylic acid + Pelargonic acid + pelargic acid + InChI=1S/C9H18O2/c1-2-3-4-5-6-7-8-9(10)11/h2-8H2,1H3,(H,10,11) + "A C9 straight-chain saturated fatty acid which occurs naturally as esters of the oil of pelargonium. Has antifungal properties, and is also used as a herbicide as well as in the preparation of plasticisers and lacquers." [] + nonylic acid + nonoic acid + pelargon + Nonanoate + C9H18O2 + CHEBI:nonanoic acid + pergonic acid + CHEBI:29019 + InChIKey=FBUKVWPVBMHYJY-UHFFFAOYSA-N + 1-nonanoic acid + CCCCCCCCC(O)=O + Pelargonsaeure + n-nonanoic acid + nonanoic acid + Nonanoic acid + Nonansaeure + CH3-[CH2]7-COOH + + + Hexan + CH3-[CH2]4-CH3 + hexane + Hexane + HEXANE + CHEBI:hexane + InChI=1S/C6H14/c1-3-5-6-4-2/h3-6H2,1-2H3 + CHEBI:29021 + C6H14 + hexane + "An unbranched alkane containing six carbon atoms." [] + InChIKey=VLKZOEOYAKHREP-UHFFFAOYSA-N + CCCCCC + n-Hexane + + + CHEBI:29036 + Cu(2+) + copper(2+) + copper, ion (Cu2+) + copper(2+) ion + "An ion of copper carrying a double positive charge." [] + Cu + Cu(II) + copper(II) cation + copper(2+) + cupric ion + InChI=1S/Cu/q+2 + Cu2+ + [Cu++] + COPPER (II) ION + copper(II) cation + CHEBI:copper(2+) + InChIKey=JPVYNHNXODAKFH-UHFFFAOYSA-N + + + [O-]C([*])=O + a carboxylate + CHEBI:29067 + CHEBI:carboxylic acid anion + CO2R + carboxylic acid anion + carboxylic acid anions + "The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated." [] + carboxylic anions + + + CHEBI:sodium(1+) + sodium(1+) ion + "A monoatomic monocation obtained from sodium." [] + SODIUM ION + [Na+] + Na(+) + Na + sodium(I) cation + sodium(1+) + sodium(1+) + sodium + Na+ + CHEBI:29101 + InChI=1S/Na/q+1 + InChIKey=FKNQFGJONOIPTF-UHFFFAOYSA-N + sodium cation + + + InChI=1S/K/q+1 + POTASSIUM ION + K(+) + [K+] + K+ + InChIKey=NPYPAHLBTDXSSS-UHFFFAOYSA-N + potassium + CHEBI:potassium(1+) + potassium(1+) ion + potassium(1+) + potassium(I) cation + CHEBI:29103 + potassium cation + K + potassium(1+) + "A monoatomic monocation obtained from potassium." [] + + + zinc + CHEBI:zinc(2+) + zinc, ion (Zn2+) + zinc(2+) + ZINC ION ON 3-FOLD CRYSTAL AXIS + Zn(2+) + zinc(2+) + InChIKey=PTFCDOFLOPIGGS-UHFFFAOYSA-N + Zn(II) + Zn + zinc(II) cation + dietary zinc + "A zinc cation that has formula Zn." [] + zinc(2+) ion + CHEBI:29105 + Zn2+ + InChI=1S/Zn/q+2 + ZINC ION + zinc cation + [Zn++] + + + calcium(2+) + CALCIUM ION + calcium(2+) ion + InChI=1S/Ca/q+2 + Ca2+ + InChIKey=BHPQYMZQTOCNFJ-UHFFFAOYSA-N + CHEBI:calcium(2+) + calcium(II) cation + Ca + "A calcium cation that has formula Ca." [] + CHEBI:29108 + [Ca++] + Ca(2+) + calcium + calcium(2+) + calcium, doubly charged positive ion + + + [IO3(OH)] + CHEBI:29149 + tetraoxoiodic acid + [H]OI(=O)(=O)=O + periodic acid + "An iodine oxoacid that has formula HIO4." [] + periodic acid + Periodsaeure + hydrogen tetraoxoiodate + InChIKey=KHIWWQKSHDUIBK-UHFFFAOYSA-N + Ueberiodsaeure + hydroxy-lambda(7)-iodanetrione + hydroxidotrioxidoiodine + HOIO3 + InChI=1S/HIO4/c2-1(3,4)5/h(H,2,3,4,5) + HIO4 + CHEBI:periodic acid + + + (3)H + hydrogen-3 + InChIKey=UFHFLCQGNIYNRP-NJFSPNSNSA-N + "The radioactive isotope of hydrogen with relative atomic mass 3.016049 and half-life of 12.33 years (from Greek taurhoiotatauomicronsigma, third)." [] + CHEBI:29238 + tritium + (3)1H + InChI=1S/H2/h1H/i1+2 + CHEBI:tritium atom + tritium atom + T + tritio + ueberschwerer Wasserstoff + tritium + [3H] + + + "An organosulfur compound in which a thiol group, -SH, is attached to a carbon atom of any aliphatic or aromatic moiety." [] + Thiol + Merkaptan + thiols + RSH + HSR + S[*] + a thiol + thiols + CHEBI:thiol + mercaptans + CHEBI:29256 + Mercaptan + thiol + + + alkyl sulfate + CHEBI:29281 + OS(=O)(=O)O[*] + alkyl sulfates + Alkyl sulfate + CHEBI:alkyl sulfate + HO4SR + + + monocarboxylic acid amide + CHEBI:monocarboxylic acid amide + acid amides + Monocarboxylic acid amide + [*]N([*])C([*])=O + CNOR3 + CHEBI:29347 + monocarboxylic acid amides + "A carboxamide derived from a monocarboxylic acid." [] + + + CHEBI:29745 + barbiturate + InChIKey=HNYOPLTXPVRDBG-UHFFFAOYSA-M + "Conjugate base of barbituric acid." [] + 2,4,6-trioxotetrahydro-2H-pyrimidin-1-ide + O=C1CC(=O)[N-]C(=O)N1 + barbiturate anion + C4H3N2O3 + InChI=1S/C4H4N2O3/c7-2-1-3(8)6-4(9)5-2/h1H2,(H2,5,6,7,8,9)/p-1 + CHEBI:barbiturate + + + -SS- + S2 + dithio + disulfanediyl group + CHEBI:29826 + CHEBI:disulfanediyl group + disulfanediyl + + + CHEBI:29917 + Sulfhydrylgruppe + HS- + -SH + sulfanyl + thiol group + thiol + Mercaptogruppe + sulfhydryl group + Thiolgruppe + thiol group + HS + Merkaptogruppe + sulphydryl group + mercapto group + CHEBI:thiol group + + + K4[Fe(CN)6] + tetrapotassium hexacyanoferrate + CHEBI:30059 + InChIKey=OCPOWIWGGAATRP-UHFFFAOYSA-N + InChI=1S/6CN.Fe.4K/c6*1-2;;;;;/q;;;;;;-4;4*+1 + "A hexacyanoferrate(4-) salt that has formula C6FeK4N6." [] + potassium hexacyanidoferrate(4-) + gelbes Blutlaugensalz + CHEBI:potassium hexacyanoferrate(4-) + potassium hexacyanidoferrate(II) + potassium hexacyanoferrate(4-) + Kaliumhexazyanoferrat(II) + tetrapotassium hexacyanidoferrate + potassium ferrocyanide + [K+].[K+].[K+].[K+].N#C[Fe-4](C#N)(C#N)(C#N)(C#N)C#N + C6FeK4N6 + + + tripotassium hexacyanidoferrate + InChI=1S/6CN.Fe.3K/c6*1-2;;;;/q;;;;;;-3;3*+1 + red prussiate + potassium hexacyanidoferrate(3-) + rotes Blutlaugensalz + K3[Fe(CN)6] + [K+].[K+].[K+].N#C[Fe-3](C#N)(C#N)(C#N)(C#N)C#N + potassium hexacyanidoferrate(III) + Kaliumhexazyanoferrat(III) + tripotassium hexacyanoferrate + InChIKey=MIMJFNVDBPUTPB-UHFFFAOYSA-N + potassium ferricyanide + CHEBI:30060 + CHEBI:potassium hexacyanoferrate(3-) + "A hexacyanoferrate(3-) salt that has formula C6FeK3N6." [] + C6FeK3N6 + potassium hexacyanoferrate(3-) + + + CHEBI:guanidinium + CHEBI:30087 + guanidinium + CH6N3 + diaminomethaniminium + guanidine + [C(NH2)3](+) + "A guanidinium ion that has formula CH6N3." [] + NC(N)=[NH2+] + InChIKey=ZRALSGWEFCBTJO-UHFFFAOYSA-O + InChI=1S/CH5N3/c2-1(3)4/h(H5,2,3,4)/p+1 + guanidinium + + + CHEBI:photon + hn + photon + . + gamma + "Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force." [] + CHEBI:30212 + foton + photon + Light + hnu + light quantum + Lichtquant + + + positron + positron + "Elementary particle not affected by the strong force having a spin 1/2, a positive elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV." [] + beta(+) + CHEBI:positron + CHEBI:30225 + e(+) + [*+] + . + + + iso-pentane + (CH3)2CH-CH2-CH3 + C5H12 + 1,1,2-trimethylethane + CCC(C)C + CHEBI:isopentane + 1,1-dimethylpropane + CHEBI:30362 + dimethylethylmethane + R-601a + isoamylhydride + 2-methylbutane + "An alkane that is butane substituted by a methyl group at position 2." [] + InChIKey=QWTDNUCVQCZILF-UHFFFAOYSA-N + InChI=1S/C5H12/c1-4-5(2)3/h5H,4H2,1-3H3 + iso-C5H12 + isopentane + isopentane + + + "A cobalt-corrinoid hexaamide that is cobalamin with the oxidation state of the central cobalt atom unspecified." [] + CHEBI:cobalamin + cobalamin + Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-cobamide + COBALAMIN + cobalamin + CHEBI:30411 + + + CHEBI:30412 + CHEBI:monoatomic dication + divalent inorganic cations + divalent cation + Divalent cation + monoatomic dication + [*++] + . + monoatomic dications + + + Siliziumdioxid + silicon dioxide + Silica, amorphous + InChI=1S/O2Si/c1-3-2 + (SiO2)n + InChIKey=VYPSYNLAJGMNEJ-UHFFFAOYSA-N + Kieselsaeureanhydrid + silicon dioxide + [SiO2] + silicic anhydride + O=[Si]=O + silica + CHEBI:silicon dioxide + silicon(IV) oxide + SiO2 + CHEBI:30563 + O2Si + "A silicon oxide made up of linear triatomic molecules in which a silicon atom is covalently bonded to two oxygens." [] + + + InChI=1S/C10H16N5O13P3.Mg/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20;/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20);/q;+2/p-4/t4-,6-,7-,10-;/m1./s1 + C10H12MgN5O13P3 + "A magnesium coordination entity that has formula C10H12MgN5O13P3." [] + [MgATP](2-) + InChIKey=CYYJCOXYBYJLIK-MCDZGGTQSA-J + [Mg++].Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP([O-])(=O)OP([O-])(=O)OP([O-])([O-])=O)[C@@H](O)[C@H]1O + MgATP(2-) + CHEBI:30617 + CHEBI:MgATP(2-) + (adenosine 5'-triphosphato)magnesium(2-) + Mg(atp)(2-) + + + CHEBI:formic acid + Ameisensaeure + hydrogen carboxylic acid + formic acid + methoic acid + [H]C(O)=O + formylic acid + Methanoic acid + bilorin + HCOOH + Formic acid + formic acid + FORMIC ACID + InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3) + InChIKey=BDAGIHXWWSANSR-UHFFFAOYSA-N + H-COOH + HCO2H + CHEBI:30751 + Acide formique + "The simplest carboxylic acid, containing a single carbon. Occurs naturally in various sources including the venom of bee and ant stings, and is a useful organic synthetic reagent. Principally used as a preservative and antibacterial agent in livestock feed. Induces severe metabolic acidosis and ocular injury in human subjects." [] + CH2O2 + aminic acid + + + 2-Hydroxytricarballylic acid + InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12) + citric acid + Citric acid + CITRIC ACID + CHEBI:citric acid + E330 + C6H8O7 + 2-hydroxypropane-1,2,3-tricarboxylic acid + "A tricarboxylic acid that is propane-1,2,3-tricarboxylic acid bearing a hydroxy substituent at position 2. It is an important metabolite in the pathway of all aerobic organisms." [] + OC(=O)CC(O)(CC(O)=O)C(O)=O + 3-Carboxy-3-hydroxypentane-1,5-dioic acid + H3cit + InChIKey=KRKNYBCHXYNGOX-UHFFFAOYSA-N + 2-hydroxypropane-1,2,3-tricarboxylic acid + CHEBI:30769 + citric acid + Citronensaeure + 2-Hydroxy-1,2,3-propanetricarboxylic acid + + + CHEBI:iron trichloride + iron trichloride + InChI=1S/3ClH.Fe/h3*1H;/q;;;+3/p-3 + iron(3+) chloride + ferric chloride + CHEBI:30808 + Cl3Fe + FeCl3 + "An iron coordination entity that has formula Cl3Fe." [] + Cl[Fe](Cl)Cl + [FeCl3] + iron trichloride + InChIKey=RBTARNINKXHZNM-UHFFFAOYSA-K + iron(III) chloride + + + CHEBI:oleate + InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- + (9Z)-octadec-9-enoate + CHEBI:30823 + (Z)-9-octadecenoic acid, ion(1-) + oleate + Oleat + C18H33O2 + (9Z)-octadecenoate + CCCCCCCC\\C=C/CCCCCCCC([O-])=O + oleic acid anion + cis-9-octadecenoate + "A C18, long straight-chain monounsaturated fatty acid anion; and the conjugate base of oleic acid, arising from deprotonation of the carboxylic acid group." [] + InChIKey=ZQPPMHVWECSIRJ-KTKRTIGZSA-M + + + E 355 + C6H10O4 + "An alpha,omega-dicarboxylic acid that is the 1,4-dicarboxy derivative of butane." [] + CHEBI:adipic acid + adipic acid + adipinic acid + OC(=O)CCCCC(O)=O + InChI=1S/C6H10O4/c7-5(8)3-1-2-4-6(9)10/h1-4H2,(H,7,8)(H,9,10) + 1,6-hexanedioic acid + Adipic acid + adipic acid + 1,4-butanedicarboxylic acid + E-355 + hexanedioic acid + INS No. 355 + CHEBI:30832 + E355 + Adipinsaeure + InChIKey=WNLRTRBMVRJNCN-UHFFFAOYSA-N + + + METHYLMALONIC ACID + Methylmalonic acid + alpha-methylmalonic acid + CC(C(O)=O)C(O)=O + 1,1-Ethanedicarboxylic acid + C4H6O4 + InChIKey=ZIYVHBGGAOATLY-UHFFFAOYSA-N + methylpropanedioic acid + methylmalonic acid + 2-methylmalonic acid + InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8) + CHEBI:methylmalonic acid + "A dicarboxylic acid that is malonic acid in which one of the methylene hydrogens is substituted by a methyl group." [] + CHEBI:30860 + 2-methylpropanedioic acid + Isosuccinic acid + + + alcohol + alcohols + "A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom." [] + CHEBI:alcohol + HOR + an alcohol + O[*] + Alcohol + CHEBI:30879 + + + gulitol + CHEBI:glucitol + Sorbitol + sorbitol + glucitol + glucitol + CHEBI:30911 + sorbitols + rel-(2R,3R,4R,5S)-hexane-1,2,3,4,5,6-hexol + C6H14O6 + + + CHEBI:30956 + TCA + trichloroethanoic acid + trichloroacetic acid + InChI=1S/C2HCl3O2/c3-2(4,5)1(6)7/h(H,6,7) + CHEBI:trichloroacetic acid + InChIKey=YNJBWRMUSHSURL-UHFFFAOYSA-N + Trichloressigsaeure + C2HCl3O2 + trichloracetic acid + Trichloroacetic acid + OC(=O)C(Cl)(Cl)Cl + trichloroacetic acid + "A monocarboxylic acid that is acetic acid in which all three methyl hydrogens are substituted by chlorine." [] + + + bile acids + Bile salt + bile acid + Gallensaeure + Gallensaeuren + CHEBI:3098 + "Any member of a group of steroid carboxylic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine." [] + Bile acid + CHEBI:bile acid + + + ClH4N + ammonium chloride + CHEBI:ammonium chloride + Cl.H4N + [Cl-].[H][N+]([H])([H])[H] + InChI=1S/ClH.H3N/h1H;1H3 + ammonium chloride + Ammonium chloride + CHEBI:31206 + "An inorganic chloride that has formula ClH4N." [] + InChIKey=NLXLAEXVIDQMFP-UHFFFAOYSA-N + NH4Cl + Ammoniumchlorid + [NH4]Cl + + + CHEBI:benzethonium chloride + benzethonii chloridum + CHEBI:31264 + cloruro de benzetonio + Neostelin green + Banagerm + Microklenz + p-diisobutyl phenoxyethoxyethyl dimethyl benzylammonium chloride + Sanizol + QAC + Antiseptol + [Cl-].CC(C)(C)CC(C)(C)c1ccc(OCCOCC[N+](C)(C)Cc2ccccc2)cc1 + benzyldimethyl(2-{2-[4-(1,1,3,3-tetramethylbutyl)phenoxy]ethoxy}ethyl)ammonium chloride + Diapp + N-benzyl-N,N-dimethyl-2-{2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethoxy}ethanaminium chloride + benzyldimethyl(2-{2-[p-(1,1,3,3-tetramethylbutyl)phenoxy]ethoxy}ethyl)ammonium chloride + benzethonium chloride + Solamin + diisobutylphenoxyethoxyethyldimethyl benzyl ammonium chloride + Quatrachlor + InChI=1S/C27H42NO2.ClH/c1-26(2,3)22-27(4,5)24-13-15-25(16-14-24)30-20-19-29-18-17-28(6,7)21-23-11-9-8-10-12-23;/h8-16H,17-22H2,1-7H3;1H/q+1;/p-1 + Disilyn + benzethonium chloride + C27H42ClNO2 + {2-[2-(4-diisobutylphenoxy)ethoxy]ethyl}dimethylbenzylammonium chloride + Phemithyn + benzyldimethyl-p-(1,1,3,3-tetramethylbutyl)phenoxyethoxy-ethylammonium chloride + N,N-dimethyl-N-(2-{2-[4-(1,1,3,3-tetramethylbutyl)phenoxy]ethoxy}ethyl)-benzenemethanaminium chloride + Inactisol + chlorure de benzethonium + Salanine + Phemerol chloride + diisobutylphenoxyethoxyethyl dimethyl benzyl ammonium chloride + Benzethonium chloride + benzetonium chloride + Anti-germ 77 + BZT + Phemeride + Kylacol + p-tert-octylphenoxyethoxyethyldimethylbenzylammonium chloride + InChIKey=UREZNYTWGJKWBI-UHFFFAOYSA-M + Hyamine 1622 + Hyamine + Polymine D + "A (synthetic) quaternary ammonium salt that is benzyldimethylamine in which the nitrogen is quaternised by a 2-{2-[p-(2,4,4-trimethylpentan-2-yl)phenoxy]ethoxy}ethyl group, with chloride as the counter-ion. An antiseptic and disinfectant, it is active against a broad spectrum of bacteria, fungi, moulds and viruses." [] + Solamine + + + InChI=1S/C20H12O5/c21-11-5-7-15-17(9-11)24-18-10-12(22)6-8-16(18)20(15)14-4-2-1-3-13(14)19(23)25-20/h1-10,21-22H + Solvent Yellow 94 + fluorescein + 2-(3-hydroxy-6-oxo-6H-xanthen-9-yl)benzoic acid + "A xanthene dye that is a highly fluorescent dye, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy." [] + D and C Yellow No. 7 + fluoresceine + Fluoreszein + resorcinolphthalein + 3,6-fluorandiol + D&C Yellow No. 7 + CHEBI:fluorescein + C20H12O5 + CHEBI:31624 + InChIKey=GNBHRKFJIUUOQI-UHFFFAOYSA-N + Japan Yellow 201 + 9-(o-carboxyphenyl)-6-hydroxy-3H-xanthen-3-one + Oc1ccc2c(Oc3cc(O)ccc3C22OC(=O)c3ccccc23)c1 + Yellow fluorescein + C.I. Solvent Yellow 94 + fluorescein + 2-(6-Hydroxy-3-oxo-3H-xanthen-9-yl)-benzoic acid + 3',6'-dihydroxy-3H-spiro[2-benzofuran-1,9'-xanthen]-3-one + 9-(o-carboxyphenyl)-6-hydroxy-3-isoxanthenone + 3',6'-dihydroxyfluoran + + + CC(=O)N(CC(O)CN(C(C)=O)c1c(I)c(C(=O)NCC(O)CO)c(I)c(C(=O)NCC(O)CO)c1I)c1c(I)c(C(=O)NCC(O)CO)c(I)c(C(=O)NCC(O)CO)c1I + CHEBI:iodixanol + InChI=1S/C35H44I6N6O15/c1-13(52)46(30-26(38)20(32(59)42-3-15(54)9-48)24(36)21(27(30)39)33(60)43-4-16(55)10-49)7-19(58)8-47(14(2)53)31-28(40)22(34(61)44-5-17(56)11-50)25(37)23(29(31)41)35(62)45-6-18(57)12-51/h15-19,48-51,54-58H,3-12H2,1-2H3,(H,42,59)(H,43,60)(H,44,61)(H,45,62) + iodixanol + 5,5'-[(2-hydroxypropane-1,3-diyl)bis(acetylimino)]bis[N,N'-bis(2,3-dihydroxypropyl)-2,4,6-triiodobenzene-1,3-dicarboxamide] + 5,5'-((2-hydroxytrimethylene)bis(acetylimino))bis(N,N'-bis(2,3-dihydroxypropyl)-2,4,6-triiodoisophthalamide) + iodixanol + "A dimeric, non-ionic, water-soluble, radiographic contrast agent, used particularly in coronary angiography." [] + CHEBI:31705 + InChIKey=NBQNWMBBSKPBAY-UHFFFAOYSA-N + iodixanolum + C35H44I6N6O15 + + + Gaultheria oil + 2-Carbomethoxyphenol + methyl salicylate + 2-Hydroxybenzoic acid methyl ester + Natural wintergreen oil + Teaberry oil + "A benzoate ester that is the methyl ester of salicylic acid." [] + Methyl o-hydroxybenzoate + Oil of wintergreen + CHEBI:31832 + Methyl salicylate + methyl salicylate + InChI=1S/C8H8O3/c1-11-8(10)6-4-2-3-5-7(6)9/h2-5,9H,1H3 + COC(=O)c1ccccc1O + Spicewood Oil + Betula oil + C8H8O3 + Methyl 2-hydroxybenzoate + InChIKey=OSWPMRLSEDHDFF-UHFFFAOYSA-N + Sweet birch oil + 2-(Methoxycarbonyl)phenol + CHEBI:methyl salicylate + + + HO4P.2K + CHEBI:32031 + [K+].[K+].OP([O-])([O-])=O + "An organic molecular entity that has formula HO4P.2K." [] + CHEBI:Potassium dibasic phosphate + Potassium dibasic phosphate + InChIKey=ZPWVASYFFYYZEW-UHFFFAOYSA-L + InChI=1S/2K.H3O4P/c;;1-5(2,3)4/h;;(H3,1,2,3,4)/q2*+1;/p-2 + Potassium dibasic phosphate + + + potash lye + CHEBI:potassium hydroxide + Aetzkali + hydroxyde de potassium + InChIKey=KWYUFKZDYYNOTN-UHFFFAOYSA-M + KOH + potasse caustique + [OH-].[K+] + HKO + InChI=1S/K.H2O/h;1H2/q+1;/p-1 + potassium hydroxide + Potassium hydroxide + Kaliumhydroxid + caustic potash + "An alkali metal hydroxide that has formula HKO." [] + potassium hydroxide + CHEBI:32035 + + + "A 1,2-benzisothiazole having a keto-group at the 3-position and two oxo substituents at the 1-position. It is used as an artificial sweetening agent." [] + 2,3-Dihydro-3-oxobenzisosulfonazole + 1,1-Dioxo-1,2-dihydro-benzo[d]isothiazol-3-one + CHEBI:saccharin + 3-Hydroxybenzisothiazole-S,S-dioxide + InChIKey=CVHZOJJKTDOEJC-UHFFFAOYSA-N + Saccharimide + o-Sulfobenzoic acid imide + C7H5NO3S + CHEBI:32111 + InChI=1S/C7H5NO3S/c9-7-5-3-1-2-4-6(5)12(10,11)8-7/h1-4H,(H,8,9) + Benzoic sulfimide + Benzosulfimide + saccharin + Benzo-2-sulphimide + Benzoic acid sulfimide + 2,3-Dihydro-3-oxobenzisosulphonazole + Benzoylsulfonic Imide + Anhydro-o-sulfaminebenzoic acid + 1,2-Benzisothiazolin-3-one 1,1-dioxide + Saccharine + O=C1NS(=O)(=O)c2ccccc12 + 1,1-Dioxo-1,2-benzisothiazol-3(2H)-one + 1,2-Benzisothiazol-3(2H)-one 1,1-dioxide + 1,2-Dihydro-2-ketobenzisosulphonazole + Saccharin + o-Sulfobenzimide + Benzosulphimide + o-Benzoic sulfimide + 1,2-Dihydro-2-ketobenzisosulfonazole + o-Benzosulfimide + 1,2-benzisothiazol-3(2H)-one 1,1-dioxide + Benzoic sulphimide + + + [Na+].O=C1[N-]S(=O)(=O)c2ccccc12 + CHEBI:Saccharin sodium + CHEBI:32112 + Saccharin sodium + Saccharin sodium anhydrous + InChI=1S/C7H5NO3S.Na/c9-7-5-3-1-2-4-6(5)12(10,11)8-7;/h1-4H,(H,8,9);/q;+1/p-1 + "An organic molecular entity that has formula C7H4NNaO3S." [] + InChIKey=WINXNKPZLFISPD-UHFFFAOYSA-M + C7H4NNaO3S + + + CCCCNc1cc(cc(c1Oc1ccccc1)S(N)(=O)=O)C(O)=O + 3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid + InChIKey=MAEIEVLCKWDQJH-UHFFFAOYSA-N + 3-(aminosulfonyl)-5-(butylamino)-4-phenoxybenzoic acid + 3-butylamino-4-(phenoxy)-5-sulfamoylbenzoic acid + InChI=1S/C17H20N2O5S/c1-2-3-9-19-14-10-12(17(20)21)11-15(25(18,22)23)16(14)24-13-7-5-4-6-8-13/h4-8,10-11,19H,2-3,9H2,1H3,(H,20,21)(H2,18,22,23) + bumetanide + bumetanide + "A member of the class of benzoic acids that is 4-phenoxybenzoic acid in which the hydrogens ortho to the phenoxy group are substituted by butylamino and sulfamoyl groups. Bumetanide is a diuretic, and is used for treatment of oedema associated with congestive heart failure, hepatic and renal disease." [] + bumetanida + 3-butylamino-4-phenoxy-5-sulfamoyl-benzoic acid + C17H20N2O5S + CHEBI:3213 + bumetanidum + 3-butylamino-4-phenoxy-5-sulfamoylbenzoic acid + CHEBI:bumetanide + + + silver nitrate + silver(1+) nitrate + CHEBI:silver(1+) nitrate + silver mononitrate + InChI=1S/Ag.NO3/c;2-1(3)4/q+1;-1 + silver(1+) nitrate + "A silver salt that has formula AgNO3." [] + CHEBI:32130 + nitric acid silver(I) salt + [Ag+].[O-]N(=O)=O + InChIKey=SQGYOTSLMSWVJD-UHFFFAOYSA-N + silver(I) nitrate + AgNO3 + + + NaHCO3 + E500 + carbonic acid monosodium salt + [Na+].OC([O-])=O + CHNaO3 + E 500 + CHO3.Na + sodium hydrogencarbonate + sodium hydrogencarbonate + Sodium hydrogencarbonate + Sodium bicarbonate + "An one-carbon compound that has formula CHO3.Na." [] + InChIKey=UIIMBOGNXHQVGW-UHFFFAOYSA-M + baking soda + bicarbonate of soda + CHEBI:32139 + sodium hydrogen carbonate + E-500 + Natriumhydrogenkarbonat + CHEBI:sodium hydrogencarbonate + sodium acid carbonate + InChI=1S/CH2O3.Na/c2-1(3)4;/h(H2,2,3,4);/q;+1/p-1 + + + Aetznatron + InChIKey=HEMHJVSKTPXQMS-UHFFFAOYSA-M + caustic soda + "An alkali metal hydroxide that has formula HNaO." [] + InChI=1S/Na.H2O/h;1H2/q+1;/p-1 + CHEBI:sodium hydroxide + Sodium hydroxide + sodium hydroxide + soude caustique + hydroxyde de sodium + sodium hydrate + NaOH + soda lye + sodium hydroxide + Natriumhydroxid + CHEBI:32145 + HNaO + [OH-].[Na+] + + + Sulpyrid + InChI=1S/C15H23N3O4S/c1-3-18-8-4-5-11(18)10-17-15(19)13-9-12(23(16,20)21)6-7-14(13)22-2/h6-7,9,11H,3-5,8,10H2,1-2H3,(H,17,19)(H2,16,20,21) + InChIKey=BGRJTUBHPOOWDU-UHFFFAOYSA-N + sulpiride + CHEBI:sulpiride + "A member of the class of benzamides obtained from formal condensation between the carboxy group of 2-methoxy-5-sulfamoylbenzoic acid and the primary amino group of (1-ethylpyrrolidin-2-yl)methylamine." [] + 5-(Aminosulfonyl)-N-((1-ethyl-2-pyrrolidinyl)methyl)-2-methoxybenzamide + N-((1-Ethyl-2-pyrrolidinyl)methyl)-5-sulfamoyl-o-anisamide + sulpiridum + C15H23N3O4S + Sulpirid + N-[(1-ethylpyrrolidin-2-yl)methyl]-2-methoxy-5-sulfamoylbenzamide + (+-)-sulpiride + N-((1-Ethyl-2-pyrrolidinyl)methyl)-2-methoxy-5-sulfamoylbenzamide + CHEBI:32168 + CCN1CCCC1CNC(=O)c1cc(ccc1OC)S(N)(=O)=O + sulpirida + sulpiride + + + CHEBI:potassium chloride + Monopotassium chloride + CHEBI:32588 + InChIKey=WCUXLLCKKVVCTQ-UHFFFAOYSA-M + sylvite + KCl + "A metal chloride salt with a K(+) counterion." [] + Klotrix + [Cl-].[K+] + muriate of potash + Kaon-Cl 10 + Klor-con + Kaliumchlorid + potassium chloride + [KCl] + InChI=1S/ClH.K/h1H;/q;+1/p-1 + ClK + potassium chloride + + + magnesium sulfate + Magnesium sulfate (1:1) + "A magnesium salt having sulfate as the counterion." [] + magnesium sulphate + MgSO4 + CHEBI:magnesium sulfate + CHEBI:32599 + InChI=1S/Mg.H2O4S/c;1-5(2,3)4/h;(H2,1,2,3,4)/q+2;/p-2 + Magnesiumsulfat + [Mg++].[O-]S([O-])(=O)=O + magnesium sulfate + InChIKey=CSNNHWWHGAXBCP-UHFFFAOYSA-L + MgO4S + magnesium sulfate anhydrous + magnesium(II) sulfate + + + "A compound formally derived from ammonia by replacing two hydrogen atoms by hydrocarbyl groups." [] + sekundaeres Amin + [H]N([*])[*] + R2NH + CHEBI:32863 + CHEBI:secondary amine + HNR2 + Secondary amine + secondary amines + secondary amine + + + Methylgruppe + CHEBI:methyl group + methyl group + alanine side-chain + group methyle + -Me + CH3- + -CH3 + "An alkyl group that is the univalent group derived from methane by removal of a hydrogen atom." [] + METHYL GROUP + grupo metilo + CHEBI:32875 + methyl + CH3 + + + R3N + tertiary amines + [*]N([*])[*] + tertiaeres Amin + Tertiary amine + CHEBI:32876 + "A compound formally derived from ammonia by replacing three hydrogen atoms by hydrocarbyl groups." [] + CHEBI:tertiary amine + NR3 + tertiary amine + + + C24H50 + CHEBI:tetracosane + CHEBI:32936 + InChIKey=POOSGDOYLQNASK-UHFFFAOYSA-N + CH3-[CH2]22-CH3 + "A straight-chain alkane containing 24 carbon atoms." [] + tetracosane + CCCCCCCCCCCCCCCCCCCCCCCC + InChI=1S/C24H50/c1-3-5-7-9-11-13-15-17-19-21-23-24-22-20-18-16-14-12-10-8-6-4-2/h3-24H2,1-2H3 + n-tetracosane + tetracosane + + + "A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups." [] + CHEBI:amine + Amine + Substituted amine + . + Amin + an amine + amine + N[*] + amines + CHEBI:32952 + + + C2H3NaO2 + "An organic sodium salt that has formula C2H3NaO2." [] + [Na+].CC([O-])=O + sodium acetate anhydrous + anhydrous sodium acetate + sodium acetate + acetic acid, sodium salt + InChI=1S/C2H4O2.Na/c1-2(3)4;/h1H3,(H,3,4);/q;+1/p-1 + sodium acetate + CHEBI:32954 + InChIKey=VMHLLURERBWHNL-UHFFFAOYSA-M + Natriumazetat + CHEBI:sodium acetate + + + CHEBI:epoxide + epoxides + Alkene oxide + "Any cyclic ether in which the oxygen atom forms part of a 3-membered ring." [] + epoxide + epoxides + C2H2OR2 + Epoxide + CHEBI:32955 + [*]C1([*])OC1([*])[*] + C2OR4 + an epoxide + Olefin oxide + + + "An inorganic group obtained by removal of one of the hydroxy groups from phosphoric acid." [] + CHEBI:32958 + -O-P(O)(OH)2 + OP(O)(=O)O-* + phosphonooxy group + phosphonooxy + (HO)2P(O)-O- + H2O4P + phosphate group + CHEBI:phosphate group + phosphooxy group + + + amides + amide + CHEBI:amide + Amide + . + CHEBI:32988 + NC([*])=O + "An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [] + + + "A calcium salt that has formula CaCl2." [] + calcium chloride anhydrous + Calcium chloride anhydrous + CHEBI:3312 + InChI=1S/Ca.2ClH/h;2*1H/q+2;;/p-2 + [CaCl2] + CaCl2 + CHEBI:calcium dichloride + InChIKey=UXVMQQNJUSDDNG-UHFFFAOYSA-L + calcium chloride + calcium dichloride + calcium dichloride + [Cl-].[Cl-].[Ca++] + + + long-chain fatty acyl-coenzyme A + "A fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any long-chain (C13 to C22) fatty acid." [] + LCFA-coenzyme As + CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCSC([*])=O + CHEBI:33184 + LCFA-coenzyme A + long-chain fatty acyl-CoA + Long-chain acyl-CoA + long-chain fatty acyl-coenzyme As + C22H35N7O17P3SR + long-chain fatty acyl-CoAs + CHEBI:long-chain fatty acyl-CoA + LCFA-CoA + LCFA-CoAs + a long-chain acyl-CoA (OLD) + + + elementary particles + elementary particle + fundamental particle + CHEBI:fundamental particle + . + CHEBI:33233 + "A particle not known to have substructure." [] + + + monoatomic entity + . + CHEBI:monoatomic entity + CHEBI:33238 + "A monoatomic entity is a molecular entity consisting of a single atom." [] + atomic entity + monoatomic entities + + + coordination entity + CHEBI:33240 + "An assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands)." [] + coordination entities + . + CHEBI:coordination entity + coordination entity + coordination compounds + + + CHEBI:33241 + oxoacid derivatives + oxoacid derivative + . + CHEBI:oxoacid derivative + + + inorganic hydrides + . + inorganic hydride + CHEBI:inorganic hydride + CHEBI:33242 + + + "An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system." [] + CHEBI:33245 + organic parent hydrides + organic fundamental parents + . + CHEBI:organic fundamental parent + organic fundamental parent + + + "Any substituent group which does not contain carbon." [] + CHEBI:33246 + CHEBI:inorganic group + inorganic groups + . + inorganic group + + + organic groups + CHEBI:33247 + "Any substituent group or skeleton containing carbon." [] + organic group + . + CHEBI:organic group + + + CHEBI:hydrocarbyl group + "A univalent group formed by removing a hydrogen atom from a hydrocarbon." [] + groupe hydrocarbyle + . + hydrocarbyl group + hydrocarbyl group + CHEBI:33248 + hydrocarbyl groups + grupos hidrocarbilo + grupo hidrocarbilo + + + organyl group + groupe organyle + . + CHEBI:33249 + organyl groups + organyl group + CHEBI:organyl group + "Any organic substituent group, regardless of functional type, having one free valence at a carbon atom." [] + grupo organilo + grupos organilo + + + element + CHEBI:33250 + atomus + atomo + atom + . + CHEBI:atom + atome + atoms + "A chemical entity constituting the smallest component of an element having the chemical properties of the element." [] + atom + elements + + + CHEBI:33252 + CHEBI:atomic nucleus + nucleo atomico + nucleus + nucleo + noyau atomique + atomic nucleus + Kern + nuclei + . + nucleus atomi + noyau + Atomkern + "A nucleus is the positively charged central portion of an atom, excluding the orbital electrons." [] + + + CHEBI:33256 + primary amide + primary amide + primary amides + . + CHEBI:primary amide + "A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [] + + + "A derivative of two oxoacids RkE(=O)l(OH)m (l =/= 0) in which two acyl groups are attached to the amino or substituted amino group." [] + secondary amide + secondary amides + CHEBI:33257 + secondary amide + . + CHEBI:secondary amide + + + elemental molecular entity + CHEBI:33259 + "A molecular entity all atoms of which have the same atomic number." [] + CHEBI:elemental molecular entity + homoatomic molecular entities + . + homoatomic entity + homoatomic molecular entity + + + CHEBI:33261 + organosulfur compound + organosulfur compounds + . + CHEBI:organosulfur compound + "An organosulfur compound is a compound containing at least one carbon-sulfur bond." [] + organosulfur compound + + + CHEBI:elemental oxygen + . + elemental oxygen + CHEBI:33262 + + + CHEBI:diatomic oxygen + diatomic oxygen + CHEBI:33263 + O2 + + + triatomic oxygen + CHEBI:33265 + CHEBI:triatomic oxygen + O3 + + + CHEBI:33266 + N2 + diatomic nitrogen + CHEBI:diatomic nitrogen + + + CHEBI:33267 + elemental nitrogen + . + CHEBI:elemental nitrogen + + + polyatomic anion + . + "An anion consisting of more than one atom." [] + CHEBI:polyatomic anion + polyatomic anions + CHEBI:33273 + + + heteroorganic entity + organoelement compounds + CHEBI:33285 + "A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms." [] + . + heteroorganic entities + CHEBI:heteroorganic entity + + + CHEBI:alkali metal molecular entity + alkali metal molecular entity + "A molecular entity containing one or more atoms of an alkali metal." [] + CHEBI:33296 + alkali metal molecular entities + . + + + lithium molecular entity + lithium compounds + CHEBI:33298 + CHEBI:lithium molecular entity + lithium molecular entity + lithium molecular entities + . + + + . + alkaline earth molecular entity + alkaline earth molecular entities + CHEBI:33299 + alkaline earth compounds + alkaline-earth compounds + "An alkaline earth molecular entity is a molecular entity containing one or more atoms of an alkaline earth metal." [] + CHEBI:alkaline earth molecular entity + alkaline earth molecular entity + + + "Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth." [] + group 15 elements + group V elements + CHEBI:33300 + pnictogen + pnictogene + CHEBI:pnictogen + nitrogenoideos + pnictogenes + . + nitrogenoides + pnictogens + + + CHEBI:33302 + CHEBI:pnictogen molecular entity + pnictogen molecular entities + pnictogen molecular entity + . + "A p-block molecular entity containing any pnictogen." [] + pnictogen molecular entity + + + group 16 elements + chalcogene + chalcogens + calcogeno + calcogenos + CHEBI:chalcogen + "Any p-block element belonging to the group 16 family of the periodic table." [] + Chalkogen + CHEBI:33303 + chalcogenes + group VI elements + anfigenos + chalcogen + . + anfigeno + Chalkogene + chalcogen + + + chalcogen molecular entity + "Any p-block molecular entity containing a chalcogen." [] + . + chalcogen molecular entity + chalcogen molecular entities + chalcogen compounds + CHEBI:chalcogen molecular entity + CHEBI:33304 + + + group IV elements + CHEBI:33306 + carbon group element + cristallogenes + CHEBI:carbon group element atom + carbon group element atom + . + cristallogene + carbon group elements + carbonoides + group 14 elements + + + CHEBI:33308 + carboxylic esters + carboxylic ester + CHEBI:carboxylic ester + "An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl." [] + [*]C(=O)O[*] + a carboxylic ester + CO2R2 + Carboxylic ester + carboxylic acid esters + + + "An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table." [] + Hauptgruppenelement + CHEBI:main group element atom + CHEBI:33318 + Hauptgruppenelemente + . + main group element + main group element atom + main group elements + + + silicon oxides + oxides of silicon + CHEBI:33327 + . + CHEBI:silicon oxide + silicon oxide + + + InChIKey=RTAQQCXQSZGOHL-UHFFFAOYSA-N + InChI=1S/Ti + titanium + "A titanium group element atom that has formula Ti." [] + CHEBI:33341 + titane + titanium atom + 22Ti + titanium + Ti + titanio + CHEBI:titanium atom + Titan + [Ti] + + + titanium group element atom + titanium group element + . + CHEBI:33345 + group 4 elements + titanium group elements + CHEBI:titanium group element atom + + + . + CHEBI:hydracid + hydracid + hydracids + hydracid + CHEBI:33405 + "A hydracid is a compound which contains hydrogen that is not bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons)." [] + + + organoarsenic compounds + CHEBI:organoarsenic compound + organoarsenic compound + organoarsenic compound + CHEBI:33406 + . + + + pnictogen oxoacids + CHEBI:pnictogen oxoacid + pnictogen oxoacid + CHEBI:33408 + . + + + CHEBI:33424 + sulfur oxoacid derivatives + CHEBI:sulfur oxoacid derivative + sulfur oxoacid derivative + sulfur oxoacid derivative + . + + + halogen oxoacid + CHEBI:33425 + halogen oxoacid + halogen oxoacids + . + CHEBI:halogen oxoacid + + + . + iodine oxoacids + iodine oxoacid + CHEBI:33428 + CHEBI:iodine oxoacid + iodine oxoacid + + + . + monoatomic monoanions + monoatomic monoanion + CHEBI:33429 + [*-] + CHEBI:monoatomic monoanion + + + CHEBI:elemental chlorine + CHEBI:33431 + elemental chlorine + . + + + monoatomic chlorine + CHEBI:33432 + Cl + CHEBI:monoatomic chlorine + atomic chlorine + + + CHEBI:33433 + monoatomic halogens + . + CHEBI:monoatomic halogen + monoatomic halogen + + + elemental halogen + CHEBI:33434 + CHEBI:elemental halogen + elemental halogen + elemental halogens + . + + + chlorine oxoanion + CHEBI:33437 + chlorine oxoanions + CHEBI:chlorine oxoanion + . + chlorine oxoanion + + + . + halogen oxoanion + CHEBI:33443 + halogen oxoanions + CHEBI:halogen oxoanion + halogen oxoanion + + + iodine oxoanions + iodine oxoanion + . + CHEBI:33445 + CHEBI:iodine oxoanion + iodine oxoanion + + + phosphorylated sugars + phospho sugars + . + phospho sugar + phospho sugar + Sugar phosphate + sugar phosphate + "Any monosaccharide containing an alcoholic hydroxy group esterified with phosphoric acid." [] + monosaccharide phosphates + phosphorylated sugar + CHEBI:phospho sugar + phosphosugars + CHEBI:33447 + phosphosugar + + + CHEBI:nitrogen oxoacid + . + oxoacids of nitrogen + nitrogen oxoacid + nitrogen oxoacids + CHEBI:33455 + + + CHEBI:33459 + pnictogen oxoanion + pnictogen oxoanion + . + pnictogen oxoanions + CHEBI:pnictogen oxoanion + + + elemental pnictogen + . + elemental pnictogens + elemental pnictogen + CHEBI:33465 + CHEBI:elemental pnictogen + + + transition metal molecular entity + transition element molecular entity + CHEBI:transition element molecular entity + . + transition element molecular entities + "A molecular entity containing one or more atoms of a transition element." [] + CHEBI:33497 + + + . + alkali metal cation + CHEBI:33504 + alkali metal cations + CHEBI:alkali metal cation + + + . + alkaline earth cation + alkaline earth cations + alkaline-earth metal cations + alkaline earth metal cation + CHEBI:alkaline earth cation + CHEBI:33513 + + + . + CHEBI:transition element cation + transition element cation + CHEBI:33515 + transition metal cation + transition element cations + + + Metal + CHEBI:33521 + metals + "An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity." [] + metal elements + . + elemental metal + CHEBI:metal atom + metal atom + elemental metals + metal element + + + . + CHEBI:33551 + organosulfonic acid + sulfonic acids + HO3SR + organosulfonic acids + "An organic derivative of sulfonic acid in which the sulfo group is linked directly to carbon." [] + OS([*])(=O)=O + CHEBI:organosulfonic acid + + + derivatives of sulfonic acid + sulfonic acid derivatives + CHEBI:sulfonic acid derivative + sulfonic acid derivative + CHEBI:33552 + sulfonic acid derivative + . + + + O3SR + CHEBI:33554 + "An organic anion obtained by deprotonation of the sufonate group(s) of any organosulfonic acid." [] + organosulfonate oxoanions + CHEBI:organosulfonate oxoanion + [O-]S([*])(=O)=O + organosulfonate oxoanion + organosulfonate + organosulfonates + . + + + CHEBI:33555 + arenesulfonic acid + arylsulfonic acid + arenesulfonic acids + "Organic derivatives of sulfonic acid in which the sulfo group is linked directly to carbon of an aryl group." [] + CHEBI:arenesulfonic acid + arylsulfonic acids + . + + + s-block element atom + s-block elements + CHEBI:s-block element atom + s-block element + . + CHEBI:33559 + + + p-block element + "Any main group element atom belonging to the p-block of the periodic table." [] + p-block elements + CHEBI:33560 + CHEBI:p-block element atom + . + p-block element atom + + + d-block element atom + CHEBI:33561 + CHEBI:d-block element atom + d-block elements + d-block element + . + + + CHEBI:33566 + a catechol + 1,2-benzenediols + CHEBI:catechols + "Any compound containing an o-diphenol component." [] + catechols + + + CHEBI:33567 + "4-(2-Aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution." [] + catecholamine + CHEBI:catecholamine + catecholamines + catecholamines + Oc1ccc(cc1O)C([*])CN[*] + Catecholamine + C8H9NO2R2 + + + CHEBI:33570 + CHEBI:benzenediols + . + benzenediols + + + Carbonsaeure + OC([*])=O + CHEBI:33575 + carboxylic acids + carboxylic acid + CHO2R + acido carboxilico + "A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid." [] + Carbonsaeuren + carboxylic acid + acidos carboxilicos + Karbonsaeure + CHEBI:carboxylic acid + RC(=O)OH + acide carboxylique + acides carboxyliques + + + main group molecular entity + main group compounds + "A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table." [] + CHEBI:main group molecular entity + . + main group molecular entities + CHEBI:33579 + + + boron group molecular entity + . + CHEBI:33581 + boron group molecular entities + CHEBI:boron group molecular entity + + + carbon group molecular entity + carbon group molecular entities + carbon group molecular entity + CHEBI:33582 + . + CHEBI:carbon group molecular entity + + + cyclic compound + CHEBI:33595 + cyclic compounds + "Any molecule that consists of a series of atoms joined together to form a ring." [] + . + CHEBI:cyclic compound + + + . + homocyclic compound + homocyclic compounds + CHEBI:33597 + CHEBI:homocyclic compound + homocyclic compound + isocyclic compounds + "A cyclic compound having as ring members atoms of the same element only." [] + + + . + "A cyclic compound in which all of the ring members are carbon atoms." [] + CHEBI:carbocyclic compound + carbocycle + carbocyclic compounds + carbocyclic compound + CHEBI:33598 + carbocyclic compound + + + "A compound having one atom as the only common member of two rings." [] + spirocycle + spiro compound + CHEBI:spiro compound + spirofused compounds + spiro-fused compounds + spirocyclic compounds + spirocyclic compound + spiro compounds + . + spirocycles + spiro compound + CHEBI:33599 + + + CHEBI:33608 + . + CHEBI:hydrogen molecular entity + hydrogen molecular entities + hydrogen molecular entity + hydrogen compounds + + + polycyclic compound + polycyclic compounds + . + CHEBI:polycyclic compound + CHEBI:33635 + + + bicyclic compound + . + CHEBI:33636 + bicyclic compounds + "A molecule that features two fused rings." [] + CHEBI:bicyclic compound + + + "Any acyclic or cyclic, saturated or unsaturated carbon compound, excluding aromatic compounds." [] + CHEBI:33653 + . + CHEBI:aliphatic compound + aliphatic compound + aliphatic compounds + + + . + CHEBI:aromatic compound + aromatics + "A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character." [] + CHEBI:33655 + aromatic compound + aromatische Verbindungen + aromatic compounds + aromatic molecular entity + + + . + aromatic hydrocarbons + arene + "Any monocyclic or polycyclic aromatic hydrocarbon." [] + CHEBI:arene + arenes + CHEBI:33658 + arene + + + organic aromatic compound + organic aromatic compounds + CHEBI:33659 + . + CHEBI:organic aromatic compound + + + CHEBI:33661 + . + monocyclic compound + CHEBI:monocyclic compound + monocyclic compounds + + + CHEBI:33663 + cyclic hydrocarbon + cyclic hydrocarbons + . + cyclic hydrocarbon + CHEBI:cyclic hydrocarbon + + + polycyclic hydrocarbon + CHEBI:33666 + polycyclic hydrocarbons + polycyclic hydrocarbon + . + CHEBI:polycyclic hydrocarbon + + + . + heteromonocyclic compounds + heteromonocyclic compound + heteromonocyclic compound + CHEBI:heteromonocyclic compound + CHEBI:33670 + + + CHEBI:33671 + . + heteropolycyclic compounds + CHEBI:heteropolycyclic compound + polyheterocyclic compounds + heteropolycyclic compound + + + CHEBI:33672 + . + CHEBI:heterobicyclic compound + "A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom." [] + heterobicyclic compounds + heterobicyclic compound + + + CHEBI:33673 + zinc group molecular entity + CHEBI:zinc group molecular entity + zinc group molecular entities + . + + + CHEBI:33674 + CHEBI:s-block molecular entity + s-block molecular entity + "An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element." [] + s-block molecular entity + s-block compounds + . + s-block molecular entities + + + CHEBI:p-block molecular entity + "A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element." [] + p-block molecular entitiy + p-block compounds + CHEBI:33675 + p-block molecular entity + . + p-block molecular entities + + + d-block molecular entity + CHEBI:33676 + "A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element." [] + d-block molecular entity + . + d-block molecular entities + d-block compounds + CHEBI:d-block molecular entity + + + CHEBI:hydrides + "Hydrides are chemical compounds of hydrogen with other chemical elements." [] + hydrides + CHEBI:33692 + . + + + oxygen hydride + CHEBI:33693 + oxygen hydrides + CHEBI:oxygen hydride + oxygen hydride + hydrides of oxygen + . + + + . + "A macromolecule formed by a living organism." [] + biopolymers + CHEBI:33694 + biomacromolecule + biomacromolecules + CHEBI:biomacromolecule + biopolymer + Biopolymere + + + CHEBI:information biomacromolecule + information macromolecules + information biomacromolecules + CHEBI:33695 + information biomacromolecule + genetically encoded biomacromolecules + information biopolymers + genetically encoded biopolymers + information macromolecule + . + + + polyatomic cations + "A cation consisting of more than one atom." [] + CHEBI:polyatomic cation + polyatomic cation + . + CHEBI:33702 + + + alpha-amino acid + alpha-Amino acid + CHEBI:33704 + Amino acid + NC([*])C(O)=O + Amino acids + alpha-amino acid + alpha-amino acids + "An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group." [] + C2H4NO2R + CHEBI:alpha-amino acid + alpha-amino carboxylic acids + + + "A non-proteinogenic amino-acid in which the amino group is located on the carbon atom at the position gamma to the carboxy group." [] + gamma-amino acid + gamma-amino acid + . + gamma-amino acids + CHEBI:33707 + CHEBI:gamma-amino acid + + + "When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue." [] + CHEBI:33708 + amino-acid residue + amino-acid residue + . + amino acid residue + CHEBI:amino-acid residue + amino-acid residues + + + "A carboxylic acid containing one or more amino groups." [] + amino acids + Aminokarbonsaeure + Aminosaeure + . + CHEBI:33709 + Aminocarbonsaeure + CHEBI:amino acid + amino acid + + + CHEBI:carbohydrate acid anion + carbohydrate acid anion + carbohydrate acid anion + carbohydrate acid anions + . + CHEBI:33721 + + + . + iron group molecular entities + CHEBI:iron group molecular entity + CHEBI:33744 + iron group molecular entity + iron group molecular entity + + + copper group molecular entity + CHEBI:copper group molecular entity + CHEBI:33745 + . + copper group molecular entities + copper group molecular entity + + + CHEBI:nickel group molecular entity + nickel group molecular entities + nickel group molecular entity + CHEBI:33747 + . + nickel group molecular entity + + + nickel molecular entities + nickel molecular entity + CHEBI:nickel molecular entity + CHEBI:33748 + . + nickel compounds + nickel molecular entity + + + trionates + CHEBI:trionate + trionate + . + CHEBI:33763 + trionate + aldotrionates + + + cobalt group molecular entity + cobalt group molecular entities + CHEBI:cobalt group molecular entity + . + cobalt group molecular entity + CHEBI:33767 + + + organic alcohol + hydroxy compounds + organic hydroxy compound + "An organic compound having at least one hydroxy group attached to a carbon atom." [] + organic hydroxy compounds + CHEBI:organic hydroxy compound + CHEBI:33822 + . + + + CHEBI:33832 + CHEBI:organic cyclic compound + "Any organic molecule that consists of atoms connected in the form of a ring." [] + organic cyclic compound + organic cyclic compounds + . + + + heteroarene + CHEBI:heteroarene + "A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2)." [] + heteroarenes + hetarenes + . + CHEBI:33833 + + + . + CHEBI:benzenoid aromatic compound + CHEBI:33836 + benzenoid aromatic compounds + benzenoid aromatic compound + benzenoid compound + + + . + complex protein + CHEBI:33837 + conjugated proteins + "Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion." [] + CHEBI:conjugated protein + conjugated protein + + + Nucleoside + a nucleoside + OC[C@H]1O[C@@H]([*])[C@H](O)[C@@H]1O + "An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents." [] + CHEBI:nucleoside + CHEBI:33838 + nucleosides + nucleoside + C5H9O4R + nucleosides + + + polymers + polymer + . + CHEBI:33839 + "A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [] + macromolecules + macromolecule + CHEBI:macromolecule + polymer molecule + macromolecule + + + monocyclic arenes + CHEBI:33847 + . + "A monocyclic aromatic hydrocarbon." [] + CHEBI:monocyclic arene + monocyclic arene + + + . + polycyclic aromatic hydrocarbons + PAHs + polycyclic arenes + CHEBI:33848 + PAH + CHEBI:polycyclic arene + "A polycyclic aromatic hydrocarbon." [] + polycyclic arene + + + phenols + "Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring." [] + Aryl alcohol + aryl alcohol + arenols + . + phenols + CHEBI:phenols + CHEBI:33853 + + + aromatic alcohol + aryl alcohols + aryl alcohol + "Any alcohol in which the alcoholic hydroxy group is attached to a carbon which is itself bonded to an aromatic ring." [] + an aromatic alcohol + CHEBI:aromatic alcohol + aromatic alcohols + CHEBI:33854 + + + CHEBI:33859 + CHO2R + CHEBI:aromatic carboxylic acid + aromatic carboxylic acids + aromatic carboxylic acid + aromatic carboxylic acid + "Any carboxylic acid in which the carboxy group is directly bonded to an aromatic ring." [] + + + C6H7N + arylamine + "An amino compound in which the amino group is linked directly to an aromatic system." [] + aromatic amines + arylamines + CHEBI:33860 + aryl amine + aromatic amine + CHEBI:aromatic amine + aryl amines + + + . + CHEBI:transition element coordination entity + transition metal coordination entities + transition element coordination entity + transition element coordination entities + CHEBI:33861 + transition metal coordination compounds + + + . + cobalt molecular entities + CHEBI:33888 + cobalt molecular entity + cobalt compounds + cobalt molecular entity + CHEBI:cobalt molecular entity + + + cobalt coordination entity + CHEBI:33890 + cobalt coordination compounds + cobalt coordination entity + . + CHEBI:cobalt coordination entity + cobalt coordination entities + + + iron coordination entity + CHEBI:iron coordination entity + . + iron coordination entities + iron coordination compounds + CHEBI:33892 + iron coordination entity + + + . + cobalt corrinoids + CHEBI:cobalt corrinoid + cobalt-corrinoids + cobalt corrinoid + CHEBI:33906 + + + metallotetrapyrrole + CHEBI:33909 + metal-tetrapyrrole complex + metal-tetrapyrrole + metallotetrapyrroles + CHEBI:metallotetrapyrrole + . + + + [Co]N1\\C2=C([*])/C3=N/C(=C([*])\\C4=N\\C(=C([*])/C5=NC([*])(C([*])([*])C5([*])[*])C1([*])C([*])([*])C2([*])[*])C([*])([*])C4([*])[*])C([*])([*])C3([*])[*] + corrinoides + Corrinoid protein + CHEBI:33913 + Korrinoid + CHEBI:corrinoid + "A derivative of the corrin nucleus, which contains four reduced or partly reduced pyrrole rings joined in a macrocycle by three =C- groups and one direct carbon-carbon bond linking alpha positions." [] + Corrinoid protein Co+ + corrinoide + C19HN4R21 + corrinoids + corrinoid + Corrinoid + corrinoid + + + InChIKey=GZCGUPFRVQAUEE-UHFFFAOYSA-N + C6H12O6 + aldohexose + Aldohexose + aldohexoses + aldohexose + CHEBI:aldohexose + "A hexose with a (potential) aldehyde group at one end." [] + OCC(O)C(O)C(O)C(O)C=O + CHEBI:33917 + InChI=1S/C6H12O6/c7-1-3(9)5(11)6(12)4(10)2-8/h1,3-6,8-12H,2H2 + . + + + CHEBI:halide salt + halide salts + halide salt + CHEBI:33958 + . + halides + + + CHEBI:33964 + silver molecular entities + silver compounds + silver molecular entity + silver molecular entity + . + CHEBI:silver molecular entity + + + . + CHEBI:33968 + silver salt + CHEBI:silver salt + silver salts + + + CHEBI:33973 + CHEBI:elemental magnesium + elemental magnesium + . + + + magnesium salt + magnesium salts + . + CHEBI:magnesium salt + CHEBI:33975 + + + CHEBI:33976 + CHEBI:magnesium coordination entity + magnesium coordination entity + magnesium coordination entities + . + magnesium coordination entity + magnesium coordination compounds + + + CHEBI:33977 + metallic base + metallic bases + . + CHEBI:metallic base + + + alkali metal hydroxides + alkali metal base + . + CHEBI:33978 + CHEBI:alkali metal hydroxide + alkali metal hydroxide + alkali metal bases + + + CsHO + caesium hydroxide + CHEBI:33988 + [OH-].[Cs+] + cesium hydrate + cesium hydroxide + "A caesium molecular entity that has formula CsHO." [] + InChIKey=HUCVOHYBFXVBRW-UHFFFAOYSA-M + caesium hydroxide + CHEBI:caesium hydroxide + InChI=1S/Cs.H2O/h;1H2/q+1;/p-1 + CsOH + + + alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid + CHEBI:(S)-AMPA + "A non-proteinogenic alpha-amino acid that has formula C7H10N2O4." [] + C7H10N2O4 + (S)-AMPA + CHEBI:34018 + Cc1onc(O)c1CC(N)C(O)=O + InChIKey=UUDAMDVQRQNNHZ-UHFFFAOYSA-N + (S)-2-Amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid + InChI=1S/C7H10N2O4/c1-3-4(6(10)9-13-3)2-5(8)7(11)12/h5H,2,8H2,1H3,(H,9,10)(H,11,12) + (S)-AMPA + + + 2-Hydroxyethyl methacrylate + 2-hydroxyethyl methacrylate + 2-Hydroxyethyl 2-methylacrylate + 2-(Methacryloyloxy)ethanol + Glycol monomethacrylate + HEMA + 2-Hydroxyethylmethacrylate + Glycol methacrylate + 2-hydroxyethyl methacrylate + InChIKey=WOBHKFSMXKNTIM-UHFFFAOYSA-N + 1,2-Ethanediol mono(2-methyl)-2-propenoate + beta-Hydroxyethyl methacrylate + "An enoate ester that is the monomethacryloyl derivative of ethylene glycol." [] + InChI=1S/C6H10O3/c1-5(2)6(8)9-4-3-7/h7H,1,3-4H2,2H3 + Ethylene glycol monomethacrylate + (hydroxyethyl)methacrylate + Hydroxyethyl methacrylate + Ethylene glycol methacrylate + CHEBI:2-hydroxyethyl methacrylate + C6H10O3 + CC(=C)C(=O)OCCO + CHEBI:34288 + + + Dextran polysulfate + Polydextran sulfate + Dextran sulfuric acid + Dextran sulfate 500 + CHEBI:dextran sulfate + Dextran sulphate + Dextran sulfuric acid ester + "A polymer composed of repeating (1->6)-alpha-linked anhydroglucose sulfate units." [] + Dextran sulfate + dextran sulfate + CHEBI:34674 + (C12H20O29S6)n + + + disodium monohydrogen phosphate + disodium hydrogen phosphate + Disodium phosphate + HO4P.2Na + disodium hydrogenphosphate + CHEBI:34683 + HNa2O4P + disodium hydrogenphosphate + InChI=1S/2Na.H3O4P/c;;1-5(2,3)4/h;;(H3,1,2,3,4)/q2*+1;/p-2 + Dibasic sodium phosphate + Na2HPO4 + "A sodium phosphate that has formula HNa2O4P." [] + InChIKey=BNIILDVGGAEEIG-UHFFFAOYSA-L + [Na+].[Na+].OP([O-])([O-])=O + CHEBI:disodium hydrogenphosphate + disodium acid orthophosphate + + + COC(=O)C(C)=C + CHEBI:methyl methacrylate + 2-Methylacrylic acid methyl ester + Methacrylsaeuremethyl ester + Methylmethacrylate + Methyl-methacrylat + Methyl 2-methyl-2-propenoate + Methyl alpha-methylacrylate + MMA + 2-(Methoxycarbonyl)-1-propene + C5H8O2 + 2-Methyl-2-propenoic acid methyl ester + Methacrylic acid methyl ester + "An enoate ester having methacrylic acid as the carboxylic acid component and methanol as the alcohol component." [] + Methyl 2-methylpropenoate + Methyl 2-methylacrylate + Methacrylate de methyle + Methyl methylacrylate + InChIKey=VVQNEPGJFQJSBK-UHFFFAOYSA-N + InChI=1S/C5H8O2/c1-4(2)5(6)7-3/h1H2,2-3H3 + CHEBI:34840 + Methyl methacrylate + methyl methacrylate + + + CHEBI:nocodazole + InChIKey=KYRVNWMVYQXFEU-UHFFFAOYSA-N + CHEBI:34892 + nocodazole + N-(5-(2-thenoyl)-2-benzimidazolyl)carbamic acid methyl ester + R-17934 + N-(5-(2-thienoyl)-2-benzimidazolyl)carbamic acid methyl ester + oncodazole + nocodazole + Nocodazole + InChI=1S/C14H11N3O3S/c1-20-14(19)17-13-15-9-5-4-8(7-10(9)16-13)12(18)11-3-2-6-21-11/h2-7H,1H3,(H2,15,16,17,19) + COC(=O)Nc1nc2cc(ccc2[nH]1)C(=O)c1cccs1 + "A member of the class of benzimidazoles that is benzimidalole which is substituted at position 2 by a (methoxycarbonyl)amino group and at position 5 by a 2-thienoyl group. It is an antineoplastic agent that exerts its effect by depolymerising microtubules." [] + nocodazol + oncobendazole + methyl (5-(2-thienylcarbonyl))-1H-benzimidazole-2-ylcarbamate + methyl [5-(2-thienylcarbonyl)-1H-benzimidazol-2-yl]carbamate + C14H11N3O3S + methyl N-(5-thenoyl-2-benzimidazolyl)carbamate + R17,934 + R 17934 + (5-(2-thienylcarbonyl)-1H-benzimidazol-2-yl)-carbamic acid methyl ester + nocodazolum + + + InChI=1S/C15H17N3O3/c1-21-12-6-4-11(5-7-12)13-8-9-14(16)18(17-13)10-2-3-15(19)20/h4-9,16H,2-3,10H2,1H3,(H,19,20) + InChIKey=ACVGNKYJVGNLIL-UHFFFAOYSA-N + CHEBI:SR95531 + "A methoxybenzene that has formula C15H17N3O3." [] + CHEBI:34968 + SR95531 + C15H17N3O3 + SR95531 + COc1ccc(cc1)-c1ccc(=N)n(CCCC(O)=O)n1 + + + CHEBI:35106 + . + nitrogen hydrides + nitrogen hydride + CHEBI:nitrogen hydride + + + "Saturated acyclic nitrogen hydrides having the general formula NnHn+2." [] + CHEBI:azane + CHEBI:35107 + azane + azanes + . + + + CHEBI:aldose phosphate + . + aldose phosphates + aldose phosphate + CHEBI:35131 + + + ketose phosphate + ketose phosphate + ketose phosphates + . + CHEBI:35132 + CHEBI:ketose phosphate + + + metalloproteine + CHEBI:metalloprotein + metalloproteins + CHEBI:35134 + metalloprotein + metalloprotein + . + + + iron protein + CHEBI:iron protein + CHEBI:35136 + iron proteins + iron protein + iron-containing proteins + . + + + CHEBI:hemoprotein + Haemprotein + hemeproteins + haem protein + CHEBI:35137 + hemoproteins + . + Haemoprotein + haemoprotein + "Conjugated proteins containing heme as the prosthetic group." [] + heme protein + hemoprotein + hemoprotein + + + aldotriose phosphate + CHEBI:aldotriose phosphate + aldotriose phosphates + . + CHEBI:35142 + aldotriose phosphate + + + CHEBI:35155 + CHEBI:elemental calcium + elemental calcium + . + + + Kalziumsalz + calcium salts + CHEBI:calcium salt + CHEBI:35156 + calcium salt + . + Kalziumsalze + + + CHEBI:sulfate salt + CHEBI:35175 + sulfate salts + sulphates + . + sulphate salts + sulfates + sulfate salt + + + CHEBI:2-oxo monocarboxylic acid anion + 2-oxo monocarboxylic acid anions + a 2-oxo carboxylate + [O-]C(=O)C([*])=O + 2-oxo monocarboxylate + C2O3R + "An oxo monocarboxylic acid anion in which the oxo group is located at the 2-position." [] + CHEBI:35179 + 2-oxo monocarboxylic acid anion + + + . + terpene + CHEBI:35186 + "A hydrocarbon of biological origin having carbon skeleton formally derived from isoprene [CH2=C(CH3)CH=CH2]." [] + Terpen + CHEBI:terpene + terpeno + terpenes + terpenes + terpene + terpenos + + + triterpenos + CHEBI:triterpene + Triterpen + "A C30 terpene." [] + . + triterpenes + triterpenes + triterpene + CHEBI:35191 + triterpeno + + + . + CHEBI:nitrogen oxide + CHEBI:35196 + nitrogen oxide + oxides of nitrogen + nitrogen oxides + + + . + CHEBI:35217 + alkaline earth coordination compounds + alkaline earth coordination entities + alkaline earth coordination entity + alkaline earth coordination entity + CHEBI:alkaline earth coordination entity + + + 1,1,1-trichloromethane + [H]C(Cl)(Cl)Cl + CHEBI:chloroform + chloroformium pro narcosi + InChIKey=HEDRZPFGACZZDS-UHFFFAOYSA-N + CHCl3 + chloroform + Chloroform + chloroform + CHEBI:35255 + chloroforme + trichloromethane + Trichlormethan + "A one-carbon compound that is methane in which three of the hydrogens are replaced by chlorines." [] + InChI=1S/CHCl3/c2-1(3)4/h1H + + + CHEBI:35259 + benzofurans + CHEBI:benzofurans + benzofurans + + + "A derivative of ammonium, NH4(+), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually organyl) groups." [] + quaternary ammonium ion + [*][N+]([*])([*])[*] + CHEBI:35267 + quaternary ammonium ions + quaternary ammonium ion + CHEBI:quaternary ammonium ion + quaternary ammonium + Quaternary amine + NR4 + + + CHEBI:quaternary ammonium salt + quaternary ammonium salt + quaternary ammonium compound + quaternary ammonium salt + . + quaternary ammonium compounds + "Derivatives of ammonium compounds, (NH4(+))Y(-), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually organyl) groups." [] + CHEBI:35273 + quaternary ammonium salts + + + ammonium ions + CHEBI:ammonium ion + . + ammonium ion + "Ammonium, NH4(+), and derivatives formed by substitution by univalent groups." [] + CHEBI:35274 + azanium ions + + + S-glycosyl compounds + CHEBI:S-glycosyl compound + S-glycosyl compound + S-glycosyl compound + S-glycosides + thioglycosides + "A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and a S atom bound to a carbon atom, thus creating a C-S bond." [] + CHEBI:35275 + thioglycoside + S-glycoside + . + + + ammonium compounds + ammonium compound + CHEBI:35276 + azanium compounds + "Compounds (NH4(+))Y(-) and derivatives, in which one or more of the hydrogens bonded to nitrogen have been replaced with univalent groups." [] + CHEBI:ammonium compound + . + + + . + betaines + CHEBI:onium betaine + "Neutral molecules having charge-separated forms with an onium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom." [] + CHEBI:35281 + onium betaine + onium betaines + + + CHEBI:ammonium betaine + "Any neutral molecule having charge-separated forms with a quaternary ammonium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom." [] + ammonium betaines + CHEBI:35284 + ammonium betaine + . + + + "Cations of structure R2C=N(+)R2." [] + iminium ion + iminium cations + iminium ions + CHEBI:iminium ion + iminium ion + CHEBI:35286 + . + + + C6H13NO2R + Acylcholine + acylcholines + "A choline ester formed from choline and a carboxylic acid." [] + C[N+](C)(C)CCOC([*])=O + acylcholine + an acylcholine + CHEBI:35287 + CHEBI:acylcholine + + + CHEBI:carbopolycyclic compound + carbopolycyclic compound + "A polyclic compound in which all of the ring members are carbon atoms." [] + CHEBI:35294 + . + carbopolycyclic compounds + + + homopolycyclic compounds + homopolycyclic compound + CHEBI:homopolycyclic compound + CHEBI:35295 + . + + + pentoside + . + CHEBI:pentoside + CHEBI:35312 + pentoside + pentosides + + + CHEBI:hexoside + . + hexoside + CHEBI:35313 + hexoside + hexosides + + + . + deoxy hexoside + deoxy hexosides + deoxy hexoside + CHEBI:35315 + CHEBI:deoxy hexoside + + + "Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from triterpenoids." [] + a steroid + . + CHEBI:35341 + steroids + CHEBI:steroid + Steroid + steroid + + + "A 17-hydroxy steroid in which the hydroxy group at position 17 has a beta-configuration." [] + 17beta-Hydroxysteroid + InChI=1S/C19H32O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h12-17,20-21H,3-11H2,1-2H3/t12?,13?,14?,15?,16?,17-,18?,19?/m0/s1 + InChIKey=CBMYJHIOYJEBSB-SQTCYDLRSA-N + 17beta-hydroxy steroid + . + 17beta-hydroxy steroids + CHEBI:17beta-hydroxy steroid + CHEBI:35343 + CC12CCC3C(CCC4CC(O)CCC34C)C1CC[C@@H]2O + + + 21-hydroxy steroids + 21-hydroxy steroid + CHEBI:21-hydroxy steroid + . + a 21-hydroxysteroid + 21-hydroxysteroids + CHEBI:35344 + 21-Hydroxysteroid + + + 11beta-Hydroxysteroid + 11beta-hydroxy steroid + 11beta-hydroxysteroids + . + CHEBI:11beta-hydroxy steroid + "The beta-stereoisomer of 11-hydroxy steroid." [] + 11beta-hydroxy steroids + CHEBI:35346 + an 11beta-hydroxysteroid + + + 3beta-sterol + 3beta-sterols + 3beta-hydroxysteroids + CHEBI:35348 + CHEBI:3beta-sterol + 3beta-Hydroxysteroid + + + CHEBI:35350 + Hydroxysteroid + CHEBI:hydroxy steroid + hydroxysteroids + hydroxy steroids + hydroxy steroid + + + CHEBI:organonitrogen compound + organonitrogen compounds + "Any heteroorganic entity containing at least one carbon-nitrogen bond." [] + CHEBI:35352 + organonitrogens + organonitrogen compound + . + + + CHEBI:dicarboximide + dicarboximides + secondary carboxamide + [*]N(C([*])=O)C([*])=O + CHEBI:35356 + dicarboximide + "An imide in which the two acyl substituents on nitrogen are carboacyl groups." [] + C2NO2R3 + + + "An amide of a sulfonic acid RS(=O)2NR'2." [] + [*]S(=O)(=O)N([*])[*] + CHEBI:35358 + sulfonamide + sulfonamides + CHEBI:sulfonamide + . + sulfonamides + NO2SR3 + + + acides gras + Fettsaeure + fatty acid + CHO2R + acido graso + CHEBI:35366 + OC([*])=O + acidos grasos + Fettsaeuren + CHEBI:fatty acid + fatty acids + "Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax." [] + Fatty acid + acide gras + fatty acids + + + CHEBI:monosaccharide + "Parent monosaccharides are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H-[CHOH]n-C(=O)[CHOH]m-H with three or more carbon atoms. The generic term 'monosaccharide' (as opposed to oligosaccharide or polysaccharide) denotes a single unit, without glycosidic connection to other such units. It includes aldoses, dialdoses, aldoketoses, ketoses and diketoses, as well as deoxy sugars, provided that the parent compound has a (potential) carbonyl group." [] + monosaccharide + Monosaccharide + CHEBI:35381 + monosaccharide + . + monosaccharides + monosacarido + Monosacharid + monosacaridos + Monosaccharid + + + CHEBI:oxoanion + "An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen." [] + oxoacid anions + oxoanion + oxoanions + . + CHEBI:35406 + oxoanion + + + D-glucoside + CHEBI:D-glucoside + D-Glucoside + D-glucosides + C6H11O6R + OC[C@H]1OC(O[*])[C@H](O)[C@@H](O)[C@@H]1O + CHEBI:35436 + + + CHEBI:nickel coordination entity + nickel coordination entities + . + nickel coordination entity + CHEBI:35438 + nickel coordination entity + nickel coordination compounds + + + cadmium dichloride + Caddy + InChIKey=YKYOUMDCQGMQQO-UHFFFAOYSA-L + Kadmiumchlorid + cadmium dichloride + cadmium chloride + CdCl2 + Dichlorocadmium + [CdCl2] + Cl[Cd]Cl + CHEBI:35456 + cadmium(II) chloride + InChI=1S/Cd.2ClH/h;2*1H/q+2;;/p-2 + cadmium(2+) chloride + "A cadmium coordination entity in which cadmium(2+) and Cl(-) ions are present in the ratio 2:1. Although considered to be ionic, it has considerable covalent character to its bonding." [] + CHEBI:cadmium dichloride + + + CHEBI:lithium salt + Lithiumsalze + Lithiumsalz + . + lithium salts + lithium salt + CHEBI:35478 + + + alkali metal salt + . + alkali metal salts + CHEBI:35479 + CHEBI:alkali metal salt + + + CHEBI:organic disulfide + organic disulfides + S2R2 + . + organic disulfide + "Compounds of structure RSSR in which R and R' are organic groups." [] + [*]SS[*] + CHEBI:35489 + disulfides + + + 1,4-benzodiazepinones + 1,4-benzodiazepinone + CHEBI:1,4-benzodiazepinone + . + CHEBI:35500 + + + CHEBI:natural product fundamental parent + natural product fundamental parent + CHEBI:35507 + natural product fundamental parents + . + + + steroid fundamental parent + steroid fundamental parents + CHEBI:steroid fundamental parent + . + CHEBI:35508 + + + [H][C@]12CCCC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])CC2)[C@H](C)CCCC(C)C + CHEBI:35515 + (5alpha)-cholestane + alpha-cholestane + CHEBI:5alpha-cholestane + 5alpha-cholestane + C27H48 + InChI=1S/C27H48/c1-19(2)9-8-10-20(3)23-14-15-24-22-13-12-21-11-6-7-17-26(21,4)25(22)16-18-27(23,24)5/h19-25H,6-18H2,1-5H3/t20-,21-,22+,23-,24+,25+,26+,27-/m1/s1 + "The 5alpha-stereoisomer of cholestane." [] + InChIKey=XIIAYQZJNBULGD-XWLABEFZSA-N + 5alpha-cholestane + + + cholestane + [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4CCCC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCCC(C)C + InChI=1S/C27H48/c1-19(2)9-8-10-20(3)23-14-15-24-22-13-12-21-11-6-7-17-26(21,4)25(22)16-18-27(23,24)5/h19-25H,6-18H2,1-5H3/t20-,21?,22+,23-,24+,25+,26+,27-/m1/s1 + InChIKey=XIIAYQZJNBULGD-LDHZKLTISA-N + "A steroid fundamental parent that has formula C27H48." [] + C27H48 + cholestane + CHEBI:35516 + CHEBI:cholestane + + + organic heterocyclic fundamental parents + CHEBI:35552 + CHEBI:heterocyclic organic fundamental parent + heterocyclic fundamental parent + heterocyclic parent hydrides + heterocyclic organic fundamental parent + heterocyclic organic fundamental parents + . + + + . + CHEBI:35555 + mancude organic heteromonocyclic parent + mancude-ring organic heteromonocyclic parents + CHEBI:mancude organic heteromonocyclic parent + mancude organic heteromonocyclic parents + + + mancude rings + . + CHEBI:mancude ring + "Any molecular entity that consists of a ring having (formally) the maximum number of noncumulative double bonds." [] + mancunide-ring systems + mancude ring + CHEBI:35568 + mancude-ring systems + + + mancude-ring organic heterocyclic parents + mancude organic heterocyclic parent + CHEBI:mancude organic heterocyclic parent + mancude organic heterocyclic parents + CHEBI:35571 + . + + + CHEBI:organic mancude parent + CHEBI:35573 + . + organic mancude-ring parents + organic mancude parents + organic mancude parent + + + carbon oxoanion + "A negative ion consisting solely of carbon and oxygen atoms, and therefore having the general formula CxOy(n-) for some integers x, y and n." [] + oxocarbon anion + . + carbon oxoanion + CHEBI:carbon oxoanion + CHEBI:35604 + carbon oxoanions + oxocarbon anions + + + carbon oxoacids + carbon oxoacid + . + CHEBI:35605 + CHEBI:carbon oxoacid + oxoacids of carbon + + + trisodium orthovanadate + sodium vanadate(V) + sodium tetraoxidovanadate(3-) + trisodium trioxido(oxo)vanadium + sodium vanadate (ortho) + sodium tetraoxidovanadate(V) + sodium pervanadate + trisodium vanadate + trisodium tetraoxovanadate + sodium tetraoxovanadate(3-) + sodium o-vanadate + Na3O4V + CHEBI:trisodium vanadate + InChI=1S/3Na.4O.V/q3*+1;;3*-1; + "An inorganic sodium salt of formula Na3VO4 containing the tetrahedral VO4(3-)" [] + vanadic acid (H3VO4), sodium salt + CHEBI:35607 + [Na+].[Na+].[Na+].[O-][V]([O-])([O-])=O + sodium vanadium oxide + vanadic acid, trisodium salt + trisodium vanadate + Na3VO4 + InChIKey=IHIXIJGXTJIKRB-UHFFFAOYSA-N + sodium vanadate + vanadate (VO4(3-)), trisodium + + + "Any ether in which the oxygen is attached to at least one aryl substituent." [] + CHEBI:aromatic ether + aromatic ether + CHEBI:35618 + . + aromatic ethers + + + beta-Lactam + beta-lactam + . + beta-lactam + CHEBI:35627 + "A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon." [] + CHEBI:beta-lactam + beta-lactams + + + Secondary alcohol + R-CHOH-R' + "A secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it." [] + CHEBI:secondary alcohol + OC([*])[*] + a secondary alcohol + secondary alcohol + CH2OR2 + CHEBI:35681 + secondary alcohols + + + aryl sulfide + aryl sulfide + aryl sulfides + CHEBI:35683 + . + CHEBI:aryl sulfide + + + Dicarboxylic acid + "An oxoacid containing two carboxy groups." [] + CHEBI:35692 + CHEBI:dicarboxylic acid + dicarboxylic acids + dicarboxylic acid + + + dicarboxylic acid anion + dicarboxylic acid anions + CHEBI:dicarboxylic acid anion + dicarboxylic acid anion + CHEBI:35693 + . + + + cobalt(II) chloride + Cl2Co + CHEBI:35696 + Kobaltdichlorid + cobalt dichloride + Kobalt chlorid + cobalt chloride + InChIKey=GVPFVAHMJGGAJG-UHFFFAOYSA-L + cobalt dichloride + cobaltous dichloride + [Cl-].[Cl-].[Co++] + CHEBI:cobalt dichloride + cobaltous chloride anhydrous + cobaltous chloride + cobalt muriate + Kobalt(II)-chlorid + InChI=1S/2ClH.Co/h2*1H;/q;;+2/p-2 + "A cobalt salt in which the cobalt metal is in the +2 oxidation state and the counter-anion is chloride. It is used as an indicator for water in desiccants." [] + dichlorocobalt + CoCl2 + cobalt(2+) chloride + + + . + CHEBI:cobalt salt + cobalt salts + cobalt salt + CHEBI:35698 + cobalt salt + + + "A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter." [] + esters + [*]OC([*])=O + ester + . + CHEBI:ester + CHEBI:35701 + Ester + + + InChIKey=RTZKZFJDLAIYFH-UHFFFAOYSA-N + 1,1'-oxybisethane + ethoxyethane + InChI=1S/C4H10O/c1-3-5-4-2/h3-4H2,1-2H3 + aether pro narcosi + ethyl ether + 3-oxapentane + Anesthetic ether + C4H10O + CHEBI:35702 + R-610 + aether + Aether + diethyl ether + 1,1'-oxydiethane + Ether + CHEBI:diethyl ether + "An ether in which the oxygen atom is linked to two ethyl groups." [] + ethyl oxide + Diethyl ether + Diethylaether + CCOCC + Pronarcol + diethyl oxide + + + CHEBI:nitro compound + CHEBI:35715 + nitro compound + nitro compounds + . + "A compound having a nitro group, -NO2 (free valence on nitrogen), which may be attached to carbon, nitrogen (as in nitramines), or oxygen (as in nitrates), among other elements (in the absence of specification, C-nitro compounds are usually implied)." [] + + + "A nitro compound having the nitro group (-NO2) attached to a carbon atom." [] + C-nitro compound + CHEBI:35716 + . + CHEBI:C-nitro compound + C-nitro compounds + + + sulfated glycosaminoglycans + . + glycosaminoglycan sulfate + sulfated glycosaminoglycan + CHEBI:sulfated glycosaminoglycan + glycosaminoglycan sulfates + CHEBI:35722 + + + carbohydrate sulfate + . + CHEBI:carbohydrate sulfate + CHEBI:35724 + carbohydrate sulfates + carbohydrate sulphates + + + CHEBI:35740 + liposaccharide + CHEBI:liposaccharide + liposaccharides + + + glycerolipids + glycerolipid + CHEBI:35741 + CHEBI:glycerolipid + "Any member of the group of lipids containing a common glycerol backbone to which at least one fatty acyl group is esterified." [] + + + tricarboxylic acid anion + "Any anion of a tricarboxylic acid formed by deprotonation of at least one carboxy group." [] + tricarboxylic acid anions + . + CHEBI:35753 + tricarboxylic acid anion + CHEBI:tricarboxylic acid anion + + + monocarboxylates + "A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated." [] + CHEBI:monocarboxylic acid anion + monocarboxylic acid anion + CO2R + CHEBI:35757 + a monocarboxylate + [O-]C([*])=O + Monocarboxylate + Carboxylate + monocarboxylic acid anions + + + CHEBI:glycerophosphoserine + Glycerophosphoserine + CHEBI:35766 + glycerophosphoserines + glycerophosphoserine + + + CHEBI:arsenic oxoanion + CHEBI:35776 + arsenic oxoanion + arsenic oxoanion + . + oxoanions of arsenic + arsenic oxoanions + + + CHEBI:35786 + sphingophospholipids + CHEBI:phosphosphingolipid + sphingophospholipid + phosphosphingolipid + phosphosphingolipids + + + seco-steroids + CHEBI:35788 + seco-steroid + CHEBI:seco-steroid + + + CHEBI:35789 + CHEBI:oxo steroid + oxo steroids + keto steroids + ketosteroids + oxo steroid + oxosteroids + + + "An azole based on a five-membered heterocyclic aromatic skeleton containing one N and one O atom." [] + oxazoles + oxazole + CHEBI:oxazole + oxazole + . + CHEBI:35790 + + + CHEBI:35800 + nitroso compounds + CHEBI:nitroso compound + "Compounds having the nitroso group, -NO, attached to carbon, or to another element, most commonly nitrogen or oxygen." [] + nitroso compound + . + + + "Compounds having the structure R2S=O (R =/= H)." [] + CHEBI:sulfoxide + . + sulfoxides + sulfoxide + CHEBI:35813 + sulfoxide + + + branched-chain fatty acid + "Any fatty acid in which the parent hydrocarbon chain has one or more alkyl substituents; a common component in animal and bacterial lipids. The fatty acyl chain is usually saturated and the substituent a methyl group; however, unsaturated BCFAs are found in marine animals, and branches other than methyl are found in microbial lipids." [] + branched fatty acids + branched fatty acid + CHEBI:branched-chain fatty acid + . + CHEBI:35819 + BCFA + Branched chain fatty acid + BCFAs + branched-chain fatty acids + + + sulfone + sulfones + CHEBI:sulfone + sulfone + CHEBI:35850 + "Compounds having the structure RS(=O)2R (R =/= H)." [] + . + + + hydroxy monocarboxylic acid + CHEBI:35868 + hydroxy monocarboxylic acids + hydroxy acid + CHEBI:hydroxy monocarboxylic acid + + + oxo monocarboxylic acid + CHEBI:oxo monocarboxylic acid + "Any monocarboxylic acid having at least one additional oxo functional group." [] + CHEBI:35871 + oxo monocarboxylic acids + + + "Anhydrides derived from carboxylic acids." [] + CHEBI:carboxylic anhydride + carboxylic anhydride + . + carboxylic anhydrides + carboxylic anhydrides + carboxylic anhydride + CHEBI:35873 + + + CHEBI:imidazopyrimidine + imidazopyrimidine + . + CHEBI:35875 + imidazopyrimidines + + + pnictogen hydride + CHEBI:35881 + . + CHEBI:pnictogen hydride + pnictogen hydride + pnictogen hydrides + + + CHEBI:oxo monocarboxylic acid anion + oxo monocarboxylic acid anions + CHEBI:35902 + oxo monocarboxylic acid anion + + + oxo carboxylic acid anion + "Any carboxylic acid anion containing at least one oxo group." [] + oxo carboxylic acid anions + CHEBI:35903 + CHEBI:oxo carboxylic acid anion + + + steryl ester + CHEBI:sterol ester + Steryl ester + sterol ester + Sterol ester + C20H31O2R + CHEBI:35915 + + + CHEBI:35969 + beta-hydroxy acids + CHEBI:3-hydroxy monocarboxylic acid + beta-hydroxy carboxylic acid + "A hydroxy monocarboxylic acid that has a hydroxy group beta to the carboxy group." [] + beta-hydroxy carboxylic acids + 3-hydroxy monocarboxylic acids + 3-hydroxy monocarboxylic acid + 3-hydroxy acid + beta-hydroxy acid + + + penams + "Natural and synthetic antibiotics containing the 4-thia-1-azabicyclo[3.2.0]heptan-7-one structure, generally assumed to have the 5R configuration unless otherwise specified." [] + CHEBI:35992 + penams + . + CHEBI:penams + + + benzoate ester + . + "Esters of benzoic acid or substituted benzoic acids." [] + benzoate ester + benzoate esters + benzoic acid esters + CHEBI:36054 + CHEBI:benzoate ester + + + CHEBI:hydroxy monocarboxylic acid anion + CHEBI:36059 + "Any monocarboxylic acid anion carrying at least one hydroxy substituent." [] + hydroxymonocarboxylic acid anions + hydroxy monocarboxylic acid anions + hydroxymonocarboxylic acid anion + hydroxy monocarboxylic acid anion + + + . + organic prosthetic group proteins + organic prosthetic group protein + CHEBI:organic prosthetic-group protein + organic prosthetic-group protein + CHEBI:36072 + + + cholanoids + bile acids and derivatives + CHEBI:cholanoid + cholanoid + CHEBI:36078 + . + + + CHEBI:36080 + CHEBI:protein + proteins + . + "A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome." [] + protein + + + inorganic chlorides + CHEBI:36093 + inorganic chloride salts + inorganic chloride + CHEBI:inorganic chloride + inorganic chloride salt + . + + + organic chloride salt + CHEBI:organic chloride salt + organic chloride salts + . + CHEBI:36094 + + + . + alicyclic ketones + alicyclic ketones + CHEBI:36132 + alicyclic ketone + CHEBI:alicyclic ketone + "A cyclic ketone in which the carbocyclic ring structure which may be saturated or unsaturated, but may not be a benzenoid or other aromatic system." [] + alicyclic ketone + + + Chinon + quinone + CHEBI:quinone + . + a quinone + quinones + CHEBI:36141 + "Compounds having a fully conjugated cyclic dione structure, such as that of benzoquinones, derived from aromatic compounds by conversion of an even number of -CH= groups into -C(=O)- groups with any necessary rearrangement of double bonds (polycyclic and heterocyclic analogues are included)." [] + quinones + quinone + + + CHEBI:disaccharide + Disaccharid + Disacharid + CHEBI:36233 + disacarido + "A compound in which two monosaccharides are joined by a glycosidic bond." [] + disacaridos + disaccharide + disaccharides + Disaccharide + + + "Members of the class of cholanic acids based on a 5beta-cholane skeleton." [] + CHEBI:5beta-cholanic acids + 5beta-cholanic acids + CHEBI:36248 + + + "A glycine or taurine amide of a bile acid." [] + bile acid conjugate + bile acid conjugates + . + CHEBI:36249 + CHEBI:bile acid conjugate + + + CHEBI:36277 + "A salt of a bile acid." [] + . + bile acid salts + bile acid salt + CHEBI:bile acid salt + + + cholan-24-oic acids + CHEBI:cholanic acids + . + cholanic acids + CHEBI:36278 + + + CHEBI:36294 + hexacyanoferrate(4-) salt + ferrocyanides + . + CHEBI:hexacyanoferrate(4-) salt + hexacyanoferrate(4-) salt + hexacyanoferrate(4-) salts + ferrocyanide salts + + + hexacyanoferrates + CHEBI:hexacyanoferrate salt + hexacyanoferrate salt + CHEBI:36295 + hexacyanoferrate salts + . + hexacyanoferrate salt + + + ferricyanide salts + CHEBI:36296 + . + hexacyanoferrate(3-) salt + hexacyanoferrate(3-) salts + hexacyanoferrate(3-) salt + CHEBI:hexacyanoferrate(3-) salt + ferricyanides + + + macrocyclic tetrapyrroles + CHEBI:cyclic tetrapyrrole + macrocyclic tetrapyrrole + CHEBI:36309 + cyclic tetrapyrroles + cyclic tetrapyrrole + . + + + CHEBI:36313 + CHEBI:glycerophosphocholine + "The glycerol phosphate ester of a phosphocholine. A nutrient with many different roles in human health." [] + sn-glycero-3-phosphocholines + glycerophosphocholines + Glycerophosphocholine + glycerophosphocholine + + + CHEBI:36314 + glycerophosphoethanolamine + CHEBI:glycerophosphoethanolamine + glycerophosphoethanolamines + sn-glycero-3-phosphoethanolamines + Glycerophosphoethanolamine + + + CHEBI:36315 + glycerophosphoinositol + glycerophosphoinositols + CHEBI:glycerophosphoinositol + phosphoinositide + phosphoinositol + Glycerophosphoinositol + "Any glycerophospholipid having the polar alcohol inositol esterified to the phosphate group at the sn-3 position of the glycerol backbone." [] + GPI + + + CHEBI:dipyrrole + CHEBI:36316 + dipyrrole + . + dipyrroles + + + lepton + CHEBI:36338 + leptons + CHEBI:lepton + . + "Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin)." [] + + + fermions + "Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi." [] + fermion + CHEBI:36340 + fermion + . + CHEBI:fermion + + + boson + "Particle of integer spin quantum number following Bose-Einstein statistics. Bosons are named after Satyendra Nath Bose." [] + boson + . + bosons + CHEBI:36341 + CHEBI:boson + + + subatomic particles + subatomic particle + "A particle smaller than an atom." [] + CHEBI:subatomic particle + CHEBI:36342 + . + + + . + nuclear particle + CHEBI:36347 + "A nucleus or any of its constituents in any of their energy states." [] + CHEBI:nuclear particle + nuclear particle + + + . + CHEBI:polyatomic entity + CHEBI:36357 + "Any molecular entity consisting of more than one atom." [] + polyatomic entity + polyatomic entities + + + . + "An ion consisting of more than one atom." [] + polyatomic ions + CHEBI:36358 + CHEBI:polyatomic ion + polyatomic ion + + + phosphorus oxoacid derivative + . + CHEBI:phosphorus oxoacid derivative + phosphorus oxoacid derivatives + CHEBI:36359 + phosphorus oxoacid derivative + + + CHEBI:phosphorus oxoacids and derivatives + phosphorus oxoacids and derivatives + phosphorus oxoacids and derivatives + . + CHEBI:36360 + + + CHEBI:alkaline earth salt + alkaline earth salt + CHEBI:36364 + . + alkaline earth salts + + + CHEBI:mancude organic heterotricyclic parent + mancude-ring organic heterotricyclic parents + . + mancude organic heterotricyclic parents + CHEBI:36416 + mancude organic heterotricyclic parent + + + C15H12ClNO2 + 2-(6-Chloro-9H-carbazol-2-yl)-propionic acid + carprofen + 6-chloro-alpha-methyl-9H-carbazole-2-acetic acid + CC(C(O)=O)c1ccc2c(c1)[nH]c1ccc(Cl)cc21 + (+-)-6-chloro-alpha-methylcarbazole-2-acetic acid + carprofeno + InChI=1S/C15H12ClNO2/c1-8(15(18)19)9-2-4-11-12-7-10(16)3-5-13(12)17-14(11)6-9/h2-8,17H,1H3,(H,18,19) + carprofen + (+/-)-2-(3-chloro-9H-carbazol-7-yl)propanoic acid + CHEBI:364453 + CHEBI:carprofen + "Propanoic acid in which one of the methylene hydrogens is substituted by a 6-chloro-9H-carbazol-2-yl group. A non-steroidal anti-inflammatory drug, it is no longer used in human medicine but is still used for treatment of arthritis in elderly dogs." [] + carprofene + carprofenum + InChIKey=PUXBGTOOZJQSKH-UHFFFAOYSA-N + 2-(6-chloro-9H-carbazol-2-yl)propanoic acid + + + CHEBI:polycyclic ether + CHEBI:36468 + polycyclic ether + polycyclic ethers + . + + + CHEBI:quinazoline alkaloid + "Any alkaloid based on a quinazoline skeleton and its substituted derivatives." [] + quinazoline alkaloids + quinazoline alkaloid + CHEBI:36470 + + + ZnO + CHEBI:36560 + InChIKey=XLOMVQKBTHCTTD-UHFFFAOYSA-N + zinc oxide + O=[Zn] + zinc oxide + Zinkoxid + "A zinc molecular entity that has formula OZn." [] + oxyde de zinc + CHEBI:zinc oxide + InChI=1S/O.Zn + OZn + oxido de cinc + + + CHEBI:36562 + . + main group coordination compounds + main-group coordination entity + CHEBI:main-group coordination entity + "A coordination entity in which the central atom to which the ligands are attached comes from groups 1, 2, 13, 14, 15, 16, 17, or 18 of the periodic table." [] + main-group coordination entities + + + CHEBI:36563 + . + CHEBI:zinc group coordination entity + zinc group coordination compounds + zinc group coordination entities + zinc group coordination entity + + + CHEBI:36565 + cadmium coordination entities + . + CHEBI:cadmium coordination entity + cadmium coordination compounds + cadmium coordination entity + + + . + "Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives." [] + CHEBI:36586 + carbonyl compound + carbonyl compounds + CHEBI:carbonyl compound + + + "Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element." [] + . + oxo compounds + CHEBI:36587 + organic oxo compound + CHEBI:organic oxo compound + organic oxo compounds + + + acid anhydride + CHEBI:36606 + acid anhydrides + acid anhydrides + CHEBI:acid anhydride + anhydride d'acide + acid anhydride + "Compounds consisting of two acyl groups bonded to the same oxygen atom acyl-O-acyl." [] + . + + + CHEBI:36608 + . + acyclic acid anhydrides + CHEBI:acyclic acid anhydride + acyclic acid anhydrides + acyclic acid anhydride + acyclic acid anhydride + acyclic anhydrides + + + acetic acid anhydride + CHEBI:acetic anhydride + acetic anhydride + "An acyclic carboxylic anhydride that has formula C4H6O3." [] + Essigsaeureanhydrid + CC(=O)OC(C)=O + InChI=1S/C4H6O3/c1-3(5)7-4(2)6/h1-2H3 + ethanoic anhydride + C4H6O3 + acetic anhydride + acetyl oxide + CHEBI:36610 + ethanoic anhydrate + InChIKey=WFDIJRYMOXRFFG-UHFFFAOYSA-N + anhydride acetique + acetanhydride + + + Triterpenoid + triterpenoides + "Any terpenoid derived from a triterpene. The term includes compounds in which the C30 skeleton of the parent triterpene has been rearranged or modified by the removal of one or more skeletal atoms (generally methyl groups)." [] + triterpenoid + CHEBI:triterpenoid + . + triterpenoids + CHEBI:36615 + + + CHEBI:acyclic carboxylic anhydride + acyclic carboxylic anhydride + acyclic carboxylic anhydride + CHEBI:36631 + acyclic carboxylic acid anhydrides + . + acyclic carboxylic anhydrides + + + CHEBI:36683 + organochlorine compound + CHEBI:organochlorine compound + organochlorine compounds + "An organochlorine compound is a compound containing at least one carbon-chlorine bond." [] + chloroorganic compounds + . + organochlorine compound + chlororganische Verbindungen + + + CHEBI:36684 + organohalogen compound + "A compound containing at least one carbon-halogen bond." [] + . + organohalogen compounds + CHEBI:organohalogen compound + + + CHEBI:heterotricyclic compound + CHEBI:36688 + heterotricyclic compound + heterotricyclic compound + . + heterotricyclic compounds + heterotricyclic compounds + + + CHEBI:36699 + "Any of a class of steroid hormones that are produced in the adrenal cortex." [] + corticosteroid hormones + CHEBI:corticosteroid hormone + . + adrenal cortex hormones + corticosteroid hormone + + + choline phosphates + CHEBI:36700 + "Any compound having phosphocholine as part of its structure." [] + phosphocholines + phosphorylcholines + CHEBI:phosphocholines + O-phosphocholines + + + 2-acyl-1-alkyl-sn-glycero-3-phosphocholines + 1-Radyl-2-acyl-sn-glycero-3-phosphocholine + 2-acyl-1-alkyl-sn-glycero-3-phosphocholine betaines + CHEBI:36702 + C[N+](C)(C)CCOP([O-])(=O)OC[C@@H](CO[*])OC([*])=O + "An alkyl,acyl-sn-glycero-3-phosphocholine in which unspecified alkyl and acyl groups are located at positions 1 and 2 respectively." [] + C9H18NO7PR2 + 2-acyl-1-alkyl-sn-glycero-3-phosphocholine + 1-O-alkyl-2-acyl-sn-glycero-3-phosphocholine + CHEBI:2-acyl-1-alkyl-sn-glycero-3-phosphocholine + 1-Organyl-2-acyl-sn-glycero-3-phosphocholine + + + 1-alkyl-2-acetyl-sn-glycero-3-phosphocholines + 1-Alkyl-2-acetyl-sn-glycero-3-phosphocholine + C10H21NO7PR + platelet-activating factor + 2-acetyl-1-alkyl-sn-glycero-3-phosphocholine zwitterion + CHEBI:2-acetyl-1-alkyl-sn-glycero-3-phosphocholine + "A 2-acyl-1-alkyl-sn-glycero-3-phosphocholine where the 2-O-acyl group is specified as acetyl; a potent phospholipid activator and mediator of many leukocyte functions, including platelet aggregation, inflammation, and anaphylaxis." [] + 2-acetyl-1-alkyl-sn-glycero-3-phosphocholines + 2-acetyl-1-alkyl-sn-glycero-3-phosphocholine + CC(=O)O[C@H](CO[*])COP([O-])(=O)OCC[N+](C)(C)C + 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine + CHEBI:36707 + + + phosphoethanolamines + phosphoethanolamine + CHEBI:36711 + CHEBI:phosphoethanolamine + + + CHEBI:36749 + dipyrrins + CHEBI:dipyrrins + "Compounds containing two pyrrole rings linked through a methine group (-CH=)." [] + dipyrrins + . + + + labdanes + labdane diterpenoid + "Any diterpenoid with a labdane skeleton." [] + labdane diterpenoids + CHEBI:labdane diterpenoid + CHEBI:36770 + + + "A salt formally resulting from the reaction of hydrochloric acid with an organic base." [] + hydrochloride salts + hydrochloride + . + CHEBI:hydrochloride + CHEBI:36807 + Hydrochlorid + hydrochlorides + + + ring assemblies + "Two or more cyclic systems (single rings or fused systems) which are directly joined to each other by double or single bonds are named ring assemblies when the number of such direct ring junctions is one less than the number of cyclic systems involved." [] + . + ring assembly + CHEBI:ring assembly + ring assembly + CHEBI:36820 + + + pseudohalide anions + pseudohalide ions + CHEBI:pseudohalide anion + pseudohalide anion + CHEBI:36828 + pseudohalides + pseudohalogen ion + . + pseudohalogen anion + + + polyatomic monoanions + CHEBI:polyatomic monoanion + polyatomic monoanion + . + CHEBI:36829 + + + CHEBI:monoanion + monoanions + . + monoanion + CHEBI:36830 + + + 3-hydroxy steroid + CHEBI:36834 + CHEBI:3-hydroxy steroid + "Any hydroxy steroid carrying a hydroxy group at position 3." [] + 3-hydroxy steroids + + + "A 3-hydroxy steroid in which the 3-hydroxy substituent is in the beta-position." [] + 3beta-hydroxy steroid + CHEBI:3beta-hydroxy steroid + a 3beta-hydroxysteroid + CHEBI:36836 + 3beta-hydroxy steroids + + + "A hydroxy steroid carrying a hydroxy group at position 17." [] + CHEBI:17-hydroxy steroid + 17-hydroxy steroids + 17-hydroxy steroid + CHEBI:36838 + + + 11-hydroxy steroids + CHEBI:11-hydroxy steroid + CHEBI:36841 + 11-hydroxy steroid + + + CHEBI:36843 + 7alpha-hydroxy steroids + "A 7-hydroxy steroid in which the hydroxy group at position 7 has an alpha-configuration." [] + CHEBI:7alpha-hydroxy steroid + 7alpha-hydroxy steroid + + + 7-hydroxy steroids + CHEBI:36844 + 7-hydroxy steroid + "A hydroxy steroid carrying a hydroxy substituent at position 7." [] + CHEBI:7-hydroxy steroid + + + 12-hydroxy steroid + CHEBI:36845 + 12-hydroxy steroids + CHEBI:12-hydroxy steroid + + + 12beta-hydroxy steroid + CHEBI:12beta-hydroxy steroid + 12beta-hydroxy steroids + CHEBI:36847 + + + CHEBI:36853 + hydroxy seco-steroid + hydroxy seco-steroids + CHEBI:hydroxy seco-steroid + + + 14-hydroxy steroid + CHEBI:14-hydroxy steroid + 14-hydroxy steroids + CHEBI:36860 + + + CHEBI:36862 + 14beta-hydroxy steroid + CHEBI:14beta-hydroxy steroid + "A 14-hydroxy steroid in which the hydroxy group has a beta-configuration." [] + 14beta-hydroxy steroids + + + inorganic radical + CHEBI:inorganic radical + inorganic radicals + CHEBI:36871 + . + + + radical anion + CHEBI:36873 + anion radical + radical anion + CHEBI:radical anion + . + radical anions + + + CHEBI:radical ion + ion radical + radical ions + "A radical that carries an electric charge." [] + radical ion + CHEBI:36875 + . + radical ion + + + CHEBI:36876 + inorganic radical anion + inorganic anion radical + inorganic radical anions + CHEBI:inorganic radical anion + . + + + CHEBI:inorganic radical ion + CHEBI:36878 + inorganic ion radical + inorganic radical ion + . + inorganic radical ions + + + 20-oxo steroids + "An oxo steroid carrying an oxo group at position 20." [] + CHEBI:36885 + CHEBI:20-oxo steroid + 20-oxo steroid + + + elemental iodine + CHEBI:36893 + CHEBI:elemental iodine + . + + + monoatomic iodine + atomic iodine + CHEBI:36897 + I + CHEBI:monoatomic iodine + + + chalcogen hydrides + CHEBI:36902 + chalcogen hydride + . + CHEBI:chalcogen hydride + chalcogen hydride + + + inorganic ions + inorganic ion + CHEBI:36914 + . + CHEBI:inorganic ion + + + CHEBI:36915 + . + CHEBI:inorganic cation + inorganic cations + inorganic cation + + + Kation + cation + CHEBI:36916 + CHEBI:cation + . + cation + Cation + "A monoatomic or polyatomic species having one or more elementary charges of the proton." [] + cations + cationes + Kationen + + + InChI=1S/C/i1+2 + carbon-14 atom + (14)6C + CHEBI:36927 + C + carbon-14 + (14)C + [14C] + "A carbon atom that has formula C." [] + InChIKey=OKTJSMMVPCPJKN-NJFSPNSNSA-N + carbon-14 + CHEBI:carbon-14 atom + carbon, isotope of mass 14 + + + aryl phosphate + CHEBI:aryl phosphate + aryl phosphates + CHEBI:36943 + + + organochalcogen compound + "An organochalcogen compound is a compound containing at least one carbon-chalcogen bond." [] + organochalcogen compounds + . + organochalcogen compound + CHEBI:36962 + CHEBI:organochalcogen compound + + + organooxygen compounds + organooxygen compound + CHEBI:36963 + . + "An organochalcogen compound containing at least one carbon-oxygen bond." [] + organooxygen compound + CHEBI:organooxygen compound + + + "A nucleotide is a nucleoside phosphate. It is a phosphate ester that has a nucleoside moiety and has at least one phosphate moiety attached to the C-5 carbon of the ribose or deoxyribose moiety." [] + nucleotide + CHEBI:36976 + Nucleotide + a nucleotide + CHEBI:nucleotide + nucleotides + + + pyridine nucleotide + pyridine nucleotides + CHEBI:pyridine nucleotide + CHEBI:36980 + + + cyclic purine nucleotide + CHEBI:36982 + cyclic purine nucleotides + CHEBI:cyclic purine nucleotide + + + nicotinamide dinucleotide + CHEBI:37007 + CHEBI:nicotinamide dinucleotide + nicotinamide dinucleotides + + + nucleoside bisphosphate + CHEBI:nucleoside bisphosphate + nucleoside bisphosphates + CHEBI:37123 + + + CHEBI:caesium molecular entity + CHEBI:37128 + caesium molecular entity + cesium compounds + caesium molecular entity + caesium molecular entities + . + caesium compounds + + + organobromine compound + bromoorganic compound + CHEBI:organobromine compound + "A compound containing at least one carbon-bromine bond." [] + organobromine compounds + . + CHEBI:37141 + + + organoiodine compound + "An organoiodine compound is a compound containing at least one carbon-iodine bond." [] + organoiodine compounds + CHEBI:organoiodine compound + organoiodine compound + CHEBI:37142 + . + + + fluororganische Verbindungen + organofluorine compound + fluoroorganic compounds + organofluorine compounds + CHEBI:organofluorine compound + fluoroorganics + "An organofluorine compound is a compound containing at least one carbon-fluorine bond." [] + CHEBI:37143 + organofluorine compound + . + fluoroorganic compound + + + glucan + Glucan + C12H22O11(C6H10O5)n + glucans + "A polysaccharide composed of glucose residues." [] + glucan + CHEBI:37163 + CHEBI:glucan + + + . + homopolysaccharides + CHEBI:37164 + homopolysaccharide + CHEBI:homopolysaccharide + homoglycan + "Glycans composed of a single type of monosaccharide residue. They are named by replacing the ending '-ose' of the sugar by '-an'." [] + homopolysaccharide + + + organic hydrides + CHEBI:37175 + . + organic hydride + CHEBI:organic hydride + + + mononuclear hydride + . + mononuclear parent hydride + CHEBI:37176 + CHEBI:mononuclear parent hydride + mononuclear hydrides + mononuclear parent hydrides + + + CHEBI:37240 + adenosine 3',5'-bisphosphates + adenosine 3',5'-bisphosphate + CHEBI:adenosine 3',5'-bisphosphate + + + . + elemental sodium + CHEBI:37246 + CHEBI:elemental sodium + + + . + CHEBI:37247 + elemental potassium + CHEBI:elemental potassium + + + elemental zinc + CHEBI:elemental zinc + . + CHEBI:37253 + + + tropane alkaloid + CHEBI:37332 + tropane alkaloids + tropanes + CHEBI:tropane alkaloid + + + mucopolysaccharides + CHEBI:mucopolysaccharide + Mucopolysaccharide + Mucopolysaccharid + mucopolisacaridos + mucopolysaccharide + "Any of the group of polysaccharides composed of alternating units from uronic acids and glycosamines, and commonly partially esterified with sulfuric acid." [] + Mukopolysaccharid + . + mucopolisacarido + CHEBI:37395 + + + CHEBI:proteoglycan + proteoglycan + "A glycoprotein in which the carbohydrate units are polysaccharides that contain amino sugars. The protein is glycosylated by one or more (up to about 100) glycosaminoglycans." [] + CHEBI:37396 + Proteoglycan + . + proteoglycans + + + CHEBI:37404 + . + CHEBI:elemental copper + elemental copper + + + cyclic ethers + "Any ether in which the oxygen atom forms part of a ring." [] + epoxy compounds + epoxy compounds + cyclic ether + CHEBI:cyclic ether + cyclic ethers + cyclic ether + CHEBI:37407 + + + CHEBI:37413 + nucleoside triphosphate analogues + nucleoside triphosphate analogue + CHEBI:nucleoside triphosphate analogue + + + dihydroxyanthraquinone + C14H8O4 + CHEBI:37484 + dihydroxy-9,10-anthracenedione + CHEBI:dihydroxyanthraquinone + dihydroxy-9,10-anthraquinone + dihydroxyanthraquinone + dihydroxyanthracene-9,10-dione + + + CHEBI:37485 + an hydroxyanthraquinone + . + CHEBI:hydroxyanthraquinones + hydroxyanthraquinones + "An anthraquinone substituted with one or more hydroxy groups." [] + + + CHEBI:37532 + CHEBI:phorbol ester + "Esters of phorbol, originally found in croton oil (from Croton tiglium, of the family Euphorbiaceae). A number of phorbol esters possess activity as tumour promoters and activate the mechanisms associated with cell growth. Some of these are used in experiments as activators of protein kinase C." [] + phorbol ester + . + phorbol ester + + + [H][C@@]12C=C(CO)C[C@]3(O)C(=O)C(C)=C[C@@]3([H])[C@@]1(O)[C@H](C)[C@@H](OC(=O)CCCCCCCCCCCCC)[C@]1(OC(C)=O)[C@@]2([H])C1(C)C + CHEBI:37537 + tetradecanoylphorbol acetate + phorbol 12-tetradecanoate 13-acetate + PMA + "A phorbol ester that has formula C36H56O8." [] + 12-Tetradecanoylphorbol 13-acetate + InChIKey=PHEDXBVPIONUQT-RGYGYFBISA-N + InChI=1S/C36H56O8/c1-7-8-9-10-11-12-13-14-15-16-17-18-29(39)43-32-24(3)35(42)27(30-33(5,6)36(30,32)44-25(4)38)20-26(22-37)21-34(41)28(35)19-23(2)31(34)40/h19-20,24,27-28,30,32,37,41-42H,7-18,21-22H2,1-6H3/t24-,27+,28-,30-,32-,34-,35-,36-/m1/s1 + (1aR,1bS,4aR,7aS,7bS,8R,9R,9aS)-9a-acetoxy-4a,7b-dihydroxy-3-(hydroxymethyl)-1,1,6,8-tetramethyl-5-oxo-1a,1b,4,4a,5,7a,7b,8,9,9a-decahydro-1H-cyclopropa[3,4]benzo[1,2-e]azulen-9-yl tetradecanoate + phorbol 13-acetate 12-myristate + 12-O-Tetradecanoylphorbol 13-acetate + C36H56O8 + CHEBI:phorbol 13-acetate 12-myristate + Phorbol 12-myristate 13-acetate + phorbol-12-myristate-13-acetate + + + fatty acyl-CoA + CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCSC([*])=O + C22H35N7O17P3SR + fatty acyl-coenzyme A + fatty acyl-coenzyme As + CHEBI:37554 + . + "An acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any fatty acid." [] + Fatty acyl CoA + CHEBI:fatty acyl-CoA + + + omega-carboxyacyl-CoA + "An acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with one of the carboxy groups of any alpha,omega-dicarboxylic acid." [] + CHEBI:37555 + . + CHEBI:omega-carboxyacyl-CoA + omega-Carboxyacyl-CoA + omega-carboxyacyl-CoA + + + "A molecular entity consisting of two or more chemical elements." [] + CHEBI:heteroatomic molecular entity + . + CHEBI:37577 + heteroatomic molecular entities + chemical compound + heteroatomic molecular entity + + + "Any heteroatomic molecular entity that is a chemical compound of halogen with other chemical elements." [] + CHEBI:halide + halides + . + halide + CHEBI:37578 + + + acid halide + acyl halide + . + "A compound consisting of an acyl group bonded to halogen." [] + acyl halide + CHEBI:acyl halide + CHEBI:37579 + + + gamma-lactonas + CHEBI:37581 + CHEBI:gamma-lactone + gamma-Laktone + gamma-lactone + gamma-lactona + "A lactone having a five-membered lactone ring." [] + gamma-lactones + 1,4-Lactone + a 1,4-lactone + . + 1,4-lactones + butyrolactones + + + sodium dihydrogenphosphate + [Na+].OP(O)([O-])=O + sodium phosphate monobasic anhydrous + CHEBI:37585 + "A sodium phosphate that has formula H2NaO4P." [] + sodium phosphate, monobasic + phosphoric acid, monosodium salt + monosodium phosphate + InChI=1S/Na.H3O4P/c;1-5(2,3)4/h;(H3,1,2,3,4)/q+1;/p-1 + NaH2PO4 + H2NaO4P + CHEBI:sodium dihydrogenphosphate + sodium dihydrogen phosphate + sodium dihydrogenphosphate + InChIKey=AJPJDKMHJJGVTQ-UHFFFAOYSA-M + + + CHEBI:37586 + sodium phosphate + . + sodium phosphate + sodium orthophosphate + phosphoric acid, sodium salt + sodium phosphates + CHEBI:sodium phosphate + sodium salt of phosphoric acid + + + [*]C(=O)N([*])[*] + CHEBI:carboxamide + CNOR3 + CHEBI:37622 + "An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom." [] + primary carboxamide + carboxamides + . + carboxamide + carboxamides + + + mannose + manno-hexose + CHEBI:mannose + mannose + C6H12O6 + CHEBI:37684 + Man + "An aldohexose that is the C-2 epimer of glucose." [] + + + indolocarbazoles + indolocarbazole alkaloids + CHEBI:37697 + . + CHEBI:indolocarbazole alkaloid + indolocarbazole alkaloid + + + CHEBI:phosphoric ester + phosphoric ester + phosphoric esters + phosphate esters + CHEBI:37734 + + + CHEBI:glycerophospholipid + phosphoglycerides + phosphatides + glycerophospholipids + Glycerophospholipid + C3H8O6PR + CHEBI:37739 + Glycerophosphodiester + "Any glycerolipid having a phosphate group ester-linked to a terminal carbon of the glycerol backbone." [] + phosphatide + glycerophospholipid + phosphoglyceride + + + aminosulfonic acid + "An organosulfonic acid containing one or more amino groups." [] + aminosulfonic acids + amino sulfonic acid + . + amino sulfonic acids + CHEBI:amino sulfonic acid + CHEBI:37793 + + + sulfuric acid derivative + sulfuric acid derivatives + CHEBI:37826 + . + sulfuric acid derivative + CHEBI:sulfuric acid derivative + + + carboxylic acyl groups + CHEBI:carboacyl group + CHEBI:37838 + carboacyl groups + . + carboacyl group + "A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid." [] + carboxylic acyl group + + + CHEBI:fluorescein isothiocyanate + "An oxaspiro compound that is an isothiocyanato derivative of fluorescein. It exists as two isomers, with the isothiocyanato group located at either the 5- or 6-position." [] + 3',6'-Dihydroxy-5(or 6)-isothiocyanatospiro(isobenzofuran-1(3H),9'-(9H)xanthene)-3-one + fluorescein isothiocyanate + fluorescein isothiocyanate + Fluoreszeinisothiocyanat + FITC + 3',6'-dihydroxy-4-isothiocyanato-3H-spiro[2-benzofuran-1,9'-xanthen]-3-one + CHEBI:37926 + + + xanthene dyes + . + CHEBI:37929 + "A dye derived by condensation of phthalic anhydride with resorcinol (and derivatives) or m-aminophenol (and derivatives)." [] + CHEBI:xanthene dye + xanthene dye + + + CHEBI:polysaccharide sulfate + polysaccharide sulfates + CHEBI:37944 + "Any carbohydrate sulfate that is a polysaccharide carrying at least one O-sulfo substituent." [] + polysaccharide sulfate + + + CHEBI:37947 + CHEBI:benzothiazoles + benzothiazoles + + + CHEBI:37948 + "A spiro compound in which at least one of the cyclic components is an oxygen heterocyle." [] + CHEBI:oxaspiro compound + oxaspiro compound + oxaspiro compounds + + + cyanine dye + "Cyanine dyes are synthetic dyes with the general formula R2N[CH=CH]nCH=N(+)R2 <-> R2N(+)=CH[CH=CH]nNR2 (n is a small number) in which the nitrogen and part of the conjugated chain usually form part of a heterocyclic system, such as imidazole, pyridine, pyrrole, quinoline and thiazole." [] + Zyaninfarbstoff + CHEBI:cyanine dye + CHEBI:37960 + . + Cyaninfarbstoff + cyanine dyes + + + [32P] + phosphorus-32 + InChIKey=OAICVXFJPJFONN-OUBTZVSYSA-N + CHEBI:37972 + InChI=1S/P/i1+1 + phosphorus-32 + Phosphorus, isotope of mass 32 + phosphorus, isotope of mass 32 + phosphorus-32 atom + "The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days." [] + P + CHEBI:phosphorus-32 atom + (32)P + (32)15P + + + [33P] + phosphorus-33 + phosphorus-33 atom + "The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2." [] + CHEBI:37973 + InChI=1S/P/i1+2 + phosphorus-33 + phosphorus, isotope of mass 33 + CHEBI:phosphorus-33 atom + P + (33)P + InChIKey=OAICVXFJPJFONN-NJFSPNSNSA-N + (33)15P + + + sulfur-35 + sulfur-35 atom + (35)S + S + sulphur-35 + CHEBI:sulfur-35 atom + (35)16S + sulfur-35 + [35S] + "The radioactive isotope of sulfur with relative atomic mass 34.9690322 and nuclear spin (3)/2. The longest-lived sulfur radionuclide with half-life of 87.5 days." [] + InChIKey=NINIDFKCEFEMDL-AKLPVKDBSA-N + CHEBI:37983 + sulfur, isotope of mass 35 + InChI=1S/S/i1+3 + + + CHEBI:Cy3 dye + . + CHEBI:37987 + [H]C(=CC([H])=C1Cc2ccccc2N1[*])C1=[N+]([*])c2ccccc2C1 + C19H15N2R2 + Cy3 dye + + + . + [H]C(C=C([H])C1=[N+]([*])c2ccccc2C1)=CC([H])=C1Cc2ccccc2N1[*] + C21H17N2R2 + CHEBI:37989 + Cy5 dye + CHEBI:Cy5 dye + + + "A macromolecule derived from one species of (real, implicit or hypothetical) monomer." [] + homopolymer + . + homopolymers + CHEBI:homopolymer macromolecule + homopolymer molecules + homopolymer macromolecule + homopolymer molecule + CHEBI:37997 + + + "A carbopolyclic compound comprising of three carbocyclic rings." [] + CHEBI:carbotricyclic compound + carbotricyclic compounds + CHEBI:38032 + carbotricyclic compound + + + CHEBI:polypyrrole + "A compound composed of two or more pyrrole units." [] + polypyrroles + CHEBI:38077 + polypyrrole + PPys + poly(pyrrole)s + + + CHEBI:38084 + "Compounds having the structure RS(=O)=NR." [] + CHEBI:sulfoximide + sulfoximides + sulfoximides + sulfoximines + . + sulfoximide + + + spirostanyl glycoside + spirostanyl glycosides + CHEBI:spirostanyl glycoside + CHEBI:38091 + spirostanyl glycoside + "Any steroid saponin that consists of a spirostan and its substituted derivatives as the aglycone moiety." [] + . + + + CHEBI:organonitrogen heterocyclic compound + . + organonitrogen heterocyclic compounds + "Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms." [] + CHEBI:38101 + heterocyclic organonitrogen compounds + organonitrogen heterocyclic compound + + + oxacycles + heterocyclic organooxygen compounds + . + organooxygen heterocyclic compounds + "Any organic heterocyclic compound containing at least one ring oxygen atom." [] + CHEBI:38104 + CHEBI:oxacycle + oxacycle + + + organosulfur heterocyclic compound + heterocyclic organosulfur compounds + . + CHEBI:organosulfur heterocyclic compound + organosulfur heterocyclic compounds + CHEBI:38106 + + + acyl fluoride + CHEBI:38110 + acid fluoride + acyl fluorides + "A compound consisting of an acyl group bonded to fluorine." [] + CHEBI:acyl fluoride + + + dialdehydes + CHEBI:38124 + CHEBI:dialdehyde + bialdehydes + . + dialdehyde + "Any aldehyde with two aldehyde groups." [] + bialdehyde + + + "Cyclic hemiacetals formed by intramolecular addition of a hydroxy group to an aldehydic or ketonic carbonyl group. They are thus 1-oxacycloalkan-2-ols or unsaturated analogues." [] + lactol + CHEBI:lactol + CHEBI:38131 + . + lactols + lactols + lactol + + + CHEBI:organic heterotetracyclic compound + organic heterotetracyclic compound + CHEBI:38163 + organic heterotetracyclic compounds + + + organic heteropentacyclic compound + organic heteropentacyclic compounds + CHEBI:organic heteropentacyclic compound + CHEBI:38164 + + + organic heterooctacyclic compound + CHEBI:organic heterooctacyclic compound + CHEBI:38165 + organic heterooctacyclic compounds + + + CHEBI:organic heteropolycyclic compound + multi-ring heterocyclic compounds + . + organic heteropolycyclic compound + organic heteropolycyclic compounds + CHEBI:38166 + + + monocyclic heteroarene + monocyclic heteroarenes + CHEBI:monocyclic heteroarene + CHEBI:38179 + + + CHEBI:polycyclic heteroarene + CHEBI:38180 + polycyclic heteroarene + polycyclic heteroarenes + + + pyridinium salt + pyridinium salts + CHEBI:38188 + CHEBI:pyridinium salt + + + tetrahydropyrroles + "Any of a class of heterocyclic amines having a saturated five-membered ring." [] + CHEBI:pyrrolidines + pyrrolidines + CHEBI:38260 + + + pyrrolidinone + CHEBI:38275 + CHEBI:pyrrolidinone + pyrrolidinones + + + azabicycloalkane + azabicycloalkanes + CHEBI:38295 + CHEBI:azabicycloalkane + + + CHEBI:thiabicycloalkane + thiabicycloalkane + CHEBI:38297 + thiabicycloalkanes + + + CHEBI:38303 + azirinopyrroloindole + CHEBI:azirinopyrroloindole + azirinopyrroloindoles + + + diazines + CHEBI:38313 + CHEBI:diazines + "Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure)." [] + + + CHEBI:beta-D-arabinoside + beta-D-arabinoside + CHEBI:38315 + beta-D-arabinosides + . + + + pyrimidones + CHEBI:38337 + CHEBI:pyrimidone + pyrimidone + "A pyrimidine carrying one or more oxo substituents." [] + + + aminopyrimidine + aminopyrimidines + "A member of the class of pyrimidines that is pyrimidine substituted by at least one amino group and its derivatives." [] + CHEBI:38338 + CHEBI:aminopyrimidine + + + thiazoles + CHEBI:38418 + 1,3-thiazole + CHEBI:1,3-thiazole + 1,3-thiazoles + + + 1-benzopyran + 1-benzopyrans + CHEBI:38443 + CHEBI:1-benzopyran + + + cyanomethane + InChI=1S/C2H3N/c1-2-3/h1H3 + MeCN + acetonitrile + methyl cyanide + ACETONITRILE + acetonitrile + InChIKey=WEVYAHXRMPXWCK-UHFFFAOYSA-N + CH3-C#N + "A nitrile that is hydrogen cyanide in which the hydrogen has been replaced by a methyl group." [] + C2H3N + CHEBI:acetonitrile + ethanenitrile + CC#N + NCMe + CHEBI:38472 + + + alkaloid ester + alkaloid esters + CHEBI:38481 + CHEBI:alkaloid ester + + + CHEBI:38530 + quinazolines + CHEBI:quinazolines + "Any organic heterobicyclic compound based on a quinazoline skeleton and its substituted derivatives." [] + + + CHEBI:38551 + . + CHEBI:cytochrome b + cytochrome b + b-type cytochrome + cytochrome b + + + CHEBI:simple protein + CHEBI:38560 + simple proteins + . + simple protein + + + CHEBI:phenethylamine alkaloid + phenethylamine alkaloid + phenethylamine alkaloids + CHEBI:38605 + + + methyloxacyclopropane + InChIKey=GOOHAUXETOMSMM-UHFFFAOYSA-N + [H]C1(C)CO1 + CHEBI:1,2-epoxypropane + epoxypropane + 1,2-Propylene oxide + C3H6O + 1,2-propylene oxide + CHEBI:38685 + 2,3-epoxypropane + 1,2-epoxypropane + "An epoxide that is oxirane substituted by a methyl group at position 2." [] + Propylene oxide + propylene oxide + methyloxirane + 1,2-epoxypropane + InChI=1S/C3H6O/c1-3-2-4-3/h3H,2H2,1H3 + 2-methyloxirane + + + CHEBI:38700 + organic sodium salt + CHEBI:organic sodium salt + organic sodium salts + . + organic sodium salt + + + CHEBI:inorganic sodium salt + CHEBI:38702 + . + inorganic sodium salt + inorganic sodium salts + + + "Any dianion containing at least one carboxy group." [] + carboxylic acid dianion + CHEBI:38716 + carboxylic acid dianions + CHEBI:carboxylic acid dianion + carboxylic acid dianion + . + + + morpholines + CHEBI:38785 + CHEBI:morpholines + "Any compound containing morpholine as part of its structure." [] + + + CHEBI:38830 + CHEBI:1-benzofurans + "A member of the class of benzofurans consisting of a 1-benzofuran skeleton and its substituted derivatives thereof." [] + 1-benzofurans + + + CHEBI:38835 + xanthenes + CHEBI:xanthenes + + + borate salt + CHEBI:38908 + . + Boratsalze + CHEBI:borate salts + borate salts + + + CHEBI:trisodium borate + trisodium borate + CHEBI:38909 + Natriumborat + InChI=1S/BO3.3Na/c2-1(3)4;;;/q-3;3*+1 + "A borate salt that has formula BNa3O3." [] + BNa3O3 + InChIKey=BSVBQGMMJUBVOD-UHFFFAOYSA-N + Na3BO3 + [Na+].[Na+].[Na+].[O-]B([O-])[O-] + sodium borate + trisodium borate + + + indole alkaloids + "An alkaloid containing an indole skeleton." [] + CHEBI:38958 + CHEBI:indole alkaloid + indole alkaloid + Indole alkaloid + . + + + CHEBI:38975 + methylbenzenes + "Any alkylbenzene that is benzene substituted with one or more methyl groups." [] + methylbenzene + CHEBI:methylbenzene + . + + + alkylbenzene + CHEBI:alkylbenzene + CHEBI:38976 + alkylbenzenes + alkylbenzene + "A monocyclic arene that is benzene substituted with one or more alkyl groups." [] + . + Alkylbenzol + + + CHEBI:MES + MES + . + CHEBI:39010 + + + "Protein component on the surface of lipoprotein." [] + CHEBI:39015 + apolipoprotein + CHEBI:apolipoprotein + apolipoproteins + . + + + CHEBI:39033 + . + PIPES + CHEBI:PIPES + + + CHEBI:NTA + CHEBI:39054 + . + nitrilotriacetate + NTA + + + CHEBI:39123 + CHEBI:calcium cation + calcium cation + calcium cations + calcium cation + Ca + + + calcium ion + calcium ion + CHEBI:39124 + CHEBI:calcium ion + calcium ions + Ca + + + magnesium cations + magnesium cation + Mg + CHEBI:magnesium cation + magnesium cation + CHEBI:39127 + + + Mg + CHEBI:magnesium ion + magnesium ions + CHEBI:39128 + magnesium ion + magnesium ion + + + . + CHEBI:39146 + trichostatin + CHEBI:trichostatin + trichostatin + trichostatins + + + CHEBI:dibenzopyran + "Any organic heteropolycyclic compound based on a skeleton consisting of a pyran ring fused with two benzene rings." [] + dibenzopyrans + dibenzopyran + CHEBI:39203 + + + CHEBI:39205 + dibenzopyrroles + dibenzopyrrole + CHEBI:dibenzopyrrole + + + CHEBI:dibenzopyridine + CHEBI:39206 + dibenzopyridines + dibenzopyridine + + + azatetracycloalkanes + "Any organic heterotetracyclic compound where at least one of the specified hetero atoms is nitrogen." [] + CHEBI:azatetracycloalkane + azatetracycloalkane + CHEBI:39266 + + + oxatetracycloalkanes + CHEBI:oxatetracycloalkane + CHEBI:39267 + "Any organic heterotetracyclic compound where at least one of the specified hetero atoms is oxygen." [] + oxatetracycloalkane + + + CHEBI:39270 + naphthofurans + naphthofuran + CHEBI:naphthofuran + + + halomethanes + CHEBI:39279 + CHEBI:halomethane + . + halomethane + halomethane + + + . + straight-chain saturated fatty acid + CHEBI:39418 + "Any saturated fatty acid lacking a side-chain." [] + CHEBI:straight-chain saturated fatty acid + straight-chain saturated fatty acid + straight-chain saturated fatty acids + + + CHEBI:pyrimidines + . + "Any compound having a pyrimidine as part of its structure." [] + pyrimidines + a pyrimidine + pyrimidines + CHEBI:39447 + + + CHEBI:cyclic ketone + Cyclic ketone + cyclic ketone + CHEBI:3992 + cyclic ketones + + + cytochrome + CHEBI:4056 + cytochromes + cytochrome + Cytochrome + CHEBI:cytochrome + "A cytochrome is a hemoprotein whose characteristic mode of action involves transfer of reducing equivalents associated with a reversible change in oxidation state of the prosthetic group. Formally, this redox change involves a single-electron, reversible equilibrium between the Fe(II) and Fe(III) states of the central iron atom." [] + cytochromes + . + + + 2-sulfanylethanol + CHEBI:41218 + mercaptoethanol + InChIKey=DGVVWUTYPXICAM-UHFFFAOYSA-N + OCCS + C2H6OS + Mercaptoethanol + Thioglycol + 2-sulfanylethanol + "An alkanethiol that has formula C2H6OS." [] + InChI=1S/C2H6OS/c3-1-2-4/h3-4H,1-2H2 + BETA-MERCAPTOETHANOL + beta-mercaptoethanol + 2-Mercaptoethanol + CHEBI:mercaptoethanol + + + BENZOIC ACID PHENYLMETHYLESTER + O=C(OCc1ccccc1)c1ccccc1 + benzyl benzoate + phenylmethyl benzoate + CHEBI:41237 + benzoic acid, phenylmethyl ester + benzoic acid, benzyl ester + "A benzoate ester obtained by the formal condensation of benzoic acid with benzyl alcohol. It has been isolated from the plant species of the genus Polyalthia." [] + benzyl benzoate + InChI=1S/C14H12O2/c15-14(13-9-5-2-6-10-13)16-11-12-7-3-1-4-8-12/h1-10H,11H2 + C14H12O2 + InChIKey=SESFRYSPDFLNCH-UHFFFAOYSA-N + Benylate + CHEBI:benzyl benzoate + + + CI Basic Violet 3 + CI 42555 + Atmonil + Basic Violet BN + crystal violet + Gentiaverm + Vianin + Basic Violet 3 + Meroxylan + Viocid + Pyoktanin + hexamethyl-p-rosaniline chloride + Calcozine Violet 6BN + CRYSTAL VIOLET + InChIKey=ZXJXZNDDNMQXFV-UHFFFAOYSA-M + Crystal violet + 4-{bis[4-(dimethylamino)phenyl]methylene}-N,N-dimethylcyclohexa-2,5-dien-1-iminium chloride + Blaues pyoktanin + N-(4-{bis[4-(dimethylamino)phenyl]methylidene}cyclohexa-2,5-dien-1-ylidene)-N-methylmethanaminium + methylrosanilinium chloride + CHEBI:crystal violet + Badil + Adergon + N-(-4-{bis[4-(dimethylamino)phenyl]methylene}2,5-cyclohexadien-1-ylidene)-N-methyltrimethanaminium chloride + (4-{bis[-(dimethylamino)phenyl]methylene}-2,5-cyclohexadien-1-ylidene)dimethylammonium chloride + "An organic chloride salt that is the monochloride salt of crystal violet cation. It has been used in creams for the topical treatment of bacterial and fungal infections, being effective against some Gram-positive bacteria (notably Staphylococcus species) and some pathogenic fungi (including Candida species) but use declined following reports of animal carcinogenicity. It has also been used for dying wood, silk, and paper, as well as a histological stain." [] + cloruro de metilrosanilina + Avermin + InChI=1S/C25H30N3.ClH/c1-26(2)22-13-7-19(8-14-22)25(20-9-15-23(16-10-20)27(3)4)21-11-17-24(18-12-21)28(5)6;/h7-18H,1-6H3;1H/q+1;/p-1 + Axuris + Bismuth Violet + Gentianaviolett + Brilliant Violet 5B + Calcozine Violet C + [Cl-].CN(C)c1ccc(cc1)C(=C1C=CC(C=C1)=[N+](C)C)c1ccc(cc1)N(C)C + CHEBI:41688 + hexamethylpararosaniline chloride + C25H30ClN3 + Gentian violet + Methylrosanilinium chloride + methylrosanilinii chloridum + methylrosaniline chloride + C.I. 42555 + Meroxyl + C.I. Basic violet 3 + chlorure de methylrosanilinium + aniline violet + + + tamoxifeno + Apo-Tamox + C26H29NO + Crisafeno + trans-Tamoxifen + tamoxifen + "A stilbenoid that has formula C26H29NO." [] + InChIKey=NKANXQFJJICGDU-QPLCGJKRSA-N + tamoxifenum + CC\\C(c1ccccc1)=C(/c1ccccc1)c1ccc(OCCN(C)C)cc1 + Tamoxifen + InChI=1S/C26H29NO/c1-4-25(21-11-7-5-8-12-21)26(22-13-9-6-10-14-22)23-15-17-24(18-16-23)28-20-19-27(2)3/h5-18H,4,19-20H2,1-3H3/b26-25- + 1-para-beta-Dimethylaminoethoxyphenyl-trans-1,2-diphenylbut-1-ene + Diemon + tamoxifen + 2-{4-[(1Z)-1,2-diphenylbut-1-en-1-yl]phenoxy}-N,N-dimethylethanamine + CHEBI:41774 + 2-{4-[(1Z)-1,2-diphenylbut-1-en-1-yl]phenoxy}-N,N-dimethylethanamine + 1-p-beta-Dimethylaminoethoxyphenyl-trans-1,2-diphenylbut-1-ene + (Z)-2-(para-(1,2-Diphenyl-1-butenyl)phenoxy)-N,N-dimethylamine + (Z)-2-(4-(1,2-Diphenyl-1-butenyl)phenoxy)-N,N-dimethylethanamine + CHEBI:tamoxifen + tamoxifene + + + CHEBI:41865 + Decanedioic acid + C10H18O4 + 1,8-dicarboxyoctane + InChI=1S/C10H18O4/c11-9(12)7-5-3-1-2-4-6-8-10(13)14/h1-8H2,(H,11,12)(H,13,14) + SEBACIC ACID + Sebacinsaeure + Sebacic acid + sebacic acid + decanedioic acid + "An alpha,omega-dicarboxylic acid that is the 1,8-dicarboxy derivative of octane." [] + 1,10-decanedioic acid + InChIKey=CXMXRPHRNRROMY-UHFFFAOYSA-N + CHEBI:sebacic acid + OC(=O)CCCCCCCCC(O)=O + + + "A hexose that has D-configuration at position 5." [] + CHEBI:4194 + D-hexose + D-hexose + D-Hexose + D-hexoses + CHEBI:D-hexose + D-hexopyranose + C6H12O6 + + + D-hexose 6-phosphate + CHEBI:D-hexose 6-phosphate + CHEBI:4195 + D-Hexose 6-phosphate + + + C23H34O5 + digoxigenin + 3beta,12beta,14-trihydroxy-5beta-card-20(22)-enolide + CHEBI:42098 + InChIKey=SHIBSTMRCDJXLN-KCZCNTNESA-N + 3-[(3S,5R,8R,9S,10S,12R,13S,14S,17R)-10,13-dimethyl-3,12,14-tris(oxidanyl)-1,2,3,4,5,6,7,8,9,11,12,15,16,17-tetradecahydrocyclopenta[a]phenanthren-17-yl]-2H-furan-5-one + [H][C@]12CC[C@]3([H])[C@]([H])(C[C@@H](O)[C@]4(C)[C@]([H])(CC[C@]34O)C3=CC(=O)OC3)[C@@]1(C)CC[C@H](O)C2 + 3-[(3S,5R,8R,9S,10S,12R,13S,14S,17R)-3,12,14-trihydroxy-10,13-dimethyl-1,2,3,4,5,6,7,8,9,11,12,15,16,17-tetradecahydrocyclopenta[a]phenanthren-17-yl]-2H-furan-5-one + CHEBI:digoxigenin + InChI=1S/C23H34O5/c1-21-7-5-15(24)10-14(21)3-4-17-18(21)11-19(25)22(2)16(6-8-23(17,22)27)13-9-20(26)28-12-13/h9,14-19,24-25,27H,3-8,10-12H2,1-2H3/t14-,15+,16-,17-,18+,19-,21+,22+,23+/m1/s1 + "A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis." [] + DIGOXIGENIN + + + CHEBI:42471 + CHEBI:forskolin + forskolin + InChIKey=OHCQJHSOBUTRHG-KGGHGJDLSA-N + colforsine + 7beta-acetoxy-8,13-epoxy-1alpha,6beta,9alpha-trihydroxylabd-14-en-11-one + colforsina + C22H34O7 + colforsin + (3R,4aR,5S,6S,6aS,10S,10aR,10bS)-3-ethenyl-6,10,10b-trihydroxy-3,4a,7,7,10a-pentamethyl-1-oxododecahydro-1H-benzo[f]chromen-5-yl acetate + Colforsin + Coleonolk + Forskolin + FORSKOLIN + [H][C@@]12[C@H](O)[C@H](OC(C)=O)[C@@]3(C)O[C@](C)(CC(=O)[C@]3(O)[C@@]1(C)[C@@H](O)CCC2(C)C)C=C + "A labdane diterpenoid isolated from the Indian Coleus plant." [] + colforsinum + InChI=1S/C22H34O7/c1-8-19(5)11-14(25)22(27)20(6)13(24)9-10-18(3,4)16(20)15(26)17(28-12(2)23)21(22,7)29-19/h8,13,15-17,24,26-27H,1,9-11H2,2-7H3/t13-,15-,16-,17-,19-,20-,21+,22-/m0/s1 + + + G 418 + C20H40N4O10 + CHEBI:geneticin + (1R,2S,3S,4R,6S)-4,6-diamino-3-[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyloxy]-2-hydroxycyclohexyl 2-amino-2,7-dideoxy-D-glycero-alpha-D-gluco-heptopyranoside + geneticin + CHEBI:42768 + Geneticin + GENETICIN + InChIKey=BRZYSWJRSDMWLG-CAXSIQPQSA-N + G418 + "An aminoglycoside antibiotic produced by Micromonospora rhodorangea. It blocks polypeptide synthesis by inhibiting the elongation step in both prokaryotic and eukaryotic cells." [] + CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@H]1[C@H](N)C[C@H](N)[C@@H](O[C@H]2O[C@H](C(C)O)[C@@H](O)[C@H](O)[C@H]2N)[C@@H]1O + antibiotic G 418 + InChI=1S/C20H40N4O10/c1-6(25)14-11(27)10(26)9(23)18(32-14)33-15-7(21)4-8(22)16(12(15)28)34-19-13(29)17(24-3)20(2,30)5-31-19/h6-19,24-30H,4-5,21-23H2,1-3H3/t6?,7-,8+,9+,10+,11-,12-,13+,14+,15+,16-,17+,18+,19+,20-/m0/s1 + + + N-Ethylmaleimide + N-ETHYLMALEIMIDE + N-ethylmaleimide + CCN1C(=O)C=CC1=O + CHEBI:44485 + N-ethylmaleimide + InChIKey=HDFGOPSGAURCEO-UHFFFAOYSA-N + NEM + C6H7NO2 + CHEBI:N-ethylmaleimide + Ethylmaleimide + 1-ethyl-1H-pyrrole-2,5-dione + "A member of the class of maleimides that is the N-ethyl derivative of maleimide." [] + InChI=1S/C6H7NO2/c1-2-7-5(8)3-4-6(7)9/h3-4H,2H2,1H3 + 1-ethyl-1H-pyrrole-2,5-dione + + + Desmopressin + DDAVP + CHEBI:desmopressin + "A synthetic analogue of vasopressin in which 3-mercaptopropionic acid replaces the cysteine residue at position 1 and D-arginine replaces the residue at position 8. An antidiuretic, it increases urine concentration and decreases urine production, and is used (usually as the trihydrate of the acetic acid salt) to prevent and control excessive thirst, urination, and dehydration caused by injury, surgery, and certain medical conditions. It is also used in the diagnosis and treatment of cranial diabetes insipidus and in tests of renal function." [] + C46H64N14O12S2 + 1-(3-mercaptopropionic acid)-8-D-arginine-vasopressin + 1-{[(4R,7S,10S,13S,16S)-7-(2-amino-2-oxoethyl)-10-(3-amino-3-oxopropyl)-13-benzyl-16-(4-hydroxybenzyl)-6,9,12,15,18-pentaoxo-1,2-dithia-5,8,11,14,17-pentaazacycloicosan-4-yl]carbonyl}-L-prolyl-D-arginylglycinamide + CHEBI:4450 + desmopressine + desmopressin + InChI=1S/C46H64N14O12S2/c47-35(62)15-14-29-40(67)58-32(22-36(48)63)43(70)59-33(45(72)60-18-5-9-34(60)44(71)56-28(8-4-17-52-46(50)51)39(66)53-23-37(49)64)24-74-73-19-16-38(65)54-30(21-26-10-12-27(61)13-11-26)41(68)57-31(42(69)55-29)20-25-6-2-1-3-7-25/h1-3,6-7,10-13,28-34,61H,4-5,8-9,14-24H2,(H2,47,62)(H2,48,63)(H2,49,64)(H,53,66)(H,54,65)(H,55,69)(H,56,71)(H,57,68)(H,58,67)(H,59,70)(H4,50,51,52)/t28-,29+,30+,31+,32+,33+,34+/m1/s1 + InChIKey=NFLWUMRGJYTJIN-PNIOQBSNSA-N + desmopresina + 1-desamino-8-D-arginine vasopressin + desmopressinum + NC(=N)NCCC[C@@H](NC(=O)[C@@H]1CCCN1C(=O)[C@@H]1CSSCCC(=O)N[C@@H](Cc2ccc(O)cc2)C(=O)N[C@@H](Cc2ccccc2)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CC(N)=O)C(=O)N1)C(=O)NCC(N)=O + desmopressin + 1-deamino-8-D-arginine vasopressin + + + tri(carboxymethyl)amine + H3nta + InChIKey=MGFYIUFZLHCRTH-UHFFFAOYSA-N + InChI=1S/C6H9NO6/c8-4(9)1-7(2-5(10)11)3-6(12)13/h1-3H2,(H,8,9)(H,10,11)(H,12,13) + Nitrilotriacetic acid + Complexon I + nitrilotriacetic acid + Trilon A + "A NTA that has formula C6H9NO6." [] + Komplexon I + NTA + Nitrilotriacetate + CHEBI:nitrilotriacetic acid + 2,2',2''-nitrilotriacetic acid + nitrilo-2,2',2''-triacetic acid + OC(=O)CN(CC(O)=O)CC(O)=O + C6H9NO6 + CHEBI:44557 + NITRILOTRIACETIC ACID + N,N-bis(carboxymethyl)glycine + alpha,alpha',alpha''-trimethylaminetricarboxylic acid + Nitrilotriessigsaeure + triglycine + N(CH2-COOH)3 + Triglycollamic acid + + + (2R)-2-hydroxy-3-[(2S,5R,6R,8S)-5-hydroxy-8-{(1R,2E)-3-[(2R,4a'R,5R,6'S,8'R,8a'S)-8'-hydroxy-6'-{(1S,3S)-1-hydroxy-3-[(2S,3R,6S)-3-methyl-1,7-dioxaspiro[5.5]undec-2-yl]butyl}-7'-methylideneoctahydro-3H,3'H-spiro[furan-2,2'-pyrano[3,2-b]pyran]-5-yl]-1-methylprop-2-en-1-yl}-10-methyl-1,7-dioxaspiro[5.5]undec-10-en-2-yl]-2-methylpropanoic acid + CHEBI:44658 + [H][C@]1(CC[C@@H](O)[C@]2(O1)O[C@@]([H])(CC(C)=C2)[C@H](C)\\C=C\\[C@@]1([H])CC[C@@]2(CC[C@@]3([H])O[C@]([H])([C@@H](O)C[C@H](C)[C@@]4([H])O[C@@]5(CCCCO5)CC[C@H]4C)C(=C)[C@@H](O)[C@]3([H])O2)O1)C[C@@](C)(O)C(O)=O + CHEBI:okadaic acid + C44H68O13 + InChI=1S/C44H68O13/c1-25-21-34(55-44(23-25)35(46)12-11-31(54-44)24-41(6,50)40(48)49)26(2)9-10-30-14-18-43(53-30)19-15-33-39(57-43)36(47)29(5)38(52-33)32(45)22-28(4)37-27(3)13-17-42(56-37)16-7-8-20-51-42/h9-10,23,26-28,30-39,45-47,50H,5,7-8,11-22,24H2,1-4,6H3,(H,48,49)/b10-9+/t26-,27-,28+,30+,31+,32+,33-,34+,35-,36-,37+,38+,39-,41-,42+,43-,44-/m1/s1 + "A polycyclic ether that has formula C44H68O13." [] + okadaic acid + (2R)-2-hydroxy-3-{(2S,5R,6R,8S)-5-hydroxy-8-[(2R,3E)-4-((2R,4a'R,5R,6'S,8'R,8a'S)-8'-hydroxy-6'-{(1S,3S)-1-hydroxy-3-[(2S,3R,6S)-3-methyl-1,7-dioxaspiro[5.5]undec-2-yl]butyl}-7'-methylideneoctahydro-3H,3'H-spiro[furan-2,2'-pyrano[3,2-b]pyran]-5-yl)but-3-en-2-yl]-10-methyl-1,7-dioxaspiro[5.5]undec-10-en-2-yl}-2-methylpropanoic acid + InChIKey=QNDVLZJODHBUFM-WFXQOWMNSA-N + 9,10-Deepithio-9,10-didehydroacanthifolicin + OKADAIC ACID + Okadaic acid + + + 1-hexadecyl-2-acetyl-sn-glycero-3-phosphocholine + PAF + 1-O-hexadecyl-2-acetyl-sn-glycero-3-phosphocholine + C16:0 PAF + C16-PAF + 1-O-hexadecyl-platelet-activating factor + C16 PAF + 1-O-hexadecyl-PAF + 2-O-acetyl-1-O-hexadecyl-sn-glycero-3-phosphocholine + (R)-7-(acetyloxy)-4-hydroxy-N,N,N-trimethyl-3,5,9-trioxa-4-phosphapentacosan-1-aminium hydroxide inner salt 4-oxide + 1-O-hexadecyl-2-acetyl-sn-glyceryl-3-phosphorylcholine + 1-O-hexadecyl-2-O-acetyl-sn-glyceryl-3-phosphorylcholine + platelet-activating factor + CHEBI:2-O-acetyl-1-O-hexadecyl-sn-glycero-3-phosphocholine + CHEBI:44811 + platelet-activating factor C16 + InChIKey=HVAUUPRFYPCOCA-AREMUKBSSA-N + 1-O-hexadecyl PAF + InChI=1S/C26H54NO7P/c1-6-7-8-9-10-11-12-13-14-15-16-17-18-19-21-31-23-26(34-25(2)28)24-33-35(29,30)32-22-20-27(3,4)5/h26H,6-24H2,1-5H3/t26-/m1/s1 + CCCCCCCCCCCCCCCCOC[C@H](COP([O-])(=O)OCC[N+](C)(C)C)OC(C)=O + C26H54NO7P + Platelet activating factor + 1-O-hexadecyl-2-O-acetyl-sn-glycero-3-phosophocholine + (2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate + "A 2-acetyl-1-alkyl-sn-glycero-3-phosphocholine betaine which has hexadecyl as the alkyl group. PAF is a potent phospholipid activator and mediator of many leukocyte functions, including platelet aggregation, inflammation, and anaphylaxis." [] + (2R)-2-acetoxy-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate + + + InChI=1S/C8H7ClN2O2S/c1-5-10-7-3-2-6(9)4-8(7)14(12,13)11-5/h2-4H,1H3,(H,10,11) + C8H7ClN2O2S + diazoxide + Diazossido + diazoxide + diazoxidum + Diazoxide + "A benzothiadiazine that is the S,S-dioxide of 2H-1,2,4-benzothiadiazine which is substituted at position 3 by a methyl group and at position 7 by chlorine. A peripheral vasodilator, it increases the concentration of glucose in the plasma and inhibits the secretion of insulin by the beta- cells of the pancreas. It is used orally in the management of intractable hypoglycaemia and intravenously in the management of hypertensive emergencies." [] + 7-chloro-3-methyl-2H-1,2,4-benzothiadiazine 1,1-dioxide + CC1=Nc2ccc(Cl)cc2S(=O)(=O)N1 + diazoxido + InChIKey=GDLBFKVLRPITMI-UHFFFAOYSA-N + Eudemine + CHEBI:4495 + CHEBI:diazoxide + + + paclitaxel + (2aR-(2aalpha,4beta,4abeta,6beta,9alpha(alpha R*,betaS*),11alpha,12alpha,12balpha))-beta-(Benzoylamino)-alpha-hydroxybenzenepropanoic acid 6,12b-bis(acetyloxy)-12-(benzoyloxy)-2a,3,4,4a,5,6,9,10,11,12,12a,12b-dodecahydro-4,11-dihydroxy-4a,8,13,13-tetramethyl-5-oxo-7,11-methano-1H-cyclodeca(3,4)benz(1,2-b)oxet-9-yl ester + C47H51NO14 + [H][C@]12[C@H](OC(=O)c3ccccc3)[C@]3(O)C[C@H](OC(=O)[C@H](O)[C@@H](NC(=O)c4ccccc4)c4ccccc4)C(C)=C([C@@H](OC(C)=O)C(=O)[C@]1(C)[C@@H](O)C[C@H]1OC[C@@]21OC(C)=O)C3(C)C + Genexol + Capxol + Genetaxyl + Ebetaxel + "A tetracyclic diterpenoid isolated originally from the bark of the Pacific yew tree, Taxus brevifolia. It is a mitotic inhibitor used in cancer chemotherapy. Note that the use of the former generic name 'taxol' is now limited, as Taxol is a registered trade mark." [] + taxol + Benzenepropanoic acid, beta-(benzoylamino)-alpha-hydroxy-,(2aR,4S,4aS,6R,9S,11S,12S,12aR,12bS)-6,12b-bis(acetyloxy)-12-(benzoyloxy)-2a,3,4,4a,5,6,9,10,11,12,12a,12b-dodecahydro-4,11-dihydroxy-4a,8,13,13-tetramethyl-5-oxo-7,11-methano-1H-cyclodeca(3,4)benz(1,2-b)oxet-9-yl ester,(alphaR,betaS)- + Intaxel + Yewtaxan + taxalbin + InChI=1S/C47H51NO14/c1-25-31(60-43(56)36(52)35(28-16-10-7-11-17-28)48-41(54)29-18-12-8-13-19-29)23-47(57)40(61-42(55)30-20-14-9-15-21-30)38-45(6,32(51)22-33-46(38,24-58-33)62-27(3)50)39(53)37(59-26(2)49)34(25)44(47,4)5/h7-21,31-33,35-38,40,51-52,57H,22-24H2,1-6H3,(H,48,54)/t31-,32-,33+,35-,36+,37+,38-,40-,45+,46-,47+/m0/s1 + Abraxane + onxol + lipopac + Plaxicel + Mitotax + Paclitaxel + cyclopax + Anzatax + CHEBI:45863 + 4alpha,10beta-bis(acetyloxy)-13alpha-[(2S,3S)-3-benzamido-2-hydroxy-3-phenylpropanoyloxy]-1,7beta-dihydroxy-9-oxo-5beta,20-epoxytax-11-en-2alpha-yl benzoate + CHEBI:paclitaxel + 5beta,20-Epoxy-1,2-alpha,4,7beta,10beta,13alpha-hexahydroxytax-11-en-9-one 4,10-diacetate 2-benzoate 13-ester with (2R,3S)-N-benzoyl-3-phenylisoserine + Taxol A + TAXOL + InChIKey=RCINICONZNJXQF-MZXODVADSA-N + paxene + + + TSA + TRICHOSTATIN A + (2E,4E,6R)-7-[4-(dimethylamino)phenyl]-N-hydroxy-4,6-dimethyl-7-oxohepta-2,4-dienamide + (2E,4E,6R)-7-[4-(dimethylamino)phenyl]-N-hydroxy-4,6-dimethyl-7-oxohepta-2,4-dienamide + "A trichostatin that has formula C17H22N2O3." [] + CHEBI:46024 + trichostatin A + (2E,4E,6R)-7-(4-(dimethylamino)phenyl)-N-hydroxy-4,6-dimethyl-7-oxo-2,4-heptadienamide + C[C@@H](C(=O)c1ccc(cc1)N(C)C)\\C=C(C)\\C=C\\C(=O)NO + C17H22N2O3 + InChIKey=RTKIYFITIVXBLE-QEQCGCAPSA-N + CHEBI:trichostatin A + InChI=1S/C17H22N2O3/c1-12(5-10-16(20)18-22)11-13(2)17(21)14-6-8-15(9-7-14)19(3)4/h5-11,13,22H,1-4H3,(H,18,20)/b10-5+,12-11+/t13-/m1/s1 + + + PhNHC(=S)NH2 + monophenyl thiourea + CHEBI:46261 + InChI=1S/C7H8N2S/c8-7(10)9-6-4-2-1-3-5-6/h1-5H,(H3,8,9,10) + "A member of the class of thioureas that is thiourea in which one of the hydrogens is replaced by a phenyl group. Depending on their genetic makeup, humans find it either very bitter-tasting or tasteless. This unusual property resulted in N-phenylthiourea being used in paternity testing prior to the advent of DNA testing." [] + PTC + phenylthiocarbamide + N-phenylthiourea + alpha-phenylthiourea + PhNHCSNH2 + N-PHENYLTHIOUREA + InChIKey=FULZLIGZKMKICU-UHFFFAOYSA-N + 1-phenylthiourea + PhNHC(S)NH2 + C7H8N2S + 1-phenyl-2-thiourea + CHEBI:N-phenylthiourea + phenyl-2-thiourea + phenylthiourea + NC(=S)Nc1ccccc1 + + + InChIKey=WQLVFSAGQJTQCK-VKROHFNGSA-N + 3beta-hydroxy-5-spirostene + "A sapogenin that is spirostan which is substituted by a hydroxy group at the 3beta position, contains a double bond at the 5-6 position, and has R- configuration at position 25. A natural product found in Dioscorea (wild yam) species, it is used as the starting point for the commercial synthesis of a number of steroids, including cortisone, pregnenolone and progesterone." [] + CHEBI:diosgenin + [H][C@]12C[C@@]3([H])[C@]4([H])CC=C5C[C@@H](O)CC[C@]5(C)[C@@]4([H])CC[C@]3(C)[C@@]1([H])[C@H](C)[C@@]1(CC[C@@H](C)CO1)O2 + CHEBI:4629 + (3beta,25R)-spirost-5-en-3-ol + diosgenin + C27H42O3 + InChI=1S/C27H42O3/c1-16-7-12-27(29-15-16)17(2)24-23(30-27)14-22-20-6-5-18-13-19(28)8-10-25(18,3)21(20)9-11-26(22,24)4/h5,16-17,19-24,28H,6-15H2,1-4H3/t16-,17+,19+,20-,21+,22+,23+,24+,25+,26+,27-/m1/s1 + nitogenin + (20R,25R)-spirost-5-en-3beta-ol + diosgenin + Diosgenin + (25R)-spirost-5-en-3beta-ol + + + ganciclovir + ganciclovirum + "An oxopurine that is guanine substituted by a [(1,3-dihydroxypropan-2-yl)oxy]methyl group at position 9. Ganciclovir is an antiviral drug used to treat or prevent AIDS-related cytomegalovirus infections." [] + 2-Amino-9-(2-hydroxy-1-hydroxymethyl-ethoxymethyl)-1,9-dihydro-purin-6-one + gancyclovir + Ganciclovir + CHEBI:465284 + 9-(1,3-DIHYDROXY-PROPOXYMETHANE)GUANINE + InChI=1S/C9H13N5O4/c10-9-12-7-6(8(17)13-9)11-3-14(7)4-18-5(1-15)2-16/h3,5,15-16H,1-2,4H2,(H3,10,12,13,17) + 2-amino-9-(2-hydroxy-1-hydroxymethylethoxymethyl)-6,9-dihydro-1H-6-purinone + 2-amino-9-{[(1,3-dihydroxypropan-2-yl)oxy]methyl}-1,9-dihydro-6H-purin-6-one + 2-amino-9-((1,3-dihydroxypropan-2-yloxy)methyl)-3H-purin-6(9H)-one + 2-amino-9-((1,3-dihydroxypropan-2-yloxy)methyl)-1H-purin-6(9H)-one + Nc1nc2n(COC(CO)CO)cnc2c(=O)[nH]1 + C9H13N5O4 + 2-amino-9-((1,3-dihydroxypropan-2-yloxy)methyl)-9H-purin-6-ol + 2-(6-Amino-purin-9-ylmethoxy)-propane-1,3-diol + 9-((2-Hydroxy-1-(hydroxymethyl)ethoxy)methyl)guanine + ganciclovir + 9-[(1,3-dihydroxy-2-propoxy)methyl]guanine + InChIKey=IRSCQMHQWWYFCW-UHFFFAOYSA-N + GA2 + CHEBI:ganciclovir + + + mineraux + mineral + "A mineral is a naturally occurring substance formed through geological processes that has a characteristic chemical composition, a highly ordered atomic structure and specific physical properties." [] + mineral + CHEBI:mineral + . + Minerale + CHEBI:46662 + minerals + minerales + + + 3,4-dihydroxy-N-[3-(4-hydroxyphenyl)-1-methylpropyl]-beta-phenylethylamine + InChIKey=JRWZLRBJNMZMFE-UHFFFAOYSA-N + CHEBI:dobutamine + dobutaminum + InChI=1S/C18H23NO3/c1-13(2-3-14-4-7-16(20)8-5-14)19-11-10-15-6-9-17(21)18(22)12-15/h4-9,12-13,19-22H,2-3,10-11H2,1H3 + DL-dobutamine + CHEBI:4670 + rac-dobutamine + dobutamina + dobutamine + CC(CCc1ccc(O)cc1)NCCc1ccc(O)c(O)c1 + dobutamine + (+-)-4-(2-((3-(p-hydroxyphenyl)-1-methylpropyl)amino)ethyl)pyrocatechol + "A catecholamine that is 4-(3-aminobutyl)phenol in which one of the hydrogens attached to the nitrogen is substituted by a 2-(3,4-dihydroxyphenyl)ethyl group. A beta1-adrenergic receptor agonist that has cardiac stimulant action without evoking vasoconstriction or tachycardia, it is used as the hydrochloride to increase the contractility of the heart in the management of acute heart failure." [] + 4-(2-{[4-(4-hydroxyphenyl)butan-2-yl]amino}ethyl)benzene-1,2-diol + 4-{2-[3-(4-Hydroxy-phenyl)-1-methyl-propylamino]-ethyl}-benzene-1,2-diol + C18H23NO3 + DOBUTAMINE + racemic-dobutamine + Dobutamine + + + . + CHEBI:HEPES + HEPES + CHEBI:46756 + + + tricine + CHEBI:46760 + CHEBI:tricine + . + + + CHEBI:dipeptide + Dipeptid + dipeptides + C4H6N2O3R2 + dipeptide + Dipeptide + CHEBI:46761 + "Any molecule that contains two amino-acid residues connected by peptide linkages." [] + + + . + CHEBI:polyether + polyether + "An organooxygen compound containing more than one ether group." [] + polyether + CHEBI:46774 + polyethers + + + CHEBI:N-alkylpyrrolidine + CHEBI:46775 + N-alkylpyrrolidine + N-alkylpyrrolidines + + + hydroxyether + . + hydroxyethers + hydroxyether + CHEBI:hydroxyether + CHEBI:46789 + + + hydroxypolyether + . + CHEBI:46792 + hydroxypolyether + hydroxypolyethers + "A hydroxyether compound containing more than one ether group." [] + CHEBI:hydroxypolyether + + + poly(ethyleneoxide) + "A polymer composed of repeating ethyleneoxy units." [] + polyethylene glycol + PEG + Polyaethylenglykole + ethylene glycol polymer + polyethylene glycols + poly(ethylene glycol) + POE + polyethylene oxide + Macrogol + Glycols, polyethylene + polyoxyethylene + Polyaethylenglykol + alpha,omega-hydroxypoly(ethylene oxide) + Polyethylene glycol + (C2H4O)n + alpha-hydro-omega-hydroxypoly(oxyethylene) + alpha-hydro-omega-hydroxypoly(oxyethylene) + CHEBI:poly(ethylene glycol) + poly(oxyethylene) + CHEBI:46793 + ethylene glycol homopolymer + alpha-hydro-omega-hydroxypoly(oxy-1,2-ethanediyl) + 1,2-ethanediol homopolymer + PEO + + + N-alkylpiperazines + CHEBI:46845 + CHEBI:N-alkylpiperazine + N-alkylpiperazine + + + N-iminopiperazines + N-iminopiperazine + CHEBI:N-iminopiperazine + CHEBI:46847 + + + CHEBI:46850 + CHEBI:organoammonium salt + organoammonium salts + organoammonium salt + + + CHEBI:46851 + N-(2-hydroxyethyl)piperazines + N-(2-hydroxyethyl)piperazine + CHEBI:N-(2-hydroxyethyl)piperazine + + + CHEBI:N-(sulfoalkyl)piperazine + CHEBI:46852 + N-(sulfoalkyl)piperazine + N-(sulfoalkyl)piperazines + + + -NH2 + AMINO GROUP + azanyl + CHEBI:amino group + CHEBI:46882 + amino + amino group + primary amine group + H2N + primary amino group + + + imidazopyridines + CHEBI:imidazopyridine + CHEBI:46908 + imidazopyridine + + + CHEBI:N-methylpiperazine + N-methylpiperazines + N-methylpiperazine + CHEBI:46920 + + + oxazinane + oxazinanes + CHEBI:46952 + CHEBI:oxazinane + + + CHEBI:46955 + CHEBI:anthracenes + anthracenes + "Compounds containing an anthracene skeleton." [] + + + CHEBI:tetrahydrofuranol + tetrahydrofuranols + CHEBI:47017 + tetrahydrofuranol + + + monohydroxytetrahydrofurans + monohydroxytetrahydrofuran + CHEBI:monohydroxytetrahydrofuran + CHEBI:47018 + + + dihydroxytetrahydrofurans + dihydroxytetrahydrofuran + CHEBI:dihydroxytetrahydrofuran + CHEBI:47019 + + + 5-Bromouracil deoxyriboside + Bromodeoxyuridine + CHEBI:472552 + 5-Bdu + 5-bromo-2'-deoxyuridine + 5-Bromodeoxyuridine + 5-Bromodesoxyuridine + BrdU + 5-bromo-2'-deoxyuridine + OC[C@H]1O[C@H](C[C@@H]1O)n1cc(Br)c(=O)[nH]c1=O + C9H11BrN2O5 + broxuridina + broxuridinum + InChIKey=WOVKYSAHUYNSMH-RRKCRQDMSA-N + 5-Bromouracil-2-deoxyriboside + Bromouracil deoxyriboside + broxuridine + "A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase." [] + CHEBI:5-bromo-2'-deoxyuridine + InChI=1S/C9H11BrN2O5/c10-4-2-12(9(16)11-8(4)15)7-1-5(14)6(3-13)17-7/h2,5-7,13-14H,1,3H2,(H,11,15,16)/t5-,6+,7+/m0/s1 + + + CHEBI:47622 + an acetyl ester + CC(=O)O[*] + acetate ester + acetates + C2H3O2R + Acetyl ester + "Any carboxylic ester where the carboxylic acid component is acetic acid." [] + CHEBI:acetate ester + acetyl esters + Acetic ester + acetate esters + acetate + + + ammonium salt + CHEBI:47704 + ammonium salt + Ammoniumsalz + ammonium salts + . + CHEBI:ammonium salt + Ammoniumsalze + + + CHEBI:47775 + "Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL)." [] + CHEBI:high-density lipoprotein cholesterol + HDL-C + alpha-lipoprotein cholesterol + high-density lipoprotein cholesterol + HDL cholesterol + . + + + glyceride + glycerides + CHEBI:47778 + acylglycerols + glycerides + CHEBI:glyceride + . + acylglycerol + glyceride + "Any ester of glycerol (propane-1,2,3-triol) with fatty acids." [] + + + CHEBI:47779 + aminoglycosides + CHEBI:aminoglycoside + aminoglycoside + + + 3-oxosteroids + CHEBI:47788 + 3-oxo steroid + 3-oxo steroids + "Any oxo steroid where an oxo substituent is located at position 3." [] + a 3-oxosteroid + 3-Oxosteroid + CHEBI:3-oxo steroid + + + . + CHEBI:47857 + CHEBI:ureas + ureas + urea derivatives + + + CHEBI:hexose 6-phosphate + CHEBI:47877 + hexose 6-phosphate + + + . + hexose phosphates + hexose phosphate + CHEBI:47878 + hexose phosphate + "A phospho sugar that is formally obtained from a hexose." [] + CHEBI:hexose phosphate + + + CHEBI:47880 + . + steroid esters + steroid ester + CHEBI:steroid ester + + + CHEBI:3-oxo monocarboxylic acid + 3-oxo monocarboxylic acids + 3-Oxo acid + CHEBI:47881 + 3-oxo monocarboxylic acid + 3-Keto acid + C3H2O3R2 + 3-oxomonocarboxylic acids + 3-oxomonocarboxylic acid + + + CHEBI:47882 + CHEBI:cyclic polypyrrole + polypyrrole macrocycles + . + cyclic polypyrroles + macrocyclic polypyrroles + cyclic polypyrrole + + + Dinucleotide + dinucleotide + C10H18O13P2R2 + CHEBI:dinucleotide + dinucleotides + dinucleotide + CHEBI:47885 + O[C@H]1[C@H]([*])O[C@H](COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@@H]([*])[C@H](O)[C@@H]2O)[C@H]1O + + + CHEBI:47891 + steroid acid + . + CHEBI:steroid acid + steroid acids + "Any steroid substituted by at least one carboxy group." [] + + + CHEBI:alkanethiol + HSR + alkanethiols + alkanethiol + alkyl thiol + Alkyl thiol + CHEBI:47908 + alkyl thiols + "An alkanethiol is a compound in which a sulfanyl group, -SH, is attached to an alkyl group." [] + S[*] + + + CHEBI:diazepine + diazepine + CHEBI:47918 + diazepines + + + CHEBI:47923 + CHEBI:tripeptide + "Any molecule that contains three amino-acid residues connected by peptide linkages." [] + tripeptides + Tripeptide + tripeptide + C6H8N3O4R3 + + + "The pyranose form of D-mannose 6-phosphate." [] + CHEBI:D-mannopyranose 6-phosphate + InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4+,5+,6?/m1/s1 + OC1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H](O)[C@@H]1O + CHEBI:48066 + 6-O-phosphono-D-mannopyranose + C6H13O9P + InChIKey=NBSCHQHZLSJFNQ-QTVWNMPRSA-N + D-mannopyranose 6-(dihydrogen phosphate) + D-mannopyranose 6-phosphate + + + acide nitrique + HNO3 + HONO2 + CHEBI:nitric acid + acide azotique + CHEBI:48107 + hydrogen trioxonitrate(1-) + InChI=1S/HNO3/c2-1(3)4/h(H,2,3,4) + hydrogen nitrate + Nitrate + Nitric acid + "A nitrogen oxoacid of formula HNO3 in which the nitrogen atom is bonded to a hydroxy group and by equivalent bonds to the remaining two oxygen atoms." [] + InChIKey=GRYLNZFGIOXLOG-UHFFFAOYSA-N + [NO2(OH)] + Salpetersaeure + hydroxidodioxidonitrogen + O[N+]([O-])=O + nitric acid + azotic acid + trioxonitric acid + + + CHEBI:48120 + "Anthracyclines are polyketides that have a tetrahydronaphthacenedione ring structure attached by a glycosidic linkage to the amino sugar daunosamine." [] + anthracycline + . + anthracyclines + CHEBI:anthracycline + anthracycline + + + CHEBI:48132 + tetracenomycins + CHEBI:tetracenomycin + tetracenomycin + . + "A polyketide based on a tetracene ring structure." [] + + + CHEBI:disulfide + "Compounds of structure RSSR'." [] + disulfide + CHEBI:48343 + disulfides + + + organic bromide salt + . + CHEBI:organic bromide salt + organic bromide salts + CHEBI:48369 + + + carbazoles + CHEBI:carbazoles + CHEBI:48513 + + + C10H14N4O2 + 3-isobutyl-1-methylxanthine + CHEBI:3-isobutyl-1-methylxanthine + CHEBI:48518 + "An oxopurine that is xanthine which is substituted at positions 1 and 3 by methyl and isobutyl groups, respectively." [] + IBMX + + + CHEBI:48546 + pyrimidinethiones + CHEBI:pyrimidinethione + pyrimidinethione + + + CHEBI:48589 + piperidones + piperidone + CHEBI:piperidones + + + CHEBI:hydroxypiperidine + hydroxypiperidine + CHEBI:48590 + hydroxypiperidines + + + cloruro de litio + Lithiumchlorid + InChI=1S/ClH.Li/h1H;/q;+1/p-1 + chlorure de lithium + CHEBI:lithium chloride + "A metal chloride salt with a Li(+) counterion." [] + lithium chloride + ClLi + LiCl + CHEBI:48607 + [Li+].[Cl-] + lithium chloride + lithii chloridum + InChIKey=KWGKDLIKAYFUFQ-UHFFFAOYSA-M + + + dimethylarsinic acid + [As(CH3)2O(OH)] + CHEBI:dimethylarsinic acid + InChIKey=OGGXGZAMXPVRFZ-UHFFFAOYSA-N + Kakodylsaeure + Dimethylarsinate + CHEBI:48765 + C2H7AsO2 + Me2As(=O)OH + InChI=1S/C2H7AsO2/c1-3(2,4)5/h1-2H3,(H,4,5) + CACODYLIC ACID + dimethylarsinic acid + C[As](C)(O)=O + "The organoarsenic compound that is arsenic acid substituted on the central arsenic atom with two methyl groups." [] + + + cadmium(II) cation + "A cadmium cation that has formula Cd." [] + InChIKey=WLZRMCYVCSSEQC-UHFFFAOYSA-N + CADMIUM ION + Cd + [Cd++] + CHEBI:48775 + Cd2+ + cadmium + cadmium(2+) + InChI=1S/Cd/q+2 + cadmium(2+) + cadmium(2+) ion + cadmium, ion (Cd2+) + Cd(2+) + CHEBI:cadmium(2+) + + + cobaltous ion + cobalt(2+) ion + InChI=1S/Co/q+2 + Co2+ + CHEBI:cobalt(2+) + InChIKey=XLJKHNWPARRRJB-UHFFFAOYSA-N + cobalt(II) cation + CHEBI:48828 + cobalt(2+) ion + cobalt(2+) + Co(2+) + [Co++] + cobalt(II) cation + COBALT (II) ION + "A cobalt cation that has formula Co." [] + Cobalt(2+) + cobalt(2+) + Co + Co(II) + + + ethidium bromide + 2,7-diamino-10-ethyl-9-phenylphenanthridinium bromide + "An organic bromide salt that has formula C21H20N3.Br." [] + Homidium bromide + EtBr + CHEBI:ethidium bromide + C21H20BrN3 + C21H20N3.Br + CHEBI:4883 + [Br-].CC[n+]1c(-c2ccccc2)c2cc(N)ccc2c2ccc(N)cc12 + InChI=1S/C21H19N3.BrH/c1-2-24-20-13-16(23)9-11-18(20)17-10-8-15(22)12-19(17)21(24)14-6-4-3-5-7-14;/h3-13,23H,2,22H2,1H3;1H + Dromilac + Ethidium bromide + 2,7-diamino-9-phenyl-10-ethylphenanthridinium bromide + InChIKey=ZMMJGEGLRURXTF-UHFFFAOYSA-N + 3,8-diamino-5-ethyl-6-phenylphenanthridinium bromide + + + CHEBI:48865 + CHEBI:thiadiazolidine + thiadiazolidines + thiadiazolidine + "A organic heteromonocyclic compound that consists of a cylcopentane ring in which two carbon atoms are replaced by a sulfur and nitrogen atom respectively." [] + + + 3-ethyl-3-methylsuccinimide + etosuximida + CHEBI:ethosuximide + Ethosuximide + ethosuximidum + (+-)-2-ethyl-2-methylsuccinimide + CHEBI:4887 + C7H11NO2 + 3-ethyl-3-methylpyrrolidine-2,5-dione + CCC1(C)CC(=O)NC1=O + ethosuximide + gamma-ethyl-gamma-methyl-succinimide + 3-methyl-3-ethylsuccinimide + alpha-ethyl-alpha-methylsuccinimide + ethosuximide + 3-ethyl-3-methyl-2,5-pyrrolidinedione + gamma-methyl-gamma-ethyl-succinimide + InChI=1S/C7H11NO2/c1-3-7(2)4-5(9)8-6(7)10/h3-4H2,1-2H3,(H,8,9,10) + "A dicarboximide that is pyrrolidine-2,5-dione in which the hydrogens at position 3 are substituted by one methyl and one ethyl group. An antiepileptic, it is used in the treatment of absence seizures and may be used for myoclonic seizures, but is ineffective against tonic-clonic seizures." [] + InChIKey=HAPOVYFOVVWLRS-UHFFFAOYSA-N + 2-methyl-2-ethylsuccinimide + alpha-methyl-alpha-ethylsuccinimide + 3-methyl-3-ethylpyrrolidine-2,5-dione + Aethosuximide + 2-ethyl-2-methylsuccinimide + + + pyridoindoles + pyridoindole + CHEBI:pyridoindole + CHEBI:48888 + + + thiazoles + CHEBI:thiazoles + "An azole in which the five-membered heterocyclic aromatic skeleton contains a N atom and one S atom." [] + CHEBI:48901 + + + (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside + Etopophos + "A furonaphthodioxole that has formula C29H32O13." [] + 4'-Demethylepipodophyllotoxin 9-(4,6-O-(R)-ethylidene-beta-D-glucopyranoside) + Etoposido + CHEBI:4911 + Lastet + InChI=1S/C29H32O13/c1-11-36-9-20-27(40-11)24(31)25(32)29(41-20)42-26-14-7-17-16(38-10-39-17)6-13(14)21(22-15(26)8-37-28(22)33)12-4-18(34-2)23(30)19(5-12)35-3/h4-7,11,15,20-22,24-27,29-32H,8-10H2,1-3H3/t11-,15+,20-,21-,22+,24-,25-,26-,27-,29+/m1/s1 + 9-((4,6-O-Ethylidine-beta-D-glucopyranosyl)oxy)-5,8,8a,9-tetrahydro-5-(4-hydroxy-3,4-dimethyloxyphenyl)furo(3',4'':6,7)naptho-(2,3-d)-1,3-dioxol-6(5aH)-one + etoposidum + (-)-etoposide + etoposide + Toposar + Vepesid + trans-Etoposide + [H][C@]12COC(=O)[C@]1([H])[C@H](c1cc(OC)c(O)c(OC)c1)c1cc3OCOc3cc1[C@H]2O[C@@H]1O[C@@H]2CO[C@@H](C)O[C@H]2[C@H](O)[C@H]1O + CHEBI:etoposide + Etoposide + C29H32O13 + Eposin + 4-demethylepipodophyllotoxin beta-D-ethylideneglucoside + InChIKey=VJJPUSNTGOMMGY-MRVIYFEKSA-N + VP-16 + etoposide + + + C9H11NO4 + CHEBI:49168 + DL-beta-(3,4-dihydroxyphenyl)alanine + 3-hydroxy-DL-tyrosine + beta-(3,4-dihydroxyphenyl)-DL-alpha-alanine + dopa + dopa + InChIKey=WTDRDQBEARUVNC-UHFFFAOYSA-N + "A hydroxyphenylalanine carrying hydroxy substituents at positions 3 and 4 of the benzene ring." [] + dl-beta-(3,4-dihydroxyphenyl)-alpha-alanine + (R,S)-dopa + DL-3,4-dopa + 2-amino-3-(3,4-dihydroxyphenyl)propanoic acid + (+-)-3-(3,4-dihydroxyphenyl)alanine + DL-dihydroxyphenylalanine + DL-dioxyphenylalanine + NC(Cc1ccc(O)c(O)c1)C(O)=O + (+-)-dopa + 3',4'-dihydroxyphenylalanine + InChI=1S/C9H11NO4/c10-6(9(13)14)3-5-1-2-7(11)8(12)4-5/h1-2,4,6,11-12H,3,10H2,(H,13,14) + 3-hydroxytyrosine + CHEBI:dopa + + + 4-allyl-2-methoxyphenol + Allylguaiacol + C10H12O2 + 2-methoxy-4-(2-propen-1-yl)phenol + 2-methoxy-4-(prop-2-en-1-yl)phenol + 4-Allylcatechol-2-methyl ether + CHEBI:eugenol + p-Eugenol + 2-Methoxy-4-allylphenol + eugenol + 1-Hydroxy-2-methoxy-4-propenylbenzene + 4-Hydroxy-3-methoxy-1-allylbenzene + eugenol + 2-Hydroxy-5-allylanisole + p-Allylguaiacol + 4-Allyl-1-hydroxy-2-methoxybenzene + 2-Methoxy-1-hydroxy-4-allylbenzene + 1-Hydroxy-2-methoxy-4-allylbenzene + CHEBI:4917 + 4-Allylguaiacol + 1,3,4-Eugenol + 2-Methoxy-4-(2-propen-1-yl)phenol + InChIKey=RRAFCDWBNXTKKO-UHFFFAOYSA-N + 1-Hydroxy-2-methoxy-4-prop-2-enylbenzene + Eugenic acid + 2-Methoxy-4-prop-2-enylphenol + InChI=1S/C10H12O2/c1-3-4-8-5-6-9(11)10(7-8)12-2/h3,5-7,11H,1,4H2,2H3 + 1-allyl-3-methoxy-4-hydroxybenzene + 1-allyl-4-hydroxy-3-methoxybenzene + COc1cc(CC=C)ccc1O + Eugenol + Caryophyllic acid + "A phenylpropanoid formally derived from guaiacol with an allyl chain substituted para to the hydroxy group." [] + + + . + piperidine antibiotics + CHEBI:piperidine antibiotic + CHEBI:49318 + piperidine antibiotic + + + CHEBI:carbocyclic antibiotic + CHEBI:49319 + carbocyclic antibiotics + carbocyclic antibiotic + + + anthracyclins + anthracyclines + anthracycline antibiotic + CHEBI:49322 + "An organic compound that has a tetrahydronaphthacenedione ring structure attached by a glycosidic linkage to the amino sugar daunosamine and which exhibits antibiotic activity." [] + anthracycline antibiotics + . + CHEBI:anthracycline antibiotic + + + beta-cyclodextrin + beta-CD + CHEBI:beta-cyclodextrin + InChI=1S/C42H70O35/c43-1-8-29-15(50)22(57)36(64-8)72-30-9(2-44)66-38(24(59)17(30)52)74-32-11(4-46)68-40(26(61)19(32)54)76-34-13(6-48)70-42(28(63)21(34)56)77-35-14(7-49)69-41(27(62)20(35)55)75-33-12(5-47)67-39(25(60)18(33)53)73-31-10(3-45)65-37(71-29)23(58)16(31)51/h8-63H,1-7H2/t8-,9-,10-,11-,12-,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23-,24-,25-,26-,27-,28-,29-,30-,31-,32-,33-,34-,35-,36-,37-,38-,39-,40-,41-,42-/m1/s1 + InChIKey=WHGYBXFWUBPSRW-FOUAGVGXSA-N + cycloheptaglucosan + C42H70O35 + cycloheptaamylose + beta-cycloamylose + cycloheptaglucan + OC[C@H]1O[C@@H]2O[C@@H]3[C@@H](CO)O[C@H](O[C@@H]4[C@@H](CO)O[C@H](O[C@@H]5[C@@H](CO)O[C@H](O[C@@H]6[C@@H](CO)O[C@H](O[C@@H]7[C@@H](CO)O[C@H](O[C@@H]8[C@@H](CO)O[C@H](O[C@H]1[C@H](O)[C@H]2O)[C@H](O)[C@H]8O)[C@H](O)[C@H]7O)[C@H](O)[C@H]6O)[C@H](O)[C@H]5O)[C@H](O)[C@H]4O)[C@H](O)[C@H]3O + CHEBI:495055 + cyclomaltoheptaose + "A cyclodextrin composed of seven alpha-(1->4) linked D-glucopyranose units." [] + betadex + beta-cyclodextrin + + + Diazepam + CN1C(=O)CN=C(c2ccccc2)c2cc(Cl)ccc12 + CHEBI:49575 + InChIKey=AAOVKJBEBIDNHE-UHFFFAOYSA-N + C16H13ClN2O + Valium + diazepam + 7-chloro-1,3-dihydro-1-methyl-5-phenyl-2H-1,4-benzodiazepin-2-one + CHEBI:diazepam + "A 1,4-benzodiazepinone that is 1,3-dihydro-2H-1,4-benzodiazepin-2-one substituted by a chloro group at position 7, a methyl group at position 1 and a phenyl group at position 5." [] + InChI=1S/C16H13ClN2O/c1-19-14-8-7-12(17)9-13(14)16(18-10-15(19)20)11-5-3-2-4-6-11/h2-9H,10H2,1H3 + methyl diazepinone + + + hydrogene + CHEBI:49637 + ETNAM H HYDROGEN ATOM + H + [H] + hydrogen atom + InChIKey=YZCKVEUIGOORGS-UHFFFAOYSA-N + InChI=1S/H + hydrogen + Wasserstoff + 1H + CHEBI:hydrogen atom + "A s-block element atom that has formula H." [] + hydrogen + hidrogeno + + + [ClO4](-) + ClO4 + perchlorate + PERCHLORATE ION + tetraoxidochlorate(1-) + ClO4(-) + InChIKey=VLTRZXGMWDSKGL-UHFFFAOYSA-M + CHEBI:perchlorate + Perchlorat + tetraoxochlorate(1-) + "A monovalent inorganic anion obtained by deprotonation of perchloric acid." [] + Chlorat(VII) + perchlorate + tetraoxochlorate(VII) + CHEBI:49706 + [O-]Cl(=O)(=O)=O + InChI=1S/ClHO4/c2-1(3,4)5/h(H,2,3,4,5)/p-1 + + + tetraoxoiodate(VII) + tetraoxidoiodate(1-) + periodate + tetraoxoiodate(1-) + InChI=1S/HIO4/c2-1(3,4)5/h(H,2,3,4,5)/p-1 + PERIODATE + periodate + "A monovalent inorganic anion obtained by deprotonation of periodic acid." [] + IO4 + InChIKey=KHIWWQKSHDUIBK-UHFFFAOYSA-M + [IO4](-) + CHEBI:49826 + IO4(-) + [O-]I(=O)(=O)=O + CHEBI:periodate + + + organic amino compounds + CHEBI:50047 + CHEBI:organic amino compound + organic amino compound + "A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups." [] + + + dihydropyridine + CHEBI:50075 + CHEBI:dihydropyridine + dihydropyridines + . + dihydropyridine + + + [Na+].CC(=O)C([O-])=O + sodium 2-oxopropanoate + pyruvic acid, sodium salt + C3H3NaO3 + CHEBI:sodium pyruvate + "An organic sodium salt that has formula C3H3NaO3." [] + Natriumpyruvat + InChIKey=DAEPDZWVDSPTHF-UHFFFAOYSA-M + sodium pyruvate + CHEBI:50144 + InChI=1S/C3H4O3.Na/c1-2(4)3(5)6;/h1H3,(H,5,6);/q;+1/p-1 + + + CHEBI:retinol + retinol + retinols + CC(C=CC=C(C)C=CC1=C(C)CCCC1(C)C)=CCO + retinol + C20H30O + CHEBI:50211 + InChIKey=FPIPGXGPPPQFEQ-UHFFFAOYSA-N + 3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-ol + "A retinoid consisting of 3,7-dimethylnona-2,4,6,8-tetraen-1-ol substituted at position 9 by a 2,6,6-trimethylcyclohex-1-en-1-yl group (geometry of the four exocyclic double bonds is not specified)." [] + InChI=1S/C20H30O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,21H,7,10,14-15H2,1-5H3 + + + C13H17N + selegiline + InChI=1S/C13H17N/c1-4-10-14(3)12(2)11-13-8-6-5-7-9-13/h1,5-9,12H,10-11H2,2-3H3 + N-methyl-N-(1-methyl-2-phenylethyl)prop-2-yn-1-amine + "A phenethylamine alkaloid that has formula C13H17N." [] + InChIKey=MEZLKOACVSPNER-UHFFFAOYSA-N + selegilina + selegilinum + CC(Cc1ccccc1)N(C)CC#C + CHEBI:selegiline + selegiline + CHEBI:50217 + + + maleate salt + . + maleate salt + "Salts from maleic acid." [] + CHEBI:50221 + CHEBI:maleate salt + maleate salts + + + thiazide + CHEBI:50264 + Thiazides + tiazidas + CHEBI:thiazide + "Heterocyclic compound with sulfur and nitrogen in the ring." [] + + + CHEBI:50265 + CHEBI:benzothiadiazine + "Heterocyclic compound of a ring with sulfur and two nitrogen atoms fused to a benzene ring. Members inhibit sodium-potassium-chloride symporters and are used as diuretics." [] + Benzothiadiazines + benzothiadiazines + benzothiadiazine + + + Cadmiumsulfat + "A cadmium salt that has formula CdO4S." [] + cadmium(2+) sulfate + CHEBI:cadmium sulfate + sulfate de cadmium + CHEBI:50292 + [Cd++].[O-]S([O-])(=O)=O + cadmium sulphate + CdSO4 + Kadmiumsulfat + InChIKey=QCUOBSQYDGUHHT-UHFFFAOYSA-L + cadmium sulfate + sulfato de cadmio + CdO4S + cadmium monosulfate + InChI=1S/Cd.H2O4S/c;1-5(2,3)4/h;(H2,1,2,3,4)/q+2;/p-2 + cadmium sulfate + + + cadmium salts + cadmium salt + CHEBI:50293 + cadmium salt + CHEBI:cadmium salt + + + CHEBI:50307 + . + furonaphthodioxole + furonaphthodioxoles + furonaphthodioxole + CHEBI:furonaphthodioxole + + + proteinogenic amino-acid side-chain groups + proteinogenic amino-acid side-chains + proteinogenic amino-acid side-chain group + CHEBI:50325 + "A univalent organyl group obtained by cleaving the bond from C-2 to the side chain of a proteinogenic amino-acid." [] + proteinogenic amino-acid side-chain + canonical amino-acid side-chains + canonical amino-acid side-chain + CHEBI:proteinogenic amino-acid side-chain group + + + organic iodide salts + . + CHEBI:organic iodide salt + CHEBI:50356 + organic iodide salt + + + . + taxane diterpenoids + taxane diterpenoid + CHEBI:taxane diterpenoid + taxane diterpenoid + CHEBI:50367 + + + CHEBI:cholestanoid + CHEBI:50401 + "Any steroid based on a cholestane skeleton and its derivatives." [] + cholestanoid + cholestanoids + + + ergostanoid + CHEBI:50403 + CHEBI:ergostanoid + ergostanoids + + + CHEBI:lipoprotein cholesterol + "Cholesterol esters and free cholesterol which are contained in or bound to lipoproteins." [] + CHEBI:50404 + lipoprotein cholesterol + + + dihydrolipoyl group + 6,8-dimercaptooctanoyl + 6,8-disulfanyloctanoyl + C8H15OS2 + CHEBI:50488 + CHEBI:dihydrolipoyl group + + + "Any compound containing the thiocarbonyl group, C=S." [] + CHEBI:50492 + thiocarbonyl compound + CHEBI:thiocarbonyl compound + thiocarbonyl compounds + + + InChI=1S/C5H11N3O2/c1-7-5(10)3-8-4(9)2-6/h2-3,6H2,1H3,(H,7,10)(H,8,9) + Fibrin + "A peptide that has formula C5H11N3O2." [] + CNC(=O)CNC(=O)CN + InChIKey=BWGVNKXGVNDBDI-UHFFFAOYSA-N + C5H11N3O2 + CHEBI:Fibrin + Fibrin + CHEBI:5054 + + + alkyl alcohols + butan-1-ols + "An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position." [] + hydroxyalkane + alkyl alcohol + CHEBI:50584 + hydroxyalkanes + CHEBI:alkyl alcohol + + + minocycline + minomycin + InChIKey=DYKFCLLONBREIL-KVUCHLLUSA-N + (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE + "A tetracycline analogue having a dimethylamino group at position 7 and lacking the methyl and hydroxy groups at position 5." [] + [H][C@@]12Cc3c(ccc(O)c3C(=O)C1=C(O)[C@]1(O)C(=O)C(C(N)=O)=C(O)[C@@H](N(C)C)[C@]1([H])C2)N(C)C + CHEBI:minocycline + minociclinum + InChI=1S/C23H27N3O7/c1-25(2)12-5-6-13(27)15-10(12)7-9-8-11-17(26(3)4)19(29)16(22(24)32)21(31)23(11,33)20(30)14(9)18(15)28/h5-6,9,11,17,27,29-30,33H,7-8H2,1-4H3,(H2,24,32)/t9-,11-,17-,23-/m0/s1 + Minocycline + minociclina + 7-Dimethylamino-6-demethyl-6-deoxytetracycline + minocycline + CHEBI:50694 + C23H27N3O7 + (4S,4aS,5aR,12aS)-4,7-bis(dimethylamino)-3,10,12,12a-tetrahydroxy-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide + + + . + an oligosaccharide + O-glycosylglycosides + oligosaccharide + CHEBI:50699 + oligosacarido + "A compound in which monosaccharide units are joined by glycosidic linkages. The term is commonly used to refer to a defined structure as opposed to a polymer of unspecified length or a homologous mixture. When the linkages are of other types the compounds are regarded as oligosaccharide analogues." [] + oligosacaridos + CHEBI:oligosaccharide + Oligosaccharide + O-glycosylglycoside + oligosaccharides + + + doxycycline + CHEBI:50845 + (4S,4aR,5S,5aR,6R,12aS)-4-(dimethylamino)-3,5,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide + Doxycyclin + doxiciclina + CHEBI:doxycycline + InChI=1S/C22H24N2O8/c1-7-8-5-4-6-9(25)11(8)16(26)12-10(7)17(27)14-15(24(2)3)18(28)13(21(23)31)20(30)22(14,32)19(12)29/h4-7,10,14-15,17,25,27-29,32H,1-3H3,(H2,23,31)/t7-,10+,14+,15-,17-,22-/m0/s1 + doxycyclinum + 6alpha-deoxy-5-oxytetracycline + InChIKey=JBIWCJUYHHGXTC-AKNGSSGZSA-N + 5-hydroxy-alpha-6-deoxytetracycline + doxycycline (anhydrous) + Vibramycin + (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE + Supracyclin + Doxycycline + "Tetracycline in which the 5beta-hydrogen is replaced by a hydroxy group, while the 6alpha-hydroxy group is replaced by hydrogen. A semi-synthetic tetracycline antibiotic, it is used to inhibit bacterial protein synthesis and treat non-gonococcal urethritis and cervicitis, exacerbations of bronchitis in patients with chronic obstructive pulmonary disease (COPD), and adult periodontitis." [] + [H][C@@]12[C@@H](C)c3cccc(O)c3C(=O)C1=C(O)[C@]1(O)C(=O)C(C(N)=O)=C(O)[C@@H](N(C)C)[C@]1([H])[C@H]2O + Jenacyclin + C22H24N2O8 + doxycycline + + + corticoides + CHEBI:50858 + corticosteroid + . + corticosteroids + CHEBI:corticosteroid + "A natural or synthetic analogue of the hormones secreted by the adrenal gland." [] + corticosteroides + + + CHEBI:5086 + CHEBI:flavoprotein + Flavoprotein + . + flavoprotein + flavoproteins + flavoprotein + "A flavin tightly bound or covalently attached to a protein chain, commonly through the 8-methyl carbon atom." [] + + + "Any molecular entity that contains carbon." [] + organic molecular entity + organic compounds + . + CHEBI:organic molecular entity + organic molecules + organic entity + CHEBI:50860 + organic molecular entities + + + thiazolidenediones + CHEBI:50990 + CHEBI:thiazolidenediones + "A thiadiazolidine in which the 1,3-thiazolidine ring is substituted by two oxo groups." [] + + + primary amino compound + "A compound formally derived from ammonia by replacing one hydrogen atom by an organyl group." [] + CHEBI:50994 + CHEBI:primary amino compound + primary amino compounds + + + secondary amino compounds + CHEBI:50995 + secondary amino compound + "A compound formally derived from ammonia by replacing two hydrogen atoms by organyl groups." [] + CHEBI:secondary amino compound + + + CHEBI:tertiary amino compound + tertiary amino compounds + CHEBI:50996 + "A compound formally derived from ammonia by replacing three hydrogen atoms by organyl groups." [] + tertiary amino compound + + + Makrocyclen + Makrozyklen + macrocycle + "A cyclic compound containing nine or more atoms as part of the cyclic system." [] + macrocycles + CHEBI:macrocycle + makrocyclische Verbindungen + makrozyklische Verbindungen + macrocycle + CHEBI:51026 + + + C15H14FN3O3 + "A benzodiazepine that has formula C15H14FN3O3." [] + flumazenil + Lanexat + flumazenil + ethyl 8-fluoro-5-methyl-6-oxo-5,6-dihydro-4H-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate + InChI=1S/C15H14FN3O3/c1-3-22-15(21)13-12-7-18(2)14(20)10-6-9(16)4-5-11(10)19(12)8-17-13/h4-6,8H,3,7H2,1-2H3 + flumazenilum + CCOC(=O)c1ncn2-c3ccc(F)cc3C(=O)N(C)Cc12 + CHEBI:5103 + Anexate + CHEBI:flumazenil + flumazenilo + InChIKey=OFBIFZUFASYYRE-UHFFFAOYSA-N + + + organic halide salt + CHEBI:organic halide salt + CHEBI:51069 + organic halide salts + + + nitrate salts + nitrate salt + CHEBI:51082 + CHEBI:nitrate salt + + + inorganic nitrates + CHEBI:inorganic nitrate salt + inorganic nitrate salt + CHEBI:51084 + inorganic nitrate salts + + + C36H30F2N2O13 + InChI=1S/C36H30F2N2O13/c1-18-2-4-24(39(14-32(43)44)15-33(45)46)30(8-18)51-6-7-52-31-9-19(3-5-25(31)40(16-34(47)48)17-35(49)50)36-20-10-22(37)26(41)12-28(20)53-29-13-27(42)23(38)11-21(29)36/h2-5,8-13,41H,6-7,14-17H2,1H3,(H,43,44)(H,45,46)(H,47,48)(H,49,50) + Fluo-4 + CHEBI:51103 + CHEBI:Fluo-4 + {[2-(2-{2-[bis(carboxymethyl)amino]-5-(2,7-difluoro-6-hydroxy-3-oxo-3H-xanthen-9-yl)phenoxy}ethoxy)-4-methylphenyl](carboxymethyl)amino}acetic acid + InChIKey=OUVXYXNWSVIOSJ-UHFFFAOYSA-N + "A xanthene dye that has formula C36H30F2N2O13." [] + Cc1ccc(N(CC(O)=O)CC(O)=O)c(OCCOc2cc(ccc2N(CC(O)=O)CC(O)=O)-c2c3cc(F)c(O)cc3oc3cc(=O)c(F)cc23)c1 + + + CHEBI:BODIPY compound + BODIPY compound + "A compound that contains a 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene skeleton." [] + CHEBI:51108 + BODIPY compounds + + + "Molecules that contain a 4-bora-3a,4a-diaza-s-indacene skeleton." [] + 4-bora-3a,4a-diaza-s-indacenes + CHEBI:4-bora-3a,4a-diaza-s-indacene + CHEBI:51109 + 4-bora-3a,4a-diaza-s-indacene + + + CHEBI:BODIPY dye + "A dye molecule that contains a 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene skeleton." [] + CHEBI:51123 + BODIPY dyes + BODIPY dye + + + CHEBI:51142 + amino groups + amine groups + CHEBI:amino groups + + + nitrogen molecular entities + CHEBI:nitrogen molecular entity + Nitrogenous compounds + CHEBI:51143 + . + nitrogen molecular entity + nitrogen compounds + + + nitrogen group + CHEBI:nitrogen group + CHEBI:51144 + nitrogen groups + nitrogen-containing group + nitrogen group + nitrogenous group + + + "An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case." [] + CHEBI:51151 + dipolar compounds + CHEBI:dipolar compound + dipolar compound + + + Prozac + CHEBI:fluoxetine + fluoxetine + (+-)-N-methyl-gamma-(4-(trifluoromethyl)phenoxy)benzenepropanamine + fluoxetina + C17H18F3NO + fluoxetinum + "A racemate comprising equimolar amounts of (R)- and (S)-fluoxetine. A selective serotonin reuptake inhibitor (SSRI), it is used (generally as the hydrochloride salt) for the treatment of depression (and the depressive phase of bipolar disorder), bullimia nervosa, and obsessive-compulsive disorder." [] + CHEBI:5118 + fluoxetine + rac-N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine + (+-)-N-methyl-3-phenyl-3-((alpha,alpha,alpha-trifluoro-p-tolyl)oxy)propylamine + + + InChI=1S/C16H15N5/c17-15(18)10-3-1-9(2-4-10)13-7-11-5-6-12(16(19)20)8-14(11)21-13/h1-8,21H,(H3,17,18)(H3,19,20) + C16H15N5 + 2-(4-(aminoiminomethyl)phenyl)-1H-indole-6-carboximidamide + InChIKey=FWBHETKCLVMNFS-UHFFFAOYSA-N + CHEBI:DAPI + 2-(4-carbamimidoylphenyl)-1H-indole-6-carboximidamide + "An indole that has formula C16H15N5." [] + DAPI + 4',6-diamidinophenyl-indole + 4',6-diamidino-2-phenylindole + NC(=N)c1ccc(cc1)-c1cc2ccc(cc2[nH]1)C(N)=N + CHEBI:51231 + + + CHEBI:magnesium halide + magnesium halides + magnesium halide + CHEBI:51234 + + + CHEBI:propidium iodide + [I-].[I-].CC[N+](C)(CC)CCC[n+]1c(-c2ccccc2)c2cc(N)ccc2c2ccc(N)cc12 + propidium diiodide + InChI=1S/C27H33N4.2HI/c1-4-31(3,5-2)17-9-16-30-26-19-22(29)13-15-24(26)23-14-12-21(28)18-25(23)27(30)20-10-7-6-8-11-20;;/h6-8,10-15,18-19,29H,4-5,9,16-17,28H2,1-3H3;2*1H/q+1;;/p-1 + C27H34I2N4 + 3,8-diamino-5-(3-(diethylmethylammonio)propyl)-6-phenylphenanthridinium diiodide + "An organic iodide salt that has formula C27H34I2N4." [] + CHEBI:51240 + InChIKey=XJMOSONTPMZWPB-UHFFFAOYSA-M + propidium iodide + 3,8-diamino-5-{3-[diethyl(methyl)ammonio]propyl}-6-phenylphenanthridinium diiodide + + + texas red + InChI=1S/C31H29ClN2O6S2/c32-41(35,36)20-9-10-21(26(17-20)42(37,38)39)27-24-15-18-5-1-11-33-13-3-7-22(28(18)33)30(24)40-31-23-8-4-14-34-12-2-6-19(29(23)34)16-25(27)31/h9-10,15-17H,1-8,11-14H2 + 5-(chlorosulfonyl)-2-(2,3,6,7,12,13,16,17-octahydro-1H,5H,11H,15H-pyrido[3,2,1-ij]quinolizino[1',9':6,7,8]chromeno[2,3-f]quinolin-4-ium-9-yl)benzenesulfonate + C31H29ClN2O6S2 + CHEBI:texas red + CHEBI:51247 + InChIKey=MPLHNVLQVRSVEE-UHFFFAOYSA-N + sulforhodamine 101 acid chloride + [O-]S(=O)(=O)c1cc(ccc1C1=c2cc3CCC[N+]4=c3c(CCC4)c2Oc2c3CCCN4CCCc(cc12)c34)S(Cl)(=O)=O + sulforhodamine 101 sulfonyl chloride + "An organic heteroheptacyclic compound that has formula C31H29ClN2O6S2." [] + + + C39H37N3O13S2 + CHEBI:Alexa Fluor 594 + CHEBI:51248 + Alexa Fluor 594 + + + acenes + CHEBI:51269 + CHEBI:acenes + "Polycyclic aromatic hydrocarbons consisting of fused benzene rings in a rectilinear arrangement and their substitution derivatives." [] + + + thioureas + CHEBI:thioureas + CHEBI:51276 + "Compounds of general formula RR'NC(=S)NR''R'''." [] + + + thioesters + "A compound of general formula RC(=O)SR'." [] + thio ester + CHEBI:51277 + COSR2 + thioester + thiol ester + [*]C(=O)S[*] + CHEBI:thioester + + + CHEBI:51285 + "Quinones containing an acene fused ring system." [] + acenoquinones + CHEBI:acenoquinone + acenoquinone + acenoquinone + + + cinchona alkaloids + CHEBI:cinchona alkaloid + "An alkaloid based on a cinchonan skeleton." [] + cinchona alkaloid + CHEBI:51323 + + + CHEBI:51336 + CHEBI:metal sulfate + "Sulfate salts where the cation is a metal ion." [] + metal sulfates + metal sulfate + + + organic monovalent group + organic univalent group + CHEBI:51447 + CHEBI:organic univalent group + + + 2-{[3-(dimethylamino)propyl](propyl)amino}-4-[(E)-(3-methyl-1,3-benzothiazol-2(3H)-ylidene)methyl]-1-phenylquinolinium + 2-{(E)-[2-{[3-(dimethylamino)propyl](propyl)amino}-1-phenylquinolin-4(1H)-ylidene]methyl}-3-methyl-1,3-benzothiazol-3-ium + InChI=1S/C32H37N4S/c1-5-20-35(22-13-21-33(2)3)31-23-25(24-32-34(4)29-18-11-12-19-30(29)37-32)27-16-9-10-17-28(27)36(31)26-14-7-6-8-15-26/h6-12,14-19,23-24H,5,13,20-22H2,1-4H3/q+1 + 2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium + InChIKey=CGNLCCVKSWNSDG-UHFFFAOYSA-N + C32H37N4S + CHEBI:51461 + (E)-2-((2-((3-(dimethylamino)propyl)(propyl)amino)-1-phenylquinolin-4(1H)-ylidene)methyl)-3-methylbenzo[d]thiazol-3-ium + CCCN(CCCN(C)C)C1=C/C(=C\\c2sc3ccccc3[n+]2C)c2ccccc2N1c1ccccc1 + "SYBR Green I is a cationic unsymmetrical cyanine dye used as a nucleic acid stain in molecular biology. SYBR Green I binds to double-stranded DNA." [] + CHEBI:SYBR Green I + SYBR Green I + + + naphthohydroquinones + CHEBI:naphthohydroquinone + naphthohydroquinone + . + naphthohydroquinone + CHEBI:51475 + + + N-acyl-amino acid + N-acylamino acid + N-acyl amino acid + N-acyl amino acids + . + N-acyl-amino-acids + acyl-amino-acids + N-acylamino acids + "A carboxamide resulting from the formal condensation of a carboxylic acid with the amino group of an amino acid." [] + acyl-amino-acid + N-acyl-amino-acid + N-acyl-amino acids + CHEBI:51569 + CHEBI:N-acyl-amino acid + acylamino acids + + + CHEBI:51570 + "Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton." [] + CHEBI:biotins + biotins + . + + + InChI=1S/C25H22N2O5/c1-26(2)15-6-9-18-21(12-15)32-22-13-16(27(3)4)7-10-19(22)23(18)17-8-5-14(24(28)29)11-20(17)25(30)31/h5-13H,1-4H3,(H-,28,29,30,31) + 5-TAMRA + C25H22N2O5 + 5-carboxytetramethylrhodamine + 2-[3,6-bis(dimethylamino)xanthenium-9-yl]-5-carboxybenzoate + InChIKey=YMZMTOFQCVHHFB-UHFFFAOYSA-N + CN(C)c1ccc2c(-c3ccc(cc3C([O-])=O)C(O)=O)c3ccc(cc3[o+]c2c1)N(C)C + CHEBI:5-carboxytetramethylrhodamine + "A tetramethylrhodamine compound having a carboxy substituent at the 5-position" [] + CHEBI:51657 + + + CHEBI:methoxybenzene + CHEBI:51683 + methoxybenzenes + methoxybenzene + . + "Any aromatic ether that consists of a benzene skeleton substituted with one or more methoxy groups." [] + + + InChIKey=WZUVPPKBWHMQCE-UHFFFAOYSA-N + CHEBI:51686 + hematoxylin + hematoxyline + CHEBI:haematoxylin + haematoxylin + hematoxilina + Oc1cc2CC3(O)COc4c(O)c(O)ccc4C3c2cc1O + "An organic heterotetracyclic compound that has formula C16H14O6." [] + C16H14O6 + InChI=1S/C16H14O6/c17-10-2-1-8-13-9-4-12(19)11(18)3-7(9)5-16(13,21)6-22-15(8)14(10)20/h1-4,13,17-21H,5-6H2 + 7,11b-dihydroindeno[2,1-c]chromene-3,4,6a,9,10(6H)-pentol + Haematoxylin + 7,11b-dihydrobenz[b]indeno[1,2-d]pyran-3,4,6a,9,10(6H)-pentol + + + [H]C(=O)C(\\[*])=C(/[*])[*] + C3HOR3 + enal + "An alpha,beta-unsaturated aldehyde of general formula R(1)R(2)C=CR(3)-CH=O in which the aldehydic C=O function is conjugated to a C=C double bond at the alpha,beta position." [] + CHEBI:51688 + CHEBI:enal + . + enals + + + C3O2R4 + enoate esters + enoate ester + [*]\\C([*])=C(\\[*])C(=O)O[*] + "An alpha,beta-unsaturated carboxylic ester of general formula R(1)R(2)C=CR(3)-C(=O)OR(4) (R(4) =/= H) in which the ester C=O function is conjugated to a C=C double bond at the alpha,beta position." [] + enoates + CHEBI:51702 + enoate + CHEBI:enoate ester + . + + + alpha,beta-unsaturated aldehyde + . + CHEBI:51718 + alpha,beta-unsaturated aldehydes + "An aldehyde of general formula R(1)R(2)C=CR(3)-CH=O or RC#C-CH=O in which the aldehydic C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position." [] + CHEBI:alpha,beta-unsaturated aldehyde + + + alpha,beta-unsaturated carboxylic ester + CHEBI:51737 + . + "A carboxylic ester of general formula R(1)R(2)C=CR(3)-C(=O)OR(4) (R(4) =/= H) or R(1)C#C-C(=O)OR(2) (R(2) =/= H) in which the ester C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position." [] + CHEBI:alpha,beta-unsaturated carboxylic ester + alpha,beta-unsaturated carboxylic esters + + + [H+].[Cl-].CN(C)c1ccc2cc3ccc(cc3nc2c1)N(C)C + N,N,N',N'-tetramethylacridine-3,6-diamine hydrochloride + 3,6-Bis(dimethylamino)acridine + Rhoduline Orange + CHEBI:acridine orange + InChI=1S/C17H19N3.ClH/c1-19(2)14-7-5-12-9-13-6-8-15(20(3)4)11-17(13)18-16(12)10-14;/h5-11H,1-4H3;1H + N3,N3,N6,N6-tetramethyl-3,6-Acridinediamine hydrochloride(1:1) + C17H20ClN3 + CHEBI:51739 + 3,6-Bis(dimethylamino)acridine hydrochloride + "Fluorescent dye useful for cell cycle determination. It is cell-permeable, and interacts with DNA and RNA by intercalation or electrostatic attractions respectively." [] + C17H19N3.ClH + InChIKey=VSTHNGLPHBTRMB-UHFFFAOYSA-N + acridine orange + + + alpha,beta-unsaturated carboxamide + CHEBI:alpha,beta-unsaturated carboxylic acid amide + alpha,beta-unsaturated monocarboxylic acid amide + "A monocarboxylic amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) or R(1)C#C-C(=O)NR(2)R(3) in which the amide C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position." [] + alpha,beta-unsaturated monocarboxylic acid amides + alpha,beta-unsaturated amide + alpha,beta-unsaturated carboxylic acid amide + . + CHEBI:51750 + + + C3NOR5 + [*]\\C([*])=C(\\[*])C(=O)N([*])[*] + "An alpha,beta-unsaturated carboxylic acid amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) in which the amide C=O function is conjugated to a C=C double bond at the alpha,beta position." [] + enamide + enamides + . + CHEBI:enamide + CHEBI:51751 + + + "An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3." [] + CHEBI:Alexa Fluor 546 + [H+].[Na+].CC1CC(C)(C)Nc2c1cc1c(Oc3c(c4=NC(C)(C)CC(C)c4cc3=C1c1c(Cl)c(SCC(=O)NCCCCCC(=O)ON3C(=O)CCC3=O)c(Cl)c(Cl)c1C(O)=O)S([O-])(=O)=O)c2S([O-])(=O)=O + C44H46Cl3N4NaO14S3 + Alexa Fluor 546 carboxylic acid, succinimidyl ester + Alexa Fluor 546 + InChIKey=ZAINTDRBUHCDPZ-UHFFFAOYSA-M + InChI=1S/C44H47Cl3N4O14S3.Na/c1-19-16-43(3,4)49-35-21(19)14-23-29(24-15-22-20(2)17-44(5,6)50-36(22)41(68(61,62)63)38(24)64-37(23)40(35)67(58,59)60)30-31(42(56)57)32(45)34(47)39(33(30)46)66-18-25(52)48-13-9-7-8-10-28(55)65-51-26(53)11-12-27(51)54;/h14-15,19-20,49H,7-13,16-18H2,1-6H3,(H,48,52)(H,56,57)(H,58,59,60)(H,61,62,63);/q;+1/p-1 + sodium 6-(2-carboxy-3,4,6-trichloro-5-{[2-({6-[(2,5-dioxopyrrolidin-1-yl)oxy]-6-oxohexyl}amino)-2-oxoethyl]thio}phenyl)-2,2,4,8,10,10-hexamethyl-3,4,5a,8,9,10,11,12a-octahydro-2H-pyrano[3,2-g:5,6-g']diquinolin-1-ium-12,14-disulfonate + CHEBI:51760 + + + CHEBI:Alexa Fluor 568 + C37H33N3O13S2 + CHEBI:51766 + Alexa Fluor 568 + Alexa Fluor 568 carboxylic acid, succinimidyl ester + + + . + aminoacridines + aminoacridine + CHEBI:aminoacridines + "Acridines which are substituted in any position by one or more amino groups or substituted amino groups. Note that the term 'aminoacridine' is the International Prorietary Name (INN) for 9-aminoacridine." [] + CHEBI:51803 + + + "A ketone of formula RC(=O)CH3 (R =/= H)." [] + . + CHEBI:51867 + CHEBI:methyl ketone + methyl ketones + methyl ketone + + + 2',7'-Bis((bis(carboxymethyl)amino)methyl)fluorescein + CHEBI:calcein + OC(=O)CN(CC(O)=O)Cc1cc2c(Oc3cc(O)c(CN(CC(O)=O)CC(O)=O)cc3C22OC(=O)c3ccccc23)cc1O + calcein + 2,2',2'',2'''-[(3',6'-dihydroxy-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-2',7'-diyl)bis(methylenenitrilo)]tetraacetic acid + oftasceinum + oftasceine + 2,7-Bis(N,N-bis(carboxymethyl)aminomethylene)fluorescein + oftasceina + CHEBI:51903 + N,N'-(3',6'-Dihydroxyspiro(phthalid-3,9'-xanthen)-2',7'-diyldimethyl)bis(iminodiessigsaeure) + C30H26N2O13 + InChIKey=DEGAKNSWVGKMLS-UHFFFAOYSA-N + "A xanthene dye that has formula C30H26N2O13." [] + InChI=1S/C30H26N2O13/c33-21-7-23-19(5-15(21)9-31(11-25(35)36)12-26(37)38)30(18-4-2-1-3-17(18)29(43)45-30)20-6-16(22(34)8-24(20)44-23)10-32(13-27(39)40)14-28(41)42/h1-8,33-34H,9-14H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42) + + + CHEBI:51915 + . + indolocarbazole + CHEBI:indolocarbazole + "Compounds based upon an indolo[2,3-a]carbazole skeleton." [] + indolocarbazoles + + + organic polycyclic compound + CHEBI:organic polycyclic compound + CHEBI:51958 + organic polycyclic compounds + + + CHEBI:organic tricyclic compound + organic tricyclic compounds + CHEBI:51959 + organic tricyclic compound + + + 4-{2-[4-(dihexadecylamino)phenyl]ethenyl}-1-methylpyridinium iodide + InChIKey=YPGZWUVVEWKKDQ-UHFFFAOYSA-M + CHEBI:4-(4-dihexadecylaminostyryl)-N-methylpyridium iodide + CHEBI:52024 + "A pyridinium salt that has formula C46H79N2.I." [] + DIASP + DiA + 4-(4-Dihexadecylaminostyryl)N-methylpyridium, iodide + 4-{2-[4-(dihexadecylamino)phenyl]vinyl}-1-methylpyridinium iodide + 4-(4-dihexadecylaminostyryl)-N-methylpyridium iodide + 4-Di-16-ASP + C46H79N2.I + C46H79IN2 + [I-].[H]C(=C([H])c1cc[n+](C)cc1)c1ccc(cc1)N(CCCCCCCCCCCCCCCC)CCCCCCCCCCCCCCCC + InChI=1S/C46H79N2.HI/c1-4-6-8-10-12-14-16-18-20-22-24-26-28-30-40-48(41-31-29-27-25-23-21-19-17-15-13-11-9-7-5-2)46-36-34-44(35-37-46)32-33-45-38-42-47(3)43-39-45;/h32-39,42-43H,4-31,40-41H2,1-3H3;1H/q+1;/p-1 + + + 3H-Indolium, 2-[3-(1,3-dihydro-3,3-dimethyl-1-octadecyl-2H-indol-2-ylidene)-1-propenyl]-3,3-dimethyl-1-octadecyl-, perchlorate + InChI=1S/C59H97N2.ClHO4/c1-7-9-11-13-15-17-19-21-23-25-27-29-31-33-35-41-50-60-54-46-39-37-44-52(54)58(3,4)56(60)48-43-49-57-59(5,6)53-45-38-40-47-55(53)61(57)51-42-36-34-32-30-28-26-24-22-20-18-16-14-12-10-8-2;2-1(3,4)5/h37-40,43-49H,7-36,41-42,50-51H2,1-6H3;(H,2,3,4,5)/q+1;/p-1 + CHEBI:dilC18(3) dye + "A Cy3 dye that has formula C59H97ClN2O4." [] + CHEBI:52029 + DilC18(3) + [O-]Cl(=O)(=O)=O.[H]C(=C([H])C1=[N+](CCCCCCCCCCCCCCCCCC)c2ccccc2C1(C)C)C([H])=C1N(CCCCCCCCCCCCCCCCCC)c2ccccc2C1(C)C + 2-[3-(3,3-dimethyl-1-octadecyl-1,3-dihydro-2H-indol-2-ylidene)prop-1-en-1-yl]-3,3-dimethyl-1-octadecyl-3H-indolium perchlorate + C59H97ClN2O4 + InChIKey=JVXZRNYCRFIEGV-UHFFFAOYSA-M + dilC18(3) dye + DiI + + + 1,6-alpha-D-Glucan + dextrano + dextrane + dextran + (1,6-alpha-D-Glucosyl)n + (1,6-alpha-D-Glucosyl)m + (1,6-alpha-D-Glucosyl)n+1 + (1,6-alpha-D-Glucosyl)m+1 + dextran + Dextran 40 + dextranum + CHEBI:52071 + CHEBI:dextran + Dextran 75 + "A (1->6)-alpha-D-glucan which has extra branching consisting of (1->2), (1->3) or (1->4) linkages." [] + dextrans + Dextran 70 + + + InChIKey=MCEXQZRGUKALLT-UHFFFAOYSA-N + [H]C(c1cc2cc(OCCOc3cc(C)ccc3N(CC(=O)OCOC(C)=O)CC(=O)OCOC(C)=O)c(cc2o1)N(CC(=O)OCOC(C)=O)CC(=O)OCOC(C)=O)=C1NC(=S)NC1=O + fura red + CHEBI:52080 + CHEBI:fura red + InChI=1S/C41H44N4O20S/c1-23-6-7-31(44(15-36(50)61-19-57-24(2)46)16-37(51)62-20-58-25(3)47)34(10-23)55-8-9-56-35-12-28-11-29(13-30-40(54)43-41(66)42-30)65-33(28)14-32(35)45(17-38(52)63-21-59-26(4)48)18-39(53)64-22-60-27(5)49/h6-7,10-14H,8-9,15-22H2,1-5H3,(H2,42,43,54,66) + "A 1-benzofuran substituted at position 2 by a (5-oxo-2-thioxoimidazolidin-4-ylidene)methyl group, and at C-5 and C-6 by heavily substituted oxygen and nitrogen functionalities respectively." [] + (acetyloxy)methyl [{2-[(acetyloxy)methoxy]-2-oxoethyl}(5-{2-[2-(bis{2-[(acetyloxy)methoxy]-2-oxoethyl}amino)-5-methylphenoxy]ethoxy}-2-[(5-oxo-2-thioxoimidazolidin-4-ylidene)methyl]-1-benzofuran-6-yl)amino]acetate + C41H44N4O20S + + + InChI=1S/C20H24BF2N5O/c1-26(2)13-12-25-20(29)10-8-15-5-6-16-14-17-7-9-19(18-4-3-11-24-18)28(17)21(22,23)27(15)16/h3-7,9,11,14,24H,8,10,12-13H2,1-2H3,(H,25,29) + CHEBI:52117 + DND-99 dye + CN(C)CCNC(=O)CCC1=[N+]2C(C=C1)=Cc1ccc(-c3ccc[nH]3)n1[B-]2(F)F + C20H24BF2N5O + LysoTracker Red DND-99 + CHEBI:DND-99 dye + "A BODIPY dye that has formula C20H24BF2N5O." [] + InChIKey=DYYUXMKNXUZBMO-UHFFFAOYSA-N + (3-{2-[(1H,1'H-2,2'-bipyrrol-5-yl-kappaN(1))methylidene]-2H-pyrrol-5-yl-kappaN}-N-[2-(dimethylamino)ethyl]propanamidato)(difluoro)boron + + + organic heteroheptacyclic compound + . + CHEBI:organic heteroheptacyclic compound + CHEBI:52157 + + + CHEBI:organic perchlorate salt + . + organic perchlorate salt + CHEBI:52165 + + + C29H32N2O12S2 + InChI=1S/C29H32N2O12S2/c32-28(33)10-3-1-5-16-30-22-14-12-20(44(36,37)38)18-24(22)42-26(30)8-7-9-27-31(17-6-2-4-11-29(34)35)23-15-13-21(45(39,40)41)19-25(23)43-27/h7-9,12-15,18-19H,1-6,10-11,16-17H2,(H3-,32,33,34,35,36,37,38,39,40,41) + CHEBI:52302 + CHEBI:Cy2 dye + 3-(6-carboxyhexyl)-2-{3-[3-(5-carboxypentyl)-6-sulfo-1,3-benzoxazol-3-ium-2-yl]prop-2-en-1-ylidene}-2,3-dihydro-1,3-benzoxazole-6-sulfonate + [H]C(=Cc1oc2cc(ccc2[n+]1CCCCCC(O)=O)S([O-])(=O)=O)C([H])=C1Oc2cc(ccc2N1CCCCCC(O)=O)S(O)(=O)=O + InChIKey=CUMZIUDGEWDTIL-UHFFFAOYSA-N + Cy2 dye + "A cyanine dye that has formula C29H32N2O12S2." [] + + + "A diterpenoid with a tetracyclic skeleton." [] + tetracyclic diterpenoids + CHEBI:tetracyclic diterpenoid + CHEBI:52557 + tetracyclic diterpenoid + + + CHEBI:acylglycerophosphoserine + CHEBI:52565 + acylglycerophosphoserine + acylglycerophosphoserines + + + inorganic hydroxides + CHEBI:52625 + CHEBI:inorganic hydroxy compound + inorganic hydroxy compound + + + CHEBI:leptomycin B + C33H48O6 + CHEBI:52646 + "A leptomycin having a (2E,10E,12E,16Z,18E)-double bond configuration as well as an ethyl substituent at position 17." [] + InChI=1S/C33H48O6/c1-9-28(14-15-29-24(5)13-16-31(36)39-29)19-22(3)12-10-11-21(2)17-25(6)32(37)27(8)33(38)26(7)18-23(4)20-30(34)35/h10-11,13-17,19-20,22,24-27,29,33,38H,9,12,18H2,1-8H3,(H,34,35)/b11-10+,15-14+,21-17+,23-20+,28-19-/t22-,24+,25-,26+,27-,29+,33-/m1/s1 + (2E,5S,6R,7S,9R,10E,12E,15R,16Z,18E)-17-ethyl-6-hydroxy-3,5,7,9,11,15-hexamethyl-19-[(2S,3S)-3-methyl-6-oxo-3,6-dihydro-2H-pyran-2-yl]-8-oxononadeca-2,10,12,16,18-pentaenoic acid + Antibiotic CI 940 + InChIKey=YACHGFWEQXFSBS-XYERBDPFSA-N + leptomycin B + antibiotic ATS 1287B + ATS 1287B + LMB + Antibiotic PD 114720 + Antibiotic CL 1957A + CC\\C(\\C=C\\[C@@H]1OC(=O)C=C[C@@H]1C)=C\\[C@H](C)C\\C=C\\C(\\C)=C\\[C@@H](C)C(=O)[C@@H](C)[C@H](O)[C@@H](C)C\\C(C)=C\\C(O)=O + + + CHEBI:52651 + "A complex, very long chain, polyunsaturated fatty acid whose core structure comprises 8-oxononadeca-2,10,12,16,18-pentaenoic acid having methyl substituents at positions 3, 5, 7, 9, 11 and 15 and a 3,6-dihydropyran-6-one-2-yl group at position 19." [] + leptomycin + CHEBI:leptomycin + leptomycins + + + CHEBI:52661 + Alexa Fluor 488 + CHEBI:Alexa Fluor 488 + . + "A fluorescent dye of absorption wavelength 495 nm and emission wavelength 519 nm, derived from a 3,6-diaminoxanthenium-4,5-disulfate." [] + + + C21H14N2O11S2 + Alexa Fluor 555 + Nc1ccc2c(-c3ccc(cc3C(O)=O)C(O)=O)c3ccc(=N)c(c3oc2c1S(O)(=O)=O)S(O)(=O)=O + CHEBI:Alexa Fluor 555 + InChI=1S/C21H14N2O11S2/c22-13-5-3-10-15(9-2-1-8(20(24)25)7-12(9)21(26)27)11-4-6-14(23)19(36(31,32)33)17(11)34-16(10)18(13)35(28,29)30/h1-7,22H,23H2,(H,24,25)(H,26,27)(H,28,29,30)(H,31,32,33) + InChIKey=IGAZHQIYONOHQN-UHFFFAOYSA-N + 4-(6-amino-3-imino-4,5-disulfo-3H-xanthen-9-yl)benzene-1,3-dicarboxylic acid + CHEBI:52673 + "A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate." [] + + + CHEBI:52718 + [H]C(=CC([H])=CC([H])=C1Cc2cc(ccc2N1CC)S(O)(=O)=O)C=C([H])C1=[N+](CCCCCC(O)=O)c2ccc(cc2C1)S([O-])(=O)=O + 2-{7-[1-(5-carboxypentyl)-5-sulfo-1,3-dihydro-2H-indol-2-ylidene]hepta-1,3,5-trien-1-yl}-1-ethyl-3H-indolium-5-sulfonate + CHEBI:Cy7 dye + InChIKey=LOPCOKFMJOYXHI-UHFFFAOYSA-N + 1-(5-carboxypentyl)-2-[7-(1-ethyl-5-sulfo-1,3-dihydro-2H-indol-2-ylidene)hepta-1,3,5-trien-1-yl]-3H-indolium-5-sulfonate + Cy7 dye + C31H34N2O8S2 + "A C7-cyanine dye having differentially-substituted 2-indolyl units at each end." [] + InChI=1S/C31H34N2O8S2/c1-2-32-25(19-23-21-27(42(36,37)38)14-16-29(23)32)11-7-4-3-5-8-12-26-20-24-22-28(43(39,40)41)15-17-30(24)33(26)18-10-6-9-13-31(34)35/h3-5,7-8,11-12,14-17,21-22H,2,6,9-10,13,18-20H2,1H3,(H2-,34,35,36,37,38,39,40,41) + + + CHEBI:52815 + InChIKey=DHRJOYDLBMLIFJ-UHFFFAOYSA-N + "A cationic heterotetracyclic fluorescent dye derived from benzo[a]phenoxazine." [] + C16H12N3O + cresyl violet + InChI=1S/C16H12N3O/c17-9-5-6-13-14(7-9)20-15-8-12(18)10-3-1-2-4-11(10)16(15)19-13/h1-8H,17-18H2/q+1 + 5,9-diaminobenzo[a]phenoxazin-7-ium + Nc1ccc2nc3c(cc(N)c4ccccc34)[o+]c2c1 + CHEBI:cresyl violet + + + CHEBI:52838 + benzothiazolium ion + benzothiazolium ion + benzothiazolium ions + CHEBI:benzothiazolium ion + + + CHEBI:gelatin + Gelatine + gelatin + CHEBI:5291 + "A mixture of peptides and proteins produced by partial hydrolysis of collagen extracted from the skin, bones, and connective tissues of animals such as domesticated cattle, chicken, pigs, and fish." [] + Gelatin + + + CHEBI:53025 + OC[C@@H]1OC(OP(O)(O)=O)[C@@H](O)[C@H](O)[C@@H]1O + "A galactose phosphate compound with undefined anomeric stereochemistry having L-configuration and the phosphate group at the 1-position." [] + InChI=1S/C6H13O9P/c7-1-2-3(8)4(9)5(10)6(14-2)15-16(11,12)13/h2-10H,1H2,(H2,11,12,13)/t2-,3+,4+,5-,6?/m0/s1 + L-galactopyranose-1-(dihydrogen phosphate) + CHEBI:L-galactose 1-phosphate + C6H13O9P + L-galactose 1-phosphate + InChIKey=HXXFSFRBOHSIMQ-DHVFOXMCSA-N + 1-O-phosphono-L-galactopyranose + + + oxysterols + oxysterol + CHEBI:53030 + CHEBI:oxysterol + "An oxygenated derivative of cholesterol" [] + + + C6H3N3O9S + Trinitrobenzenesulfonic acid + 2,4,6-trinitrobenzenesulfonic acid + InChI=1S/C6H3N3O9S/c10-7(11)3-1-4(8(12)13)6(19(16,17)18)5(2-3)9(14)15/h1-2H,(H,16,17,18) + CHEBI:53063 + Picryl sulfonic acid + InChIKey=NHJVRSWLHSJWIN-UHFFFAOYSA-N + CHEBI:2,4,6-trinitrobenzenesulfonic acid + 2,4,6-Trinitrobenzene-1-sulfonic acid + OS(=O)(=O)c1c(cc(cc1[N+]([O-])=O)[N+]([O-])=O)[N+]([O-])=O + 2,4,6-trinitrobenzenesulfonic acid + 2,4,6-Trinitrobenzenesulfonic acid + picrylsulfonic acid + "The arenesulfonic acid that is benzenesulfonic acid with three nitro substituents in the 2-, 4- and 6-positions." [] + TNBS + + + . + CHEBI:poly(ether) macromolecule + poly(ether) macromolecule + poly(ether) + CHEBI:53223 + poly(ether)s + polyether + polyethers + "A macromolecule composed of units connected by ether (-O-) linkages." [] + + + poly(alkene)s + polyalkylenes + CHEBI:poly(alkylene) macromolecule + polyalkene + poly(olefin) + poly(olefin)s + polyolefins + poly(alkylene) + poly(alkylene)s + polyolefin + poly(alkylene) macromolecule + poly(alkene) + polyalkenes + . + CHEBI:53225 + "A macromolecule composed of repeating alkane or substituted alkane units." [] + polyalkylene + + + CHEBI:polyethylene macromolecule + . + CHEBI:53226 + polyethylene + poly(ethene)s + polyethylene macromolecule + poly(ethylene)s + polyethylenes + polyethenes + "A macromolecule composed of ethane or substituted ethane units." [] + + + poly(ethylene) + CHEBI:poly(ethylene) + polyethene + CHEBI:53227 + polythene + Polyethylene + polyethylene + poly(ethene) + (C2H4)n + "A polymer composed of ethane units." [] + + + 3-(4,5-dimethylthiazole-2-yl)-2,5-diphenyltetrazolium bromide + MMT Tetrazolium + "The bromide salt of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium." [] + MTT + 3-(4,5-Dimethylthiazolyl)-2,5-diphenyltetrazolium bromide + 3-(4,5-dimethyl-1,3-thiazol-2-yl)-2,5-diphenyl-2H-tetrazol-3-ium bromide + CHEBI:53233 + Thiazolyl blue tetrazolium bromide + 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide + Thiazolyl Blue Monotetrazolium + CHEBI:3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide + Thiazolyl blue + C18H16BrN5S + [Br-].Cc1nc(sc1C)-[n+]1nc(nn1-c1ccccc1)-c1ccccc1 + InChIKey=AZKSAVLVSZKNRD-UHFFFAOYSA-M + Methylthiazoletetrazolium + 2-(4,5-dimethyl-1,3-thiazol-2-yl)-3,5-diphenyl-2H-tetrazol-3-ium bromide + TMCHB + InChI=1S/C18H16N5S.BrH/c1-13-14(2)24-18(19-13)23-21-17(15-9-5-3-6-10-15)20-22(23)16-11-7-4-8-12-16;/h3-12H,1-2H3;1H/q+1;/p-1 + 3-(4,5-Dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide + + + vinyl polymer macromolecule + vinyl polymers + vinyl polymer + . + CHEBI:vinyl polymer macromolecule + CHEBI:53242 + "A macromolecule composed of repeating -CHR-CH2- units." [] + + + Poly(N-vinyl-2-pyrrolidinone) + Poly(N-vinyl-2-pyrrolidone) + CHEBI:53248 + Vinylpyrrolidone polymer + polyvinylpyrrolidone + N-Vinylpyrrolidone polymer + CHEBI:poly(vinylpyrrolidone) + poly(vinylpyrrolidone) + 1-Vinyl-2-pyrrolidinone homopolymer + PVPON + Crospovidonum + poly(vinylpyrrolidone) + 1-Ethenyl-2-pyrrolidinone homopolymer + Poly(1-vinyl-2-pyrrolidone) + Poly-N-vinyl pyrrolidone + Povidone + poly(N-vinyl pyrrolidone) + (C6H9NO)n + Poly(1-vinylpyrrolidinone) + N-Vinylpyrrolidinone polymer + Vinylpyrrolidinone polymer + Poly(1-vinyl-2-pyrrolidinone) homopolymer + 1-Vinyl-2-pyrrolidone polymer + Poly(1-vinyl-2-pyrrolidinone) + Polyvidonum + Poly(N-vinylpyrrolidinone) + N-Vinyl-2-pyrrolidone polymer + Polyvinylpyrrolidone + N-Vinylbutyrolactam polymer + poly[1-(2-oxopyrrolidin-1-yl)ethylene] + Poly(N-vinylbutyrolactam) + Polividona + "A vinyl polymer composed of repeating -CH2-CR- units where R is a 2-oxopyrrolidin-1-yl group." [] + Poly(1-(2-oxo-1-pyrrolidinyl)ethylene) + poly(N-vinylpyrrolidone) + 1-Vinyl-2-pyrrolidinone polymer + 1-Ethenyl-2-pyrrolidinone polymers + Poly(1-ethenyl-2-pyrrolidinone) + Polividone + + + polyvinylidene + poly(vinylidene) + "A polymer composed of repeating -CR2-CR2- units." [] + CHEBI:poly(vinylidene) + poly(vinylidene)s + CHEBI:53249 + polyvinylidenes + + + poly(vinylidene fluoride) + CHEBI:53250 + "A polymer composed of repeating 1,1-difluoroethyl units." [] + poly(vinylidenefluoride) + polyvinylidenefluoride + Polyvinylidene fluoride + poly(vinylene fluoride) + polyvinylenefluoride + (C2H2F2)n + poly(1,1-difluoroethylene) + poly(vinylenefluoride) + CHEBI:poly(vinylene fluoride) + polyvinylene difluoride + + + CHEBI:poly(tetrafluoroethylene) + PTFE + Tetrafluoroethene polymer + poly(1,1,2,2-tetrafluoroethylene) + Politefo + CHEBI:53251 + Polytetrafluoroethylene + poly(tetrafluoroethene) + Poly(ethylene tetrafluoride) + "A polymer composed of repeating tetrafluoroethyl groups." [] + Tetrafluoroethylene polymer + (C2F4)n + Polytef + polytetrafluoroethene + Ptfe + poly(tetrafluoroethylene) + Fluorogold + Perfluoroethylene polymer + Teflon + Tetrafluoroethene homopolymer + polytetrafluoroethylene + Fluoro-gold + Politefum + Poly(tetrafluoroethylene) + Polytetrafluoroethene + Tetrafluoroethylene polymers + Tetrafluoroethylene homopolymer + + + InChIKey=HRXKRNGNAMMEHJ-UHFFFAOYSA-K + trisodium 2-hydroxypropane-1,2,3-tricarboxylate + C6H5Na3O7 + "The trisodium salt of citric acid." [] + CHEBI:53258 + InChI=1S/C6H8O7.3Na/c7-3(8)1-6(13,5(11)12)2-4(9)10;;;/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12);;;/q;3*+1/p-3 + citric acid trisodium salt + sodium citrate + [Na+].[Na+].[Na+].OC(CC([O-])=O)(CC([O-])=O)C([O-])=O + CHEBI:sodium citrate + trisodium citrate + + + Piroxilina + CHEBI:nitrocellulose + Cellulose tetranitrate + Pyroxyline + Collodion + CHEBI:53325 + Pyroxylinum + Cellulose nitrate + . + nitrocellulose + Pyroxylin + gun cotton + "A (1->4)-beta-D-glucan compound formed by nitrating cellulose through exposure to nitric acid or another powerful nitrating agent." [] + Nitrocellulose + + + tweens + polysorbates + CHEBI:polysorbate + CHEBI:53422 + polysorbate + "A polymer composed of PEG-ylated sorbitan [2-(1,2-dihydroxyethyl)tetrahydrofuran-3,4-diol] normally containing a total of 20 oxyethylene groups, with one or more of the terminal hydroxy groups esterified with a fatty acyl group. They are used as emulsifiers and dispersing agents in some pharmaceuticals products and as defoamers and emulsifiers in some foods." [] + . + + + Tween 20 + "A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by a dodecanoyl group." [] + polisorbato + Polyoxyethylene (20) sorbitan monolaurate + CHEBI:polysorbate 20 + Polyoxyethylene sorbitan monolaurate + polysorbate + Polysorbate + polysorbatum + Polysorbate 20 + C58H114O26 + CHEBI:53424 + polysorbate 20 + + + F-Met-leu-phe + C21H31N3O5S + "A tripeptide composed of L-Met, L-Leu and L-Phe in a linear sequence with a formyl group at the amino terminus. It acts as a potent inducer of leucocyte chemotaxis and macrophage activator as well as a ligand for the FPR receptor." [] + fMLF + CHEBI:53490 + N-Formyl-methionyl-leucyl-phenylalanine + CHEBI:N-formyl-L-methionyl-L-leucyl-L-phenylalanine + N-Formyl-Met-Leu-Phe + InChI=1S/C21H31N3O5S/c1-14(2)11-17(23-19(26)16(22-13-25)9-10-30-3)20(27)24-18(21(28)29)12-15-7-5-4-6-8-15/h4-8,13-14,16-18H,9-12H2,1-3H3,(H,22,25)(H,23,26)(H,24,27)(H,28,29)/t16-,17-,18-/m0/s1 + N-formyl-L-methionyl-L-leucyl-L-phenylalanine + N-Formylmethionine leucyl-phenylalanine + fMetLeuPhe + N-Formyl-L-methionyl-L-leucyl-L-phenylalanine + N-formyl-L-methionyl-L-leucyl-L-phenylalanine + fMLP + [H]C(=O)N[C@@H](CCSC)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc1ccccc1)C(O)=O + InChIKey=PRQROPMIIGLWRP-BZSNNMDCSA-N + + + 1-Propene homopolymer + CHEBI:53550 + Polipropene 25 + "A polymer compose of repeating propane-1,2-diyl units." [] + (C3H6)n + poly(propene) + polypropene + poly(prop-1-ene) + poly(1-methylethylene) + poly(propylene) + Polypropylene + polypropylene + CHEBI:poly(propylene) + PP + + + CHEBI:5386 + CHEBI:globin + globins + globin + Globin + . + pentacoordinate globin + + + isoxazoles + CHEBI:55373 + . + isoxazoles + "Oxazoles in which the N and O atoms are adjacent." [] + 1,2-oxazoles + CHEBI:isoxazoles + + + "Compounds containing a cyclic dicarboximide skeleton in which the two carboacyl groups on nitrogen together with the nitrogen itself form a 1H-pyrrole-2,5-dione structure." [] + CHEBI:maleimides + CHEBI:55417 + . + maleimides + + + 1,2-benzisothiazole + 1,2-benzisothiazoles + CHEBI:55505 + CHEBI:1,2-benzisothiazole + "A benzothiazole consisting of a benzene ring fused to an isothiazole." [] + + + 4'-fluoro-4-(4-hydroxy-4-(4'-chlorophenyl)piperidino)butyrophenone + 1-(3-p-fluorobenzoylpropyl)-4-p-chlorophenyl-4-hydroxypiperidine + 4-[4-(4-chlorophenyl)-4-hydroxypiperidin-1-yl]-1-(4-fluorophenyl)butan-1-one + CHEBI:5613 + InChIKey=LNEPOXFFQSENCJ-UHFFFAOYSA-N + Haldol + haloperidolum + gamma-(4-(p-chlorophenyl)-4-hydroxpiperidino)-p-fluorbutyrophenone + haloperidol + "A compound composed of a central piperidine structure with hydroxy and p-chlorophenyl substituents at position 4 and an N-linked p-fluorobutyrophenone moiety." [] + 4'-fluoro-4-(4-(p-chlorophenyl)-4-hydroxypiperidinyl)butyrophenone + 4-(4-(para-chlorophenyl)-4-hydroxypiperidino)-4'-fluorobutyrophenone + haloperidol + C21H23ClFNO2 + InChI=1S/C21H23ClFNO2/c22-18-7-5-17(6-8-18)21(26)11-14-24(15-12-21)13-1-2-20(25)16-3-9-19(23)10-4-16/h3-10,26H,1-2,11-15H2 + 4-[4-(4-chlorophenyl)-4-hydroxy-1-piperidyl]-1-(4-fluorophenyl)-butan-1-one + OC1(CCN(CCCC(=O)c2ccc(F)cc2)CC1)c1ccc(Cl)cc1 + CHEBI:haloperidol + + + CHEBI:hemiacetal + CHEBI:5653 + "A compound having the general formula RR'C(OH)OR'' (R'' =/= H)." [] + hemiacetals + OC([*])O[*] + hemiacetals + hemiacetal + CH2O2R2 + Hemiacetal + + + CHEBI:heterocyclic compound + compuestos heterociclicos + Heterocyclic compound + . + heterocyclic compound + heterocycle + compuesto heterociclico + "A cyclic compound having as ring members atoms of at least two different elements." [] + heterocyclic compounds + CHEBI:5686 + + + 2-{[{[(4S)-4-azaniumyl-4-carboxylatobutyl]amino}(iminiumyl)methyl]amino}butanedioate + CHEBI:57472 + [NH3+][C@@H](CCCNC(=[NH2+])NC(CC([O-])=O)C([O-])=O)C([O-])=O + InChI=1S/C10H18N4O6/c11-5(8(17)18)2-1-3-13-10(12)14-6(9(19)20)4-7(15)16/h5-6H,1-4,11H2,(H,15,16)(H,17,18)(H,19,20)(H3,12,13,14)/p-1/t5-,6?/m0/s1 + InChIKey=KDZOASGQNOPSCU-ZBHICJROSA-M + 2-{[{[(4S)-4-ammonio-4-carboxylatobutyl]amino}(iminio)methyl]amino}succinate + 2-(N(omega)-L-arginino)succinate + "Conjugate base of (N(omega)-L-arginino)succinic acid." [] + (N(omega)-L-arginino)succinate(1-) + C10H17N4O6 + CHEBI:(N(omega)-L-arginino)succinate(1-) + + + CHEBI:long-chain fatty acid anion + a long-chain carboxylate + [O-]C([*])=O + "A fatty acid anion with a chain length of C13 or greater." [] + long-chain fatty acid anion + CO2R + long-chain fatty acid anions + CHEBI:57560 + a long-chain fatty acid + + + . + organophosphate oxoanions + organophosphate oxoanion + CHEBI:58945 + "An organic phosphoric acid derivative in which one or more oxygen atoms of the phosphate group(s) has been deprotonated." [] + CHEBI:organophosphate oxoanion + + + [O-]C([*])=O + short-chain fatty acid anions + "Any fatty acid anion obtained by removal of a proton from the carboxy group of a short-chain fatty acid (chain length of less than C6)." [] + CO2R + a short-chain fatty acid + CHEBI:short-chain fatty acid anion + CHEBI:58951 + short-chain fatty acid anion + + + "Any fatty acid anion in which there is no C-C unsaturation." [] + a saturated fatty acid + CHEBI:saturated fatty acid anion + CHEBI:58953 + saturated fatty acid anions + . + saturated fatty acid anion + + + straight-chain fatty acids + straight-chain fatty acid + "Any fatty acid whose skeletal carbon atoms form an unbranched open chain." [] + CHEBI:straight-chain fatty acid + CHEBI:59202 + + + acetate salts + acetate salt + "Any salt prepared using acetic acid as the acid component." [] + CHEBI:59230 + CHEBI:acetate salt + + + insulin (recombinant) + InChIKey=YAJCHEVQCOHZDC-QMMNLEPNSA-N + CHEBI:insulin (human) + InChI=1S/C256H381N65O77S6/c1-29-130(23)202(311-190(337)103-258)250(391)315-200(128(19)20)246(387)286-158(75-82-197(347)348)216(357)281-154(70-77-186(261)333)220(361)306-181-115-402-403-116-182-241(382)303-176(110-323)238(379)293-161(88-122(7)8)224(365)294-167(95-139-53-61-145(328)62-54-139)227(368)282-153(69-76-185(260)332)217(358)289-160(87-121(5)6)222(363)283-157(74-81-196(345)346)219(360)301-173(101-188(263)335)233(374)297-169(97-141-57-65-147(330)66-58-141)230(371)307-180(240(381)302-174(254(395)396)102-189(264)336)114-401-400-113-179(213(354)272-106-191(338)277-152(72-79-194(341)342)215(356)280-150(51-42-84-270-256(266)267)211(352)271-107-192(339)278-165(93-137-46-36-32-37-47-137)226(367)296-166(94-138-48-38-33-39-49-138)229(370)298-170(98-142-59-67-148(331)68-60-142)236(377)318-205(134(27)326)253(394)321-85-43-52-184(321)244(385)284-151(50-40-41-83-257)221(362)319-206(135(28)327)255(397)398)309-247(388)199(127(17)18)314-234(375)163(90-124(11)12)291-228(369)168(96-140-55-63-146(329)64-56-140)295-223(364)159(86-120(3)4)288-209(350)132(25)276-214(355)156(73-80-195(343)344)285-245(386)198(126(15)16)313-235(376)164(91-125(13)14)292-232(373)172(100-144-105-269-119-275-144)300-237(378)175(109-322)279-193(340)108-273-212(353)178(112-399-404-117-183(308-242(181)383)243(384)317-204(133(26)325)251(392)304-177(111-324)239(380)316-203(131(24)30-2)249(390)310-182)305-225(366)162(89-123(9)10)290-231(372)171(99-143-104-268-118-274-143)299-218(359)155(71-78-187(262)334)287-252(393)207(208(265)349)320-248(389)201(129(21)22)312-210(351)149(259)92-136-44-34-31-35-45-136/h31-39,44-49,53-68,104-105,118-135,149-184,198-207,322-331H,29-30,40-43,50-52,69-103,106-117,257-259H2,1-28H3,(H2,260,332)(H2,261,333)(H2,262,334)(H2,263,335)(H2,264,336)(H2,265,349)(H,268,274)(H,269,275)(H,271,352)(H,272,354)(H,273,353)(H,276,355)(H,277,338)(H,278,339)(H,279,340)(H,280,356)(H,281,357)(H,282,368)(H,283,363)(H,284,385)(H,285,386)(H,286,387)(H,287,393)(H,288,350)(H,289,358)(H,290,372)(H,291,369)(H,292,373)(H,293,379)(H,294,365)(H,295,364)(H,296,367)(H,297,374)(H,298,370)(H,299,359)(H,300,378)(H,301,360)(H,302,381)(H,303,382)(H,304,392)(H,305,366)(H,306,361)(H,307,371)(H,308,383)(H,309,388)(H,310,390)(H,311,337)(H,312,351)(H,313,376)(H,314,375)(H,315,391)(H,316,380)(H,317,384)(H,318,377)(H,319,362)(H,320,389)(H,341,342)(H,343,344)(H,345,346)(H,347,348)(H,395,396)(H,397,398)(H4,266,267,270)/t130-,131-,132+,133+,134+,135+,149+,150+,151+,152+,153+,154+,155+,156+,157+,158+,159+,160+,161+,162+,163+,164+,165+,166+,167+,168+,169+,170+,171+,172+,173+,174+,175+,176+,177+,178+,179+,180+,181+,182-,183+,184+,198+,199+,200+,201+,202+,203+,204+,205+,206+,207+/m1/s1 + "A peptide hormone produced in the pancreas and involved in regulating the metabolism of carbohydrates (particularly glucose) and fats. Commonly thought of as a protein, it consists of two petide chains, one containing 21 amino acid residues and the other containing 30; the chains are joined together by 2 disulfide bonds. Recombinant insulin is identical to human insulin, but is synthesised by inserting the human insulin gene into E. coli, which then produces insulin for human use. It is used in the treatment of type I and type II diabetes." [] + Insulin recombinant + CHEBI:5931 + C256H381N65O77S6 + insulin (human) + CC[C@@H](C)[C@H](NC(=O)CN)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@H]1CSSC[C@H]2NC(=O)[C@@H](NC(=O)[C@H](CO)NC(=O)[C@@H](NC(=O)[C@H](CSSC[C@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@H](Cc3c[nH]cn3)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](N)Cc3ccccc3)C(C)C)C(N)=O)C(=O)NCC(=O)N[C@@H](CO)C(=O)N[C@@H](Cc3c[nH]cn3)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](Cc3ccc(O)cc3)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CSSC[C@H](NC(=O)[C@H](Cc3ccc(O)cc3)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](Cc3ccc(O)cc3)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CO)NC2=O)C(=O)N[C@@H](CC(N)=O)C(O)=O)C(=O)NCC(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](CCCNC(N)=N)C(=O)NCC(=O)N[C@@H](Cc2ccccc2)C(=O)N[C@@H](Cc2ccccc2)C(=O)N[C@@H](Cc2ccc(O)cc2)C(=O)N[C@@H]([C@H](C)O)C(=O)N2CCC[C@H]2C(=O)N[C@@H](CCCCN)C(=O)N[C@@H]([C@H](C)O)C(O)=O)NC1=O)[C@H](C)O)[C@H](C)CC + Insulin + + + OC([*])=O + MCFA + MCFAs + medium-chain fatty acid + CHEBI:59554 + medium-chain fatty acids + "Any fatty acid with a chain length of between C6 and C12." [] + CHEBI:medium-chain fatty acid + CHO2R + + + oxo fatty acid + CHEBI:oxo fatty acid + CHEBI:59644 + oxo fatty acids + "Any fatty acid containing at least one aldehydic or ketonic group in addition to the carboxylic acid group." [] + + + acetals + CHEBI:59769 + acetal + CHEBI:acetal + "An organooxygen compound having the structure RR'C(OR'')(OR''') (R'', R''' =/= H). Mixed acetals have R'' and R''' groups which differ." [] + + + hemiketals + hemiketal + "A hemiacetal having the structure RR'C(OH)R'' (R, R', R'' =/= H), derived from a ketone by formal addition of an alcohol to the carbonyl group." [] + CHEBI:59772 + CHEBI:hemiketal + + + CHEBI:ketal + CHEBI:59777 + "An acetal of formula R2C(OR)2 (R =/= H) derived from a ketone by replacement of the oxo group by two hydrocarbyloxy groups. The class name 'ketals', once abandoned by IUPAC, has been reinstated as a subclass of acetals." [] + ketal + ketals + + + "A ketal in the molecule of which the ketal carbon and one or both oxygen atoms thereon are members of a ring." [] + cyclic ketal + CHEBI:59779 + cyclic ketals + CHEBI:cyclic ketal + + + "A hemiacetal having the structure R2C(OH)OR (R =/= H), derived from a ketone by formal addition of an alcohol to the carbonyl group. The term 'cyclic hemiketals', once abandoned by IUPAC, has been reinstated as a subclass of hemiacetals." [] + cyclic hemiketal + CHEBI:59780 + cyclic hemiketals + CHEBI:cyclic hemiketal + + + CHEBI:N-acyl-L-alpha-amino acid anion + N-acyl-L-alpha-amino acid(1-) + [O-]C(=O)[C@H]([*])NC([*])=O + N-acyl-L-alpha-amino acid anion + N-acyl-L-amino acid + C3H2NO3R2 + "A carboxylic acid anion that is the conjugate base of an N-acyl-L-alpha-amino acid arising from deprotonation of the C-1 carboxy group." [] + CHEBI:59874 + + + "A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types." [] + chemical substance + CHEBI:59999 + CHEBI:chemical substance + Chemische Substanz + + + CHEBI:60004 + CHEBI:mixture + "A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind." [] + Mischung + mixture + + + CHEBI:polymer + Kunststoff + "A polymer is a mixture, which is composed of macromolecules of different kinds and which may be differentiated by composition, length, degree of branching etc.." [] + CHEBI:60027 + Polymer + polymer + + + isoflurane + 1-chloro-2,2,2-trifluoroethyl difluoromethyl ether + "An organofluorine compound that has formula C3H2ClF5O." [] + InChI=1S/C3H2ClF5O/c4-1(3(7,8)9)10-2(5)6/h1-2H + 2-chloro-2-difluoromethoxy-1,1,1-trifluoroethane + CHEBI:isoflurane + InChIKey=PIWKPBJCKXDKJR-UHFFFAOYSA-N + C3H2ClF5O + FC(F)OC(Cl)C(F)(F)F + Ethane + isoflurano + CHEBI:6015 + Aerrane + Isoflurane + isoflurane + Forene + isofluranum + Forane + + + "A derivative of phosphatidylinositol in which the inositol ring is phosphorylated at three unspecified positions." [] + phosphatidylinositol trisphosphates + CHEBI:60169 + CHEBI:phosphatidylinositol trisphosphate + phosphatidylinositol trisphosphate + + + divalent metal cation + CHEBI:60240 + a divalent metal cation + "A metal cation with a valence of two." [] + CHEBI:divalent metal cation + + + monovalent inorganic cation + CHEBI:monovalent inorganic cation + CHEBI:60242 + a monovalent cation + "An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one." [] + + + "R = C or H. The iminium ion resulting from the protonation of one of the imine nitrogen of guanidine or its derivatives." [] + [H][N+](C)=C(N(C)C)N(C)C + CHEBI:60251 + diaminomethaniminium ions + guanidinium ions + guanidinium ion + CHN3R5 + CHEBI:guanidinium ion + diaminomethaniminium ion + + + "Insoluble fibrous protein aggregates exhibiting beta sheet structure." [] + CHEBI:60425 + amyloid fibril + CHEBI:amyloid fibril + + + lysophosphatidylcholine + monoacylglycero-3-phosphocholine + "A compound resulting from partial hydrolysis of a phosphatidylcholine which removes one of the fatty acid groups." [] + CHEBI:lysophosphatidylcholine + lysophosphatidylcholines + CHEBI:60479 + + + C19H21N3O5 + CHEBI:6073 + Isradipine + DynaCirc (TN) + CHEBI:Isradipine + Isradipine + + + "Any pyridoindole containing a beta-carboline skeleton." [] + CHEBI:60834 + CHEBI:beta-carbolines + 9H-pyrido[3,4-b]indoles + beta-carbolines + + + CHEBI:racemate + racemic mixture + racemate + melange racemique + CHEBI:60911 + "A racemate is an equimolar mixture of a pair of enantiomers." [] + racemates + + + CHEBI:60971 + aminophospholipid + "A phospholipid that contains one or more amino groups." [] + aminolipids + aminophospholipids + amino-positive phospholipid + aminophosphoglycolipid + phosphoaminolipid + amino-positive phospholipids + aminophosphoglycolipids + phosphoaminolipids + aminolipid + CHEBI:aminophospholipid + + + "A glucoside in which the anomeric carbon of the glycosidic bond is in a beta configuration" [] + beta-glucoside + CHEBI:beta-glucoside + beta-glucosides + CHEBI:60980 + + + CHEBI:kanamycin + . + (2R,3R,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-3-[(2R,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxy-cyclohexyl]oxy-oxane-3,4,5-triol + (2R,3R,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-3-[(2R,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-2-hydroxy-cyclohexoxy]tetrahydropyran-3,4,5-triol + (2R,3R,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-3-[(2R,3S,4R,5R,6S)-4-amino-3,5-dihydroxy-6-methylol-tetrahydropyran-2-yl]oxy-2-hydroxy-cyclohexoxy]tetrahydropyran-3,4,5-triol + kanamycin + Kanamycin + CHEBI:6104 + kanamicin + N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](C[*])[C@@H](O)[C@H](O)[C@H]2[*])[C@H](O)[C@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](N)[C@H]1O + "Kanamycin is a naturally occurring antibiotic complex from Streptomyces kanamyceticus that consists of several components: kanamycin A, the major component (also usually designated as kanamycin), and kanamycins B, C, D and X the minor components." [] + + + CHEBI:oxygen radical + oxygen radicals + CHEBI:61073 + oxygen radical + "An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species." [] + + + "A nucleoside bisphosphate that has a purine nucleobase." [] + CHEBI:purine nucleoside bisphosphate + purine nucleoside bisphosphates + purine nucleoside bisphosphate + CHEBI:61078 + + + ribonucleoside bisphosphates + CHEBI:ribonucleoside bisphosphate + "A nucleoside bisphosphate where sugar of the nucleoside is ribose." [] + CHEBI:61079 + ribonucleoside bisphosphate + + + nucleobase-containing compound + CHEBI:nucleobase-containing molecular entity + nucleobase-containing molecular entity + CHEBI:61120 + "Any compound that has a nucleobase as a part." [] + nucleobase-containing molecular entities + nucleobase-containing compounds + + + (+-)-ketamine + InChIKey=YQEZLKZALYSWHR-UHFFFAOYSA-N + CHEBI:ketamine + DL-ketamine + CNC1(CCCCC1=O)c1ccccc1Cl + dl-ketamine + ketaminum + CHEBI:6121 + special K + ketamina + ketamine + NMDA + 2-(2-Chloro-phenyl)-2-methylamino-cyclohexanone + "A member of the class of cyclohexanones in which one of the hydrogens at position 2 is substituted by a 2-chlorophenyl group, while the other is substituted by a methylamino group." [] + 2-(o-chlorophenyl)-2-(methylamino)-cyclohexanone + 2-(methylamino)-2-(2-chlorophenyl)cyclohexanone + Ketamine + KETAMINE + C13H16ClNO + 2-(2-chlorophenyl)-2-(methylamino)cyclohexanone + ketamine + InChI=1S/C13H16ClNO/c1-15-13(9-5-4-8-12(13)16)10-6-2-3-7-11(10)14/h2-3,6-7,15H,4-5,8-9H2,1H3 + + + CHEBI:61293 + "A nucleotide having adenine as the base." [] + CHEBI:adenyl nucleotide + adenine nucleotide + adenyl nucleotide + + + "A purine riboncleotide where adenine is the purine." [] + CHEBI:adenyl ribonucleotide + CHEBI:61296 + adenyl ribonucleotide + adenine ribonucleotide + + + "A glycerate in which at least one of the hydroxy groups has been phosphorylated." [] + CHEBI:phosphoglycerate + phosphoglycerate + CHEBI:61304 + phosphoglycerates + + + CHEBI:C21-steroid + "A steroid compound with a structure based on a 21-carbon (pregnane) skeleton." [] + C21-steroid + CHEBI:61313 + + + beta-hydroxy carboxylic acids + 3-hydroxy carboxylic acids + CHEBI:61355 + beta-hydroxy carboxylic acid + CHEBI:3-hydroxy carboxylic acid + 3-hydroxy carboxylic acid + "Any hydroxy carboxylic acid which contains a hydroxy group located beta- to the carboxylic acid group." [] + + + poly(amide) polymer + polyamides + polyamide + poly(amide) + "A polymer, composed of poly(amide) macromolecules." [] + CHEBI:61445 + CHEBI:poly(amide) polymer + poly(amide)s + + + (3R,4R,6S)-2-(hydroxymethyl)-6-propan-2-ylsulfanyloxane-3,4,5-triol + CC(C)S[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O + CHEBI:isopropyl beta-D-thiogalactopyranoside + IPTG + InChI=1S/C9H18O5S/c1-4(2)15-9-8(13)7(12)6(11)5(3-10)14-9/h4-13H,3H2,1-2H3/t5-,6+,7+,8-,9+/m1/s1 + isopropyl beta-D-thiogalactopyranoside + isopropyl-beta-D-thiogalactoside + (3R,4R,6S)-2-(hydroxymethyl)-6-(propan-2-ylthio)oxane-3,4,5-triol + isopropyl-beta-D-thiogalactopyranoside + "An S-glycosyl compound consisting of beta-D-1-thiogalactose having an isopropyl group attached to the anomeric sulfur." [] + CHEBI:61448 + C9H18O5S + ISOPROPYL-1-BETA-D-THIOGALACTOSIDE + (3R,4R,6S)-2-(hydroxymethyl)-6-propan-2-ylsulfanyl-oxane-3,4,5-triol + InChIKey=BPHPUYQFMNQIOC-NXRLNHOXSA-N + isopropyl beta-D-1-thiogalactopyranoside + (2S,4R,5R)-2-(isopropylthio)-6-methylol-tetrahydropyran-3,4,5-triol + isopropyl thiogalactoside + (3R,4R,6S)-2-(hydroxymethyl)-6-isopropylsulfanyl-tetrahydropyran-3,4,5-triol + isopropyl beta-D-thiogalactoside + + + glycosteroids + steryl glycoside + steroid saponin + steryl glycosides + glycosteroid + sterol glycosides + steroid saponins + glycosyl steroids + steroid glycoside + steroidal glycosides + CHEBI:61655 + steroidal glycoside + "Any saponin derived from a hydroxysteroid." [] + steroid glycosides + CHEBI:steroid saponin + glycosyl steroid + sterol glycoside + + + InChIKey=NBSCHQHZLSJFNQ-KNZZERQRSA-N + "Any D-hexose 6-phosphate in which the hexose is in the pyranose form." [] + CHEBI:D-hexopyranose 6-phosphate + D-hexopyranose 6-phosphate + C6H13O9P + InChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3?,4?,5?,6?/m1/s1 + OC1O[C@H](COP(O)(O)=O)C(O)C(O)C1O + CHEBI:61667 + + + FA derivative + fatty acid derivatives + fatty acid derivative + FA derivatives + CHEBI:61697 + CHEBI:fatty acid derivative + "Any organic molecular entity derived from a fatty acid." [] + + + mannose 6-phosphate + CHEBI:mannose 6-phosphate + CHEBI:616988 + + + hydroxy-FA-coenzyme A + CHEBI:hydroxy fatty acyl-CoA + "A fatty-acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any hydroxy fatty acid." [] + hydroxy FA-CoA + hydroxy fatty acyl-CoA + hydroxy-fatty acyl-coenzyme A + hydroxy-fatty acyl-CoAs + CHEBI:61902 + + + short-chain fatty acyl-CoA + "A fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any short-chain fatty acid." [] + CHEBI:short-chain fatty acyl-CoA + SCFA-coenzyme A + SCFA-CoAs + short-chain fatty acyl-coenzyme As + SCFA-CoA + CHEBI:61905 + short-chain fatty acyl-coenzyme A + SCFA-coenzyme As + short-chain fatty acyl-CoAs + + + MCFA-coenzyme As + MCFA-CoAs + MCFA-coenzyme A + MCFA-CoA + medium-chain fatty acyl-coenzyme As + medium-chain fatty acyl-CoA + medium-chain fatty acyl-CoAs + CHEBI:61907 + medium-chain fatty acyl-coenzyme A + "A fatty acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any medium-chain fatty acid." [] + CHEBI:medium-chain fatty acyl-CoA + medium-chain fatty acyl-CoA + + + very long-chain fatty acyl-coenzyme A + very long-chain fatty acyl-CoA + VLCFA-coenzyme As + "A fatty acyl-CoA in which the fatty acyl group has a chain length greater than C22." [] + very long-chain acyl-coenzyme A + VLCFA-coenzyme A + CHEBI:very long-chain fatty acyl-CoA + very long-chain fatty acyl-coenzyme As + CHEBI:61910 + VLCFA-CoA + very long-chain acyl-CoA + VLCFA-CoAs + VLCA-coenzyme A + + + 1,1-diunsubstituted alkanesulfonate + CHEBI:1,1-diunsubstituted alkanesulfonate + [H]C([H])([*])S([O-])(=O)=O + "An alkanesulfonate in which the carbon at position 1 is attached to at least two hydrogens." [] + CH2O3SR + 1,1-diunsubstituted alkanesulfonates + 1,1-di-unsubstituted alkanesulfonate + CHEBI:62081 + 1,1-di-unsubstituted alkanesulfonates + + + CHEBI:hydroxyacyl-CoA + CHEBI:62618 + hydroxyacyl-CoAs + hydroxyacyl-coenzyme A + "An acyl-CoA that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any hydroxycarboxylic acid." [] + hydroxyacyl-CoA + + + a phospholipid derivative + phospholipid anions + anionic phospholipids + anionic phospholipid + CHEBI:anionic phospholipid + "Any organophosphate oxoanion that is a negatively charged phospholipid, e.g. phosphatidylserine(1-), phosphatidate(2-), phosphatidylglycerol(1-)." [] + phospholipid anion + CHEBI:62643 + + + aromatic esters + aromatic ester + CHEBI:aromatic ester + "An ester where the ester linkage is bonded directly to an aromatic system." [] + CHEBI:62732 + + + aromatic amide + "An amide in which the amide linkage is bonded directly to an aromatic system." [] + aromatic amides + CHEBI:62733 + CHEBI:aromatic amide + + + tyrosine derivatives + "An amino acid derivative resulting from reaction of tyrosine at the amino group or the carboxy group, any substitution of phenyl hydrogens, or from the replacement of any hydrogen of tyrosine by a heteroatom. The definition normally excludes peptides containing tyrosine residues." [] + CHEBI:62761 + tyrosine derivative + CHEBI:tyrosine derivative + + + RNI + CHEBI:reactive nitrogen species + RNS + reactive nitrogen species + "A family of nitrogen molecular entities which are highly reactive and derived from nitric oxide (.NO) and superoxide (O2.(-)) produced via the enzymatic activity of inducible nitric oxide synthase 2 (NOS2) and NADPH oxidase respectively." [] + CHEBI:62764 + + + sulfuric acid, diammonium salt + ammonium sulfate + CHEBI:62946 + InChIKey=BFNBIHQBYMNNAN-UHFFFAOYSA-N + [NH4+].[NH4+].[O-]S([O-])(=O)=O + ammonium sulphate + diazanium sulfate + CHEBI:ammonium sulfate + sulfuric acid ammonium salt (1:2) + (NH4)2SO4 + ammonium sulfate (2:1) + H8N2O4S + diammonium sulfate + mascagnite + "An inorganic sulfate salt obtained by reaction of sulfuric acid with two equivalents of ammonia. A high-melting (decomposes above 280degreeC) white solid which is very soluble in water (70.6 g/100 g water at 0degreeC; 103.8 g/100 g water at 100degreeC), it is widely used as a fertilizer for alkaline soils." [] + InChI=1S/2H3N.H2O4S/c;;1-5(2,3)4/h2*1H3;(H2,1,2,3,4) + + + C2H7NO2 + ammonium acetate + acetic acid, ammonium salt + InChI=1S/C2H4O2.H3N/c1-2(3)4;/h1H3,(H,3,4);1H3 + AcONH4 + INS No. 264 + E264 + [NH4+].CC([O-])=O + ammonium ethanoate + CHEBI:62947 + E-264 + CH3COONH4 + InChIKey=USFZMSVCRYTOJT-UHFFFAOYSA-N + CH3CO2NH4 + CHEBI:ammonium acetate + azanium acetate + ammonium acetate + NH4OAc + "An ammonium salt obtained by reaction of ammonia with acetic acid. A deliquescent white crystalline solid, it has a relatively low melting point (114degreeC) for a salt. Used as a food acidity regulator, although no longer approved for this purpose in the EU." [] + E 264 + + + Sodium dimethyl arsinate + Sodium salt of cacodylic acid + Cacodylate de sodium + Dimethylarsinic acid sodium salt + sodium dimethyl arsonide + ((Dimethylarsino)oxy)sodium As-oxide + [Na+].C[As](C)([O-])=O + Cacodylic acid sodium salt + Hydroxydimethylarsine oxide, sodium salt + sodium dimethylarsinate + InChIKey=IHQKEDIOMGYHEB-UHFFFAOYSA-M + CHEBI:62956 + sodium cacodylate + CHEBI:sodium dimethylarsinate + "The organic sodium salt of dimethylarsinate." [] + InChI=1S/C2H7AsO2.Na/c1-3(2,4)5;/h1-2H3,(H,4,5);/q;+1/p-1 + ((Dimethylarsino)oxy)sodium-As-oxide + C2H6AsNaO2 + + + [Mg++].CC([O-])=O.CC([O-])=O + Acetic acid, magnesium salt (2:1) + acetic acid magnesium salt + CHEBI:62964 + Magnesium di(acetate) + Mg Acetate + CHEBI:magnesium acetate + Mg(II) acetate + C4H6MgO4 + magnesium acetate + "The magnesium salt of acetic acid." [] + InChI=1S/2C2H4O2.Mg/c2*1-2(3)4;/h2*1H3,(H,3,4);/q;;+2/p-2 + magnesium diacetate + InChIKey=UEGPKNKPLBYCNK-UHFFFAOYSA-L + + + InChIKey=JHJLBTNAGRQEKS-UHFFFAOYSA-M + Trisodium tribromide + [Na+].[Br-] + Bromide salt of sodium + CHEBI:63004 + NaBr + BrNa + "An inorganic sodium salt having bromide as the counterion." [] + Bromnatrium + CHEBI:sodium bromide + sodium bromide + InChI=1S/BrH.Na/h1H;/q;+1/p-1 + + + C9H13O2 + branched alpha-(4-nonylphenyl)-omega-hydroxypoly(oxy-1,2-ethanediyl) + "Poly(ether) macoromolecule comprising a branched nonyl group bonded to one of the ring positions in 2-[phenoxypoly(ethoxy)]ethanol. A commericially available detergent, it is used to help crystallise proteins and extract the cytoplasmic contents of cellular culture." [] + nonyl phenoxypolyethoxylethanol + Polyethylene glycol mono(branched p-nonylphenyl) ether + Nonylphenol Ethoxylate + Tergitol-type NP-40 + CHEBI:63016 + Tergitol NP40 + CHEBI:nonyl phenoxypolyethoxylethanol + NP40 + + + CHEBI:63036 + Potassium acid phosphate + potassium dihydrogen phosphate + InChIKey=GNSKLFRGEWLPPA-UHFFFAOYSA-M + "A potassium salt in which dihydrogen phosphate(1-) is the counterion." [] + [K+].OP(O)([O-])=O + Phosphoric acid, monopotassium salt + Potassium dihydrogen phosphate + Monopotassium monophosphate + potassium dihydrogen phosphate + Monopotassium phosphate + H2KO4P + Phosphoric acid, potassium salt (1:1) + Orthophosphoric acid, monopotassium salt + Potassium dihydrogen orthophosphate + InChI=1S/K.H3O4P/c;1-5(2,3)4/h;(H3,1,2,3,4)/q+1;/p-1 + Monopotassium dihydrogen phosphate + MKP + Potassium phosphate + Monopotassium orthophosphate + Potassium phosphate monobasic + CHEBI:potassium dihydrogen phosphate + Sorensen's potassium phosphate + + + CHEBI:63039 + cesium(I) chloride + CHEBI:caesium chloride + InChI=1S/ClH.Cs/h1H;/q;+1/p-1 + Tricesium trichloride + [Cl-].[Cs+] + cesium chloride + "The inorganic chloride salt of caesium; each caesium ion is coordinated by eight chlorine ions." [] + caesium chloride + caesium monochloride + caesium(I) chloride + ClCs + caesium chloride + Cesium monochloride + InChIKey=AIYUHDOJVYHVIT-UHFFFAOYSA-M + + + CHEBI:1,3-thiazolium cation + 1,3-thiazolium cation + 1,3-thiazolium cations + CHEBI:63048 + "An organic cation resulting from protonation or quaternisation at the 3-position of any 1,3-thiazole." [] + + + CHEBI:zinc cation + zinc cations + zinc cation + "Any zinc ion that is positively charged." [] + CHEBI:63056 + + + CHEBI:cadmium cation + cadmium cation + CHEBI:63063 + "A transition element cation where the metal is specifed as cadmium." [] + cadmium cations + + + CHEBI:glycosyl compound + CHEBI:63161 + "A carbohydrate derivative arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to an oxygen, carbon, nitrogen or sulfur atom of a separate entity." [] + glycosyl compounds + glycosyl compound + + + "Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds." [] + derivatized carbohydrates + derivatized carbohydrate + CHEBI:63299 + derivatised carbohydrate + derivatised carbohydrates + carbohydrate derivative + CHEBI:carbohydrate derivative + carbohydrate derivatives + + + "An aldose derivative that is formally obtained from an aldohexose." [] + CHEBI:63354 + CHEBI:aldohexose derivative + aldohexose derivative + aldohexose derivatives + + + monosaccharide derivative + CHEBI:monosaccharide derivative + monosaccharide derivatives + CHEBI:63367 + "A carbohydrate derivative that is formally obtained from a monosaccharide." [] + + + CHEBI:63368 + aldose derivative + "A monosaccharide derivative that is formally obtained from an aldose." [] + CHEBI:aldose derivative + aldose derivatives + + + hexose derivative + CHEBI:hexose derivative + CHEBI:63385 + "A monosaccharide derivative that is formally obtained from a hexose." [] + hexose derivatives + + + CHEBI:D-hexose derivative + CHEBI:63386 + D-hexose derivatives + D-hexose derivative + "A hexose derivative that has D-configuration." [] + + + D-aldohexose derivative + CHEBI:D-aldohexose derivative + CHEBI:63387 + "An aldohexose derivative that has D-configuration." [] + D-aldohexose derivatives + + + pentose derivative + CHEBI:63409 + pentose derivatives + "A monosaccharide derivative that is formally obtained from a pentose." [] + CHEBI:pentose derivative + + + naturally occurring monoamines + "An aralylamino compound which contains one amino group connected to an aromatic ring by a two-carbon chain. Monoamines are derived from aromatic amino acids like phenylalanine, tyrosine, tryptophan, and the thyroid hormones by the action of aromatic amino acid decarboxylase enzymes." [] + CHEBI:monoamine + monoamine + CHEBI:63534 + naturally occurring monoamine + monoamines + + + CHEBI:63563 + CHEBI:oligosaccharide derivative + O-glycosylglycoside derivative + "A carbohydrate derivative that is formally obtained from an oligosaccharide." [] + oligosaccharide derivative + O-glycosylglycoside derivatives + oligosaccharide derivatives + + + pentasaccharide derivatives + "An oligosaccharide derivative that is formally obtained from a pentasaccharide." [] + CHEBI:63566 + CHEBI:pentasaccharide derivative + pentasaccharide derivative + + + tetrasaccharide derivative + "An oligosaccharide derivative that is formally obtained from a tetrasaccharide." [] + CHEBI:tetrasaccharide derivative + CHEBI:63567 + tetrasaccharide derivatives + + + CHEBI:63732 + CHEBI:1,1-diol + geminal diol + gem-diols + 1,1-diol + geminal diols + gem-diol + "Any alcohol in which two hydroxy groups are bonded to the same atom." [] + 1,1-diols + + + aldehyde hydrate + CHEBI:63733 + [H]C(O)(O)[*] + "A 1,1-diol resulting from the formal addition of water to the carbonyl group of a aldehyde." [] + CH3O2R + aldehyde hydrates + CHEBI:aldehyde hydrate + + + CHEBI:macrocyclic lactone + CHEBI:63944 + "Any lactone in which the cyclic carboxylic ester group forms a part of a cyclic macromolecule." [] + macrocyclic lactones + macrocyclic lactone + + + CC(C)C[C@H](NC(C)=O)C(=O)NC(CC(C)C)C(=O)NC(CCCNC(N)=N)C=O + InChI=1S/C20H38N6O4/c1-12(2)9-16(24-14(5)28)19(30)26-17(10-13(3)4)18(29)25-15(11-27)7-6-8-23-20(21)22/h11-13,15-17H,6-10H2,1-5H3,(H,24,28)(H,25,29)(H,26,30)(H4,21,22,23)/t15?,16-,17?/m0/s1 + Leupeptin + CHEBI:Leupeptin + C20H38N6O4 + Leupeptin + InChIKey=GDBQQVLCIARPGH-CGZBRXJRSA-N + "A peptide that has formula C20H38N6O4." [] + CHEBI:6426 + + + glutaraldehyde + PENTANEDIAL + InChI=1S/C5H8O2/c6-4-2-1-3-5-7/h4-5H,1-3H2 + CHEBI:64276 + InChIKey=SXRSQZLOMIGNAQ-UHFFFAOYSA-N + Glutaric acid dialdehyde + Glutaric dialdehyde + 1,5-Pentanedione + glutaralum + Glutardialdehyde + 1,5-Pentanedial + pentanedial + CHEBI:glutaraldehyde + Glutaral + glutaral + Glutaraldehyde + C5H8O2 + 1,3-Diformylpropane + O=CCCCC=O + "A dialdehyde comprised of pentane with aldehyde functions at C-1 and C-5." [] + + + CHEBI:64365 + aralkylamino compounds + CHEBI:aralkylamino compound + "An organic amino compound in which an aminoalkyl group is linked to an arene." [] + aralkylamino compound + + + organosulphonate salt + organosulfonate salt + organosulfonate salts + CHEBI:64382 + "Any organic salt prepared using an organosulfonic acid as the acid component." [] + CHEBI:organosulfonate salt + organosulphonate salts + + + InChIKey=UPCKIPHSXMXJOX-UHFFFAOYSA-N + N-hexanoylglycine + Hexanoylglycine + InChI=1S/C8H15NO3/c1-2-3-4-5-7(10)9-6-8(11)12/h2-6H2,1H3,(H,9,10)(H,11,12) + CCCCCC(=O)NCC(O)=O + N-(1-oxohexyl)glycine + CHEBI:64390 + N-caproylglycine + n-Hexanoylglycine + Caproylglycine + N-hexanoylglycine + C8H15NO3 + "An N-acylglycine in which the acyl group is specified as hexanoyl." [] + CHEBI:N-hexanoylglycine + + + biaryl + CHEBI:biaryl + "A ring assembly resulting from the formal oxidative coupling of two aromatic rings, resulting in the two rings being joined by a single bond." [] + biaryls + CHEBI:64459 + + + Ceramide phosphocholine + sphingomyelin + C9H19N2O6PR2 + C[N+](C)(C)CCOP([O-])(=O)OC[C@H](NC([*])=O)[C@H](O)[*] + CHEBI:sphingomyelin + "Any of a class of phospholipids in which the amino group of a sphingoid base is in amide linkage with one of several fatty acids, while the terminal hydroxy group of the sphingoid base is esterified to phosphorylcholine." [] + CHEBI:64583 + N-(acyl)-sphingosylphosphocholine + + + CHEBI:phosphagen + CHEBI:64618 + "Any of a group of guanidine or amidine phosphates that function as storage depots for high-energy phosphate in muscle with the purpose of regenerating ATP from ADP during muscular contraction." [] + phosphagen + + + "An inorganic cation with a valency of two." [] + divalent inorganic cation + CHEBI:64641 + CHEBI:divalent inorganic cation + + + "An organic molecular entity containing a single carbon atom (C1)." [] + one-carbon compound + CHEBI:64708 + one-carbon compounds + CHEBI:one-carbon compound + + + organic acids + CHEBI:64709 + organic acid + CHEBI:organic acid + "Any organic molecular entity that is acidic and contains carbon in covalent linkage." [] + + + [Na+].[Na+].[O-]C(=O)C[NH+](CC[NH+](CC([O-])=O)CC([O-])=O)CC([O-])=O + disodium 2,2',2'',2'''-(ethane-1,2-diyldiammonio)tetraacetate + CHEBI:64734 + Edetate disodium anhydrous + EDTA disodium (anh.) + disodium EDTA (anhydrous) + EDTA disodium + Na2H2EDTA + ethylenediaminetetraacetic acid disodium salt + "An organic sodium salt that is the anhydrous form of the disodium salt of ethylenediaminetetraacetic acid (EDTA)." [] + ethylenebis(iminodiacetic acid) disoidum salt + (ethylenedinitrilo)tetraacetic acid disodium salt + disodium edetate + EDTA disodium (anhydrous) + InChI=1S/C10H16N2O8.2Na/c13-7(14)3-11(4-8(15)16)1-2-12(5-9(17)18)6-10(19)20;;/h1-6H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20);;/q;2*+1/p-2 + N,N'-1,2-ethanediylbis[N-(carboxymethyl)glycine], disodium salt + Na2-EDTA + edetate disodium + C10H14N2Na2O8 + CHEBI:EDTA disodium salt (anhydrous) + disodium EDTA (anh.) + disodium edetate (anhydrous) + edetate disodium (anh.) + edetate disodium (anhydrous) + EDTA disodium salt (anh.) + InChIKey=ZGTMUACCHSMWAC-UHFFFAOYSA-L + disodium edetate (anh.) + EDTA disodium salt (anhydrous) + disodium EDTA + + + bio-conjugates + "A molecular entity consisting of at least 2 biological molecules covalently linked together." [] + CHEBI:bioconjugate + bioconjugate + CHEBI:64985 + bioconjugates + bio-conjugate + + + ketamine HCl + CHEBI:ketamine hydrochloride + [Cl-].C[NH2+]C1(CCCCC1=O)c1ccccc1Cl + CI-581 + "The hydrochloride salt of ketamine." [] + Ketaject + CL-369 + CN-52372-2 + 2-(o-chlorophenyl)-2-(methylamino)cyclohexanone hydrochloride + InChIKey=VCMGMSHEPQENPE-UHFFFAOYSA-N + CHEBI:650657 + KETAMINE HYDROCHLORIDE + 2-(2-chlorophenyl)-2-(methylamino)cyclohexanone hydrochloride + InChI=1S/C13H16ClNO.ClH/c1-15-13(9-5-4-8-12(13)16)10-6-2-3-7-11(10)14;/h2-3,6-7,15H,4-5,8-9H2,1H3;1H + Ketalar + (+-)-ketamine hydrochloride + ketamine hydrochloride + Ketanest + (+-)-2-(o-chlorophenyl)-2-(methylamino)cyclohexanone hydrochloride + C13H17Cl2NO + 1-(2-chlorophenyl)-N-methyl-2-oxocyclohexanaminium chloride + + + CHEBI:polysaccharide derivative + CHEBI:65212 + "A carbohydrate derivative that is any derivative of a polysaccharide." [] + polysaccharide derivative + polysaccharide derivatives + + + terpenoid indole alkaloid + "An indole alkaloid which is biosynthesised from L-tryptophan and isoprenoid building blocks." [] + CHEBI:65321 + CHEBI:terpenoid indole alkaloid + terpenoid indole alkaloids + + + CHEBI:monoterpenoid indole alkaloid + monoterpenoid indole alkaloids + monoterpenoid indole alkaloid + "A terpenoid indole alkaloid which is biosynthesised from L-tryptophan and diisoprenoid (usually secolaganin) building blocks." [] + CHEBI:65323 + + + Lorazepam + CHEBI:Lorazepam + Lorazepam + C15H10Cl2N2O2 + CHEBI:6539 + + + Magnesium chloride anhydrous + [MgCl2] + magnesium dichloride + Magnesium chloride + Magnesiumchlorid + CHEBI:magnesium dichloride + MgCl2 + [Mg++].[Cl-].[Cl-] + "A magnesium salt comprising of two chlorine atoms bound to a magnesium atom." [] + InChI=1S/2ClH.Mg/h2*1H;/q;;+2/p-2 + CHEBI:6636 + Cl2Mg + magnesium dichloride + InChIKey=TWRXJAOTZQYOKJ-UHFFFAOYSA-L + + + [2-hydroxy-1,1-bis(hydroxymethyl)ethyl]ammonium acetate + "An acetate salt resulting from the reaction of equimolar amounts of tris and acetic acid." [] + CHEBI:tris acetate + tris(hydroxymethyl)aminomethane acetate + 1,3-dihydroxy-2-(hydroxymethyl)propan-2-aminium acetate + tris(hydroxymethyl)aminomethane acetate salt + TRIS acetate salt + InChIKey=PIEPQKCYPFFYMG-UHFFFAOYSA-N + trizma acetate + 2-amino-2-(hydroxymethyl)propane-1,3-diol acetate + tris acetate + CC(O)=O.NC(CO)(CO)CO + C6H15NO5 + CHEBI:66869 + InChI=1S/C4H11NO3.C2H4O2/c5-4(1-6,2-7)3-8;1-2(3)4/h6-8H,1-3,5H2;1H3,(H,3,4) + + + CHEBI:66873 + C4-dicarboxylic acid + CHEBI:C4-dicarboxylic acid + C4-dicarboxylic acids + "Any dicarboxylic acid that contains four carbon atoms." [] + + + folate anions + folate anion + CHEBI:67011 + CHEBI:folates + folates + "An N-acyl-L-alpha-amino acid anion obtained by deprotonation of any folic acid." [] + folate + + + "A folate obtained by deprotonation of any tetrahydrofolic acid." [] + CHEBI:tetrahydrofolate + tetrahydrofolate anion + tetrahydrofolates + tetrahydrofolate + CHEBI:67016 + tetrahydrofolate anions + + + Tris-maleate + CHEBI:67100 + bis[1,3-dihydroxy-2-(hydroxymethyl)propan-2-aminium] (2Z)-3-carboxyprop-2-enoate + (2-Hydroxy-1,1-bis(hydroxymethyl)ethyl)ammonium hydrogen maleate + NC(CO)(CO)CO.NC(CO)(CO)CO.OC(=O)\\C=C/C(O)=O + InChIKey=POSZUTFLHGNLHX-KSBRXOFISA-N + InChI=1S/2C4H11NO3.C4H4O4/c2*5-4(1-6,2-7)3-8;5-3(6)1-2-4(7)8/h2*6-8H,1-3,5H2;1-2H,(H,5,6)(H,7,8)/b;;2-1- + CHEBI:tris maleate + 2-amino-2-(hydroxymethyl)propane-1,3-diol (2Z)-but-2-enedioate (2:1) + "A maleate salt resulting from the reaction of tris and maleic acid in the molar ratio tris:maleic acid = 2:1." [] + tris(hydroxymethyl)aminomethane maleate salt + trizma maleate + tris maleate + C12H26N2O10 + + + base analogs + base analogues + nucleobase analog + base analog + base analogue + CHEBI:nucleobase analogue + CHEBI:67142 + "A molecule that can substitute for a normal nucleobase in nucleic acids." [] + nucleobase analogue + nucleobase analogues + nucleobase analogs + + + Medroxyprogesterone 17-acetate + InChI=1S/C24H34O4/c1-14-12-18-19(22(4)9-6-17(27)13-21(14)22)7-10-23(5)20(18)8-11-24(23,15(2)25)28-16(3)26/h13-14,18-20H,6-12H2,1-5H3/t14-,18+,19-,20-,22+,23-,24-/m0/s1 + 6alpha-Methyl-4-pregnene-3,20-dion-17alpha-ol acetate + Medroxyprogesterone acetate + 17alpha-Hydroxy-6alpha-methylprogesterone acetate + 6alpha-Methyl-17alpha-hydroxyprogesterone acetate + CHEBI:6716 + 6alpha-Methyl-17-acetoxy progesterone + InChIKey=PSGAAPLEWMOORI-PEINSRQWSA-N + Methylacetoxyprogesterone + (6alpha)-17-(Acetyloxy)-6-methylpreg-4-ene-3,20-dione + C24H34O4 + CHEBI:medroxyprogesterone acetate + Medroxyacetate progesterone + [H][C@@]12C[C@H](C)C3=CC(=O)CC[C@]3(C)[C@@]1([H])CC[C@@]1(C)[C@@]2([H])CC[C@]1(OC(C)=O)C(C)=O + 6-alpha-Methyl-17-alpha-hydroxyprogesterone acetate + medroxyprogesterone acetate + 17-Acetoxy-6alpha-methylprogesterone + Metigestrona + "A steroid ester that has formula C24H34O4." [] + 6-alpha-Methyl-17-alpha-acetoxyprogesterone + (6alpha)-6-methyl-3,20-dioxopregn-4-en-17-yl acetate + + + CHEBI:azole + azole + "Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen." [] + azoles + CHEBI:68452 + + + "A deoxyribonucleoside containing a pyrimidine base." [] + pyrimidine deoxyribonucleoside + pyrimidine deoxyribonucleosides + CHEBI:pyrimidine deoxyribonucleoside + CHEBI:68472 + + + CHEBI:alkyl,acyl-sn-glycero-3-phosphocholine + C8H18NO6PR2 + "A glycerophosphocholine that is sn-glycero-3-phosphocholine in which positions 1 and 2 are substituted by unspecified acyl and alkyl groups, and in which the positions of the acyl and alkyl groups are also unspecified." [] + alkyl,acyl-sn-glycero-3-phosphocholine + CHEBI:68489 + [H][C@@](CO[*])(COP([O-])(=O)OCC[N+](C)(C)C)O[*] + alkyl,acyl-sn-glycero-3-phosphocholines + acyl,alkyl-sn-glycero-3-phosphocholine + acyl,alkyl-sn-glycero-3-phosphocholines + + + "An organic chloride salt that has formula C16H18N3S.Cl." [] + InChI=1S/C16H18N3S.ClH/c1-18(2)11-5-7-13-15(9-11)20-16-10-12(19(3)4)6-8-14(16)17-13;/h5-10H,1-4H3;1H/q+1;/p-1 + Methylene Blue anhydrous + Basic Blue 9 + chlorure de methylthioninium + bleu de methylene + cloruro de metiltioninio + Methylthioninium chloride + methylthioninium chloride + [Cl-].CN(C)c1ccc2nc3ccc(cc3[s+]c2c1)N(C)C + methylthioninii chloridum + azul de metileno + 3,7-bis(dimethylamino)phenothiazin-5-ium chloride + methylene blue + C16H18N3S.Cl + CHEBI:6872 + Methylene blue + Methylenblau + InChIKey=CXKWCBBOMKCUKX-UHFFFAOYSA-M + CHEBI:methylene blue + + + Midazolam + Cc1ncc2CN=C(c3ccccc3F)c3cc(Cl)ccc3-n12 + InChI=1S/C18H13ClFN3/c1-11-21-9-13-10-22-18(14-4-2-3-5-16(14)20)15-8-12(19)6-7-17(15)23(11)13/h2-9H,10H2,1H3 + CHEBI:6931 + Midazolam + "A diazepine that has formula C18H13ClFN3." [] + CHEBI:Midazolam + InChIKey=DDLIGBOFAVUZHB-UHFFFAOYSA-N + C18H13ClFN3 + + + Muscimol + NCc1cc(=O)[nH]o1 + "A member of the class of isoxazoles that is 1,2-oxazol-3(2H)-one substituted by an aminomethyl group at position 5. It has been isolated from mushrooms of the genus Amanita." [] + 5-(aminomethyl)-3(2H)-isoxazolone + InChI=1S/C4H6N2O2/c5-2-3-1-4(7)6-8-3/h1H,2,5H2,(H,6,7) + InChIKey=ZJQHPWUVQPJPQT-UHFFFAOYSA-N + 5-(aminomethyl)-1,2-oxazol-3(2H)-one + CHEBI:muscimol + muscimol + C4H6N2O2 + CHEBI:7035 + + + CHEBI:hexacyclic triterpenoid + CHEBI:70994 + hexacyclic triterpenoids + "A triterpenoid that consists of a hexacyclic ring system." [] + hexacyclic triterpenoid + + + [Na+].[Na+].[Na+].[Na+].[O-]P([O-])(=O)OP([O-])([O-])=O + Na4O7P2 + sodium diphosphate + Sodium pyrophosphate + InChIKey=FQENQNTWSFEDLI-UHFFFAOYSA-J + CHEBI:sodium diphosphate + "An inorganic sodium salt comprised of a diphosphate(4-) anion and four sodium(1+) cations. More commonly known as tetrasodium pyrophosphate, it finds much use in the food industry as an emulsifier and in dental hygiene as a calcium-chelating salt." [] + CHEBI:71240 + Natrium pyrophosphat + InChI=1S/4Na.H4O7P2/c;;;;1-8(2,3)7-9(4,5)6/h;;;;(H2,1,2,3)(H2,4,5,6)/q4*+1;/p-4 + TSPP + Pyrophosphoric acid tetrasodium salt + Diphosphoric acid, tetrasodium salt + Tetrasodium pyrophosphate + sodium diphosphate + + + rotenoid + rotenoids + "Members of the class of tetrahydrochromenochromene that consists of a cis-fused tetrahydrochromeno[3,4-b]chromene skeleton and its substituted derivatives. The term was originally restricted to natural products, but is now also used to describe semi-synthetic and fully synthetic compounds." [] + CHEBI:rotenoid + CHEBI:71543 + + + CHEBI:ortho ester + ortho esters + orthoesters + [*]C(O[*])(O[*])O[*] + CO3R4 + ortho ester + ortho-esters + "Any organooxygen compound that has the general formula RC(OR(1))(OR(2))(OR(3)), where R(1), R(2), R(3) =/= H." [] + CHEBI:71989 + ortho-ester + orthoester + + + "Any organic molecular entity whose stucture is based on derivatives of a phenyl-substituted 1-phenylpropane possessing a C15 or C16 skeleton, or such a structure which is condensed with a C6-C3 lignan precursors. The term is a 'superclass' comprising all members of the classes of flavonoid, isoflavonoid, neoflavonoid, chalcones, dihydrochalcones, aurones, pterocarpan, coumestans, rotenoid, flavonolignan, homoflavonoid and flavonoid oligomers. Originally restricted to natural products, the term is also applied to synthetic compounds related to them." [] + CHEBI:72544 + flavonoids + CHEBI:flavonoids + flavonoid + + + tetrahydrochromenochromenes + CHEBI:72579 + CHEBI:tetrahydrochromenochromene + tetrahydrochromenochromene + "Any organic heteropolycyclic compound consisting of a cis-fused dihydro chromene rings and its substituted derivatives." [] + + + CHEBI:rotenones + [*]c1c([*])c([*])c2C(=O)C3([*])c4c([*])c([*])c([*])c([*])c4OC([*])([*])C3([*])Oc2c1[*] + "Members of the class of rotenoid which consists of a 6a,12a-dihydrochromeno[3,4-b]chromen-12(6H)-one skeleton and its substituted products." [] + rotenones + C16O3R12 + CHEBI:72581 + + + spiroacetal + spiroketals + spiroketal + CHEBI:spiroketal + CHEBI:72600 + spiroacetals + "A cyclic ketal in which the ketal carbon is the only common atom of two rings." [] + + + organic molecule + "Any molecule that consists of at least one carbon atom as part of the electrically neutral entity." [] + CHEBI:72695 + organic molecules + CHEBI:organic molecule + + + extracellular polymeric substance + CHEBI:exopolysaccharide + CHEBI:72813 + exopolysaccharide + extracellular polymeric substances + "A biomacromolecule composed of carbohydrate residues which is secreted by a microorganism into the surrounding environment." [] + exopolysaccharides + + + C#C containing compound + CHEBI:acetylenic compound + C#C-containing compounds + acetylenic compounds + C2R2 + acetylenic compound + C#C-containing compound + C#C containing compounds + "Any organic molecule containing a C#C bond." [] + CHEBI:73474 + [*]C#C[*] + + + terminal acetylenic compounds + CHEBI:73477 + CHEBI:terminal acetylenic compound + C#CH containing compounds + C#CH containing compound + "An acetylenic compound which a carbon of the C#C moiety is attached to a hydrogen atom." [] + [H]C#C[*] + C#C-H containing compound + C2HR + terminal acetylenic compound + C#C-H containing compounds + + + "A carbonyl compound produced as a water-soluble byproduct when fatty acids are broken down for energy in the liver. There are three endogenous ketone bodies: acetone, acetoacetic acid, and (R)-3-hydroxybutyric acid; others may be produced as a result of the metabolism of synthetic triglycerides." [] + CHEBI:ketone body + ketone bodies + CHEBI:73693 + ketone body + + + wax + CHEBI:wax + CHEBI:73702 + waxes + "A chemical substance that is an organic compound or mixture of compounds that is composed of long-chain molecules and is malleable at ambient temperatures." [] + + + UNII-7I2HA1NU22 + GW501,516 + GW 501,516 + InChI=1S/C21H18F3NO3S2/c1-12-9-16(7-8-17(12)28-10-19(26)27)29-11-18-13(2)25-20(30-18)14-3-5-15(6-4-14)21(22,23)24/h3-9H,10-11H2,1-2H3,(H,26,27) + GW501516 + CHEBI:73726 + "An aromatic ether that is phenoxyacetic acid in which the phenyl group is substituted at position 2 by a methyl group and at position 4 by a (1,3-thiazol-5-ylmethyl)sulfanediyl group, and in which the 1,3-thiazolyl group is substituted at positions 2 and 4 by p-trifluoromethylphenyl and methyl groups, respectively." [] + GW 501516 + GSK-516 + GW-501,516 + GW-1516 + Endurobol + Cc1cc(SCc2sc(nc2C)-c2ccc(cc2)C(F)(F)F)ccc1OCC(O)=O + InChIKey=YDBLKRPLXZNVNB-UHFFFAOYSA-N + GW-501516 + GW-516 + C21H18F3NO3S2 + {2-methyl-4-[({4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-thiazol-5-yl}methyl)sulfanyl]phenoxy}acetic acid + CHEBI:GW 501516 + GW 1516 + GW1516 + + + CHEBI:thiosugar + CHEBI:73754 + thiosugars + "A carbohydrate derivative in which one or more of the oxygens or hydroxy groups of the parent carbohydrate is replaced by sulfur or -SR, where R can be hydrogen or any group." [] + thiosugar + + + 1,2,3,6-tetrahydro-2,6-dioxo-5-fluoro-4-pyrimidinecarboxylic acid + NSC 31712 + FOA + 5-fluoro-1,2,3,6-tetrahydro-2,6-dioxo-4-pyrimidinecarboxylic acid + 5-fluoro-6-carboxyuracil + Ro 2-9945 + 5-fluoroorotic acid + 5-fluoro-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid + CHEBI:74498 + FO + "A pyrimidinemonocarboxylic that is orotic acid which is substituted by fluorine at position 5. It is used in yeast molecular genetics to detect expression of the URA3 gene, which encodes orotine-5'-monophosphate dicarboxylase. A yeast with and active URA3 gene converts 5-fluoroorotic acid to fluorodeoxyuridine, which is toxic to cells." [] + 5-fluorouracil-4-carboxylic acid + NSC-31712 + ENT-26398 + CHEBI:5-fluoroorotic acid + + + alpha-thiolglycerol + 3-mercaptopropane-1,2-diol + CHEBI:monothioglycerol + thioglycerin + 3-mercapto-1,2-propanediol + InChIKey=PJUIMOJAAPLTRJ-UHFFFAOYSA-N + InChI=1S/C3H8O2S/c4-1-3(5)2-6/h3-6H,1-2H2 + 3-sulfanylpropane-1,2-diol + monothioglycerin + 2,3-dihydroxypropanethiol + 1-monothioglycerol + thioglycerol + CHEBI:74537 + 1-thio-2,3-propanediol + thioglycerine + C3H8O2S + monothioglycerol + monothioglycerol + 1-thioglycerol + 1-mercapto-2,3-propanediol + OCC(O)CS + 1-mercaptoglycerol + "A thiol that is glycerol in which one of the primary hydroxy groups is replaced by a thiol group." [] + + + CHEBI:furopyran + "Any organic heterobicyclic compound containing ortho-fused furan and pyran rings." [] + furopyran + CHEBI:74927 + furopyrans + + + 5-bromo-4-chloro-3-indolyl beta-D-galactoside + CHEBI:5-bromo-4-chloro-3-indolyl beta-D-galactoside + C14H15BrClNO6 + CHEBI:75055 + InChI=1S/C14H15BrClNO6/c15-5-1-2-6-9(10(5)16)7(3-17-6)22-14-13(21)12(20)11(19)8(4-18)23-14/h1-3,8,11-14,17-21H,4H2/t8-,11+,12+,13-,14-/m1/s1 + [H][C@]1(O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)Oc1c[nH]c2ccc(Br)c(Cl)c12 + X-gal + X-Gal + 5-bromo-4-chloro-3-indolyl beta-galactoside + BCIG + Indoxyl-Gal + InChIKey=OPIFSICVWOWJMJ-AEOCFKNESA-N + "An indolyl carbohydrate that is the beta-D-galactoside of 3-hydroxy-1H-indole in which the indole moiety is substituted at positions 4 and 5 by chlorine and bromine, respectively. It is used to test for the presence of an enzyme, beta-galactosidase, which cleaved the glycosidic bond to give 5-bromo-4-chloro-3-hydroxy-1H-indole, which immediately dimerises to give an intensely blue product." [] + 5-bromo-4-chloroindol-3-yl-beta-D-galactopyranoside + 5-bromo-4-chloro-1H-indol-3-yl beta-D-galactopyranoside + + + neomycin + NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2[*])[C@H](N)[C@@H](O)[C@@H]1O + CHEBI:7507 + CHEBI:neomycin + Neomycin + C22H41N5O13R2.C12H26N4O6 + "A broad-spectrum highly toxic antibiotic or mixture of antibiotics produced by a streptomyces (Streptomyces fradiae) and used medically especially to treat local infections." [] + + + Oc1cc(cc(O)c1O)C(=O)Oc1cc(cc(O)c1O)C(=O)OC[C@H]1OC(OC(=O)c2cc(O)c(O)c(OC(=O)c3cc(O)c(O)c(O)c3)c2)[C@H](OC(=O)c2cc(O)c(O)c(OC(=O)c3cc(O)c(O)c(O)c3)c2)[C@@H](OC(=O)c2cc(O)c(O)c(OC(=O)c3cc(O)c(O)c(O)c3)c2)[C@@H]1OC(=O)c1cc(O)c(O)c(OC(=O)c2cc(O)c(O)c(O)c2)c1 + C76H52O46 + tannic acid + InChIKey=LRBQNJMCXXYXIU-YIILYMKVSA-N + CHEBI:75211 + InChI=1S/C76H52O46/c77-32-1-22(2-33(78)53(32)92)67(103)113-47-16-27(11-42(87)58(47)97)66(102)112-21-52-63(119-72(108)28-12-43(88)59(98)48(17-28)114-68(104)23-3-34(79)54(93)35(80)4-23)64(120-73(109)29-13-44(89)60(99)49(18-29)115-69(105)24-5-36(81)55(94)37(82)6-24)65(121-74(110)30-14-45(90)61(100)50(19-30)116-70(106)25-7-38(83)56(95)39(84)8-25)76(118-52)122-75(111)31-15-46(91)62(101)51(20-31)117-71(107)26-9-40(85)57(96)41(86)10-26/h1-20,52,63-65,76-101H,21H2/t52-,63-,64+,65-,76?/m1/s1 + CHEBI:tannic acid + 1,2,3,4,6-pentakis-O-{3,4-dihydroxy-5-[(3,4,5-trihydroxybenzoyl)oxy]benzoyl}-D-glucopyranose + "A gallotannin obtained by acylation of the five hydroxy groups of D-glucose by 3,4-dihydroxy-5-[(3,4,5-trihydroxybenzoyl)oxy]benzoic acid (a gallic acid dimer)." [] + + + 5-bromo-4-chloroindoxyl phosphate + C8H6BrClNO4P + 5-Bromo-4-chloro-3-indoxyl phosphate + X-Phos + OP(O)(=O)Oc1c[nH]c2ccc(Br)c(Cl)c12 + 5-bromo-4-chloro-1H-indol-3-yl dihydrogen phosphate + CHEBI:5-bromo-4-chloro-3-indolyl phosphate + InChI=1S/C8H6BrClNO4P/c9-4-1-2-5-7(8(4)10)6(3-11-5)15-16(12,13)14/h1-3,11H,(H2,12,13,14) + BCIP + 5-bromo-4-chloro-3-indolyl phosphate + "An aryl phosphate that is indoxyl phopshate in which the indole moiety is substituted at positions 4 and 5 by chlorine and bromine, respectively. It is used to test for the presence of an enzyme, alkaline phosphatase, which cleaves the phosphate group to give 5-bromo-4-chloroindoxyl, which immediately dimerises to give an intensely blue product." [] + CHEBI:75508 + InChIKey=QRXMUCSWCMTJGU-UHFFFAOYSA-N + 5-Bcip + + + nifedipino + InChI=1S/C17H18N2O6/c1-9-13(16(20)24-3)15(14(10(2)18-9)17(21)25-4)11-7-5-6-8-12(11)19(22)23/h5-8,15,18H,1-4H3 + 4-(2'-Nitrophenyl)-2,6-dimethyl-1,4-dihydropyridin-3,5-dicarbonsaeuredimethylester + C17H18N2O6 + COC(=O)C1=C(C)NC(C)=C(C1c1ccccc1[N+]([O-])=O)C(=O)OC + Coracten + Procardia + Nifecor + "A dihydropyridine that has formula C17H18N2O6." [] + Nifecard + nifedipine + dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate + CHEBI:nifedipine + Nifedipres + nifedipine + nifedipinum + InChIKey=HYIMSNHJOBLJNT-UHFFFAOYSA-N + Adapine + CHEBI:7565 + Adalat + Nifedipine + + + InChI=1S/C40H30N10O6/c1-55-37-25-29(13-23-35(37)47-43-39(27-9-5-3-6-10-27)41-45(47)31-15-19-33(20-16-31)49(51)52)30-14-24-36(38(26-30)56-2)48-44-40(28-11-7-4-8-12-28)42-46(48)32-17-21-34(22-18-32)50(53)54/h3-26H,1-2H3/q+2 + 3,3'-(3,3'-dimethoxybiphenyl-4,4'-diyl)bis[2-(4-nitrophenyl)-5-phenyl-2H-tetrazol-3-ium] + InChIKey=JPXMTWWFLBLUCD-UHFFFAOYSA-N + COc1cc(ccc1-[n+]1nc(nn1-c1ccc(cc1)[N+]([O-])=O)-c1ccccc1)-c1ccc(c(OC)c1)-[n+]1nc(nn1-c1ccc(cc1)[N+]([O-])=O)-c1ccccc1 + "An organic cation that has formula C40H30N10O6." [] + CHEBI:7586 + C40H30N10O6 + CHEBI:nitro blue tetrazolium(2+) + nitro blue tetrazolium(2+) + + + chemical solution + solution + CHEBI:75958 + CHEBI:solution + "A mixture that is homogeneous, made up of at least two scattered molecular aggregates, one playing the role of solute and the other playing the role of solvent." [] + + + hexadecanoyl bioconjugate + CHEBI:palmitoyl bioconjugate + "A bioconjugate obtained by coupling of palmitic acid to another biomolecule (e.g. coenzyme A, an acyl-carrier protein, a phospholipid, an oligosaccharide, a nucleic acid etc.), which for the sake of convenience, is represented by an R group." [] + palmitoyl-R + palmitic acid bioconjugate + C16H31OR + hexadecanoyl-R + palmitoyl bioconjugate + CHEBI:76194 + CCCCCCCCCCCCCCCC([*])=O + hexadecanoic acid bioconjugate + + + aromatic ketones + "A ketone in which the carbonyl group is attached to an aromatic ring." [] + CHEBI:76224 + aryl ketones + CHEBI:aromatic ketone + aryl ketone + aromatic ketone + + + CHEBI:N-nitrosoureas + "A nitroso compound that is any urea in which one of the nitrogens is substituted by a nitroso group" [] + N-nitrosoureas + CHEBI:76551 + + + diradylglycerol + disubstituted glycerol + diorganylglycerol + CHEBI:76578 + "Any lipid that is glycerol bearing two substituent groups - either acyl, alkyl, or alk-1-enyl - at any two of the three possible positions." [] + CHEBI:disubstituted glycerol + + + "A polynucleotide comprised of inosine units connected via 3'->5' phosphodiester linkages." [] + CHEBI:76777 + poly I + inosine polynucleotide + poly(I) + CHEBI:poly(inosinic acid) + C20H24N8O15P2(C10H11N4O7P)n + poly(inosinic acid) + polyinosinic acid + + + sulfonylurea + CHEBI:76983 + N-sulfonylureas + sulfonylureas + CN2O3SR4 + "A urea in which one of the hydrogens attached to a nitrogen of the urea group is replaced by a sulfonyl group. The N-sulfonylurea moiety is a key group in various herbicides, as well as in a number of antidiabetic drugs used in the management of type 2 diabetis mellitus." [] + [*]S(=O)(=O)N([*])C(=O)N([*])[*] + N-sulfonylurea + CHEBI:N-sulfonylurea + + + "A calcium salt composed of calcium and phosphate/diphosohate ions; present in milk and used for the mineralisation of calcified tissues." [] + CHEBI:calcium phosphate + CHEBI:77635 + calcium phosphate + + + InChI=1S/C19H15N4/c1-4-10-16(11-5-1)19-20-22(17-12-6-2-7-13-17)23(21-19)18-14-8-3-9-15-18/h1-15H/q+1 + CHEBI:78021 + c1ccc(cc1)-c1nn(-c2ccccc2)[n+](n1)-c1ccccc1 + "An organic cation that is tetrazole carrying three phenyl substituents at positions 2, 3 and 5." [] + C19H15N4 + InChIKey=LNOBZXNCABUBKK-UHFFFAOYSA-N + 2,3,5-triphenyltetrazolium + CHEBI:2,3,5-triphenyltetrazolium + 2,3,5-triphenyl-2H-tetrazol-3-ium + + + CHEBI:78049 + "A fatty acid anion containing 18 carbons and one double bond. Formed by deprotonation of the carboxylic acid group. Major species at pH 7.3." [] + C18H33O2 + octadecenoate + [O-]C([*])=O + CHEBI:octadecenoate + + + CHEBI:fatty acid anion 4:0 + "Any saturated fatty acid anion containing 4 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3." [] + fatty acid anion 4:0 + CHEBI:78115 + C4H7O2 + fatty acid 4:0 + [O-]C([*])=O + + + [O-]C([*])=O + fatty acid anion 16:0 + C16H31O2 + fatty acid 16:0 + "Any saturated fatty acid anion containing 16 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3." [] + CHEBI:78123 + CHEBI:fatty acid anion 16:0 + + + InChIKey=YMBCJWGVCUEGHA-UHFFFAOYSA-M + N,N,N-Triethylethanaminium chloride + "A quarternary ammonium chloride salt in which the cation has four ethyl substituents around the central nitrogen." [] + CHEBI:78161 + CHEBI:tetraethylammonium chloride + Et4NCl + tetraethylammonium chloride + InChI=1S/C8H20N.ClH/c1-5-9(6-2,7-3)8-4;/h5-8H2,1-4H3;1H/q+1;/p-1 + [Cl-].CC[N+](CC)(CC)CC + C8H20ClN + Etamon chloride + + + CHEBI:1-alkyl-2-acyl-glycero-3-phosphocholine + C[N+](C)(C)CCOP([O-])(=O)OCC(CO[*])OC([*])=O + 1-alkyl-2-acyl-glycero-3-phosphocholine + "An alkylacylglycero-3-phosphocholine in which the alkyl and acyl groups are located at positions 1 and 2 respectively. Major species at pH 7.3." [] + 1-alkyl-2-acyl-glycero-3-phosphocholine + C9H18NO7PR2 + CHEBI:78186 + + + CHEBI:78189 + CHEBI:alkylacylglycero-3-phosphocholine + C[N+](C)(C)CCOP([O-])(=O)OCC(CO[*])O[*] + C9H18NO7PR2 + alkylacylglycero-3-phosphocholine + "A glycerophosphocholine that is glycero-3-phosphocholine carrying one alkyl and one acyl group in unspecified positions. Major species at pH 7.3." [] + monoalkylmonoacylglycero-3-phosphocholine + + + CHEBI:78574 + "Any pyrimidine that bears one or more carboxylic acid substituents." [] + CHEBI:pyrimidinecarboxylic acid + pyrimidinecarboxylic acid + pyrimidinecarboxylic acids + + + carbohydrates and their derivatives + CHEBI:78616 + carbohydrates and carbohydrate derivatives + CHEBI:carbohydrates and carbohydrate derivatives + carbohydrates and derivatives + "Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation." [] + + + CHEBI:D-fructose 1,6-bisphosphate + CHEBI:78682 + D-fructose 1,6-bisphosphate + Diphosphofructose + "A ketohexose bisphosphate that is D-fructose substituted by phosphate groups at positions 1 and 6. It is an intermediate in the glycolysis metabolic pathway." [] + + + hydrolyzable tannin + hydrolysable tannin + "A tannin that yields gallic or ellagic acids upon acid hydrolysis." [] + CHEBI:hydrolysable tannin + hydrolyzable tannins + CHEBI:78689 + hydrolysable tannins + + + polyethylene glycol mono(4-octylphenyl) ether + "A poly(ether) macromolecule that is polyethylene glycol in which one of the terminal hydroxy groups has been converted to the corresponding p-octylphenyl ether. A nonionic, non-denaturing detergent, it is used for solubilising membrane proteins during isolation of membrane-protein complexes. n ~ 8." [] + Nonidet P40 + CHEBI:78708 + Nonidet P-40 + octylphenolpoly(ethyleneglycolether) + polyethylene glycol mono(p-octylphenyl) ether + CHEBI:Nonidet P-40 + (C2H4O)nC14H22O + polyethylene glycol mono(octylphenyl) ether + + + hydroxydopamine + NCCc1cc(O)c(O)cc1O + InChI=1S/C8H11NO3/c9-2-1-5-3-7(11)8(12)4-6(5)10/h3-4,10-12H,1-2,9H2 + CHEBI:78741 + 6-hydroxydopamine + oxidopamina + oxidopamine + 6-OHDA + InChIKey=DIVDFFZHCJEHGG-UHFFFAOYSA-N + "A benzenetriol that is phenethylamine in which the hydrogens at positions 2, 4, and 5 on the phenyl ring are replaced by hydroxy groups. It occurs naturally in human urine, but is also produced as a metabolite of the drug DOPA (used for the treatment of Parkinson's disease)." [] + oxidopamine + oxidopaminum + CHEBI:oxidopamine + 2,4,5-trihydroxyphenethylamine + 5-(2-aminoethyl)benzene-1,2,4-triol + C8H11NO3 + topamine + + + olefinic compounds + CHEBI:78840 + olefinic compound + CHEBI:olefinic compound + "Any organic molecular entity that contains at least one C=C bond." [] + + + tetrasodium 3,3'-[(3,3'-dimethylbiphenyl-4,4'-diyl)didiazene-2,1-diyl]bis(5-amino-4-hydroxynaphthalene-2,7-disulfonate) + InChI=1S/C34H28N6O14S4.4Na/c1-15-7-17(3-5-25(15)37-39-31-27(57(49,50)51)11-19-9-21(55(43,44)45)13-23(35)29(19)33(31)41)18-4-6-26(16(2)8-18)38-40-32-28(58(52,53)54)12-20-10-22(56(46,47)48)14-24(36)30(20)34(32)42;;;;/h3-14,41-42H,35-36H2,1-2H3,(H,43,44,45)(H,46,47,48)(H,49,50,51)(H,52,53,54);;;;/q;4*+1/p-4/b39-37+,40-38+;;;; + C34H24N6Na4O14S4 + C34H24N6O14S4.4Na + "An organosulfonate salt that is the tetrasodium salt of 3,3'-[(3,3'-dimethylbiphenyl-4,4'-diyl)didiazene-2,1-diyl]bis(5-amino-4-hydroxynaphthalene-2,7-disulfonic acid)." [] + trypan blue + Sodium ditolyl-diazobis-8-amino-1-naphthol-3,6-disulfonate + CHEBI:trypan blue + Sodium ditolyldisazobis-8-amino-1-naphthol-3,6-disulfonate + Sodium ditolyldisazobis-8-amino-1-naphthol-3,6-disulphonate + CHEBI:78897 + InChIKey=GLNADSQYFUSGOU-GPTZEZBUSA-J + [Na+].[Na+].[Na+].[Na+].Cc1cc(ccc1\\N=N\\c1c(O)c2c(N)cc(cc2cc1S([O-])(=O)=O)S([O-])(=O)=O)-c1ccc(\\N=N\\c2c(O)c3c(N)cc(cc3cc2S([O-])(=O)=O)S([O-])(=O)=O)c(C)c1 + + + CHEBI:(omega-1)-hydroxy fatty acid + "A hydroxy fatty acid that is a straight-chain fatty acid in which one of the hydrogens attached to the carbon adjacent to the terminal methyl group (i.e. at the (omega-1) position) is replaced by a hydroxy group." [] + (omega-1)-hydroxy fatty acid + CHEBI:78954 + (omega-1)-hydroxy fatty acids + + + InChIKey=IPCSVZSSVZVIGE-UHFFFAOYSA-M + 1-pentadecanecarboxylate + CH3-[CH2]14-COO(-) + n-hexadecoate + 1-hexyldecanoate + C16H31O2 + CHEBI:palmitate + "A long-chain fatty acid anion that is the conjugate base of palmitic acid; major species at pH 7.3." [] + Hexadecanoic acid, ion(1-) + CHEBI:7896 + hexadecanoate + InChI=1S/C16H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h2-15H2,1H3,(H,17,18)/p-1 + CCCCCCCCCCCCCCCC([O-])=O + palmitate + hexadecanoate + pentadecanecarboxylate + n-hexadecanoate + + + alpha,beta-unsaturated monocarboxylic acids + 2,3-unsaturated monocarboxylic acids + "A monocarboxylic acid in which the carbon of the carboxy group is directly attached to a C=C or C#C bond." [] + CHEBI:79020 + CHEBI:alpha,beta-unsaturated monocarboxylic acid + 2,3-unsaturated monocarboxylic acid + alpha,beta-unsaturated monocarboxylic acid + + + CHEBI:monovalent inorganic anion + CHEBI:79389 + monovalent inorganic anions + monovalent inorganic anion + "Any inorganic anion with a valency of one." [] + + + Pentobarbital + InChI=1S/C11H18N2O3/c1-4-6-7(3)11(5-2)8(14)12-10(16)13-9(11)15/h7H,4-6H2,1-3H3,(H2,12,13,14,15,16) + CHEBI:7983 + CHEBI:pentobarbital + "A member of the class of barbiturates, the structure of which is that of barbituric acid substituted at C-5 by ethyl and sec-pentyl groups." [] + 5-ethyl-5-(1-methylbutyl)barbituric acid + 5-ethyl-5-(sec-pentyl)barbituric acid + Pentobarbitone + 5-Ethyl-5-(1-methyl-butyl)-pyrimidine-2,4,6-trione + InChIKey=WEXRUCMBJFQVBZ-UHFFFAOYSA-N + 5-ethyl-5-(pentan-2-yl)pyrimidine-2,4,6(1H,3H,5H)-trione + Nembutal + 5-Ethyl-5-(1-methylbutyl)-2,4,6(1H,3H,5H)-pyrimidinetrione + CCCC(C)C1(CC)C(=O)NC(=O)NC1=O + C11H18N2O3 + pentobarbital + + + C11H17N2O3.Na + Pentobarbital sodium + Pentobarbital sodium + InChI=1S/C11H18N2O3.Na/c1-4-6-7(3)11(5-2)8(14)12-10(16)13-9(11)15;/h7H,4-6H2,1-3H3,(H2,12,13,14,15,16);/q;+1/p-1 + CHEBI:Pentobarbital sodium + InChIKey=QGMRQYFBGABWDR-UHFFFAOYSA-M + CHEBI:7984 + [Na+].CCCC(C)C1(CC)C(=O)NC([O-])=NC1=O + "An organic molecular entity that has formula C11H17N2O3.Na." [] + + + Pepstatin + CC(C)CC(NC(=O)[C@H](C)NC(=O)CC(O)C(CC(C)C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)CC(C)C)C(C)C)C(C)C)C(O)CC(O)=O + InChI=1S/C34H63N5O9/c1-17(2)12-23(37-33(47)31(21(9)10)39-34(48)30(20(7)8)38-27(42)14-19(5)6)25(40)15-28(43)35-22(11)32(46)36-24(13-18(3)4)26(41)16-29(44)45/h17-26,30-31,40-41H,12-16H2,1-11H3,(H,35,43)(H,36,46)(H,37,47)(H,38,42)(H,39,48)(H,44,45)/t22-,23?,24?,25?,26?,30-,31-/m0/s1 + "A peptide that has formula C34H63N5O9." [] + InChIKey=FAXGPCHRFPCXOO-JHTFMCFMSA-N + CHEBI:Pepstatin + Pepstatin + CHEBI:7989 + C34H63N5O9 + + + [*]C#N + CHEBI:aliphatic nitrile + CHEBI:80291 + aliphatic nitrile + CNR + "Any nitrile derived from an aliphatic compound." [] + an aliphatic nitrile + + + [H][C@]12CSc3[nH]c4ccccc4c3C[C@]([H])(NC(=O)[C@H](C)NC(=O)[C@]3([H])C[C@H](O)CN3C1=O)C(=O)N[C@@H](C[C@@](C)(O)CO)C(=O)N[C@@H](C)C(=O)N[C@]([H])([C@H](C)O)C(=O)N2 + InChIKey=KPKZJLCSROULON-QKGLWVMZSA-N + C35H48N8O11S + InChI=1S/C35H48N8O11S/c1-15-27(47)38-22-10-20-19-7-5-6-8-21(19)41-33(20)55-13-24(34(53)43-12-18(46)9-25(43)31(51)37-15)40-32(52)26(17(3)45)42-28(48)16(2)36-30(50)23(39-29(22)49)11-35(4,54)14-44/h5-8,15-18,22-26,41,44-46,54H,9-14H2,1-4H3,(H,36,50)(H,37,51)(H,38,47)(H,39,49)(H,40,52)(H,42,48)/t15-,16-,17-,18-,22-,23-,24-,25-,26+,35+/m0/s1 + "A homodetic bicyclic heptapeptide having a sulfide bridge." [] + (1S,14R,18S,20S,23S,28S,31S,34R)-28-[(2R)-2,3-dihydroxy-2-methylpropyl]-18-hydroxy-34-[(1S)-1-hydroxyethyl]-23,31-dimethyl-12-thia-10,16,22,25,27,30,33,36-octaazapentacyclo[12.11.11.0(3,11).0(4,9).0(16,20)]hexatriaconta-3(11),4,6,8-tetraene-15,21,24,26,29,32,35-heptone + CHEBI:phalloidin + phalloidin + Phalloidine + cyclic(L-alanyl-D-threonyl-L-cysteinyl-cis-4-hydroxy-L-prolyl-L-alanyl-2-mercapto-L-tryptophyl-4,5-dihydroxy-L-leucyl), cyclic (3,6)-sulfide + Phalloidin + CHEBI:8040 + + + InChIKey=BHTRKEVKTKCXOH-LBSADWJPSA-N + Tauroursodeoxycholic acid + CHEBI:80774 + CHEBI:Tauroursodeoxycholic acid + InChI=1S/C26H45NO6S/c1-16(4-7-23(30)27-12-13-34(31,32)33)19-5-6-20-24-21(9-11-26(19,20)3)25(2)10-8-18(28)14-17(25)15-22(24)29/h16-22,24,28-29H,4-15H2,1-3H3,(H,27,30)(H,31,32,33)/t16-,17+,18-,19-,20+,21+,22+,24+,25+,26-/m1/s1 + "A bile acid taurine conjugate that has formula C26H45NO6S." [] + C[C@H](CCC(=O)NCCS(O)(=O)=O)[C@H]1CC[C@H]2[C@@H]3[C@@H](O)C[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C + C26H45NO6S + + + [H+].[Cl-].CNC[C@H](O)c1cccc(O)c1 + InChIKey=OCYSGIYOVXAGKQ-FVGYRXGTSA-N + C9H13NO2.HCl + 3-[(1R)-1-hydroxy-2-(methylamino)ethyl]phenol hydrochloride + CHEBI:phenylephrine hydrochloride + phenylephrine hydrochloride + InChI=1S/C9H13NO2.ClH/c1-10-6-9(12)7-3-2-4-8(11)5-7;/h2-5,9-12H,6H2,1H3;1H/t9-;/m0./s1 + Dionephrine + "A hydrochloride that has formula C9H13NO2.HCl." [] + CHEBI:8094 + Mydfrin + C9H14ClNO2 + Neo-Synephrine + + + phenylmethylsulfonyl fluoride + CHEBI:phenylmethanesulfonyl fluoride + PMSF + InChI=1S/C7H7FO2S/c8-11(9,10)6-7-4-2-1-3-5-7/h1-5H,6H2 + FS(=O)(=O)Cc1ccccc1 + Benzenemethanesulfonyl fluoride + phenylmethanesulfonyl fluoride + alpha-toluenesulphonyl fluoride + C7H7FO2S + InChIKey=YBYRMVIVWMBXKQ-UHFFFAOYSA-N + alpha-toluenesulfonyl fluoride + phenylmethanesulfonyl fluoride + Phenylmethanesulfonyl fluoride + "An acyl fluoride with phenylmethanesulfonyl as the acyl group." [] + CHEBI:8102 + + + CHEBI:Phaeomelanin + Phaeomelanin + CHEBI:81393 + + + CHEBI:Placental lactogen + Chorionic somatomammotropin hormone + Placental lactogen + CHEBI:81588 + PL + + + [K+].OC([O-])=O + E501 + "A potassium salt that is the monopotassium salt of carbonic acid. It has fungicidal properties and is used in organic farming for the control of powdery mildew and apple scab." [] + potassium bicarbonate + potassium hydrogencarbonate + CHKO3 + KHCO3 + potassium acid carbonate + potassium hydrogen carbonate + InChI=1S/CH2O3.K/c2-1(3)4;/h(H2,2,3,4);/q;+1/p-1 + InChIKey=TYJJADVDDVDEDZ-UHFFFAOYSA-M + monopotassium carbonate + CHEBI:potassium hydrogencarbonate + CHEBI:81862 + + + CHEBI:Picrotoxinin + CHEBI:8206 + "A furopyran that has formula C15H16O6." [] + C15H16O6 + InChIKey=PIMZUZSSNYHVCU-YKWPQBAZSA-N + InChI=1S/C15H16O6/c1-5(2)7-8-11(16)19-9(7)10-13(3)14(8,18)4-6-15(13,21-6)12(17)20-10/h6-10,18H,1,4H2,2-3H3/t6-,7+,8-,9-,10-,13-,14-,15+/m1/s1 + Picrotoxinin + Picrotoxinin + CC(=C)[C@@H]1[C@H]2OC(=O)[C@@H]1[C@]1(O)C[C@H]3O[C@]33C(=O)O[C@H]2[C@]13C + + + C19H20N2O3S + InChI=1S/C19H20N2O3S/c1-2-13-3-6-15(20-12-13)9-10-24-16-7-4-14(5-8-16)11-17-18(22)21-19(23)25-17/h3-8,12,17H,2,9-11H2,1H3,(H,21,22,23) + CHEBI:8228 + CCc1ccc(CCOc2ccc(CC3SC(=O)NC3=O)cc2)nc1 + "A member of the class of thiazolidenediones that is 1,3-thiazolidine-2,4-dione substituted by a benzyl group at position 5 which in turn is substituted by a 2-(5-ethylpyridin-2-yl)ethoxy group at position 4 of the phenyl ring. It exhibits hypoglycemic activity." [] + InChIKey=HYAFETHFCAUJAY-UHFFFAOYSA-N + (+-)-5-((4-(2-(5-ethyl-2-pyridinyl)ethoxy)phenyl)methyl)-2,4-thiazolidinedione + Pioglitazone + pioglitazone + pioglitazona + pioglitazone + pioglitazonum + 5-{4-[2-(5-ethylpyridin-2-yl)ethoxy]benzyl}-1,3-thiazolidine-2,4-dione + CHEBI:pioglitazone + + + 3,3'-Dimethoxybenzidine + C14H16N2O2 + CHEBI:3,3'-Dimethoxybenzidine + CHEBI:82321 + InChI=1S/C14H16N2O2/c1-17-13-7-9(3-5-11(13)15)10-4-6-12(16)14(8-10)18-2/h3-8H,15-16H2,1-2H3 + COc1cc(ccc1N)-c1ccc(N)c(OC)c1 + "A biphenyl that has formula C14H16N2O2." [] + InChIKey=JRBJSXQPQWSCCF-UHFFFAOYSA-N + ortho-Dianisidine + + + InChIKey=RZSYLLSAWYUBPE-UHFFFAOYSA-M + C37H35N2Na2O10S3 + "An organic molecular entity that has formula C37H35N2Na2O10S3." [] + InChI=1S/C37H36N2O10S3.2Na/c1-3-38(24-26-7-5-9-33(21-26)50(41,42)43)30-15-11-28(12-16-30)37(35-20-19-32(40)23-36(35)52(47,48)49)29-13-17-31(18-14-29)39(4-2)25-27-8-6-10-34(22-27)51(44,45)46;;/h5-23H,3-4,24-25H2,1-2H3,(H3,41,42,43,44,45,46,47,48,49);;/q;2*+1/p-1 + CHEBI:Fast Green FCF + [Na+].[Na+].CCN(Cc1cccc(c1)S([O-])(=O)=O)c1ccc(cc1)C(=C1C=CC(C=C1)=[N+](CC)Cc1cccc(c1)S([O-])(=O)=O)c1ccc(O)cc1S(O)(=O)=O + Fast Green FCF + CHEBI:82468 + + + "Any unsaturated fatty acid anion with one double or triple bond in the fatty acid chain." [] + monounsaturated fatty acid anions + [O-]C([*])=O + CHEBI:82680 + CHEBI:monounsaturated fatty acid anion + monounsaturated fatty acid anion + + + CHEBI:defensin + defensins + defensin + CHEBI:82761 + "A family of cysteine-rich polypeptides that function as host defence peptides and consist of 18-45 amino acids including six to eight cysteine residues." [] + + + CHEBI:monochlorobenzenes + monochlorobenzenes + "Any member of the class of chlorobenzenes containing a mono- or poly-substituted benzene ring in which only one substituent is chlorine." [] + CHEBI:83403 + + + HR + a long-chain alkane + CHEBI:83563 + long-chain alkane + [*] + "Any alkane having a chain length of at least 13 carbon atoms." [] + CHEBI:long-chain alkane + + + canonical amino acid derivatives + canonical amino-acid derivatives + proteinogenic amino-acid derivatives + proteinogenic amino-acid derivative + canonical amino-acid derivative + proteinogenic amino acid derivative + "Any derivative of a proteinogenic amino acid resulting from reaction at an amino group, carboxy group, or a side-chain functional group, or from the replacement of any hydrogen by a heteroatom." [] + proteinogenic amino acid derivatives + canonical amino acid derivative + CHEBI:proteinogenic amino acid derivative + CHEBI:83811 + + + CHEBI:non-proteinogenic amino acid + non-proteinogenic amino-acids + non-coded amino acid + non-canonical amino acids + non-canonical amino-acids + CHEBI:83820 + non-proteinogenic amino acid + non-coded amino-acids + "Any amino-acid that is not naturally encoded in the genetic code of any organism." [] + non-proteinogenic amino acids + non-coded amino-acid + non-canonical amino-acid + non-coded amino acids + non-canonical amino acid + non-proteinogenic amino-acid + + + "Any derivative of an amino acid resulting from reaction at an amino group, carboxy group, side-chain functional group, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing amino acid residues." [] + CHEBI:amino acid derivative + CHEBI:83821 + modified amino acids + amino acid derivatives + amino acid derivative + + + "Any L-alpha-amino acid which is not a member of the group of 23 proteinogenic amino acids." [] + CHEBI:83822 + non-proteinogenic L-alpha-amino acids + non-proteinogenic L-alpha-amino acid + CHEBI:non-proteinogenic L-alpha-amino acid + + + "A proteinogenic amino acid derivative resulting from the formal reaction of L-cysteine at the amino group, carboxy group, or thiol group, or from the replacement of any hydrogen of L-cysteine by a heteroatom." [] + CHEBI:L-cysteine derivative + CHEBI:83824 + L-cysteine derivative + L-cysteine derivatives + + + CHEBI:non-proteinogenic alpha-amino acid + non-proteinogenic alpha-amino-acid + CHEBI:83925 + non-proteinogenic alpha-amino acid + non-proteinogenic alpha-amino-acids + "Any alpha-amino acid which is not a member of the group of 23 proteinogenic amino acids." [] + non-proteinogenic alpha-amino acids + + + CHEBI:84055 + "Any phospho sugar that is the phosphate derivative of pentose." [] + CHEBI:pentose phosphate + pentose phosphates + pentose phosphate + + + CHEBI:L-serine derivative + "A proteinogenic amino acid derivative resulting from reaction of L-serine at the amino group or the carboxy group, or from the replacement of any hydrogen of L-serine by a heteroatom." [] + L-serine derivative + L-serine derivatives + CHEBI:84135 + + + L-phenylalanine derivatives + "A proteinogenic amino acid derivative resulting from reaction of L-phenylalanine at the amino group or the carboxy group, or from the replacement of any hydrogen of L-phenylalanine by a heteroatom." [] + L-phenylalanine derivative + CHEBI:L-phenylalanine derivative + CHEBI:84144 + + + CCCOc1ccc(cc1N)C(=O)OCCN(CC)CC + Proparacaine + CHEBI:Proparacaine + Proxymetacaine + Proparacaine + InChI=1S/C16H26N2O3/c1-4-10-20-15-8-7-13(12-14(15)17)16(19)21-11-9-18(5-2)6-3/h7-8,12H,4-6,9-11,17H2,1-3H3 + C16H26N2O3 + CHEBI:8485 + InChIKey=KCLANYCVBBTKTO-UHFFFAOYSA-N + "A benzoate ester that has formula C16H26N2O3." [] + + + [Na+].OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C([O-])=O + sodium D-gluconate + InChI=1S/C6H12O7.Na/c7-1-2(8)3(9)4(10)5(11)6(12)13;/h2-5,7-11H,1H2,(H,12,13);/q;+1/p-1/t2-,3-,4+,5-;/m1./s1 + CHEBI:sodium gluconate + Monosodium gluconate + CHEBI:84997 + D-Gluconic acid, monosodium salt + "An organic sodium salt having D-gluconate as the counterion." [] + Monosodium D-gluconate + sodium gluconate + InChIKey=UPMFZISCCZSDND-JJKGCWMISA-M + sodium (2R,3S,4R,5R)-2,3,4,5,6-pentahydroxyhexanoate + Gluconic acid sodium salt + C6H11NaO7 + + + 6-Thio-4-propyluracil + 2-Thio-6-propyl-1,3-pyrimidin-4-one + "A pyrimidinethione consisting of uracil in which the 2-oxo group is substituted by a thio group and the hydrogen at position 6 is substituted by a propyl group." [] + propylthiouracilum + 6-propyl-2-sulfanylidene-2,3-dihydropyrimidin-4(1H)-one + CHEBI:6-propyl-2-thiouracil + CHEBI:8502 + 6-Propyl-2-thio-2,4(1H,3H)pyrimidinedione + 2-Mercapto-6-propylpyrimid-4-one + C7H10N2OS + 6-propyl-2-thiouracil + 2-Thio-4-oxo-6-propyl-1,3-pyrimidine + 4-propyl-2-thiouracil + 2-Mercapto-6-propyl-4-pyrimidone + propylthiouracil + 6-propyl-2-thiouracil + 6-Propylthiouracil + 6-propyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one + InChI=1S/C7H10N2OS/c1-2-3-5-4-6(10)9-7(11)8-5/h4H,2-3H2,1H3,(H2,8,9,10,11) + InChIKey=KNAHARQHSZJURB-UHFFFAOYSA-N + CCCc1cc(=O)[nH]c(=S)[nH]1 + 2,3-dihydro-6-propyl-2-thioxo-4(1H)-pyrimidinone + propiltiouracilo + 4-Propyl-2-thiouracil + Propylthiouracil + propylthiouracile + + + ristocetina + CHEBI:ristocetin + COC(=O)[C@H]1NC(=O)[C@H]2NC(=O)[C@H](NC(=O)[C@@H]3NC(=O)[C@H]4NC(=O)[C@H](NC(=O)[C@H](N)c5ccc(O)c(Oc6cc4cc(O)c6C)c5)[C@H](O)c4ccc(Oc5cc3cc(Oc3ccc(cc3)[C@H]2O[C@@H]2C[C@@H](N)[C@@H](O)[C@H](C)O2)c5O[C@@H]2O[C@H](COC3O[C@@H](C)[C@H](O)[C@@H](O)[C@H]3O)[C@@H](O)[C@H](O)[C@H]2O[C@@H]2O[C@@H](CO)[C@H](O)[C@@H](O)[C@H]2O[C@@H]2OC[C@@H](O)[C@@H](O)[C@@H]2O)cc4)c2ccc(O)c(c2)-c2c(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)cc(O)cc12 + InChIKey=VUOPFFVAZTUEGW-FBMDODLCSA-N + ristocetin + "A heterodetic cyclic peptide that is produced by species of Amycolatopsis and Nocardia." [] + InChI=1S/C95H110N8O44/c1-30-47(109)18-37-20-49(30)139-50-19-35(9-16-46(50)108)59(97)84(125)102-64-68(113)33-5-11-40(12-6-33)137-52-21-38-22-53(81(52)145-95-83(76(121)72(117)56(143-95)29-134-91-78(123)73(118)67(112)32(3)136-91)147-94-82(75(120)71(116)55(27-105)142-94)146-92-77(122)69(114)48(110)28-133-92)138-41-13-7-34(8-14-41)80(144-57-25-44(96)66(111)31(2)135-57)65-89(130)101-63(90(131)132-4)43-23-39(106)24-51(140-93-79(124)74(119)70(115)54(26-104)141-93)58(43)42-17-36(10-15-45(42)107)60(85(126)103-65)98-87(128)62(38)99-86(127)61(37)100-88(64)129/h5-24,31-32,44,48,54-57,59-80,82-83,91-95,104-124H,25-29,96-97H2,1-4H3,(H,98,128)(H,99,127)(H,100,129)(H,101,130)(H,102,125)(H,103,126)/t31-,32-,44+,48+,54+,55-,56+,57+,59+,60+,61-,62+,63-,64+,65-,66-,67-,68+,69+,70+,71-,72+,73+,74-,75+,76-,77-,78+,79-,80+,82+,83+,91?,92-,93+,94-,95-/m0/s1 + CHEBI:85129 + C95H110N8O44 + + + CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)CCCCCCCCCCC[*] + C33H57N7O17P3SR + CHEBI:85348 + CHEBI:11,12-saturated fatty acyl-CoA + "Any fatty acyl-CoA in which the 11-12 bond of the fatty acyl group is saturated." [] + 11,12-saturated fatty acyl-CoA + + + O-decenoylcarnitines + C[N+](C)(C)CC(CC([O-])=O)OC([*])=O + "An O-acylcarnitine in which the acyl group specified is decenoyl." [] + decenoylcarnitine + C17H31NO4 + CHEBI:O-decenoylcarnitine + CHEBI:86063 + O-decenoylcarnitine + + + InChI=1S/2H3N.Ni.2H2O4S/c;;;2*1-5(2,3)4/h2*1H3;;2*(H2,1,2,3,4)/q;;+2;;/p-2 + Diammonium nickel bis(sulphate) + CHEBI:86151 + "A nickel coordination entity comprising ammonium, nickel and sulfate in which the ratio of ammonium to iron(2+) to sulfate ions is 2:1:2." [] + InChIKey=DAPUDVOJPZKTSI-UHFFFAOYSA-L + nickel ammonium sulfate (anhydrous) + ammonium nickel sulfate + ammonium nickel(2+) sulfate (2/1/2) + H8N2NiO8S2 + nickel ammonium sulfate + Ammonium disulfatonickelate(II) + ammonium nickel sulfate (anhydrous) + CHEBI:ammonium nickel sulfate + Nickel(II) ammonium sulfate + [NH4+].[NH4+].[Ni++].[O-]S([O-])(=O)=O.[O-]S([O-])(=O)=O + + + InChIKey=KIUMMUBSPKGMOY-UHFFFAOYSA-N + CHEBI:dithionitrobenzoic acid + 5-(3-carboxy-4-nitro-phenyl)disulfanyl-2-nitrobenzoic acid + 3,3'-Dithiobis(6-nitrobenzoic acid) + C14H8N2O8S2 + InChI=1S/C14H8N2O8S2/c17-13(18)9-5-7(1-3-11(9)15(21)22)25-26-8-2-4-12(16(23)24)10(6-8)14(19)20/h1-6H,(H,17,18)(H,19,20) + dithionitrobenzoic acid + Ellman's reagent + "An organic disulfide that results from the formal oxidative dimerisation of 2-nitro-5-thiobenzoic acid. An indicator used to quantify the number or concentration of thiol groups." [] + Dithiobisnitrobenzoic acid + CHEBI:86228 + 2,2'-Dinitro-5,5'-dithiodibenzoic acid + DTNB + 2,2'-Dinitro-5,5'-dithiodibenzoesaeure + 3,3'-disulfanediylbis(6-nitrobenzoic acid) + OC(=O)c1cc(SSc2ccc(c(c2)C(O)=O)[N+]([O-])=O)ccc1[N+]([O-])=O + 5,5'-dithiobis(2-nitrobenzoic acid) + + + CHEBI:86478 + "Heteroorganic entities that are microbial metabolites (or compounds derived from them) which have significant antifungal properties." [] + CHEBI:antibiotic antifungal agent + antibiotic antifungal agents + antibiotic antifungal agent + + + CHEBI:8682 + Pyronine Y + [Cl-].CN(C)c1ccc2cc3ccc(cc3oc2c1)=[N+](C)C + "An organic molecular entity that has formula C17H19N2O.Cl." [] + Pyronine + Pyronine Y + InChIKey=INCIMLINXXICKS-UHFFFAOYSA-M + CHEBI:Pyronine Y + C17H19N2O.Cl + InChI=1S/C17H19N2O.ClH/c1-18(2)14-7-5-12-9-13-6-8-15(19(3)4)11-17(13)20-16(12)10-14;/h5-11H,1-4H3;1H/q+1;/p-1 + + + CHEBI:antibiotic antifungal drug + "Any antibiotic antifungal agent used to treat fungal infections in humans or animals." [] + CHEBI:87113 + antibiotic antifungal drug + antibiotic antifungal drugs + + + "Any antibiotic antifungal agent that has been used as a fungicide." [] + antibiotic fungicide + CHEBI:87114 + CHEBI:antibiotic fungicide + antibiotic fungicides + + + (3S,4R,4aR,6S,6aR,7S,8R,8aS,8bR,9S,9aS)-4,6,7,8a,8b,9a-hexahydroxy-7-isopropyl-3,6a,9-trimethyldodecahydro-6,9-methanobenzo[1,2]pentaleno[1,6-bc]furan-8-yl 1H-pyrrole-2-carboxylate + ryanodol, 3-(1H-pyrrole-2-carboxylate) + Ryania + ryanodine + Ryanodin + Ryanodine + CHEBI:8925 + "An insecticide alkaloid isolated from South American plant Ryania speciosa." [] + C25H35NO9 + CHEBI:ryanodine + InChI=1S/C25H35NO9/c1-12(2)22(31)17(34-16(28)14-7-6-10-26-14)23(32)18(4)11-21(30)19(22,5)25(23,33)24(35-21)15(27)13(3)8-9-20(18,24)29/h6-7,10,12-13,15,17,26-27,29-33H,8-9,11H2,1-5H3/t13-,15+,17+,18-,19+,20-,21-,22+,23+,24+,25+/m0/s1 + (3S,4R,4aR,6S,6aR,7S,8R,8aS,8bR,9S,9aS)-4,6,7,8a,8b,9a-hexahydroxy-3,6a,9-trimethyl-7-(propan-2-yl)dodecahydro-6,9-methanobenzo[1,2]pentaleno[1,6-bc]furan-8-yl 1H-pyrrole-2-carboxylate + CC(C)[C@@]1(O)[C@@H](OC(=O)c2ccc[nH]2)[C@@]2(O)[C@@]3(C)C[C@]4(O)O[C@@]5([C@H](O)[C@@H](C)CC[C@]35O)[C@@]2(O)[C@@]14C + InChIKey=JJSYXNQGLHBRRK-SFEDZAPPSA-N + + + sodium dodecyl sulfate + [Na+].CCCCCCCCCCCCOS([O-])(=O)=O + CHEBI:8984 + C12H25NaO4S + sodium dodecylsulfate + "An alkyl sulfate that has formula C12H25NaO4S." [] + Sodium dodecyl sulfate + InChIKey=DBMJMQXJHONAFJ-UHFFFAOYSA-M + CHEBI:sodium dodecyl sulfate + sodium dodecyl sulphate + sodium lauryl sulphate + SDS + Sodium lauryl sulfate + InChI=1S/C12H26O4S.Na/c1-2-3-4-5-6-7-8-9-10-11-12-16-17(13,14)15;/h2-12H2,1H3,(H,13,14,15);/q;+1/p-1 + C12H25O4S.Na + SLS + + + sodium 7-deoxycholate + Sodium deoxycholate + sodium deoxycholate + desoxycholate sodium + C24H39NaO4 + sodium deoxycholate + CHEBI:9177 + deoxycholic acid sodium salt + InChI=1S/C24H40O4.Na/c1-14(4-9-22(27)28)18-7-8-19-17-6-5-15-12-16(25)10-11-23(15,2)20(17)13-21(26)24(18,19)3;/h14-21,25-26H,4-13H2,1-3H3,(H,27,28);/q;+1/p-1/t14-,15-,16-,17+,18-,19+,20+,21+,23+,24-;/m1./s1 + InChIKey=FHHPUSMSKHSNKW-SMOYURAASA-M + sodium desoxycholate + "A bile acid salt that has formula C24H39NaO4." [] + sodium 3alpha,12alpha-dihydroxy-5beta-cholan-24-oate + deoxycholate sodium + CHEBI:sodium deoxycholate + C24H39O4.Na + [Na+].[H][C@]12CC[C@@]3([H])[C@]4([H])CC[C@]([H])([C@H](C)CCC([O-])=O)[C@@]4(C)[C@@H](O)C[C@]3([H])[C@@]1(C)CC[C@@H](O)C2 + + + 1,6-Hexanedicarboxylic acid + Suberic acid + 1,6-dicarboxyhexane + hexamethylenedicarboxylic acid + octane-1,8-dioic acid + InChI=1S/C8H14O4/c9-7(10)5-3-1-2-4-6-8(11)12/h1-6H2,(H,9,10)(H,11,12) + octanedioic acid + 1,8-Octanedioic acid + CHEBI:suberic acid + Suberinsaeure + CHEBI:9300 + "An alpha,omega-dicarboxylic acid that is the 1,6-dicarboxy derivative of hexane." [] + Cork acid + Oktandisaeure + C8H14O4 + Korksaeure + InChIKey=TYFQFVWCELRYAO-UHFFFAOYSA-N + suberic acid + Octanedioic acid + OC(=O)CCCCCCC(O)=O + + + InChIKey=GKCBAIGFKIBETG-UHFFFAOYSA-N + CHEBI:9468 + 2-(Dimethylamino)ethyl p-(butylamino)benzoate + CCCCNc1ccc(cc1)C(=O)OCCN(C)C + tetracainum + tetracaina + C15H24N2O2 + tetracaine + tetracaine + p-Butylaminobenzoyl-2-dimethylaminoethanol + Diaethylaminoaethanol ester der p-butylaminobenzoesaeure + InChI=1S/C15H24N2O2/c1-4-5-10-16-14-8-6-13(7-9-14)15(18)19-12-11-17(2)3/h6-9,16H,4-5,10-12H2,1-3H3 + 2-(dimethylamino)ethyl 4-(butylamino)benzoate + Tetracaine + p-(butylamino)benzoic acid beta-(dimethylamino)ethyl ester + CHEBI:tetracaine + Amethocaine + "A benzoate ester in which 4-N-butylbenzoic acid and 2-(dimethylamino)ethanol have combined to form the ester bond; a local ester anaesthetic (ester caine) used for surface and spinal anaesthesia." [] + + + maculotoxin + "A quinazoline alkaloid that is a marine toxin isolated from fish such as puffer fish. It has been shown to exhibit potential neutotoxicity due to its ability to block voltage-gated sodium channels." [] + CHEBI:tetrodotoxin + C11H17N3O8 + OC[C@@]1(O)[C@H]2O[C@@]3(O)O[C@@H]1[C@@H]1[C@@H](O)NC(=N)N[C@]1([C@H]2O)[C@@H]3O + CHEBI:9506 + (1R,5R,6R,7R,9S,11R,12R,13S,14S)-14-(hydroxymethyl)-3-imino-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1(7,11).0(1,6)]tetradecane-5,9,12,13,14-pentol + tetrodontoxin + InChI=1S/C11H17N3O8/c12-8-13-6(17)2-4-9(19,1-15)5-3(16)10(2,14-8)7(18)11(20,21-4)22-5/h2-7,15-20H,1H2,(H3,12,13,14)/t2-,3+,4-,5+,6-,7+,9+,10-,11+/m1/s1 + octahydro-12-(hydroxymethyl)-2-imino-5,9:7,10a-dimethano-10aH-[1,3]dioxocino[6,5-d]pyrimidine-4,7,10,11,12-pentol + InChIKey=CFMYXEVWODSLAX-QYIGHCJRSA-N + tarichatoxin + fugu poison + Tetrodotoxin + spheroidine + tetrodotoxin + TTX + + + Thiamin diphosphate + Thiamin pyrophosphate + "A 1,3-thiazolium cation that is the conjugate acid of thiamine(1+) diphosphate(1)." [] + ThPP + TPP + C12H19N4O7P2S + thiamine(1+) diphosphate + Thiamine diphosphate + InChIKey=AYEKOFBPNLCAJY-UHFFFAOYSA-O + InChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1 + 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[2-(diphosphooxy)ethyl]-4-methyl-1,3-thiazol-3-ium + CHEBI:9532 + CHEBI:thiamine(1+) diphosphate + Cc1ncc(C[n+]2csc(CCOP(O)(=O)OP(O)(O)=O)c2C)c(N)n1 + + + Thiocarbohydrazide + NNC(=S)NN + InChI=1S/CH6N4S/c2-4-1(6)5-3/h2-3H2,(H2,4,5,6) + "A thiocarbonyl compound that has formula CH6N4S." [] + CH6N4S + InChIKey=LJTFFORYSFGNCT-UHFFFAOYSA-N + CHEBI:9549 + Thiocarbohydrazide + CHEBI:Thiocarbohydrazide + 1,3-Diamino-2-thiourea + + + C11H17N2O2S.Na + thiopental sodique + monosodium 5-ethyl-5-(1-methylbutyl) thiobarbiturate + sodium 5-ethyl-4,6-dioxo-5-(pentan-2-yl)-1,4,5,6-tetrahydropyrimidine-2-thiolate + sodium thiopental + tiopental sodico + sodium pentothal + sodium pentothiobarbital + C11H17N2NaO2S + Thiopental sodium + sodium 5-ethyl-5-(1-methylbutyl)-2-thiobarbiturate + sodium (+-)-5-ethyl-5-(1-methylbutyl)-2-thiobarbiturate + sodium thiopentobarbital + penthiobarbital sodium + [Na+].CCCC(C)C1(CC)C(=O)NC([S-])=NC1=O + thiopentone sodium + "An organic sodium salt having thiopental(1-) as the counter-ion." [] + thiopentalum natricum + sodium thiopentone + thiopental sodium + Pentothal + CHEBI:9561 + CHEBI:thiopental sodium + thiopental sodium + InChIKey=AWLILQARPMWUHA-UHFFFAOYSA-M + InChI=1S/C11H18N2O2S.Na/c1-4-6-7(3)11(5-2)8(14)12-10(16)13-9(11)15;/h7H,4-6H2,1-3H3,(H2,12,13,14,15,16);/q;+1/p-1 + + + Thrombin + Thrombin + CHEBI:Thrombin + CHEBI:9574 + + + 4-tert-Octylphenyl peg ether + (C2H4O)nC14H22O + "A poly(ethylene glycol) terminated with a 4-(2,4,4-trimethylpentan-3-yl) phenyl group at one end." [] + Peg 4-tert-octylphenyl ether + Poly(oxyethylene)-p-tert-octylphenyl ether + Triton X-100 + octoxinolum + Polyoxyethylene mono(octylphenyl) ether + Triton X-100 + octoxinol + CHEBI:9750 + alpha-(4-(1,1,3,3-Tetramethylbutyl)phenyl)-omega-hydroxypoly(oxy-1,2-ethanediyl) + CHEBI:Triton X-100 + Polyoxyethylene 4-(1,1,3,3-tetramethylbutyl)phenyl ether + Polyethylene glycol mono(p-(1,1,3,3-tetramethylbutyl)phenyl) ether + Octoxynol 9 + 4-(1,1,3,3-Tetramethylbutyl)phenyl hydroxypoly(oxyethylene) + Polyethylene glycol mono(p-tert-octylphenyl) ether + Peg (p-(1,1,3,3-tetramethylbutyl)phenyl) ether + Peg 4-isooctylphenyl ether + + + Trizma + tris + tris(hydroxymethyl)aminomethane + Tris amino + InChIKey=LENZDBCJOHFCAS-UHFFFAOYSA-N + CHEBI:tris + "A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC." [] + 2-amino-2-(hydroxymethyl)propane-1,3-diol + C4H11NO3 + Tris + THAM + 1,1,1-tris(hydroxymethyl)methanamine + Trometamol + CHEBI:9754 + InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2 + aminotris(hydroxymethyl)methane + 2-Amino-2-(hydroxymethyl)-1,3-propanediol + Tris buffer + Tromethamine + Tris-base + NC(CO)(CO)CO + Tris base + + + C17H20N2O2 + Mydriacyl (TN) + Tropicamide + Tropicamide + CHEBI:9757 + CHEBI:Tropicamide + + + For: buffer(v.)/buffered/buffering/buffers + CHEBI_CHMO_EXT:buffer process + BFO:occurrent and ((realizes some CHEBI:buffer) or (results_in_formation_of some CHMO:'buffer solution')) + buffer + CHEBI_CHMO_EXT:buffer_process + buffer process + + + CHEBI_CHMO_EXT:buffer solution + buffer solution + (CHEBI:solution and has_proper_part some CHEBI_EXT:buffer) or CHMO:'buffer solution' + CHEBI_CHMO_EXT:buffer_solution + buffer + + + IP3 + inositol 1,4,5-triphosphate + D-myo-inositol 1,4,5-trisphosphate + 1D-myo-inositol 1,4,5-trisphosphate + InsP3 + CHEBI_EXT:1D-myo-inositol 1,4,5-trisphosphate + CHEBI_EXT:1D_myo_inositol_1_4_5_trisphosphate + D-myo-inositol 1,4,5-triphosphate + inositol 1,4,5-trisphosphate + CHEBI:'1D-myo-inositol 1,4,5-trisphosphate' or CHEBI:'1D-myo-inositol 1,4,5-trisphosphate(6-)' + Ins(1,4,5)P3 + 1,4,5-Insp3 + 1D-myo-inositol 1,4,5-triphosphate + + + CHEBI_EXT:22695 + base + CHEBI_EXT:base + "A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base)." [] + + + CHEBI_EXT:chromophore + CHEBI_EXT:23240 + chromophore + "The part (atom or group of atoms) of a molecular entity in which the electronic transition responsible for a given spectral band is approximately localized." [] + + + CHEBI_EXT:cofactor + CHEBI_EXT:23357 + "An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group)." [] + cofactor + + + CHEBI_EXT:drug + drug + "Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances." [] + CHEBI_EXT:23888 + + + "A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction." [] + enzyme inhibitor + CHEBI_EXT:enzyme inhibitor + CHEBI_EXT:23924 + + + fat-soluble vitamin + "Vitamins like A, D, E and K that dissolve in fats and are stored in body tissues. Unlike the water-soluble vitamins, these are stored in the body for long periods of time and generally pose a greater risk for toxicity when consumed in excess." [] + CHEBI_EXT:fat-soluble vitamin + CHEBI_EXT:24020 + + + CHEBI_EXT:24432 + CHEBI_EXT:biological role + "A role played by the molecular entity or part thereof within a biological context." [] + biological role + + + CHEBI_EXT:hormone + hormone + "Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds." [] + CHEBI_EXT:24621 + + + CHEBI_EXT:24869 + ionophore + CHEBI_EXT:ionophore + "A compound which can carry specific ions through membranes of cells or organelles." [] + + + CHEBI_EXT:25078 + CHEBI_EXT:luciferin + "A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase." [] + luciferin + + + CHEBI_EXT:25212 + metabolite + CHEBI_EXT:metabolite + "Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites." [] + + + CHEBI_EXT:25435 + "An agent that increases the frequency of mutations above the normal background level, usually by interacting directly with DNA and causing it damage, including base substitution." [] + CHEBI_EXT:mutagen + mutagen + + + CHEBI_EXT:25512 + CHEBI_EXT:neurotransmitter + "An endogenous compound that is used to transmit information across the synapse between a neuron and another cell." [] + neurotransmitter + + + CHEBI_EXT:26130 + "An endogenous molecular entity that results in a colour of an organism as the consequence of the selective absorption of light." [] + biological pigment + CHEBI_EXT:biological pigment + + + prosthetic group + CHEBI_EXT:prosthetic group + CHEBI_EXT:26348 + "A tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity." [] + + + "Poisonous substance produced by a biological organism such as a microbe, animal or plant." [] + toxin + CHEBI_EXT:toxin + CHEBI_EXT:27026 + + + CHEBI_EXT:detergent + CHEBI_EXT:27780 + detergent + "A surfactant (or a mixture containing one or more surfactants) having cleaning properties in dilute solutions." [] + + + CHEBI:2-oxoglutarate(1-) or CHEBI:2-oxoglutarate(2-) + 2-ketoglutarate + alpha-ketoglutarate + CHEBI_EXT:2-oxoglutarate + CHEBI_EXT:2_oxoglutarate + 2-oxoglutarate + + + "An organic substance that is distributed in foodstuffs, is distinct from the main organic components of food (protein, carbohydrate and fat) and is needed for the normal nutrition of the organism in question. The term \"vitamines\" (from vita + amines) was coined in 1912 by Casimir Funk, who believed that these compounds were amines." [] + CHEBI_EXT:vitamin + vitamin + CHEBI_EXT:33229 + + + CHEBI_EXT:33232 + "Intended use of the molecular entity or part thereof by humans." [] + application + CHEBI_EXT:application + + + CHEBI_EXT:molecular messenger + molecular messenger + CHEBI_EXT:33280 + + + CHEBI_EXT:antimicrobial agent + "A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans." [] + antimicrobial agent + CHEBI_EXT:33281 + + + CHEBI_EXT:antibacterial agent + antibacterial agent + "A substance that kills or slows the growth of bacteria." [] + CHEBI_EXT:33282 + + + CHEBI_EXT:nutrient + CHEBI_EXT:33284 + nutrient + "A nutrient is a chemical element needed by all life forms." [] + + + CHEBI_EXT:food + food + "Any material that can be ingested by an organism." [] + CHEBI_EXT:33290 + + + CHEBI_EXT:33893 + reagent + "A substance used in a chemical reaction to detect, measure, examine, or produce other substances." [] + CHEBI_EXT:reagent + + + CHEBI_EXT:35195 + "A substance which lowers the surface tension of the medium in which it is dissolved, and/or the interfacial tension with other phases, and, accordingly, is positively adsorbed at the liquid/vapour and/or at other interfaces." [] + surfactant + CHEBI_EXT:surfactant + + + CHEBI_EXT:tracer + "A role played by a foreign substance mixed with or attached to a given substance to enable the distribution or location of the latter to be determined subsequently." [] + CHEBI_EXT:35204 + tracer + + + inhibitor + CHEBI_EXT:35222 + "A substance that diminishes the rate of a chemical reaction." [] + CHEBI_EXT:inhibitor + + + "A small molecule which increases (activator) or decreases (inhibitor) the activity of an (allosteric) enzyme by binding to the enzyme at the regulatory site (which is different from the substrate-binding catalytic site)." [] + CHEBI_EXT:effector + CHEBI_EXT:35224 + effector + + + buffer + CHEBI_EXT:35225 + "Any substance or mixture of substances that, in solution (typically aqueous), resists change in pH upon addition of small amounts of acid or base." [] + CHEBI_EXT:buffer + + + CHEBI_EXT:35470 + CHEBI_EXT:central nervous system drug + central nervous system drug + "A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system." [] + + + CHEBI_EXT:35472 + anti-inflammatory drug + CHEBI_EXT:anti-inflammatory drug + "A substance that reduces or suppresses inflammation." [] + + + CHEBI_EXT:35480 + CHEBI_EXT:analgesic + analgesic + "An agent capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms." [] + + + central nervous system depressant + CHEBI_EXT:35488 + CHEBI_EXT:central nervous system depressant + "A loosely defined group of drugs that tend to reduce the activity of the central nervous system." [] + + + "An agent that promotes the excretion of urine through its effects on kidney function." [] + CHEBI_EXT:35498 + diuretic + CHEBI_EXT:diuretic + + + xenobiotic + CHEBI_EXT:35703 + CHEBI_EXT:xenobiotic + "A xenobiotic (Greek, xenos \"foreign\"; bios \"life\") is a compound that is foreign to a living organism. Principal xenobiotics include: drugs, carcinogens and various compounds that have been introduced into the environment by artificial means." [] + + + CHEBI_EXT:immunosuppressive agent + CHEBI_EXT:35705 + "An agent that suppresses immune function by one of several mechanisms of action. Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of T-cells or by inhibiting the activation of helper cells. In addition, an immunosuppressive agent is a role played by a compound which is exhibited by a capability to diminish the extent and/or voracity of an immune response." [] + immunosuppressive agent + + + sedative + "A central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety." [] + CHEBI_EXT:sedative + CHEBI_EXT:35717 + + + CHEBI_EXT:antifungal agent + antifungal agent + "An antimicrobial agent that destroys fungi by suppressing their ability to grow or reproduce." [] + CHEBI_EXT:35718 + + + neurotransmitter agent + CHEBI_EXT:neurotransmitter agent + "A substance used for its pharmacological action on any aspect of neurotransmitter systems. Neurotransmitter agents include agonists, antagonists, degradation inhibitors, uptake inhibitors, depleters, precursors, and modulators of receptor function." [] + CHEBI_EXT:35942 + + + acid + CHEBI_EXT:37527 + CHEBI_EXT:acid + "An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid)." [] + + + CHEBI_EXT:37670 + CHEBI_EXT:protease inhibitor + protease inhibitor + "A compound which inhibits or antagonizes the biosynthesis or actions of proteases (endopeptidases)." [] + + + CHEBI_EXT:protein kinase inhibitor + "An EC 2.7.* (P-containing group transferase) inhibitor that interferes with the action of protein kinases." [] + protein kinase inhibitor + CHEBI_EXT:37699 + + + CHEBI_EXT:37886 + CHEBI_EXT:adrenergic agonist + adrenergic agonist + "An agent that selectively binds to and activates adrenergic receptors." [] + + + CHEBI_EXT:37958 + dye + CHEBI_EXT:dye + + + adrenergic agent + "Any agent that acts on an adrenergic receptor or affects the life cycle of an adrenergic transmitter." [] + CHEBI_EXT:adrenergic agent + CHEBI_EXT:37962 + + + CHEBI_EXT:calcium channel blocker + calcium channel blocker + "One of a class of drugs that acts by selective inhibition of calcium influx through cell membranes or on the release and binding of calcium in intracellular pools." [] + CHEBI_EXT:38215 + + + "Any agent that affects the transport of molecular entities across a biological membrane." [] + CHEBI_EXT:membrane transport modulator + CHEBI_EXT:38632 + membrane transport modulator + + + CHEBI_EXT:sodium channel blocker + "An agent that inhibits sodium influx through cell membranes." [] + sodium channel blocker + CHEBI_EXT:38633 + + + calcium channel modulator + CHEBI_EXT:calcium channel modulator + CHEBI_EXT:38808 + "A membrane transport modulator that is able to regulate intracellular calcium levels." [] + + + anaesthetic + CHEBI_EXT:anaesthetic + CHEBI_EXT:38867 + "Substance which produces loss of feeling or sensation." [] + + + CHEBI_EXT:sodium channel modulator + CHEBI_EXT:39000 + sodium channel modulator + + + CHEBI_EXT:39442 + "A role played by a fluorescent molecular entity used to study the microscopic environment by fluorescence spectroscopy." [] + CHEBI_EXT:fluorescent probe + fluorescent probe + + + solvent + CHEBI_EXT:solvent + CHEBI_EXT:46787 + "A liquid that can dissolve other substances (solutes) without any change in their chemical composition." [] + + + CHEBI_EXT:indicator + indicator + CHEBI_EXT:47867 + "Anything used in a scientific experiment to indicate the presence of a substance or quality, change in a body, etc." [] + + + "A drug used for its effects on dopamine receptors, on the life cycle of dopamine, or on the survival of dopaminergic neurons." [] + CHEBI_EXT:dopaminergic agent + dopaminergic agent + CHEBI_EXT:48560 + + + dopaminergic antagonist + "A drug that binds to but does not activate dopamine receptors, thereby blocking the actions of dopamine or exogenous agonists." [] + CHEBI_EXT:dopaminergic antagonist + CHEBI_EXT:48561 + + + agonist + CHEBI_EXT:48705 + CHEBI_EXT:agonist + "Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own." [] + + + CHEBI_EXT:50112 + "Any hormone that is responsible for controlling sexual characteristics and reproductive function." [] + CHEBI_EXT:sex hormone + sex hormone + + + CHEBI_EXT:50113 + CHEBI_EXT:androgen + androgen + "A sex hormone that stimulates or controls the development and maintenance of masculine characteristics in vertebrates by binding to androgen receptors." [] + + + CHEBI_EXT:estrogen + CHEBI_EXT:50114 + "A hormone that stimulates or controls the development and maintenance of female sex characteristics in mammals by binding to oestrogen receptors. The oestrogens are named for their importance in the oestrous cycle. The oestrogens that occur naturally in the body, notably estrone, estradiol, estriol, and estetrol are steroids. Other compounds with oestrogenic activity are produced by plants (phytoestrogens) and fungi (mycoestrogens); synthetic compounds with oestrogenic activity are known as xenoestrogens." [] + estrogen + + + probe + "A role played by a molecular entity used to study the microscopic environment." [] + CHEBI_EXT:probe + CHEBI_EXT:50406 + + + visual indicator + "Anything used in a scientific experiment that gives a visual change to indicate the presence of a substance or quality, change in a body, etc." [] + CHEBI_EXT:visual indicator + CHEBI_EXT:50408 + + + CHEBI_EXT:50410 + colour indicator + CHEBI_EXT:colour indicator + + + one-colour indicator + "A colour indicator that is colourless on one side of the transition interval." [] + CHEBI_EXT:50411 + CHEBI_EXT:one-colour indicator + + + CHEBI_EXT:potassium channel blocker + potassium channel blocker + CHEBI_EXT:50509 + "An agent that inhibits cell membrane glycoproteins that are selectively permeable to potassium ions." [] + + + potassium channel modulator + CHEBI_EXT:50510 + CHEBI_EXT:potassium channel modulator + + + CHEBI_EXT:immunomodulator + CHEBI_EXT:50846 + immunomodulator + "Biologically active substance whose activity affects or plays a role in the functioning of the immune system." [] + + + genotoxin + CHEBI_EXT:50902 + CHEBI_EXT:genotoxin + "A role played by a chemical compound to induce direct or indirect DNA damage. Such damage can potentially lead to the formation of a malignant tumour, but DNA damage does not lead inevitably to the creation of cancerous cells." [] + + + carcinogenic agent + CHEBI_EXT:50903 + CHEBI_EXT:carcinogenic agent + "A role played by a chemical compound which is known to induce a process of carcinogenesis by corrupting normal cellular pathways, leading to the acquistion of tumoral capabilities." [] + + + CHEBI_EXT:teratogenic agent + "A role played by a chemical compound in biological systems with adverse consequences in embryo developments, leading to birth defects, embryo death or altered development, growth retardation and functional defect." [] + teratogenic agent + CHEBI_EXT:50905 + + + CHEBI_EXT:role + role + "A role is particular behaviour which a material entity may exhibit." [] + CHEBI_EXT:50906 + + + fixative + CHEBI_EXT:50913 + "Any compound used for the purpose of preserving biological tissues from decay in such a way as to allow for the preparation of thin, stained sections for subsequent histological study." [] + CHEBI_EXT:fixative + + + chemical role + CHEBI_EXT:chemical role + CHEBI_EXT:51086 + "A role played by the molecular entity or part thereof within a chemical context." [] + + + CHEBI_EXT:51121 + CHEBI_EXT:fluorescent dye + fluorescent dye + + + "A fluorescent dye used to stain biological specimens." [] + fluorochrome + CHEBI_EXT:fluorochrome + CHEBI_EXT:51217 + + + GABA agonist + CHEBI_EXT:GABA agonist + CHEBI_EXT:51373 + "A drug that binds to and activates gamma-aminobutyric acid receptors." [] + + + CHEBI_EXT:GABA agent + "A substance, such as agonists, antagonists, degradation or uptake inhibitors, depleters, precursors, and modulators of receptor function, used for its pharmacological actions on GABAergic systems." [] + GABA agent + CHEBI_EXT:51374 + + + biochemical role + CHEBI_EXT:biochemical role + CHEBI_EXT:52206 + "A biological role played by the molecular entity or part thereof within a biochemical context." [] + + + biophysical role + CHEBI_EXT:biophysical role + CHEBI_EXT:52208 + + + "A role played by the molecular entity or part thereof which causes the development of a pathological process." [] + CHEBI_EXT:52209 + aetiopathogenetic role + CHEBI_EXT:aetiopathogenetic role + + + CHEBI_EXT:pharmacological role + CHEBI_EXT:52210 + pharmacological role + "A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties." [] + + + CHEBI_EXT:52211 + physiological role + CHEBI_EXT:physiological role + + + CHEBI_EXT:52215 + "A chemical role played by the molecular entity or part thereof in a photochemical process." [] + CHEBI_EXT:photochemical role + photochemical role + + + CHEBI_EXT:photobiochemical role + CHEBI_EXT:52216 + photobiochemical role + "A role played by a molecular entity or part thereof in a photobiochemical process." [] + + + CHEBI_EXT:pharmaceutical + CHEBI_EXT:52217 + pharmaceutical + "Any substance introduced into a living organism with therapeutic or diagnostic purpose." [] + + + CHEBI_EXT:52290 + mitogen + CHEBI_EXT:mitogen + "A chemical substance that encourages a cell to commence cell division, triggering mitosis." [] + + + CHEBI_EXT:EC 6.3.2.* (acid--D-amino-acid ligase) inhibitor + EC 6.3.2.* (acid--D-amino-acid ligase) inhibitor + "Any inhibitor of an acid--D-amino-acid ligase (EC 6.3.2.*)." [] + CHEBI_EXT:59105 + + + CHEBI_EXT:59132 + CHEBI_EXT:antigen + antigen + "Any substance that stimulates an immune response in the body, such as through antibody production or by presentation to a T-cell receptor after binding to a major histocompability complex (MHC)." [] + + + amphiphile + "A surfactant molecule possessing both hydrophilic and lipophilic properties." [] + CHEBI_EXT:amphiphile + CHEBI_EXT:59941 + + + EC 3.4.* (hydrolases acting on peptide bond) inhibitor + CHEBI_EXT:60258 + CHEBI_EXT:EC 3.4.* (hydrolases acting on peptide bond) inhibitor + "A hydrolase inhibitor that interferes with the action of any hydrolase acting on peptide bonds (peptidase), EC 3.4.*.*)." [] + + + thyroid hormone + "Any hormone produced by the thyroid gland" [] + CHEBI_EXT:thyroid hormone + CHEBI_EXT:60311 + + + CHEBI_EXT:adjuvant + adjuvant + CHEBI_EXT:60809 + "Any pharmacological or immunological agent that modifies the effect of other agents such as drugs or vaccines while having few if any direct effects when given by itself." [] + + + immunogen + "A type of antigen capable on its own of inducing an immune response." [] + CHEBI_EXT:immunogen + CHEBI_EXT:60816 + + + CHEBI_EXT:60832 + "Any substance that interacts with tubulin to inhibit or promote polymerisation of microtubules." [] + tubulin modulator + CHEBI_EXT:tubulin modulator + + + "Any substance that interacts with tubulin to promote polymerisation of microtubules." [] + microtubule-stabilising agent + CHEBI_EXT:microtubule-stabilising agent + CHEBI_EXT:61950 + + + CHEBI_EXT:62488 + signalling molecule + CHEBI_EXT:signalling molecule + "A molecular messenger in which the molecule is specifically involved in transmitting information between cells. Such molecules are released from the cell sending the signal, cross over the gap between cells by diffusion, and interact with specific receptors in another cell, triggering a response in that cell by activating a series of enzyme controlled reactions which lead to changes inside the cell." [] + + + "The chemical role played by a substance that stabilizes an emulsion by increasing its kinetic stability." [] + CHEBI_EXT:emulsifier + emulsifier + CHEBI_EXT:63046 + + + oxidising agent + "A substance that removes electrons from another reactant in a redox reaction." [] + CHEBI_EXT:oxidising agent + CHEBI_EXT:63248 + + + CHEBI_EXT:64047 + food additive + CHEBI_EXT:food additive + "Any substance which is added to food to preserve or enhance its flavour and/or appearance." [] + + + cysteine protease inhibitor + "Any protease inhibitor that restricts the action of a cysteine protease." [] + CHEBI_EXT:64152 + CHEBI_EXT:cysteine protease inhibitor + + + CHEBI_EXT:64338 + K-ATP channel agonist + "A compound which acts as an agonist at the ATP-sensitive K+ channel." [] + CHEBI_EXT:K-ATP channel agonist + + + "Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism." [] + CHEBI_EXT:64909 + CHEBI_EXT:poison + poison + + + CHEBI_EXT:67079 + "Any compound that has anti-inflammatory effects." [] + anti-inflammatory agent + CHEBI_EXT:anti-inflammatory agent + + + CHEBI_EXT:PPAR modulator + PPAR modulator + CHEBI_EXT:70781 + "Any compound which acts on the peroxisome proliferator-activated receptor." [] + + + CHEBI_EXT:EC 2.* (transferase) inhibitor + "An enzyme inhibitor that inhibits the action of a transferase (EC 2.*)" [] + EC 2.* (transferase) inhibitor + CHEBI_EXT:71300 + + + PPARbeta/delta agonist + "A PPAR modulator which activates the peroxisome proliferator-activated receptor-beta/delta." [] + CHEBI_EXT:73730 + CHEBI_EXT:PPARbeta/delta agonist + + + CHEBI_EXT:chromogenic compound + "Colourless, endogenous or exogenous pigment precursors that may be transformed by biological mechanisms into coloured compounds. They are used in biochemical assays and in diagnosis as indicators, particularly in the form of enzyme substrates." [] + CHEBI_EXT:75050 + chromogenic compound + + + CHEBI_EXT:EC 6.3.2.2 (glutamate--cysteine ligase) inhibitor + CHEBI_EXT:75599 + "An acid--amino-acid ligase inhibitor that inhibits the action of a glutamate--cysteine ligase (EC 6.3.2.2)" [] + EC 6.3.2.2 (glutamate--cysteine ligase) inhibitor + + + CHEBI_EXT:EC 6.3.* (C-N bond-forming ligase) inhibitor + CHEBI_EXT:75600 + "A ligase inhibitor that interferes with the action of a C-N bond-forming ligase (EC 6.3.*.*)." [] + EC 6.3.* (C-N bond-forming ligase) inhibitor + + + EC 6.* (ligase) inhibitor + "Any enzyme inhibitor that interferes with the action of a ligase (EC 6.*.*.*). Ligases are enzymes that catalyse the joining of two molecules with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [] + CHEBI_EXT:EC 6.* (ligase) inhibitor + CHEBI_EXT:75603 + + + CHEBI_EXT:76219 + CHEBI_EXT:fluorogen + "A non-fluorescent small compound which become fluorescent only when complexed to a fluorogen activating protein (FAP)." [] + fluorogen + + + "A transferase inhibitor that inhibits the action of a phosphorus-containing group transferase (EC 2.7.*.*)." [] + CHEBI_EXT:EC 2.7.* (P-containing group transferase) inhibitor + EC 2.7.* (P-containing group transferase) inhibitor + CHEBI_EXT:76668 + + + CHEBI_EXT:EC 3.* (hydrolase) inhibitor + CHEBI_EXT:76759 + EC 3.* (hydrolase) inhibitor + "Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*)." [] + + + "An EC 3.4.* (hydrolases acting on peptide bond) inhibitor that interferes with the action of any cysteine endopeptidase (EC 3.4.22.*)." [] + CHEBI_EXT:76796 + CHEBI_EXT:EC 3.4.22.* (cysteine endopeptidase) inhibitor + EC 3.4.22.* (cysteine endopeptidase) inhibitor + + + CHEBI_EXT:77182 + CHEBI_EXT:food colouring + food colouring + "A food additive that imparts colour to food. In European countries, E-numbers for permitted food colours are from E 100 to E 199, divided into yellows (E 100-109), oranges (E 110-119), reds (E 120-129), blues and violets (E 130-139), greens (E 140-149), browns and blacks (E 150-159), and others (E 160-199)." [] + + + CHEBI_EXT:77608 + "A diuretic that acts on the ascending loop of Henle in the kidney." [] + loop diuretic + CHEBI_EXT:loop diuretic + + + CHEBI_EXT:food component + "Any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants." [] + food component + CHEBI_EXT:78295 + + + potassium channel opener + "A potassium channel modulator that opens the potassium channel." [] + CHEBI_EXT:potassium channel opener + CHEBI_EXT:79085 + + + "An EC 2.7.11.* (protein-serine/threonine kinase) inhibitor that interferes with the action of mitogen-activated protein kinase (EC 2.7.11.24)." [] + CHEBI_EXT:EC 2.7.11.24 (mitogen-activated protein kinase) inhibitor + EC 2.7.11.24 (mitogen-activated protein kinase) inhibitor + CHEBI_EXT:79091 + + + CHEBI_EXT:82824 + calpain inhibitor + CHEBI_EXT:calpain inhibitor + "An EC 3.4.22.* (cysteine endopeptidase) inhibitor that interferes with the action of any calpain." [] + + + "Any compound that acts as an agonist towards the liver X receptors." [] + CHEBI_EXT:liver X receptor agonist + CHEBI_EXT:86029 + liver X receptor agonist + + + adenosine diphosphate + ADP + CHEBI_EXT:ADP + CHEBI:ADP or CHEBI:ADP(3-) or CHEBI:dADP or CHEBI:dADP(3-) + CHEBI_EXT:ADP + + + ATP + CHEBI_EXT:ATP + CHEBI:ATP or CHEBI:ATP(3-) or CHEBI:ATP(4-) or CHEBI:dATP or CHEBI:dATP(3-) or CHEBI:dATP(4-) + adenosine triphosphate + CHEBI_EXT:ATP + + + CHEBI_EXT:D-lysine + D-lysine + CHEBI_EXT:D_lysine + CHEBI:'D-lysine' or CHEBI:'D-lysine residue' + + + CHEBI_EXT:EDTA + CHEBI_EXT:EDTA + CHEBI:'ethylenediaminetetraacetic acid' or CHEBI:EDTA(2-) or CHEBI:EDTA(3-) + EDTA + + + CHEBI_EXT:EDTA sodium salt + CHEBI:'EDTA disodium salt (anhydrous)' or CHEBI:'EDTA trisodium salt' + EDTA sodium salt + CHEBI_EXT:EDTA_sodium_salt + + + CHEBI_EXT:EGTA + CHEBI_EXT:EGTA + EGTA + CHEBI:'ethylene glycol bis(2-aminoethyl)tetraacetate' or CHEBI:'ethylene glycol bis(2-aminoethyl)tetraacetic acid' + + + CHEBI:'fura-2 dye' or CHEBI:fura-2(5-) + Fura-2 + CHEBI_EXT:Fura_2 + CHEBI_EXT:Fura-2 + + + GDP + guanosine diphosphate + CHEBI_EXT:GDP + CHEBI:GDP or CHEBI:GDP(2-) or CHEBI:GDP(3-) or CHEBI:dGDP or CHEBI:dGDP(2-) + CHEBI_EXT:GDP + + + CHEBI_EXT:GTP + GTP + CHEBI:GTP or CHEBI:GTP(3-) or CHEBI:GTP(4-) or CHEBI:dGTP or CHEBI:dGTP(3-) or CHEBI:dGTP(4-) + CHEBI_EXT:GTP + guanosine triphosphate + + + CHEBI_EXT:L_glutamine + CHEBI_EXT:L-glutamine + CHEBI:'L-glutamine' or CHEBI:'L-glutamine residue' + L-glutamine + + + CHEBI_EXT:NADH + NADH + CHEBI_EXT:NADH + CHEBI:NADH or CHEBI:NADH(2-) + + + CHEBI_EXT:NADP + CHEBI:NADP or CHEBI:NADP(3-) + NADP + CHEBI_EXT:NADP + + + CHEBI_EXT:NADPH + NADPH + CHEBI_EXT:NADPH + CHEBI:NADPH or CHEBI:NADPH(4-) + + + CHEBI_EXT:NMDA + CHEBI_EXT:NMDA + NMDA + CHEBI:'N-methyl-D-aspartic acid' or is_conjugate_base_of some CHEBI:'N-methyl-D-aspartic acid' + + + CHEBI_EXT:TO_PRO_3 + CHEBI_EXT:TO-PRO-3 + CHEBI:To-Pro-3 or CHEBI:To-Pro-3(2+) + TO-PRO-3 + + + CHEBI_EXT:ToTo + CHEBI_EXT:ToTo + ToTo + CHEBI:'ToTo-1' or CHEBI:'ToTo-1(4+)' or CHEBI:'ToTo-3' or CHEBI:'ToTo-3(4+)' + + + CHEBI_EXT:UTP + uridine triphosphate + CHEBI:UTP or CHEBI:UTP(3-) or CHEBI:UTP(4-) or CHEBI:dUTP or CHEBI:dUTP(3-) or CHEBI:dUTP(4-) + CHEBI_EXT:UTP + UTP + + + poly(acrylic) + CHEBI_EXT:acrylic + CHEBI_EXT:acrylic + polyacrylate + poly(acrylate) + CHEBI:'acrylic macromolecule' or CHEBI:'acrylic polymer' + polyacrylic + acrylic + + + (CHEBI:adenine or CHEBI:'adenin-9-yl group' or CHEBI:adenosine or CHEBI:'2'-deoxyadenosine' or CHEBI:'5'-deoxyadenosine' or CHEBI:'adenosyl group' or CHEBI:'adenosine residue' or CHEBI:'5'-adenylyl group' or CHEBI:AMP or CHEBI:'AMP residue' or CHEBI:'AMP 3'-end residue' or CHEBI:'AMP 5'-end residue' or CHEBI:'dAMP residue' or CHEBI:'dAMP 3'-end residue' or CHEBI:'dAMP 5'-end residue') or +(is_conjugate_acid_of some (CHEBI:adenine or CHEBI:'adenin-9-yl group' or CHEBI:adenosine or CHEBI:'2'-deoxyadenosine' or CHEBI:'5'-deoxyadenosine' or CHEBI:'adenosyl group' or CHEBI:'adenosine residue' or CHEBI:'5'-adenylyl group' or CHEBI:AMP or CHEBI:'AMP residue' or CHEBI:'AMP 3'-end residue' or CHEBI:'AMP 5'-end residue' or CHEBI:'dAMP residue' or CHEBI:'dAMP 3'-end residue' or CHEBI:'dAMP 5'-end residue')) +(is_conjugate_base_of some (CHEBI:adenine or CHEBI:'adenin-9-yl group' or CHEBI:adenosine or CHEBI:'2'-deoxyadenosine' or CHEBI:'5'-deoxyadenosine' or CHEBI:'adenosyl group' or CHEBI:'adenosine residue' or CHEBI:'5'-adenylyl group' or CHEBI:AMP or CHEBI:'AMP residue' or CHEBI:'AMP 3'-end residue' or CHEBI:'AMP 5'-end residue' or CHEBI:'dAMP residue' or CHEBI:'dAMP 3'-end residue' or CHEBI:'dAMP 5'-end residue')) + adenosine + adenyl + For: A, adenine, adenosine + adenine + adenylyl + adenosyl + CHEBI_EXT:adenine_nucleobase_or_nucleoside_or_nucleotide_molecular_entity_or_group + CHEBI_EXT:adenine nucleobase/nucleoside/nucleotide molecular entity or group + adenine nucleobase/nucleoside/nucleotide molecular entity or group + + + CHEBI:alloisoleucine or CHEBI:'alloisoleucine residue' + CHEBI_EXT:alloisoleucine + alloisoleucyl + CHEBI_EXT:alloisoleucine + alloisoleucine + + + aluminum + aluminium + CHEBI_EXT:aluminium + CHEBI_EXT:aluminum + Al + CHEBI:'aluminium atom' or CHEBI:'elemental aluminium' + + + For: anaesthetic/anesthetic (as modifier) + anesthetic + CHEBI_EXT:anaesthetic agent, process or quality + CHEBI_EXT:anaesthetic_agent_or_process_or_quality + anaesthetic + anaesthetic agent, process or quality + CHEBI_EXT:anaesthetic or CHEBI_EXT:anaesthetic_process_or_quality + + + CHEBI_EXT:anaesthetic_process + CHEBI_EXT:anaesthetic process + For: anaesthetisation/anaesthetise/anaesthetised/anaesthetises/anaesthetising/anesthetization/anesthetize/anesthetized/anesthetizes/anesthetizing + anaesthetic process + anesthetization + anaesthetisation + BFO:occurrent and realizes some CHEBI:anaesthetic + + + anaesthetic process or quality + anaesthesia + CHEBI_EXT:anaesthetic process or quality + CHEBI_EXT:anaesthetic_process or (BFO:quality and causally_effected_by some CHEBI_EXT:anaesthetic) + anesthesia + CHEBI_EXT:anaesthetic_process_or_quality + For: anaesthesia/anesthesia + + + CHEBI_EXT:anxiolytic_process_or_quality + CHEBI_EXT:anxiolytic process or quality + (BFO:occurrent and realizes some (BFO:function and inheres_in some CHEBI_EXT:'anxiolytic drug')) or (BFO:quality and causally_effected_by some CHEBI_EXT:'anxiolytic drug') + anxiolytic process or quality + anxiolysis + For: anxiolysis + + + Ar + argon + CHEBI_EXT:argon + CHEBI:'argon atom' or CHEBI:'elemental argon' + CHEBI_EXT:argon + + + CHEBI_EXT:biochemical + CHEBI:'chemical entity' and bearer_of some CHEBI:'biochemical role' + CHEBI_EXT:biochemical + biochemical + + + CHEBI_EXT:cadmium + CHEBI_EXT:cadmium + cadmium + CHEBI:'cadmium atom' or CHEBI:'elemental cadmium' or CHEBI:'cadmium cation' + Cd + + + CHEBI:'calcium atom' or CHEBI:'elemental calcium' + CHEBI_EXT:calcium + Ca + calcium + CHEBI_EXT:calcium + + + CHEBI_EXT:carbon + CHEBI:'carbon atom' or CHEBI:'elemental carbon' + C + CHEBI_EXT:carbon + carbon + + + carboxyl + CHEBI:'carboxy group' or CHEBI:'carboxylato group' + carboxylate + CHEBI_EXT:carboxy_or_carboxylato_group + CHEBI_EXT:carboxy or carboxylato group + For: carboxyl + carboxy or carboxylato group + + + CHEBI_EXT:chemical substance or polyatomic entity + CHEBI_EXT:chemical_substance_or_polyatomic_entity + chemical substance or polyatomic entity + chemical substance + chemical + CHEBI:'chemical substance' or CHEBI:'polyatomic entity' + + + Cl + CHEBI:'chlorine atom' or CHEBI:'elemental chlorine' + CHEBI_EXT:chlorine + CHEBI_EXT:chlorine + chlorine + + + CHEBI_EXT:citrate + CHEBI_EXT:citrate + CHEBI:citrate(1-) or CHEBI:citrate(2-) or CHEBI:citrate(3-) or CHEBI:'citrate salt' + citrate + + + CHEBI_EXT:cobalt + cobalt + Co + CHEBI:'cobalt atom' or CHEBI:'cobalt cation' + CHEBI_EXT:cobalt + + + CHEBI_EXT:copper + Cu + copper + CHEBI:'copper atom' or CHEBI:'elemental copper' + CHEBI_EXT:copper + + + epoxy + CHEBI:'cyclic ether' or CHEBI:'epoxy group' + CHEBI_EXT:cyclic_ether_or_epoxy_group + CHEBI_EXT:cyclic ether or epoxy group + cyclic ether or epoxy group + + + cytidine + cytosine nucleobase/nucleoside/nucleotide molecular entity or group + CHEBI_EXT:cytosine_nucleobase_or_nucleoside_or_nucleotide_molecular_entity_or_group + (CHEBI:cytosine or CHEBI:'cytosin1-yl group' or CHEBI:cytidine or CHEBI:'2'-deoxycytidine' or CHEBI:'cytidyl group' or CHEBI:'cytidine residue' or CHEBI:'5'-cytidylyl group' or CHEBI:CMP or CHEBI:'CMP residue' or CHEBI:'CMP 3'-end residue' or CHEBI:'CMP 5'-end residue' or CHEBI:'dCMP residue' or CHEBI:'dCMP 3'-end residue' or CHEBI:'dCMP 5'-end residue') or +(is_conjugate_acid_of some (CHEBI:cytosine or CHEBI:'cytosin1-yl group' or CHEBI:cytidine or CHEBI:'2'-deoxycytidine' or CHEBI:'cytidyl group' or CHEBI:'cytidine residue' or CHEBI:'5'-cytidylyl group' or CHEBI:CMP or CHEBI:'CMP residue' or CHEBI:'CMP 3'-end residue' or CHEBI:'CMP 5'-end residue' or CHEBI:'dCMP residue' or CHEBI:'dCMP 3'-end residue' or CHEBI:'dCMP 5'-end residue')) or +(is_conjugate_base_of some (CHEBI:cytosine or CHEBI:'cytosin1-yl group' or CHEBI:cytidine or CHEBI:'2'-deoxycytidine' or CHEBI:'cytidyl group' or CHEBI:'cytidine residue' or CHEBI:'5'-cytidylyl group' or CHEBI:CMP or CHEBI:'CMP residue' or CHEBI:'CMP 3'-end residue' or CHEBI:'CMP 5'-end residue' or CHEBI:'dCMP residue' or CHEBI:'dCMP 3'-end residue' or CHEBI:'dCMP 5'-end residue')) + cytosyl + cytosine + CHEBI_EXT:cytosine nucleobase/nucleoside/nucleotide molecular entity or group + cytidyl + For: C, cytosine, cytidine + + + deoxyadenosine triphosphate + dATP + CHEBI_EXT:dATP + CHEBI:dATP or CHEBI:dATP(3-) or CHEBI:dATP(4-) + CHEBI_EXT:dATP + + + deoxycytidine triphosphate + CHEBI_EXT:dCTP + CHEBI:dCTP or CHEBI:dCTP(3-) or CHEBI:dCTP(4-) + CHEBI_EXT:dCTP + dCTP + + + CHEBI_EXT:dGTP + dGTP + deoxyguanosine triphosphate + CHEBI:dGTP or CHEBI:dGTP(3-) or CHEBI:dGTP(4-) + CHEBI_EXT:dGTP + + + deoxyribonucleoside triphosphate + CHEBI_EXT:dNTP + dNTP + CHEBI_EXT:dNTP + (CHEBI:deoxyribonucleotide and has_proper_part some (CHEBI:'triphosphate group' or CHEBI:'triphosphate group(4-)')) or +CHEBI:'2'-deoxyribonucleoside 5'-triphosphate' or CHEBI:'2'-deoxyribonucleoside 5'-triphosphate(4-)' + + + CHEBI:dUTP or CHEBI:dUTP(3-) or CHEBI:dUTP(4-) + dUTP + CHEBI_EXT:dUTP + CHEBI_EXT:dUTP + deoxyuridine triphosphate + + + CHEBI_EXT:deoxyadenosine nucleoside or nucleotide residue + For: dA, deoxyadenosine + (CHEBI:'2'-deoxyadenosine' or CHEBI:'5'-deoxyadenosine' or CHEBI:'dAMP residue' or CHEBI:'dAMP 3'-end residue' or CHEBI:'dAMP 5'-end residue') or +(is_conjugate_acid_of some (CHEBI:'2'-deoxyadenosine' or CHEBI:'5'-deoxyadenosine' or CHEBI:'dAMP residue' or CHEBI:'dAMP 3'-end residue' or CHEBI:'dAMP 5'-end residue')) +(is_conjugate_base_of some (CHEBI:'2'-deoxyadenosine' or CHEBI:'5'-deoxyadenosine' or CHEBI:'dAMP residue' or CHEBI:'dAMP 3'-end residue' or CHEBI:'dAMP 5'-end residue')) + CHEBI_EXT:deoxyadenosine_nucleoside_or_nucleotide_residue + deoxyadenosine nucleoside or nucleotide residue + deoxyadenosine + dA + + + CHEBI_EXT:deoxycholate/deoxycholic acid + deoxycholate/deoxycholic acid + DOC + CHEBI_EXT:deoxycholate_or_deoxycholic_acid + CHEBI:deoxycholate or CHEBI:'deoxycholic acid' + + + deoxycytidine nucleoside or nucleotide residue + dC + (CHEBI:'2'-deoxycytidine' or CHEBI:'dCMP residue' or CHEBI:'dCMP 3'-end residue' or CHEBI:'dCMP 5'-end residue') or +(is_conjugate_acid_of some (CHEBI:'2'-deoxycytidine' or CHEBI:'dCMP residue' or CHEBI:'dCMP 3'-end residue' or CHEBI:'dCMP 5'-end residue')) or +(is_conjugate_base_of some (CHEBI:'2'-deoxycytidine' or CHEBI:'dCMP residue' or CHEBI:'dCMP 3'-end residue' or CHEBI:'dCMP 5'-end residue')) + CHEBI_EXT:deoxycytidine nucleoside or nucleotide residue + deoxycytidine + CHEBI_EXT:deoxycytidine_nucleoside_or_nucleotide_residue + + + CHEBI_EXT:deoxyguanosine_nucleoside_or_nucleotide_residue + CHEBI_EXT:deoxyguanosine nucleoside or nucleotide residue + deoxyguanosine nucleoside or nucleotide residue + For: dG, deoxyguanosine + dG + deoxyguanosine + (CHEBI:'2'-deoxyguanosine' or CHEBI:'3'-deoxyguanosine' or CHEBI:'guanyl deoxyribonucleotide residue') or +(is_conjugate_acid_of some (CHEBI:guanosine or CHEBI:'2'-deoxyguanosine' or CHEBI:'3'-deoxyguanosine' or CHEBI:'guanyl deoxyribonucleotide residue')) or +(is_conjugate_base_of some (CHEBI:guanosine or CHEBI:'2'-deoxyguanosine' or CHEBI:'3'-deoxyguanosine' or CHEBI:'guanyl deoxyribonucleotide residue')) + + + CHEBI_EXT:diuretic_agent_or_process + CHEBI_EXT:diuretic or (BFO:occurrent and realizes some (BFO:function and inheres_in some CHEBI_EXT:diuretic)) + CHEBI_EXT:diuretic agent or process + diuretic agent or process + diuretic + For: diuretic (as modifier) + + + CHEBI:'eosin b' or CHEBI:'eosin b(2-)' or CHEBI:'eosin YS dye' + eosin + CHEBI_EXT:eosin + CHEBI_EXT:eosin + + + CHEBI_EXT:gadolinium + Gd + CHEBI:'gadolinium atom' or CHEBI:'elemental gadolinium' + CHEBI_EXT:gadolinium + gadolinium + + + CHEBI_EXT:glutamate + CHEBI_EXT:glutamate + CHEBI:glutamate(1-) or CHEBI:glutamate(2-) or CHEBI:'glutamate residue' + glutamate + + + CHEBI:'glycerol 1-phosphate' or CHEBI:'glycerol 1-phosphate(2-)' + glycerol 1-phosphate + CHEBI_EXT:glycerol 1-phosphate + CHEBI_EXT:glycerol_1_phosphate + + + CHEBI_EXT:gold + CHEBI:'gold atom' or CHEBI:'elemental gold' + CHEBI_EXT:gold + gold + Au + + + guanosine + guanylyl + guanosyl + guanine nucleobase/nucleoside/nucleotide molecular entity or group + CHEBI_EXT:guanine nucleobase/nucleoside/nucleotide molecular entity or group + guanine + For: G, guanine, guanosine + (CHEBI:guanine or CHEBI:'guanin-9-yl group' or CHEBI:guanosine or CHEBI:'2'-deoxyguanosine' or CHEBI:'3'-deoxyguanosine' or CHEBI:'guanosyl group' or CHEBI:'guanosine residue' or CHEBI:'5'-guanylyl group' or CHEBI:'GMP residue' or CHEBI:'GMP 3'-end residue' or CHEBI:'GMP 5'-end residue' or CHEBI:'guanyl deoxyribonucleotide residue') or +(is_conjugate_acid_of some (CHEBI:guanine or CHEBI:'guanin-9-yl group' or CHEBI:guanosine or CHEBI:'2'-deoxyguanosine' or CHEBI:'3'-deoxyguanosine' or CHEBI:'guanosyl group' or CHEBI:'guanosine residue' or CHEBI:'5'-guanylyl group' or CHEBI:'GMP residue' or CHEBI:'GMP 3'-end residue' or CHEBI:'GMP 5'-end residue' or CHEBI:'guanyl deoxyribonucleotide residue')) or +(is_conjugate_base_of some (CHEBI:guanine or CHEBI:'guanin-9-yl group' or CHEBI:guanosine or CHEBI:'2'-deoxyguanosine' or CHEBI:'3'-deoxyguanosine' or CHEBI:'guanosyl group' or CHEBI:'guanosine residue' or CHEBI:'5'-guanylyl group' or CHEBI:'GMP residue' or CHEBI:'GMP 3'-end residue' or CHEBI:'GMP 5'-end residue' or CHEBI:'guanyl deoxyribonucleotide residue')) + CHEBI_EXT:guanine_nucleobase_or_nucleoside_or_nucleotide_molecular_entity_or_group + guanyl + + + CHEBI_EXT:homopolymer + CHEBI:homopolymer or CHEBI:'homopolymer macromolecule' + homopolymer + CHEBI_EXT:homopolymer + + + H + hydrogen + CHEBI_EXT:hydrogen + CHEBI:'hydrogen atom' or CHEBI:'elemental hydrogen' + CHEBI_EXT:hydrogen + + + CHEBI_EXT:iridium + Ir + CHEBI_EXT:iridium + CHEBI:'iridium atom' or CHEBI:iridium(3+) + iridium + + + CHEBI_EXT:iron + Fe + CHEBI:'iron atom' or CHEBI:'elemental iron' + iron + CHEBI_EXT:iron + + + krypton + CHEBI_EXT:krypton + CHEBI:'krypton atom' or CHEBI:'elemental krypton' + Kr + CHEBI_EXT:krypton + + + lead + Pb + CHEBI_EXT:lead + CHEBI:'lead atom' or CHEBI:'elemental lead' + CHEBI_EXT:lead + + + Li + CHEBI_EXT:lithium + CHEBI_EXT:lithium + lithium + CHEBI:'lithium atom' or CHEBI:lithide or CHEBI:lithium(1+) + + + magnesium + CHEBI:'magnesium atom' or CHEBI:'elemental magnesium' + Mg + CHEBI_EXT:magnesium + CHEBI_EXT:magnesium + + + CHEBI:maleate(1-) or CHEBI:maleate(2-) or CHEBI:'maleate salt' + maleate + CHEBI_EXT:maleate + CHEBI_EXT:maleate + + + CHEBI_EXT:manganese + CHEBI_EXT:manganese + CHEBI:'manganese atom' or CHEBI:'elemental manganese' + manganese + Mn + + + Hg + CHEBI_EXT:mercury + mercury + CHEBI:'mercury atom' or CHEBI:'elemental mercury' + CHEBI_EXT:mercury + + + CHEBI_EXT:metal + CHEBI:'metal atom' or CHEBI:'metal cation' + CHEBI_EXT:metal + metal + + + Ni + CHEBI_EXT:nickel + nickel + CHEBI_EXT:nickel + CHEBI:'nickel atom' or CHEBI:'nickel ion' + + + N + CHEBI_EXT:nitrogen + CHEBI_EXT:nitrogen + nitrogen + CHEBI:'nitrogen atom' or CHEBI:'elemental nitrogen' + + + CHEBI_EXT:nucleoprotein + CHEBI:'molecular entity' and (has_proper_part some CHEBI:'nucleic acid') and (has_proper_part some CHEBI:protein) + CHEBI_EXT:nucleoprotein + nucleoprotein + + + NTP + nucleoside triphosphate + CHEBI_EXT:nucleotide_triphosphate + (CHEBI:nucleotide and has_proper_part some (CHEBI:'triphosphate group' or CHEBI:'triphosphate group(4-)')) or +CHEBI:'2'-deoxyribonucleoside 5'-triphosphate' or CHEBI:'ribonucleoside 5'-triphosphate' + CHEBI_EXT:NTP + + + CHEBI_EXT:ornithine + Orn + CHEBI_EXT:ornithine + CHEBI:ornithine or CHEBI:'ornithine residue' + ornithine + + + O + CHEBI_EXT:oxygen + oxygen + CHEBI_EXT:oxygen + CHEBI:'oxygen atom' or CHEBI:'elemental oxygen' + + + CHEBI_EXT:palladium + CHEBI:palladium or CHEBI:'elemental palladium' + Pd + palladium + CHEBI_EXT:palladium + + + paraformaldehyde + CHEBI_EXT:paraformaldehye + CHEBI:'paraformaldehyde macromolecule' or CHEBI:'paraformaldehyde polymer' + CHEBI_EXT:paraformaldehyde + + + CHEBI_EXT:phosphate + CHEBI_EXT:phosphate + CHEBI:phosphate or CHEBI:'phosphate ion' + phosphate + + + CHEBI_EXT:phosphatidylcholine + CHEBI:phosphatidylcholine or CHEBI:phosphatidylcholine(1+) + CHEBI_EXT:phosphatidylcholine + phosphatidylcholine + + + CHEBI_EXT:phosphohistone + CHEBI:histone and has_proper_part some (CHEBI:'phosphate group' or CHEBI:'phosphate group(2-)') + phosphohistone + CHEBI_EXT:phosphohistone + + + phosphoprotein + CHEBI_EXT:phosphoprotein + CHEBI:protein and has_proper_part some (CHEBI:'phosphate group' or CHEBI:'phosphate group(2-)') + CHEBI_EXT:phosphoprotein + + + CHEBI_EXT:phosphotyrosine + CHEBI_EXT:phosphotyrosine + O(4)-phosphotyrosine + phosphotyrosine + CHEBI:'O(4)-phosphotyrosine' or CHEBI:'O(4)-phosphonatotyrosine(2-)' or (CHEBI:'amino-acid residue' and is_substituent_group_from some CHEBI:'O(4)-phosphotyrosine' or CHEBI:'O(4)-phosphonatotyrosine(2-)') + O-phosphotyrosine + + + Pt + CHEBI_EXT:platinum + platinum + CHEBI_EXT:platinum + CHEBI:platinum or CHEBI:'elemental platinum' or CHEBI:'platinum cation' + + + polyC + CHEBI_EXT:poly(C acid) + CHEBI_EXT:polyC_acid + pC + poly(C) + poly(C acid) + CHEBI:'poly(cytidylic acid)' or CHEBI:'poly(deoxycytidylic acid)' + + + CHEBI:'poly(methyl methacrylate) macromolecule' or CHEBI:'poly(methyl methacrylate) polymer' + CHEBI_EXT:poly(methyl methacrylate) + poly(methyl methacrylate) + polymethymethacrylate + CHEBI_EXT:poly_methyl_methacrylate + Plexiglas + Plexiglass + + + poly(vinyl alcohol) + CHEBI_EXT:poly(vinyl alcohol) + Gelvatol + CHEBI:'poly(vinyl alcohol) macromolecule' or CHEBI:'poly(vinyl alcohol) polymer + CHEBI_EXT:poly_vinyl_alcohol + + + CHEBI:'polyacrylamide macromolecule' or CHEBI:'polyacrylamide polymer' + CHEBI_EXT:polyacrylamide + polyacrylamide + CHEBI_EXT:polyacrylamide + + + molecular + CHEBI:group or CHEBI:'polyatomic entity' + polyatomic entity or group + CHEBI_EXT:polyatomic entity or group + CHEBI_EXT:polyatomic_entity_or_group + + + CHEBI_EXT:polycarbonate + polycarbonate + CHEBI_EXT:polycarbonate + CHEBI:'polycarbonate macromolecule' or CHEBI:'polycarbonate polymer' + + + polyester + CHEBI_EXT:polyester + CHEBI:'polyester macromolecule' or CHEBI:'polyester polymer' + CHEBI_EXT:polyester + + + CHEBI:'polystyrene macromolecule' or CHEBI:'polystyrene polymer' + polystyrene + CHEBI_EXT:polystyrene + CHEBI_EXT:polystyrene + + + K + CHEBI:'potassium atom' or CHEBI:'elemental potassium' or CHEBI:potassium(1+) + potassium + CHEBI_EXT:potassium + CHEBI_EXT:potassium + + + potassium phosphate + CHEBI_EXT:potassium_phosphate + CHEBI_EXT:potassium phosphate + CHEBI:'potassium dibasic phosphate' or CHEBI:'potassium dihydrogen phosphate' + + + CHEBI:purine or is_substituent_group_from some CHEBI:purine + CHEBI_EXT:purine + purine + CHEBI_EXT:purine + + + CHEBI:pyrimidine or is_substituent_group_from some CHEBI:pyrimidine + pyrimidine + CHEBI_EXT:pyrimidine + CHEBI_EXT:pyrimidine + + + radiolabel process + CHEBI_EXT:radiolabel_process + For: radiolabel(v.)/radiolabeled/radiolabelled/radiolabeling/radiolabelling/radiolabels + BFO:occurrent and realizes some (BFO:function and inheres_in some CHEBI:'radioactive label') + CHEBI_EXT:radiolabel process + radiolabel + + + CHEBI_EXT:residue + residue + CHEBI:'amino-acid residue' or CHEBI:'nucleotide residue' + CHEBI_EXT:residue + + + CHEBI_EXT:ribonucleoprotein + CHEBI:'molecular entity' and (has_proper_part some (CHEBI:'ribonucleic acid' or SO_EXT:'ribonucleic acid')) and (has_proper_part some CHEBI:protein) + ribonucleoprotein + RNP + CHEBI_EXT:ribonucleoprotein + + + (CHEBI:ribonucleotide and has_proper_part some (CHEBI:'triphosphate group' or CHEBI:'triphosphate group(4-)')) or CHEBI:'ribonucleoside 5'-triphosphate' + CHEBI_EXT:rNTP + CHEBI_EXT:ribonucleoside_triphosphate + rNTP + + + CHEBI_EXT:saline sodium citrate + SSC + CHEBI:solution and (has_proper_part some CHEBI:salt) and (has_proper_part some CHEBI:'sodium citrate') + saline sodium citrate + CHEBI_EXT:saline_sodium_citrate + + + saline + saline solution + salt solution + CHEBI_EXT:saline_solution + CHEBI_EXT:saline solution + CHEBI:solution and has_proper_part some CHEBI:salt + + + For: sedative (as modifier) + sedative + CHEBI_EXT:sedative_agent_or_process_or_quality + CHEBI_EXT:sedative or CHEBI_EXT:sedative_process_or_quality + CHEBI_EXT:sedative agent, process or quality + sedative agent, process or quality + + + For: sedation + sedative process or quality + CHEBI_EXT:sedative_process or (BFO:quality and causally_effected_by some CHEBI_EXT:sedative) + CHEBI_EXT:sedative_process_or_quality + sedation + CHEBI_EXT:sedative process or quality + + + selenoprotein + CHEBI_EXT:selenoprotein + CHEBI:protein and has_proper_part some CHEBI:'selenocysteine residue' + CHEBI_EXT:selenoprotein + + + CHEBI_EXT:silver + silver + CHEBI_EXT:silver + CHEBI:'silver atom' or CHEBI:'silver ion' or CHEBI:'elemental silver' + Ag + + + succinate + CHEBI_EXT:succinate + CHEBI_EXT:succinate + CHEBI:succinate(1-) or CHEBI:succinate(2-) or CHEBI:'succinate salt' + + + sulfur + S + CHEBI_EXT:sulfur + CHEBI:'sulfur atom' or CHEBI:'elemental sulfur' + CHEBI_EXT:sulfur + + + CHEBI_EXT:tartrate + CHEBI:tartrate(1-) or CHEBI:tartrate(2-) or CHEBI:tartrate + tartrate + CHEBI_EXT:tartrate + + + thioglycolate + thioglycollate + CHEBI:thioglycolate(1-) or CHEBI:thioglycolate(2-) + CHEBI_EXT:thioglycolate + mercaptoacetate + CHEBI_EXT:thioglycolate + + + thymidine + thymine nucleobase/nucleoside/nucleotide molecular entity or group + (CHEBI:thymine or CHEBI:'thymin-1-yl group' or CHEBI:thymidine or CHEBI:'thymidyl group' or CHEBI:'5'-thymidylyl group' or CHEBI:'dTMP residue' or CHEBI:'dTMP 3'-end residue' or CHEBI:'dTMP 5'-end residue') or +(is_conjugate_acid_of some (CHEBI:thymine or CHEBI:'thymin-1-yl group' or CHEBI:thymidine or CHEBI:'thymidyl group' or CHEBI:'5'-thymidylyl group' or CHEBI:'dTMP residue' or CHEBI:'dTMP 3'-end residue' or CHEBI:'dTMP 5'-end residue')) or +(is_conjugate_base_of some (CHEBI:thymine or CHEBI:'thymin-1-yl group' or CHEBI:thymidine or CHEBI:'thymidyl group' or CHEBI:'5'-thymidylyl group' or CHEBI:'dTMP residue' or CHEBI:'dTMP 3'-end residue' or CHEBI:'dTMP 5'-end residue')) + thymine + thymidyl + For: T, dT, thymine, thymidine + CHEBI_EXT:thymine nucleobase/nucleoside/nucleotide molecular entity or group + thyminyl + CHEBI_EXT:thymine_nucleobase_or_nucleoside_or_nucleotide_molecular_entity_or_group + + + TNBS + CHEBI_EXT:trinitrobenzenesulfonic_acid + trinitrobenzenesulfonic acid + trinitrobenzene sulfonic acid + CHEBI_EXT:trinitrobenzenesulfonic acid + CHEBI:'2,4,5-trinitrobenzenesulfonic acid' or CHEBI:'2,4,6-trinitrobenzenesulfonic acid' + + + W + CHEBI_EXT:tungsten + CHEBI_EXT:tungsten + tungsten + CHEBI:'tungsten atom' or CHEBI:'tungsten cation' + + + For: U, uracil, uridine + uracil + uracil nucleobase/nucleoside/nucleotide molecular entity or group + CHEBI_EXT:uracil nucleobase/nucleoside/nucleotide molecular entity or group + (CHEBI:uracil or CHEBI:'uracil-1-yl group' or CHEBI:uridine or CHEBI:'uridyl group' or CHEBI:'uridine residue' or CHEBI:'5'-uridylyl group' or CHEBI:'UMP residue' or CHEBI:'UMP 3'-end residue' or CHEBI:'UMP 5'-end residue' or CHEBI:'dUMP residue' or CHEBI:'dUMP 3'-end residue' or CHEBI:dUMP 5'-end residue) or +(is_conjugate_acid_of some (CHEBI:uracil or CHEBI:'uracil-1-yl group' or CHEBI:uridine or CHEBI:'uridyl group' or CHEBI:'uridine residue' or CHEBI:'5'-uridylyl group' or CHEBI:'UMP residue' or CHEBI:'UMP 3'-end residue' or CHEBI:'UMP 5'-end residue' or CHEBI:'dUMP residue' or CHEBI:'dUMP 3'-end residue' or CHEBI:dUMP 5'-end residue)) or +(is_conjugate_base_of some (CHEBI:uracil or CHEBI:'uracil-1-yl group' or CHEBI:uridine or CHEBI:'uridyl group' or CHEBI:'uridine residue' or CHEBI:'5'-uridylyl group' or CHEBI:'UMP residue' or CHEBI:'UMP 3'-end residue' or CHEBI:'UMP 5'-end residue' or CHEBI:'dUMP residue' or CHEBI:'dUMP 3'-end residue' or CHEBI:dUMP 5'-end residue)) + uridine + uridyl + CHEBI_EXT:uracil_nucleobase_or_nucleoside_or_nucleotide_molecular_entity_or_group + uridylyl + + + polyvinyl + vinyl polymer + CHEBI_EXT:vinyl polymer + CHEBI:'vinyl polymer' or CHEBI:'vinyl polymer macromolecule' + CHEBI_EXT:vinyl_polymer + + + CHEBI:'zinc atom' or CHEBI:'elemental zinc' + Zn + CHEBI_EXT:zinc + zinc + CHEBI_EXT:zinc + + + CHEBI_GO_EXT:agonist + CHEBI_EXT:agonist or GO_EXT:'bearer of receptor agonist activity' or (has_prototype o positively_regulates some (BFO:occurrent or BFO:dependent_continuant)) + CHEBI_GO_EXT:agonist + agonist + + + CHEBI_GO_EXT:antagonist + antagonist + CHEBI_GO_EXT:antagonist + CHEBI_EXT:antagonist or GO_EXT:'bearer of receptor antagonist activity' or (has_prototype o negatively_regulates some (BFO:occurrent or BFO:dependent_continuant)) + + + CHEBI_EXT:antioxidant or GO_EXT:'bearer of antioxidant activity' + CHEBI_GO_EXT:antioxidant + antioxidant + CHEBI_GO_EXT:antioxidant + + + CHEBI_GO_EXT:biological process, quality or role + biological process, quality or role + CHEBI:'biological role' or GO:biological_process or (BFO:dependent_continuant and regulated_by some GO:'regulation of biological quality') + CHEBI_GO_EXT:biological_process_or_quality_or_role + biologically + biology + For: biological/biologically/biology + biological + + + inhibitor of cyclin-dependent protein kinase + inhibitor of CDK + CDK inhibitor + CHEBI_EXT:'EC 2.7.11.22 (cyclin-dependent kinase) inhibitor' or GO_EXT:'bearer of cyclin-dependent protein serine/threonine kinase inhibitor activity' + cyclin-dependent protein kinase inhibitor + CHEBI_GO_EXT:cyclin_dependent_kinase_inhibitor + CHEBI_GO_EXT:cyclin-dependent kinase inhibitor + cyclin-dependent kinase inhibitor + inhibitor of cyclin-dependent kinase + + + CHEBI_EXT:'enzyme inhibitor' or GO_EXT:'bearer of enzyme inhibitor activity' + enzyme inhibitor + CHEBI_GO_EXT:enzyme inhibitor + CHEBI_GO_EXT:enzyme_inhibitor + inhibitor of enzyme + For: enzyme inhibitor(s), inhibitor(s) of enzyme(s) + + + haemoglobin + hemoglobin + CHEBI_GO_EXT:hemoglobin + CHEBI:hemoglobin or GO:'hemoglobin complex' + CHEBI_GO_EXT:hemoglobin + + + For: high-density lipoprotein particle(s), high-density lipoprotein(s), HDL(s), HDL lipoprotein(s) + high-density lipoprotein particle + CHEBI_GO_EXT:high_density_lipoprotein_particle + HDL lipoprotein + HDL particle + CHEBI_GO_EXT:high-density lipoprotein particle + high-density lipoprotein + CHEBI:'high-density lipoprotein' or GO:'high-density lipoprotein particle' + HDL + + + For: HDAC inhibitor(s), histone deacetylase inhibitor(s), inhibitor(s) of HDAC(s), inhibitor(s) of histone deacetylase(s) + CHEBI_GO_EXT:histone_deacetylase_inhibitor + HDAC inhibitor + CHEBI_GO_EXT:histone deacetylase inhibitor + CHEBI_EXT:'EC 3.5.1.98 (histone deacetylase) inhibitor' or GO_EXT:'bearer of histone deacetylase inhibitor activity' + inhibitor of HDAC + inhibitor of histone deacetylase + histone deacetylase inhibitor + + + CHEBI_GO_EXT:hormone + hormone + CHEBI_EXT:hormone or GO_EXT:'bearer of hormone activity' + For: hormonal/hormonally/hormone/hormones + CHEBI_GO_EXT:hormone + + + CHEBI_EXT:ligand or CHEBI:'chemical entity' and has_prototype o participates_in some GO:binding) + CHEBI_GO_EXT:ligand + CHEBI_GO_EXT:ligand + ligand + + + CHEBI_GO_EXT:ligase_inhibitor + CHEBI_EXT:'EC 6.* (ligase) inhibitor' GO_EXT:'bearer of ligase inhibitor activity' + inhibitor of ligase + inhibitor of synthetase + synthetase inhibitor + CHEBI_GO_EXT:ligase inhibitor + For: inhibitor(s) of ligase(s), ligase inhibitor(s) + ligase inhibitor + + + CHEBI:lipoprotein or GO:'lipoprotein particle' + CHEBI_GO_EXT:lipoprotein_particle + CHEBI_GO_EXT:lipoprotein particle + lipoprotein particle + For: lipoprotein(s) + lipoprotein + + + LDL + LDL particle + CHEBI_GO_EXT:low-density lipoprotein particle + CHEBI_GO_EXT:low_density_lipoprotein_particle + LDL lipoprotein + CHEBI:'low-density lipoprotein' or GO:'low-density lipoprotein particle' + low-density lipoprotein particle + low-density lipoprotein + For: low-density lipoprotein(s), low-density lipoprotein particle(s), LDL(s), LDL lipoprotein(s) + + + CHEBI_GO_EXT:neomycin_or_neomycin_phosphotransferase + For: neo + CHEBI_GO_EXT:neomycin or neomycin phosphotransferase + neo + neomycin or neomycin phosphotransferase + CHEBI:neomycin or (CHEBI:'chemical entity' and bearer_of some GO_EXT:'bearer of kanamycin kinase activity') + + + For: peptidase inhibitor(s), protease inhibitor(s), proteinase inhibitor(s) + peptidase/protease/proteinase inhibitor + protease inhibitor + inhibitor of peptidase + CHEBI_GO_EXT:peptidase/protease/proteinase inhibitor + proteinase inhibitor + CHEBI_EXT:'EC 3.4.* (hydrolases acting on peptide bond) inhibitor' or GO_EXT:'bearer of peptidase inhibitor activity' + inhibitor of protease + peptidase inhibitor + CHEBI_GO_EXT:peptidase_or_protease_or_proteinase_inhibitor + inhibitor of proteinase + + + CHEBI_GO_EXT:phosphoprotein phosphatase inhibitor + phosphoprotein phosphatase inhibitor + CHEBI_EXT:'EC 3.1.3.16 (phosphoprotein phosphatase) inhibitor' or GO_EXT:'bearer of phosphoprotein phosphatase inhibitor activity' + inhibitor of phosphoprotein phosphohydrolase + phosphoprotein phosphohydrolase inhibitor + inhibitor of protein phosphatase + CHEBI_GO_EXT:phosphoprotein_phosphatase_inhibitor + protein phosphatase inhibitor + inhibitor of phosphoprotein phosphatase + + + radioligand + CHEBI:'chemical entity' and (has_prototype o participates_in some GO:binding) and (has_proper_part some CHEBI_EXT:'radioactive label') + CHEBI_GO_EXT:radioligand + CHEBI_GO_EXT:radioligand + + + CHEBI_GO_EXT:very_low_density_lipoprotein_particle + VLDL lipoprotein + CHEBI_GO_EXT:very-low-density lipoprotein particle + For: very-low-density lipoprotein(s), very-low-density lipoprotein particle(s), VLDL(s), VLDL lipoprotein(s) + VLDL + very-low-density lipoprotein + CHEBI:'very-low-density lipoprotein' or GO:'very-low-density lipoprotein particle' + very-low-density lipoprotein particle + VLDL particle + + + For: growth hormone(s), GH(s) + growth hormone + CHEBI_GO_PR_EXT:growth hormone + CHEBI_EXT:'growth hormone' or GO_EXT:'bearer of growth hormone activity' or PR_EXT:somatotropin + Gh + CHEBI_GO_PR_EXT:growth_hormone + + + CHEBI_GO_SO_EXT:enzyme + For: enzymatic/enzymatically/enzyme/enzymes + CHEBI_GO_SO_EXT:enzyme + (CHEBI_EXT:catalyst and bearer_of some CHEBI:'biological role') or GO_EXT:'bearer of catalytic activity' or bearer_of some SO:enzymatic + enzyme + + + CHEBI_MOP_EXT:oxidising_agent_or_oxidation + oxidant + CHEBI_EXT:'oxidising agent' or MOP:oxidation + For: oxidant (as modifier) + CHEBI_MOP_EXT:oxidation or oxidizing agent + oxidation or oxidizing agent + + + GBP28 + adipocyte, C1q and collagen domain-containing protein + CHEBI:Adiponectin or PR_EXT:adiponectin + ACRP30 + adipocyte complement-related 30 kDa protein + APM1 + adiponectin + CHEBI_PR_EXT:adiponectin + 30 kDa adipocyte complement-related protein + adipocyte-specific protein AdipoQ + CHEBI_PR_EXT:adiponectin + AdipoQ + ACDC + gelatin-binding protein + apM-1 + adipose most abundant gene transcript 1 protein + + + amyloid beta protein + beta amyloid + CHEBI_PR_EXT:amyloid_beta + beta-amyloid + beta-amyloid protein + Abeta + CHEBI:'beta-amyloid' or PR_EXT:'amyloid beta peptide' + beta-APP + amyloid beta + CHEBI_PR_EXT:amyloid beta + amyloid beta peptide + + + beta-APP40 + beta-amyloid peptide 40 + CHEBI_PR_EXT:amyloid_beta_40 + Abeta40 + beta-amyloid 40 + CHEBI:'beta-amyloid polypeptide 40' or PR_EXT:'beta-amyloid protein 40' + beta-amyloid protein 40 + CHEBI_PR_EXT:amyloid beta 40 + amyloid beta 40 + Abeta(1-40) + APP-40 + + + Abeta(1-42) + CHEBI:'beta-amyloid polypeptide 42' or PR_EXT:'beta-amyloid protein 42' + APP-42 + beta-amyloid protein 42 + amyloid beta 42 + CHEBI_PR_EXT:amyloid beta 42 + beta-amyloid peptide 42 + Abeta42 + beta-amyloid 42 + beta-APP42 + CHEBI_PR_EXT:amyloid_beta_42 + + + angiotensin + CHEBI:angiotensin or PR_EXT:'angiotensinogen proteolytic cleavage product' + CHEBI_PR_EXT:angiotensin + CHEBI_PR_EXT:angiotensin + + + [Arg8]-vasopressin + AVP-NPII + CHEBI_PR_EXT:arginine vasopressin + argipressin + 8-arginine-vasopressin + CHEBI:argipressin or PR_EXT:'vasopressin-neurophysin 2-copeptin' + AVP + 8-L-arginine vasopressin + CHEBI_PR_EXT:arginine_vasopressin + arginine vasopressin + + + calcitonin gene-related polypeptide + calcitonin-related polypeptide + CHEBI_PR_EXT:calcitonin_gene_related_peptide + calcitonin gene-related peptide + CHEBI_PR_EXT:calcitonin gene-related peptide + calcitonin-related peptide + CHEBI:'calcitonin gene-related peptide 1' or CHEBI:'calcitonin gene-related peptide 2' or PR_EXT:'calcitonin gene-related peptide 1' or PR_EXT:'calcitonin gene-related peptide 2' + CGRP + + + CHEBI:Collagen or PR_EXT:'collagen alpha chain' + CHEBI_PR_EXT:collagen + CHEBI_PR_EXT:collagen + collagen + + + F10 + CHEBI_PR_EXT:Factor X + FX + CHEBI_PR_EXT:factor_X + Stuart factor + Stuart-Prower factor + Factor X + coagulation factor X + CHEBI:'Factor X' or PR_EXT:'coagulation factor X' + + + CHEBI_PR_EXT:gastrin + gastrin + CHEBI_PR_EXT:gastrin + CHEBI:gastrin or PR_EXT:gastrin + GAST + GAS + + + glucagon + GCG + CHEBI_PR_EXT:glucagon + CHEBI:glucagon or PR_EXT:glucagon + CHEBI_PR_EXT:glucagon + + + IGF-I + CHEBI_PR_EXT:insulin_like_growth_factor_1 + somatomedin C + IGF1 + insulin-like growth factor 1 + IGF-1 + CHEBI_PR_EXT:insulin-like growth factor 1 + insulin-like growth factor I + CHEBI:'Insulin-like growth factor I' or PR_EXT:'insulin-like growth factor I' + + + somatomedin A + CHEBI_PR_EXT:insulin_like_growth_factor_2 + IGF2 + IGF-II + insulin-like growth factor 2 + CHEBI_PR_EXT:insulin-like growth factor 2 + CHEBI:'Insulin-like growth factor II' or PR_EXT:'insulin-like growth factor II' + IGF-2 + insulin-like growth factor II + + + CHEBI_PR_EXT:leptin + OB + CHEBI:Leptin or PR_EXT:leptin + obesity factor + OBS + leptin + CHEBI_PR_EXT:leptin + obese protein + LEP + + + CHEBI_PR_EXT:myoglobin + MB + myoglobin + CHEBI:myoglobin or PR_EXT:myoglobin + CHEBI_PR_EXT:myoglobin + + + CHEBI:'Parathyroid hormone' or PR_EXT:'parathyroid hormone' + parathormone + parathyrin + parathyroid hormone + PTH + CHEBI_PR_EXT:parathyroid hormone + CHEBI_PR_EXT:parathyroid_hormone + + + CHEBI_PR_EXT:prolactin + luteotropic hormone + prolactin + CHEBI:Prolactin or PR_EXT:prolactin + PRL + luteotropin + CHEBI_PR_EXT:prolactin + + + CHEBI_PR_EXT:protein + CHEBI_PR_EXT:protein + protein + CHEBI:'protein' or PR_EXT:'protein' + + + blood coagulation factor II + CHEBI_PR_EXT:prothrombin + CHEBI:Prothrombin or PR_EXT:prothrombin + Cf2 + coagulation factor II + prothrombin + F2 + CHEBI_PR_EXT:prothrombin + + + CHEBI:somatostatin or PR_EXT:somatostatin + GHRIH + SST + somatotropin release-inhibiting hormone + growth hormone release-inhibiting hormone + growth hormone release-inhibiting factor + SRIF + SMST + somatostatin + SRIH + somatotropin release-inhibiting factor + GHIH + CHEBI_PR_EXT:somatostatin + growth hormone-inhibiting hormone + CHEBI_PR_EXT:somatostatin + + + CHEBI_PR_EXT:thioredoxin + CHEBI_PR_EXT:thioredoxin + thioredoxin + TRX + TXN + CHEBI:thioredoxin or PR_EXT:thioredoxin or PR_EXT:'thioredoxin, mitochondrial' + TRDX + + + thromboplastin + CHEBI_PR_EXT:thromboplastin + CHEBI_PR_EXT:thromboplastin + CHEBI:'Coagulation Factor Xa' or PR_EXT:'tissue factor' + + + CHEBI_PR_EXT:vasopressin + vasopressin-neurophysin 2-copeptin + antidiuretic hormone + vasopressin + CHEBI_PR_EXT:vasopressin + CHEBI:vasopressin or PR_EXT:'vasopressin-neurophysin 2-copeptin' + ADH + + + carboxy terminus + For: C/carboxy-terminal/termini/terminus + C-terminus + C-terminus or C-terminal region + CHEBI_SO_EXT:C-terminus or C-terminal region + CHEBI_SO_EXT:C_terminus_or_C_terminal_region + (CHEBI:'carboxy group' and proper_part_of some CHEBI:'C-terminal amino-acid residue') or (SO_EXT:region and has_part some CHEBI:'C-terminal amino-acid residue') or (SO_EXT:region and bearer_of some (PATO:orientation and toward some CHEBI:'C-terminal amino-acid residue')) + + + CHEBI_SO_EXT:DNA + CHEBI:'deoxyribonucleic acid' or (is_region_part_of some CHEBI:'deoxyribonucleic acid') or (bearer_of some SO:DNA) + DNA + CHEBI_SO_EXT:DNA + + + For: N/amino-terminal/termini/terminus + CHEBI_SO_EXT:N_terminus_or_N_terminal_region + CHEBI_SO_EXT:N-terminus or N-terminal region + amino terminus + N-terminus or N-terminal region + (CHEBI:'amino group' and proper_part_of some CHEBI:'N-terminal amino-acid residue') or (SO_EXT:region and has_part some CHEBI:'N-terminal amino-acid residue') or (SO_EXT:region and bearer_of o toward some CHEBI:'N-terminal amino-acid residue') + N-terminus + + + RNA + CHEBI_SO_EXT:RNA + CHEBI:'ribonucleic acid' or (is_region_part_of some CHEBI:'ribonucleic acid') or bearer_of some SO:RNA + CHEBI_SO_EXT:RNA + + + alanine + Ala + CHEBI:alanine or CHEBI:'alanine residue' or SO_EXT:alanine + CHEBI_SO_EXT:alanine + CHEBI_SO_EXT:alanine + + + amino acid + CHEBI_SO_EXT:amino_acid + aa + CHEBI_SO_EXT:amino acid + CHEBI:'amino acid' or CHEBI:'amino-acid residue' or SO_EXT:amino_acid + + + CHEBI_SO_EXT:arginine + arginine + CHEBI_SO_EXT:arginine + CHEBI:arginine or CHEBI:'arginine residue' or SO_EXT:arginine + Arg + + + CHEBI_SO_EXT:asparagine + CHEBI_SO_EXT:asparagine + Asn + asparagine + CHEBI:asparagine or CHEBI:'asparagine residue' or SO_EXT:asparagine + + + CHEBI:aspartate(1-) or CHEBI:aspartate(2-) or CHEBI:'aspartate residue' or CHEBI_SO_EXT:aspartic_acid + aspartate or aspartic acid + Asp + CHEBI_SO_EXT:aspartate_or_aspartic_acid + CHEBI_SO_EXT:aspartate or aspartic acid + + + CHEBI:'aspartic acid' or CHEBI:'aspartic acid residue' or SO_EXT:aspartic_acid + For: aspartic acid(s) + aspartic acid + CHEBI_SO_EXT:aspartic_acid + CHEBI_SO_EXT:aspartic acid + + + CHEBI:nucleobase or (CHEBI:group and is_substituent_group_from some CHEBI:nucleobase) or SO_EXT:base + nucleic acid base + CHEBI_SO_EXT:base + base + nucleobase + CHEBI_SO_EXT:base + + + biomarker + CHEBI:biomarker or SO_EXT:'genetic marker' + CHEBI_SO_EXT:biomarker + CHEBI_SO_EXT:biomarker + + + CHEBI_SO_EXT:cysteine + CHEBI:cysteine or CHEBI:'cysteine residue' or SO_EXT:cysteine + CHEBI_SO_EXT:cysteine + cysteine + Cys + + + CHEBI_SO_EXT:deoxyoligonucleotide + deoxyoligonucleotide + CHEBI_SO_EXT:deoxyoligonucleotide + CHEBI_SO_EXT:oligonucleotide and (CHEBI:'deoxyribonucleic acid' or bearer_of some SO:DNA) + + + deoxyribonucleotide + CHEBI:deoxyribonucleotide or CHEBI:'deoxyribonucleotide residue' or (CHEBI_SO_EXT:nucleotide and bearer_of some SO:DNA) + deoxynucleotide + deoxynucleotidyl + CHEBI_SO_EXT:deoxyribonucleotide + CHEBI_SO_EXT:deoxyribonucleotide + + + dinucleotide + CHEBI_SO_EXT:dinucleotide + CHEBI:dinucleotide or (SO:region and (has_sequence_unit_part exactly 2 (CHEBI_SO_EXT:nucleotide) and (has_sequence_unit_part only (CHEBI_SO_EXT:nucleotide)) + CHEBI_SO_EXT:dinucleotide + + + CHEBI_SO_EXT:double_stranded_DNA + dsDNA + double-stranded DNA + CHEBI_SO_EXT:double-stranded DNA + CHEBI:'double-stranded DNA' or (is_region_part_of some CHEBI:'double-stranded DNA') or (SO_EXT:DNA and bearer_of some (SO:double or SO:double_stranded_cDNA)) or SO_EXT:double_stranded_DNA_chromosome or SO_EXT:ds_DNA_viral_sequence + + + CHEBI_SO_EXT:double-stranded RNA + double-stranded RNA + CHEBI_SO_EXT:double_stranded_RNA + CHEBI:'double-stranded RNA' or (is_region_part_of some CHEBI:'double-stranded RNA') or (SO_EXT:RNA and bearer_of some SO:double) or SO_EXT:double_stranded_RNA_chromosome or SO_EXT:ds_RNA_viral_sequence + dsRNA + + + epitope + CHEBI_SO_EXT:epitope + CHEBI_EXT:epitope or SO_EXT:epitope + CHEBI_SO_EXT:epitope + + + Glu + For: Glu + CHEBI_SO_EXT:glutamate_or_glutamic_acid + CHEBI_SO_EXT:glutamate or glutamic acid + glutamate or glutamic acid + CHEBI_EXT:glutamate or CHEBI_SO_EXT:glutamic_acid + + + glutamic acid + CHEBI_SO_EXT:glutamic acid + CHEBI:'glutamic acid' or CHEBI:'glutamic acid residue' or SO_EXT:'glutamic acid' + CHEBI_SO_EXT:glutamic_acid + + + CHEBI_SO_EXT:glutamine + glutamine + CHEBI:glutamine or CHEBI:'glutamine residue' or SO_EXT:glutamine + Gln + CHEBI_SO_EXT:glutamine + + + glycine + CHEBI_SO_EXT:glycine + CHEBI:glycine or CHEBI:'glycine residue' or SO_EXT:glycine + CHEBI_SO_EXT:glycine + Gly + + + For: hexamer(s), hexameric, hexanucleotide(s) + CHEBI_SO_EXT:hexanucleotide + CHEBI_SO_EXT:hexanucleotide + (CHEBI:oligonucleotide or SO:oligonucleotide) and (has_sequence_unit_part exactly 6 CHEBI_SO_EXT:nucleotide) and (has_sequence_unit_part only CHEBI_SO_EXT:nucleotide) + hexanucleotide + hexamer + + + His + histidine + CHEBI_SO_EXT:histidine + CHEBI_SO_EXT:histidine + CHEBI:histidine or CHEBI:'histidine residue' or SO_EXT:histidine + + + CHEBI_SO_EXT:inosine + CHEBI:inosine or CHEBI:'inosyl group' or CHEBI:'inosine 5'-phosphate(1-) residue' or CHEBI:'IMP residue' or SO_EXT:inosine + inosine + CHEBI_SO_EXT:inosine + + + CHEBI_SO_EXT:isoleucine + CHEBI:isoleucine or CHEBI:'isoleucine residue' or SO:isoleucine + Ile + isoleucine + CHEBI_SO_EXT:isoleucine + + + CHEBI:leucine or CHEBI:'leucine residue' or SO_EXT:leucine + CHEBI_SO_EXT:leucine + CHEBI_SO_EXT:leucine + Leu + leucine + + + CHEBI:lysine or CHEBI:'lysine residue' or SO_EXT:lysine + Lys + CHEBI_SO_EXT:lysine + lysine + CHEBI_SO_EXT:lysine + + + messenger RNA + CHEBI_SO_EXT:mRNA + mRNA + CHEBI_SO_EXT:mRNA + CHEBI:'messenger RNA' or SO_EXT:mRNA + + + Met + CHEBI_SO_EXT:methionine + methionine + CHEBI_SO_EXT:methionine + CHEBI:methionine or CHEBI:'methionine residue' or SO_EXT:methionine + + + For: indicator/indicators, label(n.)/labels(n.), mark(n.)/marker/marks(n.), tag(n.)/tags(n.) + molecular tag + molecular marker + molecular indicator + CHEBI_SO_EXT:molecular_indicator_or_label_or_marker_or_tag + CHEBI_EXT:indicator or CHEBI_EXT:label or SO_EXT:'genetic marker' or SO_EXT:tag + molecular indicator/label/marker/tag + molecular label + CHEBI_SO_EXT:molecular indicator/label/marker/tag + + + molecular marking process + molecular tagging process + CHEBI_SO_EXT:molecular label/mark/tag process + molecular label/mark/tag process + CHEBI_SO_EXT:molecular_label_or_mark_or_tag_process + BFO:occurrent and results_in_formation_of some (BFO:independent_continuant and has_proper_part (CHEBI_EXT:label or SO_EXT:'genetic marker' or SO_EXT:tag)) + molecular labeling process + For: label(v.)/labeled/labeling/labelled/labelling/labels(v.), mark(v.)/marked(v.)/marking/marks(v.), tag(v.)/tagged/tagging/tags(v.) + + + CHEBI_SO_EXT:molecular probe + molecular probe + CHEBI_SO_EXT:molecular_probe + CHEBI_EXT:probe or SO_EXT:probe + + + CHEBI_SO_EXT:nonanucleotide + nonanucleotide + CHEBI_SO_EXT:nonanucleotide + nonamer + (CHEBI:oligonucleotide or SO:oligonucleotide) and (has_sequence_unit_part exactly 9 CHEBI_SO_EXT:nucleotide) and (has_sequence_unit_part only CHEBI_SO_EXT:nucleotide) + + + CHEBI_SO_EXT:nucleic acid + CHEBI:'nucleic acid' or bearer_of some SO:nucleic_acid + nucleic acid + CHEBI_SO_EXT:nucleic_acid + + + nt + CHEBI_SO_EXT:nucleotide + nucleotide + CHEBI_SO_EXT:nucleotide + CHEBI:nucleotide or CHEBI:'nucleotide residue' or is_sequence_unit_part_of some CHEBI_SO_EXT:'nucleic acid' + + + oligonucleotide + CHEBI_SO_EXT:oligonucleotide + oligo + CHEBI_SO_EXT:oligonucleotide + CHEBI:oligonucleotide or SO_EXT:oligo + + + CHEBI_SO_EXT:peptide_or_peptide_region + CHEBI:peptide or bearer_of some SO:peptidyl + peptide + peptide or peptide region + peptidyl + CHEBI_SO_EXT:peptide or peptide region + + + CHEBI_SO_EXT:phenylalanine + CHEBI:phenylalanine or CHEBI:'phenylalanine residue' or SO_EXT:phenylalanine + CHEBI_SO_EXT:phenylalanine + Phe + phenylalanine + + + CHEBI_SO_EXT:polypeptide + CHEBI_SO_EXT:polypeptide + CHEBI:polypeptide or SO_EXT:polypeptide + polypeptide + + + CHEBI:proline or CHEBI:'proline residue' or SO_EXT:proline + CHEBI_SO_EXT:proline + CHEBI_SO_EXT:proline + Pro + proline + + + ribosomal RNA + CHEBI_SO_EXT:rRNA + CHEBI:'ribosomal RNA" or SO_EXT:rRNA + CHEBI_SO_EXT:rRNA + rRNA + + + CHEBI_SO_EXT:riboprobe + CHEBI_SO_EXT:riboprobe + CHEBI_SO_EXT:RNA and CHEBI_SO_EXT:molecular_probe + riboprobe + + + Sec + CHEBI_SO_EXT:selenocysteine + selenocysteine + CHEBI_SO_EXT:selenocysteine + CHEBI:selenocysteine or CHEBI:'selenocysteine residue' or SO_EXT:selenocysteine + + + CHEBI_SO_EXT:serine + Ser + CHEBI:serine or CHEBI:'serine residue' or SO_EXT:serine + CHEBI_SO_EXT:serine + serine + + + single-stranded DNA + CHEBI:'single-stranded DNA' or (is_region_part_of some CHEBI:'single-stranded DNA') or (SO_EXT:DNA and bearer_of some (SO:single or SO:single_stranded_cDNA)) or SO_EXT:single_stranded_DNA_chromosome + ssDNA + CHEBI_SO_EXT:single-stranded DNA + CHEBI_SO_EXT:single_stranded_DNA + + + CHEBI:'transfer RNA' or SO_EXT:tRNA + transfer RNA + CHEBI_SO_EXT:tRNA + For: transfer RNA(s), tRNA(s) + CHEBI_SO_EXT:tRNA + tRNA + + + CHEBI:tRNA(Trp) or SO_EXT:'tryptophanyl tRNA' + tryptophanyl tRNA + CHEBI_SO_EXT:tRNA_Trp + tRNA(Trp) + CHEBI_SO_EXT:tRNA(Trp) + + + CHEBI_SO_EXT:threonine + CHEBI_SO_EXT:threonine + CHEBI:threonine or CHEBI:'threonine residue' or SO_EXT:threonine + threonine + Thr + + + CHEBI_SO_EXT:tripeptide + CHEBI:tripeptide or (SO_EXT:region and (has_sequence_unit_part exactly 3 CHEBI_SO_EXT:amino_acid) and (has_sequence_unit_part only CHEBI_SO_EXT:amino_acid) + CHEBI_SO_EXT:tripeptide + tripeptide + + + tryptophan + CHEBI_SO_EXT:tryptophan + CHEBI:tryptophan or CHEBI:'tryptophan residue' or SO_EXT:tryptophan + CHEBI_SO_EXT:tryptophan + Trp + + + CHEBI_SO_EXT:tyrosine + CHEBI_SO_EXT:tyrosine + tyrosine + CHEBI:tyrosine or CHEBI:'tyrosine residue' or SO_EXT:tyrosine + Tyr + + + CHEBI:valine or CHEBI:'valine residue' or SO_EXT:valine + CHEBI_SO_EXT:valine + CHEBI_SO_EXT:valine + valine + Val + + + CHEBI_UBERON_EXT:triglyceride_or_adipose_tissue + CHEBI:triglyceride or UBERON:'adipose tissue' + For: fat/fats/fatty + fat + CHEBI_UBERON_EXT:fat + fatty + + + CHEBI extension classes + + + CHEMINF_GO_EXT:bearer of chemical binding or bond formation + binder + For: binder(s) + BFO:independent_continuant and has_prototype o participates_in some CHEMINF_GO_EXT:chemical_binding_or_bond_formation + bearer of chemical binding or bond formation + CHEMINF_GO_EXT:bearer_of_chemical_binding_or_bond_formation + + + (BFO:occurrent and ((results_in_formation_of some CHEMINF:'chemical bond') or (realizes some GO_EXT:binding))) or GO:binding or MOP:'formation of covalent bond' or MOP:metallation + bond formation + binding + For: (chemical) bind/binding/binds/bond(v.)/bonded/bonding/bonds(v.)/bound + CHEMINF_GO_EXT:chemical_binding_or_bond_formation + chemical binding or bond formation + CHEMINF_GO_EXT:chemical binding or bond formation + + + bodily fluid or bodily fluid experimental method + serology + serological + (CHMO:'experimental method' and has_input some 'bodily fluid') or UBERON:'bodily fluid' + CHMO_UBERON_EXT:bodily fluid or bodily fluid experimental method + For: serology/serological/serologically + CHMO_UBERON_EXT:bodily_fluid_or_bodily_fluid_experimental_method + + + cell + CL:cell + "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] + CL:0000000 + + + unpassaged cultured cell + primary cultured cell + primary cell culture cell + primary cell line cell + CL:primary cultured cell + "A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged." [ReO:mhb] + CL:0000001 + + + "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [CARO:mah] + native cell + CL:0000003 + CL:native cell + + + neuronal receptor cell + CL:neuronal receptor cell + CL:0000006 + neuronal receptor cell (sensu Animalia) + + + CL:0000007 + "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] + CL:early embryonic cell + early embryonic cell + + + cultured cell + "A cell in vitro that is or has been maintained or propagated as part of a cell culture." [ReO:mhb] + CL:cultured cell + CL:0000010 + + + germ line stem cell + germline stem cell + CL:0000014 + CL:germ line stem cell + + + CL:0000015 + CL:male germ cell + male germ cell + + + spermatocyte + CL:spermatocyte + "A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids." [GOC:tfm, MESH:A05.360.490.890.880] + CL:0000017 + + + nematoblast + CL:spermatid + "A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa." [MESH:A05.360.490.890.860] + spermatid + CL:0000018 + + + CL:sperm + sperm cell + "A mature male germ cell that develops from a spermatid." [GOC:tfm, MESH:A05.360.490.890] + CL:0000019 + sperm + spermatozoon + spermatozoid + + + spermatogonium + CL:spermatogonium + "An euploid male germ cell of an early stage of spermatogenesis." [MESH:A05.360.490.890.900] + CL:0000020 + + + CL:female germ cell + female germ cell + "Female germ cell is a germ cell that supports female gamete production." [GOC:tfm, PMID:11023867, PMID:20454446] + CL:0000021 + + + CL:0000023 + oogonium + "A female germ cell that has entered meiosis." [GOC:tfm, ISBN:0721662544] + CL:oocyte + oocyte + + + CL:0000025 + egg cell + CL:egg cell + "A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization." [GOC:tfm, ISBN:0721662544] + mature oocyte + ovum + + + CL:0000031 + CL:neuroblast + "A cell that will develop into a neuron often after a migration phase." [http://en.wikipedia.org/wiki/Neuroblast] + neuroblast + + + CL:0000034 + "A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [GOC:tfm, MESH:A11.872] + stem cell + CL:stem cell + + + single fate stem cell + unipotential stem cell + CL:0000035 + unipotent stem cell + CL:single fate stem cell + "A stem cell that self-renews as well as give rise to a single mature cell type." [GOC:tfm] + + + CL:epithelial fate stem cell + epithelial fate stem cell + CL:0000036 + + + hematopoietic stem cell + hemopoietic stem cell + CL:0000037 + CL:hematopoietic stem cell + "A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Hematopoietic_stem_cell, PMID:19022770] + blood forming stem cell + colony forming unit hematopoietic + HSC + + + CFU-E + BFU-E + CL:0000038 + blast forming unit erythroid + "A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative)." [GOC:add, ISBN:0721601464] + erythroid progenitor cell + erythroid stem cell + colony forming unit erythroid + burst forming unit erythroid + CL:erythroid progenitor cell + + + "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." [GOC:tfm, ISBN:0721662544] + CL:germ line cell + germ line cell + CL:0000039 + + + CL:0000047 + CL:neuronal stem cell + "Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors." [GOC:tfm, http://en.wikipedia.org/wiki/Neural_stem_cell, MESH:D058953, PMID:15247488] + NSC + neuronal stem cell + neural stem cell + + + multipotent stem cell + multi-fate stem cell + CL:0000048 + multi fate stem cell + multifate stem cell + CL:multi fate stem cell + "A stem cell that can give rise to multiple lineages of cells." [GOC:add] + multipotent cell + + + CL:totipotent stem cell + totipotent stem cell + CL:0000052 + totipotential stem cell + "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] + + + non-terminally differentiated cell + CL:0000055 + "A precursor cell with a limited number of potential fates." [SANBI:mhl] + blast cell + CL:non-terminally differentiated cell + + + CL:0000056 + "A precursor cell of the myogenic lineage that develops from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes." [GOC:tfm, MESH:A11.635] + CL:myoblast + myoblast + + + CL:0000057 + fibroblast + CL:fibroblast + "A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped." [http://en.wikipedia.org/wiki/Fibroblast, ISBN:0517223651, MESH:A11.329.228, MESH:D005347] + + + CL:0000059 + ameloblast + "Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell." [GO_REF:0000034, GOC:tfm, MESH:A11.436.107] + CL:ameloblast + amelocyte + enamel secreting cell + + + osteoblast + CL:osteoblast + "Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell." [GO_REF:0000034, MESH:A11.329.629] + CL:0000062 + + + CL:ciliated cell + CL:0000064 + ciliated cell + "A cell that has a filiform extrusion of the cell surface." [GOC:tfm] + + + epithelial cell + CL:0000066 + CL:epithelial cell + epitheliocyte + "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina." [FB:ma, GOC:tfm, MESH:A11.436] + + + "An epithelial cell that has a cillia." [GOC:tfm] + CL:ciliated epithelial cell + ciliated epithelial cell + CL:0000067 + + + duct epithelial cell + CL:0000068 + CL:duct epithelial cell + + + CL:blood vessel endothelial cell + CL:0000071 + "An endothelial cell that lines the vasculature." [GOC:tfm] + blood vessel endothelial cell + cuboidal endothelial cell of vascular tree + + + CL:non-branched duct epithelial cell + CL:0000072 + non-branched duct epithelial cell + + + CL:0000075 + CL:columnar/cuboidal epithelial cell + columnar/cuboidal epithelial cell + + + CL:0000076 + CL:squamous epithelial cell + squamous epithelial cell + + + CL:mesothelial cell + CL:0000077 + "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." [GOC:tfm, ISBN:0721662544] + mesotheliocyte + mesothelial cell + + + CL:stratified epithelial cell + stratified epithelial cell + CL:0000079 + + + CL:circulating cell + "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add] + circulating cell + CL:0000080 + + + blood cell + "A cell found predominately in the blood." [GOC:add, GOC:tfm] + CL:blood cell + CL:0000081 + + + CL:epithelial cell of lung + epithelial cell of lung + CL:0000082 + + + "An epithelial cell of the pancreas." [GOC:tfm] + pancreas epithelial cell + CL:epithelial cell of pancreas + epithelial cell of pancreas + pancreatic epithelial cell + CL:0000083 + + + mature T cell + T-lymphocyte + "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex." [GOC:add, GOC:tfm, ISBN:0781735149] + T cell + immature T cell + T lymphocyte + T-cell + CL:0000084 + CL:T cell + + + CL:osteoclast + "A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149, PMID:10428500, PMID:15055519, PMID:17380158] + osteoclast + chondroclast + CL:0000092 + + + CL:granulocyte + "A leukocyte with abundant granules in the cytoplasm." [GOC:amm, GOC:tfm, http://en.wikipedia.org/wiki/Granulocyte, MESH:A11.118.637.415, MESH:D006098] + granular leucocyte + granulocyte + polymorphonuclear leukocyte + CL:0000094 + granular leukocyte + + + CL:0000095 + CL:neuron associated cell + neuron associated cell + + + polynuclear neutrophilic leukocyte + mature neutrophil leucocyte + CL:mature neutrophil + CL:0000096 + polymorphonuclear neutrophil + polynuclear neutrophilic leucocyte + mature neutrophil + "A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive." [GOC:add, GOC:tfm, http://www.cap.org, MESH:A11.118.637.415.583, MESH:D009504, PMID:11138776, PMID:12560239, PMID:15514007, PMID:7880385] + mature neutrophilic leukocyte + mature neutrophil leukocyte + mature neutrophilic leucocyte + mature neutrocyte + PMN + + + mast cell + CL:mast cell + tissue basophil + labrocyte + mastocyte + CL:0000097 + "A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development." [GOC:add, GOC:dsd, GOC:tfm, ISBN:068340007X, MESH:A11.329.427, MESH:D008407, PMCID:PMC1312421, PMCID:PMC2855166, PMID:15153310, PMID:16455980, PMID:19671378, PMID:212366338, PMID:9354811] + histaminocyte + + + CL:sensory epithelial cell + sensory epithelial cell + CL:0000098 + "A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells." [GOC:tfm, ISBN:0517223651, ISBN:0721662544] + + + "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions." [GOC:tfm, MESH:A08.663.358] + CL:0000099 + CL:interneuron + interneuron + + + CL:motor neuron + motoneuron + CL:0000100 + "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement." [MESH:A08.663.655.500, PMID:16875686] + motor neuron + + + "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] + sensory neuron + CL:sensory neuron + CL:0000101 + + + bipolar neuron + CL:bipolar neuron + CL:0000103 + "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body." [GOC:tfm, ISBN:0444009442] + + + CL:cholinergic neuron + CL:0000108 + "A neuron that uses acetylcholine as a vesicular neurotransmitter." [GOC:tfm] + cholinergic neuron + + + peptidergic neuron + CL:0000110 + CL:peptidergic neuron + + + "An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm." [GOC:tfm, http://en.wikipedia.org/wiki/Endothelial_cell, https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855, MESH:D042783, PMID:21275341] + endotheliocyte + CL:0000115 + CL:endothelial cell + endothelial cell + + + CL:0000117 + CL:CNS neuron (sensu Vertebrata) + CNS neuron (sensu Vertebrata) + + + CL:0000120 + granule cell + CL:granule cell + + + Purkinje neuron + Purkinje cell + Purkinje's cell + CL:0000121 + CL:Purkinje cell + cerebellum Purkinje cell + cerebellar Purkinje cell + "The output neuron of the cerebellar cortex." [MESH:A08.186.211.132.810.428.200.212.600] + + + glial cell + CL:glial cell + CL:0000125 + "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons." [MESH:A08.637] + neuroglia + neuroglial cell + + + macroglial cell + CL:0000126 + CL:macroglial cell + macrogliocyte + "A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together." [GOC:tfm, ISBN:0721662544] + + + astrocyte + CL:astrocyte + astrocytic glia + CL:0000127 + "A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury." [GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Astrocyte, MESH:A08.637.200, MESH:D001253, PMID:11746784, PMID:12162730, PMID:12898703, PMID:20942978] + + + oligodendrocyte + OLs + CL:0000128 + "A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system." [http://en.wikipedia.org/wiki/Oligodendrocyte, MESH:A08.637.600, MESH:D009836] + CL:oligodendrocyte + oligodendroglia + + + microgliocyte + MF.microglia.CNS + hortega cells + CL:microglial cell + "A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Microglia, ISBN:0721601464, MESH:D017628, PMID:11517395, PMID:12430718, PMID:14561199, PMID:14612429, PMID:16177057, PMID:19461673, PMID:2089275] + microglia + brain-resident macrophage + CL:0000129 + microglial cell + + + CL:mesenchymal cell + mesenchymal progenitor cells + stem cells, mesenchymal + CFU-F + "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. This cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." [FB:ma, GOC:dsd, http://en.wikipedia.org/wiki/Mesenchymal_stem_cell, http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells, PMCID:PMC2613570, PMID:10102814j, PMID:16923606, PMID:17986482, PMID:19960544] + MSC + mesenchymal stromal cells + CL:0000134 + mesenchymal stromal cell + mesenchymal precursor cell + mesenchymal stem cell + mesenchymal cell + + + fibrocyte + "An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes." [GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Fibrocyte, ISBN:0412046911, ISBN:0517223651, PMID:11641248, PMID:15010326, PMID:17607298, PMID:18222966, PMID:8790603, PMID:9551999] + CL:fibrocyte + CL:0000135 + + + "A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides." [MESH:A11.329.114] + CL:0000136 + CL:fat cell + adipose cell + adipocyte + fat cell + + + "A mature osteoblast that has become embedded in the bone matrix. They occupy a small cavity, called lacuna, in the matrix and are connected to adjacent osteocytes via protoplasmic projections called canaliculi." [GOC:tfm, MESH:A11.329.629.500] + CL:osteocyte + CL:0000137 + osteocyte + + + chondrocyte + CL:chondrocyte + CL:0000138 + "Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell." [GO_REF:0000034, MESH:A11.329.171] + cartilage cell + + + professional antigen presenting cell + CL:professional antigen presenting cell + "A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response." [GOC:add, ISBN:0781735149] + CL:0000145 + + + CL:simple columnar epithelial cell + CL:0000146 + simple columnar epithelial cell + + + "A pigment cell is a cell that contains pigment granules." [GOC:tfm] + CL:0000147 + chromatocyte + CL:pigment cell + chromatophore + pigment cell + + + melanocyte + CL:0000148 + CL:melanocyte + "A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance." [SANBI:mhl] + + + CL:0000150 + CL:glandular epithelial cell + "A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules." [GOC:tfm] + glandular epithelial cell + + + "A cell that specializes in controlled release of one or more substances." [GOC:tfm, ISBN:0721662544] + CL:0000151 + CL:secretory cell + secretory cell + + + CL:GAG secreting cell + hyaluronic acid secreting cell + GAG secreting cell + "A cell that secretes glycosaminoglycans." [GOC:tfm] + CL:0000153 + + + CL:0000154 + protein secreting cell + CL:protein secreting cell + + + CL:0000157 + "A cell that specializes in secretion of surfactant in the alveoli of the lung." [GOC:tfm, ISBN:0721662544] + CL:surfactant secreting cell + surfactant secreting cell + + + CL:Clara cell + CL:0000158 + bronchiolar non-ciliated cell + Clara cell + Clara cell of bronchiole + "Epithelial progenitor cell of the lung. Clara cells are dome-shaped with short microvilli but no cilia. They function to protect the bronchiolar epithelium. Clara cells also multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium." [GOC:tfm, PMID:12107102, PMID:7905712] + + + CL:0000159 + seromucus secreting cell + CL:seromucus secreting cell + + + CL:0000160 + CL:goblet cell + chalice cell + goblet cell + "A cell of the epithelial lining that produce and secrete mucins." [MESH:A03.492.411.369.320] + + + CL:0000163 + endocrinocyte + endocrine cell + CL:endocrine cell + "A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions." [MESH:A06.407] + + + CL:0000164 + enteroendocrine cell + CL:enteroendocrine cell + "An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas." [GOC:tfm, SANBI:mhl] + + + CL:0000165 + CL:neuroendocrine cell + "An endocrine cell that has the specialized function to produce and secrete hormones in response to neuronal signals." [MESH:A06.688] + neuroendocrine cell + neurosecretory cell + + + CL:chromaffin cell + CL:0000166 + "A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system." [MESH:A06.224.161] + phaeochromocyte + chromaffin cell + + + peptide hormone secreting cell + CL:0000167 + CL:peptide hormone secreting cell + + + CL:0000168 + CL:insulin secreting cell + insulin secreting cell + + + CL:type B pancreatic cell + B-cell of pancreatic islet + beta cell islet + pancreatic B-cell + pancreatic islet core + pancreatic B cell + CL:0000169 + type B enteroendocrine cell + type B pancreatic cell + beta cell of pancreatic islet + insulin-secreting cell + "A cell that secretes insulin and is located towards the center of the islets of Langerhans." [GOC:tfm, http://en.wikipedia.org/wiki/Pancreatic_b_cell, ISBN:0517223651] + pancreatic beta cell + + + CL:glucagon secreting cell + CL:0000170 + glucagon-secreting cell + "A cell that secretes glucagon." [GOC:tfm] + glucagon secreting cell + + + alpha cell of iselt of Langerhans + pancreatic A cell + "A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon." [GOC:tfm, ISBN:0721662544] + pancreatic alpha cell + CL:0000171 + CL:pancreatic A cell + + + CL:somatostatin secreting cell + somatostatin secreting cell + CL:0000172 + + + delta cell of islet + pancreatic delta cell + pancreatic D-cell + "A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin." [FMA:0517223651, GOC:tfm] + somatostatin-secreting pancreatic cell + CL:pancreatic D cell + delta cell of pancreatic islet + pancreatic D cell + CL:0000173 + D-cell of pancreatic islet + + + CL:0000174 + steroid hormone secreting cell + CL:steroid hormone secreting cell + + + CL:0000177 + CL:testosterone secreting cell + testosterone secreting cell + + + CL:0000178 + Leydig cell + interstitial cell of Leydig + CL:Leydig cell + "A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis." [GOC:tfm, PMID:12050120] + + + CL:metabolising cell + "A cell whose primary function is intermediary metabolism." [FB:ma] + metabolising cell + CL:0000181 + + + hepatocyte + "The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated." [GOC:tfm, http://en.wikipedia.org/wiki/Hepatocyte, ISBN:0412046911, MESH:A11.436.348, PMID:19717280] + CL:hepatocyte + CL:0000182 + + + contractile cell + CL:contractile cell + "A cell whose primary function is to shorten." [FB:ma] + CL:0000183 + + + myoepithelial cell + "Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament." [GOC:tfm, ISBN:0721662544] + CL:0000185 + basket epithelial cell + myoepitheliocyte + CL:myoepithelial cell + + + CL:muscle cell + muscle fiber + CL:0000187 + "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." [MESH:A11.620] + myocyte + muscle cell + + + skeletal muscle cell + CL:0000188 + "A somatic cell located in skeletal muscle." [GOC:tfm] + CL:skeletal muscle cell + + + CL:slow muscle cell + CL:0000189 + slow muscle cell + slow muscle fiber + "A muscle cell that develops tension more slowly than a fast-twitch fiber." [GOC:tfm, ISBN:0323052908] + + + "A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron ." [GOC:tfm, ISBN:0323052908] + fast muscle cell + glycolytic muscle fiber + CL:fast muscle cell + CL:0000190 + + + myocytes, smooth muscle + CL:smooth muscle cell + smooth muscle cell + smooth muscle fiber + "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast)." [http://en.wikipedia.org/wiki/Smooth_muscle_cell, MESH:A11.620.520, MESH:D032389, PMID:9315361] + SMCs + non-striated muscle cell + CL:0000192 + + + receptor cell + CL:0000197 + CL:receptor cell + + + nociceptor + CL:0000198 + pain receptor cell + CL:pain receptor cell + nocireceptor + "The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings." [MESH:A08.800.550.700.650] + + + CL:mechanoreceptor cell + mechanoreceptor + CL:0000199 + "A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system." [MESH:A08.800.550.700.500] + mechanoreceptor cell + + + CL:0000202 + "A mechanoreceptor cell located in the inner ear that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." [MESH:A08.663.650.250] + cochlear hair cell + auditory hair cell + inner ear hair cell + CL:auditory hair cell + auditory receptor cell + inner ear receptor cell + + + "A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood." [MESH:A08.800.550.700.120] + CL:0000206 + chemoreceptor cell + CL:chemoreceptor cell + + + CL:0000207 + olfactory receptor cell + Schultze's cell + olfactory sensory neuron + CL:olfactory receptor cell + olfactory receptor neuron + + + taste bud cell + CL:0000209 + CL:taste receptor cell + taste receptor cell + "A cell type found in the spherical or ovoid clusters of receptor cells found mainly in the epithelium of the tongue and constituting the end organs of the sense of taste." [GOC:tfm, ISBN:0618947256] + + + CL:0000210 + CL:photoreceptor cell + photoreceptor cell + "A cell specialized to detect and transduce light." [MESH:A08.663.650.650] + + + CL:electrically active cell + "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] + CL:0000211 + electrically active cell + + + CL:0000212 + "A cell that takes up and metabolizes substances." [CL:CVS] + absorptive cell + CL:absorptive cell + + + boundary cell + "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] + CL:lining cell + CL:0000213 + lining cell + + + synovial cell + "A meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid." [GOC:tfm, ISBN:0721662544, PMID:17942474] + hyaluronic acid secreting cell + CL:synovial cell + synoviocyte + CL:0000214 + + + "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] + CL:0000215 + barrier cell + CL:barrier cell + + + CL:0000216 + "A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier." [MESH:A05.360.444.849.789] + CL:Sertoli cell + Sertoli cell + + + CL:0000217 + CL:insulating cell + insulating cell + + + CL:0000218 + CL:myelinating Schwann cell + neurilemmal cell + myelinating Schwann cell + "A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons." [GOC:cvs, GOC:tfm, MESH:A08.637.800] + + + motile cell + CL:0000219 + CL:motile cell + "A cell that moves by its own activities." [FB:ma] + + + "A cell of the outer of the three germ layers of the embryo." [MESH:A16.254.425.273] + ectoderm cell + CL:0000221 + ectodermal cell + CL:ectodermal cell + + + mesodermal cell + "A cell of the middle germ layer of the embryo." [MESH:A16.254.425.660] + CL:mesodermal cell + CL:0000222 + mesoblast + mesoderm cell + + + endoderm cell + CL:endodermal cell + endodermal cell + "A cell of the inner of the three germ layers of the embryo." [MESH:A16.254.425.407] + CL:0000223 + + + CL:anucleate cell + non-nucleated cell + anucleate cell + CL:0000225 + "A cell that lacks a nucleus." [FB:ma] + + + single nucleate cell + CL:0000226 + "A cell with a single nucleus." [FB:ma, GOC:tfm] + CL:single nucleate cell + + + CL:0000228 + syncytium + syncitium + "A cell with more than one nucleus." [FB:ma] + syncytial cell + CL:multinucleate cell + multinucleate cell + + + erythrocyte + "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen." [GOC:tfm, MESH:A11.118.290] + CL:0000232 + red blood cell + CL:erythrocyte + RBC + + + platelet + "A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Platelet, MESH:A11.118.188, MESH:D001792, PMID:11110672, PMID:16987572, PMID:17204662, PMID:17479180, PMID:20414831] + anucleate thrombocyte + blood platelet + CL:platelet + CL:0000233 + enucleate thrombocyte + + + phagocyte + "Any cell capable of ingesting particulate matter via phagocytosis." [GOC:add, ISBN:0721601464] + CL:phagocyte + CL:0000234 + + + macrophage + "A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells." [GO_REF:0000031, GOC:add, GOC:tfm, PMID:16213494, PMID:1919437] + CL:macrophage + histiocyte + CL:0000235 + + + "A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149] + B-lymphocyte + B cell + B-cell + B lymphocyte + CL:0000236 + CL:B cell + + + CL:0000237 + keratinizing barrier epithelial cell + CL:keratinizing barrier epithelial cell + + + CL:brush border epithelial cell + CL:0000239 + brush border epithelial cell + + + stratified squamous epithelial cell + CL:stratified squamous epithelial cell + CL:0000240 + + + glial cell (sensu Vertebrata) + CL:0000243 + "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Form the myelin insulation of nervous pathways, guide neuronal migration during development, and exchange metabolites with neurons. Neuroglia have high-affinity transmitter uptake systems, voltage-dependent and transmitter-gated ion channels, and can release transmitters, but their role in signaling (as in many other functions) is unclear." [MESH:A08.637] + CL:glial cell (sensu Vertebrata) + + + eukaryotic cell + CL:eukaryotic cell + CL:0000255 + + + CL:0000287 + CL:eye photoreceptor cell + eye photoreceptor cell + + + gamete + haploid nucleated cell + CL:0000300 + haploid germ cell + CL:gamete + "A mature sexual reproductive cell having a single set of unpaired chromosomes." [GOC:tfm, ISBN:0721662544] + + + lens cell + crystallin accumulating cell + CL:crystallin accumulating cell + CL:0000306 + + + CL:0000311 + CL:keratin accumulating cell + keratin accumulating cell + + + keratinized cell of epidermis + malpighian cell + CL:0000312 + "An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell." [GOC:dsd, http://en.wikipedia.org/wiki/Keratinocyte, MESH:A11.436.397, MESH:D015603, PMID:15582983, PMID:15749908, PMID:19727116] + keratinocyte + CL:keratinocyte + + + mucous cell + CL:mucus secreting cell + mucus secreting cell + CL:0000319 + + + CL:pneumocyte + CL:0000322 + "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates." [GOC:tfm, PMID:20054144] + alveolar epithelial cell + pneumocyte + pneumonocyte + + + CL:0000323 + lysozyme secreting cell + CL:lysozyme secreting cell + + + "A cell that is specialised to accumulate a particular substance(s)." [FB:ma] + stuff accumulating cell + CL:stuff accumulating cell + CL:0000325 + + + extracellular matrix secreting cell + CL:extracellular matrix secreting cell + CL:0000327 + + + CL:0000328 + CL:myelin accumulating cell + myelin accumulating cell + + + CL:0000329 + oxygen accumulating cell + CL:oxygen accumulating cell + + + CL:0000335 + mesenchyme condensation cell + "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] + CL:mesenchyme condensation cell + + + hair follicle dermal papilla cell + CL:hair follicle dermal papilla cell + "A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling." [GOC:tfm, PMID:9893172] + CL:0000346 + + + CL:0000349 + CL:extraembryonic cell + extraembryonic cell + + + CL:0000351 + CL:trophoblast cell + trophoblast cell + "A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface." [GOC:tfm, MESH:A11.936] + trophoblastic cell + + + "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." [GOC:tfm, ISBN:0618947256] + epiblast cell + CL:0000352 + CL:epiblast cell + + + CL:blastoderm cell + blastoderm cell + CL:0000353 + "An undifferentiated cell produced by early cleavages of the fertilized egg (zygote)." [MESH:A11.104] + blastomere + + + CL:0000359 + vascular smooth muscle cell + "A smooth muscle cell assocatiated with the vasculature." [GOC:dsd, GOC:tfm] + CL:vascular associated smooth muscle cell + vascular associated smooth muscle cell + VSMC + + + cell of epidermis + CL:epidermal cell + CL:0000362 + epidermal cell + "An epithelial cell of the integument (the outer layer of an organism)." [Flybase:dsj, MA:ma] + + + zygote + CL:zygote + CL:0000365 + "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." [ISBN:0471245208] + + + CL:support cell (sensu Nematoda and Protostomia) + support cell (sensu Nematoda and Protostomia) + CL:0000378 + + + hemocyte (sensu Nematoda and Protostomia) + CL:0000387 + CL:hemocyte (sensu Nematoda and Protostomia) + + + CL:electrically responsive cell + "A cell whose function is determined by its response to an electric signal." [FB:ma] + CL:0000393 + electrically responsive cell + + + CL:0000398 + polygonal cell + CL:polygonal cell + + + CNS interneuron + CL:CNS interneuron + CL:0000402 + + + "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] + CL:electrically signaling cell + electrically signaling cell + CL:0000404 + + + CL:male gamete + male gamete + CL:0000408 + + + CL:polyploid cell + polyploid cell + CL:0000412 + "A cell whose nucleus, or nuclei, each contain more than two haploid genomes." [FB:ma] + + + CL:haploid cell + CL:0000413 + haploid cell + "A cell whose nucleus contains a single haploid genome." [FB:ma, GOC:tfm] + + + diploid cell + "A cell whose nucleus has two haploid genomes." [FB:ma] + CL:0000415 + CL:diploid cell + + + CL:endopolyploid cell + endopolyploid cell + CL:0000417 + + + CL:excretory cell + "A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids." [GOC:tfm, PMID:19783135] + excretory cell + CL:0000424 + + + CL:apoptosis fated cell + CL:0000445 + apoptosis fated cell + + + CL:carbohydrate secreting cell + carbohydrate secreting cell + CL:0000447 + + + white fat cell + CL:white fat cell + white adipose cell + "Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole." [GOC:tfm, MESH:A11.329.114.500] + white adipocyte + white fat cell + CL:0000448 + + + brown adipocyte + "A cell from the thermogenic form of adipose tissue found in newborns of many species, including humans, and in hibernating mammals. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation." [MESH:A10.165.114.322] + brown fat cell + brown adipose cell + CL:0000449 + CL:brown fat cell + + + veiled cell + CL:0000451 + CL:dendritic cell + interdigitating cell + "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative)." [GOC:add, ISBN:0781735149] + dendritic cell + + + CL:biogenic amine secreting cell + biogenic amine secreting cell + CL:0000457 + + + 5-HT secreting cell + "A cell type that secretes 5-Hydroxytryptamine (serotonin)." [GOC:tfm, PMID:19630576] + serotonin secreting cell + CL:serotonin secreting cell + 5-Hydroxytryptamine secreting cell + CL:0000458 + + + "A cell whose primary function is to protect the organism." [JB:jb] + CL:defensive cell + CL:0000473 + defensive cell + + + CL:follicle cell + follicle cell + CL:0000477 + ovarian follicle cell + + + visible light photoreceptor cell + CL:visible light photoreceptor cell + "A photoreceptor cell that detects visible light." [GOC:tfm] + CL:0000488 + + + photopic photoreceptor cell + CL:photopic photoreceptor cell + CL:0000490 + + + "A CD4-positive, alpha-beta T cell that cooperates with other lymphocytes via direct contact or cytokine release to initiate a variety of immune functions." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, ISBN:0781735149, MESH:A11.118.637.555.567.569.200.400] + CD4-positive helper T-lymphocyte + CD4-positive T-helper cell + CD4-positive helper T-cell + CL:0000492 + CD4-positive helper T lymphocyte + CD4-positive helper T cell + CL:CD4-positive helper T cell + + + blue sensitive photoreceptor cell + "A photoreceptor cell that is sensitive to blue light." [GO:tfm] + CL:blue sensitive photoreceptor cell + CL:0000495 + + + stromal cell + CL:stromal cell + "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere." [GOC:tfm, MESH:A11.329.830] + CL:0000499 + + + CL:0000502 + "A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin." [MESH:A03.492.766.440.175] + D cell + CL:type D enteroendocrine cell + type D enteroendocrine cell + + + "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix." [GOC:tfm, ISBN:0517223651, MESH:A03.492.411.369.700] + CL:paneth cell + paneth cell + CL:0000510 + + + "A peptide hormone secreting cell that secretes androgen binding protein." [GO:tfm] + CL:androgen binding protein secreting cell + CL:0000511 + androgen binding protein secreting cell + + + CL:0000515 + "A myoblast that differentiates into skeletal muscle fibers." [SANBI:mhl] + skeletal muscle myoblast + skeletal myoblast + CL:skeletal muscle myoblast + + + CL:0000519 + CL:phagocyte (sensu Nematoda and Protostomia) + phagocyte (sensu Nematoda and Protostomia) + "A phagocyte from organisms in the Nematoda or Protostomia clades." [GOC:tfm] + + + fungal cell + CL:0000521 + CL:fungal cell + + + input neuron + CL:0000526 + CL:afferent neuron + "A neuron which conveys sensory information centrally from the periphery." [GOC:tfm, MESH:A08.663.650] + afferent neuron + + + CL:efferent neuron + CL:0000527 + "A neuron which sends impulses peripherally to activate muscles or secretory cells." [MESH:A08.663.655] + output neuron + efferent neuron + + + pigmented epithelial cell + CL:pigmented epithelial cell + CL:0000529 + + + primary neuron + CL:0000530 + CL:primary neuron + + + nerve cell + CL:neuron + neuron + "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [http://en.wikipedia.org/wiki/Neuron, MESH:A08.663, MESH:D009474] + CL:0000540 + + + CL:melanoblast + "A cell that originates from the neural crest and differentiates into a pigment cell." [GOC:tfm, SANBI:mhl] + melanoblast + CL:0000541 + + + CL:lymphocyte + "A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [GOC:add, ISBN:0683073696, ISBN:0781735149] + CL:0000542 + lymphocyte + + + "A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19375293, PMID:20303875, PMID:22343568] + T helper cells type 1 + Th1 cell + CL:T-helper 1 cell + Th1 T-lymphocyte + Th1 T-cell + Th1 T cell + Th1 CD4+ T cell + T(H)-1 cell + CL:0000545 + Th1 T lymphocyte + T-helper 1 cell + helper T cell type 1 + + + T-helper 2 cell + T helper cells type 2 + Th2 T cell + Th2 cell + CL:0000546 + Th2 T-lymphocyte + T(H)-2 cell + "A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive, CXCR3-negative, CCR6-negative, and is capable of producing interleukin-4." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19375293, PMID:20103781, PMID:22343568] + Th2 T-cell + Th2 T lymphocyte + CL:T-helper 2 cell + helper T cell type 2 + + + "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." [ISBN:0721601464, MESH:A11.118.290.350.200, PMID:1638021] + rubriblast + CL:0000547 + CL:proerythroblast + proerythroblast + pronormoblast + + + CL:animal cell + CL:0000548 + animal cell + + + basophilic erythroblast + basophilic normoblast + early normoblast + prorubricyte + "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." [GOC:tfm, ISBN:0721601464] + CL:basophilic erythroblast + early erythroblast + CL:0000549 + + + megacaryocyte + "A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm." [http://en.wikipedia.org/wiki/Megakaryocyte, ISBN:0721601464, MESH:D008533] + megalokaryocyte + CL:megakaryocyte + CL:0000556 + megalocaryocyte + megakaryocyte + + + CL:0000558 + "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [GOC:add, GOC:tfm, PMID:15946868, PMID:2037622] + reticulocyte + CL:reticulocyte + + + CL:amacrine cell + CL:0000561 + amacrine neuron + amacrine cell + "Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons." [GOC:tfm, MESH:A08.663.358.050] + + + "A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell." [GOC:tfm, ISBN:0721662544, MESH:A11.070] + amine precursor uptake and decarboxylation cell + CL:0000568 + CL:APUD cell + APUD cell + + + CL:0000573 + retinal cone cell + CL:retinal cone cell + "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision." [MESH:A08.663.650.650.670.100] + + + "Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells." [GO_REF:0000031, MESH:A11.118.637.555.652] + CL:monocyte + CL:0000576 + monocyte + + + CL:experimentally modified cell in vitro + CL:0000578 + experimentally modified cell in vitro + "A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure." [FB:ma, ReO:mhb] + + + CL:0000581 + "A macrophage resident in the peritoneum under non-inflammatory conditions. Markers include F4/80-high, CD11b-high, CD68-positive, SIGNR1-positive, CD115-high, MHC-II-negative, and Dectin-1-positive." [MESH:A11.329.372.630, PMID:15771589, PMID:19201820] + peritoneal macrophage + CL:peritoneal macrophage + + + CL:0000584 + enterocyte + CL:enterocyte + "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen." [SANBI:mhl] + + + CL:germ cell + CL:0000586 + germ cell + "The reproductive cell in multicellular organisms." [MESH:A05.360.490] + + + "A bulbous cell that is medially placed in one row in the organ of Corti. In contrast to the outer hair cells, the inner hair cells are fewer in number, have fewer sensory hairs, and are less differentiated." [MESH:A08.663.650.250.250] + cochlear inner hair cell + CL:cochlear inner hair cell + CL:0000589 + + + CL:0000593 + "A steroid hormone secreting cell that secretes androgen." [GOC:tfm] + CL:androgen secreting cell + androgen secreting cell + + + CL:0000598 + pyramidal neuron + CL:pyramidal cell + pyramidal cell + projection neuron + "A projection neuron in the cerebral cortex and the hippocampus. Pyramidal cells have a pyramid-shaped soma with the apex and an apical dendrite pointed toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their cortical region." [GOC:tfm, MESH:A08.186.211.577.405.700] + + + CL:outer hair cell + outer hair cell + "A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea." [MESH:A08.663.650.250.315] + cochlear outer hair cell + CL:0000601 + + + CL:0000604 + retinal rod cell + CL:retinal rod cell + "One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision." [MESH:A08.663.650.650.670.650] + + + vestibular receptor cell + vestibular hair cell + "A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem." [GOC:tfm, MESH:A08.663.650.250.380] + CL:vestibular hair cell + CL:0000609 + + + natural killer cell + CL:0000623 + NK cell + CL:natural killer cell + "A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells." [GOC:add, ISBN:0781735149, PMID:15771571] + + + CL:0000624 + CL:CD4-positive, alpha-beta T cell + CD4-positive, alpha-beta T cell + "A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor." [GOC:add, ISBN:0781735149] + CD4-positive, alpha-beta T lymphocyte + CD4-positive, alpha-beta T-cell + CD4-positive, alpha-beta T-lymphocyte + + + transporting cell + CL:0000627 + CL:transporting cell + "A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances." [TAIR:sr] + + + supportive cell + "A cell whose primary function is to support other cell types." [FB:ma, GOC:tfm] + CL:supportive cell + CL:0000630 + + + CL:0000635 + CL:Deiter's cell + Deiters cell + outer phalangeal cell + "The outer phalangeal cells of the organ of Corti. This cell holds the base of the hair cell in a cup-shaped depression." [GOC:tfm, http://www.britannica.com/EBchecked/topic/156177/Deiters-cell, ISBN:0721662544] + Deiter's cell + + + CL:Mueller cell + CL:0000636 + Mueller cell + + + CL:basal cell + basal cell + "Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament." [GOC:tfm, ISBN:0517223651] + CL:0000646 + + + CL:0000649 + "A cell with delicate radiating processes known as desmosomes that form intercellular bridges between other cells of this type. This cell type forms the stratum spinosum (prickle cell layer. A function of this cell is to generate keratin." [GOC:tfm, ISBN:0721662544, ISBN:0815332181] + prickle cell of epidermis + prickle cell + CL:prickle cell + + + "A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries." [GOC:tfm, http://www.copewithcytokines.de/cope.cgi?key=mesangial%20cells] + CL:0000650 + CL:mesangial cell + mesangial cell + + + "This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation." [GOC:tfm, http://en.wikipedia.org/wiki/Pinealocyte, ISBN:0517223651, PMID:16687276] + CL:pinealocyte + pinealocyte + CL:0000652 + + + podocyte + glomerular podocyte + "A glomerular visceral epithelial cell is a specialized kidney epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells." [GOC:tfm] + CL:glomerular visceral epithelial cell + CL:0000653 + glomerular visceral epithelial cell + + + CL:primary oocyte + primary oocyte + "A primary oocyte is an oocyte that has not completed female meosis I." [GOC:tfm, ISBN:0721662544] + primary oogonium + CL:0000654 + + + primary spermatocyte + CL:0000656 + CL:primary spermatocyte + "A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes." [GOC:tfm, ISBN:0721662544] + + + CL:collagen secreting cell + CL:0000667 + "An extracellular matrix secreting cell that secretes collagen." [GOC:tfm] + collagen secreting cell + + + ARC + pericyte cell + pericyte + adventitial reticular cell + "An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells." [GOC:dsd, GOC:tfm, ISBN:0721662544, MESH:D020286, PMID:16807374, PMID:17986482, PMID:20024907] + CL:pericyte cell + CL:0000669 + pericyte of Rouget + cell of Rouget + adventitial cell + + + CL:primordial germ cell + primordial germ cell + "A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells." [GOC:tfm, PMID:1381289] + CL:0000670 + gonocyte + primitive germ cell + + + CL:female gamete + CL:0000675 + female gamete + "A mature sexual reproductive cell of the female germline." [GOC:tfm] + + + CL:cap cell + cap cell + CL:0000676 + + + CL:0000677 + "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules." [JB:jb] + CL:gut absorptive cell + gut absorptive cell + + + muscle precursor cell + CL:muscle precursor cell + CL:0000680 + + + CL:radial glial cell + radial glial cell + "A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration." [GOC:dph] + CL:0000681 + + + CL:M cell of gut + M-cell + "An absorptive cell of the gut epithelium that endocytoses microorganisms and intact macromolecules from the gut lumen and transports them to the subepithelial space where they are presented to antigen-presenting cells and lymphocytes." [GOC:jb, GOC:tfm] + CL:0000682 + M cell of gut + microfold cell + + + R1 photoreceptor cell + CL:0000687 + CL:R1 photoreceptor cell + + + CL:dopaminergic neuron + dopaminergic cell + CL:0000700 + "A neuron that releases dopamine as a neurotransmitter." [GOC:dhill] + dopaminergic neuron + + + R6 photoreceptor cell + CL:R6 photoreceptor cell + CL:0000705 + + + "Epithelial cells derived from neural plate and neural crest." [GOC:tfm] + CL:0000710 + neurecto-epithelial cell + CL:neurecto-epithelial cell + + + CL:stratum granulosum cell + stratum granulosum cell + CL:0000712 + + + somatic stem cell + CL:somatic stem cell + CL:0000723 + "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] + + + "Muscle cell which has as its direct parts myofilaments organized into sarcomeres." [GOC:tfm, ISBN:0721662544] + striated muscle cell + CL:0000737 + CL:striated muscle cell + + + CL:leukocyte + "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [GOC:add, GOC:tfm, ISBN:978-0-323-05290-0] + CL:0000738 + leukocyte + immune cell + leucocyte + white blood cell + + + CL:0000740 + "The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve." [GOC:dph] + RGC + retinal ganglion cell + CL:retinal ganglion cell + ganglion cell of retina + gangliocyte + + + "Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification)." [GO_REF:0000034, PMID:15951842] + hypertrophic chondrocyte + CL:hypertrophic chondrocyte + CL:0000743 + + + CL:0000745 + CL:horizontal cell + horizontal cell + "A neuron that laterally connects other neurons in the inner nuclear layer of the retina." [ISBN:0195088433] + + + CL:0000746 + "Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei." [GOC:mtg_cardiacconduct_nov11, GOC:tfm, ISBN:0323052908, PMID:22426062, PMID:4711263] + CL:cardiac muscle cell + cardiac muscle cell + cardiac myocyte + heart muscle cell + cardiac muscle fiber + cardiomyocyte + + + "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer." [PMID:14689473] + CL:0000748 + CL:retinal bipolar neuron + retinal bipolar neuron + + + ON-bipolar cell + CL:0000749 + CL:ON-bipolar cell + "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors." [PMID:14689473] + + + OFF-bipolar cell + CL:0000750 + CL:OFF-bipolar cell + "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the outer half of the inner plexiform layer. These cells hyperpolarize in response to light stimulation of their corresponding photoreceptors." [PMID:14689473] + + + CL:rod bipolar cell + CL:0000751 + rod bipolar cell + "A bipolar neuron found in the retina and having connections with rod photoreceptor cells and neurons in the inner plexiform layer." [GOC:tfm, PMID:14689473] + + + CL:cone retinal bipolar cell + "A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer." [PMID:14689473] + cone retinal bipolar cell + CL:0000752 + + + myeloid cell + "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." [GOC:add] + CL:myeloid cell + CL:0000763 + + + erythropoietic cell + CL:0000764 + CL:erythroid lineage cell + erythroid lineage cell + "A immature or mature cell in the lineage leading to and including erythrocytes." [GOC:add, GOC:tfm] + + + erythroblast + CL:0000765 + normoblast + "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." [GOC:add, ISBN:0721601464, PMID:18174176] + CL:erythroblast + + + CL:0000766 + CL:myeloid leukocyte + "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] + myeloid leukocyte + + + "Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive." [GOC:add, GOC:amm, GOC:dsd, GOC:tfm, ISBN:0721601464, MESH:D001491, PMCID:PMC2626675, PMID:11927641, PMID:19741522, PMID:21236338, PMID:9933081] + CL:0000767 + basophilic leukocyte + basophil + CL:basophil + basophilic leucocyte + + + eosinophilic leukocyte + eosinophilic granulocyte + CL:eosinophil + "Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive." [GOC:add, GOC:amm, GOC:dsd, GOC:tfm, ISBN:0721601464, PMCID:PMC2626675, PMID:10914487, PMID:1662676] + eosinophil + eosinophilic leucocyte + eosinocyte + CL:0000771 + + + neutrophil leukocyte + neutrophilic leucocyte + neutrocyte + "Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes." [GOC:add, GOC:amm, GOC:tfm, ISBN:0721601464] + neutrophil leucocyte + CL:0000775 + neutrophil + neutrophilic leukocyte + CL:neutrophil + + + "Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking." [GOC:add, ISBN:0721601464] + immatuer neutrophilic leukocyte + CL:0000776 + immature neutrophil leukocyte + immature neutrocyte + immature neutrophilic leucocyte + immature neutrophil + immature neutrophil leucocyte + CL:immature neutrophil + + + alpha-beta T cell + alpha-beta T-lymphocyte + "A T cell that expresses an alpha-beta T cell receptor complex." [GOC:add, GOC:tfm, ISBN:0781735149] + CL:0000789 + CL:alpha-beta T cell + alpha-beta T lymphocyte + alpha-beta T-cell + + + CL:mature alpha-beta T cell + mature alpha-beta T cell + "A alpha-beta T cell that has a mature phenotype." [GOC:add, GOC:tfm, ISBN:0781735149] + mature alpha-beta T-lymphocyte + CL:0000791 + mature alpha-beta T-cell + mature alpha-beta T lymphocyte + + + memory T lymphocyte + memory T-lymphocyte + memory T cell + "A distinctly differentiated long-lived T cell that has the phenotype CD45RO-positive and CD127-positive." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, ISBN:0781735149] + CL:memory T cell + CL:0000813 + memory T-cell + + + regulatory T-lymphocyte + regulatory T lymphocyte + "A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release." [GO_REF:0000031, GOC:add] + regulatory T-cell + CL:regulatory T cell + regulatory T cell + CL:0000815 + + + CL:promyelocyte + "A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative." [GOC:add, GOC:amm, GOC:tfm, http://www.cap.org, ISBN:0721601464] + promyelocyte + CL:0000836 + + + CL:myeloid lineage restricted progenitor cell + CL:0000839 + myeloid lineage restricted progenitor cell + "A progenitor cell restricted to the myeloid lineage." [GOC:add, GOC:tfm, PMID:19022770] + + + CL:mononuclear cell + mononuclear cell + CL:0000842 + "A leukocyte with a single non-segmented nucleus in the mature form." [GOC:add] + + + vestibular dark cell + "An epithelial cell of the vestibular sensory organ that is characterized by intense enzymatic activities and numerous basal membrane infoldings." [PMID:11223304] + CL:vestibular dark cell + CL:0000846 + + + CL:sensory hair cell + "Hair cell is a mechanoreceptor cell that is sensitive to movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." [SANBI:mhl] + sensory hair cell + CL:0000855 + + + CL:0000857 + CL:slow muscle myoblast + slow muscle myoblast + "A skeletal muscle myoblast that differentiates into slow muscle fibers." [SANBI:mhl] + + + CL:0000861 + elicited macrophage + free macrophage + CL:elicited macrophage + "A macrophage which develops from an inflammatory monocyte and is recruited into the tissues in response to injury and infection as part of an inflammatory response. Markers include CD11b-positive, CD68-positive, and F4/80-positive." [GO_REF:0000031, GOC:add, GOC:ana, GOC:tfm, PMID:15771589] + wandering histiocyte + + + "A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells." [GO_REF:0000031, GOC:ana, PMID:19770654] + resting histiocyte + fixed macrophage + CL:0000864 + CL:tissue-resident macrophage + tissue-resident macrophage + + + CL:0000878 + central nervous system macrophage + CL:central nervous system macrophage + "A tissue-resident macrophage found in the central nervous system." [GO_REF:0000031, PMID:16322748] + CNS macrophage + + + CL:thymocyte + thymic lymphocyte + thymocyte + CL:0000893 + "An immature T cell located in the thymus." [GO_REF:0000031, GOC:add, GOC:tfm, PMID:12415312] + + + CL:0000898 + naive T-cell + "Mature T cell not yet exposed to antigen with the phenotype CCR7-positive, CD45RA-positive, and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19100699] + CL:naive T cell + naive T lymphocyte + naive T cell + naive T-lymphocyte + + + CL:effector T cell + effector T-cell + effector T lymphocyte + CL:0000911 + "A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response." [GOC:PAM-ADD, GOC:tfm, ISBN:0877799148, PMID:18395547] + effector T cell + effector T-lymphocyte + + + CL:0000912 + helper T lymphocyte + helper T-cell + helper T cell + T-helper cell + helper T-lymphocyte + "A effector T cell that provides help in the form of secreted cytokines to other immune cells." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:18395547] + CL:helper T cell + + + "A lymphocyte of B lineage is a lymphocyte that expresses CD19 on the cell surface. An additional defining characteristic is the commitment to express an immunoglobulin complex." [GO_REF:0000031, GOC:add, GOC:rhs, GOC:tfm, ISBN:0781735149] + CL:lymphocyte of B lineage + lymphocyte of B lineage + CL:0000945 + + + hematopoietic cell + haemopoietic cell + CL:hematopoietic cell + hemopoietic cell + "A cell of a hematopoietic lineage." [GO_REF:0000031, GOC:add] + haematopoietic cell + CL:0000988 + + + "Granule cell that is part of the cerebellum." [GOC:mah] + CL:0001031 + cerebellar granule cell + CL:cerebellar granule cell + + + cell in vitro + CL:0001034 + "A cell that is maintained or propagated in a controlled artificial environment for use in an investigation." [ReO:mhb] + CL:cell in vitro + + + CL:bone cell + "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] + CL:0001035 + bone cell + + + "A CD4-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative." [GOC:add, PMID:22343568] + CL:0001051 + CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T-cell + CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T lymphocyte + CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell + CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T-lymphocyte + CL:CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell + + + CL:hematopoietic lineage restricted progenitor cell + hematopoietic lineage restricted progenitor cell + "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] + CL:0002031 + + + small alveolar cells + squamous alveolar lining cell + type 1 alveolar epithelial cells + type 1 pneumocyte + "A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange." [GOC:tfm, http://www.copewithcytokines.de, PMID:20054144] + type I alveolar epithelial cells + squamous alveolar cell + pulmonary alveolar type I cell + CL:type I pneumocyte + AT1 + CL:0002062 + lung type 1 cells + type I alveolar cells + ATI + type I pneumocyte + membranous pneumocytes + + + TII + ATII + "A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli." [GOC:tfm, http://www.copewithcytokines.de, ISBN:0412046911, PMID:8540632] + type 2 alveolocyte + type 2 pneumocyte + lung type II cell + type II alveolar epithelial cell + CL:type II pneumocyte + great alveolar cell + type II alveolocyte + type 2 alveolar epithelial cell + type II alveolar cell + AT2 + CL:0002063 + type II pneumocyte + lung type 2 cell + cuboidal type II cell + granular pneumocyte + + + CL:type A enterocrine cell + CL:0002067 + type A enterocrine cell + "An enterocrine cell that produces glucagon." [GOC:tfm, ISBN:0412046911] + + + "An epithelial cell derived from endoderm." [FMA:69075, GOC:tfm] + endo-epithelial cell + CL:0002076 + CL:endo-epithelial cell + + + "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] + CL:0002077 + ecto-epithelial cell + CL:ecto-epithelial cell + + + CL:0002078 + epithelial mesenchymal cell + "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] + CL:meso-epithelial cell + meso-epithelial cell + + + "A leukocyte that lacks granules." [GOC:tfm] + CL:nongranular leukocyte + agranular leukocyte + CL:0002087 + nongranular leukocyte + + + CL:bone marrow cell + CL:0002092 + bone marrow cell + "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." [GOC:tfm, ISBN:0618947256] + + + CL:0002139 + "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." [GOC:dsd, GOC:tfm, PMID:12768659] + CL:endothelial cell of vascular tree + vascular endothelial cell + endothelial cell of vascular tree + + + CL:0002159 + CL:general ecto-epithelial cell + general ecto-epithelial cell + "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] + + + CL:0002165 + "A supporting cell that is attached to the basement membrane and forms rows that support the hair cells." [GOC:tfm, ISBN:0618947256] + phalangeal cell + CL:phalangeal cell + + + epithelial cell of stomach + CL:0002178 + CL:epithelial cell of stomach + "An epithelial cell found in the lining of the stomach." [GOC:tfm] + + + "A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane." [GOC:tfm, ISBN:0517223651] + CL:0002187 + basal cell of epidermis + CL:basal cell of epidermis + + + CL:granulocytopoietic cell + CL:0002191 + granulocytopoietic cell + "A cell involved in the formation of a granulocyte." [GOC:tfm] + + + CL:epithelial cell of tracheobronchial tree + "An epithelial cell of the tracheobronchial tree." [GOC:tfm] + epithelial cell of tracheobronchial tree + CL:0002202 + + + red muscle cell + red muscle fiber + oxidative muscle fiber + CL:0002210 + "A slow muscle cell that contains high levels of myoglobin and oxygen storing proteins giving the cell a red appearance." [GOC:tfm, ISBN:0517223651] + CL:red muscle cell + + + type 1 muscle cell + slow-twitch muscle fiber + slow twitch fiber + type I muscle cell + type I muscle fiber + "A slow muscle cell that has large amounts of myoglobin, stores energy as triglycerides, generates ATP by the oxidative method and is resistant to fatigue." [GOC:tfm, ISBN:0517223651] + CL:type I muscle cell + intermediate muscle fiber + CL:0002211 + type 1 muscle fiber + slow twitch muscle fiber + slow twitch muscle cell + + + type 2 muscle cell + type II muscle cell + CL:type II muscle cell + CL:0002212 + type II muscle fiber + type 2 muscle fiber + "A fast muscle fiber cell that stores energy in the form of glycogen and creatine phosphate." [GOC:tfm] + + + "A muscle cell with low content of myoglobin and other oxygen storing proteins. This muscle cell has a white appearance." [GOC:tfm, ISBN:0517223651] + white muscle cell + CL:white muscle cell + CL:0002213 + + + fatigue resistant fast twitch muscle cell + fast twitch A + type 2a muscle fiber + "A type II muscle cell that contains large amounts of myoglobin, has many mitochondria and very many blood capillaries. Type II A cells are red, have a very high capacity for generating ATP by oxidative metabolic processes, split ATP at a very rapid rate, have a fast contraction velocity and are resistant to fatigue." [GOC:tfm] + type 2a muscle cell + CL:type IIa muscle cell + type IIa muscle cell + type IIa muscle fiber + CL:0002214 + + + type 2b muscle cell + type 2b muscle fiber + "A type II muscle cell that contains a low content of myoglobin, relatively few mitochondria, relatively few blood capillaries and large amounts of glycogen. Type II B fibres are white, geared to generate ATP by anaerobic metabolic processes, not able to supply skeletal muscle fibres continuously with sufficient ATP, fatigue easily, split ATP at a fast rate and have a fast contraction velocity." [GOC:tfm, http://en.wikipedia.org/wiki/Skeletal_muscle, ISBN:0517223651] + type IIb muscle cell + CL:0002215 + CL:type IIb muscle cell + type IIb muscle fiber + + + vertebrate lens cell + "A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye." [GOC:tfm, ISBN:0721662544] + CL:vertebrate lens cell + CL:0002222 + + + lens epithelial cell + CL:lens epithelial cell + "A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth." [GOC:tfm, http://en.wikipedia.org/wiki/Lens_%28anatomy%29#Lens_epithelium, ISBN:0721662544] + CL:0002224 + + + primary lens fiber + CL:0002228 + "An elongating cell that rapidly obliterates the lumen of the lens vesicle. Subsequently, differentiation of this cell type at the lens equator leads to the formation of secondary fiber cells that come to overlie the primary fibers." [GOC:tfm, PMID:10711704] + CL:primary lens fiber + primary lens fibre + + + prostate epithelial cell + "An epithelial cell of the prostate." [GOC:tfm] + epithelial cell of prostate + CL:0002231 + CL:epithelial cell of prostate + + + CL:nucleate cell + nucleate cell + CL:0002242 + "A cell containing at least one nucleus." [GOC:tfm] + + + CL:pluripotent stem cell + CL:0002248 + "A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta." [GOC:tfm, PMID:19343304] + pluripotent stem cell + + + epithelial cell of alimentary canal + CL:0002251 + CL:epithelial cell of alimentary canal + "An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus." [GOC:tfm, ISBN:0721662544] + + + epithelial cell of small intestine + CL:epithelial cell of small intestine + CL:0002254 + "An epithelial cell of the small intestine." [GOC:tfm] + + + epithelial cell of thyroid gland + "An epithelial cell of thyroid gland." [GOC:tfm] + CL:epithelial cell of thyroid gland + CL:0002257 + + + CL:0002262 + "An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver." [GOC:tfm, ISBN:0618947256] + endothelial cell of sinusoid + CL:endothelial cell of sinusoid + + + CL:0002274 + "A cell type that secretes histamine." [GOC:tfm] + CL:histamine secreting cell + histamine secreting cell + + + epithelial cell of thymus gland + thymic epithelial cell + CL:epithelial cell of thymus + epithelial reticular cell + epithelial reticular cell of thymus + "An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies." [FMA:72208, GOC:tfm] + epithelial cell of thymus + CL:0002293 + + + CL:0002315 + supporting cell of cochlea + CL:supporting cell of cochlea + "An epithelial supporting cell located in the cochlea." [GOC:tfm] + + + neural cell + CL:0002319 + "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] + CL:neural cell + + + CL:0002320 + connective tissue cell + CL:connective tissue cell + "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] + + + embryonic cell + "A cell of the embryo." [FMA:0618947256] + CL:0002321 + CL:embryonic cell + + + "A stem cell of embryonic origin." [GOC:dsd, GOC:tfm, ISBN:068340007X, PMID:18179856] + CL:embryonic stem cell + CL:0002322 + ESC + embryonic stem cell + + + CL:0002327 + mammary epithelial cell + CL:mammary epithelial cell + breast epithelial cell + "An epithelial cell of the mammary gland." [GOC:tfm, PMID:19022771] + + + CL:0002328 + CL:bronchial epithelial cell + "An epithelial cell of the bronchus." [GOC:tfm] + bronchial epithelial cell + + + CL:cortical thymic epithelial cell + "An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells." [GOC:tfm, PMID:18403190] + cortical thymic epithelial cell + cTEC + CL:0002364 + + + CL:medullary thymic epithelial cell + mTEC + CL:0002365 + medullary thymic epithelial cell + "An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output." [GOC:tfm, PMID:18180458] + + + airway epithelial cell + CL:respiratory epithelial cell + respiratory epithelial cell + CL:0002368 + "An endo-epithelial cell of the respiratory tract." [GOC:tfm] + + + fungal spore + CL:0002369 + CL:fungal spore + "A differentiated form of a fungus produced during or as a result of an asexual or sexual reproductive process; usually a cell with a thick cell wall that stores and protects one or more nuclei. Spores may be produced in response to, and are characteristically resistant to, adverse environmental conditions." [FAO:0000019, GOC:tfm] + + + CL:somatic cell + somatic cell + "A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell)." [GOC:tfm, ISBN:0721662544] + CL:0002371 + + + "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] + single cell sarcomere + CL:0002372 + CL:myotube + myotube + myotubule + + + CL:ear hair cell + ear hair cell + ear receptor cell + CL:0002374 + "A hair cell of the ear that contains the organs of balance and hearing." [GOC:dph, GOC:tfm, ISBN:0192801023] + + + mature T-cell + "A T cell that expresses a T cell receptor complex and has completed T cell selection." [GOC:tfm] + CD3epsilon T cell + CL:0002419 + CD3e-positive T cell + mature T cell + CL:mature T cell + + + CL:0002420 + CL:immature T cell + "A T cell that has not completed T cell selection." [GOC:tfm] + immature T cell + immature T-cell + + + CL:mammary stem cell + CL:0002451 + mammary stem cell + "A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi." [GOC:hjd, GOC:tfm, PMID:15987436, PMID:16397499, PMID:17851544] + + + peritubular myoid cell + CL:peritubular myoid cell + "The flattened smooth myoepithelial cells of mesodermal origin that lie just outside the basal lamina of the seminiferous tubule." [GOC:cjm, GOC:tfm, MP:0006420] + CL:0002481 + + + hair follicle melanocyte + CL:hair follicle melanocyte + "A melanocyte that produces pigment within the hair follicle." [GOC:tfm, MP:0004381] + CL:0002483 + + + "A melanocyte that produces pigment in the epithelium." [GOC:tfm, MP:0009388] + epithelial melanocyte + CL:epithelial melanocyte + CL:0002484 + + + CL:strial intermediate cell + "A melanocyte located between the epithelial marginal cell layer and the mesodermal basal cell layer within the intrastrial space; the predominant cellular component of the electrogenic machinery that generates an endocochlear potential (80-100 mV) ." [GOC:tfm, MP:0000048] + CL:0002486 + strial intermediate cell + + + CL:trophoblast giant cell + giant trophoblast cell + trophoblast giant cell + "A trophoblast cell that has a large volume of cytoplasm, is polyploidy and is usually mononuclear but is also occasionally multi-nucleate. This cell type is important in establishing maternal physiology and remodeling of the vasculature of the placenta." [GOC:tfm, MP:0001714, MP:19876834] + CL:0002488 + + + CL:organ of Corti supporting cell + CL:0002490 + organ of Corti supporting cell + "A supporting cell of the organ of Corti." [GOC:tfm, MP:0004300] + + + CL:0002491 + "A specialized cell involved in auditory sensory perception." [GOC:tfm] + CL:auditory epithelial cell + auditory epithelial cell + + + strial marginal cell + CL:0002492 + CL:strial marginal cell + "A polarized columnar cell that covesr the lateral surface of the cochlear duct, secretes potassium ions and forms a continuous sheet in contact with the endolymph; marginal cells form extensive interdigitations with the basal and intermediate cells in the normal adult stria." [GOC:tfm, MP:0004366] + + + cardiocyte + "A cell located in the heart, including both muscle and non muscle cells." [GOC:tfm] + CL:0002494 + CL:cardiocyte + heart cell + + + neonatal cardiomyocyte + fetal cardiomyocyte + CL:0002495 + embryonic cardiomyocyte + CL:fetal cardiomyocyte + "A fetal and neonatal heart cell that undergoes proliferation and is not yet terminally differentiated into a binucleate or a multinucleate cardiac myocyte." [GOC:tfm, MP:0008788] + + + CL:primary trophoblast giant cell + CL:0002497 + primary trophoblast giant cell + "A trophoblast giant cell derived from the mural trophectoderm." [GOC:tfm, PMCID:PMC85124] + + + CL:secondary trophoblast giant cell + secondary trophoblast giant cell + CL:0002498 + "A trophoblast giant cell that is derived from ectoplacental cone and, later in gestation, the spongiotrophoblast." [GOC:tfm, PMCID:PMC85124] + + + CL:kidney epithelial cell + kidney epithelial cell + "An epithelial cell of the kidney." [GOC:tfm, KUPO:SJ] + CL:0002518 + + + "A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both." [GOC:tfm] + CL:0002522 + CL:renal filtration cell + renal filtration cell + + + mesenchymal stem cell of the bone marrow + CL:mesenchymal stem cell of the bone marrow + "A mesenchymal stem cell that is part of the bone marrow." [GOC:tfm] + CL:0002540 + + + CL:0002551 + fibroblast of dermis + CL:fibroblast of dermis + + + hair follicle cell + "An animal cell that is part of a hair follicle." [GOC:tfm] + CL:hair follicle cell + CL:0002559 + + + CL:0002561 + outer root sheath cell + "An epithelial cell that is part of the outer root sheath." [GOC:tfm] + CL:outer root sheath cell + + + CL:0002563 + CL:intestinal epithelial cell + intestinal epithelial cell + "An epithelial cell of the intestine." [GOC:tfm] + + + CL:Schwann cell + CL:0002573 + "A glial cell that ensheathes axons of neuron in the peripheral nervous system and are necessary for their maintainance and function." [GOC:tfm] + Schwann cell + + + CL:0002584 + "An epithelial cell of the kidney cortex." [GOC:tfm] + CL:renal cortical epithelial cell + renal cortical epithelial cell + + + smooth muscle cell of the coronary artery + CL:smooth muscle cell of the coronary artery + CL:0002592 + "A smooth muscle cell of the coronary artery." [GOC:tfm] + + + astrocyte of the cerebral cortex + CL:0002605 + CL:astrocyte of the cerebral cortex + "An astrocyte of the cerebral cortex." [GOC:tfm] + + + "A neuron of the hippocampus." [GOC:tfm] + CL:0002608 + hippocampal neuron + CL:hippocampal neuron + + + CL:neuron of cerebral cortex + CL:0002609 + neuron of cerebral cortex + "A CNS neuron of the cerebral cortex." [GOC:tfm] + cortical neuron + + + CL:0002613 + CL:striatum neuron + "A neuron of the striatum." [GOC:tfm] + striatum neuron + + + CL:skin fibroblast + "A fibroblast of skin." [GOC:tfm] + CL:0002620 + skin fibroblast + + + "A cell of the seminiferous tubule epithelium." [GOC:tfm] + seminiferous tubule epithelial cell + CL:0002625 + CL:seminiferous tubule epithelial cell + + + "An immature astrocyte." [GOC:dsd] + CL:immature astrocyte + immature astrocyte + CL:0002626 + immature astrocytic glia + + + mature astrocyte + mature astrocytic glia + CL:0002627 + activated astrocyte + "A mature astrocyte that is capable of producing cytokines." [GOC:dsd, PMID:12898703, PMID:8734446] + CL:mature astrocyte + + + reactive microglia + CL:0002629 + CL:mature microglial cell + mature microglia + mature microglial cell + "A mature microglial cell that has changed shape to an amoeboid morphology and is capable of cytokine production and antigen presentation." [GOC:dsd, PMID:11517395, PMID:14612429, PMID:15246020, PMID:16177057, PMID:18396103, PMID:20021364] + activated microglia + + + CL:epithelial cell of lower respiratory tract + epithelial cell of lower respiratory tract + CL:0002632 + + + otic fibrocyte + "A fibrocyte of the cochlea that has specialized structural and molecular adaptions." [GOC:tfm, PMID:18353863] + CL:0002665 + CL:otic fibrocyte + + + type II otic fibrocyte + type II spiral ligament fibrocyte + CL:0002666 + CL:type 2 otic fibrocyte + "An otic fibrocyte that underlies the spiral prominence and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." [GOC:tfm, PMID:18353863] + type 2 otic fibrocyte + + + CL:0002670 + type 1 otic fibrocyte + CL:type 1 otic fibrocyte + "An otic fibrocyte that underlies the stria vascularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." [GOC:tfm, PMID:18353863] + type I spiral ligament fibrocyte + type I otic fibrocyte + + + CL:retinal progenitor cell + retinal progenitor cell + "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." [GOC:tfm, PMID:20959166, PMID:21148186] + CL:0002672 + + + CL:0002681 + CL:kidney cortical cell + kidney cortical cell + + + CL:renal principal cell + "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the cells apical membrane is regulated by aldosterone and vasopressin. In mammals these cells are located in the renal collecting ducts." [CL:CVS] + renal principal cell + CL:0005009 + + + CL:auditory epithelial support cell + "A non-sensory cell that extends from the basement membrane to the apical surface of the auditory epithelium and provides support for auditory hair cells." [CL:CVS, GOC:tfm] + auditory epithelial support cell + CL:0005014 + + + inner phalangeal cell + CL:inner phalangeal cell + CL:0005015 + "An auditory epithelial support cell that surrounds the nerve fibers and synapses of the auditory inner hair cells." [CL:CVS] + + + CL:0007010 + preosteoblast + osteoprogenitor cell + "Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells." [GO_REF:0000034] + CL:preosteoblast + + + "Muscle precursor cell that is adjacent to the notochord and part of the presomitic mesoderm." [PMID:8951054] + adaxial cell + CL:adaxial cell + CL:0007016 + + + non-striated muscle cell + CL:0008000 + CL:non-striated muscle cell + "Any muscle cell in which the fibers are not organised into sarcomeres." [GOC:DOS] + + + CL:hematopoietic precursor cell + hematopoietic precursor cell + "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." [GOC:dos] + CL:0008001 + + + CL:skeletal muscle fiber + CL:0008002 + "A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." [GOC:tfm, ISBN:0323052908] + skeletal muscle fiber + + + CL:visceral muscle cell + "A muscle cell that is part of some visceral muscle" [GOC:dos] + CL:0008007 + visceral muscle cell + + + spinal sensory neuron + "A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord." [GOC:nv, GOC:pr] + CL:0009000 + CL:sensory neuron of spinal nerve + sensory neuron of spinal nerve + + + inflammatory cell + CL:inflammatory cell + CL:0009002 + "Any cell participating in the inflammatory response to a foreign substance, e.g. neutrophil, macrophage." [] + + + "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [] + CL:0009004 + CL:retinal cell + retinal cell + + + CL:stromal cell of bone marrow + CL:0010001 + stromal cell of bone marrow + "a stromal cell that is part_of a bone marrow" [] + bone marrow stromal cell + + + CL:epithelial cell of alveolus of lung + epithelial cell of alveolus of lung + CL:0010003 + alveolus of lung epithelial cell + "a epithelial cell that is part_of a alveolus of lung" [] + + + camera type eye photoreceptor cell + CL:camera type eye photoreceptor cell + CL:0010009 + + + cerebral cortex neuron + "a neuron that is part_of a cerebral cortex" [] + CL:cerebral cortex neuron + CL:0010012 + + + CL:0011001 + CL:spinal cord motor neuron + "A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement." [GOC:nv] + spinal cord motor neuron + + + CL:lens fiber cell + lens fiber cell + "A vetebrate lens cell that is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye." [GO:0070307, GOC:nv] + lens fibre cell + CL:0011004 + + + "Astrocyte-like radial glial cell that extends vertically throughout the retina, with the nucleus are usually in the middle of the inner nuclear layer.\n" [PMID:21911394] + CL:Muller cell + Muller cell + Muller glia + Müller cell + CL:0011107 + + + "Neuron found in the spriral ganglion." [] + CL:0011113 + spiral ganglion neuron + CL:spiral ganglion neuron + + + astrocyte of the forebrain + CL:astrocyte of the forebrain + "An astrocyte of the forebrain." [] + forebrain astrocyte + CL:0012000 + + + neuron of the forebrain + "A CNS neuron of the forebrain." [] + forebrain neuron + CL:neuron of the forebrain + CL:0012001 + + + "A rod-like cell in the inner ear, having their heads joined and their bases on the basilar membrane widely separated so as to form a spiral tunnel known as the tunnel of Corti." [GOC:tfm, PMID:12417662] + cochlear pillar cell + CL:1000191 + pillar cell + pillar cell of corti + CL:pillar cell + rod cell of Corti + pillar cell of cochlea + + + CL:trophectodermal cell + trophectodermal cell + CL:1000274 + trophectoderm cell + + + CL:1000415 + CL:epithelial cell of gall bladder + "An epithelial cell that is part of the gallbladder." [GOC:tfm] + epithelial cell of gall bladder + + + CL:1000426 + chromaffin cell of adrenal gland + CL:chromaffin cell of adrenal gland + "A chromaffin cell that is part of the adrenal gland." [GOC:tfm] + + + epidermal stem cell + "A somatic stem cell that is part of the epidermis." [GOC:tfm] + CL:stem cell of epidermis + stem cell of epidermis + CL:1000428 + + + epithelial cell of nephron + CL:1000449 + "An epithelial cell that is part of the nephron." [GOC:tfm] + CL:epithelial cell of nephron + + + Bowmans capsule epithelial cell + epithelial cell of glomerular capsule + epithelial cell of Bowman's capsule + CL:1000450 + CL:epithelial cell of glomerular capsule + "An epithelial cell that is part of the glomerular capsule." [GOC:tfm] + + + "An epithelial cell that is part of the visceral layer of glomerular capsule." [GOC:tfm] + CL:epithelial cell of visceral layer of glomerular capsule + CL:1000451 + epithelial cell of visceral layer of glomerular capsule + + + epithelial cell of renal collecting tubule + CL:1000454 + "An epithelial cell that is part of the collecting duct of renal tubule." [GOC:tfm] + kidney collecting duct epithelial cell + CL:kidney collecting duct epithelial cell + + + skin melanocyte + "A melanocyte that is part of the skin of body." [GOC:tfm] + CL:1000458 + melanocyte of skin + CL:melanocyte of skin + + + CL:1000497 + CL:kidney cell + kidney cell + + + kidney medulla cell + CL:kidney medulla cell + CL:1000504 + + + kidney tubule cell + CL:kidney tubule cell + CL:1000507 + + + kidney glomerular epithelial cell + CL:kidney glomerular epithelial cell + CL:1000510 + + + kidney corpuscule cell + CL:1000612 + CL:kidney corpuscule cell + + + CL:1000617 + kidney inner medulla cell + CL:kidney inner medulla cell + + + CL:1000746 + glomerular cell + CL:glomerular cell + + + kidney collecting duct cell + CL:kidney collecting duct cell + CL:1001225 + + + kidney collecting duct principal cell + CL:1001431 + CL:kidney collecting duct principal cell + + + "A neuron residing in the olfactory bulb that serve to process and refine signals arising from olfactory sensory neurons" [PMID:18603310] + CL:olfactory bulb interneuron + CL:1001434 + olfactory bulb interneuron + + + CL:sensory neuron of dorsal root ganglion + CL:1001451 + "A sensory neuron of the dorsal root ganglia that senses body position and sends information about how much the muscle is stretched to the spinal cord." [MP:0004297] + sensory neuron of dorsal root ganglion + proprioceptive neuron + + + medium spiny neuron + "the inhibitory projection neurons located in the striatum that integrate glutamatergic signals arising from the cerebral cortex and thalamus" [MP:0008462] + CL:1001474 + medium-sized densely spiny neuron + CL:medium spiny neuron + + + CL:1001502 + CL:mitral cell + "the large glutaminergic nerve cells whose dendrites synapse with axons of the olfactory receptor neurons in the glomerular layer of the olfactory bulb, and whose axons pass centrally in the olfactory tract to the olfactory cortex" [MP:0009954] + mitral cell + + + "A pyramidal cell of the hippocampus." [GOC:pr, PMID:19342486] + hippocampus (CA) pyramidal neuron + CL:1001571 + hippocampus (CA) pyramidal cell + CL:hippocampal pyramidal neuron + hippocampal pyramidal neuron + + + brain cortex glial cell + "Glial cell of cerebral cortex." [NPX:PDR] + cerebral cortex glial cells + CL:1001579 + CL:cerebral cortex glial cell + cerebrum cortex glial cell + cerebral cortex glial cell + + + articular chondrocyte + CL:1001607 + CL:articular chondrocyte + "Chondrocyte forming the hyaline cartilage found in joints." [NPX:PDR] + + + "Fibroblast from foreskin." [NPX:PDR] + foreskin fibroblast + CL:1001608 + CL:foreskin fibroblast + + + CL:1001610 + "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes." [NPX:PDR] + bone marrow hematopoietic cells + CL:bone marrow hematopoietic cell + bone marrow hematopoietic cell + bone marrow poietic cells + + + CL:1001611 + CL:cerebellar neuron + cerebellar neuron + cerebellum neuron + "Neuron of the cerebellum." [NPX:PDR] + + + liver cell + CL_EXT:liver cell + For: hepatic cell(s), liver cell(s) + CL_EXT:liver_cell + hepatic cell + CL:cell and ((proper_part_of some UBERON:liver) or (derives_from o proper_part_of some UBERON:liver)) + + + CL_EXT:neural_crest_cell + CL:'migratory neural crest cell' or CL:'premigratory neural crest cell' + neural crest cell + CL_EXT:neural crest cell + NCC + For: NCC(s), neural crest cell(s) + + + CL:cell or GO:cell + CL_GO_EXT:cell + cell + CL_GO_EXT:cell + For: cell(s), cellular(ly) + + + lens fibre + CL_UBERON_EXT:lens fiber + lens fiber + CL:'lens fiber cell' or UBERON:'lens fiber' + For: lens fiber(s)/fibre(s) +Not for: lens fiber/fibre cell, primary lens fiber(s)/fibre(s), secondary lens fiber(s)/fibre(s) + CL_UBERON_EXT:lens_fiber + + + CL_UBERON_EXT:lymphocyte_or_lymphoid_progenitor_or_system_or_tissue + CL:'common lymphoid progenitor' or CL:'early lymphoid progenitor' or CL:'lymphoid lineage restricted progenitor cell' or CL:lymphocyte or UBERON:'lymphoid system' or UBERON:'lymphoid tissue' + lymphocyte, lymphoid progenitor, or lymphoid system or tissue + CL_UBERON_EXT:lymphocyte, lymphoid progenitor, or lymphoid system or tissue + For: lymphoid + lymphoid + + + CL extension classes + + + reproductive physiological process + "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732] + GO:0000003 + GO:reproduction + reproduction + + + GO:0000041 + GO:transition metal ion transport + transition metal transport + transition metal ion transport + "The directed movement of transition metal ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver." [ISBN:0198506732] + + + mitotic sister chromatid segregation + "The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets." [GOC:ai, GOC:jl] + GO:mitotic sister chromatid segregation + GO:0000070 + mitotic chromosome segregation + + + cell cycle checkpoint + GO:cell cycle checkpoint + GO:0000075 + "A cell cycle process that controls cell cycle progression by monitoring the integrity of specific cell cycle events. A cell cycle checkpoint begins with detection of deficiencies or defects and ends with signal transduction." [GOC:mtg_cell_cycle] + + + GO:DNA damage checkpoint + GO:0000077 + "A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds." [GOC:mtg_cell_cycle] + DNA damage checkpoint + + + "The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex." [GOC:mtg_cell_cycle] + GO:0000086 + G2/M transition of mitotic cell cycle + mitotic G2/M transition + GO:G2/M transition of mitotic cell cycle + + + ubiquitin ligase complex + GO:0000151 + "A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex." [GOC:jh2, PMID:9529603] + GO:ubiquitin ligase complex + + + "A ubiquitin ligase complex found in the nucleus." [GOC:mah] + GO:0000152 + nuclear ubiquitin ligase complex + GO:nuclear ubiquitin ligase complex + + + "A protein complex that has protein serine/threonine phosphatase activity that is polycation-stimulated (PCS), being directly stimulated by protamine, polylysine, or histone H1; it constitutes a subclass of several enzymes activated by different histones and polylysine, and consists of catalytic, scaffolding, and regulatory subunits. The catalytic and scaffolding subunits form the core enzyme, and the holoenzyme also includes the regulatory subunit." [GOC:mah, ISBN:0198547684, PMID:17245430] + protein phosphatase type 2A complex + GO:protein phosphatase type 2A complex + GO:0000159 + protein phosphatase 2 complex + + + MAPKKK cascade + GO:MAPK cascade + MAPK signalling + mitogen-activated protein kinase cascade + MAPK signal transduction + MAP kinase kinase kinase cascade + MAP kinase cascade + MAPK cascade + MAPK signaling + "An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell." [GOC:bf, GOC:mtg_signaling_feb11, PMID:20811974, PMID:9561267] + GO:0000165 + + + nuclear-transcribed mRNA catabolic process, nonsense-mediated decay + mRNA catabolism, nonsense-mediated + GO:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay + "The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins." [GOC:krc, GOC:ma, PMID:10025395] + nuclear mRNA catabolic process, nonsense-mediated decay + mRNA catabolic process, nonsense-mediated + mRNA degradation, nonsense-mediated decay + nonsense-mediated mRNA decay + mRNA breakdown, nonsense-mediated decay + GO:0000184 + + + GO:0000187 + GO:activation of MAPK activity + MAPK activation + activation of MAPK activity + activation of MAP kinase + "The initiation of the activity of the inactive enzyme MAP kinase (MAPK)." [PMID:9561267] + + + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." [GOC:mah] + microtubule cytoskeleton organization and biogenesis + microtubule cytoskeleton organisation + microtubule cytoskeleton organization + GO:microtubule cytoskeleton organization + GO:0000226 + microtubule dynamics + + + astral microtubule + "Any of the spindle microtubules that radiate in all directions from the spindle poles and are thought to contribute to the forces that separate the poles and position them in relation to the rest of the cell." [ISBN:0815316194] + GO:astral microtubule + GO:0000235 + + + leptotene + "The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible." [GOC:mtg_cell_cycle] + GO:leptotene + GO:0000237 + + + GO:0000238 + "The cell cycle phase which follows leptotene during prophase I of meiosis, and during which each chromosome pairs with its homolog; the two become aligned and crossing over may occur." [GOC:mtg_cell_cycle] + zygotene + GO:zygotene + + + "The cell cycle phase which follows zygotene during prophase I of meiosis, and during which crossing over occurs between a chromatid in one partner and another chromatid in the homologous chromosome." [GOC:mtg_cell_cycle] + GO:pachytene + GO:0000239 + pachytene + + + "The cell cycle phase which follows pachytene during prophase I of meiosis, during which the homologous chromosomes begin to separate and the synaptonemal complex dissolves." [GOC:mtg_cell_cycle] + GO:0000240 + diplotene + GO:diplotene + + + polysaccharide catabolic process + polysaccharide catabolism + "The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [CHEBI:18154, GOC:go_curators] + GO:0000272 + GO:polysaccharide catabolic process + polysaccharide breakdown + polysaccharide degradation + + + M-phase + GO:M phase + GO:0000279 + "A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase." [GOC:mtg_cell_cycle] + M phase + + + GO:0000280 + nuclear division + GO:nuclear division + karyokinesis + "The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei." [GOC:mah] + + + GO:storage vacuole + "A vacuole that functions primarily in the storage of materials, including nutrients, pigments, waste products, and small molecules." [GOC:krc] + GO:0000322 + storage vacuole + + + GO:lytic vacuole + lytic vacuole + GO:0000323 + "A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases." [GOC:krc] + + + RNA splicing, via transesterification reactions + spliceosomal catalysis + RNA splicing factor activity, transesterification mechanism + GO:0000375 + pre-mRNA splicing factor activity + "Splicing of RNA via a series of two transesterification reactions." [GOC:krc] + GO:RNA splicing, via transesterification reactions + + + GO:RNA splicing, via transesterification reactions with bulged adenosine as nucleophile + "Splicing of RNA via a series of two transesterification reactions with a bulged adenosine residue from the intron branch point as the initiating nucleophile. When the initial RNA for the splicing reaction is a single molecule (cis splicing), the excised intron is released in a lariat structure." [GOC:krc, PMID:11377794] + RNA splicing, via transesterification reactions with bulged adenosine as nucleophile + lariat RNA biosynthesis + lariat RNA formation + GO:0000377 + + + alternative nuclear mRNA splicing, via spliceosome + "The process of generating multiple mRNA molecules from a given set of exons by differential use of exons from the primary transcript(s) to form multiple mature mRNAs that vary in their exon composition." [GOC:krc, PMID:12110900] + GO:0000380 + GO:alternative mRNA splicing, via spliceosome + alternative mRNA splicing, via spliceosome + + + nuclear mRNA splicing, via spliceosome + mRNA splicing, via spliceosome + "The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced." [GOC:krc, ISBN:0198506732, ISBN:0879695897] + splicing AT-AC intron + GO:mRNA splicing, via spliceosome + splicing GT-AG intron + GO:0000398 + + + mitochondrion autophagy + mitophagy + GO:mitophagy + "The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions." [GOC:autophagy, PMID:15798367, PMID:19289147, PMID:23065344] + GO:0000422 + + + GO:0000502 + proteasome + GO:proteasome complex + proteasome complex + "A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core." [GOC:rb, http://en.wikipedia.org/wiki/Proteasome] + + + GO:embryonic axis specification + GO:0000578 + "The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo." [GOC:dph, GOC:go_curators, GOC:sdb_2009, GOC:tb] + embryonic axis determination + embryonic axis specification + + + Rad51-dependent recombinational repair + homologous recombinational repair + GO:double-strand break repair via homologous recombination + Rhp51-dependent recombinational repair + HDR + homology-directed repair + "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC:elh, PMID:10357855] + GO:0000724 + HRR + double-strand break repair via homologous recombination + + + "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC:elh] + GO:recombinational repair + recombinational repair + GO:0000725 + + + GO:0000732 + strand displacement + GO:strand displacement + D-loop processing + displacement loop processing + D-loop dissociation + displacement loop dissociation + "The rejection of the broken 3' single-strand DNA molecule that formed heteroduplex DNA with its complement in an intact duplex DNA. The Watson-Crick base pairing in the original duplex is restored. The rejected 3' single-strand DNA molecule reanneals with its original complement to reform two intact duplex molecules." [PMID:10357855] + + + GO:0000768 + cell-cell fusion + GO:syncytium formation by plasma membrane fusion + syncytium formation by plasma membrane fusion + "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." [GOC:mtg_muscle, GOC:tb] + + + kinetochore + "A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules." [GOC:elh] + GO:kinetochore + GO:0000776 + + + GO:chromatin + chromosome scaffold + chromatin + "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] + GO:0000785 + + + "A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures." [GOC:elh] + GO:0000786 + GO:nucleosome + nucleosome + + + GO:nuclear chromatin + nuclear chromatin + GO:0000790 + "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus." [GOC:elh, PMID:20404130] + + + "A dispersed and relatively uncompacted form of chromatin." [GOC:elh] + GO:0000791 + euchromatin + GO:euchromatin + + + "A compact and highly condensed form of chromatin." [GOC:elh] + GO:heterochromatin + heterochromatin + GO:0000792 + + + condensed chromosome + "A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure." [GOC:elh] + mitotic chromosome + metaphase chromosome + GO:condensed chromosome + GO:0000793 + cytoplasmic mitotic chromosome + + + "A proteinaceous scaffold found between homologous chromosomes during meiosis." [GOC:elh] + GO:synaptonemal complex + synaptonemal complex + GO:0000795 + + + "A proteinaceous core found between sister chromatids during meiotic prophase." [GOC:elh] + GO:0000800 + axial element + lateral element + GO:lateral element + + + "A structural unit of the synaptonemal complex that spans the regions between the lateral elements and connects them." [GOC:elh] + GO:transverse filament + GO:0000802 + transverse filament + + + sex chromosome + "A chromosome involved in sex determination." [GOC:elh] + GO:0000803 + GO:sex chromosome + + + GO:0000805 + GO:X chromosome + X chromosome + "The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males." [GOC:mah, ISBN:0582227089] + + + GO:0000806 + "The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males." [GOC:mah, ISBN:0582227089] + GO:Y chromosome + Y chromosome + + + "A heterotetrameric protein complex that associates with replication origins, where it is required for the initiation of DNA replication, and with replication forks." [GOC:rb, GOC:rn, PMID:12730134, PMID:16990792, PMID:17467990] + GO:0000811 + Go, Ichi, Ni and San complex + GINS complex + GO:GINS complex + + + GO:0000819 + GO:sister chromatid segregation + sister chromatid segregation + "The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets." [GOC:ai, GOC:elh] + + + cell morphogenesis + cellular morphogenesis + GO:0000902 + GO:cell morphogenesis + "The developmental process in which the size or shape of a cell is generated and organized." [GOC:clt, GOC:dph, GOC:go_curators, GOC:tb] + + + GO:0000904 + GO:cell morphogenesis involved in differentiation + cell morphogenesis involved in differentiation + "The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history." [GOC:go_curators] + + + GO:0000910 + "The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells." [GOC:mtg_cell_cycle] + cytokinesis + cell cycle cytokinesis + GO:cytokinesis + cytokinesis involved in cell cycle + + + GO:0000922 + "Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules." [GOC:clt] + spindle pole + GO:spindle pole + + + nuclear-transcribed mRNA catabolic process + nuclear mRNA degradation + nuclear mRNA breakdown + GO:nuclear-transcribed mRNA catabolic process + GO:0000956 + "The chemical reactions and pathways resulting in the breakdown of nuclear-transcribed mRNAs in eukaryotic cells." [GOC:krc] + nuclear mRNA catabolism + + + "A DNA synthesis process that uses RNA as the initial template for synthesis of DNA, but which also includes an RNase activity to remove the RNA strand of an RNA-DNA heteroduplex produced by the RNA-dependent synthesis step and use of the initial DNA strand as a template for DNA synthesis." [GOC:txnOH, PMID:20358252] + GO:0001171 + reverse transcription + GO:reverse transcription + + + skeletal system development + GO:skeletal system development + GO:0001501 + skeletal development + "The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton)." [GOC:dph, GOC:jid, GOC:tb, http://www.stedmans.com/] + + + cartilage condensation + GO:0001502 + "The condensation of mesenchymal cells that have been committed to differentiate into chondrocytes." [ISBN:0878932437] + GO:cartilage condensation + + + osteogenesis + ossification + GO:ossification + "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:mtg_mpo, PMID:17572649] + bone biosynthesis + GO:0001503 + bone formation + + + neurotransmitter import + "The directed movement of neurotransmitters into neurons or glial cells. This process leads to inactivation and recycling of neurotransmitters." [ISBN:0123668387] + neurotransmitter uptake + GO:0001504 + GO:neurotransmitter uptake + + + GO:regulation of neurotransmitter levels + "Any process that modulates levels of neurotransmitter." [GOC:jl] + GO:0001505 + regulation of neurotransmitter levels + + + GO:action potential + "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] + GO:0001508 + action potential + + + GO:angiogenesis + "Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels." [ISBN:0878932453] + blood vessel formation from pre-existing blood vessels + angiogenesis + GO:0001525 + + + cornified envelope + GO:0001533 + "A type of plasma membrane that has been modified through addition of distinct intracellular and extracellular components, including ceramide, found in cornifying epithelial cells (corneocytes)." [GOC:add, PMID:11112355, PMID:11590230, PMID:15803139] + GO:cornified envelope + + + ovarian follicle development + GO:ovarian follicle development + follicular phase + GO:0001541 + "The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure." [GOC:go_curators] + + + blood vessel development + GO:blood vessel development + GO:0001568 + "The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood." [GOC:hjd, UBERON:0001981] + + + vasculogenesis + GO:vasculogenesis + GO:0001570 + "The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes." [PMID:8999798] + vascular morphogenesis + + + GO:microtubule bundle formation + "A process that results in a parallel arrangement of microtubules." [GOC:dph] + microtubule bundle formation + microtubule bundling + GO:0001578 + + + sensory transduction of bitter taste + sensory detection of chemical stimulus during perception of bitter taste + perception of bitter taste, sensory transduction of chemical stimulus + "The series of events required for a bitter taste stimulus to be received and converted to a molecular signal." [GOC:go_curators] + bitter taste detection + GO:0001580 + detection of chemical stimulus involved in sensory perception of bitter taste + sensory detection of bitter taste + sensory transduction of chemical stimulus during perception of bitter taste + perception of bitter taste, detection of chemical stimulus + GO:detection of chemical stimulus involved in sensory perception of bitter taste + + + perception of sweet taste, detection of chemical stimulus + sensory transduction of chemical stimulus during perception of sweet taste + sensory detection of sweet taste + sweet taste detection + GO:0001582 + "The series of events required for a sweet taste stimulus to be received and converted to a molecular signal." [GOC:go_curators] + sensory transduction of sweet taste + sensory detection of chemical stimulus during perception of sweet taste + GO:detection of chemical stimulus involved in sensory perception of sweet taste + detection of chemical stimulus involved in sensory perception of sweet taste + perception of sweet taste, sensory transduction of chemical stimulus + + + GO:eye development + GO:0001654 + eye development + "The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight." [GOC:jid, GOC:jl] + + + branching involved in ureteric bud morphogenesis + GO:branching involved in ureteric bud morphogenesis + "The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules." [GOC:dph, PMID:16916378] + ureteric bud branching + GO:0001658 + + + GO:temperature homeostasis + thermoregulation + "A homeostatic process in which an organism modulates its internal body temperature." [GOC:jl] + temperature homeostasis + GO:0001659 + + + GO:0001667 + amoeboidal cell migration + "Cell migration that is accomplished by extension and retraction of a pseudopodium." [GOC:dph] + ameboid cell migration + ameboidal-type cell migration + GO:ameboidal-type cell migration + amoeboid cell migration + + + acrosomal vesicle + "A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome." [ISBN:0124325653, ISBN:0198506732] + acrosome + acrosomal granule + GO:0001669 + GO:acrosomal vesicle + + + GO:0001676 + long-chain fatty acid metabolism + "The chemical reactions and pathways involving long-chain fatty acids, A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [CHEBI:15904, GOC:ajp] + GO:long-chain fatty acid metabolic process + long-chain fatty acid metabolic process + + + GO:0001708 + "The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment." [GOC:go_curators] + GO:cell fate specification + cell fate specification + + + GO:cell fate determination + "A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment." [ISBN:0878932437] + cell fate determination + GO:0001709 + + + GO:endodermal cell fate specification + "The cell fate determination process that results in a cell becoming capable of differentiating autonomously into an endoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:go_curators] + GO:0001714 + endodermal cell fate specification + endoderm cell fate specification + + + GO:0001715 + ectoderm cell fate specification + ectodermal cell fate specification + "The cell fate determination process that results in a cell becoming becomes capable of differentiating autonomously into an ectoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:go_curators] + GO:ectodermal cell fate specification + + + sex chromatin + "Chromatin that is part of a sex chromosome." [GOC:dos, ISBN:0198506732] + GO:0001739 + GO:sex chromatin + + + XY body + GO:0001741 + GO:XY body + "A structure found in a male mammalian spermatocyte containing an unpaired X chromosome that has become densely heterochromatic, silenced and localized at the nuclear periphery." [GOC:hjd] + + + GO:photoreceptor outer segment + "The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes." [ISBN:0824072820] + photoreceptor outer segment + GO:0001750 + + + "The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms." [GOC:go_curators] + GO:0001754 + eye photoreceptor cell differentiation + GO:eye photoreceptor cell differentiation + + + "The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo." [GOC:ascb_2009, GOC:dph, GOC:tb, ISBN:0878932437] + GO:0001755 + GO:neural crest cell migration + neural crest cell migration + + + GO:0001763 + branching morphogenesis + GO:morphogenesis of a branching structure + morphogenesis of a branching structure + "The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes." [ISBN:0721662544] + + + neuron migration + "The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature." [CL:0000540, GOC:go_curators] + GO:0001764 + GO:neuron migration + neuron chemotaxis + neuron guidance + neuronal migration + + + "The change in morphology and behavior of a microglial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, PMID:10626665, PMID:10695728, PMID:12580336, PMID:9893949] + GO:0001774 + microglial cell activation + GO:microglial cell activation + + + GO:0001775 + GO:cell activation + "A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:mgi_curators] + cell activation + + + GO:0001816 + "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] + cytokine production + GO:cytokine production + + + GO:kidney development + GO:0001822 + kidney development + nephrogenesis + "The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine." [GOC:dph, GOC:mtg_kidney_jan10, ISBN:0124020607, ISBN:0721662544] + + + GO:blastocyst development + GO:0001824 + blastocyst development + "The process whose specific outcome is the progression of the blastocyst over time, from its formation to the mature structure. The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm." [GOC:dph, ISBN:0124020607, ISBN:0198542771] + + + EMT + GO:0001837 + "A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell." [GOC:dph, PMID:14701881] + GO:epithelial to mesenchymal transition + epithelial-mesenchymal transition + epithelial to mesenchymal transition + + + "The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes." [GOC:add, ISBN:068340007X] + GO:liver development + GO:0001889 + liver development + + + "The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin." [GOC:add, ISBN:068340007X] + GO:0001890 + placental development + GO:placenta development + placentation + placenta development + + + GO:tissue homeostasis + tissue homeostasis + "A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function." [GOC:add, GOC:isa_complete] + GO:0001894 + + + "The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs." [GOC:add, PMID:12019563] + GO:0001917 + photoreceptor inner segment + GO:photoreceptor inner segment + + + regulation of protein amino acid phosphorylation + GO:regulation of protein phosphorylation + regulation of protein phosphorylation + "Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein." [GOC:hjd] + GO:0001932 + + + up regulation of protein amino acid phosphorylation + positive regulation of protein phosphorylation + positive regulation of protein amino acid phosphorylation + up-regulation of protein amino acid phosphorylation + GO:positive regulation of protein phosphorylation + GO:0001934 + "Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein." [GOC:hjd] + upregulation of protein amino acid phosphorylation + + + "The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open." [GOC:dph, UBERON:0002073] + GO:0001942 + hair follicle development + GO:hair follicle development + + + GO:vasculature development + vascular system development + vasculature development + "The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism." [GOC:dph, UBERON:0002409] + GO:0001944 + + + heart looping + GO:0001947 + cardiac looping + "The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation." [GOC:dph, PMID:12094232] + GO:heart looping + + + GO:endochondral ossification + GO:0001958 + "Replacement ossification wherein bone tissue replaces cartilage." [GO_REF:0000034, ISBN:0878932437] + endochondral ossification + + + "The directed movement of a motile cell or organism in response to touch." [GOC:dph] + thigmotaxis + GO:0001966 + stereotaxis + taxis in response to touch stimulus + GO:thigmotaxis + + + GO:0001967 + suckling behavior + "Specific behavior of a newborn or infant mammal that results in the derivation of nourishment from the breast." [GOC:dph, GOC:pr] + nursing behavior + GO:suckling behavior + + + "The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube." [GOC:dph, GOC:jl, GOC:tb, ISBN:0198506732] + GO:morphogenesis of an epithelium + morphogenesis of an epithelium + GO:0002009 + epithelium morphogenesis + + + GO:0002011 + GO:morphogenesis of an epithelial sheet + "The process in which the anatomical structures of an epithelial sheet are generated and organized. An epithelial sheet is a flat surface consisting of closely packed epithelial cells." [GOC:jl] + morphogenesis of an epithelial sheet + + + regulation of heart rate + regulation of heart contraction rate + "Any process that modulates the frequency or rate of heart contraction." [GOC:dph, GOC:tb, PMID:10358008] + GO:0002027 + cardiac chronotropy + GO:regulation of heart rate + regulation of rate of heart contraction + + + GO:epithelial cell development + GO:0002064 + "The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface." [GOC:dph] + epithelial cell development + + + epithelial cell maturation + GO:epithelial cell maturation + GO:0002070 + "The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell to attain its fully functional state. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface." [GOC:dph] + + + GO:osteoblast development + osteoblast development + "The process whose specific outcome is the progression of an osteoblast over time, from its formation to the mature structure. Osteoblast development does not include the steps involved in committing a cranial neural crest cell or an osteoprogenitor cell to an osteoblast fate. An osteoblast is a cell that gives rise to bone." [GOC:dph] + GO:0002076 + + + "A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates." [GOC:dph, GOC:tb, PMID:12458206] + regulation of respiratory gaseous exchange by neurological system process + GO:regulation of respiratory gaseous exchange by neurological system process + neurological control of breathing + GO:0002087 + + + GO:manchette + GO:0002177 + manchette + "A conical shaped array of microtubules that completely covers the nucleus of a spermatid, thought to be involved in sperm head elongation." [PMID:15018141] + + + GO:0002218 + "Any process that initiates an innate immune response. Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. Examples of this process include activation of the hypersensitive response of Arabidopsis thaliana and activation of any NOD or TLR signaling pathway in vertebrate species." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, GOC:mtg_sensu, ISBN:0781735149, PMID:15199967, PMID:16177805] + activation of innate immune response + GO:activation of innate immune response + + + pathogen receptor signaling pathway + pattern recognition receptor signaling pathway + GO:pattern recognition receptor signaling pathway + PAMP receptor signaling pathway + GO:0002221 + pathogen receptor signalling pathway + "Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species, or damage-associated molecular pattern (DAMPs), endogenous molecules released from damaged cells." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967] + PRR signaling pathway + + + TLR signaling pathway + toll-like receptor signaling pathway + GO:toll-like receptor signaling pathway + toll-like receptor signalling pathway + GO:0002224 + "Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149, PMID:12467241, PMID:12524386, PMID:12855817, PMID:15585605, PMID:15728447] + + + adaptive immune response + GO:0002250 + acquired immune response + "An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory)." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] + GO:adaptive immune response + + + GO:0002252 + immune effector process + "Any process of the immune system that can potentially contribute to an immune response." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] + GO:immune effector process + + + GO:0002253 + GO:activation of immune response + "Any process that initiates an immune response." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] + activation of immune response + + + myeloid leucocyte activation + myeloid leukocyte activation + GO:0002274 + GO:myeloid leukocyte activation + "A change in the morphology or behavior of a myeloid leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:add, ISBN:0781735149] + + + GO:immune system process + "Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05] + GO:0002376 + immune system process + + + GO:inflammatory response to antigenic stimulus + GO:0002437 + inflammatory response to antigenic stimulus + "An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes." [GOC:add, ISBN:0781735149] + + + GO:0002443 + GO:leukocyte mediated immunity + immune cell effector process + "Any process involved in the carrying out of an immune response by a leukocyte." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] + leucocyte immune effector process + cellular immune response + cell-mediated immune response + immune cell mediated immunity + leucocyte mediated immunity + leukocyte mediated immunity + leukocyte immune effector process + + + GO:lymphocyte mediated immunity + lymphocyte mediated immunity + "Any process involved in the carrying out of an immune response by a lymphocyte." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] + GO:0002449 + + + adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains + "An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains, and allowing for enhanced responses upon subsequent exposures to the same antigen (immunological memory). Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies). An example of this is the adaptive immune response found in Mus musculus." [GOC:add, GOC:mtg_sensu, ISBN:0781735149] + GO:adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains + GO:0002460 + + + tolerance induction + GO:0002507 + "A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it." [GO_REF:0000022, GOC:jal, GOC:mtg_15nov05, ISBN:0781735149] + GO:tolerance induction + + + GO:immune system development + immune system development + GO:0002520 + "The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process." [GOC:add, GOC:dph] + + + acute inflammatory response + GO:acute inflammatory response + GO:0002526 + "Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] + + + Factor XII activation + Hageman factor activation + "Any process that activates Factor XII (Hageman factor). Factor XII is a protein synthesized by the liver that circulates in an inactive form until it encounters collagen or basement membrane or activated platelets (as occurs at the site of endothelial injury). Factor XII then undergoes a conformational change (becoming factor XIIa), exposing an active serine center that can subsequently cleave protein substrates and activate a variety of mediator systems. Factor XII is a participant in the clotting cascade as well as the kinin cascade." [GOC:jal, ISBN:0721601871] + GO:0002542 + GO:Factor XII activation + + + GO:regulation of acute inflammatory response + regulation of acute inflammatory response + "Any process that modulates the frequency, rate, or extent of an acute inflammatory response." [GOC:add] + GO:0002673 + + + upregulation of acute inflammatory response + positive regulation of acute inflammatory response + up-regulation of acute inflammatory response + up regulation of acute inflammatory response + GO:positive regulation of acute inflammatory response + GO:0002675 + "Any process that activates or increases the frequency, rate, or extent of an acute inflammatory response." [GOC:add] + + + regulation of immune system process + GO:0002682 + GO:regulation of immune system process + "Any process that modulates the frequency, rate, or extent of an immune system process." [GOC:add] + + + up regulation of immune system process + "Any process that activates or increases the frequency, rate, or extent of an immune system process." [GOC:add] + up-regulation of immune system process + positive regulation of immune system process + GO:positive regulation of immune system process + GO:0002684 + upregulation of immune system process + + + cytoplasmic pathogen receptor signaling pathway + "Any series of molecular signals generated as a consequence of a cytoplasmic pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species, or damage-associated molecular pattern (DAMPs), endogenous molecules released from damaged cells." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967] + cytoplasmic pattern recognition receptor signalling pathway + cytoplasmic PRR signaling pathway + GO:0002753 + GO:cytoplasmic pattern recognition receptor signaling pathway + cytoplasmic PAMP receptor signaling pathway + cytoplasmic pattern recognition receptor signaling pathway + + + GO:immune response-activating signal transduction + GO:0002757 + immune response-activating signal transduction + "The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately leading to activation or perpetuation of an immune response." [GOC:add] + + + GO:innate immune response-activating signal transduction + GO:0002758 + "The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately leading to activation or perpetuation of an innate immune response." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05] + innate immune response-activating signal transduction + + + "The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately leading to the activation, perpetuation, or inhibition of an immune response." [GOC:add, ISBN:0781735149, PMID:15771571] + GO:immune response-regulating signaling pathway + immune response-regulating signaling pathway + immune response-regulating signalling pathway + GO:0002764 + + + peptide secretion + "The controlled release of a peptide from a cell or a tissue." [GOC:add] + GO:peptide secretion + GO:0002790 + + + GO:regulation of peptide secretion + GO:0002791 + regulation of peptide secretion + "Any process that modulates the frequency, rate, or extent of peptide secretion." [GOC:add] + + + GO:0003002 + GO:regionalization + pattern formation + regionalization + "The pattern specification process that results in the subdivision of an axis or axes in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment." [GOC:dph, GOC:isa_complete] + + + reproductive developmental process + GO:developmental process involved in reproduction + "A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring." [GOC:dph, GOC:isa_complete] + developmental process involved in reproduction + GO:0003006 + + + GO:heart morphogenesis + heart morphogenesis + "The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." [GOC:dph, GOC:isa_complete] + GO:0003007 + cardiac morphogenesis + + + "A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective." [GOC:mtg_cardio] + organ system process + system process + GO:0003008 + GO:system process + + + muscle system process + GO:muscle system process + GO:0003012 + muscle physiological process + "A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers." [GOC:mtg_cardio] + + + "A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism." [GOC:mtg_cardio] + GO:circulatory system process + circulatory system process + GO:0003013 + + + excretory system process + renal system process + GO:renal system process + kidney system process + "A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila)." [GOC:cjm, GOC:mtg_cardio, GOC:mtg_kidney_jan10] + GO:0003014 + + + heart process + "A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." [GOC:mtg_cardio] + GO:heart process + GO:0003015 + cardiac process + + + GO:glomerular filtration + GO:0003094 + "The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein." [GOC:mtg_cardio, GOC:sart, ISBN:0721643949] + glomerular filtration + + + GO:renal water transport + renal water transport + GO:0003097 + "The directed movement of water (H2O) by the kidney." [GOC:mtg_cardio] + + + GO:embryonic heart tube morphogenesis + "The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart." [GOC:mtg_heart] + embryonic heart tube morphogenesis + GO:0003143 + + + GO:outflow tract morphogenesis + "The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries." [GOC:mtg_heart, UBERON:0004145] + GO:0003151 + outflow tract morphogenesis + + + "The progression of a cardiac septum over time, from its initial formation to the mature structure." [GOC:mtg_heart] + GO:0003279 + GO:cardiac septum development + cardiac septum development + heart septum development + + + ventricular septum development + GO:ventricular septum development + GO:0003281 + "The progression of the ventricular septum over time from its formation to the mature structure." [GOC:mtg_heart] + interventricular septum development + + + GO:retinal pigment epithelium development + GO:0003406 + RPE development + retinal pigment epithelium development + "The progression of the retinal pigment epithelium over time, from its initial formation to the mature structure. The retinal pigment epithelium is the melanin-containing layer of cells between the retina and the choroid that absorbs scattered and reflected light and removes waste products produced by the photoreceptor cells." [GOC:ascb_2009, GOC:dph, GOC:tb] + + + GO:0003408 + GO:optic cup formation involved in camera-type eye development + optic cup formation involved in camera-type eye development + "The developmental process pertaining to the initial formation of the optic cup, a two-walled vesicle formed from the optic vesicle." [GOC:ascb_2009, GOC:dph, GOC:tb] + + + "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators] + molecular_function + GO:molecular_function + GO:0003674 + molecular function + + + "Interacting selectively and non-covalently with any nucleic acid." [GOC:jl] + GO:nucleic acid binding + GO:0003676 + nucleic acid binding + + + GO:0005488 + "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732] + GO:binding + binding + + + alpha-2 macroglobulin receptor-associated protein activity + GO:0005515 + protein degradation tagging activity + protein amino acid binding + GO:protein binding + "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC:go_curators] + protein tagging activity + protein binding + + + "The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together." [GOC:go_curators, NIF_Subcellular:sao-1337158144] + GO:0005575 + cellular_component + cell or subcellular entity + cellular component + subcellular entity + GO:cellular_component + + + extracellular region + "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators] + GO:extracellular region + extracellular + GO:0005576 + + + fibrinogen + "A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds." [ISBN:0198547684] + fibrinogen complex + GO:fibrinogen complex + GO:0005577 + + + terminal complement complex + TCC + "A protein complex produced by sequentially activated components of the complement cascade inserted into a target cell membrane and forming a pore leading to cell lysis via ion and water flow." [GOC:add, ISBN:0198547684, ISBN:068340007X, ISBN:0781735149] + GO:membrane attack complex + MAC + membrane attack complex + GO:0005579 + + + laminin-2 complex + GO:0005607 + "A laminin complex composed of alpha2, beta1 and gamma1 polypeptide chains." [GOC:jl, PMID:10842354] + GO:laminin-2 complex + + + GO:0005610 + laminin-5 complex + "A laminin complex composed of alpha3, beta3 and gamma2 polypeptide chains." [GOC:jl, PMID:10842354] + GO:laminin-5 complex + + + extracellular space + "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN:0198547684] + intercellular space + GO:extracellular space + GO:0005615 + + + cell wall + GO:cell wall + GO:0005618 + "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins." [GOC:giardia, http://en.wikipedia.org/wiki/Microbial_cyst, ISBN:0198547684, PMID:15134259] + + + GO:0005622 + intracellular + nucleocytoplasm + internal to cell + GO:intracellular + protoplast + protoplasm + "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732] + + + GO:nucleus + GO:0005634 + "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] + cell nucleus + nucleus + + + nuclear envelope + GO:0005635 + "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN:0198547684] + GO:nuclear envelope + + + perinuclear membrane + nuclear outer membrane + GO:nuclear outer membrane + GO:0005640 + "The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes." [ISBN:0198547684] + + + GO:nuclear pore + nuclear pore complex + nucleopore + "Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined." [ISBN:0198547684] + GO:0005643 + NPC + nuclear pore + + + nucleoplasm + "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC:ma, ISBN:0124325653] + GO:0005654 + GO:nucleoplasm + + + eukaryotic pre-replicative complex + GO:0005656 + nuclear pre-replicative complex + "A protein-DNA complex assembled at eukaryotic DNA replication origins during late mitosis and G1, allowing the origin to become competent, or 'licensed', for replication. The complex normally includes the origin recognition complex (ORC), Cdc6, Cdt1 and the MiniChromosome Maintenance (Mcm2-7) proteins." [PMID:15222894] + GO:nuclear pre-replicative complex + pre-RC + + + replication fork + "The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes." [GOC:mah, ISBN:0198547684] + replication focus + GO:replication fork + GO:0005657 + + + DNA replication factor A complex + "A conserved heterotrimeric complex that binds nonspecifically to single-stranded DNA and is required for multiple processes in eukaryotic DNA metabolism, including DNA replication, DNA repair, and recombination. In all eukaryotic organisms examined the complex is composed of subunits of approximately 70, 30, and 14 kDa." [PMID:9242902] + GO:0005662 + GO:DNA replication factor A complex + replication protein A + RPA + + + GO:transcription factor complex + "A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription." [GOC:jl] + transcription factor complex + GO:0005667 + + + "A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex." [GOC:ew, GOC:krc, PMID:14500720, PMID:22308316, PMID:22572993, PMID:7813015] + GO:0005675 + GO:holo TFIIH complex + holo TFIIH complex + + + chromosome + GO:0005694 + GO:chromosome + "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684] + + + GO:chiasma + "A connection formed between chromatids, visible during meiosis, thought to be the point of the interchange involved in crossing-over." [ISBN:0198506732] + chiasma + GO:0005712 + + + "An electron dense structure that is associated with meiotic chromosomes." [GOC:elh] + recombination nodule + GO:recombination nodule + GO:0005713 + + + GO:early recombination nodule + "An electron dense structure that is associated with meiotic chromosomes in leptotene or zygotene during meiosis I." [GOC:elh] + early recombination nodule + GO:0005714 + + + nuclear heterochromatin + "A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin." [ISBN:0198506732] + GO:0005720 + GO:nuclear heterochromatin + + + centromeric heterochromatin + pericentric heterochromatin + GO:pericentric heterochromatin + GO:0005721 + centric heterochromatin + "Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3." [PMID:12019236, PMID:20206496, PMID:22729156] + + + nucleolus + GO:nucleolus + GO:0005730 + "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN:0198506732] + + + NOR + GO:nucleolus organizer region + nucleolus organizer complex + "A region of a chromosome where nucleoli form during interphase, and where genes encoding the largest rRNA precursor transcript are tandemly arrayed." [PMID:14504406] + nucleolus organiser region + nucleolus organizer region + GO:0005731 + + + GO:cytoplasm + GO:0005737 + cytoplasm + "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684] + + + "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [GOC:giardia, ISBN:0198506732] + mitochondria + GO:mitochondrion + mitochondrion + GO:0005739 + + + GO:0005741 + GO:mitochondrial outer membrane + mitochondrial outer membrane + outer mitochondrial membrane + "The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope." [GOC:ai] + + + GO:mitochondrial inner membrane + GO:0005743 + inner mitochondrial membrane + mitochondrial inner membrane + "The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae." [GOC:ai] + + + GO:mitochondrial proton-transporting ATP synthase complex + GO:0005753 + "A proton-transporting ATP synthase complex found in the mitochondrial membrane." [GOC:mah, GOC:mtg_sensu] + mitochondrial proton-transporting ATP synthase complex + mitochondrial respiratory chain complex V + + + "The region between the inner and outer lipid bilayers of the mitochondrial envelope." [GOC:mah] + mitochondrial intermembrane space + GO:0005758 + mitochondrial membrane lumen + GO:mitochondrial intermembrane space + mitochondrial envelope lumen + + + mitochondrial lumen + GO:mitochondrial matrix + GO:0005759 + mitochondrial matrix + "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation." [GOC:as, ISBN:0198506732] + + + GO:lysosome + GO:0005764 + lysosome + "A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [GOC:mah, ISBN:0198506732] + + + GO:lysosomal membrane + GO:0005765 + "The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm." [GOC:ai] + lysosomal membrane + + + GO:0005767 + "Vacuole formed by the fusion of a lysosome with an organelle (autosome) or with a primary phagosome." [GOC:jl, ISBN:0815316194] + secondary lysosome + GO:secondary lysosome + + + GO:0005768 + "A membrane-bounded organelle to which materials ingested by endocytosis are delivered." [ISBN:0198506732, PMID:19696797] + endosome + GO:endosome + + + GO:0005769 + GO:early endosome + "A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways." [GOC:mah, NIF_Subcellular:nlx_subcell_20090701, PMID:19696797] + early endosome + + + "A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center." [NIF_Subcellular:nlx_subcell_20090702, PMID:11964142, PMID:2557062] + prevacuolar compartment + GO:late endosome + late endosome + GO:0005770 + + + GO:vacuole + vacuolar carboxypeptidase Y + vacuole + "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732] + GO:0005773 + + + GO:0005774 + "The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell." [GOC:ai] + vacuolar membrane + GO:vacuolar membrane + + + autophagosome + autophagic vacuole + GO:0005776 + "A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy." [GOC:autophagy, ISBN:0198547684, PMID:11099404] + GO:autophagosome + initial autophagic vacuole + + + peroxisome + GO:0005777 + GO:peroxisome + "A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism." [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576] + peroxisomal + + + "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732] + endoplasmic reticulum + ER + GO:endoplasmic reticulum + GO:0005783 + + + "The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae." [ISBN:0198506732] + rough ER + rough endoplasmic reticulum + RER + GO:rough endoplasmic reticulum + GO:0005791 + + + Golgi complex + GO:Golgi apparatus + Golgi apparatus + "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions." [ISBN:0198506732] + GO:0005794 + + + GO:cis-Golgi network + cis Golgi network + forming face + Golgi cis face + cis-Golgi network + Golgi cis-face + GO:0005801 + "The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum." [ISBN:0198506732, ISBN:0815316194] + + + Golgi trans face + TGN + trans Golgi network + late Golgi + Golgi trans-face + GO:trans-Golgi network + "The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination." [GOC:vw, ISBN:0815316194] + maturing face + GO:0005802 + trans-Golgi network + + + centrosome + "A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle." [GOC:mah, ISBN:0198547684] + GO:centrosome + GO:0005813 + + + centriole + "A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle." [ISBN:0198547684] + GO:centriole + GO:0005814 + + + microtubule organising centre + GO:microtubule organizing center + GO:0005815 + microtubule organizing center + "An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides." [GOC:vw, http://en.wikipedia.org/wiki/Microtubule_organizing_center, ISBN:0815316194, PMID:17072892, PMID:17245416] + MTOC + + + GO:spindle + GO:0005819 + "The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart." [ISBN:0198547684] + spindle + + + cytosol + GO:0005829 + "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC:hjd, GOC:jl] + GO:cytosol + + + ribosome + "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732] + ribosomal RNA + GO:ribosome + GO:0005840 + + + polysome + "A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro." [ISBN:0198506732, NIF_Subcellular:sao1038025871] + GO:polysome + polyribosome + GO:0005844 + + + cytoskeleton + GO:cytoskeleton + GO:0005856 + "Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." [GOC:mah, ISBN:0198547684, PMID:16959967] + + + microtubulus + GO:0005874 + "Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle." [ISBN:0879693568] + GO:microtubule + microtubuli + microtubule + + + GO:0005875 + "Any multimeric complex connected to a microtubule." [GOC:jl] + GO:microtubule associated complex + microtubule associated complex + + + spindle microtubule + GO:0005876 + "Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole." [ISBN:0815316194] + GO:spindle microtubule + + + "Any microtubule in the cytoplasm of a cell." [GOC:mah] + GO:cytoplasmic microtubule + GO:0005881 + cytoplasmic microtubule + + + intermediate filament associated protein + "A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins." [http://www.cytochemistry.net/Cell-biology/intermediate_filaments.htm, ISBN:0198506732] + type I intermediate filament associated protein + intermediate filament + type II intermediate filament associated protein + GO:0005882 + GO:intermediate filament + + + GO:neurofilament + type IV intermediate filament + "A type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter." [ISBN:0198506732, ISBN:0716731363, ISBN:0815316194] + neurofilament + GO:0005883 + + + GO:0005884 + "A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane." [GOC:mah, ISBN:0198506732, PMID:10666339] + GO:actin filament + actin filament + microfilament + + + GO:0005886 + "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] + cell membrane + GO:plasma membrane + plasma membrane + cytoplasmic membrane + plasmalemma + cellular membrane + + + "A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm." [GOC:mah, ISBN:0721662544, PMID:16645198] + caveolar membrane + GO:0005901 + caveolae + caveola + GO:caveola + + + GO:0005902 + "Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells." [ISBN:0813516194] + GO:microvillus + microvilli + microvillus + + + GO:0005911 + GO:cell-cell junction + "A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals." [GOC:dgh, GOC:hb, GOC:mah] + intercellular junction + cell-cell junction + + + GO:0005912 + adherens junction + GO:adherens junction + "A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments." [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732] + + + GO:0005913 + GO:cell-cell adherens junction + cell-cell adherens junction + "An adherens junction which connects a cell to another cell." [GOC:hb] + + + macula communicans + GO:gap junction + GO:0005921 + electrical synapse + gap junction plaque + gap junction macula + electrotonic synapse + intercellular gap junction channel + "A cell-cell junction that is composed of an array of small channels that permit small molecules to pass from one cell to another. At gap junctions, the membranes of two adjacent cells are separated by a uniform narrow gap of about 2-4 nm that is spanned by channel-forming proteins called connexins, which form hexagonal tubes called connexons." [GOC:mah, GOC:mtg_muscle, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_g.html, ISBN:0815332181] + zonula communicans + gap junction + communicating junction + + + hemi-adherens junction + GO:cell-substrate adherens junction + cell-substrate adherens junction + GO:0005924 + "An adherens junction which connects a cell to the extracellular matrix." [GOC:hb] + + + adhesion plaque + hemi-adherens junction + GO:0005925 + "Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments." [ISBN:0124325653, ISBN:0815316208] + focal contact + GO:focal adhesion + focal adhesion + + + GO:cilium + eukaryotic flagellum + flagellum + microtubule-based flagellum + GO:0005929 + cilium + "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body." [GOC:cilia, GOC:kmv, GOC:vw, ISBN:0198547684] + + + axoneme + flagellar axoneme + GO:0005930 + "The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." [GOC:bf, GOC:cilia, ISBN:0198547684] + ciliary axoneme + GO:axoneme + flagellum axoneme + cilium axoneme + + + GO:0005938 + cell cortex + peripheral cytoplasm + cell periphery + "The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins." [GOC:mah, ISBN:0815316194] + GO:cell cortex + + + glycine cleavage complex + glycine synthase complex + glycine decarboxylase complex + GO:0005960 + glycine dehydrogenase complex (decarboxylating) + glycine dehydrogenase (decarboxylating) complex + GO:glycine cleavage complex + "A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T." [GOC:mah, MetaCyc:GCVMULTI-CPLX] + glycine cleavage system + + + GO:carbohydrate metabolic process + carbohydrate metabolic process + carbohydrate metabolism + "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC:mah, ISBN:0198506732] + GO:0005975 + + + "The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [CHEBI:18154, ISBN:0198547684] + GO:0005976 + GO:polysaccharide metabolic process + glycan metabolic process + polysaccharide metabolic process + glycan metabolism + polysaccharide metabolism + + + glycogen metabolic process + glycogen metabolism + GO:glycogen metabolic process + "The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages." [ISBN:0198506732] + GO:0005977 + + + GO:glycogen catabolic process + glycogen catabolism + "The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues." [ISBN:0198506732] + GO:0005980 + glycogen degradation + glycogen breakdown + glycogenolysis + glycogen catabolic process + + + monosaccharide metabolism + GO:monosaccharide metabolic process + GO:0005996 + "The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides." [ISBN:0198506732] + monosaccharide metabolic process + + + GO:0006006 + GO:glucose metabolic process + glucose metabolic process + cellular glucose metabolic process + glucose metabolism + "The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides." [ISBN:0198506732] + + + glucose catabolism + GO:0006007 + glucose degradation + glucose catabolic process + glucose breakdown + "The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose." [GOC:ai] + GO:glucose catabolic process + + + "The chemical reactions and pathways involving proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans." [GOC:mah, ISBN:0198506732] + GO:0006029 + proteoglycan metabolism + proteoglycan metabolic process + GO:proteoglycan metabolic process + + + GO:alcohol metabolic process + GO:0006066 + "The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." [CHEBI:30879, ISBN:0198506732] + alcohol metabolism + alcohol metabolic process + + + GO:cellular glucan metabolic process + GO:0006073 + "The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues." [ISBN:0198547684] + cellular glucan metabolic process + cellular glucan metabolism + + + GO:organic acid metabolic process + "The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732] + organic acid metabolic process + organic acid metabolism + GO:0006082 + + + lactate metabolism + GO:0006089 + GO:lactate metabolic process + 2-hydroxypropanoate metabolic process + alpha-hydroxypropionate metabolism + "The chemical reactions and pathways involving lactate, the anion of lactic acid." [ISBN:0198547684] + lactate metabolic process + alpha-hydroxypropionate metabolic process + 2-hydroxypropanoate metabolism + + + GO:pyruvate metabolic process + pyruvate dehydrogenase bypass + pyruvate metabolic process + GO:0006090 + "The chemical reactions and pathways involving pyruvate, 2-oxopropanoate." [GOC:go_curators] + pyruvate metabolism + + + generation of precursor metabolites and energy + metabolic energy generation + "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances." [GOC:jl] + GO:generation of precursor metabolites and energy + GO:0006091 + intermediary metabolism + + + gluconeogenesis + "The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol." [MetaCyc:GLUCONEO-PWY] + GO:gluconeogenesis + glucose biosynthetic process + glucose biosynthesis + GO:0006094 + + + Embden-Meyerhof pathway + "The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules." [GOC:bf, GOC:dph, ISBN:0201090910, ISBN:0716720094, ISBN:0879010479, Wikipedia:Glycolysis] + modifed Embden-Meyerhof pathway + GO:0006096 + anaerobic glycolysis + glycolysis + Embden-Meyerhof-Parnas pathway + glycolytic process + GO:glycolytic process + + + "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." [ISBN:0198506732] + GO:tricarboxylic acid cycle + Krebs cycle + citric acid cycle + TCA cycle + GO:0006099 + tricarboxylic acid cycle + + + GO:citrate metabolic process + GO:0006101 + citrate metabolism + citrate metabolic process + "The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboyxlate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle." [ISBN:0198506732] + + + GO:regulation of carbohydrate metabolic process + GO:0006109 + regulation of carbohydrate metabolism + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates." [GOC:go_curators] + regulation of carbohydrate metabolic process + + + "Any process that modulates the frequency, rate or extent of glycolysis." [GOC:go_curators] + regulation of glycolytic process + GO:0006110 + GO:regulation of glycolytic process + + + GO:0006112 + energy reserve metabolic process + energy reserve metabolism + "The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen." [GOC:mah] + GO:energy reserve metabolic process + + + oxidative phosphorylation + GO:0006119 + "The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis." [ISBN:0198506732, ISBN:0471331309] + GO:oxidative phosphorylation + respiratory-chain phosphorylation + + + GO:0006139 + "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai] + nucleobase, nucleoside, nucleotide and nucleic acid metabolic process + nucleobase-containing compound metabolic process + GO:nucleobase-containing compound metabolic process + cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process + nucleobase, nucleoside and nucleotide metabolic process + cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism + nucleobase, nucleoside, nucleotide and nucleic acid metabolism + + + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleotides." [GOC:go_curators] + regulation of nucleotide metabolic process + regulation of nucleotide metabolism + GO:0006140 + GO:regulation of nucleotide metabolic process + + + "The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] + GO:purine nucleotide metabolic process + purine nucleotide metabolic process + GO:0006163 + purine nucleotide metabolism + + + purine nucleotide synthesis + GO:purine nucleotide biosynthetic process + purine nucleotide formation + purine nucleotide biosynthesis + purine nucleotide biosynthetic process + GO:0006164 + "The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] + purine nucleotide anabolism + + + "The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate." [GOC:ai] + GO:nucleoside diphosphate phosphorylation + GO:0006165 + nucleoside diphosphate phosphorylation + + + GO:0006259 + DNA metabolic process + DNA metabolism + cellular DNA metabolism + "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] + GO:DNA metabolic process + + + "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC:mah] + GO:DNA replication + DNA replication + GO:0006260 + + + "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC:mah, ISBN:0198506732] + GO:0006261 + GO:DNA-dependent DNA replication + DNA-dependent DNA replication + + + mitochondrial DNA replication + mitochondrial DNA synthesis + GO:0006264 + "The process in which new strands of DNA are synthesized in the mitochondrion." [GOC:ai] + GO:mitochondrial DNA replication + replication of mitochondrial DNA + mtDNA replication + mtDNA synthesis + + + DNA ligation + "The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase." [ISBN:0815316194] + GO:DNA ligation + GO:0006266 + + + "The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action." [ISBN:071673706X, ISBN:0815316194] + DNA-dependent DNA replication initiation + GO:0006270 + DNA replication initiation + GO:DNA replication initiation + + + "The process in which a DNA strand is synthesized from template DNA during replication by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand." [ISBN:071673706X, ISBN:0815316194] + DNA strand elongation during DNA replication + DNA replication elongation + DNA strand elongation involved in DNA replication + GO:DNA strand elongation involved in DNA replication + GO:0006271 + + + GO:leading strand elongation + leading strand elongation + GO:0006272 + "The synthesis of DNA from a template strand in the 5' to 3' direction; leading strand elongation is continuous as it proceeds in the same direction as the replication fork." [ISBN:071673706X, ISBN:0815316194] + + + lagging strand elongation + "The synthesis of DNA from a template strand in a net 3' to 5' direction. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork." [ISBN:071673706X, ISBN:0815316194] + GO:0006273 + GO:lagging strand elongation + + + "The process in which the number of copies of a gene is increased in certain cells as extra copies of DNA are made in response to certain signals of cell development or of stress from the environment." [ISBN:0721601464] + GO:DNA amplification + DNA amplification + GO:0006277 + + + "A DNA replication process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strands." [GOC:mah, ISBN:0198506732] + RNA-dependent DNA replication + GO:0006278 + GO:RNA-dependent DNA replication + + + meiotic DNA synthesis + DNA replication involved in S phase involved in meiotic cell cycle + premeiotic DNA synthesis + meiotic DNA replication + meiotic nuclear cell cycle DNA replication + nuclear cell cycle DNA replication involved in meiotic cell cycle + DNA replication involved in S-phase involved in meiotic cell cycle + GO:0006279 + DNA replication during S phase involved in meiotic cell cycle + meiotic cell cycle DNA replication + premeiotic DNA replication + "The replication of DNA that precedes meiotic cell division." [GO_REF:0000060, GOC:ai, GOC:TermGenie] + GO:premeiotic DNA replication + + + DNA repair + "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID:11563486] + GO:0006281 + GO:DNA repair + + + transcription-coupled NER + transcription-coupled repair + GO:0006283 + "The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway." [PMID:10197977, PMID:11900249] + TCR + GO:transcription-coupled nucleotide-excision repair + TC-NER + transcription-coupled nucleotide-excision repair + + + intrastrand cross-link repair + NER + "A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts)." [PMID:10197977] + GO:0006289 + pyrimidine-dimer repair, DNA damage excision + GO:nucleotide-excision repair + nucleotide-excision repair + + + MMR + mismatch repair + GO:mismatch repair + GO:0006298 + MutS/MutL/MutH pathway + mismatch repair, MutL-like pathway + "A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination." [ISBN:0198506732, PMID:11687886] + + + GO:0006302 + GO:double-strand break repair + double-strand break repair + "The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix." [GOC:elh] + + + DNA modification + GO:0006304 + GO:DNA modification + "The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties." [GOC:jl, GOC:ma] + + + DNA alkylation + GO:0006305 + GO:DNA alkylation + "The addition of alkyl groups to many positions on all four bases of DNA. Alkylating agents can also modify the bases of incoming nucleotides in the course of DNA synthesis." [ISBN:0716735970] + + + GO:0006306 + GO:DNA methylation + DNA methylation + "The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine." [GOC:ems, ISBN:0198506732] + + + "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN:0198506732] + GO:0006310 + GO:DNA recombination + DNA recombination + + + GO:DNA packaging + DNA condensation + DNA packaging + DNA organization + GO:0006323 + "Any process in which DNA and associated proteins are formed into a compact, orderly structure." [GOC:mah, ISBN:0815316194] + DNA organisation + + + establishment or maintenance of chromatin architecture + chromatin organisation + "Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin." [GOC:mah] + GO:chromatin organization + GO:0006325 + chromatin organization + + + chromatin assembly/disassembly + GO:0006333 + "The formation or destruction of chromatin structures." [GOC:mah] + chromatin assembly or disassembly + GO:chromatin assembly or disassembly + + + GO:nucleosome assembly + GO:0006334 + nucleosome modeling + nucleosome assembly + "The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA." [GOC:mah] + histone chaperone + + + "Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation." [GOC:jid, PMID:12697820] + GO:chromatin remodeling + GO:0006338 + chromatin modeling + chromatin remodeling + chromatin remodelling + chromatin modelling + + + TGS + GO:chromatin silencing + GO:0006342 + transcriptional gene silencing + chromatin-mediated silencing + heterochromatic silencing + "Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin." [GOC:mah, PMID:10219245] + chromatin silencing + chromatin-mediated maintenance of transcriptional inactivation + + + regulation of gene expression by DNA imprinting + GO:regulation of gene expression by genetic imprinting + regulation of gene expression by genetic imprinting + "Heritable alterations in the activity of a gene that depend on whether it passed through the paternal or the maternal germline, but that are not encoded by DNA itself." [GOC:ems, ISBN:0198506732, PMID:11498578] + GO:0006349 + + + transcription regulator activity + GO:0006351 + cellular transcription, DNA-dependent + DNA-dependent transcription + "The cellular synthesis of RNA on a template of DNA." [GOC:jl, GOC:txnOH] + transcription, DNA-templated + GO:transcription, DNA-templated + transcription, DNA-dependent + + + GO:regulation of transcription, DNA-templated + regulation of transcription, DNA-dependent + regulation of cellular transcription, DNA-dependent + GO:0006355 + regulation of gene-specific transcription + "Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] + regulation of transcription, DNA-templated + + + global transcription regulation from Pol II promoter + GO:regulation of transcription from RNA polymerase II promoter + regulation of transcription from RNA polymerase II promoter + regulation of gene-specific transcription from RNA polymerase II promoter + regulation of global transcription from Pol II promoter + regulation of transcription from RNA polymerase II promoter, global + "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH] + regulation of transcription from Pol II promoter + GO:0006357 + + + GO:0006366 + general transcription from RNA polymerase II promoter + RNA polymerase II transcription factor activity + specific transcription from RNA polymerase II promoter + "The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs)." [GOC:jl, GOC:txnOH, ISBN:0321000382] + transcription from Pol II promoter + GO:transcription from RNA polymerase II promoter + transcription from RNA polymerase II promoter + gene-specific transcription from RNA polymerase II promoter + + + RNA processing + GO:0006396 + GO:RNA processing + "Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules." [GOC:mah] + + + GO:mRNA processing + "Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide." [GOC:mah] + mRNA maturation + mRNA processing + GO:0006397 + + + GO:RNA catabolic process + GO:0006401 + RNA catabolic process + RNA breakdown + "The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732] + RNA catabolism + RNA degradation + + + GO:0006402 + mRNA degradation + "The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes." [ISBN:0198506732] + mRNA breakdown + mRNA catabolism + mRNA catabolic process + GO:mRNA catabolic process + mRNA decay + + + "The directed movement of RNA from the nucleus to the cytoplasm." [GOC:ma] + RNA export from nucleus + GO:0006405 + GO:RNA export from nucleus + RNA export out of nucleus + RNA transport from nucleus to cytoplasm + RNA export from cell nucleus + RNA-nucleus export + + + mRNA export from cell nucleus + "The directed movement of mRNA from the nucleus to the cytoplasm." [GOC:ma] + mRNA-nucleus export + mRNA export from nucleus + GO:0006406 + mRNA export out of nucleus + mRNA transport from nucleus to cytoplasm + GO:mRNA export from nucleus + + + GO:translation + GO:0006412 + translation + "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] + protein synthesis + protein translation + protein formation + protein anabolism + protein biosynthesis + protein biosynthetic process + + + GO:translational initiation + GO:0006413 + translational initiation + "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] + translation initiation + + + translational elongation + GO:0006414 + translation elongation + "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] + GO:translational elongation + + + translation termination + "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] + GO:0006415 + GO:translational termination + translational complex disassembly + translational termination + + + GO:0006417 + regulation of translation + regulation of protein synthesis + regulation of protein formation + GO:regulation of translation + regulation of protein biosynthesis + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA." [GOC:isa_complete] + regulation of protein anabolism + + + translational readthrough + natural nonsense suppression + GO:translational readthrough + "The continuation of translation beyond a stop codon by the use of a special tRNA that recognizes the UAG and UGA codons as modified amino acids, rather than as termination codons." [GOC:jsg, PMID:11179232] + GO:0006451 + + + chaperone activity + co-chaperonin activity + protein folding + non-chaperonin molecular chaperone ATPase activity + GO:protein folding + GO:0006457 + "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure." [GOC:go_curators, GOC:rb] + glycoprotein-specific chaperone activity + chaperonin ATPase activity + protein complex assembly, multichaperone pathway + co-chaperone activity + + + "The aggregation, arrangement and bonding together of a set of components to form a protein complex." [GOC:ai] + chaperone activity + GO:0006461 + protein complex formation + GO:protein complex assembly + protein complex assembly + + + "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:go_curators] + GO:0006464 + GO:cellular protein modification process + process resulting in protein modification + protein tagging activity + cellular protein modification process + + + protein amino acid phosphorylation + GO:protein phosphorylation + "The process of introducing a phosphate group on to a protein." [GOC:hb] + GO:0006468 + protein phosphorylation + + + GO:0006476 + protein amino acid deacetylation + protein deacetylation + GO:protein deacetylation + "The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." [GOC:ai] + + + GO:protein methylation + "The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom." [GOC:ai] + GO:0006479 + protein methylation + protein amino acid methylation + + + GO:proteolysis + "The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds." [GOC:bf, GOC:mah] + peptidolysis + proteolysis + GO:0006508 + + + ubiquitin-dependent proteolysis + GO:ubiquitin-dependent protein catabolic process + "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein." [GOC:go_curators] + ubiquitin-dependent protein breakdown + ubiquitin-dependent protein catabolic process + ubiquitin-dependent protein degradation + ubiquitin-dependent protein catabolism + GO:0006511 + + + peptide metabolic process + GO:peptide metabolic process + "The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." [CHEBI:16670, GOC:go_curators] + GO:0006518 + peptide metabolism + + + GO:0006520 + "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells." [CHEBI:33709, GOC:curators, ISBN:0198506732] + amino acid metabolic process + cellular amino acid metabolism + amino acid and derivative metabolism + GO:cellular amino acid metabolic process + cellular amino acid metabolic process + cellular amino acid and derivative metabolic process + + + alanine metabolism + GO:alanine metabolic process + alanine metabolic process + "The chemical reactions and pathways involving alanine, 2-aminopropanoic acid." [GOC:go_curators] + GO:0006522 + + + GO:0006523 + alanine anabolism + GO:alanine biosynthetic process + "The chemical reactions and pathways resulting in the formation of alanine, 2-aminopropanoic acid." [GOC:go_curators] + alanine biosynthesis + alanine biosynthetic process + alanine formation + alanine synthesis + + + GO:0006536 + glutamic acid metabolism + GO:glutamate metabolic process + glutamic acid metabolic process + "The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid." [GOC:go_curators] + glutamate metabolism + glutamate metabolic process + + + glutamate synthesis + glutamate biosynthetic process + glutamate formation + GO:0006537 + "The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid." [GOC:go_curators] + GO:glutamate biosynthetic process + glutamate anabolism + glutamate biosynthesis + glutamic acid biosynthetic process + glutamic acid biosynthesis + + + glutamine metabolism + glutamine metabolic process + "The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid." [GOC:ai] + GO:glutamine metabolic process + GO:0006541 + + + glutamine biosynthesis + "The chemical reactions and pathways resulting in the formation of glutamine, 2-amino-4-carbamoylbutanoic acid." [GOC:ai] + GO:glutamine biosynthetic process + glutamine formation + glutamine synthesis + glutamine biosynthetic process + glutamine anabolism + GO:0006542 + + + cellular amino acid derivative metabolism + "The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents." [CHEBI:83821, GOC:ai] + modified amino acid metabolic process + cellular modified amino acid metabolism + amino acid derivative metabolic process + GO:0006575 + modified amino acid metabolism + GO:cellular modified amino acid metabolic process + cellular amino acid derivative metabolic process + cellular modified amino acid metabolic process + + + melanin metabolic process + melanin metabolism + GO:melanin metabolic process + "The chemical reactions and pathways involving melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom." [GOC:go_curators] + GO:0006582 + + + GO:lipid metabolic process + "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC:ma] + lipid metabolic process + GO:0006629 + lipid metabolism + + + GO:fatty acid metabolic process + GO:0006631 + "The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN:0198547684] + fatty acid metabolic process + fatty acid metabolism + + + "A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC:mah, ISBN:0198506732, MetaCyc:FAO-PWY] + fatty acid beta-oxidation + GO:fatty acid beta-oxidation + GO:0006635 + + + neutral lipid metabolism + GO:0006638 + "The chemical reactions and pathways involving neutral lipids, lipids only soluble in solvents of very low polarity." [ISBN:0198547684] + GO:neutral lipid metabolic process + neutral lipid metabolic process + + + glyceride metabolic process + acylglycerol metabolic process + GO:acylglycerol metabolic process + GO:0006639 + "The chemical reactions and pathways involving acylglycerol, any mono-, di- or triester of glycerol with (one or more) fatty acids." [ISBN:0198506732] + acylglycerol metabolism + glyceride metabolism + + + triacylglycerol metabolism + triglyceride metabolic process + "The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins." [ISBN:0198506732] + GO:0006641 + triglyceride metabolism + GO:triglyceride metabolic process + triacylglycerol metabolic process + + + steroid anabolism + steroidogenesis + GO:steroid biosynthetic process + steroid biosynthetic process + steroid biosynthesis + "The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification." [GOC:go_curators] + steroid synthesis + steroid formation + GO:0006694 + + + "The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones." [GOC:ai] + cholesterol biosynthetic process + cholesterol anabolism + cholesterol synthesis + GO:cholesterol biosynthetic process + cholesterol formation + cholesterol biosynthesis + GO:0006695 + + + "The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile." [GOC:go_curators] + GO:0006699 + bile acid synthesis + bile acid biosynthesis + bile acid formation + bile acid anabolism + bile acid biosynthetic process + GO:bile acid biosynthetic process + + + aromatic compound metabolism + GO:cellular aromatic compound metabolic process + cellular aromatic compound metabolic process + GO:0006725 + "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells." [GOC:ai, ISBN:0198506732] + + + coenzyme metabolism + GO:0006732 + "The chemical reactions and pathways involving coenzymes, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed." [ISBN:0198506732] + coenzyme metabolic process + GO:coenzyme metabolic process + + + oxidoreduction coenzyme metabolic process + "The chemical reactions and pathways involving coenzymes that are required, in addition to an enzyme and a substrate, for an oxidoreductase reaction to proceed." [GOC:mah] + oxidoreduction coenzyme metabolism + GO:0006733 + GO:oxidoreduction coenzyme metabolic process + + + reduced NADP metabolic process + oxidized nicotinamide adenine dinucleotide phosphate metabolism + reduced NADP metabolism + NADP metabolic process + NAD phosphorylation and dephosphorylation + NADP (oxidized) metabolism + NADPH metabolism + oxidized NADP metabolism + reduced nicotinamide adenine dinucleotide phosphate metabolic process + NADP (reduced) metabolic process + GO:NADP metabolic process + reduced nicotinamide adenine dinucleotide phosphate metabolism + GO:0006739 + nicotinamide adenine dinucleotide phosphate metabolism + nicotinamide adenine dinucleotide phosphate metabolic process + NADP (reduced) metabolism + "The chemical reactions and pathways involving nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; metabolism may be of either the oxidized form, NADP, or the reduced form, NADPH." [GOC:mah] + NADPH metabolic process + NADP metabolism + oxidized nicotinamide adenine dinucleotide phosphate metabolic process + NADP (oxidized) metabolic process + oxidized NADP metabolic process + + + oxidized nicotinamide adenine dinucleotide phosphate biosynthesis + oxidized nicotinamide adenine dinucleotide phosphate biosynthetic process + reduced NADP biosynthesis + reduced NADP biosynthetic process + "The chemical reactions and pathways resulting in the formation of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; biosynthesis may be of either the oxidized form, NADP, or the reduced form, NADPH." [GOC:mah] + NADP biosynthesis + NADP formation + NADP synthesis + NADP biosynthetic process + NADP anabolism + NADP (reduced) biosynthesis + NADP (reduced) biosynthetic process + GO:NADP biosynthetic process + nicotinamide adenine dinucleotide phosphate biosynthesis + nicotinamide adenine dinucleotide phosphate biosynthetic process + GO:0006741 + reduced nicotinamide adenine dinucleotide phosphate biosynthesis + reduced nicotinamide adenine dinucleotide phosphate biosynthetic process + NADP (oxidized) biosynthetic process + NADP (oxidized) biosynthesis + oxidized NADP biosynthetic process + oxidized NADP biosynthesis + NADPH biosynthetic process + NADPH biosynthesis + + + "The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle." [CHEBI:16856, ISBN:0198506732] + glutathione metabolic process + GO:0006749 + glutathione metabolism + GO:glutathione metabolic process + + + glutathione formation + glutathione biosynthesis + GO:0006750 + glutathione anabolism + "The chemical reactions and pathways resulting in the formation of glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins." [CHEBI:16856, GOC:ai, GOC:al, GOC:pde, ISBN:0198506732] + glutathione biosynthetic process + GO:glutathione biosynthetic process + glutathione synthesis + + + "The chemical reactions and pathways involving any phosphorylated nucleoside." [GOC:mah] + GO:nucleoside phosphate metabolic process + nucleoside phosphate metabolism + GO:0006753 + nucleoside phosphate metabolic process + + + ATP biosynthetic process + ATP anabolism + ATP biosynthesis + ATP formation + GO:ATP biosynthetic process + GO:0006754 + "The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [GOC:go_curators, ISBN:0198506732] + ATP synthesis + + + GO:ATP generation from ADP + ADP phosphorylation + "The process of introducing a phosphate group into ADP, adenosine diphosphate, to produce ATP." [GOC:ai] + GO:0006757 + ATP generation from ADP + + + sulphur metabolism + GO:0006790 + "The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione." [GOC:ai] + GO:sulfur compound metabolic process + sulfur compound metabolic process + sulphur metabolic process + sulfur metabolism + + + GO:phosphorus metabolic process + GO:0006793 + phosphorus metabolism + phosphorus metabolic process + "The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4)." [GOC:ai] + + + GO:phosphate-containing compound metabolic process + phosphate-containing compound metabolic process + "The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid." [GOC:ai] + phosphate metabolism + phosphate metabolic process + GO:0006796 + + + "The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide." [GOC:cab2] + xenobiotic metabolism + GO:0006805 + GO:xenobiotic metabolic process + xenobiotic metabolic process + + + GO:nitrogen compound metabolic process + "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium." [CHEBI:51143, GOC:go_curators, GOC:jl, ISBN:0198506732] + nitrogen compound metabolism + GO:0006807 + nitrogen compound metabolic process + + + GO:0006810 + transport + "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore." [GOC:dph, GOC:jl, GOC:mah] + auxiliary transport protein activity + GO:transport + transport accessory protein activity + + + GO:0006811 + GO:ion transport + ion transport + "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + + + "The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + cation transport + GO:0006812 + GO:cation transport + + + K+ conductance + low voltage-dependent potassium channel auxiliary protein activity + GO:0006813 + potassium ion transport + potassium transport + "The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + GO:potassium ion transport + low voltage-gated potassium channel auxiliary protein activity + + + GO:calcium ion transport + "The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + calcium ion transport + calcium transport + GO:0006816 + + + GO:anion transport + GO:0006820 + "The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + anion transport + + + GO:0006821 + chloride transport + "The directed movement of chloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc] + GO:chloride transport + + + GO:0006826 + GO:iron ion transport + iron transport + iron ion transport + "The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + + + GO:water transport + GO:0006833 + water transport + "The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + + + GO:0006836 + neurotransmitter transport + GO:neurotransmitter transport + "The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [GOC:ai] + + + GO:0006837 + GO:serotonin transport + "The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems." [GOC:ai] + serotonin transport + + + "The transport of substances that occurs outside cells." [GOC:go_curators] + extracellular transport + GO:0006858 + GO:extracellular transport + + + GO:amino acid transport + amino acid transport + GO:0006865 + "The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + + + lipid transport + GO:lipid transport + "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [ISBN:0198506732] + GO:0006869 + + + regulation of pH + hydrogen ion homeostasis + GO:regulation of pH + GO:0006885 + "Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell." [GOC:dph, GOC:go_curators, GOC:tb] + + + intracellular protein transport + "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell." [GOC:mah] + GO:0006886 + GO:intracellular protein transport + copper-induced intracellular protein transport + + + vesicle exocytosis + exocytosis + "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell. Steps that prepare vesicles for fusion with the membrane (e.g. docking and priming) are included in this process. This is the process in which most molecules are secreted from eukaryotic cells." [GOC:mah, ISBN:0716731363] + nonselective vesicle exocytosis + GO:exocytosis + GO:0006887 + + + GO:endocytosis + "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle." [GOC:mah, ISBN:0198506732, ISBN:0716731363] + plasma membrane invagination + nonselective vesicle endocytosis + endocytosis + GO:0006897 + vesicle endocytosis + + + "An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles." [GOC:mah, ISBN:0716731363] + GO:receptor-mediated endocytosis + receptor-mediated endocytosis + receptor mediated endocytosis + GO:0006898 + + + membrane evagination + "The evagination of a membrane, resulting in formation of a vesicle." [GOC:jid, GOC:tb] + membrane budding + vesicle formation + nonselective vesicle assembly + GO:membrane budding + GO:0006900 + vesicle biosynthesis + vesicle budding + + + vesicle fusion + GO:0006906 + "Fusion of the membrane of a transport vesicle with its target membrane." [GOC:jid] + GO:vesicle fusion + + + pinocytosis + GO:pinocytosis + "An endocytosis process that results in the uptake of liquid material by cells from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, called pinosomes, formed by invagination of the plasma membrane." [ISBN:0198506732] + GO:0006907 + fluid-phase endocytosis + + + GO:phagocytosis + phagocytosis + "An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles." [ISBN:0198506732] + GO:0006909 + + + "The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis." [GOC:curators, ISBN:0781735149] + phagocytosis, engulfment + GO:phagocytosis, engulfment + GO:0006911 + phagosome formation + phagosome biosynthesis + + + GO:nucleocytoplasmic transport + GO:0006913 + "The directed movement of molecules between the nucleus and the cytoplasm." [GOC:go_curators] + nucleocytoplasmic transport + + + GO:0006914 + "The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation." [GOC:autophagy, ISBN:0198547684, PMID:11099404, PMID:9412464] + autophagy + GO:autophagy + + + GO:apoptotic process + apoptotic programmed cell death + "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263] + induction of apoptosis by p53 + apoptotic process + apoptotic cell death + signaling (initiator) caspase activity + induction of apoptosis + commitment to apoptosis + GO:0006915 + apoptosis activator activity + programmed cell death by apoptosis + + + GO:movement of cell or subcellular component + "The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore." [GOC:dgh, GOC:dph, GOC:jl, GOC:mlg] + cellular component motion + movement of cell or subcellular component + GO:0006928 + cell movement + cellular component movement + + + chemotaxis + GO:0006935 + "The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." [ISBN:0198506732] + taxis in response to chemical stimulus + GO:chemotaxis + + + GO:0006936 + "A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis." [GOC:ef, GOC:mtg_muscle, ISBN:0198506732] + muscle contraction + GO:muscle contraction + + + GO:syncytium formation + syncytium formation + "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division." [ISBN:0198506732] + GO:0006949 + + + GO:response to stress + response to biotic stress + response to stress + GO:0006950 + response to abiotic stress + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] + + + physiological defense response + GO:defense response + GO:0006952 + "Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." [GOC:go_curators] + antimicrobial peptide activity + defence response + defense response + defense/immunity protein activity + + + GO:acute-phase response + GO:0006953 + "An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals." [ISBN:0198506732] + acute-phase response + + + GO:inflammatory response + GO:0006954 + inflammatory response + "The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages." [GO_REF:0000022, GOC:mtg_15nov05, ISBN:0198506732] + + + GO:0006955 + immune response + GO:immune response + "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05] + + + GO:0006956 + complement activation + complement activity + "Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] + GO:complement activation + complement response + complement cascade + + + GO:humoral immune response + humoral immune response + "An immune response mediated through a body fluid." [GOC:hb, ISBN:0198506732] + GO:0006959 + + + GO:0006968 + cellular defence response + GO:cellular defense response + "A defense response that is mediated by cells." [GOC:ebc] + cellular defense response + + + cellular response to DNA damage stimulus + GO:0006974 + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC:go_curators] + cellular DNA damage response + response to genotoxic stress + GO:cellular response to DNA damage stimulus + DNA damage response + + + organelle organization + organelle organisation + organelle organization and biogenesis + GO:0006996 + GO:organelle organization + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] + + + nuclear organization and biogenesis + nuclear organization + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus." [GOC:dph, GOC:ems, GOC:jl, GOC:mah] + nuclear organisation + nuclear morphology + GO:0006997 + GO:nucleus organization + nucleus organization and biogenesis + nucleus organization + + + nuclear envelope organization + nuclear envelope organization and biogenesis + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope." [GOC:dph, GOC:ems, GOC:jl, GOC:mah] + GO:nuclear envelope organization + GO:0006998 + nuclear envelope organisation + + + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear pore." [GOC:dph, GOC:jid, GOC:jl, GOC:mah] + nuclear pore organisation + nuclear pore organization and biogenesis + nuclear pore complex organization and biogenesis + nuclear pore organization + GO:nuclear pore organization + GO:0006999 + + + mitochondrion organization and biogenesis + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components." [GOC:dph, GOC:jl, GOC:mah, GOC:sgd_curators, PMID:9786946] + GO:0007005 + mitochondrion organization + GO:mitochondrion organization + mitochondrion organisation + mitochondria organization + + + GO:0007010 + cytoskeleton organization and biogenesis + cytoskeleton organisation + cytoskeleton organization + cytoskeletal regulator activity + cytoskeletal organization and biogenesis + GO:cytoskeleton organization + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:dph, GOC:jl, GOC:mah] + + + GO:0007015 + GO:actin filament organization + actin filament organization + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking." [GOC:mah] + actin filament organisation + + + GO:microtubule-based process + microtubule-based process + GO:0007017 + "Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins." [GOC:mah] + + + "A microtubule-based process that is mediated by motor proteins and results in the movement of organelles, other microtubules, or other particles along microtubules." [GOC:cjm, ISBN:0815316194] + microtubule-based movement + GO:0007018 + GO:microtubule-based movement + + + "The removal of tubulin heterodimers from one or both ends of a microtubule." [ISBN:0815316194] + GO:microtubule depolymerization + microtubule disassembly + microtubule depolymerization + GO:0007019 + microtubule shortening + + + microtubule stabilization + GO:0007026 + down-regulation of microtubule depolymerization + GO:negative regulation of microtubule depolymerization + negative regulation of microtubule depolymerization + negative regulation of microtubule disassembly + down regulation of microtubule depolymerization + downregulation of microtubule depolymerization + "Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol." [GOC:mah, ISBN:0815316194] + + + "The directed movement of substances into, out of or within a vacuole." [GOC:ai] + vacuolar transport + GO:vacuolar transport + GO:0007034 + + + "The directed movement of substances into, out of or within a lysosome." [GOC:ai] + GO:lysosomal transport + GO:0007041 + lysosomal transport + + + cell-cell junction assembly + GO:0007043 + intercellular junction assembly + "The aggregation, arrangement and bonding together of a set of components to form a junction between cells." [GOC:ai] + GO:cell-cell junction assembly + + + cell-division cycle + "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators, GOC:mtg_cell_cycle] + GO:cell cycle + GO:0007049 + cell cycle + + + GO:0007050 + cell cycle arrest + termination of cell cycle + cessation of cell cycle + GO:cell cycle arrest + arrest of cell cycle progression + "A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M)." [GOC:dph, GOC:mah, GOC:tb] + + + spindle organisation + spindle organization + spindle organization and biogenesis + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart." [GOC:mah] + GO:0007051 + GO:spindle organization + + + GO:mitotic spindle organization + spindle organization and biogenesis during mitosis + mitotic spindle organization and biogenesis + mitotic spindle organisation + mitotic spindle organization + GO:0007052 + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle." [GOC:mah] + + + "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." [GOC:jl, GOC:mah, GOC:mtg_cell_cycle, GOC:vw] + chromosome transmission + chromosome segregation + GO:chromosome segregation + chromosome division + GO:0007059 + + + "A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell." [GOC:dph, GOC:ma, GOC:mah, ISBN:0198547684] + mitosis + mitotic nuclear division + GO:mitotic nuclear division + GO:0007067 + + + "A form of asexual reproduction, occurring in certain bacteria and fungi (e.g. yeasts) and some primitive animals in which an individual arises from a daughter cell formed by pinching off a part of the parent cell. The budlike outgrowths so formed may sometimes remain attached to the parent cell." [ISBN:0198506732] + GO:0007114 + GO:cell budding + cell budding + + + "One of the two nuclear divisions that occur as part of the meiotic cell cycle." [GOC:dph, GOC:mah, PMID:9334324] + GO:meiotic nuclear division + GO:0007126 + meiotic nuclear division + + + GO:meiosis I + meiosis I + GO:0007127 + "The first meiotic nuclear division in which homologous chromosomes are paired and segregated from each other, producing two haploid daughter nuclei." [GOC:dph, GOC:jl, GOC:mtg_cell_cycle, PMID:9334324] + + + GO:meiotic prophase I + "The cell cycle phase which is the first stage of meiosis I and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell." [GOC:mtg_cell_cycle] + meiotic prophase I + GO:0007128 + + + "The meiotic cell cycle process where side by side pairing and physical juxtaposition of homologous chromosomes is created during meiotic prophase. Synapsis begins when the chromosome arms begin to pair from the clustered telomeres and ends when synaptonemal complex or linear element assembly is complete." [GOC:mtg_cell_cycle, PMID:22582262, PMID:23117617] + synapsis + GO:synapsis + chromosomal pairing + GO:0007129 + homologous chromosome pairing at meiosis + chromosomal synapsis + + + "The cell cycle process in which the synaptonemal complex is formed. This is a structure that holds paired chromosomes together during prophase I of meiosis and that promotes genetic recombination." [ISBN:0198506732] + synaptonemal complex assembly + synaptonemal complex formation + GO:synaptonemal complex assembly + GO:0007130 + + + GO:0007131 + gene conversion with reciprocal crossover + reciprocal meiotic recombination + GO:reciprocal meiotic recombination + "The cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate. This results in the equal exchange of genetic material between non-sister chromatids in a pair of homologous chromosomes. These reciprocal recombinant products ensure the proper segregation of homologous chromosomes during meiosis I and create genetic diversity." [PMID:2087779] + + + GO:meiotic metaphase I + GO:0007132 + "The cell cycle phase, following prophase I, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis I." [GOC:mtg_cell_cycle] + meiotic metaphase I + + + GO:meiosis II + GO:0007135 + meiosis II + "The second nuclear division of meiosis, in which the two chromatids in each chromosome are separated, resulting in four daughter nuclei from the two nuclei produced in meiosis II." [GOC:dph, GOC:mah, ISBN:0198547684] + + + meiotic metaphase II + "The cell cycle phase, following prophase II, during which chromosomes become aligned on the equatorial plate of the cell as part of meiosis II." [GOC:mtg_cell_cycle] + GO:0007137 + GO:meiotic metaphase II + + + "A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline." [GOC:dph, GOC:mah] + male meiosis + GO:male meiosis + GO:0007140 + + + GO:0007143 + female meiotic division + GO:female meiotic division + "A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline." [GOC:dph, GOC:ems, GOC:mah] + + + GO:cell communication + GO:0007154 + "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:mah] + cell communication + + + cell adhesion + cell adhesion molecule activity + GO:0007155 + GO:cell adhesion + "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules." [GOC:hb, GOC:pf] + + + GO:0007159 + "The attachment of a leukocyte to another cell via adhesion molecules." [GOC:go_curators] + GO:leukocyte cell-cell adhesion + leukocyte cell-cell adhesion + leukocyte cell adhesion + leukocyte adhesion + + + down-regulation of cell adhesion + GO:negative regulation of cell adhesion + negative regulation of cell adhesion + downregulation of cell adhesion + cell adhesion receptor inhibitor activity + GO:0007162 + down regulation of cell adhesion + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion." [GOC:go_curators] + + + signalling pathway + GO:signal transduction + GO:0007165 + signal transduction + signaling pathway + "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] + + + cell surface receptor signaling pathway + GO:0007166 + "A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:mah, GOC:pr, GOC:signaling] + cell surface receptor linked signaling pathway + cell surface receptor linked signal transduction + cell surface receptor linked signalling pathway + GO:cell surface receptor signaling pathway + + + GO:0007167 + enzyme linked receptor protein signaling pathway + enzyme linked receptor protein signalling pathway + "Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, ISBN:0185316194] + GO:enzyme linked receptor protein signaling pathway + + + GO:transmembrane receptor protein tyrosine kinase signaling pathway + "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:ceb, GOC:signaling] + GO:0007169 + transmembrane receptor protein tyrosine kinase signalling pathway + transmembrane receptor protein tyrosine kinase signaling pathway + + + transmembrane receptor protein serine/threonine kinase signaling pathway + GO:0007178 + GO:transmembrane receptor protein serine/threonine kinase signaling pathway + "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses serine/threonine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling] + transmembrane receptor protein serine/threonine kinase signalling pathway + + + transforming growth factor beta receptor signaling pathway + TGF-beta receptor signaling pathway + GO:transforming growth factor beta receptor signaling pathway + TGF-beta receptor signalling pathway + TGFbeta receptor signalling pathway + GO:0007179 + transforming growth factor beta receptor signalling pathway + TGFbeta receptor signaling pathway + "A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mah, GOC:signaling] + + + G-protein coupled receptor protein signaling pathway + "A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576)." [GOC:bf, GOC:mah, PMID:16902576PMID\:24568158, Wikipedia:G_protein-coupled_receptor] + G-protein coupled receptor signaling pathway + GO:0007186 + GPCR signaling pathway + G-protein-coupled receptor protein signalling pathway + G-protein coupled receptor protein signal transduction + G protein coupled receptor protein signalling pathway + GO:G-protein coupled receptor signaling pathway + G protein coupled receptor protein signaling pathway + GPCR signalling pathway + G-protein-coupled receptor protein signaling pathway + G-protein coupled receptor signalling pathway + + + "The series of molecular signals generated as a consequence of a dopamine receptor binding to one of its physiological ligands." [GOC:mah] + dopamine receptor signaling pathway + GO:dopamine receptor signaling pathway + dopamine receptor signalling pathway + GO:0007212 + + + 4-aminobutyrate signalling pathway + GABA signaling pathway + 4-aminobutanoate signalling pathway + GABA signalling pathway + 4-aminobutyrate signaling pathway + 4-aminobutanoate signaling pathway + GO:gamma-aminobutyric acid signaling pathway + "The series of molecular signals generated by the binding of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, to a cell surface receptor." [GOC:mah] + GO:0007214 + gamma-aminobutyric acid signalling pathway + gamma-aminobutyric acid signaling pathway + + + N signaling pathway + Notch signalling pathway + GO:0007219 + Notch signaling pathway + N signalling pathway + GO:Notch signaling pathway + Notch receptor signaling pathway + "A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, GOC:signaling] + Notch-receptor signalling pathway + Notch receptor signalling pathway + Notch-receptor signaling pathway + + + "A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened." [GOC:mah, PMID:15205520] + GO:smoothened signaling pathway + smoothened signaling pathway + hedgehog signaling pathway + Shh signaling pathway + smoothened signalling pathway + GO:0007224 + + + GO:0007259 + JAK-STAT signal transduction + JAK-STAT cascade + "Any process in which STAT proteins (Signal Transducers and Activators of Transcription) and JAK (Janus Activated Kinase) proteins convey a signal to trigger a change in the activity or state of a cell. The JAK-STAT cascade begins with activation of STAT proteins by members of the JAK family of tyrosine kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins." [GOC:bf, GOC:jl, GOC:signaling, PMID:12039028] + GO:JAK-STAT cascade + + + GO:0007264 + small GTPase-mediated signal transduction + GO:small GTPase mediated signal transduction + small GTPase mediated signal transduction + "Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals." [GOC:mah] + + + GO:0007265 + GO:Ras protein signal transduction + Ras protein signal transduction + "A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state." [GOC:bf] + Ras mediated signal transduction + + + cell-cell signalling + GO:cell-cell signaling + GO:0007267 + cell-cell signaling + "Any process that mediates the transfer of information from one cell to another." [GOC:mah] + + + GO:0007268 + "The vesicular release of classical neurotransmitter molecules from a neuron, across a chemical synapse, the subsequent activation of neurotransmitter receptors of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." [GOC:jl, MeSH:D009435] + neurotransmission + GO:synaptic transmission + synaptic transmission + + + GO:0007275 + GO:multicellular organismal development + "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb] + multicellular organismal development + + + GO:0007276 + gametogenesis + gamete generation + GO:gamete generation + "The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell." [GOC:ems, GOC:mtg_sensu] + + + GO:germ cell development + "The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism." [GOC:go_curators] + germ-cell development + germ cell development + GO:0007281 + + + GO:spermatogenesis + "The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis." [GOC:jid, ISBN:9780878933846] + GO:0007283 + generation of spermatozoa + spermatogenesis + + + GO:spermatid development + GO:0007286 + spermatid cell development + "The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure." [GOC:dph, GOC:go_curators] + spermatid development + spermiogenesis + + + GO:female gamete generation + female gamete generation + "Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction." [GOC:dph, ISBN:0198506732] + GO:0007292 + + + GO:acrosome reaction + "The discharge, by sperm, of a single, anterior secretory granule following the sperm's attachment to the zona pellucida surrounding the oocyte. The process begins with the fusion of the outer acrosomal membrane with the sperm plasma membrane and ends with the exocytosis of the acrosomal contents into the egg." [GOC:dph, PMID:3886029] + GO:0007340 + acrosome reaction + + + "The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry." [GOC:dph, GOC:jid] + determination of left/right symmetry + determination of left/right asymmetry + GO:0007368 + GO:determination of left/right symmetry + + + GO:gastrulation + GO:0007369 + gastrulation + "A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm." [GOC:curators, ISBN:9780878933846] + + + pattern formation + GO:0007389 + pattern specification process + pattern biosynthesis + "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate." [GOC:go_curators, GOC:isa_complete, ISBN:0521436125] + GO:pattern specification process + + + GO:0007398 + "The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation." [GOC:dph, GOC:tb] + ectoderm development + GO:ectoderm development + + + nervous system development + pan-neural process + GO:0007399 + GO:nervous system development + "The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state." [GOC:dgh] + + + GO:axonogenesis + neuron long process generation + "De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon." [GOC:dph, GOC:jid, GOC:pg, GOC:pr, ISBN:0198506732] + axon morphogenesis + GO:0007409 + axonogenesis + + + GO:0007411 + axon pathfinding + "The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues." [ISBN:0878932437] + axon chemotaxis + axon guidance + GO:axon guidance + + + synaptogenesis + synapse biogenesis + "The aggregation, arrangement and bonding together of a set of components to form a synapse." [GOC:mah] + GO:synapse assembly + synapse assembly + GO:0007416 + + + "The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord." [GOC:bf, GOC:jid, ISBN:0582227089] + GO:central nervous system development + central nervous system development + CNS development + GO:0007417 + + + GO:0007420 + "The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.)." [GOC:dph, GOC:jid, GOC:tb, UBERON:0000955] + brain development + GO:brain development + + + "The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure." [GOC:go_curators] + GO:0007423 + sense organ development + GO:sensory organ development + sensory organ development + + + GO:0007444 + "The process whose specific outcome is the progression of the imaginal disc over time, from its formation to the metamorphosis to form adult structures. Imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult structures (legs, antennae, wings, etc.)." [GOC:bf, ISBN:0879694238] + imaginal disc development + GO:imaginal disc development + + + GO:endoderm development + "The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues." [GOC:dph, GOC:tb] + GO:0007492 + endoderm development + + + "The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine." [GOC:jid, UBERON:0001045] + midgut development + GO:0007494 + GO:midgut development + + + mesoderm development + GO:mesoderm development + GO:0007498 + "The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue." [GOC:dph, GOC:tb] + + + cardiac development + GO:heart development + heart development + GO:0007507 + "The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." [GOC:jid, UBERON:0000948] + + + "The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work." [GOC:jid, ISBN:0198506732] + muscle organ development + GO:muscle organ development + GO:0007517 + + + "A process in which non-proliferating myoblasts fuse to existing fibers or to myotubes to form new fibers. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:mtg_muscle] + GO:myoblast fusion + GO:0007520 + myoblast fusion + + + GO:0007530 + sex determination + "Any process that establishes and transmits the specification of sexual status of an individual organism." [ISBN:0198506732] + GO:sex determination + + + GO:primary sex determination + "The sex determination process that results in the initial specification of sexual status of an individual organism." [GOC:mah] + GO:0007538 + primary sex determination + + + "The sex determination processes that take place after the initial transmission of the sexual phenotype to specific information pathways." [GOC:mah] + GO:0007545 + GO:processes downstream of sex determination signal + processes downstream of sex determination signal + + + somatic processes downstream of sex determination signal + GO:somatic processes downstream of sex determination signal + GO:0007546 + "The events determining the somatic sexual phenotype after the initial transmission of that phenotype to soma-specific information pathways." [GOC:ems] + + + GO:sex differentiation + "The establishment of the sex of an organism by physical differentiation." [GOC:ai] + GO:0007548 + sex differentiation + + + "Compensating for the two-fold variation in X:autosome chromosome ratios between sexes by a global activation or inactivation of all, or most of, genes on one or both of the X chromosomes." [GOC:ems, ISBN:0140512888, PMID:11498577] + dosage compensation + GO:dosage compensation + GO:0007549 + + + GO:0007565 + gestation + "The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth." [ISBN:0192800825] + carrying of young + female pregnancy + GO:female pregnancy + + + GO:0007566 + blastocyst implantation + embryo implantation + GO:embryo implantation + "Attachment of the blastocyst to the uterine lining." [GOC:isa_complete, http://www.medterms.com] + + + "The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs." [ISBN:0198506732] + GO:parturition + parturition + GO:0007567 + giving birth + + + ageing + aging + "A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death (GO:0016265) and may succeed developmental maturation (GO:0021700)." [GOC:PO_curators] + GO:0007568 + GO:aging + + + "An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469)." [GOC:PO_curators] + cell aging + cell ageing + GO:cell aging + GO:0007569 + + + response to nutrient + GO:0007584 + response to nutrients + GO:response to nutrient + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus." [GOC:go_curators] + + + GO:respiratory gaseous exchange + GO:0007585 + "The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms." [ISBN:0198506732] + respiratory gaseous exchange + + + "The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [GOC:isa_complete, ISBN:0198506732] + digestion + GO:digestion + GO:0007586 + + + "The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds." [ISBN:0192801023] + GO:excretion + GO:0007588 + excretion + + + GO:0007589 + body fluid secretion + GO:body fluid secretion + "The controlled release of a fluid by a cell or tissue in an animal." [GOC:ai, GOC:dph, GOC:mah, GOC:tb] + + + lactation + "The secretion of milk by the mammary gland." [ISBN:0198506732] + GO:lactation + GO:0007595 + + + GO:blood coagulation + blood clotting + "The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers." [http://www.graylab.ac.uk/omd/, ISBN:0198506732] + blood coagulation + GO:0007596 + + + "A protein activation cascade that contributes to blood coagulation and consists of the self-limited process linking exposure and activation of tissue factor to the activation of clotting factor X." [GOC:add, GOC:mah, GOC:pde] + GO:0007598 + GO:blood coagulation, extrinsic pathway + blood coagulation, extrinsic pathway + + + GO:hemostasis + "The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part." [ISBN:0198506732] + hemostasis + GO:0007599 + + + sensory perception + GO:0007600 + "The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:ai, GOC:dph] + GO:sensory perception + + + GO:visual perception + GO:0007601 + sensory visual perception + "The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image." [GOC:ai] + vision + sense of sight + visual perception + + + GO:0007602 + opsin + GO:phototransduction + phototransduction + "The sequence of reactions within a cell required to convert absorbed photons into a molecular signal." [GOC:go_curators] + + + GO:0007605 + "The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound." [GOC:ai] + hearing + sensory perception of sound + perception of sound + GO:sensory perception of sound + + + chemosensory perception + GO:sensory perception of chemical stimulus + GO:0007606 + sensory perception of chemical stimulus + "The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:ai] + + + GO:sensory perception of smell + scent perception + smell perception + olfaction + sensory perception of smell + sense of smell + "The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process." [GOC:ai, http://www.onelook.com/] + GO:0007608 + + + behavior + behaviour + "The internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] + behavioral response to stimulus + GO:behavior + behavioural response to stimulus + GO:0007610 + + + GO:learning or memory + GO:0007611 + learning or memory + "The acquisition and processing of information and/or the storage and retrieval of this information over time." [GOC:jid, PMID:8938125] + + + GO:learning + GO:0007612 + "Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience." [ISBN:0582227089, ISBN:0721662544] + learning + + + GO:memory + GO:0007613 + memory + "The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task)." [GOC:curators, http://www.onelook.com/, ISBN:0582227089] + + + GO:0007616 + GO:long-term memory + long-term memory + "The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation." [http://hebb.mit.edu/courses/9.03/lecture4.html, ISBN:0582227089] + + + GO:0007618 + "The pairwise union of individuals for the purpose of sexual reproduction, ultimately resulting in the formation of zygotes." [GOC:jl, ISBN:0387520546] + GO:mating + mating + + + GO:copulation + "The act of sexual union between male and female, involving the transfer of sperm." [ISBN:0721662544] + copulation + GO:0007620 + + + circadian process + GO:0007623 + circadian rhythm + GO:circadian rhythm + "Any biological process in an organism that recurs with a regularity of approximately 24 hours." [GOC:bf, GOC:go_curators] + circadian response + response to circadian rhythm + + + "The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [GOC:dph] + locomotion in response to stimulus + locomotory behaviour + GO:0007626 + GO:locomotory behavior + locomotory behavior + locomotory behavioral response to stimulus + locomotory behavioural response to stimulus + behavior via locomotion + + + feeding behavior + "Behavior associated with the intake of food." [GOC:mah] + behavioural response to food + GO:feeding behavior + feeding behaviour + GO:0007631 + behavioral response to food + + + chemosensory behavior + behavioral response to chemical stimulus + behavioural response to chemical stimulus + chemosensory behaviour + GO:0007635 + "Behavior that is dependent upon the sensation of chemicals." [GOC:go_curators] + GO:chemosensory behavior + + + GO:0008015 + GO:blood circulation + "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." [GOC:mtg_heart, ISBN:0192800825] + blood circulation + hemolymph circulation + + + GO:regulation of heart contraction + "Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body." [GOC:dph, GOC:go_curators, GOC:tb] + regulation of heart contraction + regulation of cardiac contraction + GO:0008016 + + + GO:synaptic vesicle + synaptic vesicle + GO:0008021 + "A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane." [PMID:10099709, PMID:12563290] + + + GO:axo-dendritic transport + GO:0008088 + axo-dendritic transport + "The directed movement of organelles or molecules along microtubules in neuron projections." [ISBN:0815316194] + + + protein localisation + GO:0008104 + protein localization + establishment and maintenance of protein localization + "Any process in which a protein is transported to, or maintained in, a specific location." [GOC:ai] + GO:protein localization + + + biological_process + "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete] + GO:0008150 + biological process + physiological process + GO:biological_process + + + metabolic process + GO:0008152 + GO:metabolic process + "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] + metabolism + + + GO:0008154 + GO:actin polymerization or depolymerization + actin polymerization or depolymerization + "Assembly or disassembly of actin filaments by the addition or removal of actin monomers from a filament." [GOC:mah] + + + "The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." [ISBN:0198547684] + steroid metabolism + GO:0008202 + steroid metabolic process + GO:steroid metabolic process + + + "The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues." [ISBN:0198506732] + GO:0008203 + cholesterol metabolism + cholesterol metabolic process + GO:cholesterol metabolic process + + + "The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." [GOC:go_curators] + bile acid metabolic process + GO:bile acid metabolic process + bile acid metabolism + GO:0008206 + + + GO:0008213 + GO:protein alkylation + protein amino acid alkylation + protein alkylation + "The addition of an alkyl group to a protein amino acid. An alkyl group is any group derived from an alkane by removal of one hydrogen atom." [GOC:ma] + + + regulation of blood pressure + control of blood pressure + "Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure." [GOC:dph, GOC:mtg_cardio, ISBN:0721643949] + GO:regulation of blood pressure + blood pressure homeostasis + blood pressure regulation + GO:0008217 + + + bioluminescence + "The production of light by certain enzyme-catalyzed reactions in cells." [ISBN:0198506732] + GO:bioluminescence + GO:0008218 + + + GO:cell death + "Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as \"apoptotic bodies\"); and/or (3) its corpse (or its fragments) have been engulfed by an adjacent cell in vivo." [GOC:mah, GOC:mtg_apoptosis] + accidental cell death + cell death + GO:0008219 + necrosis + + + "A protein complex that is required for sister chromatid cohesion in eukaryotes. The cohesin complex forms a molecular ring complex, and is composed of structural maintenance of chromosomes (SMC) and kleisin proteins. For example, in yeast, the complex is composed of the SMC proteins Smc1p and Smc3p, and the kleisin protein Scc1p. In vertebrates, the complex is composed of the SMC1 (SMC1A or SMC1B) and SMC3 heterodimer attached via their hinge domains to a kleisin (RAD21, REC8 or RAD21L) which links them, and one STAG protein (STAG1, STAG2 or STAG3)." [GOC:sp, PMID:9887095] + SMC/kleisin ring complex + cohesin complex + SMC complex + GO:0008278 + GO:cohesin complex + + + GO:ATP-sensitive potassium channel complex + "A protein complex that comprises four pore-forming (Kir6.x) and four regulatory sulphonylurea receptor (SURx) subunits and forms a transmembrane channel through which ions may pass. The opening and closing of the channel is regulated by ATP: binding of ATP to the Kir6.x subunit inhibits channel activity, whereas binding of Mg2+-complexed ATP or ADP to the SURx subunit stimulates channel activity." [GOC:bhm, PMID:16308567, PMID:16956886] + ATP-sensitive potassium channel complex + GO:0008282 + + + GO:0008283 + "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [GOC:mah, GOC:mb] + cell proliferation + GO:cell proliferation + + + "A complex, normally consisting of a catalytic and a regulatory subunit, which catalyzes the removal of a phosphate group from a serine or threonine residue of a protein." [GOC:bf] + GO:0008287 + GO:protein serine/threonine phosphatase complex + protein serine/threonine phosphatase complex + + + GO:caspase complex + caspase complex + GO:0008303 + cysteine-type endopeptidase complex + "A protein complex that is located in the cytosol and contains one or more cysteine-type endopeptidases (also called caspases), which give the complex a peptidase activity with specificity for the hydrolysis of aspartyl bonds. These complexes may be involved e.g. in apoptotic or inflammation processes." [GOC:cna, GOC:mtg_apoptosis] + + + "A protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands." [PMID:17543136] + GO:integrin complex + integrin complex + GO:0008305 + laminin receptor protein + + + Pavlovian conditioning + conditional learning + classical conditioning + conditional response + "Learning by associating a stimulus (the cause) with a particular outcome (the effect)." [ISBN:0582227089] + associative learning + GO:0008306 + GO:associative learning + + + GO:0008355 + olfactory learning + "Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs in response to (repeated) exposure to an olfactory cue." [ISBN:0582227089] + GO:olfactory learning + + + GO:0008356 + asymmetric cytokinesis + asymmetrical cell division + "The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity." [PMID:11672519] + asymmetric cell division + GO:asymmetric cell division + asymmetrical cytokinesis + + + "The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA." [GOC:krc, GOC:mah] + GO:RNA splicing + RNA splicing + GO:0008380 + pre-mRNA splicing factor activity + + + GO:gonad development + gonadogenesis + GO:0008406 + "The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones." [GOC:ems, ISBN:0198506732] + gonad development + + + GO:proteasome regulatory particle, lid subcomplex + GO:0008541 + proteasome regulatory particle, lid subcomplex + "The subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex." [GOC:rb] + + + "The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands." [GOC:ceb] + GO:fibroblast growth factor receptor signaling pathway + fibroblast growth factor receptor signaling pathway + FGFR signaling pathway + FGF receptor signalling pathway + fibroblast growth factor receptor signalling pathway + FGF receptor signaling pathway + GO:0008543 + + + testicular development + "The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure." [GOC:jid] + testis development + GO:0008584 + male gonad development + GO:male gonad development + + + GO:0008594 + photoreceptor development + GO:photoreceptor cell morphogenesis + photoreceptor cell morphogenesis + "The process in which the structures of a photoreceptor cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a photoreceptor cell, a sensory cell that reacts to the presence of light. An example of this is found in Drosophila melanogaster." [GOC:jid, GOC:mah] + + + GO:anterior/posterior axis specification, embryo + anterior/posterior axis determination, embryo + GO:0008595 + "The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238] + anterior/posterior axis specification, embryo + + + lipid synthesis + lipid anabolism + GO:0008610 + "The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [GOC:go_curators] + lipogenesis + lipid biosynthesis + lipid formation + GO:lipid biosynthetic process + lipid biosynthetic process + + + GO:carbohydrate transport + GO:0008643 + "The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC:ai] + carbohydrate transport + + + GO:hexose transport + GO:0008645 + hexose transport + "The directed movement of hexose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Hexoses are any aldoses with a chain of six carbon atoms in the molecule." [GOC:ai] + + + cellular amino acid synthesis + GO:cellular amino acid biosynthetic process + "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents." [ISBN:0198506732] + cellular amino acid biosynthesis + cellular amino acid formation + cellular amino acid biosynthetic process + amino acid biosynthetic process + cellular amino acid anabolism + GO:0008652 + + + Barr body formation + dosage compensation by inactivation of X chromosome + "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex." [GOC:jl, GOC:pr, ISBN:0140512888, PMID:11498577] + GO:dosage compensation by inactivation of X chromosome + X chromosome inactivation + GO:0009048 + + + breakdown + catabolism + catabolic process + "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684] + GO:catabolic process + degradation + GO:0009056 + + + macromolecule breakdown + biopolymer catabolic process + macromolecule catabolic process + GO:0009057 + GO:macromolecule catabolic process + "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah] + macromolecule catabolism + macromolecule degradation + + + synthesis + biosynthetic process + GO:biosynthetic process + formation + GO:0009058 + biosynthesis + "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] + anabolism + + + biopolymer biosynthetic process + macromolecule synthesis + macromolecule formation + macromolecule biosynthetic process + "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah] + GO:macromolecule biosynthetic process + macromolecule anabolism + macromolecule biosynthesis + GO:0009059 + + + fatty acid catabolic process + GO:0009062 + fatty acid degradation + "The chemical reactions and pathways resulting in the breakdown of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes." [GOC:go_curators] + fatty acid catabolism + fatty acid breakdown + GO:fatty acid catabolic process + + + GO:glutamine family amino acid metabolic process + glutamine family amino acid metabolism + glutamine family amino acid metabolic process + GO:0009064 + "The chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." [GOC:ai] + + + "The chemical reactions and pathways involving any amino acid that requires pyruvate for its synthesis, e.g. alanine." [GOC:jl] + pyruvate family amino acid metabolic process + pyruvate family amino acid metabolism + GO:pyruvate family amino acid metabolic process + GO:0009078 + + + "The chemical reactions and pathways resulting in the formation of any amino acid that requires pyruvate for its synthesis, e.g. alanine." [GOC:jl] + pyruvate family amino acid biosynthetic process + GO:pyruvate family amino acid biosynthetic process + pyruvate family amino acid biosynthesis + pyruvate family amino acid anabolism + pyruvate family amino acid formation + GO:0009079 + pyruvate family amino acid synthesis + + + GO:0009081 + branched-chain amino acid metabolic process + GO:branched-chain amino acid metabolic process + "The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine." [CHEBI:22918, GOC:ai] + branched chain family amino acid metabolism + + + glutamine family amino acid anabolism + GO:glutamine family amino acid biosynthetic process + glutamine family amino acid biosynthesis + glutamine family amino acid synthesis + GO:0009084 + glutamine family amino acid formation + glutamine family amino acid biosynthetic process + "The chemical reactions and pathways resulting in the formation of amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." [GOC:ai] + + + glycoprotein metabolic process + "The chemical reactions and pathways involving glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732] + GO:glycoprotein metabolic process + GO:0009100 + glycoprotein metabolism + + + glycoprotein biosynthetic process + glycoprotein anabolism + glycoprotein synthesis + glycoprotein biosynthesis + GO:glycoprotein biosynthetic process + GO:0009101 + "The chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732] + glycoprotein formation + + + coenzyme biosynthetic process + coenzyme synthesis + coenzyme biosynthesis + GO:0009108 + coenzyme formation + coenzyme anabolism + GO:coenzyme biosynthetic process + "The chemical reactions and pathways resulting in the formation of coenzymes, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed." [GOC:ai] + + + GO:0009116 + "The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine)." [GOC:ma] + GO:nucleoside metabolic process + nucleoside metabolic process + nucleoside metabolism + + + GO:nucleotide metabolic process + GO:0009117 + nucleotide metabolism + nucleotide metabolic process + "The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates)." [GOC:ma] + + + regulation of nucleoside metabolism + GO:regulation of nucleoside metabolic process + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleosides." [GOC:go_curators] + regulation of nucleoside metabolic process + GO:0009118 + + + "The chemical reactions and pathways involving any ribonucleoside, a nucleoside in which purine or pyrimidine base is linked to a ribose (beta-D-ribofuranose) molecule." [CHEBI:18254, GOC:jl] + GO:ribonucleoside metabolic process + ribonucleoside metabolism + ribonucleoside metabolic process + GO:0009119 + + + nucleoside monophosphate metabolism + GO:0009123 + "The chemical reactions and pathways involving a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + GO:nucleoside monophosphate metabolic process + nucleoside monophosphate metabolic process + + + nucleoside monophosphate formation + GO:0009124 + GO:nucleoside monophosphate biosynthetic process + "The chemical reactions and pathways resulting in the formation of a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + nucleoside monophosphate anabolism + nucleoside monophosphate synthesis + nucleoside monophosphate biosynthetic process + nucleoside monophosphate biosynthesis + + + purine nucleoside monophosphate metabolism + GO:0009126 + GO:purine nucleoside monophosphate metabolic process + "The chemical reactions and pathways involving purine nucleoside monophosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + purine nucleoside monophosphate metabolic process + + + purine nucleoside monophosphate anabolism + GO:0009127 + purine nucleoside monophosphate biosynthesis + GO:purine nucleoside monophosphate biosynthetic process + purine nucleoside monophosphate biosynthetic process + purine nucleoside monophosphate formation + purine nucleoside monophosphate synthesis + "The chemical reactions and pathways resulting in the formation of purine nucleoside monophosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + + + nucleoside diphosphate metabolic process + GO:0009132 + GO:nucleoside diphosphate metabolic process + nucleoside diphosphate metabolism + "The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + + + GO:0009135 + GO:purine nucleoside diphosphate metabolic process + purine nucleoside diphosphate metabolic process + "The chemical reactions and pathways involving purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + purine nucleoside diphosphate metabolism + + + GO:nucleoside triphosphate metabolic process + nucleoside triphosphate metabolic process + nucleoside triphosphate metabolism + "The chemical reactions and pathways involving a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + GO:0009141 + + + "The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + nucleoside triphosphate formation + nucleoside triphosphate synthesis + nucleoside triphosphate biosynthetic process + nucleoside triphosphate biosynthesis + nucleoside triphosphate anabolism + GO:nucleoside triphosphate biosynthetic process + GO:0009142 + + + "The chemical reactions and pathways involving purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + purine nucleoside triphosphate metabolism + GO:purine nucleoside triphosphate metabolic process + GO:0009144 + purine nucleoside triphosphate metabolic process + + + purine nucleoside triphosphate synthesis + GO:purine nucleoside triphosphate biosynthetic process + purine nucleoside triphosphate formation + GO:0009145 + purine nucleoside triphosphate biosynthesis + purine nucleoside triphosphate biosynthetic process + purine nucleoside triphosphate anabolism + "The chemical reactions and pathways resulting in the formation of purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + + + purine ribonucleotide metabolic process + "The chemical reactions and pathways involving a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] + purine ribonucleotide metabolism + GO:purine ribonucleotide metabolic process + GO:0009150 + + + purine ribonucleotide formation + purine ribonucleotide synthesis + purine ribonucleotide anabolism + GO:0009152 + purine ribonucleotide biosynthesis + GO:purine ribonucleotide biosynthetic process + purine ribonucleotide biosynthetic process + "The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] + + + ribonucleoside monophosphate anabolism + GO:0009156 + ribonucleoside monophosphate synthesis + "The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + ribonucleoside monophosphate formation + GO:ribonucleoside monophosphate biosynthetic process + ribonucleoside monophosphate biosynthesis + ribonucleoside monophosphate biosynthetic process + + + ribonucleoside monophosphate metabolic process + ribonucleoside monophosphate metabolism + GO:ribonucleoside monophosphate metabolic process + GO:0009161 + "The chemical reactions and pathways involving a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + + + nucleoside formation + nucleoside synthesis + nucleoside anabolism + GO:nucleoside biosynthetic process + GO:0009163 + nucleoside biosynthesis + nucleoside biosynthetic process + "The chemical reactions and pathways resulting in the formation of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside)." [GOC:jl, ISBN:0140512713] + + + "The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates)." [GOC:go_curators] + nucleotide formation + GO:0009165 + nucleotide synthesis + GO:nucleotide biosynthetic process + nucleotide anabolism + nucleotide biosynthetic process + nucleotide biosynthesis + + + purine ribonucleoside monophosphate metabolic process + GO:0009167 + GO:purine ribonucleoside monophosphate metabolic process + "The chemical reactions and pathways involving purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + purine ribonucleoside monophosphate metabolism + + + purine ribonucleoside monophosphate biosynthetic process + purine ribonucleoside monophosphate anabolism + GO:purine ribonucleoside monophosphate biosynthetic process + purine ribonucleoside monophosphate biosynthesis + purine ribonucleoside monophosphate formation + purine ribonucleoside monophosphate synthesis + GO:0009168 + "The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + + + purine ribonucleoside diphosphate metabolic process + GO:0009179 + GO:purine ribonucleoside diphosphate metabolic process + "The chemical reactions and pathways involving purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + purine ribonucleoside diphosphate metabolism + + + GO:0009185 + GO:ribonucleoside diphosphate metabolic process + ribonucleoside diphosphate metabolic process + "The chemical reactions and pathways involving a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + ribonucleoside diphosphate metabolism + + + GO:ribonucleoside triphosphate metabolic process + GO:0009199 + ribonucleoside triphosphate metabolic process + ribonucleoside triphosphate metabolism + "The chemical reactions and pathways involving a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + + + "The chemical reactions and pathways resulting in the formation of a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + ribonucleoside triphosphate anabolism + GO:ribonucleoside triphosphate biosynthetic process + ribonucleoside triphosphate formation + ribonucleoside triphosphate synthesis + ribonucleoside triphosphate biosynthetic process + GO:0009201 + ribonucleoside triphosphate biosynthesis + + + "The chemical reactions and pathways involving purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + GO:0009205 + GO:purine ribonucleoside triphosphate metabolic process + purine ribonucleoside triphosphate metabolism + purine ribonucleoside triphosphate metabolic process + + + purine ribonucleoside triphosphate biosynthesis + purine ribonucleoside triphosphate anabolism + GO:purine ribonucleoside triphosphate biosynthetic process + GO:0009206 + purine ribonucleoside triphosphate biosynthetic process + purine ribonucleoside triphosphate formation + "The chemical reactions and pathways resulting in the formation of purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732] + purine ribonucleoside triphosphate synthesis + + + GO:0009251 + glucan degradation + glucan catabolic process + "The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues." [GOC:go_curators] + glucan catabolism + GO:glucan catabolic process + glucan breakdown + + + ribonucleotide metabolic process + GO:0009259 + ribonucleotide metabolism + GO:ribonucleotide metabolic process + "The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] + + + ribonucleotide biosynthetic process + "The chemical reactions and pathways resulting in the formation of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732] + ribonucleotide anabolism + GO:ribonucleotide biosynthetic process + ribonucleotide biosynthesis + ribonucleotide synthesis + ribonucleotide formation + GO:0009260 + + + genetic transfer + "In the absence of a sexual life cycle, the process involved in the introduction of genetic information to create a genetically different individual." [GOC:clt] + GO:0009292 + GO:genetic transfer + + + GO:0009293 + "The transfer of genetic information to a bacterium from a bacteriophage or between bacterial or yeast cells mediated by a phage vector." [ISBN:0198506732] + GO:transduction + transduction + + + GO:DNA mediated transformation + DNA mediated transformation + "The introduction and uptake of foreign genetic material (DNA or RNA) into a cell, and often the expression of that genetic material." [ISBN:0716720094, Wikipedia:Transformation_(genetics)] + GO:0009294 + DNA-mediated transformation + + + GO:0009306 + protein secretion + GO:protein secretion + "The controlled release of proteins from a cell." [GOC:ai] + + + response to electromagnetic radiation stimulus + response to radiation stimulus + response to radiation + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation." [GOC:jl, Wikipedia:Electromagnetic_radiation] + GO:response to radiation + GO:0009314 + + + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light." [GOC:go_curators, ISBN:0582227089] + GO:response to light stimulus + GO:0009416 + response to light stimulus + + + GO:fertilization + GO:0009566 + "The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)." [GOC:tb, ISBN:0198506732] + fertilization + syngamy + + + perception of external stimulus + "The series of events in which an external stimulus is received by a cell and converted into a molecular signal." [GOC:hb] + detection of external stimulus + GO:detection of external stimulus + GO:0009581 + + + perception of abiotic stimulus + GO:detection of abiotic stimulus + detection of abiotic stimulus + GO:0009582 + "The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal." [GOC:hb] + + + GO:detection of light stimulus + detection of light stimulus + GO:0009583 + detection of light + perception of light + "The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal." [GOC:go_curators] + + + perception of chemical substance + GO:detection of chemical stimulus + detection of chemical substance + perception of chemical stimulus + "The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal." [GOC:jl] + GO:0009593 + chemoperception + detection of chemical stimulus + + + response to external stimulus + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus." [GOC:hb] + response to environmental stimulus + GO:0009605 + GO:response to external stimulus + + + GO:response to abiotic stimulus + response to abiotic stimulus + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus." [GOC:hb] + GO:0009628 + + + GO:response to light intensity + GO:0009642 + response to light intensity + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light intensity stimulus." [GOC:go_curators] + + + response to darkness + GO:response to absence of light + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an absence of light stimuli." [GOC:go_curators] + response to absence of light + GO:0009646 + + + "The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:go_curators, ISBN:0521436125] + anatomical structure morphogenesis + morphogenesis + anatomical structure organization + GO:0009653 + GO:anatomical structure morphogenesis + + + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism." [GOC:sm] + GO:0009719 + GO:response to endogenous stimulus + response to endogenous stimulus + + + embryonal development + GO:0009790 + embryogenesis + "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] + embryo development + GO:embryo development + + + axis determination + "The establishment, maintenance and elaboration of a pattern along a line or around a point." [GOC:dph, GOC:go_curators, GOC:isa_complete] + axis specification + GO:0009798 + GO:axis specification + + + GO:0009799 + specification of symmetry + GO:specification of symmetry + determination of symmetry + "The establishment of an organism's body plan or part of an organism such that a similar arrangement in form and relationship of parts around a common axis, or around each side of a plane is created." [GOC:go_curators] + + + GO:0009855 + "The establishment of an organism's body plan or part of an organism with respect to a single longitudinal plane. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry." [GOC:go_curators] + determination of bilateral asymmetry + GO:determination of bilateral symmetry + determination of bilateral symmetry + + + ventral/lateral system + "The process that results in the patterns of cell differentiation that will arise in an embryo." [GOC:go_curators, ISBN:0521436125] + embryonic pattern specification + GO:0009880 + GO:embryonic pattern specification + + + "Morphogenesis of an organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:dgh, GOC:go_curators, ISBN:0471245208, ISBN:0721662544] + GO:0009887 + GO:organ morphogenesis + organ morphogenesis + + + tissue development + histogenesis + GO:0009888 + GO:tissue development + "The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure." [ISBN:0471245208] + + + regulation of biosynthesis + regulation of formation + GO:0009889 + regulation of synthesis + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators] + regulation of biosynthetic process + GO:regulation of biosynthetic process + regulation of anabolism + + + down-regulation of biosynthetic process + negative regulation of biosynthesis + negative regulation of anabolism + down regulation of biosynthetic process + GO:0009890 + downregulation of biosynthetic process + negative regulation of formation + negative regulation of biosynthetic process + "Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators] + GO:negative regulation of biosynthetic process + negative regulation of synthesis + + + positive regulation of anabolism + up-regulation of biosynthetic process + GO:positive regulation of biosynthetic process + positive regulation of biosynthesis + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators] + up regulation of biosynthetic process + GO:0009891 + upregulation of biosynthetic process + positive regulation of synthesis + positive regulation of formation + positive regulation of biosynthetic process + + + negative regulation of metabolic process + downregulation of metabolic process + down regulation of metabolic process + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] + GO:negative regulation of metabolic process + down-regulation of metabolic process + GO:0009892 + negative regulation of metabolism + + + positive regulation of metabolic process + positive regulation of metabolism + GO:positive regulation of metabolic process + up-regulation of metabolic process + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] + up regulation of metabolic process + upregulation of metabolic process + GO:0009893 + + + regulation of degradation + "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] + regulation of catabolism + regulation of catabolic process + regulation of breakdown + GO:regulation of catabolic process + GO:0009894 + + + GO:cytoplasmic side of plasma membrane + cytoplasmic side of plasma membrane + GO:0009898 + internal side of plasma membrane + internal leaflet of plasma membrane + "The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface." [GOC:dos, GOC:tb] + + + epidermal cell differentiation + hypodermal cell differentiation + "The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis." [GOC:dph, GOC:go_curators, GOC:mtg_sensu, GOC:sdb_2009, GOC:tb] + GO:0009913 + GO:epidermal cell differentiation + + + GO:hormone transport + hormone transport + "The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:tb] + GO:0009914 + + + anterior/posterior axis determination + "The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism." [GOC:dph, GOC:go_curators, GOC:tb] + GO:0009948 + anterior/posterior axis specification + GO:anterior/posterior axis specification + + + GO:0009952 + "The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism." [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb] + anterior/posterior pattern formation + anterior/posterior pattern specification + GO:anterior/posterior pattern specification + + + dorsal-ventral pattern formation + GO:0009953 + GO:dorsal/ventral pattern formation + dorsoventral pattern formation + dorsal/ventral pattern formation + "The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism." [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb] + + + regulation of signaling pathway + GO:0009966 + "Any process that modulates the frequency, rate or extent of signal transduction." [GOC:sm] + GO:regulation of signal transduction + regulation of signalling pathway + regulation of signal transduction + + + GO:0009967 + positive regulation of signal transduction + "Any process that activates or increases the frequency, rate or extent of signal transduction." [GOC:sm] + up-regulation of signal transduction + positive regulation of signaling pathway + GO:positive regulation of signal transduction + up regulation of signal transduction + upregulation of signal transduction + positive regulation of signalling pathway + + + GO:cell surface + cell bound + cell surface + "The external part of the cell wall and/or plasma membrane." [GOC:jl, GOC:mtg_sensu, GOC:sm] + cell associated + GO:0009986 + + + GO:0009987 + "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] + cellular process + cellular physiological process + GO:cellular process + cell physiology + + + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus." [GOC:go_curators] + GO:0009991 + response to extracellular stimulus + GO:response to extracellular stimulus + + + endosome membrane + GO:0010008 + "The lipid bilayer surrounding an endosome." [GOC:mah] + GO:endosome membrane + endosomal membrane + + + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus." [GOC:sm] + GO:response to organic substance + response to organic substance + GO:0010033 + + + "The infolding of a membrane, resulting in formation of a vesicle." [GOC:tb] + GO:0010324 + GO:membrane invagination + membrane invagination + + + GO:0010369 + GO:chromocenter + chromocenter + "A region in which centric, heterochromatic portions of one or more chromosomes form a compact structure." [PMID:12384572, PMID:15053486, PMID:16831888] + + + GO:DNA methylation on cytosine within a CG sequence + cytosine methylation within a CG sequence + "The covalent transfer of a methyl group to C-5 or N-4 of a cytosine located within a CG sequence in a DNA molecule." [GOC:dph, GOC:tb, PMID:17239600] + GO:0010424 + DNA methylation on cytosine within a CG sequence + + + GO:0010463 + "The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." [GOC:dph, GOC:tb] + GO:mesenchymal cell proliferation + mesenchymal cell proliferation + + + GO:0010467 + "The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] + GO:gene expression + gene expression + + + regulation of gene expression + GO:regulation of gene expression + regulation of gene product expression + GO:0010468 + "Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] + + + "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome." [GOC:tb] + GO:proteasomal protein catabolic process + proteasomal protein catabolic process + proteasome-mediated protein catabolism + GO:0010498 + proteasome-mediated protein catabolic process + + + GO:regulation of macromolecule biosynthetic process + "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] + GO:0010556 + regulation of macromolecule biosynthetic process + + + "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] + GO:positive regulation of macromolecule biosynthetic process + GO:0010557 + positive regulation of macromolecule biosynthetic process + + + GO:negative regulation of macromolecule biosynthetic process + GO:0010558 + negative regulation of macromolecule biosynthetic process + "Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] + + + "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus." [GOC:dph, GOC:tb] + positive regulation of phosphorus metabolic process + GO:positive regulation of phosphorus metabolic process + GO:0010562 + + + GO:regulation of cell cycle process + "Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events." [GOC:dph, GOC:tb] + regulation of cell cycle process + GO:0010564 + + + GO:positive regulation of macromolecule metabolic process + positive regulation of macromolecule metabolic process + GO:0010604 + "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] + + + negative regulation of macromolecule metabolic process + GO:negative regulation of macromolecule metabolic process + "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] + GO:0010605 + + + posttranscriptional regulation of gene expression + "Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript." [GOC:dph, GOC:tb] + GO:posttranscriptional regulation of gene expression + GO:0010608 + + + developmental programmed cell death + "The activation of endogenous cellular processes that result in the death of a cell as part of its development." [GOC:dph, GOC:tb] + GO:developmental programmed cell death + GO:0010623 + + + positive regulation of gene expression + "Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] + GO:0010628 + GO:positive regulation of gene expression + + + GO:0010629 + negative regulation of gene expression + GO:negative regulation of gene expression + "Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] + + + GO:0010631 + epithelial cell migration + "The orderly movement of an epithelial cell from one site to another, often during the development of a multicellular organism." [GOC:ascb_2009, GOC:BHF, GOC:dph, GOC:tb] + GO:epithelial cell migration + + + "Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle." [GOC:dph, GOC:tb] + GO:0010639 + negative regulation of organelle organisation + negative regulation of organelle organization + negative regulation of organelle organization and biogenesis + GO:negative regulation of organelle organization + + + GO:0010646 + regulation of cell communication + GO:regulation of cell communication + "Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:dph, GOC:tb] + + + positive regulation of cell communication + GO:0010647 + "Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:dph, GOC:tb] + GO:positive regulation of cell communication + + + regulation of cellular carbohydrate metabolic process + GO:regulation of cellular carbohydrate metabolic process + GO:0010675 + "Any process that modulates the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:dph, GOC:tb] + + + GO:regulation of hormone levels + GO:0010817 + regulation of hormone levels + "Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action." [GOC:BHF, GOC:dph, GOC:tb] + + + "The cellular component assembly that is part of the initial shaping of the component during its developmental progression." [GOC:dph, GOC:tb] + cellular component assembly involved in morphogenesis + GO:0010927 + GO:cellular component assembly involved in morphogenesis + + + regulation of cell death + GO:0010941 + "Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:dph, GOC:tb] + GO:regulation of cell death + + + positive regulation of cell death + GO:0010942 + GO:positive regulation of cell death + "Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:dph, GOC:tb] + + + negative regulation of cell cycle process + "Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events." [GOC:dph, GOC:tb] + GO:negative regulation of cell cycle process + GO:0010948 + + + GO:positive regulation of protein processing + GO:0010954 + positive regulation of protein maturation by peptide bond cleavage + "Any process that increases the rate, frequency or extent of protein maturation by peptide bond cleavage." [GOC:dph, GOC:mah, GOC:tb] + positive regulation of protein processing + + + establishment of localization by movement along microtubule + momvement along microtubule + "The movement of organelles or other particles from one location in the cell to another along microtubules." [GOC:dph, GOC:mah, GOC:tb] + GO:0010970 + microtubule-based transport + GO:establishment of localization by movement along microtubule + + + "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis] + GO:programmed cell death + GO:0012501 + programmed cell death + caspase-independent apoptosis + PCD + regulated cell death + + + GO:0012506 + GO:vesicle membrane + "The lipid bilayer surrounding any membrane-bounded vesicle in the cell." [GOC:mah] + vesicle membrane + + + oligodendrocyte development + "The process aimed at the progression of an oligodendrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An oligodendrocyte is a type of glial cell involved in myelinating the axons in the central nervous system." [GOC:dgh, GOC:ef] + GO:oligodendrocyte development + oligodendrocyte cell development + GO:0014003 + + + "The multiplication or reproduction of glial cells by cell division, resulting in the expansion of their population. Glial cells exist throughout the nervous system, and include Schwann cells, astrocytes, and oligodendrocytes among others." [GOC:ef, ISBN:0878932585] + GO:0014009 + glial cell proliferation + GO:glial cell proliferation + glia proliferation + + + GO:0014010 + GO:Schwann cell proliferation + "The multiplication or reproduction of Schwann cells, resulting in the expansion of their population. Schwann cells are a type of glial cell in the peripheral nervous system." [GOC:ef, ISBN:0878932585] + Schwann cell proliferation + + + GO:0014018 + GO:neuroblast fate specification + "The process in which a cell becomes capable of differentiating autonomously into a neuroblast in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed." [GOC:ef, ISBN:0878932585] + neuroblast fate specification + + + GO:0014019 + GO:neuroblast development + neuroblast development + "The process aimed at the progression of a neuroblast over time, from initial commitment of the cell to a specific state, to the mature neuroblast. It does not include processes where the neuroblast turns into a glial cell or a neuron." [GOC:ef, ISBN:0878932585] + + + GO:mesenchymal cell development + "The process aimed at the progression of a mesenchymal cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." [GOC:dh, GOC:ef] + mesenchymal cell development + GO:0014031 + + + GO:neural crest cell development + "The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." [GOC:dh, GOC:ef] + GO:0014032 + neural crest cell development + + + "Any process that modulates the frequency, rate or extent of neuron maturation, the process leading to the attainment of the full functional capacity of a neuron. This process is independent of morphogenetic change." [GOC:ef] + GO:regulation of neuron maturation + GO:0014041 + regulation of neuron maturation + + + gamma-aminobutyric acid secretion + GABA secretion + GO:0014051 + "The regulated release of gamma-aminobutyric acid by a cell or a tissue. The gamma-aminobutyric acid is the principal inhibitory neurotransmitter in the brain but is also found in several extraneural tissues." [GOC:ef] + GO:gamma-aminobutyric acid secretion + + + PI3K cascade + phosphatidylinositol 3-kinase signal transduction + "A series of reactions within the signal-receiving cell, mediated by the intracellular phosphatidylinositol 3-kinase (PI3K). Many cell surface receptor linked signaling pathways signal through PI3K to regulate numerous cellular functions." [GOC:ef, http://www.biocarta.com, PMID:22525052, Wikipedia:PI3K] + phosphatidylinositol 3-kinase cascade + GO:phosphatidylinositol 3-kinase signaling + PI3K signaling + GO:0014065 + PI 3-kinase cascade + phosphatidylinositol 3-kinase signaling + PI3K signal transduction + phosphoinositide 3-kinase cascade + + + "The postsynaptic density is a region that lies adjacent to the cytoplasmic face of the postsynaptic membrane at excitatory synapse. It forms a disc that consists of a range of proteins with different functions, some of which contact the cytoplasmic domains of ion channels in the postsynaptic membrane. The proteins making up the disc include receptors, and structural proteins linked to the actin cytoskeleton. They also include signalling machinery, such as protein kinases and phosphatases. The postsynaptic density may be part of a neuron or a muscle cell or a glial cell." [GOC:BHF, GOC:ef, GOC:jid, GOC:pr, GOC:sjp, http://molneuro.kaist.ac.kr/psd, PMID:14532281, Wikipedia:Postsynaptic_density] + post-synaptic density + GO:0014069 + post synaptic density + GO:postsynaptic density + postsynaptic density + + + "The process whose specific outcome is the progression of a striated muscle over time, from its formation to the mature structure. Striated muscle contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. Skeletal muscle myoblasts fuse to form myotubes and eventually multinucleated muscle fibers. The fusion of cardiac cells is very rare and can only form binucleate cells." [CL:0000737, GOC:dph, GOC:mtg_muscle] + GO:striated muscle tissue development + striated muscle tissue development + GO:0014706 + + + "Any process in which striated muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." [GOC:mtg_muscle] + GO:striated muscle adaptation + striated muscle adaptation + GO:0014888 + striated muscle plasticity + + + GO:0015031 + GO:protein transport + "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + protein transport + + + actin cytoskeleton + "The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes." [GOC:jl, ISBN:0395825172, ISBN:0815316194] + GO:actin cytoskeleton + GO:0015629 + + + "The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + gas transport + GO:0015669 + GO:gas transport + + + oxygen transport + GO:oxygen transport + GO:0015671 + "The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + + + GO:monovalent inorganic cation transport + "The directed movement of inorganic cations with a valency of one into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic cations are atoms or small molecules with a positive charge which do not contain carbon in covalent linkage." [GOC:ai] + monovalent inorganic cation transport + GO:0015672 + + + ammonium transport + ammonia transport + "The directed movement of ammonium into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals." [ISBN:0198506732] + GO:ammonium transport + GO:0015696 + + + GO:inorganic anion transport + "The directed movement of inorganic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage." [GOC:krc] + inorganic anion transport + GO:0015698 + + + bicarbonate transport + GO:bicarbonate transport + GO:0015701 + "The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc] + + + GO:iodide transport + GO:0015705 + iodide transport + "The directed movement of iodide into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc] + + + organic anion transport + "The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage." [GOC:ai, GOC:krc] + GO:0015711 + GO:organic anion transport + + + monocarboxylic acid transport + GO:0015718 + GO:monocarboxylic acid transport + "The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc] + + + "The directed movement of monosaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides." [GOC:ai] + GO:monosaccharide transport + monosaccharide transport + GO:0015749 + + + GO:0015758 + "The directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + glucose transport + GO:glucose transport + + + gamma-aminobutyric acid transport + 4-aminobutanoate transport + 4-aminobutyrate transport + "The directed movement of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators, ISBN:0198506732] + GO:gamma-aminobutyric acid transport + GO:0015812 + GABA transport + + + "The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + GO:0015833 + GO:peptide transport + peptide transport + + + "The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [CHEBI:25375, GOC:mah] + GO:0015844 + GO:monoamine transport + monoamine transport + + + organic acid transport + GO:organic acid transport + GO:0015849 + "The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [ISBN:0198506732] + + + "The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom." [CHEBI:33822, GOC:ai] + organic alcohol transport + organic hydroxy compound transport + GO:organic hydroxy compound transport + GO:0015850 + + + "The directed movement of fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Fatty acids are aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [GOC:ai] + GO:0015908 + GO:fatty acid transport + fatty acid transport + + + GO:0015918 + GO:sterol transport + sterol transport + "The directed movement of sterols into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC:ai] + + + GO:0015931 + "The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + nucleobase-containing compound transport + GO:nucleobase-containing compound transport + nucleobase, nucleoside, nucleotide and nucleic acid transport + + + "The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released." [GOC:mah] + GO:0015980 + energy derivation by oxidation of organic compounds + chemoorganotrophy + GO:energy derivation by oxidation of organic compounds + + + GO:membrane + "A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] + membrane + GO:0016020 + + + "The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:go_curators] + integral component of membrane + transmembrane + GO:0016021 + GO:integral component of membrane + + + cytoplasmic membrane bounded vesicle + "A membrane-bounded vesicle found in the cytoplasm of the cell." [GOC:ai, GOC:mah] + cytoplasmic membrane-enclosed vesicle + GO:cytoplasmic, membrane-bounded vesicle + GO:0016023 + cytoplasmic, membrane-bounded vesicle + + + GO:rhabdomere + "The specialized microvilli-containing organelle on the apical surfaces of a photoreceptor cell containing the visual pigment rhodopsin and most of the proteins involved in phototransduction." [GOC:hb, GOC:sart, PMID:8646774] + GO:0016028 + rhabdomere + + + GO:light absorption + GO:0016037 + absorption of light + light absorption + "The reception of a photon by a cell." [GOC:go_curators] + + + lipid catabolism + lipolysis + lipid degradation + lipid catabolic process + lipid breakdown + GO:lipid catabolic process + "The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [GOC:go_curators] + GO:0016042 + + + cellular component organisation at cellular level + "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] + cellular component organisation in other organism + cellular component organization + GO:cellular component organization + cell organization and biogenesis + cellular component organization in other organism + GO:0016043 + cell organisation + cellular component organization at cellular level + + + GO:0016050 + vesicle organization + GO:vesicle organization + vesicle organisation + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle." [GOC:mah] + vesicle organization and biogenesis + + + anabolic carbohydrate metabolism + "The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [ISBN:0198506732] + carbohydrate anabolism + carbohydrate biosynthesis + anabolic carbohydrate metabolic process + carbohydrate biosynthetic process + carbohydrate formation + GO:carbohydrate biosynthetic process + GO:0016051 + carbohydrate synthesis + + + carbohydrate catabolism + GO:carbohydrate catabolic process + catabolic carbohydrate metabolism + carbohydrate catabolic process + carbohydrate breakdown + GO:0016052 + "The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [ISBN:0198506732] + carbohydrate degradation + catabolic carbohydrate metabolic process + + + organic acid biosynthetic process + "The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732] + organic acid anabolism + GO:organic acid biosynthetic process + organic acid biosynthesis + organic acid formation + organic acid synthesis + GO:0016053 + + + GO:organic acid catabolic process + "The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732] + organic acid breakdown + organic acid catabolism + organic acid catabolic process + organic acid degradation + GO:0016054 + + + Wnt receptor signaling pathway + frizzled signalling pathway + Wg signalling pathway + GO:0016055 + Wg signaling pathway + frizzled signaling pathway + GO:Wnt signaling pathway + Wnt-activated signaling pathway + "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state." [GOC:dph, GOC:go_curators, PMID:11532397] + Wnt signaling pathway + Wingless signaling pathway + Wnt receptor signalling pathway + Wingless signalling pathway + + + GO:immunoglobulin mediated immune response + "An immune response mediated by immunoglobulins, whether cell-bound or in solution." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] + immunoglobulin mediated immune response + antibody-mediated immune response + GO:0016064 + + + GO:RNA metabolic process + RNA metabolism + GO:0016070 + RNA metabolic process + "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732] + + + GO:0016071 + mRNA metabolic process + GO:mRNA metabolic process + mRNA metabolism + "The chemical reactions and pathways involving mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes." [ISBN:0198506732] + + + GO:0016125 + GO:sterol metabolic process + "The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [ISBN:0198547684] + sterol metabolic process + sterol metabolism + + + "The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC:go_curators] + GO:0016126 + sterol biosynthesis + sterol synthesis + GO:sterol biosynthetic process + sterol anabolism + sterol biosynthetic process + sterol formation + + + vesicle-mediated transport + GO:0016192 + protein sorting along secretory pathway + vesicular transport + GO:vesicle-mediated transport + vesicle transport + vesicle trafficking + "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] + + + GO:endosomal transport + endosome transport + "The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." [ISBN:0198506732] + GO:0016197 + endosomal transport + + + GO:0016234 + inclusion body + GO:inclusion body + cellular inclusion + "A discrete intracellular part formed of aggregated molecules such as proteins or other biopolymers." [GOC:mah, PMID:11121744] + + + posttranscriptional gene silencing by siRNA + GO:RNA interference + "The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes." [GOC:ems, PMID:11201747, PMID:11713190, PMID:18771919] + RNAi + RNA interference + GO:0016246 + + + GO:0016264 + GO:gap junction assembly + gap junction assembly + "Assembly of gap junctions, which are found in most animal tissues, and serve as direct connections between the cytoplasms of adjacent cells. They provide open channels through the plasma membrane, allowing ions and small molecules (less than approximately a thousand daltons) to diffuse freely between neighboring cells, but preventing the passage of proteins and nucleic acids." [GOC:jid, ISBN:0716731363] + + + death + GO:death + "A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism." [GOC:mah, GOC:mtg_apoptosis, ISBN:0877797099] + GO:0016265 + + + tissue death + "A permanent cessation of all vital functions of a tissue." [GOC:dph, GOC:mtg_apoptosis] + GO:0016271 + GO:tissue death + + + "The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide." [ISBN:0198506732] + GO:phosphorylation + phosphorylation + GO:0016310 + + + GO:dephosphorylation + dephosphorylation + GO:0016311 + "The process of removing one or more phosphoric (ester or anhydride) residues from a molecule." [ISBN:0198506732] + + + basolateral plasma membrane + "The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis." [GOC:go_curators] + GO:0016323 + GO:basolateral plasma membrane + + + apical plasma membrane + GO:apical plasma membrane + GO:0016324 + "The region of the plasma membrane located at the apical end of the cell." [GOC:curators] + + + GO:morphogenesis of embryonic epithelium + "The process in which the anatomical structures of embryonic epithelia are generated and organized." [GOC:jl] + morphogenesis of embryonic epithelium + GO:0016331 + + + single organismal cell-cell adhesion + GO:single organismal cell-cell adhesion + GO:0016337 + "The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism." [GOC:hb] + + + GO:posttranscriptional gene silencing + post-transcriptional gene silencing + quelling + PTGS + cosuppression + GO:0016441 + "The inactivation of gene expression by a posttranscriptional mechanism." [GOC:mah, PMID:15020054] + posttranscriptional gene silencing + + + GO:somatic cell DNA recombination + GO:0016444 + "Recombination occurring within or between DNA molecules in somatic cells." [GOC:ma] + somatic cell DNA recombination + + + "Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression." [GOC:dos, GOC:dph, GOC:jid, GOC:tb] + gene silencing + GO:0016458 + GO:gene silencing + + + GO:proton-transporting two-sector ATPase complex + "A large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of protons across a membrane. The complex comprises a membrane sector (F0, V0, or A0) that carries out proton transport and a cytoplasmic compartment sector (F1, V1, or A1) that catalyzes ATP synthesis or hydrolysis. Two major types have been characterized: V-type ATPases couple ATP hydrolysis to the transport of protons across a concentration gradient, whereas F-type ATPases, also known as ATP synthases, normally run in the reverse direction to utilize energy from a proton concentration or electrochemical gradient to synthesize ATP. A third type, A-type ATPases have been found in archaea, and are closely related to eukaryotic V-type ATPases but are reversible." [GOC:mah, ISBN:0716743663, PMID:16691483] + GO:0016469 + vacuolar hydrogen-transporting ATPase + hydrogen-transporting two-sector ATPase complex + proton-transporting two-sector ATPase complex + + + "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, http://en.wikipedia.org/wiki/Cell_migration] + GO:0016477 + GO:cell migration + cell migration + + + "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, or within the cytoplasm of a cell." [GOC:ai] + GO:cytoplasmic transport + GO:0016482 + cytoplasmic transport + + + protein maturation by peptide bond hydrolysis + GO:protein processing + "Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein." [GOC:curators, GOC:jl, GOC:jsg] + protein maturation by peptide bond cleavage + GO:0016485 + protein maturation by proteolysis + protein processing + peptidolysis during protein maturation + + + "A SWI/SNF-type complex that contains nine or more proteins, including both conserved (core) and nonconserved components; the Swi2/Snf2 ATPase is one of the core components." [GOC:mah, PMID:12672490] + SWI-SNF complex + SWI/SNF complex + GO:0016514 + GO:SWI/SNF complex + + + GO:sarcoplasm + sarcoplasm + GO:0016528 + "The cytoplasm of a muscle cell; includes the sarcoplasmic reticulum." [ISBN:0198547684] + + + protein autoprocessing + "Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein." [GOC:ai, PMID:9335337] + GO:protein autoprocessing + GO:0016540 + + + protein ubiquitinylation + "The process in which one or more ubiquitin groups are added to a protein." [GOC:ai] + GO:0016567 + protein ubiquitination + protein ubiquitylation + GO:protein ubiquitination + + + chromatin modification + GO:0016568 + GO:chromatin modification + "The alteration of DNA, protein, or sometimes RNA, in chromatin, which may result in changing the chromatin structure." [GOC:mah, PMID:20404130] + + + GO:covalent chromatin modification + GO:0016569 + "The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups." [GOC:mah] + covalent chromatin modification + + + "The covalent alteration of one or more amino acid residues within a histone protein." [GOC:krc] + histone modification + GO:0016570 + GO:histone modification + + + "The modification of histones by addition of methyl groups." [GOC:ai] + histone methylation + GO:0016571 + GO:histone methylation + + + "Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins." [GOC:ma, PMID:10330182] + GO:nuclear body + GO:0016604 + nuclear body + + + GO:PML body + PML NB + ND10 + nuclear dot + PML body + "A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection." [GOC:ma, PMID:10944585] + PML nuclear body + GO:0016605 + + + antibiotic metabolism + "The chemical reactions and pathways involving an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms." [GOC:cab2] + antibiotic metabolic process + GO:antibiotic metabolic process + GO:0016999 + + + antibiotic catabolic process + antibiotic degradation + GO:0017001 + GO:antibiotic catabolic process + antibiotic breakdown + antibiotic catabolism + "The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms." [GOC:go_curators] + + + GO:regulation of transforming growth factor beta receptor signaling pathway + regulation of TGF-beta receptor signaling pathway + GO:0017015 + regulation of transforming growth factor beta receptor signalling pathway + regulation of transforming growth factor beta receptor signaling pathway + "Any process that modulates the frequency, rate or extent of activity of any TGF-beta receptor signaling pathway." [GOC:mah] + regulation of TGFbeta receptor signaling pathway + + + transcriptional repressor complex + "A protein complex that possesses activity that prevents or downregulates transcription." [GOC:mah] + GO:0017053 + GO:transcriptional repressor complex + + + branched-chain alpha-ketoacid dehydrogenase complex + 3-methyl-2-oxobutanoate dehydrogenase (lipoamide) complex + BCADH + GO:3-methyl-2-oxobutanoate dehydrogenase (lipoamide) complex + GO:0017086 + "A protein complex that catalyzes the reaction 3-methyl-2-oxobutanoate + lipoamide = S-(2-methylpropanoyl)-dihydrolipoamide + carbon dioxide (CO2). This requires thiamine diphosphate; the enzyme also acts on (S)-3-methyl-2-oxopentanoate and 4-methyl-2-oxo-pentanoate." [EC:1.2.4.4] + + + drug metabolic process + GO:0017144 + drug metabolism + GO:drug metabolic process + "The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice." [GOC:cab2] + + + stem cell division + GO:stem cell division + GO:0017145 + "The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types." [GOC:jid, ISBN:0582227089] + stem cell renewal + + + GO:0017156 + GO:calcium ion regulated exocytosis + calcium ion-dependent exocytosis + calcium ion regulated exocytosis + "The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell, induced by a rise in cytosolic calcium-ion levels." [GOC:go_curators] + + + GO:peptidyl-lysine methylation + peptidyl-lysine methylation + "The methylation of peptidyl-lysine to form either the mono-, di- or trimethylated derivative." [GOC:ai] + GO:0018022 + + + GO:peptidyl-lysine trimethylation + peptidyl-lysine trimethylation + "The methylation of peptidyl-lysine to form peptidyl-N6,N6,N6-trimethyl-L-lysine." [RESID:AA0074] + GO:0018023 + + + GO:0018027 + "The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine." [RESID:AA0075] + GO:peptidyl-lysine dimethylation + peptidyl-lysine dimethylation + + + GO:protein amidation + protein amidation + protein amino acid amidation + GO:0018032 + "Addition of an amide group from a glycine to a protein amino acid." [UniProtKB-KW:KW-0027] + + + heterocycle biosynthesis + heterocycle synthesis + "The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [ISBN:0198547684] + heterocycle anabolism + GO:heterocycle biosynthetic process + heterocycle biosynthetic process + GO:0018130 + heterocycle formation + + + GO:0018193 + peptidyl-amino acid modification + GO:peptidyl-amino acid modification + "The alteration of an amino acid residue in a peptide." [GOC:mah] + + + "The modification of peptidyl-lysine." [GOC:go_curators] + GO:0018205 + peptidyl-lysine modification + GO:peptidyl-lysine modification + + + GO:0018958 + "The chemical reactions and pathways involving a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring." [CHEBI:33853, ISBN:0198506732] + phenol-containing compound metabolism + carbolic acid metabolic process + hydroxybenzene metabolism + hydroxybenzene metabolic process + carbolic acid metabolism + GO:phenol-containing compound metabolic process + phenol-containing compound metabolic process + + + GO:host + host + GO:0018995 + host organism + "Any organism in which another organism, especially a parasite or symbiont, spends part or all of its life cycle and from which it obtains nourishment and/or protection." [ISBN:0198506732] + + + reproductive behaviour + reproductive behavior + GO:0019098 + "The specific behavior of an organism that is associated with reproduction." [GOC:jl, GOC:pr] + GO:reproductive behavior + + + nonribosomal peptide formation + nonribosomal peptide synthesis + nonribosomal peptide biosynthesis + nonribosomal peptide anabolism + GO:0019184 + non-ribosomal peptide synthesis + GO:nonribosomal peptide biosynthetic process + "The biosynthetic process in which peptide bond formation occurs in the absence of the translational machinery. Examples include the synthesis of antibiotic peptides, and glutathione." [ISBN:0198506732] + nonribosomal peptide biosynthetic process + non-ribosomal peptide biosynthesis + non-ribosomal peptide biosynthetic process + nonribosomal peptide synthetase + non-ribosomal peptide formation + + + regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process + regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism + GO:0019219 + GO:regulation of nucleobase-containing compound metabolic process + "Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] + regulation of nucleobase-containing compound metabolic process + + + regulation of phosphate metabolism + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:go_curators] + GO:regulation of phosphate metabolic process + regulation of phosphate metabolic process + GO:0019220 + + + "A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:19295629] + cytokine-mediated signaling pathway + cytokine and chemokine mediated signaling pathway + cytokine mediated signalling pathway + GO:cytokine-mediated signaling pathway + GO:0019221 + + + GO:regulation of metabolic process + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] + regulation of metabolism + regulation of metabolic process + GO:0019222 + + + GO:proprioception + proprioception + "The series of events by which an organism senses the position, location, orientation, and movement of the body and its parts. Proprioception is mediated by proprioceptors, sensory nerve terminals found in muscles, tendons, and joint capsules, which give information concerning movements and position of the body. The receptors in the labyrinth are sometimes also considered proprioceptors." [http://www.onelook.com/, ISBN:072168677X] + GO:0019230 + + + "The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process." [http://www.onelook.com/] + sensory perception of pain + nociception + GO:sensory perception of pain + GO:0019233 + + + lactate anabolism + GO:0019249 + lactate formation + GO:lactate biosynthetic process + lactate biosynthetic process + lactate biosynthesis + lactate synthesis + "The chemical reactions and pathways resulting in the formation of lactate, the anion of lactic acid." [GOC:go_curators] + + + hexose metabolism + GO:0019318 + hexose metabolic process + GO:hexose metabolic process + "The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule." [ISBN:0198506732] + + + GO:0019319 + hexose biosynthesis + "The chemical reactions and pathways resulting in the formation of hexose, any monosaccharide with a chain of six carbon atoms in the molecule." [ISBN:0198506732] + GO:hexose biosynthetic process + hexose anabolism + hexose biosynthetic process + hexose synthesis + hexose formation + + + GO:hexose catabolic process + "The chemical reactions and pathways resulting in the breakdown of hexose, any monosaccharide with a chain of six carbon atoms in the molecule." [ISBN:0198506732] + hexose breakdown + hexose catabolic process + GO:0019320 + hexose catabolism + hexose degradation + + + nicotinamide nucleotide synthesis + nicotinamide nucleotide biosynthesis + GO:0019359 + nicotinamide nucleotide anabolism + GO:nicotinamide nucleotide biosynthetic process + "The chemical reactions and pathways resulting in the formation of nicotinamide nucleotides, any nucleotide that contains combined nicotinamide." [GOC:go_curators] + nicotinamide nucleotide biosynthetic process + nicotinamide nucleotide formation + + + "The chemical reactions and pathways involving a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base." [GOC:jl] + pyridine nucleotide metabolism + pyridine nucleotide metabolic process + GO:0019362 + GO:pyridine nucleotide metabolic process + + + pyridine nucleotide anabolism + GO:pyridine nucleotide biosynthetic process + pyridine nucleotide biosynthetic process + pyridine nucleotide formation + GO:0019363 + pyridine nucleotide synthesis + pyridine nucleotide biosynthesis + "The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base." [GOC:jl, GOC:pde, GOC:vw] + + + GO:0019395 + "The removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydrogen." [ISBN:0198506732, MetaCyc:FAO-PWY] + GO:fatty acid oxidation + fatty acid oxidation + + + triglyceride anabolism + GO:0019432 + triglyceride biosynthesis + triglyceride synthesis + GO:triglyceride biosynthetic process + triacylglycerol biosynthetic process + triacylglycerol biosynthesis + triglyceride biosynthetic process + triglyceride formation + "The chemical reactions and pathways resulting in the formation of a triglyceride, any triester of glycerol." [ISBN:0198506732] + + + aromatic compound synthesis + "The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring." [GOC:ai] + GO:0019438 + GO:aromatic compound biosynthetic process + aromatic compound biosynthetic process + aromatic compound formation + aromatic compound biosynthesis + aromatic compound anabolism + + + aromatic compound degradation + aromatic compound catabolic process + GO:0019439 + "The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring." [GOC:ai] + aromatic compound catabolism + aromatic compound breakdown + GO:aromatic compound catabolic process + + + "The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification." [GOC:ma] + protein metabolism + GO:protein metabolic process + protein metabolic process + protein metabolic process and modification + protein metabolism and modification + GO:0019538 + + + organophosphate metabolic process + organophosphate metabolism + GO:0019637 + "The chemical reactions and pathways involving organophosphates, any phosphate-containing organic compound." [ISBN:0198506732] + GO:organophosphate metabolic process + + + ribose phosphate metabolism + GO:ribose phosphate metabolic process + GO:0019693 + ribose phosphate metabolic process + "The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar." [GOC:ai] + + + "Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions." [GOC:signaling] + GO:0019722 + GO:calcium-mediated signaling + calcium-mediated signalling + calcium ion signaling + calcium signalling + calcium signaling + calcium-mediated signaling + + + B-cell mediated immune effector process + GO:0019724 + "Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149] + B lymphocyte mediated immune effector process + B cell mediated immunity + GO:B cell mediated immunity + B-cell mediated immunity + B-lymphocyte mediated immune effector process + B-lymphocyte mediated immunity + B lymphocyte mediated immunity + + + GO:0019725 + "Any process involved in the maintenance of an internal steady state at the level of the cell." [GOC:isa_complete, GOC:jl, ISBN:0395825172] + cellular homeostasis + GO:cellular homeostasis + + + secondary metabolic process + GO:0019748 + "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients." [GOC:go_curators] + secondary metabolite metabolic process + secondary metabolite metabolism + GO:secondary metabolic process + secondary metabolism + + + GO:carboxylic acid metabolic process + carboxylic acid metabolism + carboxylic acid metabolic process + GO:0019752 + "The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [ISBN:0198506732] + + + immunoglobulin complex + GO:immunoglobulin complex + GO:0019814 + "A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, GOC:jl, ISBN:0781765196] + + + GO:0019827 + "The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types." [GOC:mah, ISBN:0878932437] + maintenance of pluripotency + stem cell population maintenance + GO:stem cell population maintenance + + + GO:0019835 + holin + bacteriocin activity + cytolysis + GO:cytolysis + bacteriolytic toxin activity + lysin activity + "The rupture of cell membranes and the loss of cytoplasm." [UniProtKB-KW:KW-0204] + necrosis + autolysin activity + + + GO:0019866 + organelle inner membrane + GO:organelle inner membrane + "The inner, i.e. lumen-facing, lipid bilayer of an organelle envelope; usually highly selective to most ions and metabolites." [GOC:mah] + + + outer membrane + GO:0019867 + "The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites." [GOC:go_curators] + GO:outer membrane + + + antigen processing + antigen processing and presentation + GO:antigen processing and presentation + GO:0019882 + antigen presentation + "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149, PMID:15771591, PMID:15928678] + + + "The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:dos, GOC:jl, GOC:mah] + extrinsic component of membrane + peripheral membrane protein + GO:0019898 + extrinsic to membrane + GO:extrinsic component of membrane + + + lipid storage + GO:lipid storage + storage of lipids + lipid retention + retention of lipids + "The accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development." [GOC:dph, GOC:mah, GOC:tb, PMID:11102830] + GO:0019915 + sequestration of lipids + + + second-messenger-mediated signal transduction + second messenger mediated signalling + GO:second-messenger-mediated signaling + second-messenger-mediated signalling + second messenger-mediated signalling + second messenger-mediated signaling + GO:0019932 + "Any intracellular signal transduction in which the signal is passed on within the cell via a second messenger; a small molecule or ion that can be quickly generated or released from intracellular stores, and can diffuse within the cell. Second-messenger signaling includes production or release of the second messenger, and effectors downstream of the second messenger that further transmit the signal within the cell." [GOC:signaling, ISBN:0815316194, PMID:15221855, Wikipedia:Second_messenger_system] + second-messenger-mediated signaling + second messenger mediated signaling + + + modification-dependent protein breakdown + modification-initiated protein catabolism + modification-dependent protein degradation + GO:0019941 + modification-initiated proteolysis + protein degradation tagging activity + modification-initiated protein catabolic process + modification-dependent proteolysis + "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein." [GOC:go_curators] + GO:modification-dependent protein catabolic process + modification-dependent protein catabolic process + modification-dependent protein catabolism + + + "A reproduction process that creates a new organism by combining the genetic material of two organisms. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two different individuals (parents) join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny." [GOC:jl, http://en.wikipedia.org/wiki/Sexual_reproduction, ISBN:0387520546] + sexual reproduction + GO:sexual reproduction + GO:0019953 + + + asexual reproduction + GO:asexual reproduction + "The biological process in which new individuals are produced by either a single cell or a group of cells, in the absence of any sexual process." [ISBN:0387520546] + GO:0019954 + + + GO:telencephalon development + "The process whose specific outcome is the progression of the telencephalon over time, from its formation to the mature structure. The telencephalon is the paired anteriolateral division of the prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695] + cerebrum development + telencephalon development + GO:0021537 + + + developmental maturation + GO:0021700 + "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] + GO:developmental maturation + + + glial cell development + GO:0021782 + GO:glial cell development + "The process aimed at the progression of a glial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] + + + GO:layer formation in cerebral cortex + layer formation in cerebral cortex + GO:0021819 + cerebral cortex lamination + "The detachment of cells from radial glial fibers at the appropriate time when they cease to migrate and form distinct layer in the cerebral cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:12626695] + + + GO:0021905 + "The process whose specific outcome is the creation of the forebrain-midbrain boundary." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06, PMID:11262869] + forebrain-midbrain boundary formation + GO:forebrain-midbrain boundary formation + + + pineal gland development + "The progression of the pineal gland over time from its initial formation until its mature state. The pineal gland is an endocrine gland that secretes melatonin and is involved in circadian rhythms." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] + GO:pineal gland development + GO:0021982 + epiphysis development + + + neurogenesis + GO:neurogenesis + nervous system cell generation + GO:0022008 + neural cell differentiation + "Generation of cells within the nervous system." [GO_REF:0000021, GOC:cls, GOC:curators, GOC:dgh, GOC:dph, GOC:jid, GOC:mtg_15jun06] + + + cell cycle process + "The cellular process that ensures successive accurate and complete genome replication and chromosome segregation." [GOC:isa_complete, GOC:mtg_cell_cycle] + GO:cell cycle process + GO:0022402 + + + GO:cell cycle phase + GO:0022403 + cell cycle phase + "One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GOC:mtg_cell_cycle] + + + molting cycle process + GO:0022404 + "A multicellular organismal process involved in the periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin." [GOC:isa_complete] + GO:molting cycle process + + + GO:0022405 + GO:hair cycle process + hair cycle process + "A multicellular organismal process involved in the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." [GOC:isa_complete] + + + GO:regulation of cell-cell adhesion + regulation of cell-cell adhesion + GO:0022407 + "Any process that modulates the frequency, rate or extent of attachment of a cell to another cell." [GOC:isa_complete] + + + down regulation of cell-cell adhesion + down-regulation of cell-cell adhesion + "Any process that stops, prevents or reduces the rate or extent of cell adhesion to another cell." [GOC:isa_complete] + GO:negative regulation of cell-cell adhesion + GO:0022408 + downregulation of cell-cell adhesion + negative regulation of cell-cell adhesion + + + GO:cellular component disassembly + cell structure disassembly + "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] + cellular component disassembly at cellular level + cellular component disassembly + GO:0022411 + + + GO:cellular process involved in reproduction in multicellular organism + "A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism." [GOC:isa_complete] + reproductive cellular process in multicellular organism + GO:0022412 + cellular process involved in reproduction in multicellular organism + + + "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete] + GO:0022414 + GO:reproductive process + reproductive process + + + GO:0022600 + GO:digestive system process + digestive system process + "A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [GOC:isa_complete, GOC:jid, GOC:mtg_cardio] + + + "The progression of physiological phases, occurring in the endometrium during the menstrual cycle that recur at regular intervals during the reproductive years. The menstrual cycle is an ovulation cycle where the endometrium is shed if pregnancy does not occur." [GOC:dph, GOC:isa_complete, GOC:jid] + menstrual cycle phase + GO:0022601 + GO:menstrual cycle phase + + + menstrual cycle process + GO:ovulation cycle process + estrous cycle process + ovulation cycle process + "A process involved in the sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years." [GOC:isa_complete] + GO:0022602 + + + "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] + cellular component assembly at cellular level + GO:0022607 + GO:cellular component assembly + cellular component assembly + cell structure assembly + + + GO:0022610 + "The attachment of a cell or organism to a substrate or other organism." [GOC:isa_complete] + GO:biological adhesion + biological adhesion + + + DNA strand elongation + GO:0022616 + GO:DNA strand elongation + "The DNA metabolic process in which a DNA strand is synthesized by adding nucleotides to the 3' end of an existing DNA stand." [GOC:isa_complete] + + + GO:0022900 + electron transport chain + GO:electron transport chain + "A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient." [GOC:mtg_electron_transport] + + + "A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate." [GOC:mtg_signal, GOC:signaling] + signal transmission via phosphorylation event + GO:0023014 + signal transduction via phosphorylation event + signal transduction by protein phosphorylation + GO:signal transduction by protein phosphorylation + + + GO:0023051 + regulation of signalling process + regulation of signaling + regulation of signaling process + "Any process that modulates the frequency, rate or extent of a signaling process." [GOC:mtg_signal] + GO:regulation of signaling + + + signalling + signalling process + signaling + "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] + biological signaling + signaling process + GO:0023052 + GO:signaling + + + positive regulation of signaling + GO:positive regulation of signaling + positive regulation of signaling process + "Any process that activates, maintains or increases the frequency, rate or extent of a signaling process." [GOC:mtg_signal] + positive regulation of signalling process + GO:0023056 + + + GO:0023061 + "The process in which a signal is secreted or discharged into the extracellular medium from a cellular source." [GOC:mtg_signal] + signal release + signal secretion + GO:signal release + + + metal ion transport + GO:metal ion transport + "The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + GO:0030001 + + + striated muscle fiber + GO:myofibril + GO:0030016 + striated muscle fibre + "The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism." [ISBN:0815316194] + myofibril + + + GO:cell projection organization + cell projection organization and biogenesis + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] + cell projection organisation + cell projection organization + GO:0030030 + cell surface structure organization and biogenesis + + + formation of a cell surface projection + "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] + GO:0030031 + GO:cell projection assembly + cell projection assembly + cell projection biogenesis + + + GO:actin filament polymerization + "Assembly of actin filaments by the addition of actin monomers to a filament." [GOC:mah] + actin polymerizing activity + actin filament polymerization + actin polymerization + GO:0030041 + + + GO:0030054 + "A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix." [GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732] + GO:cell junction + cell junction + + + cell-substrate junction + cell-matrix junction + GO:0030055 + GO:cell-substrate junction + "A cell junction that forms a connection between a cell and the extracellular matrix." [GOC:hb, GOC:mah] + + + hemi-adherens junction + hemidesmosome + GO:hemidesmosome + GO:0030056 + "A cell-substrate junction (attachment structure) found in epithelial cells that links intermediate filaments to extracellular matrices via transmembrane complexes. In vertebrates, hemidesmosomes mediate contact between the basal side of epithelial cells and the basal lamina. In C. elegans, hemidesmosomes connect epithelial cells to distinct extracellular matrices on both the apical and basal cell surfaces." [GOC:kmv, ISBN:0815316208, PMID:20205195] + + + GO:peptide hormone secretion + "The regulated release of a peptide hormone from a cell." [GOC:mah] + peptide hormone secretion + GO:0030072 + + + GO:0030073 + insulin secretion + GO:insulin secretion + "The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin." [GOC:mah, ISBN:0198506732] + + + GO:0030097 + "The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates." [GOC:dgh, ISBN:0198506732] + hematopoiesis + blood cell formation + GO:hemopoiesis + hemopoiesis + haemopoiesis + blood cell biosynthesis + + + "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages." [GOC:add, ISBN:0781735149] + GO:0030099 + myeloid cell differentiation + GO:myeloid cell differentiation + + + GO:0030104 + water homeostasis + "Any process involved in the maintenance of an internal steady state of water within an organism or cell." [GOC:dph, GOC:mah, GOC:tb] + GO:water homeostasis + osmoregulation + regulation of osmotic pressure + + + regulation of Wnt-activated signaling pathway + GO:regulation of Wnt signaling pathway + regulation of frizzled signalling pathway + regulation of Wnt receptor signaling pathway + GO:0030111 + regulation of Wnt receptor signalling pathway + regulation of Wnt signaling pathway + regulation of frizzled signaling pathway + "Any process that modulates the frequency, rate or extent of the activity of the Wnt signal transduction pathway." [GOC:dph, GOC:mah, GOC:tb] + + + constitutive secretory pathway transport vesicle + "Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell." [GOC:mah, PMID:22160157] + transport vesicle + GO:transport vesicle + GO:0030133 + + + coated vesicle + GO:coated vesicle + "Small membrane-bounded organelle formed by pinching off of a coated region of membrane. Some coats are made of clathrin, whereas others are made from other proteins." [ISBN:0815316194] + GO:0030135 + + + GO:endocytic vesicle + endocytotic transport vesicle + GO:0030139 + "A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting." [GOC:go_curators, PMID:19696797] + endocytotic vesicle + endocytic vesicle + + + GO:secretory granule + GO:0030141 + secretory granule + "A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules." [GOC:mah, ISBN:0198596732] + + + GO:cell differentiation + "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732] + GO:0030154 + cell differentiation + + + GO:regulation of cell adhesion + regulation of cell adhesion + "Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix." [GOC:mah] + GO:0030155 + cell adhesion receptor regulator activity + + + regulation of proteolysis + regulation of peptidolysis + GO:0030162 + GO:regulation of proteolysis + "Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein." [GOC:mah] + + + protein catabolic process + protein degradation + protein breakdown + pheromone catabolism + GO:protein catabolic process + pheromone catabolic process + GO:0030163 + protein catabolism + "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:mah] + + + GO:protein denaturation + "Structural change in proteins which destroys the native, active configuration without rupture of peptide bonds." [GOC:kd, ISBN:3110145359] + protein denaturation + GO:0030164 + + + GO:proteoglycan biosynthetic process + proteoglycan biosynthetic process + "The chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans." [GOC:mah, ISBN:0198506732] + proteoglycan anabolism + proteoglycan synthesis + GO:0030166 + proteoglycan biosynthesis + proteoglycan formation + + + "A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug." [http://www.graylab.ac.uk/omd/] + GO:platelet activation + platelet activation + GO:0030168 + blood coagulation, platelet activation + + + GO:0030182 + neuron differentiation + "The process in which a relatively unspecialized cell acquires specialized features of a neuron." [GOC:mah] + GO:neuron differentiation + + + regulation of blood coagulation + GO:regulation of blood coagulation + "Any process that modulates the frequency, rate or extent of blood coagulation." [GOC:mah] + GO:0030193 + + + negative regulation of blood coagulation + GO:0030195 + downregulation of blood coagulation + down regulation of blood coagulation + "Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation." [GOC:mah] + down-regulation of blood coagulation + GO:negative regulation of blood coagulation + + + keratinocyte cell differentiation + keratinocyte differentiation + GO:keratinocyte differentiation + GO:0030216 + "The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte." [GOC:dph, GOC:mah, GOC:sdb_2009, GOC:tb] + + + erythrocyte differentiation + erythrocyte cell differentiation + "The process in which a myeloid precursor cell acquires specializes features of an erythrocyte." [GOC:mah] + GO:erythrocyte differentiation + GO:0030218 + red blood cell differentiation + RBC differentiation + erythropoiesis + + + "The specification of female sex of an individual organism." [GOC:mah, ISBN:0198506732] + GO:0030237 + female sex determination + GO:female sex determination + + + GO:0030238 + male sex determination + GO:male sex determination + "The specification of male sex of an individual organism." [GOC:mah] + + + lipid modification + GO:0030258 + "The covalent alteration of one or more fatty acids in a lipid, resulting in a change in the properties of the lipid." [GOC:mah] + GO:lipid modification + + + "The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells." [GOC:mah, ISBN:0815316194] + chromosome condensation + nuclear chromosome condensation + GO:0030261 + eukaryotic chromosome condensation + GO:chromosome condensation + + + apoptotic chromosome condensation + pyknosis + "The compaction of chromatin during apoptosis." [GOC:mah] + GO:0030263 + GO:apoptotic chromosome condensation + + + dynein complex + "Any of several large complexes that contain two or three dynein heavy chains and several light chains, and have microtubule motor activity." [ISBN:0815316194] + GO:0030286 + GO:dynein complex + + + "Uptake of cholesterol into the blood by absorption from the small intestine." [GOC:mah] + GO:0030299 + GO:intestinal cholesterol absorption + intestinal cholesterol absorption + + + cholesterol transport + GO:cholesterol transport + GO:0030301 + "The directed movement of cholesterol, cholest-5-en-3-beta-ol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah, ISBN:0198506732] + + + GO:external encapsulating structure + GO:0030312 + external encapsulating structure + "A structure that lies outside the plasma membrane and surrounds the entire cell. This does not include the periplasmic space." [GOC:go_curators] + + + transverse tubule + GO:0030315 + triad + GO:T-tubule + "Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane." [GOC:mtg_muscle, ISBN:0815316194] + T-tubule + + + respiratory tube development + GO:respiratory tube development + GO:0030323 + "The process whose specific outcome is the progression of the respiratory tube over time, from its formation to the mature structure. The respiratory tube is assumed to mean any tube in the respiratory tract." [GOC:jid] + + + lung development + GO:lung development + GO:0030324 + "The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax." [GOC:jid, UBERON:0002048] + + + membrane disassembly + membrane catabolism + "The controlled breakdown of any cell membrane in the context of a normal process such as autophagy." [GOC:mah] + membrane degradation + GO:membrane disassembly + membrane breakdown + GO:0030397 + + + GO:axon + GO:0030424 + "The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter." [GOC:nln, ISBN:0198506732] + axon + + + dendrite + GO:0030425 + GO:dendrite + "A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body." [GOC:dos, GOC:mah, GOC:nln, ISBN:0198506732] + + + sleep + diapause + GO:sleep + GO:0030431 + lethargus + "Any process in which an organism enters and maintains a periodic, readily reversible state of reduced awareness and metabolic activity. Usually accompanied by physical relaxation, the onset of sleep in humans and other mammals is marked by a change in the electrical activity of the brain." [ISBN:0192800981] + dormancy + + + sporulation resulting in formation of a cellular spore + cellular spore formation by sporulation + spore formation + "The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction." [GOC:mah, GOC:pamgo_curators, ISBN:0072992913] + spore biosynthesis + GO:sporulation resulting in formation of a cellular spore + GO:0030435 + spore differentiation + + + BMP receptor signaling pathway + GO:BMP signaling pathway + "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, ISBN:0878932437, PR:000000034] + BMP signaling pathway + BMP signalling pathway + bone morphogenetic protein signaling pathway + GO:0030509 + bone morphogenetic protein signalling pathway + + + GO:0030510 + "Any process that modulates the frequency, rate or extent of the activity of any BMP receptor signaling pathway." [GOC:mah] + regulation of bone morphogenetic protein signalling pathway + regulation of BMP signaling pathway + regulation of BMP receptor signaling pathway + regulation of bone morphogenetic protein signaling pathway + GO:regulation of BMP signaling pathway + regulation of BMP signalling pathway + + + GO:intracellular receptor signaling pathway + GO:0030522 + intracellular receptor-mediated signaling pathway + intracellular receptor signaling pathway + intracellular receptor-mediated signalling pathway + intracellular receptor mediated signaling pathway + "Any series of molecular signals initiated by a ligand binding to an receptor located within a cell." [GOC:bf, GOC:mah] + + + GO:intracellular ribonucleoprotein complex + "An intracellular macromolecular complex containing both protein and RNA molecules." [GOC:krc, GOC:vesicles] + intracellular ribonucleoprotein complex + GO:0030529 + + + immune cell chemotaxis + leukocyte chemotaxis + leucocyte chemotaxis + GO:leukocyte chemotaxis + GO:0030595 + "The movement of a leukocyte in response to an external stimulus." [GOC:add, GOC:jl] + + + "The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way." [GOC:bf, GOC:mah, GOC:vw] + protein binding, bridging + GO:0030674 + GO:protein binding, bridging + + + "The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell." [GOC:mah] + GO:0030705 + cytoskeleton-dependent intracellular transport + GO:cytoskeleton-dependent intracellular transport + + + ovulation + GO:0030728 + GO:ovulation + "The release of a mature ovum/oocyte from an ovary." [GOC:bf, ISBN:0878932437] + + + regulation of nucleotide catabolism + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of nucleotides." [GOC:mah] + GO:0030811 + regulation of nucleotide catabolic process + regulation of nucleotide degradation + regulation of nucleotide breakdown + GO:regulation of nucleotide catabolic process + + + GO:0030849 + "Any chromosome other than a sex chromosome." [GOC:mah] + autosome + GO:autosome + + + prostate development + prostate gland development + GO:prostate gland development + GO:0030850 + "The process whose specific outcome is the progression of the prostate gland over time, from its formation to the mature structure. The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid." [PMID:11839751] + + + epithelial cell differentiation + "The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium." [GOC:ecd, PMID:11839751] + GO:epithelial cell differentiation + GO:0030855 + + + nucleolar chromatin + "The portion of nuclear chromatin associated with the nucleolus; includes the DNA encoding the ribosomal RNA." [GOC:mah] + GO:0030874 + GO:nucleolar chromatin + + + GO:0030879 + GO:mammary gland development + "The process whose specific outcome is the progression of the mammary gland over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. Its development starts with the formation of the mammary line and ends as the mature gland cycles between nursing and weaning stages." [PMID:9576833] + mammary gland development + + + GO:forebrain development + GO:0030900 + prosencephalon development + "The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions)." [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=forebrain] + forebrain development + + + GO:0031012 + extracellular matrix + GO:extracellular matrix + "A structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals and bacteria) or be part of the cell (as in plants)." [GOC:mah, NIF_Subcellular:nlx_subcell_20090513] + + + dense core granule + "Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted." [NIF_Subcellular:sao772007592, PMID:14690495] + GO:dense core granule + dense core vesicle + GO:0031045 + + + gene silencing by RNA + "Any process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:mah, GOC:tb, PMID:15020054] + GO:gene silencing by RNA + RNA-mediated gene silencing + GO:0031047 + + + "The process in which the anatomical structures of the hair follicle are generated and organized." [GOC:ln] + GO:hair follicle morphogenesis + GO:0031069 + hair follicle morphogenesis + + + GO:0031080 + Nup107-160 complex + GO:nuclear pore outer ring + nuclear pore outer ring + "A subcomplex of the nuclear pore complex (NPC) that forms the outer rings of the core scaffold, a lattice-like structure that gives the NPC its shape and strength. In S. cerevisiae, the two outer rings each contain multiple copies of the following proteins: Nup133p, Nup120p, Nup145Cp, Nup85p, Nup84p, Seh1p, and Sec13p. In vertebrates, the two outer rings each contain multiple copies of the following proteins: Nup133, Nup160, Nup96, Nup75, Nup107, Seh1, Sec13, Nup43, Nup37, and ALADIN. Components are arranged in 8-fold symmetrical 'spokes' around the central transport channel. A single 'spoke', can be isolated and is sometimes referred to as the Nup84 complex (S. cerevisiae) or the Nup107-160 complex (vertebrates)." [GOC:dgf, PMID:18046406, PMID:19524430, PMID:20947011, PMID:22419078] + Nup84 complex + Nup107-120 complex + + + GO:0031090 + intracellular membrane + organelle membrane + "A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle." [GOC:dos, GOC:mah] + GO:organelle membrane + + + regeneration + GO:0031099 + "The regrowth of a lost or destroyed body part, such as an organ or tissue." [GOC:mah] + GO:regeneration + + + GO:microtubule polymerization or depolymerization + microtubule polymerization or depolymerization + GO:0031109 + "Assembly or disassembly of microtubules by the addition or removal of tubulin heterodimers from a microtubule." [GOC:mah] + + + "Any process that modulates the frequency, rate or extent of microtubule polymerization or depolymerization by the addition or removal of tubulin heterodimers from a microtubule." [GOC:mah] + GO:0031110 + regulation of microtubule polymerization or depolymerization + GO:regulation of microtubule polymerization or depolymerization + + + down-regulation of microtubule polymerization or depolymerization + GO:negative regulation of microtubule polymerization or depolymerization + GO:0031111 + negative regulation of microtubule polymerization or depolymerization + downregulation of microtubule polymerization or depolymerization + down regulation of microtubule polymerization or depolymerization + "Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization or depolymerization." [GOC:mah] + + + GO:regulation of microtubule depolymerization + GO:0031114 + regulation of microtubule disassembly + "Any process that modulates the frequency, rate or extent of microtubule depolymerization." [GOC:mah] + regulation of microtubule depolymerization + + + pseudopodium + "A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding." [ISBN:0198506732] + GO:0031143 + GO:pseudopodium + pseudopod + + + "The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites)." [GOC:mah] + neuron projection development + GO:0031175 + GO:neuron projection development + + + "The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane." [GOC:mah] + GO:0031224 + intrinsic component of membrane + GO:intrinsic component of membrane + + + "The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos, GOC:mah] + GO:anchored component of membrane + GO:0031225 + anchored component of membrane + anchored to membrane + + + GO:0031253 + membrane projection + "The portion of the plasma membrane surrounding a cell surface projection." [GOC:mah] + cell projection membrane + membrane extension + GO:cell projection membrane + + + GO:0031261 + DNA replication preinitiation complex + "A protein-DNA complex assembled at eukaryotic DNA replication origins immediately prior to the initiation of DNA replication. The preinitiation complex is formed by the assembly of additional proteins onto an existing prereplicative complex. In budding yeast, the additional proteins include Cdc45p, Sld2p, Sld3p, Dpb11p, DNA polymerases, and others; in fission yeast the GINS complex is present." [GOC:bf, GOC:hjd, GOC:jl, GOC:pr, GOC:rb, GOC:vw, PMID:12694535, PMID:15194812] + pre-IC + GO:DNA replication preinitiation complex + + + GO:regulation of cellular metabolic process + regulation of cellular metabolism + regulation of cellular metabolic process + GO:0031323 + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] + + + negative regulation of cellular metabolic process + GO:negative regulation of cellular metabolic process + GO:0031324 + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] + down regulation of cellular metabolic process + down-regulation of cellular metabolic process + negative regulation of cellular metabolism + downregulation of cellular metabolic process + + + up regulation of cellular metabolic process + positive regulation of cellular metabolism + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] + GO:0031325 + GO:positive regulation of cellular metabolic process + positive regulation of cellular metabolic process + upregulation of cellular metabolic process + up-regulation of cellular metabolic process + + + regulation of cellular biosynthetic process + regulation of cellular anabolism + GO:0031326 + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] + regulation of cellular synthesis + regulation of cellular formation + regulation of cellular biosynthesis + GO:regulation of cellular biosynthetic process + + + negative regulation of cellular formation + GO:negative regulation of cellular biosynthetic process + negative regulation of cellular biosynthetic process + down-regulation of cellular biosynthetic process + negative regulation of cellular biosynthesis + GO:0031327 + down regulation of cellular biosynthetic process + negative regulation of cellular anabolism + downregulation of cellular biosynthetic process + negative regulation of cellular synthesis + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] + + + GO:positive regulation of cellular biosynthetic process + positive regulation of cellular anabolism + GO:0031328 + up regulation of cellular biosynthetic process + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] + positive regulation of cellular biosynthesis + positive regulation of cellular synthesis + positive regulation of cellular formation + upregulation of cellular biosynthetic process + positive regulation of cellular biosynthetic process + up-regulation of cellular biosynthetic process + + + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] + GO:0031329 + regulation of cellular degradation + regulation of cellular catabolism + regulation of cellular breakdown + regulation of cellular catabolic process + GO:regulation of cellular catabolic process + + + GO:regulation of defense response + GO:0031347 + regulation of defense response + "Any process that modulates the frequency, rate or extent of a defense response." [GOC:mah] + + + up-regulation of defense response + positive regulation of defense response + "Any process that activates or increases the frequency, rate or extent of a defense response." [GOC:mah] + GO:0031349 + upregulation of defense response + up regulation of defense response + GO:positive regulation of defense response + + + GO:0031399 + regulation of protein modification process + GO:regulation of protein modification process + "Any process that modulates the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." [GOC:mah, GOC:tb] + + + positive regulation of protein modification process + up regulation of protein modification + GO:positive regulation of protein modification process + up-regulation of protein modification + GO:0031401 + "Any process that activates or increases the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." [GOC:mah, GOC:tb] + upregulation of protein modification + + + cytoplasmic vesicle + GO:0031410 + "A vesicle formed of membrane or protein, found in the cytoplasm of a cell." [GOC:mah] + GO:cytoplasmic vesicle + + + GO:0031424 + keratinization + GO:keratinization + "The process in which the cytoplasm of the outermost cells of the vertebrate epidermis is replaced by keratin. Keratinization occurs in the stratum corneum, feathers, hair, claws, nails, hooves, and horns." [GOC:dph, GOC:ebc, GOC:sdb_2009, GOC:tb] + + + chromatin assembly + GO:0031497 + GO:chromatin assembly + establishment of chromatin architecture + "The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus." [http://www.infobiogen.fr/services/chromcancer/IntroItems/ChromatinEducEng.html, PMID:20404130] + + + GO:0031498 + "The controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, other proteins, and sometimes RNA." [http://www.infobiogen.fr/services/chromcancer/IntroItems/ChromatinEducEng.html, PMID:20404130] + GO:chromatin disassembly + chromatin disassembly + + + establishment and maintenance of protein complex localization + protein complex localisation + GO:0031503 + protein complex localization + "A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location." [GOC:mah] + GO:protein complex localization + + + establishment of heterochromatin architecture + heterochromatin assembly + GO:heterochromatin assembly + GO:0031507 + heterochromatin formation + "The assembly of chromatin into heterochromatin, a compact and highly condensed form that is often, but not always, transcriptionally silent." [GOC:mah] + + + immotile primary cilium + GO:nonmotile primary cilium + nonmotile primary cilium + GO:0031513 + sensory cilium + "A primary cilium which contains a variable array of axonemal microtubules but does not contain molecular motors. Nonmotile primary cilia are found on many different cell types and function as sensory organelles that concentrate and organize sensory signaling molecules." [GOC:dgh, GOC:kmv, PMID:17009929, PMID:20144998] + nonmotile primary cilia + + + motile cilium + motile secondary cilium + microtubule-based flagellum + GO:0031514 + "A cilium which has a variable arrangement of axonemal microtubules, contains molecular motors, and beats with a characteristic whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface. Motile cilia are typically found in multiple copies on epithelial cells that line the lumenal ducts of various tissues. Motile cilia may also function as sensory organelles." [GOC:dgh, GOC:kmv, PMID:17009929, PMID:20144998] + motile cilia + GO:motile cilium + + + Polycomb Group protein complex + GO:0031519 + "A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure." [PMID:9372908] + PcG protein complex + GO:PcG protein complex + + + regulation of DNA-dependent transcription, termination + GO:0031554 + regulation of DNA-templated transcription, termination + transcription antiterminator activity + regulation of transcription termination, DNA-dependent + GO:regulation of DNA-templated transcription, termination + regulation of termination of DNA-dependent transcription + "Any process that modulates the frequency, rate, extent, or location of DNA-templated transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA." [GOC:mlg, GOC:txnOH] + + + "Regulation of transcription through variation in where transcription termination occurs." [GOC:dh, GOC:mlg, ISBN:0198542682] + transcriptional attenuation + GO:transcriptional attenuation + GO:0031555 + + + GO:0031564 + transcriptional readthrough + transcription antitermination + "Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond a termination site." [ISBN:0198577788, PMID:12456320] + GO:transcription antitermination + + + DNA integrity checkpoint + "A cell cycle process that controls cell cycle progression in response to changes in DNA structure by monitoring the integrity of the DNA. The DNA integrity checkpoint begins with detection of DNA damage, defects in DNA structure or DNA replication, and progresses through signal transduction and ends with cell cycle effector processes." [GOC:mtg_cell_cycle] + GO:0031570 + GO:DNA integrity checkpoint + + + spindle checkpoint + GO:0031577 + GO:spindle checkpoint + "A cell cycle checkpoint that originates from the mitotic or meiotic spindle." [GOC:mtg_cell_cycle] + + + heat generation + GO:0031649 + "Any homeostatic process in which an organism produces heat, thereby raising its internal temperature." [GOC:mah] + GO:heat generation + + + GO:response to nutrient levels + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients." [GOC:mah] + response to nutrient levels + GO:0031667 + + + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus." [GOC:mah] + cellular response to extracellular stimulus + GO:cellular response to extracellular stimulus + GO:0031668 + + + GO:cellular response to nutrient levels + cellular response to nutrient levels + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients." [GOC:mah] + GO:0031669 + + + GO:0031670 + GO:cellular response to nutrient + cellular response to nutrient + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus." [GOC:mah] + + + "A two-stranded helical polymer of the protein actin." [GOC:mah] + F-actin + GO:filamentous actin + filamentous actin + GO:0031941 + + + "Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space." [GOC:mah, GOC:pz] + GO:nuclear membrane + GO:0031965 + nuclear membrane + + + GO:0031966 + mitochondrial membrane + GO:mitochondrial membrane + "Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope." [GOC:mah, NIF_Subcellular:sao1045389829] + + + GO:organelle envelope + "A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes." [GOC:mah, GOC:pz] + GO:0031967 + organelle envelope + + + GO:0031968 + "The outer, i.e. cytoplasm-facing in a cellular organelle, lipid bilayer of an organelle envelope." [GOC:mah] + organelle outer membrane + GO:organelle outer membrane + + + organelle envelope lumen + GO:0031970 + GO:organelle envelope lumen + "The region between the inner and outer lipid bilayers of an organelle envelope." [GOC:mah] + organelle intermembrane space + + + "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." [GOC:add, GOC:mah] + GO:membrane-enclosed lumen + GO:0031974 + membrane-enclosed lumen + + + GO:0031975 + "A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers." [GOC:mah, GOC:pz] + GO:envelope + envelope + + + GO:vesicle + vesicle + "Any small, fluid-filled, spherical organelle enclosed by membrane or protein." [GOC:mah, GOC:pz] + GO:0031982 + + + GO:0031984 + suborganelle compartment + organelle subcompartment + GO:organelle subcompartment + "A compartment that consists of a lumen and an enclosing membrane, and is part of an organelle." [GOC:mah, GOC:pz] + + + GO:0031988 + GO:membrane-bounded vesicle + membrane-enclosed vesicle + membrane-bounded vesicle + "Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer." [GOC:mah] + + + GO:0032042 + mitochondrial DNA metabolic process + GO:mitochondrial DNA metabolic process + mtDNA metabolic process + mtDNA metabolism + "The chemical reactions and pathways involving mitochondrial DNA." [GOC:mah] + mitochondrial DNA metabolism + + + "Any process that modulates the frequency, rate or extent of a response to an external stimulus." [GOC:mah] + regulation of response to external stimulus + GO:regulation of response to external stimulus + GO:0032101 + + + negative regulation of response to external stimulus + down-regulation of response to external stimulus + "Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus." [GOC:mah] + down regulation of response to external stimulus + GO:negative regulation of response to external stimulus + GO:0032102 + downregulation of response to external stimulus + + + up-regulation of response to external stimulus + "Any process that activates, maintains or increases the rate of a response to an external stimulus." [GOC:mah] + upregulation of response to external stimulus + GO:0032103 + up regulation of response to external stimulus + GO:positive regulation of response to external stimulus + positive regulation of response to external stimulus + + + GO:activation of protein kinase activity + activation of protein kinase activity + protein kinase activation + GO:0032147 + "Any process that initiates the activity of an inactive protein kinase." [GOC:mah] + + + GO:0032196 + transposition + GO:transposition + "Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites." [GOC:jp, ISBN:1555812090] + + + "Any process involved in a type of transpositional recombination which occurs via an RNA intermediate." [GOC:jp, ISBN:1555812090] + retrotransposition + Class I transposition + GO:0032197 + transposition, RNA-mediated + GO:transposition, RNA-mediated + retrotransposon transposition + RNA-mediated transposition + + + "The process in which a methyl group is covalently attached to a molecule." [GOC:mah] + methylation + GO:0032259 + GO:methylation + + + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell." [GOC:mah] + GO:regulation of cellular protein metabolic process + regulation of cellular protein metabolic process + GO:0032268 + regulation of cellular protein metabolism + + + upregulation of cellular protein metabolic process + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell." [GOC:mah] + positive regulation of cellular protein metabolic process + GO:0032270 + GO:positive regulation of cellular protein metabolic process + up regulation of cellular protein metabolic process + up-regulation of cellular protein metabolic process + positive regulation of cellular protein metabolism + + + "A nonmotile primary cilium that has a 9+0 microtubule array and forms the portion of the axoneme traversing the boundary between the photoreceptor inner and outer segments." [PMID:15917207, PMID:8718680] + GO:0032391 + photoreceptor connecting cilium + photoreceptor cilium + GO:photoreceptor connecting cilium + + + GO:0032392 + "The process in which a transformation is induced in the geometry of a DNA double helix, resulting in a change in twist, writhe, or both, but with no change in linking number. Includes the unwinding of double-stranded DNA by helicases." [GOC:mah] + DNA geometric change + GO:DNA geometric change + + + "An actin-based protrusion from the apical surface of auditory and vestibular hair cells and of neuromast cells. These protrusions are supported by a bundle of cross-linked actin filaments (an actin cable), oriented such that the plus (barbed) ends are at the tip of the protrusion, capped by a tip complex which bridges to the plasma. Bundles of stereocilia act as mechanosensory organelles." [GOC:ecd, PMID:15661519, PMID:7840137] + GO:stereocilium + stereocilium + GO:0032420 + + + GO:melanosome organization + melanosome organization and biogenesis + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a melanosome. A melanosome is a tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored." [GOC:vk] + melanosome organization + melanosome organisation + GO:0032438 + + + protein modification by small protein conjugation + GO:protein modification by small protein conjugation + "A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to a target protein." [GOC:mah] + GO:0032446 + + + external side of mitochondrial outer membrane + "The external (cytoplasmic) face of the mitochondrial outer membrane." [GOC:mah] + GO:0032473 + external leaflet of mitochondrial outer membrane + GO:cytoplasmic side of mitochondrial outer membrane + external side of mitochondrial envelope + cytosolic side of mitochondrial outer membrane + cytoplasmic side of mitochondrial outer membrane + + + GO:0032501 + multicellular organismal process + GO:multicellular organismal process + organismal physiological process + "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] + + + GO:0032502 + developmental process + GO:developmental process + "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] + + + GO:0032505 + GO:reproduction of a single-celled organism + reproduction of a single-celled organism + "The biological process in which new individuals are produced by one or two single-celled organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:isa_complete] + + + GO:0032507 + maintenance of protein localization in cell + GO:maintenance of protein location in cell + maintenance of protein location in cell + "Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere." [GOC:isa_complete, GOC:mah] + + + GO:0032508 + DNA unwinding + duplex DNA melting + "The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands." [GOC:isa_complete, GOC:mah] + DNA duplex unwinding + GO:DNA duplex unwinding + + + "The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication." [GOC:mah, GOC:txnOH] + RNA formation + RNA biosynthesis + GO:RNA biosynthetic process + RNA synthesis + RNA biosynthetic process + RNA anabolism + GO:0032774 + + + DNA methylation on cytosine + GO:0032776 + GO:DNA methylation on cytosine + "The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule." [GOC:pf] + + + "The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-)." [GOC:vk] + monocarboxylic acid metabolism + monocarboxylic acid metabolic process + GO:0032787 + GO:monocarboxylic acid metabolic process + monocarboxylate metabolic process + + + receptor biosynthetic process + receptor anabolism + GO:0032800 + "The chemical reactions and pathways resulting in the formation of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:mah] + receptor synthesis + receptor biosynthesis + receptor formation + GO:receptor biosynthetic process + + + GO:0032806 + carboxy-terminal domain protein kinase complex + CTDK complex + GO:carboxy-terminal domain protein kinase complex + "A protein complex that phosphorylates amino acid residues of RNA polymerase II C-terminal domain repeats; phosphorylation occurs mainly on Ser2 and Ser5." [PMID:15047695, PMID:16721054, PMID:17079683] + + + GO:0032878 + "Any process that modulates the frequency, rate or extent of the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns." [GOC:mah] + regulation of establishment or maintenance of cell polarity + GO:regulation of establishment or maintenance of cell polarity + + + "Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location." [GOC:mah] + GO:regulation of localization + GO:0032879 + regulation of localization + regulation of localisation + + + regulation of protein localisation + regulation of protein localization + GO:regulation of protein localization + GO:0032880 + "Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location." [GOC:dph, GOC:mah, GOC:tb] + + + GO:0032886 + "Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton." [GOC:mah] + GO:regulation of microtubule-based process + regulation of microtubule-based process + + + GO:0032924 + GO:activin receptor signaling pathway + "A series of molecular signals initiated by the binding of an extracellular ligand to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:rl, GOC:signaling] + activin receptor signaling pathway + activin receptor signalling pathway + + + cellular secretion + "The controlled release of a substance by a cell." [GOC:mah] + GO:secretion by cell + secretion by cell + GO:0032940 + + + secretion by tissue + GO:0032941 + GO:secretion by tissue + expulsion of gland contents + "The controlled release of a substance by a tissue." [GOC:mah] + tissue secretion + + + GO:0032943 + "The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form." [GOC:add] + GO:mononuclear cell proliferation + mononuclear cell proliferation + + + GO:collagen metabolic process + collagen metabolism + GO:0032963 + "The chemical reactions and pathways involving collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%)." [GOC:mah, ISBN:0198506732] + collagen metabolic process + + + GO:macromolecular complex disassembly + cellular macromolecular complex disassembly + GO:0032984 + cellular macromolecule complex disassembly + macromolecule complex disassembly + "The disaggregation of a macromolecular complex into its constituent components." [GOC:mah] + macromolecular complex disassembly + + + GO:protein-DNA complex disassembly + "The disaggregation of a protein-DNA complex into its constituent components." [GOC:mah] + DNA-protein complex disassembly + protein-DNA complex disassembly + GO:0032986 + + + cellular component morphogenesis + cellular structure morphogenesis + GO:cellular component morphogenesis + GO:0032989 + "The process in which cellular structures, including whole cells or cell parts, are generated and organized." [GOC:dph, GOC:mah, GOC:tb] + + + GO:0032990 + GO:cell part morphogenesis + "The process in which the anatomical structures of a cell part are generated and organized." [GOC:mah] + cell part morphogenesis + + + GO:0032991 + GO:macromolecular complex + "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together." [GOC:mah] + macromolecule complex + macromolecular complex + + + GO:protein-DNA complex + GO:0032993 + protein-DNA complex + DNA-protein complex + "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] + + + macromolecule localisation + GO:macromolecule localization + macromolecule localization + "Any process in which a macromolecule is transported to, or maintained in, a specific location." [GOC:mah] + GO:0033036 + + + GO:regulation of organelle organization + regulation of organelle organization and biogenesis + "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle." [GOC:mah] + regulation of organelle organisation + regulation of organelle organization + GO:0033043 + + + CAF-1 complex + chromatin assembly factor 1 complex + "A conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair; specifically facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). In many species the CAF-1 subunits are designated p150, p60, and p48." [PMID:17065558, PMID:17083276] + GO:CAF-1 complex + GO:0033186 + + + DNA helicase complex + "A protein complex that possesses DNA helicase activity." [GOC:mah] + GO:DNA helicase complex + GO:0033202 + + + GO:0033256 + "A protein complex containing an inhibitory-kappaB (I-kappaB/IKB) protein and one or more copies of an NF-kappaB protein. In the resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm." [GOC:bf, GOC:mah, PMID:9407099] + I-kappaB/NF-kappaB complex + GO:I-kappaB/NF-kappaB complex + + + nuclear cell cycle DNA replication + DNA replication during S phase + DNA replication involved in S-phase + DNA replication involved in S phase + "The DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle." [GOC:mtg_cell_cycle] + nuclear DNA replication + GO:nuclear DNA replication + GO:0033260 + + + GO:0033267 + axon part + "A part of an axon, a cell projection of a neuron." [GOC:jl] + GO:axon part + + + "A cell cycle checkpoint that ensures accurate chromosome replication and segregation by preventing progression through a meiotic cell cycle until conditions are suitable for the cell to proceed to the next stage." [GOC:mtg_cell_cycle] + meiotic cell cycle checkpoint + GO:0033313 + GO:meiotic cell cycle checkpoint + + + GO:carbohydrate homeostasis + carbohydrate homeostasis + GO:0033500 + "A homeostatic process involved in the maintenance of an internal steady state of a carbohydrate within an organism or cell." [GOC:mah] + + + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] + GO:cellular response to stress + GO:0033554 + cellular response to stress + + + GO:multicellular organismal response to stress + "Any process that results in a change in state or activity of a multicellular organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] + GO:0033555 + multicellular organismal response to stress + + + "The multiplication or reproduction of mammary gland epithelial cells, resulting in the expansion of a cell population. Mammary gland epithelial cells make up the covering of surfaces of the mammary gland. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk." [GOC:dph, GOC:mah] + GO:mammary gland epithelial cell proliferation + GO:0033598 + mammary gland epithelial cell proliferation + + + GO:0033674 + upregulation of kinase activity + "Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] + up-regulation of kinase activity + up regulation of kinase activity + GO:positive regulation of kinase activity + positive regulation of kinase activity + + + homotypic cell-cell adhesion + GO:0034109 + GO:homotypic cell-cell adhesion + "The attachment of a cell to a second cell of the identical type via adhesion molecules." [GOC:add] + + + toll-like receptor 5 signaling pathway + GO:0034146 + GO:toll-like receptor 5 signaling pathway + toll-like receptor 5 signalling pathway + TLR5 signaling pathway + "Any series of molecular signals generated as a consequence of binding to toll-like receptor 5." [GOC:add, PMID:16551253, PMID:17328678] + + + beta-amyloid polypeptide formation from APP + "The generation of beta-amyloid by cleavage of the amyloid precursor protein (APP)." [GOC:mah] + beta-amyloid polypeptide formation from amyloid precursor protein + beta-amyloid formation + GO:0034205 + GO:beta-amyloid formation + + + "A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC:mah] + ion transmembrane transport + GO:ion transmembrane transport + transmembrane ion transport + GO:0034220 + ion membrane transport + + + GO:regulation of cellular amide metabolic process + GO:0034248 + regulation of cellular amide metabolic process + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides." [GOC:mah] + regulation of amide metabolism + + + cell junction assembly + GO:0034329 + GO:cell junction assembly + "A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction." [GOC:mah] + + + cell junction organization + GO:0034330 + cell junction assembly and maintenance + GO:cell junction organization + cell junction organisation + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix." [GOC:dph, GOC:jl, GOC:mah] + cell junction biogenesis + + + adherens junction organization + GO:0034332 + adherens junction organisation + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments." [GOC:dph, GOC:jl, GOC:mah] + GO:adherens junction organization + adherens junction assembly and maintenance + + + GO:0034333 + "The aggregation, arrangement and bonding together of a set of components to form an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments." [GOC:mah] + adherens junction assembly + adherens junction formation + GO:adherens junction assembly + + + nuclear periphery + "The portion of the nuclear lumen proximal to the inner nuclear membrane." [GOC:krc, GOC:mah] + GO:nuclear periphery + GO:0034399 + + + "The removal of one or more electrons from a lipid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydrogen." [GOC:BHF, GOC:mah] + GO:lipid oxidation + GO:0034440 + lipid oxidation + + + GO:0034613 + cellular protein localization + GO:cellular protein localization + "Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GOC:mah] + cellular protein localisation + + + "The aggregation, arrangement and bonding together of a set of macromolecules to form a complex, carried out at the cellular level." [GOC:mah] + cellular macromolecular complex assembly + cellular macromolecule complex assembly + GO:cellular macromolecular complex assembly + GO:0034622 + + + cellular nitrogen compound metabolism + "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah] + GO:0034641 + GO:cellular nitrogen compound metabolic process + cellular nitrogen compound metabolic process + + + cellular macromolecule anabolism + "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells." [CHEBI:33694, GOC:mah] + GO:0034645 + cellular macromolecule biosynthetic process + GO:cellular macromolecule biosynthetic process + cellular macromolecule formation + cellular macromolecule synthesis + cellular macromolecule biosynthesis + cellular biopolymer biosynthetic process + + + GO:nucleobase-containing compound biosynthetic process + nucleobase, nucleoside, nucleotide and nucleic acid anabolism + nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis + nucleobase-containing compound biosynthetic process + GO:0034654 + "The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah] + nucleobase, nucleoside, nucleotide and nucleic acid formation + + + nucleobase, nucleoside, nucleotide and nucleic acid catabolic process + nucleobase-containing compound catabolic process + nucleobase, nucleoside, nucleotide and nucleic acid breakdown + GO:0034655 + nucleobase, nucleoside, nucleotide and nucleic acid degradation + GO:nucleobase-containing compound catabolic process + nucleobase, nucleoside, nucleotide and nucleic acid catabolism + "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah] + + + alpha6-beta1 integrin complex + "An integrin complex that comprises one alpha6 subunit and one beta1 subunit." [PMID:12297042] + GO:integrin alpha6-beta1 complex + VLA-6 complex + integrin alpha6-beta1 complex + GO:0034675 + + + GO:integrin alphav-beta3 complex + "An integrin complex that comprises one alphav subunit and one beta3 subunit." [PMID:12297042] + alphav-beta3 integrin complex + GO:0034683 + integrin alphav-beta3 complex + + + GO:integrin alphaM-beta2 complex + GO:0034688 + alphaM-beta2 integrin complex + integrin alphaM-beta2 complex + "An integrin complex that comprises one alphaM subunit and one beta2 subunit." [PMID:12297042] + + + ion channel complex + GO:ion channel complex + GO:0034702 + "A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient." [GOC:mah, ISBN:071673706X] + + + "An ion channel complex through which cations pass." [GOC:mah] + GO:cation channel complex + cation channel complex + GO:0034703 + + + potassium channel complex + GO:0034705 + "An ion channel complex through which potassium ions pass." [GOC:mah] + GO:potassium channel complex + + + GO:methyltransferase complex + methyltransferase complex + "A protein complex that possesses methyltransferase activity." [GOC:mah] + GO:0034708 + + + GO:nucleosome organization + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of one or more nucleosomes." [GOC:mah] + GO:0034728 + nucleosome organization + nucleosome organisation + + + histone H4K20me + histone H4 K20 methylation + GO:histone H4-K20 methylation + histone H4-K20 methylation + GO:0034770 + histone lysine H4 K20 methylation + "The modification of histone H4 by addition of one or more methyl groups to lysine at position 20 of the histone." [GOC:mah] + + + GO:histone H4-K20 dimethylation + histone H4-K20 dimethylation + "The modification of histone H4 by addition of two methyl groups to lysine at position 20 of the histone." [GOC:mah] + GO:0034772 + histone lysine H4 K20 dimethylation + histone H4 K20 dimethylation + + + histone lysine H4 K20 trimethylation + histone H4-K20 trimethylation + "The modification of histone H4 by addition of three methyl groups to lysine at position 20 of the histone." [GOC:mah] + histone H4 K20 trimethylation + GO:0034773 + GO:histone H4-K20 trimethylation + + + GO:histone lysine methylation + histone lysine methylation + "The modification of a histone by addition of one or more methyl groups to a lysine residue." [GOC:mah, GOC:pr] + GO:0034968 + + + GO:0034982 + mitochondrial protein modification + "The peptide cleavage of mitochondrial proteins, including cleavage contributing to their import." [GOC:curators] + GO:mitochondrial protein processing + mitochondrial protein processing + + + GO:histone methyltransferase complex + "A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins." [GOC:bf] + histone methyltransferase complex + GO:0035097 + + + GO:ESC/E(Z) complex + ESC/E(Z) complex + PRC2 complex + "A multimeric protein complex that can methylate lysine-27 and lysine-9 residues of histone H3. In Drosophila the core subunits of the complex include ESC, E(Z), CAF1 (NURF-55) and SU(Z)12. In mammals the core subunits of the complex include EED, EZH2, SUZ12 and RBBP4." [GOC:bf, GOC:sp, PMID:12408863, PMID:12408864, PMID:20064375] + Extra Sex Combs/Enhancer of Zeste complex + GO:0035098 + + + GO:0035102 + GO:PRC1 complex + PRC1 complex + Polycomb repressive complex 1 + "A multiprotein complex that mediates monoubiquitination of lysine residues of histone H2A (lysine-118 in Drosophila or lysine-119 in mammals). The complex is required for stable long-term maintenance of transcriptionally repressed states and is involved in chromatin remodeling." [GOC:bf, PMID:10412979] + + + operant conditioning + GO:0035106 + GO:operant conditioning + "Learning to anticipate future events on the basis of past experience with the consequences of one's own behavior." [PMID:14662373] + instrumental conditioning + + + embryonic hematopoiesis + GO:embryonic hemopoiesis + GO:0035162 + embryonic haematopoiesis + embryonic haemopoiesis + embryonic hemopoiesis + "The stages of blood cell formation that take place within the embryo." [GOC:bf] + + + "Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation." [GOC:mah, PMID:15020054, PMID:15066275, PMID:15066283] + posttranscriptional gene silencing by RNA + GO:0035194 + sense-PTGS + GO:posttranscriptional gene silencing by RNA + RNA-mediated posttranscriptional gene silencing + + + GO:0035239 + GO:tube morphogenesis + tube morphogenesis + "The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." [GOC:bf, PMID:14624839] + + + GO:gonad morphogenesis + gonad morphogenesis + "The process in which the anatomical structures of the gonads are generated and organized. A gonad is an animal organ producing gametes, e.g. the testes or the ovary in mammals." [ISBN:0198612001] + GO:0035262 + + + GO:tube development + GO:0035295 + "The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts." [PMID:12526790] + tube development + + + GO:transcriptionally active chromatin + transcriptionally active chromatin + GO:0035327 + "The ordered and organized complex of DNA and protein that forms regions of the chromosome that are being actively transcribed." [GOC:sart, PMID:17965872] + + + GO:transcriptionally silent chromatin + transcriptionally inactive chromatin + transcriptionally silent chromatin + GO:0035328 + "The ordered and organized complex of DNA and protein that forms regions of the chromosome that are not being actively transcribed." [GOC:sart, PMID:17965872] + + + GO:0035376 + sterol import + "The directed movement of a sterol into a cell or organelle. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC:bf, PMID:19793923] + GO:sterol import + sterol influx + sterol uptake + + + sterol transmembrane transport + GO:sterol transmembrane transport + sterol membrane transport + "The directed movement of a sterol across a membrane into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC:vw] + GO:0035382 + + + "Signaling between cells of the same type. The signal produced by the signaling cell binds to a receptor on, and affects a cell of the same type." [GOC:bf, ISBN:3527303782] + autocrine signalling + GO:autocrine signaling + autocrine signaling + GO:0035425 + + + protein-endoplasmic reticulum retention + protein-ER retention + retention of protein in ER + maintenance of protein localization in endoplasmic reticulum + GO:maintenance of protein localization in endoplasmic reticulum + maintenance of protein location in endoplasmic reticulum + maintenance of protein location in ER + retention of protein in endoplasmic reticulum + maintenance of protein localisation in endoplasmic reticulum + GO:0035437 + maintenance of protein localization in ER + "Any process in which a protein is maintained in the endoplasmic reticulum and prevented from moving elsewhere. These include sequestration within the endoplasmic reticulum, protein stabilization to prevent transport elsewhere and the active retrieval of proteins that escape the endoplasmic reticulum." [GOC:bf, GOC:vw] + + + intracellular signaling pathway + intracellular signaling cascade + GO:intracellular signal transduction + "The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell." [GOC:bf, GOC:jl, GOC:signaling, ISBN:3527303782] + signal transduction via intracellular signaling cascade + intracellular signaling chain + GO:0035556 + intracellular signal transduction + + + GO:protein deacylation + GO:0035601 + protein deacylation + "The removal of an acyl group, any group or radical of the form RCO- where R is an organic group, from a protein amino acid." [GOC:se, PMID:12080046] + protein amino acid deacylation + + + PDGFR-alpha signaling pathway + alphaPDGF receptor signaling pathway + "A series of molecular signals initiated by the binding of a ligand to an alpha-type platelet-derived growth factor receptor (PDGFalpha) on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:yaf, PMID:10372961, PR:000002030] + PDGF receptor-alpha signaling pathway + GO:platelet-derived growth factor receptor-alpha signaling pathway + GO:0035790 + platelet-derived growth factor receptor-alpha signaling pathway + platelet-derived growth factor receptor-alpha signalling pathway + + + platelet-derived growth factor receptor-beta signalling pathway + "A series of molecular signals initiated by the binding of a ligand to a beta-type platelet-derived growth factor receptor (PDGFbeta) on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:signaling, GOC:yaf, PMID:10372961, PR:000002035] + betaPDGF receptor signaling pathway + PDGFR-beta signaling pathway + GO:0035791 + GO:platelet-derived growth factor receptor-beta signaling pathway + platelet-derived growth factor receptor-beta signaling pathway + PDGF receptor-beta signaling pathway + + + "A DNA recombination process that results in the unidirectional transfer of genetic material from a donor sequence to a highly homologous acceptor." [GOC:mah, PMID:17846636] + gene conversion + GO:0035822 + GO:gene conversion + + + "A DNA recombination process that results in the equal exchange of genetic material between the recombining DNA molecules." [GOC:mah, PMID:11139492, PMID:17304215] + chromosomal crossover + GO:0035825 + reciprocal DNA recombination + GO:reciprocal DNA recombination + + + glial cell-derived neurotrophic factor receptor signalling pathway + glial cell line-derived neurotrophic factor receptor signalling pathway + glial cell derived neurotrophic factor receptor signaling pathway + GO:glial cell-derived neurotrophic factor receptor signaling pathway + "The series of molecular signals generated as a consequence of a glial cell-derived neurotrophic factor receptor binding to one of its physiological ligands." [GOC:yaf, PMID:12953054] + glial cell-derived neurotrophic factor receptor signaling pathway + GDNF receptor signaling pathway + GO:0035860 + + + nucleotide-binding domain, leucine rich repeat containing receptor signal transduction pathway + NLR signaling pathway + nucleotide-binding domain leucine-rich repeat containing receptor signaling pathway + nucleotide-binding domain, leucine rich repeat containing receptor signalling pathway + NOD-like receptor signaling pathway + "A series of molecular signals generated as a consequence of a nucleotide-binding domain, leucine rich repeat containing receptor (NLR) binding to one of its physiological ligands. NLRs are cytoplasmic receptors defined by their tripartite domain architecture that contains: a variable C-terminus, a middle nucleotide-binding domain, and a LRR domain that is variable in the repeats composition and number. The NLR signaling pathway begins with binding of a ligand to a NLR receptor and ends with regulation of a downstream cellular process." [GOC:sj, PMID:18280719, Reactome:168643] + GO:0035872 + GO:nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway + nucleotide-binding domain, leucine rich repeat containing receptor signal transduction + nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway + + + "A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport." [GOC:cilia, GOC:clt, PMID:21750193] + microtubule basal body + GO:ciliary basal body + cilium basal body + GO:0036064 + ciliary basal body + cilial basal body + + + indirect ossification + "Ossification that requires the replacement of a preexisting tissue prior to bone tissue formation." [GO_REF:0000034] + GO:replacement ossification + GO:0036075 + replacement ossification + + + response to platelet-derived growth factor + response to PDGF stimulus + GO:0036119 + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a platelet-derived growth factor stimulus." [GOC:yaf] + response to platelet-derived growth factor stimulus + GO:response to platelet-derived growth factor + + + GO:0036120 + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a platelet-derived growth factor stimulus." [GOC:yaf] + cellular response to PDGF stimulus + GO:cellular response to platelet-derived growth factor stimulus + cellular response to platelet-derived growth factor stimulus + + + histone H3-K9 dimethylation + GO:histone H3-K9 dimethylation + histone lysine H3 K9 dimethylation + histone H3 K9 dimethylation + "The modification of histone H3 by addition of two methyl groups to lysine at position 9 of the histone." [GOC:vw] + GO:0036123 + + + "The modification of histone H3 by addition of three methyl groups to lysine at position 9 of the histone." [GOC:vw] + histone H3-K9 trimethylation + GO:histone H3-K9 trimethylation + GO:0036124 + + + sperm cilium + GO:0036126 + GO:sperm flagellum + sperm tail + sperm flagellum + "A microtubule-based flagellum (or cilium) that is part of a sperm, a mature male germ cell that develops from a spermatid." [GOC:cilia, GOC:sart, PMID:8441407] + + + protein modification + "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:bf, GOC:jl] + GO:protein modification process + protein modification process + GO:0036211 + + + GO:0036268 + "Self-propelled movement of an organism from one location to another through water, often by means of active fin movement." [GOC:cvs, PMID:22459995] + GO:swimming + swimming + + + "The specific behavior of an organism that combines cognitive functions and physical movement. For example, driving a car, throwing a ball, or playing a musical instrument." [GOC:nhn, GOC:pr, PMID:17159989, Wikipedia:Psychomotor_learning] + GO:0036343 + GO:psychomotor behavior + psychomotor behavior + + + light adaption + "The ability of a photoreceptor to adjust to varying levels of light." [GOC:gap, PMID:16039565] + GO:light adaption + GO:0036367 + + + "A protein-DNA complex that forms at the origin of replication during the initial step of DNA replication and allows the origin to become competent, or 'licensed', for replication." [GOC:bf, GOC:bhm, GOC:jh2, Wikipedia:Pre-replication_complex] + pre-replication complex + GO:pre-replicative complex + pre-replicative complex + pre-RC + GO:0036387 + + + growth factor complex + GO:0036454 + GO:growth factor complex + "A protein complex that has growth factor activity." [GOC:bm] + + + "The transfer of information from one cell to another, where the signal travels from the signal-producing cell to the receiving cell by passive diffusion or bulk flow in intercellular fluid. The signaling cell and the receiving cell are usually in the vicinity of each other." [GOC:mtg_signaling_feb11, ISBN:3527303782] + paracrine signaling + GO:0038001 + paracrine signalling + GO:paracrine signaling + + + nodal signalling pathway + nodal signaling + nodal signaling pathway + "A series of molecular signals initiated by the binding of a nodal protein to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:vk, PMID:17287255] + GO:0038092 + GO:nodal signaling pathway + + + "A series of molecular signals initiated by the binding of interleukin-7 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling] + GO:0038111 + interleukin-7-mediated signaling pathway + interleukin-7-mediated signalling pathway + IL-7-mediated signaling pathway + GO:interleukin-7-mediated signaling pathway + + + neurotrophin signaling pathway + GO:neurotrophin signaling pathway + neurotrophin receptor signaling pathway + GO:0038179 + "A series of molecular signals initiated by the binding of a neurotrophin to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Neurotrophins are a family of secreted growth factors that induce the survival, development, and function of neurons." [GOC:bf, GOC:jc, GOC:signaling, PMID:17466268, PR:000021998, Wikipedia:Neurotrophin] + + + GO:growth + GO:0040007 + growth + non-developmental growth + growth pattern + "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma] + + + GO:regulation of growth + GO:0040008 + "Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development." [GOC:ems, GOC:mah] + regulation of growth + + + locomotion + GO:locomotion + GO:0040011 + "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh] + + + regulation of locomotion + GO:0040012 + GO:regulation of locomotion + "Any process that modulates the frequency, rate or extent of locomotion of a cell or organism." [GOC:ems] + + + GO:embryonic cleavage + GO:0040016 + embryonic cleavage + "The first few specialized divisions of an activated animal egg." [GOC:clt, ISBN:0070524300] + + + GO:regulation of meiotic nuclear division + "Any process that modulates the frequency, rate or extent of meiosis, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes." [GOC:ems, GOC:ma] + regulation of meiotic nuclear division + GO:0040020 + + + "Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence." [PMID:10521337, PMID:11498582] + regulation of gene expression, epigenetic + GO:regulation of gene expression, epigenetic + GO:0040029 + + + regulation of FGF receptor signaling pathway + regulation of FGF receptor signalling pathway + regulation of FGFR signaling pathway + GO:0040036 + GO:regulation of fibroblast growth factor receptor signaling pathway + regulation of fibroblast growth factor receptor signaling pathway + "Any process that modulates the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity." [GOC:go_curators] + + + GO:0042044 + GO:fluid transport + "The directed movement of substances that are in liquid form in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + fluid transport + + + olfactory behaviour + behavioural response to scent + behavioural response to smell + GO:0042048 + behavioral response to scent + behavioral response to smell + "The behavior of an organism in response to an odor." [GOC:jid, GOC:pr] + GO:olfactory behavior + behavioural response to odour + olfactory behavior + + + GO:0042052 + "The assembly and arrangement of a rhabdomere within a cell. The rhabdomere is the organelle on the apical surface of a photoreceptor cell that contains the visual pigments." [PMID:3076112, PMID:3937883] + rhabdomere organization + GO:rhabdomere development + rhabdomere development + + + intraflagellar transport involved in cilium organization + intraciliary transport + intraflagellar transport involved in microtubule-based flagellum organisation + intraflagellar transport + "The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins." [GOC:cilia, GOC:kmv, PMID:17981739, PMID:18180368, PMID:22869374] + GO:0042073 + GO:intraciliary transport + + + GO:T-helper 1 type immune response + GO:0042088 + Th1 immune response + "An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin." [GOC:add, ISBN:0781735149] + T-helper 1 type immune response + + + T lymphocyte receptor complex + T-cell receptor complex + "A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains." [GOC:mah, ISBN:0781735149] + TCR + GO:T cell receptor complex + T cell receptor complex + GO:0042101 + T-lymphocyte receptor complex + TCR complex + + + T-lymphocyte activation + "The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [GOC:mgi_curators, ISBN:0781735140] + T lymphocyte activation + T-cell activation + T cell activation + GO:T cell activation + GO:0042110 + + + GO:macrophage activation + GO:0042116 + "A change in morphology and behavior of a macrophage resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, ISBN:0781735149, PMID:14506301] + macrophage activation + + + "Any process that modulates the frequency, rate or extent of cell proliferation." [GOC:jl] + GO:0042127 + regulation of cell proliferation + GO:regulation of cell proliferation + + + displacement loop formation + D-loop formation + D-loop biosynthesis + displacement loop biosynthesis + "The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules." [GOC:elh, PMID:10357855] + GO:0042148 + Rad51-mediated strand invasion + strand invasion + GO:strand invasion + + + lipoprotein metabolism + "The chemical reactions and pathways involving any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids." [ISBN:0198506732] + GO:0042157 + lipoprotein metabolic process + GO:lipoprotein metabolic process + + + lipoprotein biosynthetic process + lipoprotein anabolism + GO:0042158 + lipoprotein biosynthesis + GO:lipoprotein biosynthetic process + lipoprotein formation + "The chemical reactions and pathways resulting in the formation of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids." [ISBN:0198506732] + lipoprotein synthesis + + + response to chemical stimulus + response to chemical + GO:0042221 + GO:response to chemical + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus." [GOC:jl] + response to chemical substance + + + GO:tissue regeneration + tissue regeneration + "The regrowth of lost or destroyed tissues." [GOC:curators] + GO:0042246 + + + GO:purine nucleoside metabolic process + purine nucleoside metabolic process + GO:0042278 + "The chemical reactions and pathways involving one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside)." [GOC:jl, ISBN:0140512713] + purine nucleoside metabolism + + + "The periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin, etc." [GOC:jl, ISBN:0198506732] + molting cycle + GO:molting cycle + GO:0042303 + + + regulation of phosphorylation + "Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule." [GOC:jl] + GO:regulation of phosphorylation + GO:0042325 + + + up regulation of phosphorylation + "Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule." [GOC:jl] + upregulation of phosphorylation + positive regulation of phosphorylation + GO:0042327 + GO:positive regulation of phosphorylation + up-regulation of phosphorylation + + + GO:0042330 + GO:taxis + directed movement in response to stimulus + "The directed movement of a motile cell or organism in response to an external stimulus." [GOC:jl, ISBN:0192801023] + taxis + + + ciliogenesis + microtubule-based flagellum assembly + GO:cilium assembly + GO:0042384 + "The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732] + cilium assembly + cilium biogenesis + + + GO:regulation of membrane potential + GO:0042391 + "Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732] + regulation of membrane potential + + + cellular modified amino acid biosynthesis + cellular amino acid derivative anabolism + cellular modified amino acid synthesis + "The chemical reactions and pathways resulting in the formation of compounds derived from amino acids, organic acids containing one or more amino substituents." [CHEBI:83821, GOC:ai] + cellular modified amino acid formation + cellular modified amino acid biosynthetic process + cellular amino acid derivative biosynthesis + cellular amino acid derivative biosynthetic process + cellular modified amino acid anabolism + cellular amino acid derivative synthesis + GO:0042398 + amino acid derivative biosynthetic process + cellular amino acid derivative formation + GO:cellular modified amino acid biosynthetic process + + + melanin biosynthesis + "The chemical reactions and pathways resulting in the formation of melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom." [CHEBI:25179, GOC:curators] + melanin anabolism + melanin synthesis + GO:melanin biosynthetic process + melanin formation + melanin biosynthetic process + GO:0042438 + + + GO:0042440 + pigment metabolic process + "The chemical reactions and pathways involving pigment, any general or particular coloring matter in living organisms, e.g. melanin." [GOC:jl, ISBN:0198506732] + GO:pigment metabolic process + pigment metabolism + + + GO:hormone metabolic process + GO:0042445 + hormone metabolism + "The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." [CHEBI:24621, GOC:jl] + hormone metabolic process + + + hormone biosynthetic process + hormone anabolism + "The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." [CHEBI:24621, GOC:jl] + hormone formation + GO:hormone biosynthetic process + GO:0042446 + hormone biosynthesis + hormone synthesis + + + GO:0042451 + purine nucleoside anabolism + purine nucleoside biosynthetic process + GO:purine nucleoside biosynthetic process + purine nucleoside synthesis + purine nucleoside formation + purine nucleoside biosynthesis + "The chemical reactions and pathways resulting in the formation of any purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside)." [GOC:go_curators] + + + ribonucleoside anabolism + GO:0042455 + ribonucleoside biosynthesis + ribonucleoside formation + ribonucleoside biosynthetic process + GO:ribonucleoside biosynthetic process + ribonucleoside synthesis + "The chemical reactions and pathways resulting in the formation of any ribonucleoside, a nucleoside in which purine or pyrimidine base is linked to a ribose (beta-D-ribofuranose) molecule." [CHEBI:18254, GOC:jl] + + + GO:0042461 + GO:photoreceptor cell development + "Development of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light." [GOC:go_curators] + photoreceptor morphogenesis + photoreceptor cell development + + + GO:0042462 + GO:eye photoreceptor cell development + eye photoreceptor cell development + "Development of a photoreceptor, a sensory cell in the eye that reacts to the presence of light. They usually contain a pigment that undergoes a chemical change when light is absorbed, thus stimulating a nerve." [GOC:jl, ISBN:0192800981] + + + "A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells." [GOC:jl, PMID:11584301] + melanosome + GO:0042470 + GO:melanosome + + + neuron maturation + GO:neuron maturation + GO:0042551 + "A developmental process, independent of morphogenetic (shape) change, that is required for a neuron to attain its fully functional state." [GOC:dph, GOC:jl] + + + mini-chromosome maintenance complex + MCM complex + GO:MCM complex + GO:0042555 + "A hexameric protein complex required for the initiation and regulation of DNA replication." [GOC:jl, PMID:11282021] + + + immunoglobulin complex, circulating + antibody + GO:0042571 + "An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component." [GOC:add, ISBN:0781735149] + GO:immunoglobulin complex, circulating + + + GO:microbody + microbody + "Cytoplasmic organelles, spherical or oval in shape, that are bounded by a single membrane and contain oxidative enzymes, especially those utilizing hydrogen peroxide (H2O2)." [ISBN:0198506732] + GO:0042579 + + + GO:0042583 + GO:chromaffin granule + chromaffin granule + "Specialized secretory vesicle found in the cells of adrenal glands and various other organs, which is concerned with the synthesis, storage, metabolism, and secretion of epinephrine and norepinephrine." [GOC:jl, PMID:19158310, PMID:1961743] + + + homeostasis + GO:0042592 + homeostatic process + GO:homeostatic process + "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172] + + + GO:0042593 + glucose homeostasis + "Any process involved in the maintenance of an internal steady state of glucose within an organism or cell." [GOC:go_curators] + GO:glucose homeostasis + + + GO:MHC protein complex + "A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen." [GOC:add, GOC:jl, ISBN:0781735149, PMID:15928678, PMID:16153240] + MHC protein complex + GO:0042611 + + + "A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen." [GOC:add, GOC:jl, ISBN:0120781859, PMID:15928678] + GO:0042613 + GO:MHC class II protein complex + MHC class II protein complex + + + GO:0042622 + photoreceptor outer segment membrane + "The membrane surrounding the outer segment of a vertebrate photoreceptor." [GOC:jl] + GO:photoreceptor outer segment membrane + + + GO:0042632 + "Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell." [GOC:go_curators] + cholesterol homeostasis + GO:cholesterol homeostasis + + + GO:hair cycle + GO:0042633 + "The cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." [GOC:go_curators, PMID:12230507] + hair cycle + + + anagen + "The growth phase of the hair cycle. Lasts, for example, about 3 to 6 years for human scalp hair." [PMID:12230507] + GO:anagen + GO:0042640 + + + "The process in which a relatively unspecialized cell acquires the specialized features of a retinal cone cell." [GOC:go_curators] + retinal cone cell differentiation + GO:0042670 + GO:retinal cone cell differentiation + + + GO:0042671 + GO:retinal cone cell fate determination + "The process in which a cell becomes capable of differentiating autonomously into a retinal cone cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators] + retinal cone cell fate determination + + + "The process in which a relatively unspecialized cell acquires specialized features of a muscle cell." [CL:0000187, GOC:go_curators] + GO:muscle cell differentiation + muscle cell differentiation + GO:0042692 + + + muscle cell fate specification + "The process in which a cell becomes capable of differentiating autonomously into a muscle cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [CL:0000187, GOC:go_curators] + GO:muscle cell fate specification + GO:0042694 + + + GO:0042697 + "Cessation of menstruation, occurring in (e.g.) the human female usually around the age of 50." [GOC:curators, PMID:18495681] + menopause + GO:menopause + + + ovulation cycle + GO:0042698 + GO:ovulation cycle + "The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years." [ISBN:0721662544] + + + GO:fibrinolysis + GO:0042730 + "A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin." [GOC:jl, PMID:15842654] + fibrinolysis + + + GO:0042752 + regulation of circadian rhythm + "Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours." [GOC:dph, GOC:jl, GOC:tb] + GO:regulation of circadian rhythm + + + GO:0042755 + "The specific behavior of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue." [GOC:jl, GOC:pr, ISBN:01928006X] + eating behavior + eating behaviour + GO:eating behavior + + + GO:0042756 + drinking behavior + GO:drinking behavior + drinking behaviour + "The specific behavior of an organism relating to the intake of liquids, especially water." [GOC:curators, GOC:pr] + + + "A cascade of processes induced by the detection of DNA damage within a cell." [GOC:go_curators] + response to DNA damage stimulus by intracellular signaling cascade + GO:0042770 + GO:signal transduction in response to DNA damage + signal transduction in response to DNA damage + DNA damage response, signal transduction + + + amide transport + "The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, ISBN:0198506732] + GO:amide transport + GO:0042886 + + + GO:regulation of apoptotic process + GO:0042981 + apoptosis regulator activity + regulation of apoptotic process + "Any process that modulates the occurrence or rate of cell death by apoptotic process." [GOC:jl, GOC:mtg_apoptosis] + + + amyloid precursor protein metabolism + GO:0042982 + "The chemical reactions and pathways involving amyloid precursor protein (APP), the precursor of beta-amyloid, a glycoprotein associated with Alzheimer's disease." [GOC:go_curators] + amyloid precursor protein metabolic process + APP metabolic process + APP metabolism + GO:amyloid precursor protein metabolic process + + + "The chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of beta-amyloid, a glycoprotein associated with Alzheimer's disease." [GOC:go_curators] + amyloid precursor protein anabolism + GO:0042983 + amyloid precursor protein biosynthesis + amyloid precursor protein formation + GO:amyloid precursor protein biosynthetic process + APP biosynthesis + APP biosynthetic process + amyloid precursor protein biosynthetic process + amyloid precursor protein synthesis + + + GO:amyloid precursor protein catabolic process + APP catabolic process + APP catabolism + amyloid precursor protein degradation + amyloid precursor protein catabolism + amyloid precursor protein breakdown + "The chemical reactions and pathways resulting in the breakdown of amyloid precursor protein (APP), the precursor of beta-amyloid, a glycoprotein associated with Alzheimer's disease." [GOC:go_curators] + GO:0042987 + amyloid precursor protein catabolic process + + + "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] + GO:cell projection + cell projection + cellular projection + GO:0042995 + + + "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] + GO:0043005 + nerve fiber + neuron projection + neuronal cell projection + GO:neuron projection + neuron protrusion + neuron process + + + neuronal cell soma + "The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites." [GOC:go_curators] + GO:0043025 + GO:neuronal cell body + neuronal cell body + neuron cell body + + + peptide anabolism + peptide biosynthesis + GO:0043043 + peptide biosynthetic process + peptide synthesis + GO:peptide biosynthetic process + "The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide." [CHEBI:16670, GOC:dph, GOC:jl] + peptide formation + + + "Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process." [GOC:jl, GOC:mtg_apoptosis] + upregulation of apoptosis + pro-apoptosis + up regulation of apoptosis + up-regulation of apoptosis + positive regulation of apoptotic process + GO:0043065 + GO:positive regulation of apoptotic process + + + GO:regulation of programmed cell death + "Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] + GO:0043067 + regulation of programmed cell death + + + up-regulation of programmed cell death + up regulation of programmed cell death + GO:positive regulation of programmed cell death + positive regulation of programmed cell death + "Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] + GO:0043068 + upregulation of programmed cell death + + + GO:positive regulation of catalytic activity + GO:0043085 + upregulation of enzyme activity + positive regulation of catalytic activity + positive regulation of enzyme activity + up regulation of enzyme activity + "Any process that activates or increases the activity of an enzyme." [GOC:jl, GOC:tb] + up-regulation of enzyme activity + + + GO:receptor metabolic process + receptor metabolic process + GO:0043112 + "The chemical reactions and pathways involving a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:jl] + receptor metabolism + + + GO:receptor clustering + GO:0043113 + receptor clustering + "The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response." [GOC:bf, GOC:jl, GOC:pr, PMID:19747931, PMID:21453460] + + + GO:proteasome-mediated ubiquitin-dependent protein catabolic process + proteasome pathway + proteasomal ubiquitin-dependent protein catabolic process + proteasomal ubiquitin-dependent protein breakdown + GO:0043161 + proteasome-mediated ubiquitin-dependent protein catabolic process + proteasomal ubiquitin-dependent protein catabolism + proteasomal pathway + "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome." [GOC:go_curators] + proteasomal processing + proteasomal ubiquitin-dependent protein degradation + + + macromolecule metabolic process + biopolymer metabolic process + GO:0043170 + "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [CHEBI:33694, GOC:mah] + macromolecule metabolism + GO:macromolecule metabolic process + + + synaptic bouton + GO:0043195 + "Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it." [GOC:dph, GOC:mc, GOC:nln, PMID:10218156, PMID:8409967] + terminal button + bouton + terminal bouton + presynaptic bouton + GO:terminal bouton + + + perikaryon + GO:0043204 + cell soma cytoplasm + GO:perikaryon + "The portion of the cell soma (cell body) that excludes the nucleus." [GOC:jl] + + + GO:organelle + organelle + "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:go_curators] + GO:0043226 + + + membrane-enclosed organelle + GO:0043227 + membrane-bounded organelle + "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] + GO:membrane-bounded organelle + + + non-membrane-enclosed organelle + "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] + GO:0043228 + non-membrane-bounded organelle + GO:non-membrane-bounded organelle + + + "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] + intracellular organelle + GO:0043229 + GO:intracellular organelle + + + "Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi." [GOC:jl, PMID:9914479] + extracellular organelle + GO:0043230 + GO:extracellular organelle + + + GO:0043231 + intracellular membrane-enclosed organelle + intracellular membrane-bounded organelle + "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] + GO:intracellular membrane-bounded organelle + + + intracellular non-membrane-enclosed organelle + GO:0043232 + intracellular non-membrane-bounded organelle + GO:intracellular non-membrane-bounded organelle + "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] + + + organelle lumen + GO:0043233 + "The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen." [GOC:jl, GOC:mah] + GO:organelle lumen + + + protein-protein complex + "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical." [GOC:go_curators, http://www.ebi.ac.uk/intact/complex/documentation/] + protein complex + GO:0043234 + GO:protein complex + + + "Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:go_curators] + GO:0043235 + GO:receptor complex + receptor complex + + + GO:0043241 + "The disaggregation of a protein complex into its constituent components. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups." [GOC:jl] + GO:protein complex disassembly + protein complex disassembly + + + negative regulation of protein complex disassembly + "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components." [GOC:jl] + GO:0043242 + down regulation of protein complex disassembly + downregulation of protein complex disassembly + GO:negative regulation of protein complex disassembly + down-regulation of protein complex disassembly + + + GO:regulation of protein complex disassembly + GO:0043244 + regulation of protein complex disassembly + "Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components." [GOC:jl] + + + GO:0043256 + "A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha, beta and gamma. Provides an integral part of the structural scaffolding of basement membranes." [GOC:jl, http://www.sdbonline.org/fly/newgene/laminna1.htm, PMID:10842354] + GO:laminin complex + laminin complex + + + GO:0043277 + efferocytosis + GO:apoptotic cell clearance + apoptotic cell clearance + "The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte." [GOC:rk, PMID:14685684] + apoptotic cell removal + programmed cell clearance + + + contractile fiber + contractile fibre + GO:contractile fiber + GO:0043292 + "Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle." [GOC:go_curators, ISBN:0815316194] + + + "The process of assisting in the disassembly of non-covalent linkages in a protein or protein aggregate, often where the proteins are in a non-functional or denatured state." [GOC:mlg] + GO:protein unfolding + GO:0043335 + protein unfolding + + + regulation of MAP kinase activity + GO:0043405 + Regulation of MAPK activity + regulation of mitogen activated protein kinase activity + regulation of mitogen-activated protein kinase activity + GO:regulation of MAP kinase activity + "Any process that modulates the frequency, rate or extent of MAP kinase activity." [GOC:dph, GOC:go_curators] + + + GO:positive regulation of MAP kinase activity + positive regulation of mitogen activated protein kinase activity + GO:0043406 + up-regulation of MAPK activity + "Any process that activates or increases the frequency, rate or extent of MAP kinase activity." [GOC:dph, GOC:go_curators] + up regulation of MAPK activity + positive regulation of MAP kinase activity + upregulation of MAPK activity + positive regulation of mitogen-activated protein kinase activity + + + regulation of MAPKKK cascade + regulation of MAPK cascade + GO:0043408 + GO:regulation of MAPK cascade + regulation of mitogen-activated protein kinase cascade + regulation of mitogen-activated protein kinase kinase kinase cascade + "Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade." [GOC:go_curators] + regulation of mitogen activated protein kinase cascade + regulation of mitogen activated protein kinase kinase kinase cascade + regulation of MAP kinase kinase kinase cascade + regulation of MAP kinase cascade + + + positive regulation of MAP kinase cascade + positive regulation of MAP kinase kinase kinase cascade + GO:0043410 + positive regulation of mitogen-activated protein kinase cascade + upregulation of MAPKKK cascade + upregulation of MAPK cascade + positive regulation of mitogen-activated protein kinase kinase kinase cascade + positive regulation of MAPKKK cascade + up regulation of MAPKKK cascade + stimulation of MAPK cascade + positive regulation of mitogen activated protein kinase kinase kinase cascade + positive regulation of MAPK cascade + "Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade." [GOC:go_curators] + GO:positive regulation of MAPK cascade + up-regulation of MAPKKK cascade + up-regulation of MAPK cascade + + + GO:0043412 + macromolecule modification + GO:macromolecule modification + "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties." [GOC:go_curators] + + + GO:0043414 + "The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule." [GOC:go_curators] + macromolecule methylation + GO:macromolecule methylation + + + ketoacid metabolism + oxoacid metabolism + ketoacid metabolic process + GO:0043436 + keto acid metabolic process + GO:oxoacid metabolic process + oxo acid metabolic process + "The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons)." [CHEBI:24833] + oxoacid metabolic process + oxo acid metabolism + keto acid metabolism + + + GO:0043467 + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances." [GOC:jl] + regulation of generation of precursor metabolites and energy + GO:regulation of generation of precursor metabolites and energy + + + GO:regulation of carbohydrate catabolic process + GO:0043470 + regulation of carbohydrate catabolic process + "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates." [GOC:mlg] + + + "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates, carried out by individual cells." [GOC:jl] + regulation of cellular carbohydrate catabolic process + GO:0043471 + GO:regulation of cellular carbohydrate catabolic process + + + "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells." [GOC:jl] + pigmentation + GO:pigmentation + GO:0043473 + + + "Any process that modulates the frequency, rate or extent of RNA splicing, the process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA." [GOC:jl] + regulation of RNA splicing + GO:0043484 + GO:regulation of RNA splicing + + + AKT signal transduction + PKB signaling + protein kinase B signaling cascade + protein kinase B signalling cascade + PKB signalling cascade + AKT signaling + AKT signalling cascade + GO:0043491 + GO:protein kinase B signaling + "A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B (also called AKT), which occurs as a result of a single trigger reaction or compound." [GOC:bf, PMID:20517722] + protein kinase B signal transduction + AKT signaling cascade + PKB signal transduction + protein kinase B signaling + PKB signaling cascade + + + GO:protein anchor + GO:0043495 + "Interacting selectively and non-covalently with both a protein or protein complex and a membrane, in order to maintain the localization of the protein at a specific location on the membrane." [GOC:go_curators] + protein anchor + anchoring + + + muscle plasticity + muscle adaptation + GO:muscle adaptation + GO:0043500 + "A process in which muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." [GOC:mtg_muscle, PMID:11181628, PMID:11449884, PMID:12605307] + + + GO:skeletal muscle adaptation + skeletal muscle plasticity + "Any process in which skeletal muscles change their phenotypic profiles in response to altered functional demands and a variety of signals." [GOC:mtg_muscle, PMID:11181628, PMID:11449884, PMID:12605307] + GO:0043501 + skeletal muscle adaptation + + + GO:interleukin-12 complex + "A protein complex that is composed of an interleukin-12 alpha (p35, product of the IL12A gene) and an interleukin-12 beta subunit (p40, product of the IL12B gene) and is secreted into the extracellular space." [GOC:add, GOC:ebc, GOC:mah, PMID:12948519, PMID:1381512] + interleukin-12 complex + IL-12 complex + GO:0043514 + + + regulation of kinase activity + GO:0043549 + GO:regulation of kinase activity + "Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:bf] + + + regulation of respiratory gaseous exchange + "Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment." [GOC:jl] + GO:regulation of respiratory gaseous exchange + GO:0043576 + + + ear development + "The process whose specific outcome is the progression of the ear over time, from its formation to the mature structure. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals." [GOC:jl, ISBN:0192801023] + GO:0043583 + GO:ear development + hearing organ development + + + nasus development + GO:0043584 + GO:nose development + "The process whose specific outcome is the progression of the nose over time, from its formation to the mature structure. The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)." [GOC:jl, http://www.mercksource.com/] + nose development + + + skin development + "The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue." [GOC:jl, UBERON:0002097] + GO:skin development + animal skin development + GO:0043588 + + + GO:0043603 + "The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells." [CHEBI:32988] + amide metabolism + cellular amide metabolic process + GO:cellular amide metabolic process + + + "The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [CHEBI:32988] + amide biosynthetic process + GO:amide biosynthetic process + GO:0043604 + + + cellular protein complex assembly + "The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell." [GOC:jl] + GO:0043623 + GO:cellular protein complex assembly + + + GO:cellular protein complex disassembly + "The disaggregation of a protein complex into its constituent components, occurring at the level of an individual cell. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups." [GOC:jl] + cellular protein complex disassembly + GO:0043624 + + + GO:RNA polyadenylation + RNA polyadenylation + GO:0043631 + "The enzymatic addition of a sequence of adenylyl residues at the 3' end of an RNA molecule." [GOC:jl] + + + GO:modification-dependent macromolecule catabolic process + GO:0043632 + modification-dependent macromolecule catabolic process + "The chemical reactions and pathways resulting in the breakdown of a macromolecule, initiated by covalent modification of the target molecule." [GOC:jl] + + + dicarboxylic acid metabolic process + GO:0043648 + GO:dicarboxylic acid metabolic process + dicarboxylic acid metabolism + dicarboxylate metabolic process + "The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-)." [ISBN:0198506732] + dicarboxylate metabolism + + + dicarboxylic acid formation + GO:0043650 + dicarboxylic acid anabolism + dicarboxylate biosynthetic process + dicarboxylate biosynthesis + "The chemical reactions and pathways resulting in the formation of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups." [ISBN:0198506732] + dicarboxylic acid synthesis + GO:dicarboxylic acid biosynthetic process + dicarboxylic acid biosynthesis + dicarboxylic acid biosynthetic process + + + GO:engulfment of apoptotic cell + engulfment of apoptotic cell corpse + engulfment of cell corpse + GO:0043652 + engulfment of apoptotic cell + "The removal of the apoptotic cell by phagocytosis, by a neighboring cell or by a phagocyte." [GOC:rk, PMID:15536015] + + + nerve ending + "Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it." [GOC:dph, GOC:jl] + GO:0043679 + GO:axon terminus + axon terminus + axon terminal specialization + axon terminal + motor endplate + + + "The process in which a cell becomes capable of differentiating autonomously into a photoreceptor cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:mtg_sensu] + GO:photoreceptor cell fate determination + GO:0043703 + photoreceptor cell fate determination + + + macromolecular complex organization + macromolecular complex subunit organisation + macromolecular complex subunit organization + cellular macromolecular complex subunit organisation + GO:macromolecular complex subunit organization + "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a macromolecular complex." [GOC:mtg_mpo] + cellular macromolecular complex organization + GO:0043933 + cellular macromolecular complex subunit organization + + + GO:sporulation + sporulation + "The process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure. A spore is a structure that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction." [GOC:pamgo_curators] + GO:0043934 + + + glucan metabolic process + GO:glucan metabolic process + "The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues." [GOC:jl] + glucan metabolism + GO:0044042 + + + GO:0044057 + "Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system." [GOC:jl] + regulation of system process + GO:regulation of system process + + + GO:regulation of respiratory system process + GO:0044065 + "Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system." [GOC:jl] + regulation of respiratory system process + + + GO:cellular component biogenesis + cellular component biogenesis + "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] + GO:0044085 + cellular component biogenesis at cellular level + + + GO:membrane biogenesis + membrane biogenesis + "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane." [GOC:jl] + GO:0044091 + + + GO:positive regulation of molecular function + GO:0044093 + positive regulation of molecular function + "Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GO:jl] + + + GO:other organism + "A secondary organism with which the first organism is interacting." [GOC:jl] + other organism + GO:0044215 + + + single multicellular organismal metabolic process + GO:0044236 + "The chemical reactions and pathways in a single multicellular organism that occur at the tissue, organ, or organismal level. These processes, unlike cellular metabolism, can include transport of substances between cells when that transport is required." [GOC:go_curators] + multicellular organismal metabolism + GO:multicellular organismal metabolic process + multicellular organismal metabolic process + + + "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] + intermediary metabolism + GO:0044237 + GO:cellular metabolic process + cellular metabolic process + cellular metabolism + + + GO:primary metabolic process + GO:0044238 + primary metabolic process + primary metabolism + "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] + + + cellular lipid catabolism + cellular lipid catabolic process + GO:cellular lipid catabolic process + cellular lipid breakdown + "The chemical reactions and pathways resulting in the breakdown of lipids, as carried out by individual cells." [GOC:jl] + cellular lipid degradation + GO:0044242 + + + cellular polysaccharide breakdown + cellular polysaccharide degradation + cellular polysaccharide catabolic process + GO:0044247 + GO:cellular polysaccharide catabolic process + "The chemical reactions and pathways resulting in the breakdown of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, as carried out by individual cells." [CHEBI:18154, GOC:jl] + cellular polysaccharide catabolism + + + cellular degradation + cellular catabolic process + cellular catabolism + "The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:jl] + GO:cellular catabolic process + GO:0044248 + cellular breakdown + + + cellular biosynthesis + cellular anabolism + GO:cellular biosynthetic process + "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] + GO:0044249 + cellular biosynthetic process + cellular formation + cellular synthesis + + + cellular lipid metabolism + cellular lipid metabolic process + GO:0044255 + GO:cellular lipid metabolic process + "The chemical reactions and pathways involving lipids, as carried out by individual cells." [GOC:jl] + + + "The chemical reactions and pathways resulting in the breakdown of a protein by individual cells." [GOC:jl] + cellular protein degradation + cellular protein catabolism + GO:0044257 + cellular protein catabolic process + GO:cellular protein catabolic process + cellular protein breakdown + + + GO:multicellular organismal macromolecule metabolic process + GO:0044259 + multicellular organismal macromolecule metabolic process + organismal macromolecule metabolism + "The chemical reactions and pathways involving macromolecules, large molecules including proteins, nucleic acids and carbohydrates, in multicellular organisms occurring at the tissue, organ, or organismal level." [GOC:jl] + + + cellular biopolymer metabolic process + GO:cellular macromolecule metabolic process + cellular macromolecule metabolism + GO:0044260 + cellular macromolecule metabolic process + "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells." [CHEBI:33694, GOC:mah] + + + cellular carbohydrate metabolism + GO:0044262 + "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:jl] + GO:cellular carbohydrate metabolic process + cellular carbohydrate metabolic process + + + cellular glycan metabolic process + "The chemical reactions and pathways involving polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages, as carried out by individual cells." [GOC:jl] + GO:cellular polysaccharide metabolic process + cellular polysaccharide metabolism + cellular glycan metabolism + cellular polysaccharide metabolic process + GO:0044264 + + + "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells." [CHEBI:33694, GOC:jl] + cellular biopolymer catabolic process + cellular macromolecule catabolism + cellular macromolecule degradation + GO:0044265 + GO:cellular macromolecule catabolic process + cellular macromolecule catabolic process + cellular macromolecule breakdown + + + cellular protein metabolic process + GO:cellular protein metabolic process + GO:0044267 + "The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification." [GOC:jl] + cellular protein metabolism + + + GO:0044270 + GO:cellular nitrogen compound catabolic process + "The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds." [GOC:jl, ISBN:0198506732] + cellular nitrogen compound catabolic process + + + "The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds." [GOC:jl, ISBN:0198506732] + GO:cellular nitrogen compound biosynthetic process + GO:0044271 + cellular nitrogen compound biosynthetic process + + + GO:0044272 + sulfur compound formation + sulfur compound synthesis + sulfur compound biosynthesis + sulfur compound anabolism + "The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione." [GOC:jl] + sulfur compound biosynthetic process + GO:sulfur compound biosynthetic process + + + cellular carbohydrate catabolism + GO:cellular carbohydrate catabolic process + "The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:jl] + cellular carbohydrate catabolic process + cellular carbohydrate breakdown + cellular carbohydrate degradation + GO:0044275 + + + small molecule metabolic process + GO:0044281 + small molecule metabolism + "The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw] + GO:small molecule metabolic process + + + GO:small molecule catabolic process + "The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:vw] + GO:0044282 + small molecule catabolic process + small molecule catabolism + + + GO:0044283 + small molecule biosynthetic process + "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw] + small molecule biosynthesis + GO:small molecule biosynthetic process + + + GO:0044297 + cell soma + GO:cell body + "The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections." [GOC:go_curators] + cell body + + + GO:climbing fiber + GO:0044301 + climbing fibre + climbing fiber + "The axon of inferior olive neuron that projects to the cerebellar cortex, largely via the inferior cerebellar peduncle. They range in diameter from 1-3 um and are myelinated until they enter the granule cell layer. They give off collaterals to the deep cerebellar nuclei. They synapse extensively with the dendrites of Purkinje cells in the molecular layer, where each fiber branches repeatedly to \"climb\" along the Purkinje cell dendritic tree. Each Purkinje cell is innervated by only a single climbing fiber." [NIF_Subcellular:nlx_subcell_20090203] + + + neuron projection terminal + neuron terminal specialization + nerve terminal + "The specialized, terminal region of a neuron projection such as an axon or a dendrite." [GOC:jl] + neuron projection terminus + GO:0044306 + GO:neuron projection terminus + + + "A specialized axon terminus which is produced by retinal cone cells. Pedicles are large, conical, flat end-feet (8-10 micrometers diameter) of the retinal cone axon that lie more or less side by side on the same plane at the outer edge of the outer plexiform layer (OPL)." [http://webvision.med.utah.edu/photo2.html, PMID:10939333] + GO:cone cell pedicle + cone pedicle + cone cell pedicle + GO:0044316 + + + rod photoreceptor spherule + rod cell spherule + rod spherule + GO:0044317 + GO:rod spherule + "A specialized neuron projection which is the site of synaptic transmission produced by retinal rod cells. Rod spherules are small round enlargements of the axon (3-5 micrometers diameter) or even extensions of the cell body." [http://webvision.med.utah.edu/photo2.html] + + + "Any constituent part of the extracellular matrix, the structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals) or be part of the cell (as often seen in plants)." [GOC:jl] + GO:extracellular matrix component + GO:0044420 + extracellular matrix component + extracellular matrix part + + + GO:extracellular region part + GO:0044421 + extracellular structure + "Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite." [GOC:jl] + extracellular region part + + + organelle part + GO:0044422 + GO:organelle part + "Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane." [GOC:jl] + + + GO:intracellular part + GO:0044424 + intracellular part + "Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [GOC:jl] + + + "Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:jl] + GO:membrane part + membrane part + GO:0044425 + + + GO:chromosomal part + "Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [GOC:jl] + chromosomal part + GO:0044427 + chromosome part + chromosomal component + chromosome component + + + GO:nuclear part + nuclear part + nucleus component + nuclear subcomponent + "Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated." [GOC:jl] + GO:0044428 + + + "Any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [GOC:jl] + mitochondrial subcomponent + mitochondrial part + mitochondrion component + GO:0044429 + GO:mitochondrial part + + + cytoskeletal element + GO:0044430 + GO:cytoskeletal part + cytoskeletal part + "Any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice." [GOC:jl] + cytoskeleton component + + + Golgi subcomponent + Golgi apparatus part + GO:0044431 + Golgi component + "Any constituent part of the Golgi apparatus, a compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack." [GOC:jl] + GO:Golgi apparatus part + + + "Any constituent part of a vacuole, a closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material." [GOC:jl] + vacuolar part + GO:vacuolar part + GO:0044437 + vacuole component + + + GO:0044440 + endosomal part + endosome component + endosomal subcomponent + GO:endosomal part + "Any constituent part of an endosome, a membrane-bounded organelle to which materials ingested by endocytosis are delivered." [GOC:mah, PMID:19696797] + + + GO:0044441 + cilial part + "Any constituent part of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:cilia, GOC:jl] + ciliary part + GO:ciliary part + microtubule-based flagellum part + cilium part + + + GO:0044444 + cytoplasmic part + GO:cytoplasmic part + cytoplasm component + "Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [GOC:jl] + + + GO:0044446 + "A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane." [GOC:jl] + GO:intracellular organelle part + intracellular organelle part + + + GO:0044450 + GO:microtubule organizing center part + microtubule organizing center part + "Any constituent part of a microtubule organizing center, a region in a eukaryotic cell, such as a centrosome or basal body, from which microtubules grow." [GOC:jl] + MTOC component + microtubule organizing centre component + + + GO:nucleoplasm part + GO:0044451 + nucleoplasm part + "Any constituent part of the nucleoplasm, that part of the nuclear content other than the chromosomes or the nucleolus." [GOC:jl] + + + GO:0044452 + GO:nucleolar part + nucleolus component + "Any constituent part of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis." [GOC:jl] + nucleolar part + + + GO:0044454 + "Any constituent part of a nuclear chromosome, a chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact." [GOC:jl] + GO:nuclear chromosome part + nuclear chromosome part + + + GO:0044455 + GO:mitochondrial membrane part + mitochondrial membrane part + "Any constituent part of a mitochondrial membrane, either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope." [GOC:jl] + + + GO:0044456 + synapse part + synaptic component + GO:synapse part + "Any constituent part of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell." [GOC:jl] + + + plasma membrane part + "Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [GOC:jl] + GO:plasma membrane part + GO:0044459 + + + cell projection part + "Any constituent part of a cell projection, a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl] + GO:0044463 + GO:cell projection part + + + cellular subcomponent + GO:cell part + GO:0044464 + cell part + "Any constituent part of a cell, the basic structural and functional unit of all organisms." [GOC:jl] + protoplast + + + secondary metabolite biosynthetic process + GO:secondary metabolite biosynthetic process + secondary metabolite biosynthesis + GO:0044550 + "The chemical reactions and pathways resulting in the formation of secondary metabolites, the compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon." [GOC:jl] + + + "A biological process that involves only one organism." [GOC:jl] + GO:0044699 + GO:single-organism process + single-organism process + single organism process + + + single organism signaling + "A signaling process occurring within a single organism." [GOC:jl] + GO:single organism signaling + GO:0044700 + + + GO:single organism reproductive process + "A biological process that directly contributes to the process of producing new individuals, involving a single organism." [GOC:jl] + GO:0044702 + single organism reproductive process + + + GO:multi-organism reproductive process + "A biological process that directly contributes to the process of producing new individuals, involving another organism." [GOC:jl] + multi-organism reproductive process + GO:0044703 + + + "A multicellular organism process which involves another multicellular organism of the same or different species." [GOC:jl] + GO:0044706 + multi-multicellular organism process + GO:multi-multicellular organism process + + + "A biological process occurring within a single, multicellular organism." [GOC:jl] + GO:single-multicellular organism process + GO:0044707 + single-multicellular organism process + + + GO:single-organism behavior + single-organism behavior + GO:0044708 + "The specific behavior of a single organism in response to external or internal stimuli." [GOC:jl, GOC:pr] + + + GO:0044710 + single-organism metabolic process + GO:single-organism metabolic process + "A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism." [GOC:jl] + + + "A biosynthetic process - chemical reactions and pathways resulting in the formation of substances - involving a single organism." [GOC:jl] + GO:0044711 + GO:single-organism biosynthetic process + single-organism biosynthetic process + + + "A catabolic process - chemical reactions and pathways resulting in the breakdown of substances - which involves a single organism." [GOC:jl] + GO:single-organism catabolic process + GO:0044712 + single-organism catabolic process + + + "The chemical reactions and pathways involving carbohydrates, occurring within a single organism." [GOC:jl] + GO:single-organism carbohydrate metabolic process + single-organism carbohydrate metabolic process + GO:0044723 + + + GO:single-organism carbohydrate catabolic process + single-organism carbohydrate catabolic process + "The chemical reactions and pathways resulting in the breakdown of carbohydrates, occurring within a single organism." [GOC:jl] + GO:0044724 + + + DNA methylation or demethylation + GO:0044728 + GO:DNA methylation or demethylation + changes in DNA methylation + "The process of adding or removing a methyl group from one or more nucleotides within an DNA molecule." [GOC:jl] + + + autolysosome + GO:autolysosome + degrading autophagic vacuole + AVd + autophagolysosome + GO:0044754 + "A type of secondary lysosome in which a primary lysosome has fused with the outer membrane of an autophagosome. It is involved in the second step of autophagy in which it degrades contents with acidic lysosomal hydrolases." [GOC:sart, NIF_Subcellular:sao8444068431, PMID:19008921] + + + GO:single-organism cellular process + "Any process that is carried out at the cellular level, occurring within a single organism." [GOC:jl] + single-organism cellular process + GO:0044763 + + + multi-organism cellular process + GO:0044764 + "Any process that is carried out at the cellular level which involves another organism of the same or different species." [GOC:jl] + GO:multi-organism cellular process + + + "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism." [GOC:jl] + single-organism transport + GO:0044765 + GO:single-organism transport + + + GO:single-organism developmental process + GO:0044767 + "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism." [GOC:jl] + single-organism developmental process + + + cell cycle phase transition + cell cycle transition + GO:0044770 + "The cell cycle process by which a cell commits to entering the next cell cycle phase." [GOC:mtg_cell_cycle] + GO:cell cycle phase transition + + + "The cell cycle process by which a cell commits to entering the next mitotic cell cycle phase." [GOC:mtg_cell_cycle] + mitotic cell cycle phase transition + GO:mitotic cell cycle phase transition + GO:0044772 + + + microtubule-based flagellum organization + GO:cilium organization + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:jl] + cilium organization + GO:0044782 + + + GO:0044786 + cell cycle DNA replication + "The DNA-dependent DNA replication that takes place as part of the cell cycle." [GOC:mtg_cell_cycle] + GO:cell cycle DNA replication + + + nuclear transcription factor complex + GO:0044798 + GO:nuclear transcription factor complex + "A protein complex, located in the nucleus, that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription." [GOC:jl] + + + GO:single-organism membrane fusion + "The membrane organization process that joins two lipid bilayers to form a single membrane, involving only one organism." [GOC:jl] + GO:0044801 + single-organism membrane fusion + + + GO:single-organism membrane organization + single-organism membrane organization + GO:0044802 + "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane, involving only one organism." [GOC:jl] + + + DNA packaging complex + GO:DNA packaging complex + "A protein complex that plays a role in the process of DNA packaging." [GOC:jl] + GO:0044815 + + + GO:cell quiescence + "A specialized resting state that cells enter in response to cues from the cell's environment. Quiescence is characterized by the absence of cell growth and division, by a reprogramming of global gene expression, and by changes characteristic of the organism and specific cell type. Depending on external conditions, quiescence may persist until cell death or cells may resume cell growth and division. In some cell types or under certain conditions, cellular metabolism may proceed." [GOC:jb, GOC:mah] + cell quiescence + cell cycle quiescence + G0 phase + GO:0044838 + cellular quiescence + + + cell cycle G2/M phase transition + GO:cell cycle G2/M phase transition + "The cell cycle process by which a cell in G2 phase commits to M phase." [GOC:jl, GOC:mtg_cell_cycle] + GO:0044839 + + + biological phase + GO:biological phase + GO:0044848 + "A distinct period or stage in a biological process or cycle." [GOC:jl] + + + GO:estrous cycle + estrous cycle + GO:0044849 + "A type of ovulation cycle, which occurs in most mammalian therian females, where the endometrium is resorbed if pregnancy does not occur." [GOC:jl, Wikipedia:Estrous_cycle] + + + GO:0044851 + "The cyclical periods of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." [GOC:jl] + hair cycle phase + GO:hair cycle phase + + + "A membrane raft that is part of the plasma membrane." [GOC:jl] + GO:0044853 + GO:plasma membrane raft + plasma membrane raft + + + "The chemical reactions and pathways resulting in the formation of glycerolipids, any lipid with a glycerol backbone." [GOC:ai] + glycerolipid anabolism + glycerolipid biosynthetic process + glycerolipid formation + glycerolipid synthesis + GO:0045017 + GO:glycerolipid biosynthetic process + glycerolipid biosynthesis + + + "A process of exocytosis in which soluble proteins and other substances are initially stored in secretory vesicles for later release. It is found mainly in cells that are specialized for secreting products such as hormones, neurotransmitters, or digestive enzymes rapidly on demand." [GOC:mah, ISBN:0716731363] + GO:regulated exocytosis + regulated exocytosis + GO:0045055 + regulated secretory pathway + + + nonspecific immune response + innate immunity + "Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens." [GO_REF:0000022, GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu] + GO:0045087 + GO:innate immune response + innate immune response + + + GO:0045088 + GO:regulation of innate immune response + "Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection." [GOC:ebc] + regulation of innate immune response + + + up regulation of innate immune response + GO:0045089 + GO:positive regulation of innate immune response + "Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection." [GOC:ebc] + positive regulation of innate immune response + upregulation of innate immune response + up-regulation of innate immune response + + + "A filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells. The keratins are the most diverse classes of IF proteins, with a large number of keratin isoforms being expressed. Each type of epithelium always expresses a characteristic combination of type I and type II keratins." [ISBN:0716731363] + GO:keratin filament + acidic keratin + basic/neutral keratin + keratin filament + GO:0045095 + + + type III intermediate filament + GO:type III intermediate filament + GO:0045098 + "A type of intermediate filament, typically made up of one or more of the proteins vimentin, desmin, glial fibrillary acidic protein (GFAP), and peripherin. Unlike the keratins, the type III proteins can form both homo- and heteropolymeric IF filaments." [ISBN:0716731363] + + + "The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents." [ISBN:0198506732] + GO:0045120 + pronucleus + GO:pronucleus + + + GO:0045121 + "Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions." [PMID:16645198, PMID:20044567] + lipid raft + glycolipid-enriched membrane domain + GEM domain + membrane raft + GO:membrane raft + + + leukocyte cellular extravasation + cellular extravasation + transendothelial leukocyte migration + GO:0045123 + immune cell cellular extravasation + leucocyte cellular extravasation + GO:cellular extravasation + "The migration of a leukocyte from the blood vessels into the surrounding tissue." [GOC:jl] + + + meiotic chromosome segregation + "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle." [GOC:ai, GOC:mah] + GO:0045132 + GO:meiotic chromosome segregation + + + "The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field." [ISBN:0716731185] + cell fate commitment + GO:cell fate commitment + GO:0045165 + + + cell-cell signalling during cell fate commitment + cell-cell signalling resulting in cell fate commitment + cell-cell signaling involved in cell fate commitment + GO:cell-cell signaling involved in cell fate commitment + cell fate commitment, cell-cell signaling + cell-cell signaling resulting in cell fate commitment + "Signaling at long or short range between cells that results in the commitment of a cell to a certain fate." [GOC:dph, GOC:go_curators, GOC:tb] + GO:0045168 + cell-cell signaling during in cell fate commitment + cell fate commitment, cell-cell signalling + + + "The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue." [GOC:mah, ISBN:0815316194] + GO:apical part of cell + GO:0045177 + apical part of cell + + + basal part of cell + GO:basal part of cell + "The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue." [GOC:mah, ISBN:0185316194] + GO:0045178 + + + protein recruitment + establishment of protein localization + GO:0045184 + "The directed movement of a protein to a specific location." [GOC:bf] + establishment of protein localisation + protein positioning + GO:establishment of protein localization + + + maintenance of protein localization + GO:0045185 + "Any process in which a protein is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of proteins that do move away." [GOC:bf] + maintenance of protein location + GO:maintenance of protein location + + + electrotonic synapse + GO:synapse + "The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell; the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane." [ISBN:0198506732] + GO:0045202 + synaptic junction + synapse + + + GO:cell-cell junction organization + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] + GO:0045216 + intercellular junction assembly and maintenance + cell-cell junction biogenesis + cell-cell junction organisation + cell-cell junction organization + cell-cell junction assembly and maintenance + + + GO:tricarboxylic acid cycle enzyme complex + tricarboxylic acid cycle enzyme complex + "Any of the heteromeric enzymes that act in the TCA cycle." [GOC:mah] + TCA cycle enzyme complex + GO:0045239 + + + alpha-ketoglutarate dehydrogenase complex + GO:dihydrolipoyl dehydrogenase complex + dihydrolipoyl dehydrogenase complex + 2-oxoglutarate dehydrogenase complex + GO:0045240 + "A protein complex that possesses alpha-ketoglutarate dehydrogenase activity." [GOC:mah] + + + GO:electron transfer flavoprotein complex + GO:0045251 + "A protein complex containing flavin adenine dinucleotide (FAD) and acyl-CoA dehydrogenase, which form a system that oxidizes an acyl-CoA molecule and reduces ubiquinone and other acceptors in the mitochondrial electron transport system." [ISBN:0198506732] + electron transfer flavoprotein complex + + + GO:0045254 + pyruvate dehydrogenase complex + GO:pyruvate dehydrogenase complex + pyruvate dehydrogenase complex (lipoamide) + "Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA; comprises subunits possessing three catalytic activities: pyruvate dehydrogenase (E1), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3)." [ISBN:0716720094] + + + "A proton-transporting two-sector ATPase complex that catalyzes the phosphorylation of ADP to ATP during oxidative phosphorylation. The complex comprises a membrane sector (F0) that carries out proton transport and a cytoplasmic compartment sector (F1) that catalyzes ATP synthesis by a rotational mechanism; the extramembrane sector (containing 3 a and 3 b subunits) is connected via the d-subunit to the membrane sector by several smaller subunits. Within this complex, the g and e subunits and the 9-12 c subunits rotate by consecutive 120 degree angles and perform parts of ATP synthesis. This movement is driven by the hydrogen ion electrochemical potential gradient." [EC:3.6.3.14, ISBN:0198547684, ISBN:0716743663] + proton-transporting F-type ATPase complex + proton-transporting ATP synthase complex + GO:proton-transporting ATP synthase complex + hydrogen-translocating F-type ATPase complex + GO:0045259 + hydrogen-transporting ATP synthase complex + + + leukocyte activation + "A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor." [GOC:add] + leucocyte activation + immune cell activation + GO:leukocyte activation + GO:0045321 + + + oxidative metabolism + GO:cellular respiration + oxidative metabolic process + "The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration)." [GOC:das, ISBN:0140513590, ISBN:0198506732] + cellular respiration + GO:0045333 + + + "The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products." [GOC:mah, PMID:10968780] + GO:bone resorption + bone resorption + GO:0045453 + + + "Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features." [GOC:go_curators] + regulation of cell differentiation + GO:regulation of cell differentiation + GO:0045595 + + + GO:0045664 + GO:regulation of neuron differentiation + regulation of neuron differentiation + "Any process that modulates the frequency, rate or extent of neuron differentiation." [GOC:go_curators] + + + GO:0045786 + negative regulation of cell cycle progression + "Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle." [GOC:dph, GOC:go_curators, GOC:tb] + downregulation of progression through cell cycle + negative regulation of cell cycle + down regulation of progression through cell cycle + GO:negative regulation of cell cycle + negative regulation of progression through cell cycle + down-regulation of progression through cell cycle + + + negative regulation of gene expression, epigenetic + GO:0045814 + "Any epigenetic process that stops, prevents or reduces the rate of gene expression." [GOC:go_curators] + downregulation of gene expression, epigenetic + GO:negative regulation of gene expression, epigenetic + down-regulation of gene expression, epigenetic + down regulation of gene expression, epigenetic + + + downregulation of meiosis + GO:negative regulation of meiotic nuclear division + negative regulation of meiotic nuclear division + GO:0045835 + down-regulation of meiosis + negative regulation of meiosis + "Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis." [GOC:go_curators] + down regulation of meiosis + + + regulation of protein kinase activity + "Any process that modulates the frequency, rate or extent of protein kinase activity." [GOC:go_curators] + GO:0045859 + GO:regulation of protein kinase activity + + + GO:positive regulation of protein kinase activity + up-regulation of protein kinase activity + positive regulation of protein kinase activity + "Any process that activates or increases the frequency, rate or extent of protein kinase activity." [GOC:go_curators] + up regulation of protein kinase activity + upregulation of protein kinase activity + GO:0045860 + + + up-regulation of proteolysis + up regulation of proteolysis + GO:positive regulation of proteolysis + positive regulation of proteolysis + "Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein." [GOC:go_curators] + GO:0045862 + upregulation of proteolysis + positive regulation of peptidolysis + + + inhibition of gene-specific transcription + negative regulation of transcription, DNA-dependent + down-regulation of transcription, DNA-dependent + down regulation of gene-specific transcription + transcription repressor activity + downregulation of gene-specific transcription + "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] + GO:0045892 + negative regulation of transcription, DNA-templated + down-regulation of gene-specific transcription + negative regulation of gene-specific transcription + down regulation of transcription, DNA-dependent + GO:negative regulation of transcription, DNA-templated + downregulation of transcription, DNA-dependent + negative regulation of cellular transcription, DNA-dependent + + + up-regulation of gene-specific transcription + activation of gene-specific transcription + up-regulation of transcription, DNA-dependent + positive regulation of transcription, DNA-templated + positive regulation of gene-specific transcription + up regulation of gene-specific transcription + GO:positive regulation of transcription, DNA-templated + GO:0045893 + upregulation of transcription, DNA-dependent + transcription activator activity + "Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] + positive regulation of transcription, DNA-dependent + positive regulation of cellular transcription, DNA-dependent + upregulation of gene-specific transcription + up regulation of transcription, DNA-dependent + + + GO:0045934 + down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process + "Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] + GO:negative regulation of nucleobase-containing compound metabolic process + negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism + down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process + negative regulation of nucleobase-containing compound metabolic process + negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process + downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process + + + up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process + positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process + "Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] + GO:0045935 + positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism + positive regulation of nucleobase-containing compound metabolic process + GO:positive regulation of nucleobase-containing compound metabolic process + upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process + up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process + + + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:go_curators] + positive regulation of phosphate metabolic process + up-regulation of phosphate metabolic process + GO:0045937 + up regulation of phosphate metabolic process + GO:positive regulation of phosphate metabolic process + positive regulation of phosphate metabolism + upregulation of phosphate metabolic process + + + ADP metabolic process + "The chemical reactions and pathways involving ADP, adenosine 5'-diphosphate." [GOC:go_curators] + GO:ADP metabolic process + ADP metabolism + GO:0046031 + + + ATP metabolism + ATP metabolic process + GO:0046034 + "The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator." [GOC:go_curators] + GO:ATP metabolic process + + + GO:0046128 + GO:purine ribonucleoside metabolic process + purine ribonucleoside metabolism + purine ribonucleoside metabolic process + "The chemical reactions and pathways involving any ribonucleoside, a nucleoside in which purine base is linked to a ribose (beta-D-ribofuranose) molecule." [GOC:ai] + + + GO:purine ribonucleoside biosynthetic process + GO:0046129 + purine ribonucleoside formation + "The chemical reactions and pathways resulting in the formation of any purine ribonucleoside, a nucleoside in which purine base is linked to a ribose (beta-D-ribofuranose) molecule." [GOC:ai] + purine ribonucleoside biosynthetic process + purine ribonucleoside synthesis + purine ribonucleoside anabolism + purine ribonucleoside biosynthesis + + + pigment anabolism + pigment biosynthetic process + GO:pigment biosynthetic process + pigment synthesis + pigment biosynthesis + "The chemical reactions and pathways resulting in the formation of a pigment, any general or particular coloring matter in living organisms, e.g. melanin." [ISBN:0198506732] + GO:0046148 + pigment formation + + + "The chemical reactions and pathways resulting in the formation of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." [CHEBI:30879, GOC:ai] + alcohol biosynthetic process + alcohol formation + GO:alcohol biosynthetic process + alcohol biosynthesis + alcohol synthesis + GO:0046165 + alcohol anabolism + + + GO:phenol-containing compound biosynthetic process + phenol-containing compound formation + phenol-containing compound biosynthesis + GO:0046189 + "The chemical reactions and pathways resulting in the formation of a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring." [CHEBI:33853, GOC:ai] + phenol-containing compound synthesis + phenol-containing compound biosynthetic process + phenol-containing compound anabolism + + + glucose import + "The directed movement of the hexose monosaccharide glucose into a cell or organelle." [GOC:ai] + GO:0046323 + GO:glucose import + glucose uptake + + + GO:lateral inhibition + GO:0046331 + lateral inhibition + "Signaling between cells of equivalent developmental potential that results in these cells adopting different developmental fates. An example is the suppression by cells with a particular fate of the adoption of the same fate by surrounding cells." [GOC:bf, GOC:kmv] + + + monosaccharide synthesis + monosaccharide biosynthetic process + monosaccharide anabolism + monosaccharide biosynthesis + GO:monosaccharide biosynthetic process + GO:0046364 + monosaccharide formation + "The chemical reactions and pathways resulting in the formation of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms." [ISBN:0198506732] + + + "The chemical reactions and pathways resulting in the breakdown of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms." [ISBN:0198506732] + monosaccharide catabolic process + monosaccharide degradation + GO:0046365 + GO:monosaccharide catabolic process + monosaccharide catabolism + monosaccharide breakdown + + + "The chemical reactions and pathways resulting in the formation of ribose phosphate, any phosphorylated ribose sugar." [GOC:ai] + ribose phosphate formation + GO:0046390 + GO:ribose phosphate biosynthetic process + ribose phosphate synthesis + ribose phosphate biosynthesis + ribose phosphate biosynthetic process + ribose phosphate anabolism + + + carboxylic acid synthesis + carboxylic acid formation + GO:0046394 + carboxylic acid biosynthetic process + GO:carboxylic acid biosynthetic process + carboxylic acid biosynthesis + carboxylic acid anabolism + "The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups." [ISBN:0198506732] + + + GO:0046395 + carboxylic acid degradation + carboxylic acid catabolic process + GO:carboxylic acid catabolic process + carboxylic acid catabolism + carboxylic acid breakdown + "The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups." [ISBN:0198506732] + + + neutral lipid formation + "The chemical reactions and pathways resulting in the formation of neutral lipids, lipids only soluble in solvents of very low polarity." [GOC:ai] + GO:neutral lipid biosynthetic process + GO:0046460 + neutral lipid anabolism + neutral lipid biosynthetic process + neutral lipid synthesis + neutral lipid biosynthesis + + + acylglycerol biosynthetic process + acylglycerol biosynthesis + acylglycerol formation + GO:0046463 + GO:acylglycerol biosynthetic process + acylglycerol synthesis + "The chemical reactions and pathways resulting in the formation of acylglycerol, any mono-, di- or triester of glycerol with (one or more) fatty acids." [GOC:ai] + acylglycerol anabolism + + + GO:0046483 + GO:heterocycle metabolic process + heterocycle metabolism + "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [CHEBI:5686, ISBN:0198506732] + heterocycle metabolic process + + + "The chemical reactions and pathways involving glycerolipids, any lipid with a glycerol backbone. Diacylglycerol and phosphatidate are key lipid intermediates of glycerolipid biosynthesis." [GOC:ai, PMID:8906569] + GO:0046486 + glycerolipid metabolism + GO:glycerolipid metabolic process + glycerolipid metabolic process + + + GO:nicotinamide nucleotide metabolic process + "The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide." [ISBN:0198506732] + nicotinamide nucleotide metabolism + nicotinamide nucleotide metabolic process + GO:0046496 + + + "The specialization of organization of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. An example of this process is found in Drosophila melanogaster." [GOC:ai, ISBN:0198506732] + photoreceptor cell differentiation + GO:photoreceptor cell differentiation + GO:0046530 + + + perception of umami taste, detection of chemical stimulus + perception of umami taste, sensory transduction of chemical stimulus + sensory transduction of chemical stimulus during perception of umami taste + "The series of events required for a umami taste stimulus to be received and converted to a molecular signal. Umami taste is the savory taste of meats and other foods that are rich in glutamates." [GOC:ai, GOC:dos, PMID:11894099] + sensory detection of umami taste + umami taste detection + GO:0046535 + sensory detection of chemical stimulus during perception of umami taste + sensory transduction of umami taste + GO:detection of chemical stimulus involved in sensory perception of umami taste + detection of chemical stimulus involved in sensory perception of umami taste + + + GO:0046541 + saliva secretion + GO:saliva secretion + "The regulated release of saliva from the salivary glands. In man, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin." [GOC:curators, UBERON:0001836] + salivation + + + "Development of a rod cell, one of the sensory cells in the eye that reacts to the presence of light. Rod cells contain the photopigment rhodopsin or porphyropsin and are responsible for vision in dim light." [ISBN:0198506732] + GO:0046548 + GO:retinal rod cell development + retinal rod cell development + + + retinal cone cell development + GO:retinal cone cell development + GO:0046549 + "Development of a cone cell, one of the sensory cells in the eye that reacts to the presence of light. Cone cells contain the photopigment iodopsin or cyanopsin and are responsible for photopic (daylight) vision." [ISBN:0198506732] + + + GO:lymphocyte activation + "A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, ISBN:0781735140] + GO:0046649 + lymphocyte activation + + + "The expansion of a lymphocyte population by cell division." [GOC:ai] + GO:0046651 + lymphocyte proliferation + GO:lymphocyte proliferation + + + "The establishment of the sex of a female organism by physical differentiation." [GOC:bf] + GO:0046660 + female sex differentiation + GO:female sex differentiation + + + male sex differentiation + "The establishment of the sex of a male organism by physical differentiation." [GOC:bf] + GO:male sex differentiation + GO:0046661 + + + GO:0046700 + heterocycle breakdown + "The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [GOC:ai] + heterocycle degradation + heterocycle catabolic process + heterocycle catabolism + GO:heterocycle catabolic process + + + "The controlled release of acid by a cell or a tissue." [GOC:ai] + acid secretion + GO:0046717 + GO:acid secretion + + + GO:0046777 + protein amino acid autophosphorylation + protein autophosphorylation + "The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation)." [ISBN:0198506732] + GO:protein autophosphorylation + + + bone remodelling + GO:0046849 + bone remodeling + GO:bone remodeling + "The continuous turnover of bone matrix and mineral that involves first, an increase in resorption (osteoclastic activity) and later, reactive bone formation (osteoblastic activity). The process of bone remodeling takes place in the adult skeleton at discrete foci. The process ensures the mechanical integrity of the skeleton throughout life and plays an important role in calcium homeostasis. An imbalance in the regulation of bone resorption and bone formation results in many of the metabolic bone diseases, such as osteoporosis." [GOC:curators] + + + GO:0046879 + GO:hormone secretion + "The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells." [ISBN:0198506732] + hormone secretion + + + GO:regulation of hormone secretion + "Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell." [GOC:ai] + regulation of hormone secretion + GO:0046883 + + + "The controlled release of a substance by a cell or a tissue." [GOC:ai] + GO:0046903 + GO:secretion + secretion + + + GO:intracellular transport + "The directed movement of substances within a cell." [GOC:ai] + intracellular transport + GO:0046907 + + + pore complex + pore-forming toxin activity + channel-forming toxin activity + "Any small opening in a membrane that allows the passage of gases and/or liquids." [ISBN:0198506732] + GO:pore complex + pore + GO:0046930 + + + pore complex assembly + pore complex biogenesis + pore-forming toxin activity + pore formation + GO:pore complex assembly + GO:0046931 + "The aggregation, arrangement and bonding together of a set of components to form a pore complex. A pore complex is a small opening in a membrane that allows the passage of liquids and/or gases." [GOC:jl, GOC:mah] + pore biosynthesis + + + GO:nucleotide phosphorylation + nucleotide phosphorylation + GO:0046939 + "The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside." [GOC:ai] + + + carboxylic acid transport + GO:carboxylic acid transport + GO:0046942 + "The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:ai] + + + unconditional response + nonassociative learning + GO:nonassociative learning + "A simple form of learning whereby the repeated presence of a stimulus leads to a change in the probability or strength of the response to that stimulus. There is no association of one type of stimulus with another, rather it is a generalized response to the environment." [ISBN:0582227089] + GO:0046958 + + + "A decrease in a behavioral response to a repeated stimulus. This is exemplified by the failure of a person to show a startle response to a loud noise that has been repeatedly presented." [ISBN:0582227089] + GO:habituation + GO:0046959 + habituation + + + protein heterodimerization activity + GO:0046982 + "Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer." [GOC:ai] + GO:protein heterodimerization activity + + + GO:protein dimerization activity + GO:0046983 + "The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits." [ISBN:0198506732] + protein dimerization activity + + + GO:0048008 + PDGFR signaling pathway + PDGF receptor signalling pathway + "The series of molecular signals generated as a consequence of a platelet-derived growth factor receptor binding to one of its physiological ligands." [GOC:ceb] + PDGF receptor signaling pathway + GO:platelet-derived growth factor receptor signaling pathway + platelet-derived growth factor receptor signaling pathway + + + "The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin." [GOC:ceb] + GO:ephrin receptor signaling pathway + Eph receptor signaling pathway + GO:0048013 + Eph receptor signalling pathway + ephrin receptor signaling pathway + + + phosphoinositide-mediated signalling + phosphatidylinositol-mediated signal transduction + GO:0048015 + GO:phosphatidylinositol-mediated signaling + "A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives." [GOC:bf, GOC:ceb, ISBN:0198506732] + phosphatidylinositol-mediated signaling + phosphoinositide-mediated signaling + phosphatidylinositol-mediated signalling + + + inositol lipid-mediated signalling + inositol lipid-mediated signaling + inositol lipid-mediated signal transduction + "A series of molecular signals in which a cell uses an inositol-containing lipid to convert a signal into a response. Inositol lipids include the phosphoinositides (phosphatidylinositol and its phosphorylated derivatives), ceramides containing inositol, and inositol glycolipids." [GOC:bf, GOC:ceb, PMID:16088939] + GO:0048017 + GO:inositol lipid-mediated signaling + + + "A process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers." [GOC:dph, GOC:jid, GOC:tb, http://www.mercksource.com, PMID:11891290] + GO:0048167 + GO:regulation of synaptic plasticity + regulation of synaptic plasticity + + + GO:0048180 + "A nonsteroidal regulator, composed of two covalently linked inhibin beta subunits, inhibin beta-A and inhibin beta-B (sometimes known as activin beta or activin/inhibin beta). There are three forms of activin complex, activin A, which is composed of 2 inhibin beta-A subunits, activin B, which is composed of 2 inhibin beta-B subunits, and activin AB, which is composed of an inhibin beta-A and an inhibin beta-B subunit." [GOC:go_curators, http://www.mercksource.com, http://www.stedmans.com/] + GO:activin complex + activin complex + + + "Generation of the male gamete; specialised haploid cells produced by meiosis and along with a female gamete takes part in sexual reproduction." [GOC:dph, GOC:jid] + GO:0048232 + GO:male gamete generation + male gamete generation + + + "The movement of a macrophage in response to an external stimulus." [GOC:jid] + GO:macrophage chemotaxis + macrophage chemotaxis + GO:0048246 + + + determination of adaxial identity + GO:determination of dorsal identity + "Determination of the identity of part of an organism or organ where those parts are of the type that occur in the dorsal region. Identity is considered to be the aggregate of characteristics by which a structure is recognized." [GOC:jid] + GO:0048263 + determination of dorsal identity + + + GO:organelle fusion + organelle fusion + GO:0048284 + "The creation of a single organelle from two or more organelles." [GOC:jid] + + + GO:organelle fission + "The creation of two or more organelles by division of one organelle." [GOC:jid] + GO:0048285 + organelle fission + + + lung alveolus development + "The process whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways." [GOC:mtg_lung, PMID:9751757] + GO:lung alveolus development + alveologenesis + alveolarization + GO:0048286 + + + "The process whose specific outcome is the progression of the axial mesoderm over time, from its formation to the mature structure. The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord." [GOC:dgh] + GO:0048318 + axial mesoderm development + GO:axial mesoderm development + + + paraxial mesoderm development + "The process whose specific outcome is the progression of the paraxial mesoderm over time, from its formation to the mature structure. The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube." [GOC:dgh] + GO:0048339 + GO:paraxial mesoderm development + + + terminal differentiation + "The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:go_curators] + GO:0048468 + cell development + GO:cell development + + + cell maturation + "A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state." [GOC:go_curators] + GO:cell maturation + GO:0048469 + functional differentiation + + + GO:0048471 + perinuclear region of cytoplasm + GO:perinuclear region of cytoplasm + "Cytoplasm situated near, or occurring around, the nucleus." [GOC:jid] + + + ovum development + GO:oogenesis + GO:0048477 + oogenesis + "The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster." [GOC:kmv, GOC:mtg_sensu, GOC:pr] + + + rhythm + rhythmic process + GO:rhythmic process + GO:0048511 + "Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism." [GOC:jid] + + + organogenesis + "Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:dph, GOC:jid] + GO:0048513 + animal organ development + development of an organ + GO:animal organ development + + + "Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] + upregulation of biological process + positive regulation of biological process + up regulation of biological process + GO:positive regulation of biological process + positive regulation of physiological process + GO:0048518 + up-regulation of biological process + + + negative regulation of physiological process + downregulation of biological process + "Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] + down-regulation of biological process + negative regulation of biological process + down regulation of biological process + GO:0048519 + GO:negative regulation of biological process + + + upregulation of cellular process + GO:0048522 + GO:positive regulation of cellular process + up regulation of cellular process + "Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] + positive regulation of cellular physiological process + positive regulation of cellular process + up-regulation of cellular process + + + negative regulation of cellular physiological process + GO:0048523 + GO:negative regulation of cellular process + down-regulation of cellular process + "Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid] + downregulation of cellular process + down regulation of cellular process + negative regulation of cellular process + + + GO:0048534 + haemopoietic or lymphoid organ development + haematopoietic or lymphoid organ development + GO:hematopoietic or lymphoid organ development + "The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation." [GOC:add, GOC:rl, ISBN:0781735149] + hemopoietic or lymphoid organ development + hematopoietic or lymphoid organ development + + + GO:mucosal-associated lymphoid tissue development + GO:0048537 + mucosal-associated lymphoid tissue development + "The process whose specific outcome is the progression of mucosal-associated lymphoid tissue over time, from its formation to the mature structure. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes." [GOC:add, ISBN:0781735149] + + + thymus development + GO:0048538 + "The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components." [GOC:add, ISBN:0781735149] + GO:thymus development + + + bone marrow development + "The process whose specific outcome is the progression of the bone marrow over time, from its formation to the mature structure." [GOC:add, ISBN:0781735149] + GO:bone marrow development + GO:0048539 + + + GALT development + GO:Peyer's patch development + Peyer's patch development + gut-associated lymphoid tissue development + "The process whose specific outcome is the progression of Peyer's patches over time, from their formation to the mature structure. Peyer's patches are typically found as nodules associated with gut epithelium with distinct internal structures including B- and T-zones for the activation of lymphocytes." [GOC:add, ISBN:0781735149] + GO:0048541 + + + GO:digestive tract development + GO:0048565 + "The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed." [GOC:go_curators] + digestive tract development + + + embryonic organ development + GO:0048568 + "Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:jid] + GO:embryonic organ development + embryonic organogenesis + + + GO:regulation of response to stimulus + "Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] + regulation of response to stimulus + GO:0048583 + + + "Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] + up regulation of response to stimulus + GO:positive regulation of response to stimulus + positive regulation of response to stimulus + upregulation of response to stimulus + GO:0048584 + up-regulation of response to stimulus + + + negative regulation of response to stimulus + GO:negative regulation of response to stimulus + GO:0048585 + down-regulation of response to stimulus + down regulation of response to stimulus + "Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:jid] + downregulation of response to stimulus + + + "The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another." [GOC:go_curators] + GO:0048589 + GO:developmental growth + developmental growth + + + GO:eye morphogenesis + "The process in which the anatomical structures of the eye are generated and organized." [GOC:jid, GOC:mtg_sensu] + GO:0048592 + eye morphogenesis + + + GO:embryonic morphogenesis + embryonic anatomical structure morphogenesis + GO:0048598 + embryonic morphogenesis + "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." [GOC:jid, GOC:mtg_sensu] + + + "The reproductive developmental process whose specific outcome is the progression of structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures." [GOC:dph, GOC:isa_complete, GOC:jid] + GO:0048608 + reproductive structure development + GO:reproductive structure development + + + multicellular organismal reproductive process + GO:0048609 + reproductive process in a multicellular organism + GO:multicellular organismal reproductive process + "The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs." [GOC:dph, GOC:jid, GOC:tb] + + + GO:0048645 + organ formation + GO:organ formation + "The process pertaining to the initial formation of an organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment. Organs are a natural part or structure in an animal or a plant, capable of performing some special action (termed its function), which is essential to the life or well-being of the whole. The heart and lungs are organs of animals, and the petal and leaf are organs of plants. In animals the organs are generally made up of several tissues, one of which usually predominates, and determines the principal function of the organ." [GOC:dph, GOC:jid] + + + GO:0048646 + "The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph, GOC:jid, GOC:tb] + formation of an anatomical structure involved in morphogenesis + anatomical structure formation involved in morphogenesis + GO:anatomical structure formation involved in morphogenesis + + + GO:0048664 + "The process in which a cell becomes capable of differentiating autonomously into a neuron regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:dph] + neuron fate determination + GO:neuron fate determination + + + "The process in which a cell becomes capable of differentiating autonomously into a neuron in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed." [GOC:dph] + neuron fate specification + GO:0048665 + GO:neuron fate specification + + + GO:0048666 + "The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." [GOC:dph] + neuron development + GO:neuron development + + + neuron morphogenesis involved in differentiation + GO:cell morphogenesis involved in neuron differentiation + GO:0048667 + "The process in which the structures of a neuron are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a neuron." [GOC:dph, GOC:tb] + cell morphogenesis involved in neuron differentiation + + + "The process in which the anatomical structures of a tissue are generated and organized." [GOC:dph, GOC:jid] + tissue morphogenesis + GO:tissue morphogenesis + GO:0048729 + + + GO:system development + system development + GO:0048731 + "The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process." [GOC:dph, GOC:jid] + + + GO:gland development + gland development + GO:0048732 + "The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion." [GOC:jid] + + + "The process whose specific outcome is the progression of an appendage over time, from its formation to the mature structure. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch." [GOC:jid, GOC:rc] + appendage development + GO:0048736 + GO:appendage development + + + heart muscle development + "The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure." [GOC:dph, GOC:jid, GOC:lm] + GO:cardiac muscle tissue development + GO:0048738 + cardiac muscle tissue development + + + GO:smooth muscle tissue development + "The process whose specific outcome is the progression of smooth muscle over time, from its formation to the mature structure." [GOC:dph, GOC:jid, GOC:lm] + GO:0048745 + smooth muscle tissue development + + + "The process whose specific outcome is the progression of the muscle fiber over time, from its formation to the mature structure. In skeletal muscle, fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast." [GOC:dph, GOC:jid, GOC:lm, GOC:mtg_muscle] + myofiber development + muscle fiber development + GO:muscle fiber development + myofibre development + GO:0048747 + muscle fibre development + + + pigment granule organization and biogenesis + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pigment granule." [GOC:rc] + pigment granule organization + pigment granule organisation + GO:pigment granule organization + GO:0048753 + + + branching morphogenesis of an epithelial tube + tubulogenesis + "The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder." [GOC:dgh, GOC:dph, GOC:jid] + GO:branching morphogenesis of an epithelial tube + GO:0048754 + + + GO:0048770 + GO:pigment granule + pigment granule + "A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes." [GOC:jid, GOC:mh] + + + tissue remodeling + GO:0048771 + GO:tissue remodeling + "The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling." [GOC:ebc] + + + "The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites." [GOC:mah] + GO:neuron projection morphogenesis + GO:0048812 + neurite morphogenesis + neuron projection morphogenesis + + + GO:0048821 + erythrocyte development + red blood cell development + GO:erythrocyte development + RBC development + "The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure." [GOC:devbiol] + + + GO:0048839 + "The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure." [GOC:sr] + inner ear development + GO:inner ear development + + + "The process whose specific outcome is the progression of the otolith over time, from its formation to the mature structure." [GOC:sr] + otolith development + GO:0048840 + GO:otolith development + + + forebrain morphogenesis + GO:forebrain morphogenesis + GO:0048853 + prosencephalon morphogenesis + "The process in which the anatomical structures of the forebrain are generated and organized. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions)." [GOC:cvs, GOC:dgh, GOC:dph, GOC:jid] + + + GO:anatomical structure development + "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GO_REF:0000021, GOC:mtg_15jun06] + development of an anatomical structure + anatomical structure development + GO:0048856 + + + GO:0048858 + GO:cell projection morphogenesis + "The process in which the anatomical structures of a cell projection are generated and organized." [GO_REF:0000021, GOC:mtg_15jun06] + cell projection morphogenesis + + + GO:0048859 + "The process in which the limits of an anatomical structure are generated. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GO_REF:0000021, GOC:mtg_15jun06] + formation of anatomical boundary + GO:formation of anatomical boundary + + + stem cell development + GO:0048864 + "The process whose specific outcome is the progression of the stem cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to its specific fate." [CL:0000034, GOC:isa_complete] + GO:stem cell development + + + stem cell fate specification + GO:stem cell fate specification + "The process in which a cell becomes capable of differentiating autonomously into a stem cell in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed." [CL:0000034, GOC:isa_complete] + GO:0048866 + + + "A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition." [GOC:isa_complete] + GO:0048869 + GO:cellular developmental process + cellular developmental process + + + GO:cell motility + movement of a cell + cell motility + GO:0048870 + "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another." [GOC:dgh, GOC:dph, GOC:isa_complete, GOC:mlg] + cell movement + cell locomotion + + + "Any process involved in the maintenance of an internal steady state at the level of the multicellular organism." [GOC:isa_complete] + multicellular organismal homeostasis + GO:0048871 + GO:multicellular organismal homeostasis + + + GO:chemical homeostasis + "Any biological process involved in the maintenance of an internal steady state of a chemical." [GOC:isa_complete] + chemical homeostasis + GO:0048878 + + + sensory system development + GO:0048880 + GO:sensory system development + "The process whose specific outcome is the progression of a sensory system over time from its formation to the mature structure." [GOC:dgh] + + + beta-amyloid metabolic process + GO:beta-amyloid metabolic process + "The chemical reactions and pathways involving beta-amyloid, a glycoprotein associated with Alzheimer's disease, and its precursor, amyloid precursor protein (APP)." [GOC:ai] + GO:0050435 + beta-amyloid metabolism + + + nucleic acid transport + GO:0050657 + GO:nucleic acid transport + "The directed movement of nucleic acids, single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai, ISBN:0198506732] + + + GO:0050658 + GO:RNA transport + "The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + RNA transport + + + "The regulated release of cytokines from a cell. Cytokines are any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity." [GOC:ai, GOC:bf, ISBN:0198599471] + GO:0050663 + cytokine secretion + GO:cytokine secretion + + + "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances." [ISBN:0721662544] + GO:0050673 + epithelial cell proliferation + GO:epithelial cell proliferation + + + GO:regulation of inflammatory response + "Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents." [GOC:ai] + GO:0050727 + regulation of inflammatory response + + + positive regulation of inflammatory response + GO:0050729 + up-regulation of inflammatory response + GO:positive regulation of inflammatory response + up regulation of inflammatory response + "Any process that activates or increases the frequency, rate or extent of the inflammatory response." [GOC:ai] + upregulation of inflammatory response + + + "Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons." [GOC:ai] + GO:0050767 + GO:regulation of neurogenesis + regulation of neurogenesis + + + regulation of immune response + GO:0050776 + "Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus." [GOC:ai] + GO:regulation of immune response + + + up regulation of immune response + GO:0050778 + "Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus." [GOC:ai] + GO:positive regulation of immune response + up-regulation of immune response + positive regulation of immune response + upregulation of immune response + + + GO:regulation of biological process + "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] + regulation of biological process + GO:0050789 + regulation of physiological process + + + GO:0050790 + GO:regulation of catalytic activity + regulation of catalytic activity + regulation of enzyme activity + "Any process that modulates the activity of an enzyme." [GOC:ai] + + + "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:go_curators] + regulation of developmental process + GO:regulation of developmental process + GO:0050793 + + + GO:0050794 + regulation of cellular process + GO:regulation of cellular process + regulation of cellular physiological process + "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators] + + + GO:ion homeostasis + negative regulation of crystal biosynthesis + GO:0050801 + "Any process involved in the maintenance of an internal steady state of ions within an organism or cell." [GOC:ai] + ion homeostasis + negative regulation of crystal formation + electrolyte homeostasis + + + GO:regulation of synapse structure or activity + "Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell)." [GOC:ai] + regulation of synapse structure or activity + GO:0050803 + + + GO:modulation of synaptic transmission + regulation of synaptic transmission + "Any process that modulates the frequency or rate of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse." [GOC:ai] + modulation of synaptic transmission + GO:0050804 + + + up-regulation of synaptic transmission + GO:positive regulation of synaptic transmission + positive regulation of synaptic transmission + up regulation of synaptic transmission + GO:0050806 + "Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse." [GOC:ai] + upregulation of synaptic transmission + + + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell)." [GOC:ai, GOC:pr] + GO:synapse organization + synapse organization and biogenesis + synapse organisation + GO:0050808 + synapse morphogenesis + synapse development + synapse organization + + + coagulation + GO:0050817 + "The process in which a fluid solution, or part of it, changes into a solid or semisolid mass." [ISBN:0198506732] + GO:coagulation + clotting + + + "Any process that modulates the frequency, rate or extent of coagulation, the process in which a fluid solution, or part of it, changes into a solid or semisolid mass." [GOC:ai] + GO:0050818 + regulation of coagulation + regulation of clotting + GO:regulation of coagulation + + + down-regulation of coagulation + "Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation." [GOC:ai] + GO:negative regulation of coagulation + negative regulation of coagulation + GO:0050819 + anticoagulant activity + negative regulation of clotting. + downregulation of coagulation + down regulation of coagulation + + + neurological system process + GO:neurological system process + "A organ system process carried out by any of the organs or tissues of neurological system." [GOC:ai, GOC:mtg_cardio] + GO:0050877 + neurophysiological process + pan-neural process + + + regulation of body fluid levels + GO:regulation of body fluid levels + GO:0050878 + "Any process that modulates the levels of body fluids." [GOC:ai, GOC:dph, GOC:tb] + + + "Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism." [GOC:dph, GOC:mtg_muscle, GOC:tb] + GO:0050879 + multicellular organismal movement + GO:multicellular organismal movement + + + GO:cognition + "The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory." [http://www.onelook.com/, ISBN:0721619908] + cognition + GO:0050890 + + + GO:0050892 + "Any process in which nutrients are taken up from the contents of the intestine." [GOC:ai, GOC:dph] + intestinal absorption + GO:intestinal absorption + + + "Any neural process required for an organism to sense and interpret the dimensions of a sensory experience: modality, location, intensity and affect." [GOC:dph, ISBN:0721662544] + GO:0050893 + GO:sensory processing + sensory processing + + + physiological response to stimulus + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [GOC:ai, GOC:bf] + response to stimulus + GO:0050896 + GO:response to stimulus + + + leukocyte trafficking + leucocyte migration + immune cell migration + GO:0050900 + "The movement of a leukocyte within or between different tissues and organs of the body." [GOC:add, ISBN:0781735149, PMID:14680625, PMID:14708592, PMID:7507411, PMID:8600538] + leukocyte migration + leucocyte trafficking + immune cell trafficking + GO:leukocyte migration + + + neuromuscular physiological process + neuromotor process + GO:neuromuscular process + neuromuscular process + "Any process pertaining to the functions of the nervous and muscular systems of an organism." [GOC:ai] + GO:0050905 + + + sensory transduction + GO:detection of stimulus involved in sensory perception + sensory perception, sensory transduction of stimulus + sensory perception, stimulus detection + detection of stimulus involved in sensory perception + sensory detection of stimulus + "The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal." [GOC:ai, GOC:dos, GOC:dph] + GO:0050906 + + + sensory perception, sensory detection of chemical stimulus + sensory transduction of chemical stimulus during sensory perception + sensory perception, sensory transduction of chemical stimulus + sensory detection of chemical stimulus + GO:detection of chemical stimulus involved in sensory perception + "The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception." [GOC:ai, GOC:dos] + GO:0050907 + detection of chemical stimulus involved in sensory perception + sensory detection of chemical stimulus during sensory perception + sensory transduction of chemical stimulus + + + sensory perception of taste + GO:0050909 + gustation + taste + GO:sensory perception of taste + "The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process." [GOC:ai, http://www.onelook.com/] + sense of taste + taste perception + + + perception of taste, detection of chemical stimulus + perception of taste, sensory detection of chemical stimulus + "The series of events involved in the perception of taste in which a gustatory chemical stimulus is received and converted into a molecular signal." [GOC:ai] + sensory transduction of chemical stimulus during perception of taste + sensory detection of taste + sensory transduction of taste + sensory detection of chemical stimulus during perception of taste + GO:0050912 + perception of taste, sensory transduction of chemical stimulus + GO:detection of chemical stimulus involved in sensory perception of taste + detection of chemical stimulus involved in sensory perception of taste + + + GO:sensory perception of bitter taste + bitter taste perception + "The series of events required to receive a bitter taste stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:ai] + GO:0050913 + sensory perception of bitter taste + + + sweet taste perception + sensory perception of sweet taste + "The series of events required to receive a sweet taste stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:ai] + GO:sensory perception of sweet taste + GO:0050916 + + + "The series of events required to receive an umami taste stimulus, convert it to a molecular signal, and recognize and characterize the signal. Umami taste is the savory taste of meats and other foods that are rich in glutamates. This is a neurological process." [GOC:ai] + umami taste perception + sensory perception of umami taste + GO:0050917 + GO:sensory perception of umami taste + + + GO:positive chemotaxis + chemoattraction + GO:0050918 + positive chemotaxis + "The directed movement of a motile cell or organism towards a higher concentration of a chemical." [GOC:ai, GOC:bf, GOC:isa_complete] + + + GO:0050953 + sensory perception of light stimulus + GO:sensory perception of light stimulus + "The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:ai] + + + "The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." [GOC:ai] + GO:0050954 + chemi-mechanical coupling + sensory perception of mechanical stimulus + GO:sensory perception of mechanical stimulus + mechanosensory perception + perception of mechanical stimulus + + + taction + GO:sensory perception of touch + sensory perception of touch + tactile sense + perception of touch + tactition + "The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach)." [GOC:ai] + GO:0050975 + + + microtubule severing + GO:0051013 + "The process in which a microtubule is broken down into smaller segments." [GOC:ai, PMID:14657234] + GO:microtubule severing + microtubule severing activity + + + actin cable assembly + actin cable formation + actin bundling activity + "The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness." [GOC:ai] + GO:actin filament bundle assembly + GO:0051017 + actin filament bundle assembly + + + "The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + GO:0051028 + mRNA transport + GO:mRNA transport + + + "Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue." [GOC:ai] + GO:regulation of secretion + regulation of secretion + GO:0051046 + + + GO:0051049 + "Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + regulation of transport + GO:regulation of transport + + + nuclear envelope catabolism + GO:0051081 + nuclear envelope breakdown + "The controlled breakdown of the nuclear envelope in the context of a normal process." [GOC:ai] + nuclear envelope degradation + GO:nuclear envelope disassembly + nuclear envelope disassembly + + + "Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:ai] + GO:regulation of sequence-specific DNA binding transcription factor activity + GO:0051090 + regulation of sequence-specific DNA binding transcription factor activity + + + "Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:ai] + up-regulation of transcription factor activity + positive regulation of sequence-specific DNA binding transcription factor activity + GO:positive regulation of sequence-specific DNA binding transcription factor activity + up regulation of transcription factor activity + GO:0051091 + upregulation of transcription factor activity + + + GO:0051092 + positive regulation of NF-kappaB transcription factor activity + GO:positive regulation of NF-kappaB transcription factor activity + NF-kappaB activation + "Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB." [GOC:dph, GOC:tb, PMID:15087454, PMID:15170030] + activation of NF-kappaB + activation of NF-kappaB transcription factor + + + regulation of cellular component organization + regulation of cellular component organisation + regulation of cell organisation + GO:0051128 + GO:regulation of cellular component organization + "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai] + regulation of cellular component organization and biogenesis + regulation of cell organization + + + negative regulation of cellular component organization + down-regulation of cell organization + "Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai] + down regulation of cell organization + negative regulation of cellular component organization and biogenesis + downregulation of cell organization + negative regulation of cell organisation + GO:0051129 + GO:negative regulation of cellular component organization + + + GO:0051145 + nonstriated muscle cell differentiation + smooth muscle cell differentiation + GO:smooth muscle cell differentiation + "The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell; smooth muscle lacks transverse striations in its constituent fibers and are almost always involuntary." [CL:0000192, GOC:ai] + + + nuclear export + GO:0051168 + export from nucleus + GO:nuclear export + nucleus export + substance nuclear export + "The directed movement of substances out of the nucleus." [GOC:ai] + + + "The directed movement of substances into, out of, or within the nucleus." [GOC:ai] + GO:0051169 + GO:nuclear transport + nucleus transport + nuclear transport + + + nuclear import + substance nuclear import + import into nucleus + "The directed movement of substances into the nucleus." [GOC:ai] + GO:0051170 + nucleus import + GO:nuclear import + + + regulation of nitrogen compound metabolic process + regulation of nitrogen metabolism + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] + GO:regulation of nitrogen compound metabolic process + regulation of nitrogen metabolic process + GO:0051171 + + + negative regulation of nitrogen metabolic process + down-regulation of nitrogen metabolic process + negative regulation of nitrogen compound metabolic process + GO:negative regulation of nitrogen compound metabolic process + down regulation of nitrogen metabolic process + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] + GO:0051172 + downregulation of nitrogen metabolic process + negative regulation of nitrogen metabolism + + + GO:0051173 + upregulation of nitrogen metabolic process + positive regulation of nitrogen compound metabolic process + GO:positive regulation of nitrogen compound metabolic process + positive regulation of nitrogen metabolic process + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] + up-regulation of nitrogen metabolic process + positive regulation of nitrogen metabolism + up regulation of nitrogen metabolic process + + + GO:regulation of phosphorus metabolic process + regulation of phosphorus metabolism + GO:0051174 + regulation of phosphorus metabolic process + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus." [GOC:ai] + + + GO:0051179 + localization + GO:localization + "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to or maintained in a specific location." [GOC:ai] + establishment and maintenance of localization + establishment and maintenance of position + localisation + + + "The chemical reactions and pathways involving a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate." [GOC:ai] + cofactor metabolism + cofactor metabolic process + GO:0051186 + GO:cofactor metabolic process + + + cofactor anabolism + "The chemical reactions and pathways resulting in the formation of a cofactor, a substance that is required for the activity of an enzyme or other protein." [GOC:ai] + cofactor biosynthetic process + cofactor formation + GO:0051188 + cofactor synthesis + cofactor biosynthesis + GO:cofactor biosynthetic process + + + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a cofactor." [GOC:ai] + regulation of cofactor metabolism + GO:0051193 + GO:regulation of cofactor metabolic process + regulation of cofactor metabolic process + + + regulation of coenzyme metabolic process + regulation of coenzyme metabolism + GO:regulation of coenzyme metabolic process + GO:0051196 + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a coenzyme." [GOC:ai] + + + cartilage organ development + GO:0051216 + GO:cartilage development + cartilage element development + cartilage biogenesis + cartilage development + cartilage biosynthesis + "The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." [DOI:10.1371/journal.pone.0051070, GOC:cjm, http://www.onelook.com] + cartilage formation + chondrogenesis + + + sequestering of protein in cytoplasm + sequestration of protein in cytoplasm + retention of protein in cytoplasm + cytoplasmic storage of protein + cytoplasmic sequestering of protein + GO:0051220 + maintenance of protein location in cytoplasm + storage of protein in cytoplasm + "The selective interaction of a protein with specific molecules in the cytoplasm, thereby inhibiting its transport into other areas of the cell." [GOC:ai] + cytoplasmic retention of protein + GO:cytoplasmic sequestering of protein + cytoplasmic sequestration of protein + + + "Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + regulation of protein transport + GO:0051223 + GO:regulation of protein transport + + + "The aggregation, arrangement and bonding together of a set of components to form the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart." [GOC:ai, GOC:expert_rg, GOC:mtg_sensu, GOC:tb] + spindle assembly + spindle biosynthesis + bipolar spindle formation + GO:spindle assembly + GO:0051225 + bipolar spindle biosynthesis + spindle formation + + + establishment of localisation + "The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location." [GOC:ai] + GO:0051234 + GO:establishment of localization + establishment of localization + + + "Any process in which a cell, substance or cellular entity, such as a protein complex or organelle, is maintained in a location and prevented from moving elsewhere." [GOC:ai, GOC:dph, GOC:tb] + GO:maintenance of location + maintenance of location + GO:0051235 + + + RNA recruitment + GO:establishment of RNA localization + "The directed movement of RNA to a specific location." [GOC:ai] + establishment of RNA localization + RNA positioning + GO:0051236 + establishment of RNA localisation + + + "Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai, GOC:dph, GOC:tb] + regulation of multicellular organismal process + GO:regulation of multicellular organismal process + GO:0051239 + + + down regulation of multicellular organismal process + down-regulation of multicellular organismal process + GO:negative regulation of multicellular organismal process + negative regulation of multicellular organismal process + "Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai] + GO:0051241 + downregulation of multicellular organismal process + + + GO:regulation of protein metabolic process + regulation of protein metabolism + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein." [GOC:ai] + GO:0051246 + regulation of protein metabolic process + + + GO:positive regulation of protein metabolic process + up regulation of protein metabolic process + positive regulation of protein metabolic process + positive regulation of protein metabolism + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein." [GOC:ai] + up-regulation of protein metabolic process + GO:0051247 + upregulation of protein metabolic process + + + regulation of RNA metabolism + GO:regulation of RNA metabolic process + GO:0051252 + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA." [GOC:ai] + regulation of RNA metabolic process + + + GO:negative regulation of RNA metabolic process + down regulation of RNA metabolic process + GO:0051253 + downregulation of RNA metabolic process + negative regulation of RNA metabolism + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA." [GOC:ai] + negative regulation of RNA metabolic process + down-regulation of RNA metabolic process + + + positive regulation of RNA metabolism + GO:0051254 + positive regulation of RNA metabolic process + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA." [GOC:ai] + up regulation of RNA metabolic process + GO:positive regulation of RNA metabolic process + up-regulation of RNA metabolic process + upregulation of RNA metabolic process + + + protein polymer formation + "The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein." [GOC:ai] + protein polymer biosynthesis + protein polymer biosynthetic process + GO:protein polymerization + protein polymerization + GO:0051258 + + + protein oligomer formation + protein oligomer assembly + protein multimerization + GO:protein oligomerization + protein oligomerization + protein oligomer biosynthesis + protein oligomer biosynthetic process + GO:0051259 + "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." [GOC:ai] + + + GO:0051260 + protein homooligomer biosynthesis + protein homooligomer biosynthetic process + "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." [GOC:ai] + protein homooligomer assembly + protein homooligomerization activity + GO:protein homooligomerization + protein homooligomer formation + protein homooligomerization + + + GO:protein depolymerization + GO:0051261 + protein polymer degradation + "The process in which protein polymers, compounds composed of a large number of component monomers, are broken down. Depolymerization occurs by the successive removal of monomers from an existing poly- or oligomeric protein." [GOC:ai] + protein polymer breakdown + protein polymer catabolic process + protein polymer catabolism + protein depolymerization + + + GO:0051262 + protein tetramer biosynthetic process + protein tetramer biosynthesis + "The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits." [GOC:ecd] + protein tetramer formation + protein tetramer assembly + protein tetramerization + GO:protein tetramerization + + + GO:0051270 + regulation of cellular component movement + GO:regulation of cellular component movement + "Any process that modulates the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl] + regulation of cell movement + regulation of cellular component motion + + + "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] + GO:0051276 + GO:chromosome organization + chromosome organization + nuclear genome maintenance + maintenance of genome integrity + chromosome organisation + chromosome organization and biogenesis + + + protein heterotetramer biosynthesis + "The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical." [GOC:go_curators] + protein heterotetramer biosynthetic process + protein heterotetramer formation + GO:protein heterotetramerization + protein heterotetramerization + protein heterotetramer assembly + GO:0051290 + + + "The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer." [GOC:ai] + protein heterooligomer formation + protein heterooligomer biosynthetic process + protein heterooligomer biosynthesis + GO:protein heterooligomerization + GO:0051291 + protein heterooligomerization + protein heterooligomer assembly + + + nuclear pore formation + nuclear pore complex formation + nuclear pore assembly + "The aggregation, arrangement and bonding together of a set of components to form a nuclear pore complex." [GOC:ai, GOC:mah] + GO:0051292 + nuclear pore complex biosynthesis + nuclear pore biosynthesis + nuclear pore complex biogenesis + nuclear pore biogenesis + NPC assembly + nuclear pore complex assembly + GO:nuclear pore complex assembly + + + GO:0051301 + GO:cell division + "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells." [GOC:di, GOC:go_curators, GOC:pr] + cell division + + + GO:0051302 + "Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells." [GOC:go_curators] + regulation of cell division + GO:regulation of cell division + + + GO:0051318 + G1 phase + GO:G1 phase + "The cell cycle 'gap' phase which is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis." [GOC:mtg_cell_cycle] + + + "The cell cycle phase, following G1, during which DNA synthesis takes place." [GOC:mtg_cell_cycle] + GO:S phase + S phase + S-phase + GO:0051320 + + + GO:0051322 + "The cell cycle phase, following metaphase, during which the chromosomes separate and migrate towards the poles of the spindle." [GOC:mtg_cell_cycle] + GO:anaphase + anaphase + + + GO:0051323 + GO:metaphase + "The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell." [GOC:mtg_cell_cycle] + metaphase + + + GO:0051324 + "The cell cycle phase which is the first stage of M phase of meiosis and mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell." [GOC:mtg_cell_cycle] + prophase + GO:prophase + + + "The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs." [GOC:mtg_cell_cycle] + GO:0051325 + GO:interphase + karyostasis + interphase + + + GO:0051326 + telophase + GO:telophase + "The cell cycle phase which follows anaphase during M phase of mitosis and meiosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts." [GOC:mtg_cell_cycle] + + + GO:regulation of transferase activity + GO:0051338 + transferase regulator + "Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [EC:2.-.-.-, GOC:ai] + regulation of transferase activity + + + GO:0051347 + positive regulation of transferase activity + upregulation of transferase activity + up regulation of transferase activity + "Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." [GOC:ai] + GO:positive regulation of transferase activity + up-regulation of transferase activity + transferase activator + + + GO:0051382 + kinetochore biogenesis + kinetochore biosynthesis + kinetochore formation + "The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules." [GOC:ai] + GO:kinetochore assembly + kinetochore assembly + + + GO:kinetochore organization + GO:0051383 + kinetochore organization + kinetochore organisation + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] + kinetochore organization and biogenesis + + + programmed cell death of neuronal cells by apoptosis + programmed cell death, neurons + programmed cell death of neurons by apoptosis + neuronal cell apoptosis + GO:neuron apoptotic process + neuronal cell programmed cell death by apoptosis + programmed cell death, neuronal cells + "Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [CL:0000540, GOC:mtg_apoptosis, MeSH:A.08.663] + apoptosis of neuronal cells + neuron apoptotic process + apoptosis of neurons + neuron programmed cell death by apoptosis + GO:0051402 + + + GO:0051445 + regulation of progression through meiotic cell cycle + GO:regulation of meiotic cell cycle + modulation of meiotic cell cycle progression + meiotic cell cycle modulation + regulation of meiotic cell cycle + regulation of meiotic cell cycle progression + "Any process that modulates the rate or extent of progression through the meiotic cell cycle." [GOC:ai, GOC:dph, GOC:tb] + meiotic cell cycle regulation + meiotic cell cycle regulator + + + "Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle." [GOC:ai, GOC:dph, GOC:tb] + downregulation of progression through meiotic cell cycle + negative regulation of meiotic cell cycle + down regulation of progression through meiotic cell cycle + GO:0051447 + down-regulation of progression through meiotic cell cycle + negative regulation of progression through meiotic cell cycle + GO:negative regulation of meiotic cell cycle + negative regulation of meiotic cell cycle progression + + + "The multiplication or reproduction of myoblasts, resulting in the expansion of a myoblast cell population. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:ai, GOC:mtg_muscle] + GO:0051450 + GO:myoblast proliferation + myoblast proliferation + + + regulation of cytoskeleton organisation + regulation of cytoskeleton organization + "Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:ai] + GO:regulation of cytoskeleton organization + GO:0051493 + regulation of cytoskeleton organization and biogenesis + + + GO:negative regulation of cytoskeleton organization + "Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:ai] + down-regulation of cytoskeleton organization + negative regulation of cytoskeleton organization and biogenesis + down regulation of cytoskeleton organization + GO:0051494 + negative regulation of cytoskeleton organization + downregulation of cytoskeleton organization + negative regulation of cytoskeleton organisation + + + GO:0051546 + "The directed movement of a keratinocyte, epidermal cells which synthesize keratin, from one site to another." [ISBN:0721662544] + GO:keratinocyte migration + keratinocyte migration + + + histone H3 K9 methylation + histone H3K9me + GO:0051567 + histone lysine H3 K9 methylation + histone H3-K9 methylation + GO:histone H3-K9 methylation + "The modification of histone H3 by addition of one or more methyl groups to lysine at position 9 of the histone." [GOC:ai, GOC:pr] + + + GO:0051598 + "A checkpoint that acts during late prophase I (pachytene) and prevents segregation of homologous chromosomes until recombination is completed, ensuring proper distribution of the genetic material to the gametes." [PMID:14718568] + pachytene checkpoint + meiotic recombination checkpoint + GO:meiotic recombination checkpoint + + + GO:proteolysis involved in cellular protein catabolic process + GO:0051603 + "The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells." [GOC:ai, GOC:dph, GOC:tb] + peptidolysis involved in cellular protein catabolism + peptidolysis during cellular protein catabolic process + peptidolysis during cellular protein catabolism + peptidolysis involved in cellular protein catabolic process + proteolysis involved in cellular protein catabolic process + proteolysis during cellular protein catabolic process + proteolysis during cellular protein catabolism + + + GO:0051604 + "Any process leading to the attainment of the full functional capacity of a protein." [GOC:ai] + protein maturation + GO:protein maturation + + + GO:detection of stimulus + "The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal." [GOC:add, GOC:ai, GOC:dph, GOC:mah] + perception of stimulus + stimulus detection + stimulus sensing + GO:0051606 + detection of stimulus + + + "The directed movement of serotonin into a cell, typically presynaptic neurons or glial cells. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems." [GOC:ai] + 5-hydroxytryptamine uptake + GO:0051610 + 5HT uptake + serotonin uptake + serotonin import + GO:serotonin uptake + 5-HT uptake + + + organelle localisation + "Any process in which an organelle is transported to, and/or maintained in, a specific location." [GOC:ai] + establishment and maintenance of organelle localization + GO:0051640 + organelle localization + GO:organelle localization + + + establishment and maintenance of cellular localization + cellular localisation + establishment and maintenance of localization in cell or cell membrane + GO:0051641 + cellular localization + GO:cellular localization + "A localization process that takes place at the cellular level; as a result of a cellular localization process, a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within or in the membrane of a cell." [GOC:ai, GOC:mah] + + + vesicle localization + cytoplasmic vesicle localization + establishment and maintenance of vesicle localization + "Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location." [GOC:ai] + GO:vesicle localization + GO:0051648 + vesicle localisation + + + establishment of localisation in cell + "The directed movement of a substance or cellular entity, such as a protein complex or organelle, to a specific location within, or in the membrane of, a cell." [GOC:ai, GOC:dph, GOC:tb] + GO:0051649 + GO:establishment of localization in cell + establishment of localization in cell + establishment of cellular localization + + + establishment of vesicle localization + GO:establishment of vesicle localization + GO:0051650 + "The directed movement of a vesicle to a specific location." [GOC:ai] + establishment of vesicle localisation + + + GO:maintenance of location in cell + GO:0051651 + maintenance of location in cell + maintenance of cellular localization + maintenance of localization in cell + "Any process in which a substance or cellular entity, such as a protein complex or organelle, is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere." [GOC:ai] + + + "The directed movement of an organelle to a specific location." [GOC:ai] + establishment of organelle localisation + establishment of organelle localization + GO:establishment of organelle localization + GO:0051656 + + + GO:multi-organism process + interaction between organisms + physiological interaction between organisms + multi-organism process + physiological interaction with other organism + GO:0051704 + "A biological process which involves another organism of the same or different species." [GOC:jl] + + + behavioral interaction between organisms + "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] + GO:multi-organism behavior + behavioural interaction with other organism + behavioral interaction with other organism + GO:0051705 + behavioural interaction between organisms + multi-organism behavior + + + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell." [GOC:bf, GOC:jl] + GO:cellular response to stimulus + cellular response to stimulus + GO:0051716 + + + cell cycle modulation + cell cycle regulation + modulation of cell cycle progression + control of cell cycle progression + regulation of cell cycle progression + cell cycle regulator + tumor suppressor + regulation of progression through cell cycle + GO:0051726 + "Any process that modulates the rate or extent of progression through the cell cycle." [GOC:ai, GOC:dph, GOC:tb] + regulation of cell cycle + GO:regulation of cell cycle + + + formation of actin crosslink + actin bundling + actin crosslinking + GO:actin crosslink formation + GO:0051764 + actin crosslink formation + "The process in which two or more actin filaments are connected together by proteins that act as crosslinks between the filaments. The crosslinked filaments may be on the same or differing axes." [GOC:ai] + + + down-regulation of cell division + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell division." [GOC:ai] + GO:negative regulation of cell division + GO:0051782 + negative regulation of cell division + downregulation of cell division + down regulation of cell division + + + GO:regulation of nuclear division + GO:0051783 + "Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information." [GOC:ai] + regulation of nuclear division + + + negative regulation of nuclear division + "Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information." [GOC:ai] + GO:negative regulation of nuclear division + GO:0051784 + down regulation of nuclear division + down-regulation of nuclear division + downregulation of nuclear division + + + GO:0051866 + general adaptation syndrome + general adaptation syndrome, physiological response + GO:general adaptation syndrome + physiological response during general adaptation syndrome + physiological process during general adaptation syndrome + general adaptation syndrome, physiological process + "General adaptation syndrome is the set of changes in various organ systems of the body, especially the pituitary-endocrine system, in response to a wide range of strong external stimuli, both physiological and psychological. It is described as having three stages: alarm reaction, where the body detects the external stimulus; adaptation, where the body engages defensive countermeasures against the stressor; and exhaustion, where the body begins to run out of defenses." [http://www.onelook.com, PMID:14847556, Wikipedia:General_adaptation_syndrome] + + + general adaptation syndrome, behavioral process + behavioural process during general adaptation syndrome + GO:0051867 + general adaptation syndrome, behavioural response + behavioral response during general adaptation syndrome + GO:general adaptation syndrome, behavioral process + "The set of behavioral processes that occur as part of the general adaptation syndrome, the response of the body to a strong, stressful stimulus." [GOC:ai] + general adaptation syndrome, behavioral response + behavioral process during general adaptation syndrome + general adaptation syndrome, behavioural process + behavioural response during general adaptation syndrome + + + GO:pigment granule localization + GO:0051875 + "Any process in which a pigment granule is transported to, and/or maintained in, a specific location within the cell." [GOC:ai] + pigment granule localization + pigment granule localisation + + + "The process in which membrane potential decreases with respect to its steady-state potential, usually from negative potential to a more positive potential. For example, the initial depolarization during the rising phase of an action potential is in the direction from the negative steady-state resting potential towards the positive membrane potential that will be the peak of the action potential." [GOC:dh, Wikipedia:Depolarization] + GO:membrane depolarization + membrane depolarization + GO:0051899 + + + GO:0051904 + pigment granule transport + pigment granule translocation + GO:pigment granule transport + "The directed movement of pigment granules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] + + + GO:0051905 + GO:establishment of pigment granule localization + establishment of pigment granule localisation + "The directed movement of a pigment granule to a specific location." [GOC:ai] + establishment of pigment granule localization + + + "Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue." [GOC:ai] + GO:regulation of nervous system development + regulation of nervous system development + GO:0051960 + + + "The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate." [CL:0000187, GOC:devbiol] + GO:0055001 + GO:muscle cell development + muscle cell development + + + striated muscle cell development + GO:0055002 + "The process whose specific outcome is the progression of a striated muscle cell over time, from its formation to the mature structure. Striated muscle cells contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle." [CL:0000737, GOC:devbiol] + GO:striated muscle cell development + + + "An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane." [GOC:dph, GOC:jid, GOC:kmv, GOC:rph, PMID:10930469, PMID:15601896, PMID:16246101, PMID:21556374, PMID:21562044] + recycling endosome + endosomal recycling compartment + ERC + GO:0055037 + GO:recycling endosome + endosome recycling compartment + + + monovalent inorganic cation homeostasis + "Any process involved in the maintenance of an internal steady state of monovalent inorganic cations within an organism or cell." [GOC:ai, GOC:jid, GOC:mah] + GO:monovalent inorganic cation homeostasis + GO:0055067 + + + cation homeostasis + "Any process involved in the maintenance of an internal steady state of cations within an organism or cell." [GOC:ceb, GOC:jid, GOC:mah] + GO:0055080 + GO:cation homeostasis + + + transmembrane transport + "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other" [GOC:dph, GOC:jid] + GO:transmembrane transport + GO:0055085 + membrane transport + + + "The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide." [GOC:vw] + nucleobase, nucleoside and nucleotide metabolism + nucleobase-containing small molecule metabolic process + nucleobase, nucleoside and nucleotide metabolic process + GO:nucleobase-containing small molecule metabolic process + GO:0055086 + + + GO:0055088 + lipid homeostasis + GO:lipid homeostasis + "Any process involved in the maintenance of an internal steady state of lipid within an organism or cell." [GOC:BHF, GOC:rl] + + + GO:0055092 + sterol homeostasis + GO:sterol homeostasis + "Any process involved in the maintenance of an internal steady state of sterol within an organism or cell." [GOC:BHF, GOC:rl] + + + GO:0055114 + oxidation reduction + oxidoreductase process + "A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons." [GOC:dhl, GOC:ecd, GOC:jh2, GOC:jid, GOC:mlg, GOC:rph] + oxidation-reduction process + GO:oxidation-reduction process + + + "An automatic response to a stimulus beginning with a nerve impulse from a receptor and ending with the action of an effector such as a gland or a muscle. Signaling never reaches a level of consciousness." [GOC:dph, ISBN:087797099] + GO:0060004 + GO:reflex + reflex + + + Sertoli cell development + GO:Sertoli cell development + "The process whose specific outcome is the progression of a Sertoli cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a Sertoli cell fate." [GOC:dph] + GO:0060009 + + + GO:0060013 + GO:righting reflex + "A reflex process in which an animal immediately tries to turn over after being placed in a supine position." [GOC:dph, PMID:8635460] + righting reflex + righting response + + + palatum development + palate development + GO:palate development + "The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities." [GOC:dph, ISBN:0721662544] + GO:0060021 + + + "The morphogenetic process in which an epithelium narrows along one axis and lengthens in a perpendicular axis." [GOC:dgf, GOC:dph, PMID:12062082] + GO:convergent extension + GO:0060026 + convergent extension + + + GO:anatomical structure regression + GO:0060033 + anatomical structure regression + "The developmental process in which an anatomical stucture is destroyed as a part of its normal progression." [GOC:dph] + + + retina development in camera-style eye + retinal development + retina development in camera-type eye + GO:0060041 + GO:retina development in camera-type eye + "The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [GOC:bf, GOC:dph, ISBN:0815340729] + + + heart contraction + "The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body." [GOC:dph] + heart beating + GO:0060047 + hemolymph circulation + GO:heart contraction + cardiac contraction + + + GO:0060070 + "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes." [GOC:bf, GOC:dph, PMID:11532397, PMID:19619488] + canonical Wnt signaling pathway + Wnt receptor signaling pathway through beta-catenin + canonical Wnt receptor signaling pathway + GO:canonical Wnt signaling pathway + Wnt receptor signalling pathway through beta-catenin + canonical Wnt-activated signaling pathway + Wnt receptor signaling pathway via beta-catenin + + + GO:0060073 + GO:micturition + urine voiding + urination + micturition + "The regulation of body fluids process in which parasympathetic nerves stimulate the bladder wall muscle to contract and expel urine from the body." [GOC:dph] + + + "A synapse in which an action potential in the presynaptic cell increases the probability of an action potential occurring in the postsynaptic cell." [GOC:dph, GOC:ef] + excitatory synapse + GO:0060076 + GO:excitatory synapse + + + membrane hyperpolarization + GO:0060081 + GO:membrane hyperpolarization + "The process in which membrane potential increases with respect to its steady-state potential, usually from negative potential to a more negative potential. For example, during the repolarization phase of an action potential the membrane potential often becomes more negative or hyperpolarized before returning to the steady-state resting potential." [GOC:dph] + + + GO:binding, bridging + binding, bridging + "The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way." [GOC:mtg_MIT_16mar07, GOC:vw] + GO:0060090 + molecular adaptor activity + + + "The process whose specific outcome is the progression of an inner ear receptor cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:dph] + inner ear hair cell development + GO:inner ear receptor cell development + GO:0060119 + inner ear receptor cell development + + + ciliary membrane + cilial membrane + cilium membrane + GO:ciliary membrane + "The portion of the plasma membrane surrounding a cilium." [GOC:cilia, GOC:dph, GOC:rph] + GO:0060170 + + + GO:0060173 + "The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin." [GOC:dgh, GOC:dph, PMID:11487378] + GO:limb development + limb development + + + limb bud formation + "The process pertaining to the initial formation of a limb bud from unspecified parts. This process begins with the formation of a local condensation of mesenchyme cells within the prospective limb field, and ends when a limb bud is recognizable." [GOC:dgh, GOC:dph] + limb formation + GO:limb bud formation + GO:0060174 + limbbud formation + + + GO:primitive hemopoiesis + primitive haematopoiesis + primitive hemopoiesis + primitive haemopoiesis + GO:0060215 + "A first transient wave of blood cell production that, in vertebrates, gives rise to erythrocytes (red blood cells) and myeloid cells." [GOC:bf, GOC:dph, PMID:15378083, PMID:15617691] + primitive hematopoiesis + + + definitive hematopoiesis + GO:definitive hemopoiesis + definitive haematopoiesis + GO:0060216 + definitive hemopoiesis + definitive haemopoiesis + "A second wave of blood cell production that, in vertebrates, generates long-term hemopoietic stem cells that continously provide erythroid, myeloid and lymphoid lineages throughout adulthood." [GOC:bf, GOC:dph, PMID:15378083, PMID:15617691] + + + camera-type eye photoreceptor cell differentiation + "The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell in a camera-type eye." [GOC:ascb_2009, GOC:dph, GOC:tb] + GO:camera-type eye photoreceptor cell differentiation + GO:0060219 + + + GO:delamination + delamination + "The process of negative regulation of cell adhesion that results in a cell or sheet of cells splitting off from an existing epithelial sheet." [GOC:dph, PMID:16962574, PMID:18343170] + GO:0060232 + + + "A homeostatic process involved in the maintenance of an internal steady state within a defined anatomical structure of an organism, including control of cellular proliferation and death and control of metabolic function. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph] + GO:0060249 + GO:anatomical structure homeostasis + anatomical structure maintenance + anatomical structure homeostasis + + + GO:0060255 + regulation of macromolecule metabolic process + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb] + GO:regulation of macromolecule metabolic process + + + "Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:dph, GOC:tb] + GO:regulation of cell development + GO:0060284 + regulation of cell development + + + "A process that modulates synaptic plasticity such that synapses are changed resulting in the increase in the rate, or frequency of synaptic transmission at the synapse." [GOC:dgh, GOC:dph] + GO:long-term synaptic potentiation + long-term synaptic potentiation + GO:0060291 + LTP + + + "Erythrocyte differentiation which occurs as part of the process of definitive hemopoiesis." [GOC:add, GOC:BHF, GOC:dph] + definitive erythropoiesis + GO:0060318 + definitive erythrocyte differentiation + GO:definitive erythrocyte differentiation + definitive RBC differentiation + definitive red blood cell differentiation + + + primitive erythropoiesis + GO:0060319 + GO:primitive erythrocyte differentiation + primitive RBC differentiation + primitive erythrocyte differentiation + primitive red blood cell differentiation + "Erythrocyte differentiation which occurs as part of the process of primitive hemopoiesis." [GOC:add, GOC:BHF, GOC:dph] + + + head development + "The biological process whose specific outcome is the progression of a head from an initial condition to its mature state. The head is the anterior-most division of the body." [GOC:dph] + GO:0060322 + GO:head development + + + cell chemotaxis + "The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." [GOC:dph] + GO:cell chemotaxis + GO:0060326 + + + GO:regulation of cellular localization + GO:0060341 + regulation of cellular localization + regulation of cellular localisation + "Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell." [GOC:dph, GOC:tb] + + + GO:bone morphogenesis + GO:0060349 + bone morphogenesis + "The process in which bones are generated and organized." [GOC:dph] + + + "The process in which a nerve invades a tissue and makes functional synaptic connection within the tissue." [GOC:dph, GOC:sart] + innervation + GO:0060384 + GO:innervation + + + SMAD protein signal transduction + GO:SMAD protein signal transduction + "The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell." [GOC:BHF, GOC:dph, GOC:tb] + GO:0060395 + + + growth hormone receptor signalling pathway + GO:growth hormone receptor signaling pathway + "The series of molecular signals generated as a consequence of growth hormone receptor binding to its physiological ligand." [GOC:BHF, GOC:dph, PMID:11445442] + GH receptor signaling pathway + growth hormone receptor signaling pathway + cellular response to growth hormone + GO:0060396 + + + lung morphogenesis + GO:0060425 + GO:lung morphogenesis + "The process in which the anatomical structures of the lung are generated and organized." [GOC:dph] + + + GO:0060428 + pulmonary epithelium development + GO:lung epithelium development + lung epithelium development + "The biological process whose specific outcome is the progression of the lung epithelium from an initial condition to its mature state. This process begins with the formation of lung epithelium and ends with the mature structure. The lung epithelium is the specialized epithelium that lines the inside of the lung." [GOC:dph, GOC:mtg_lung] + + + GO:epithelium development + GO:0060429 + epithelium development + "The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure." [GOC:dph, GOC:mtg_lung] + + + GO:0060430 + GO:lung saccule development + lung saccule development + "The biological process whose specific outcome is the progression of a lung saccule from an initial condition to its mature state. The lung saccule is the primitive gas exchange portion of the lung composed of type I and type II cells." [GOC:dph, GOC:mtg_lung] + + + lung formation + primary lung bud formation + GO:primary lung bud formation + GO:0060431 + "The morphogenetic process in which the foregut region specified to become the lung forms the initial left and right buds." [GOC:dph, GOC:mtg_lung] + + + bronchiole development + "The biological process whose specific outcome is the progression of a bronchiole from an initial condition to its mature state. This process begins with the formation of the bronchiole and ends with the mature structure. A bronchiole is the first airway branch that no longer contains cartilage; it is a branch of the bronchi." [GOC:dph, GOC:mtg_lung] + GO:bronchiole development + GO:0060435 + + + GO:0060438 + GO:trachea development + trachea development + "The process whose specific outcome is the progression of a trachea over time, from its formation to the mature structure. The trachea is the portion of the airway that attaches to the bronchi as it branches." [GOC:dph] + + + lung branching morphogenesis + GO:0060441 + GO:epithelial tube branching involved in lung morphogenesis + epithelial tube branching involved in lung morphogenesis + "The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units." [GOC:dph, GOC:mtg_lung] + + + pharyngeal development + GO:pharynx development + GO:0060465 + "The biological process whose specific outcome is the progression of a pharynx from an initial condition to its mature state. The pharynx is the part of the digestive system immediately posterior to the mouth." [GOC:dph, GOC:rk] + pharynx development + + + "A secretory vesicle that is stored under the cell membrane of an egg. These vesicles fuse with the egg plasma membrane as part of egg activation and are part of the block to polyspermy." [GOC:dph] + GO:cortical granule + GO:0060473 + cortical vesicle + cortical granule + + + mesenchyme development + "The process whose specific outcome is the progression of a mesenchymal tissue over time, from its formation to the mature structure. A mesenchymal tissue is made up of loosely packed stellate cells." [GOC:dph] + mesenchymal development + GO:0060485 + GO:mesenchyme development + + + "The progression of muscle tissue over time, from its initial formation to its mature state. Muscle tissue is a contractile tissue made up of actin and myosin fibers." [GOC:dph] + muscle tissue development + GO:0060537 + GO:muscle tissue development + + + GO:skeletal muscle organ development + skeletal muscle organ development + "The progression of a skeletal muscle organ over time from its initial formation to its mature state. A skeletal muscle organ includes the skeletal muscle tissue and its associated connective tissue." [GOC:dph] + GO:0060538 + + + "The progression of the diaphragm over time from its initial formation to the mature structure. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs." [GOC:dph] + GO:diaphragm development + diaphragm development + GO:0060539 + + + "Any apoptotic process that contributes to the shaping of an anatomical structure." [GOC:dph, GOC:mtg_apoptosis] + apoptotic process involved in morphogenesis + GO:0060561 + apoptosis involved in development + GO:apoptotic process involved in morphogenesis + morphogenetic apoptosis + + + epithelial tube morphogenesis + GO:epithelial tube morphogenesis + GO:0060562 + "The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." [GOC:dph] + + + "The morphogenetic process in which an epithelial sheet bends along a linear axis." [GOC:dph] + morphogenesis of an epithelial fold + GO:0060571 + folding of an epithelial sheet + GO:morphogenesis of an epithelial fold + epithelial folding + + + morphogenesis of an epithelial bud + GO:0060572 + GO:morphogenesis of an epithelial bud + "The morphogenetic process in which a bud forms from an epithelial sheet. A bud is a protrusion that forms form the sheet by localized folding." [GOC:dph] + + + adipogenesis + GO:adipose tissue development + adipose tissue development + "The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat." [GOC:dph] + GO:0060612 + + + GO:chorio-allantoic fusion + chorio-allantoic fusion + GO:0060710 + "The cell-cell adhesion process in which the cells of the chorion fuse to the cells of the allantois." [GOC:dph] + + + "The process in which the labyrinthine layer of the placenta progresses, from its formation to its mature state." [GOC:dph] + GO:labyrinthine layer development + labyrinthine layer development + GO:0060711 + + + "The developmental process in which an ectodermal placode forms. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm." [GOC:dph, GOC:sdb_2009, GOC:tb] + GO:0060788 + GO:ectodermal placode formation + ectodermal placode formation + + + GO:0060789 + "The developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud." [GOC:dph, GOC:sdb_2009, GOC:tb] + GO:hair follicle placode formation + hair follicle placode formation + + + inactivation of paternal X chromosome + GO:0060817 + GO:inactivation of paternal X chromosome + "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes specifically on the paternal X-chromosome in the XX sex." [GOC:dph, GOC:sdb_2009, GOC:tb] + + + GO:inactivation of X chromosome by genetic imprinting + "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by genetic imprinting." [GOC:dph, GOC:sdb_2009, GOC:tb] + GO:0060819 + inactivation of X chromosome by genetic imprinting + + + GO:artery development + GO:0060840 + artery development + "The progression of the artery over time, from its initial formation to the mature structure. An artery is a blood vessel that carries blood away from the heart to a capillary bed." [GOC:dph, GOC:sdb_2009, GOC:tb] + + + "The progression of the semicircular canal from its initial formation to the mature structure." [GOC:dph, GOC:sdb_2009, GOC:tb] + GO:0060872 + semicircular canal development + GO:semicircular canal development + + + kidney morphogenesis + GO:kidney morphogenesis + GO:0060993 + "Morphogenesis of a kidney. A kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." [GOC:dph, GOC:mtg_kidney_jan10] + + + cellular membrane organization + membrane organization and biogenesis + membrane organization + GO:membrane organization + cellular membrane organisation + "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:dph, GOC:tb] + membrane organisation + GO:0061024 + + + cellular membrane fusion + GO:membrane fusion + "The membrane organization process that joins two lipid bilayers to form a single membrane." [GOC:dph, GOC:tb] + GO:0061025 + membrane fusion + + + "Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury." [GOC:BHF, GOC:dph] + GO:0061041 + regulation of wound healing + GO:regulation of wound healing + + + "Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury." [GOC:dph] + GO:0061045 + negative regulation of wound healing + GO:negative regulation of wound healing + + + "The progression of a muscle structure over time, from its formation to its mature state. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms." [GOC:dph] + GO:0061061 + muscle structure development + GO:muscle structure development + + + GO:morphogenesis of a branching epithelium + "The process in which the anatomical structures of a branched epithelium are generated and organized." [GOC:dph] + morphogenesis of a branching epithelium + GO:0061138 + + + GO:0061448 + "The progression of a connective tissue over time, from its formation to the mature structure." [GOC:BHF] + connective tissue development + GO:connective tissue development + + + "The process whose specific outcome is the progression of a myeloid cell over time, from its formation to the mature structure." [GOC:dph] + GO:0061515 + GO:myeloid cell development + myeloid cell development + + + macrophage proliferation + GO:0061517 + GO:macrophage proliferation + "The expansion of a macrophage population by cell division." [GOC:dph, PMID:12614284, PMID:19466391] + + + "The expansion of a microglial cell population by cell division." [GOC:dph, PMID:17344397] + GO:microglial cell proliferation + GO:0061518 + microglial cell proliferation + + + GO:hindgut development + hindgut development + "The process whose specific outcome is the progression of the hindgut over time, from its formation to the mature structure. The hindgut is part of the alimentary canal that lies posterior to the midgut." [GOC:dph] + GO:0061525 + + + "The process in which the anatomical structures of a rhabdomere are generated and organized. The rhabdomere is the organelle on the apical surface of a photoreceptor cell that contains the visual pigments." [GOC:dph, PMID:22113834] + GO:rhabdomere morphogenesis + rhabdomere morphogenesis + GO:0061541 + + + "A process that results in the assembly, arrangement of constituent parts, or disassembly of an actin filament bundle." [GOC:dph] + GO:0061572 + actin filament cable organization + GO:actin filament bundle organization + actin filament bundle organization + + + "The process in which a neuron growth cone is directed to a specific target site in response to an attractive chemical signal." [GOC:dph, GOC:krc] + GO:chemoattraction of axon + GO:0061642 + chemoattraction of axon + + + GO:histone H3-K9 modification + histone H3-K9 modification + GO:0061647 + "The modification of histone H3 at a lysine in position 9 of the histone." [GOC:vw] + + + GO:transferase complex, transferring phosphorus-containing groups + transferase complex, transferring phosphorus-containing groups + "A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." [GOC:bhm, GOC:dph] + GO:0061695 + + + mitochondrion degradation + mitochondrion disassembly + "The disaggregation of a mitochondrion into its constituent components." [GOC:autophagy, PMID:25009776] + GO:mitochondrion disassembly + GO:0061726 + + + GO:motor learning + GO:0061743 + motor learning + "Any process in which an organism acquires a novel neuromuscular action or movement as the result of experience." [GOC:bf, GOC:PARL, Wikipedia:Motor_learning] + + + GO:0061744 + GO:motor behavior + "The specific neuromuscular movement of a single organism in response to external or internal stimuli." [GOC:bf, GOC:PARL, PMID:25318560] + motor behavior + + + GO:0065003 + macromolecular complex assembly + "The aggregation, arrangement and bonding together of a set of macromolecules to form a complex." [GOC:jl] + GO:macromolecular complex assembly + macromolecule complex assembly + + + DNA-protein complex assembly + GO:protein-DNA complex assembly + "The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex." [GOC:jl] + protein-DNA complex assembly + GO:0065004 + + + GO:0065007 + GO:biological regulation + biological regulation + "Any process that modulates a measurable attribute of any biological process, quality or function." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] + + + GO:0065008 + regulation of biological quality + regulation of biological characteristic + GO:regulation of biological quality + regulation of biological attribute + "Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] + + + GO:0065009 + GO:regulation of molecular function + "Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GOC:isa_complete] + regulation of a molecular function + regulation of molecular function + + + "An organelle lumen that is part of an intracellular organelle." [GOC:mah] + GO:intracellular organelle lumen + GO:0070013 + intracellular organelle lumen + + + "The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans)." [GOC:BHF, GOC:rl] + GO:0070091 + GO:glucagon secretion + glucagon secretion + + + "Any process that modulates the frequency, rate or extent of the regulated release of glucagon." [GOC:BHF, GOC:mah] + GO:0070092 + GO:regulation of glucagon secretion + regulation of glucagon secretion + + + GO:anchoring junction + anchoring junction + GO:0070161 + "A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix." [ISBN:0815332181] + anchoring cell junction + + + chromosome organization involved in meiotic cell cycle + GO:chromosome organization involved in meiotic cell cycle + "A process of chromosome organization that is involved in a meiotic cell cycle." [GOC:mah] + chromosome organisation involved in meiosis + GO:0070192 + meiotic chromosome organization + + + GO:0070193 + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synaptonemal complex. A synaptonemal complex is a proteinaceous scaffold formed between homologous chromosomes during meiosis." [GOC:mah] + GO:synaptonemal complex organization + synaptonemal complex organization + synaptonemal complex organisation + + + GO:0070194 + synaptonemal complex disassembly + GO:synaptonemal complex disassembly + "The controlled breakdown of a synaptonemal complex." [GOC:mah] + + + GO:regulation of establishment of protein localization + regulation of establishment of protein localization + GO:0070201 + "Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location." [GOC:BHF, GOC:mah] + regulation of establishment of protein localisation + + + GO:0070268 + "A type of programmed cell death that occurs in the epidermis, morphologically and biochemically distinct from apoptosis. It leads to the formation of corneocytes, i.e. dead keratinocytes containing an amalgam of specific proteins (e.g., keratin, loricrin, SPR and involucrin) and lipids (e.g., fatty acids and ceramides), which are necessary for the function of the cornified skin layer (mechanical resistance, elasticity, water repellence and structural stability)." [GOC:krc, PMID:18846107] + cornification + GO:cornification + + + GO:pigment cell development + "The process whose specific outcome is the progression of a pigment cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a pigment cell fate." [GOC:cvs] + pigment cell development + GO:0070285 + + + nephron absorption + GO:renal absorption + renal reabsorption + GO:0070293 + renal absorption + "A renal system process in which water, ions, glucose and proteins are taken up from the collecting ducts, glomerulus and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures (e.g. protein absorption is observed in nephrocytes in Drosophila, see PMID:23264686)." [GOC:dph, GOC:mah, GOC:yaf] + + + "A renal system process in which water is taken up from the collecting ducts and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures." [GOC:dph, GOC:mah] + GO:renal water absorption + renal water reabsorption + renal water absorption + nephron water absorption + GO:0070295 + + + GO:0070307 + GO:lens fiber cell development + "The process whose specific outcome is the progression of a lens fiber cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a lens fiber cell fate. A lens fiber cell is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye." [GOC:mah, PMID:7693735] + lens fibre cell development + lens fiber cell development + + + GO:exocytic vesicle + GO:0070382 + exocytic constitutive secretory pathway transport vesicle + exocytic vesicle + "A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis." [GOC:kad, GOC:mah] + exocytotic vesicle + + + nucleotide-binding oligomerization domain containing signaling pathway + "Any series of molecular signals generated as a consequence of binding to a nucleotide-binding oligomerization domain containing (NOD) protein." [GOC:add, PMID:17944960, PMID:18585455] + GO:0070423 + nucleotide-binding oligomerization domain containing signalling pathway + NOD signaling pathway + GO:nucleotide-binding oligomerization domain containing signaling pathway + + + GO:nucleotide-binding oligomerization domain containing 2 signaling pathway + NOD2 signaling pathway + GO:0070431 + nucleotide-binding oligomerization domain containing 2 signalling pathway + nucleotide-binding oligomerization domain containing 2 signaling pathway + "Any series of molecular signals generated as a consequence of binding to nucleotide-binding oligomerization domain containing 2 (NOD2)." [GOC:add, PMID:17944960, PMID:18585455] + + + immune cell aggregation + white blood cell aggregation + leucocyte aggregation + leukocyte aggregation + white corpuscle aggregation + "The adhesion of one leukocyte to one or more other leukocytes via adhesion molecules." [GOC:sl, PMID:12972508] + GO:leukocyte aggregation + GO:0070486 + + + T-cell aggregation + T lymphocyte aggregation + "The adhesion of one T cell to one or more other T cells via adhesion molecules." [GOC:sl, PMID:12972508] + GO:0070489 + T-lymphocyte aggregation + T cell aggregation + GO:T cell aggregation + + + interleukin-1-mediated signalling pathway + GO:interleukin-1-mediated signaling pathway + interleukin-1-mediated signaling pathway + IL-1-mediated signaling pathway + GO:0070498 + "A series of molecular signals initiated by the binding of interleukin-1 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mah, GOC:signaling] + + + regulation of microtubule cytoskeleton organization + regulation of microtubule cytoskeleton organisation + "Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." [GOC:mah] + regulation of microtubule dynamics + GO:0070507 + GO:regulation of microtubule cytoskeleton organization + + + GO:calcium ion import + "The directed movement of calcium ions into a cell or organelle." [GOC:mah] + calcium ion import + calcium ion uptake + GO:0070509 + transmembrane calcium influx + + + GO:platelet aggregation + platelet aggregation + "The adhesion of one platelet to one or more other platelets via adhesion molecules." [GOC:BHF, GOC:vk] + thrombocyte aggregation + blood platelet aggregation + GO:0070527 + + + SWI/SNF superfamily-type complex + GO:0070603 + SWI-SNF global transcription activator complex + SWI/SNF-type complex + "A protein complex that contains an ortholog of the Saccharomyces ATPase Swi2/Snf2 as one of the core components and mediates assembly of nucleosomes, changes to the spacing or structure of nucleosomes, or some combination of those activities in a manner that requires ATP." [GOC:krc, GOC:mah, PMID:16155938] + SWI-SNF-type complex + GO:SWI/SNF superfamily-type complex + SWI2/SNF2 superfamily ATP-dependent chromatin remodeling complex + + + regulation of protein maturation by peptide bond cleavage + GO:0070613 + "Any process that modulates the frequency, rate or extent of protein processing, any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein." [GOC:mah] + regulation of protein processing + GO:regulation of protein processing + + + "A protein modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to or removed from a target protein." [GOC:mah] + GO:0070647 + GO:protein modification by small protein conjugation or removal + protein modification by small protein conjugation or removal + + + GO:0070661 + leukocyte proliferation + "The expansion of a leukocyte population by cell division." [GOC:add] + GO:leukocyte proliferation + + + GO:0070727 + cellular macromolecule localisation + cellular macromolecule localization + GO:cellular macromolecule localization + "Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GOC:mah] + + + histone H3 K27 methylation + histone lysine H3 K27 methylation + GO:0070734 + histone H3K27me + histone H3-K27 methylation + GO:histone H3-K27 methylation + "The modification of histone H3 by addition of one or more methyl groups to lysine at position 27 of the histone." [GOC:mah, GOC:pr] + + + gamma-secretase complex + GO:gamma-secretase complex + GO:0070765 + gamma-secretase complex (APH1B, PSEN1, PSENEN, NCSTN) + "A protein complex that has aspartic-type endopeptidase activity, and contains a catalytic subunit, presenilin (PS), that is a prototypical member of the GxGD-type aspartyl peptidases. The complex also contains additional subunits, including nicastrin, APH-1, PEN-2, and a regulatory subunit, CD147. Gamma-secretase cleaves several transmembrane proteins including the cell surface receptor Notch and the beta-amyloid precursor protein." [GOC:mah, PMID:15286082, PMID:15890777, PMID:17047368] + + + GO:heterochromatin organization + heterochromatin organisation + GO:0070828 + "Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin, a compact and highly condensed form of chromatin." [GOC:mah] + heterochromatin organization + + + GO:divalent metal ion transport + GO:0070838 + divalent metal ion transport + "The directed movement of divalent metal cations, any metal ion with a +2 electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] + + + GO:0070841 + GO:inclusion body assembly + inclusion body assembly + "The aggregation, arrangement and bonding together of a set of components to form an inclusion body." [GOC:BHF, GOC:mah] + + + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus." [GOC:BHF, GOC:mah] + GO:response to growth factor + GO:0070848 + response to growth factor + response to growth factor stimulus + + + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus." [GOC:mah] + GO:cellular response to chemical stimulus + cellular response to chemical stimulus + GO:0070887 + + + "The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] + GO:organelle assembly + organelle assembly + GO:0070925 + + + neuron cell death + "The process of cell death in a neuron." [GOC:BHF, GOC:mah] + GO:0070997 + neuronal cell death + neuron death + GO:neuron death + + + GO:DNA conformation change + "A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule." [GOC:mah] + DNA conformation modification + GO:0071103 + DNA conformation change + + + GO:0071159 + GO:NF-kappaB complex + NF-kappaB complex + "A protein complex that consists of a homo- or heterodimer of members of a family of structurally related proteins that contain a conserved N-terminal region called the Rel homology domain (RHD). In the nucleus, NF-kappaB complexes act as transcription factors. In unstimulated cells, NF-kappaB dimers are sequestered in the cytoplasm by IkappaB monomers; signals that induce NF-kappaB activity cause degradation of IkappaB, allowing NF-kappaB dimers to translocate to the nucleus and induce gene expression." [ISBN:0849327946] + + + GO:0071214 + cellular response to abiotic stimulus + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus." [GOC:mah] + GO:cellular response to abiotic stimulus + + + GO:0071310 + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus." [GOC:mah] + cellular response to organic substance + GO:cellular response to organic substance + + + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus." [GOC:mah] + GO:0071363 + cellular response to growth factor stimulus + GO:cellular response to growth factor stimulus + + + GO:0071478 + GO:cellular response to radiation + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation." [GOC:mah] + cellular response to radiation + cellular response to radiation stimulus + cellular response to electromagnetic radiation stimulus + + + cellular response to light stimulus + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light." [GOC:mah] + GO:0071482 + GO:cellular response to light stimulus + + + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light intensity stimulus." [GOC:mah] + GO:0071484 + cellular response to light intensity + GO:cellular response to light intensity + + + GO:0071485 + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an absence of light stimuli." [GOC:mah] + cellular response to darkness + GO:cellular response to absence of light + cellular response to absence of light + + + GO:cellular response to endogenous stimulus + GO:0071495 + cellular response to endogenous stimulus + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism." [GOC:mah] + + + GO:cellular response to external stimulus + GO:0071496 + cellular response to external stimulus + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus." [GOC:mah] + cellular response to environmental stimulus + + + GO:genetic imprinting + genetic imprinting + DNA imprinting + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules by a mechanism that is mediated by DNA, is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence." [GOC:mah, GOC:vw] + GO:0071514 + + + "The adhesion of one lymphocyte to one or more other lymphocytes via adhesion molecules." [GOC:sl] + GO:lymphocyte aggregation + lymphocyte aggregation + GO:0071593 + + + "The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon." [CHEBI:50860, GOC:mah] + GO:0071702 + organic substance transport + GO:organic substance transport + + + organic molecular entity metabolic process + "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [CHEBI:50860, GOC:mah] + GO:organic substance metabolic process + organic substance metabolism + GO:0071704 + organic substance metabolic process + organic molecular entity metabolism + + + "The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [CHEBI:51143, GOC:mah] + GO:nitrogen compound transport + GO:0071705 + nitrogen compound transport + + + IgG immunoglobulin complex + GO:IgG immunoglobulin complex + "A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196] + GO:0071735 + + + "A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196] + GO:IgG immunoglobulin complex, circulating + IgG immunoglobulin complex, circulating + GO:0071736 + + + IgM immunoglobulin complex + GO:0071753 + "A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:20176268] + GO:IgM immunoglobulin complex + + + IgY immunoglobulin complex + GO:IgY immunoglobulin complex + GO:0071760 + "A protein complex composed of two identical immunoglobulin heavy chains of the IgY isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgY immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196] + + + protein complex subunit organization + GO:0071822 + "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] + GO:protein complex subunit organization + protein complex subunit organisation + + + protein-DNA complex subunit organization + "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA complex." [GOC:mah] + protein-DNA complex subunit organisation + GO:protein-DNA complex subunit organization + GO:0071824 + DNA-protein complex subunit organization + + + cellular component organisation or biogenesis + cellular component organisation or biogenesis at cellular level + cellular component organization or biogenesis + GO:cellular component organization or biogenesis + GO:0071840 + cellular component organization or biogenesis at cellular level + "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] + + + cessation of mitotic cell cycle + "The process in which the mitotic cell cycle is halted during one of the normal phases (G1, S, G2, M)." [GOC:mah] + GO:0071850 + termination of mitotic cell cycle + mitotic cell cycle arrest + arrest of mitotic cell cycle progression + GO:mitotic cell cycle arrest + + + DNA synthesis + DNA biosynthetic process + DNA formation + DNA biosynthesis + "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC:mah] + GO:DNA biosynthetic process + DNA anabolism + GO:0071897 + + + GO:0071900 + regulation of protein serine/threonine kinase activity + GO:regulation of protein serine/threonine kinase activity + "Any process that modulates the rate, frequency, or extent of protein serine/threonine kinase activity." [GOC:mah] + + + GO:0071902 + positive regulation of protein serine/threonine kinase activity + GO:positive regulation of protein serine/threonine kinase activity + "Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity." [GOC:mah] + + + "The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures." [GOC:mah] + GO:0071944 + GO:cell periphery + cell periphery + + + GO:0072006 + nephrogenesis + nephron development + "The process whose specific outcome is the progression of the nephron over time, from its formation to the mature structure. A nephron is the functional unit of the kidney." [GOC:mtg_kidney_jan10] + GO:nephron development + + + GO:0072089 + "The multiplication or reproduction of stem cells, resulting in the expansion of a stem cell population. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [GOC:mtg_kidney_jan10] + stem cell proliferation + GO:stem cell proliferation + + + "The chemical reactions and pathways resulting in the breakdown of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group." [CHEBI:25384, GOC:mah] + GO:0072329 + GO:monocarboxylic acid catabolic process + monocarboxylic acid catabolic process + + + monocarboxylic acid synthesis + monocarboxylic acid anabolism + GO:0072330 + "The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group." [CHEBI:25384, GOC:mah] + monocarboxylic acid biosynthesis + monocarboxylic acid formation + GO:monocarboxylic acid biosynthetic process + monocarboxylic acid biosynthetic process + + + GO:0072350 + GO:tricarboxylic acid metabolic process + "The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing three carboxyl (COOH) groups or anions (COO-)." [CHEBI:27093, GOC:mah] + tricarboxylic acid metabolic process + tricarboxylic acid metabolism + + + GO:cardiovascular system development + "The process whose specific outcome is the progression of the cardiovascular system over time, from its formation to the mature structure. The cardiovascular system is the anatomical system that has as its parts the heart and blood vessels." [GOC:mah, UBERON:0004535] + GO:0072358 + cardiovascular system development + + + GO:0072372 + primary cilium + GO:primary cilium + "A cilium found on many different cell types that is typically present in a single copy per cell. A primary cilium may have a variable array of axonemal microtubules and may or may not contain molecular motors." [GOC:curators, PMID:17009929, PMID:20144998] + + + GO:0072376 + GO:protein activation cascade + protein activation cascade + "A response to a stimulus that consists of a sequential series of modifications to a set of proteins where the product of one reaction acts catalytically in the following reaction. The magnitude of the response is typically amplified at each successive step in the cascade. Modifications typically include proteolysis or covalent modification, and may also include binding events." [GOC:add, GOC:mah, GOC:pde] + protein activitory cascade + protein activation pathway + + + "The directed movement of inorganic cations with a valency of two into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic cations are atoms or small molecules with a positive charge which do not contain carbon in covalent linkage." [GOC:mah] + GO:0072511 + divalent inorganic cation transport + GO:divalent inorganic cation transport + + + GO:0072521 + purine-containing compound metabolism + GO:purine-containing compound metabolic process + purine-containing compound metabolic process + "The chemical reactions and pathways involving a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof." [CHEBI:26401, GOC:mah] + purine and derivative metabolic process + + + GO:0072522 + purine-containing compound anabolism + purine-containing compound synthesis + GO:purine-containing compound biosynthetic process + purine-containing compound biosynthesis + purine-containing compound formation + purine-containing compound biosynthetic process + "The chemical reactions and pathways resulting in the formation of a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof." [CHEBI:26401, GOC:mah] + purine and derivative biosynthetic process + + + GO:0072524 + GO:pyridine-containing compound metabolic process + pyridine-containing compound metabolism + pyridine and derivative metabolic process + pyridine-containing compound metabolic process + "The chemical reactions and pathways involving a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof." [CHEBI:26421, GOC:mah] + + + pyridine-containing compound biosynthesis + pyridine-containing compound synthesis + GO:0072525 + pyridine-containing compound anabolism + pyridine and derivative biosynthetic process + "The chemical reactions and pathways resulting in the formation of a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof." [CHEBI:26421, GOC:mah] + pyridine-containing compound biosynthetic process + pyridine-containing compound formation + GO:pyridine-containing compound biosynthetic process + + + GO:0072583 + clathrin-dependent endocytosis + clathrin coated pit-dependent endocytosis + GO:clathrin-mediated endocytosis + clathrin-mediated endocytosis + "An endocytosis process that begins when material is taken up into clathrin-coated pits, which then pinch off to form clathrin-coated endocytic vesicles." [GOC:BHF, GOC:mah, PMID:18498251, PMID:8970738, PMID:9234965] + + + ROS metabolic process + reactive oxygen species metabolism + GO:0072593 + "The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers." [CHEBI:26523, GOC:mah] + GO:reactive oxygen species metabolic process + reactive oxygen species metabolic process + + + maintenance of protein localization in organelle + GO:0072595 + "Any process in which a protein is maintained in a specific location a specific location on or in an organelle, and is prevented from moving elsewhere. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle." [GOC:mah] + maintenance of protein localisation to organelle + maintenance of protein localization to organelle + GO:maintenance of protein localization in organelle + + + GO:protein localization to membrane + "A process in which a protein is transported to, or maintained in, a specific location in a membrane." [GOC:mah] + GO:0072657 + protein localization in membrane + protein localization to membrane + protein localisation in membrane + + + neutrophil extravasation + "The migration of a neutrophil from the blood vessels into the surrounding tissue." [CL:0000775, GOC:BHF] + GO:0072672 + GO:neutrophil extravasation + + + GO:0072686 + "A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules." [GOC:mah, GOC:vw, PMID:11408572, PMID:18367542, PMID:8027178] + mitotic spindle + GO:mitotic spindle + + + GO:meiotic spindle + GO:0072687 + meiotic spindle + "A spindle that forms as part of meiosis. Several proteins, such as budding yeast Spo21p, fission yeast Spo2 and Spo13, and C. elegans mei-1, localize specifically to the meiotic spindle and are absent from the mitotic spindle." [GOC:mah, GOC:vw, PMID:11408572, PMID:18367542, PMID:8027178] + + + spore-bearing organ development + fruiting structure development + "The process whose specific outcome is the progression of a spore-bearing organ over time, from its formation to the mature structure. A spore-bearing organ is an anatomical structure that produces new spores." [GOC:mah, GOC:mcc, GOC:pamgo_curators] + GO:spore-bearing organ development + GO:0075259 + + + GO:ascus development + GO:0075317 + "The process that leads to the development of ascus, a sac-like structure produced by fungi of the phylum Ascomycota (sac fungi) in which sexually produced spores (ascospores), usually four or eight in number, are formed." [GOC:di, GOC:mah, GOC:mcc, GOC:pamgo_curators] + ascus development + + + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [PMID:19211694] + GO:0080090 + regulation of primary metabolic process + GO:regulation of primary metabolic process + + + GO:0080134 + regulation of response to stress + "Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:dhl] + GO:regulation of response to stress + + + GO:primitive streak formation + primitive streak formation + "The developmental process pertaining to the initial formation of the primitive streak from unspecified parts. The primitive streak is a ridge of cells running along the midline of the embryo where the mesoderm ingresses. It defines the anterior-posterior axis." [GOC:dph, GOC:sdb_2009, GOC:tb] + GO:0090009 + + + "Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb] + regulation of peptide transport + GO:0090087 + GO:regulation of peptide transport + + + GO:0090092 + GO:regulation of transmembrane receptor protein serine/threonine kinase signaling pathway + "Any process that modulates the rate, frequency, or extent of the series of molecular signals generated as a consequence of a transmembrane receptor serine/threonine kinase binding to its physiological ligand." [GOC:dph, GOC:tb] + regulation of transmembrane receptor protein serine/threonine kinase signaling pathway + regulation of transmembrane receptor protein serine/threonine kinase signalling pathway + + + "The progression of the cochlea over time from its formation to the mature structure. The cochlea is the snail-shaped portion of the inner ear that is responsible for the detection of sound." [GOC:dph, GOC:tb] + GO:0090102 + GO:cochlea development + cochlea development + + + GO:organelle membrane fusion + GO:0090174 + organelle membrane fusion + "The joining of two lipid bilayers to form a single organelle membrane." [GOC:ascb_2009, GOC:dph, GOC:tb] + + + GO:fibroblast growth factor production + "The appearance of a fibroblast growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:BHF] + GO:0090269 + fibroblast growth factor production + + + GO:0090276 + GO:regulation of peptide hormone secretion + "Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules." [GOC:tb] + regulation of peptide hormone secretion + + + GO:regulation of cellular response to growth factor stimulus + GO:0090287 + "Any process that modulates the rate, frequency, or extent of a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus." [GOC:tb] + regulation of cellular response to growth factor stimulus + + + GO:nucleic acid metabolic process + GO:0090304 + nucleic acid metabolic process + "Any cellular metabolic process involving nucleic acids." [GOC:dph, GOC:tb] + + + GO:mitotic spindle assembly + GO:0090307 + spindle assembly involved in mitosis + mitotic spindle assembly + "The aggregation, arrangement and bonding together of a set of components to form the spindle that contributes to the process of mitosis." [GOC:tb, GOC:vw] + + + GO:organophosphate biosynthetic process + organophosphate biosynthetic process + GO:0090407 + "The chemical reactions and pathways resulting in the biosynthesis of deoxyribose phosphate, the phosphorylated sugar 2-deoxy-erythro-pentose." [GOC:chem_mtg] + + + "The expansion of one cell sheet over other cells or yolk." [GOC:dph, GOC:tb] + epiboly + GO:epiboly + GO:0090504 + + + GO:BAF-type complex + GO:0090544 + BAF-type complex + "A SWI/SNF-type complex that contains a subunit from the BAF (Brahma-Associated Factor) family." [GOC:krc, GOC:tb] + + + GO:0090575 + GO:RNA polymerase II transcription factor complex + RNA polymerase II transcription factor complex + "A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II." [GOC:tb] + + + sensory organ morphogenesis + "Morphogenesis of a sensory organ. A sensory organ is defined as a tissue or set of tissues that work together to receive and transmit signals from external or internal stimuli. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:kmv, ISBN:978-0199210893] + GO:sensory organ morphogenesis + GO:0090596 + + + GO:0090601 + "The process in which nucleated precursor cells lose their nucleus." [GOC:tb] + GO:enucleation + enucleation + + + "Any process involved in the balance between food intake (energy input) and energy expenditure." [GOC:yaf, PMID:15919751] + GO:0097009 + GO:energy homeostasis + energy homeostasis + + + GO:0097060 + "A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell." [GOC:BHF, PMID:20410104] + GO:synaptic membrane + synaptic membrane + + + "The process aimed at the progression of a vascular smooth muscle cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels." [GOC:BHF] + GO:vascular smooth muscle cell development + vascular smooth muscle cell development + GO:0097084 + + + "Any apoptotic process in a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types." [CL:0000134, GOC:mtg_apoptosis, GOC:yaf, PMID:18231833] + GO:0097152 + mesenchymal cell apoptotic process + GO:mesenchymal cell apoptotic process + + + GO:0097159 + organic cyclic compound binding + "Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure." [CHEBI:33832, GOC:sjw, PMID:7583672] + GO:organic cyclic compound binding + + + GO:0097205 + GO:renal filtration + "A renal system process in which fluid circulating through the body is filtered through a barrier system." [GOC:pr, GOC:sart] + renal filtration + + + sperm part + "Any constituent part of a sperm, a mature male germ cell that develops from a spermatid." [GOC:cjm] + GO:0097223 + GO:sperm part + + + GO:0097285 + "Any apoptotic process in a specific cell type." [GOC:mtg_apoptosis] + cell-type specific apoptotic process + GO:cell-type specific apoptotic process + + + MCM core complex + GO:0097373 + "A protein complex that contains Mcm4, Mcm6, and Mcm7 proteins, and possesses DNA helicase activity. In the heterohexameric MCM complex, the Mcm4/6/7 proteins form a stable core, and Mcm2, Mcm3, and Mcm5 are more peripherally associated." [GOC:mah, PMID:10770926, PMID:15007098, PMID:9305914] + GO:MCM core complex + MCM4/6/7 complex + + + GO:0097374 + sensory neuron axon guidance + "The process in which the migration of an axon growth cone of a sensory neuron is directed to a specific target site in response to a combination of attractive and repulsive cues. A sensory neuron is an afferent neuron conveying sensory impulses." [CL:0000101, GOC:pr] + GO:sensory neuron axon guidance + + + "A prolongation or process extending from a glial cell." [GOC:mc] + glial projection + GO:0097386 + glial cell projection + GO:glial cell projection + glial process + + + "Intracellular mass of paired, helically wound protein filaments (also called PHF) lying in the cytoplasm of neuronal cell bodies and neuritic cell processes. Neurofibrillary tangles contain an abnormally phosphorylated form of a microtubule-associated protein, tau. The shape of these inclusions may resemble a flame or a star." [NIF_Subcellular:nlx_subcell_20090201, NIF_Subcellular:nlx_subcell_20090202, NIF_Subcellular:sao2409833926] + GO:0097418 + GO:neurofibrillary tangle + neurofibrillary tangle + + + "An arrangement of closely apposed microtubules running parallel to each other." [NIF_Subcellular:sao1872343973] + microtubule bundle + microtubule fascicle + GO:0097427 + GO:microtubule bundle + + + "Either of the ends of a mitotic spindle, a spindle that forms as part of mitosis, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules." [GOC:vw] + mitotic spindle pole + GO:mitotic spindle pole + GO:0097431 + + + GO:apical dendrite + GO:0097440 + "A dendrite that emerges near the apical pole of a neuron. In bipolar neurons, apical dendrites are located on the opposite side of the soma from the axon." [NIF_Subcellular:sao273773228] + apical dendrite + + + dendritic tree + GO:0097447 + GO:dendritic tree + "The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches." [NIF_Subcellular:sao172297168] + + + astrocyte process + vellous process + peripheral astrocyte process + "A prolongation or process extending from the soma of an astrocyte and wrapping around neurons." [NIF_Subcellular:sao1630537580] + GO:0097449 + GO:astrocyte projection + astrocyte projection + + + "Any constituent part of a neuron, the basic cellular unit of nervous tissue. A typical neuron consists of a cell body (often called the soma), an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [GOC:pr, http://en.wikipedia.org/wiki/Neuron] + neuron part + GO:0097458 + GO:neuron part + + + GO:ribbon synapse + "Type of synapse characterized by an electron-dense ribbon, lamella (bar) or spherical body in the presynaptic process cytoplasm." [NIF_Subcellular:sao1884931180] + ribbon synapse + GO:0097470 + + + rod photoreceptor apoptotic process + "Any apoptotic process in a retinal rod cell, one of the two photoreceptor cell types of the vertebrate retina." [CL:0000604, GOC:jc, PMID:17202487] + retinal rod cell apoptotic process + GO:retinal rod cell apoptotic process + GO:0097473 + + + membrane leaflet + leaflet of membrane bilayer + "Any of the two layers of lipid molecules that constitute a membrane." [GOC:cjm] + GO:leaflet of membrane bilayer + GO:0097478 + + + "The process in which the migration of a neuron projection is directed to a specific target site in response to a combination of attractive and repulsive cues." [GOC:BHF, GOC:rl, PMID:22790009] + neuron projection guidance + neuron process guidance + GO:0097485 + neuronal cell projection guidance + GO:neuron projection guidance + neuron protrusion guidance + + + "A branched cellular projection (or cytoplasmic extension) that is extended from the surface of a dendritic immune cell, and which enables the cell to sample luminal pathogens and increase the surface area for antigen presentation to T cells." [CL:0000451, GOC:BHF, GOC:cjm, PMID:12200351] + GO:dendritic cell dendrite + dendritic cell dendrite + GO:0097511 + + + myeloid leukocyte migration + GO:myeloid leukocyte migration + GO:0097529 + "The movement of a myeloid leukocyte within or between different tissues and organs of the body." [GOC:cvs, PMID:22342843, PMID:24157461] + + + GO:0097530 + "The movement of a granulocyte within or between different tissues and organs of the body." [GOC:cvs, PMID:24163421, PMID:24193336] + granulocyte migration + GO:granulocyte migration + + + GO:0097546 + cilium base + flagellar base + cilial base + "Area of the cilium (also called flagellum) where the basal body and the axoneme are anchored to the plasma membrane. The ciliary base encompasses the distal part of the basal body, transition fibers and transition zone and is structurally and functionally very distinct from the rest of the cilium. In this area proteins are sorted and filtered before entering the cilium, and many ciliary proteins localize specifically to this area." [GOC:cilia, PMID:22653444] + GO:ciliary base + ciliary base + flagellum base + + + renaturation + GO:annealing activity + annealing activity + "A nucleic acid binding activity that brings together complementary sequences of nucleic acids so that they pair by hydrogen bonds to form a double-stranded polynucleotide." [GOC:mba, http://en.wikipedia.org/wiki/Nucleic_acid_thermodynamics#Annealing] + GO:0097617 + + + GO:0097659 + "The cellular synthesis of RNA on a template of nucleic acid (DNA or RNA)." [GOC:pr, GOC:txnOH, GOC:vw] + GO:nucleic acid-templated transcription + nucleic acid-templated transcription + + + STAT cascade + kinase-STAT cascade + STAT signalling pathway + GO:STAT cascade + "An intracellular signal transduction process in which STAT proteins (Signal Transducers and Activators of Transcription) convey a signal to trigger a change in the activity or state of a cell. The STAT cascade begins with activation of STAT proteins by kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins." [GOC:rjd, PMID:21534947, PMID:24587195] + GO:0097696 + kinase activated-STAT cascade + + + GO:side of membrane + GO:0098552 + "A cellular component consisting of one leaflet of a membrane bilayer and any proteins embedded or anchored in it or attached to its surface." [GOC:dos] + side of membrane + + + cytoplasmic side of membrane + GO:0098562 + GO:cytoplasmic side of membrane + "The side of a membrane that faces the cytoplasm." [GOC:dos] + + + GO:bounding membrane of organelle + bounding membrane of organelle + "The lipid bilayer that forms the outer-most layer of an organelle." [GOC:dos] + GO:0098588 + + + GO:0098589 + region of membrane + "A membrane that is a part of a larger membrane. Examples include the apical region of the plasma membrane of an epithelial cell and the various regions of the endoplasmic reticulum membrane." [GOC:dos] + GO:membrane region + membrane region + + + GO:0098590 + "A membrane that is a (regional) part of the plasma membrane." [GOC:dos] + region of plasma membrane + plasma membrane region + GO:plasma membrane region + + + GO:single organism cell adhesion + GO:0098602 + "The attachment, via cell adhesion molecules, of a cell to either another cell of the same organism, or to an underlying substrate of the same organism such as the extracellular matrix." [GOC:dos] + single organism cell adhesion + + + "The attachment of one cell to another cell via adhesion molecules." [GOC:dos] + GO:0098609 + GO:cell-cell adhesion + cell-cell adhesion + + + GO:0098636 + protein complex involved in cell adhesion + GO:protein complex involved in cell adhesion + "Any protein complex that is capable of carrying out some part of the process of cell-cell adhesion." [GOC:dos] + cell adhesion complex + + + anion transmembrane transport + "A process in which an anion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC:dos, GOC:vw] + GO:0098656 + GO:anion transmembrane transport + + + "The directed movement of some substance from outside of a cell into the cytoplasmic compartment. This may occur via transport across the plasma membrane or via endocytosis." [GOC:dos] + uptake + GO:0098657 + import into cell + GO:import into cell + + + inorganic ion transmembrane transport + "A process in which an inorganic ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC:mah] + transmembrane inorganic ion transport + GO:inorganic ion transmembrane transport + GO:0098660 + inorganic ion membrane transport + + + "A process in which an inorganic anion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC:mah] + GO:inorganic anion transmembrane transport + transmembrane inorganic anion transport + inorganic anion transmembrane transport + inorganic anion membrane transport + GO:0098661 + + + "Any subdivision of a chromosome along its length." [GOC:dos] + chromosome region + GO:0098687 + chromosomal region + GO:chromosomal region + + + GO:asymmetric stem cell division + "Division of a stem cell during which it retains its identity and buds off a daughter cell with a new identity." [GOC:dos, PMID:18513950] + asymmetric stem cell division + GO:0098722 + + + maintenance of cell number + "Any process by which the numbers of cells of a particular type in a tissue are maintained." [GOC:dos] + GO:0098727 + GO:maintenance of cell number + + + GO:0098732 + "The removal of an acyl group, any group or radical of the form RCO- where R is an organic group, from a macromolecule." [GOC:dos] + GO:macromolecule deacylation + macromolecule deacylation + + + GO:cell aggregation + GO:0098743 + "The clustering together and adhesion of initially separate cells to form an aggregate. Examples include the clustering of unicellular organisms or blood cells in suspension and the condensation of mesenchymal cells during cartilage formation." [GOC:dos] + cell aggregation + + + GO:detoxification + GO:0098754 + detoxification + "Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." [GOC:dos] + + + meiotic cell cycle phase + GO:meiotic cell cycle phase + "One of the distinct periods or stages into which the meiotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GOC:dos] + GO:0098762 + + + GO:0098763 + mitotic cell cycle phase + "One of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GOC:dos] + GO:mitotic cell cycle phase + + + "A meiotic cell cycle phase prior to a during which some part of meiosis I nuclear division or the proceeding cytokinesis occurs." [GOC:dos] + GO:0098764 + meiosis I cell cycle phase + GO:meiosis I cell cycle phase + + + GO:0098765 + meiosis II cell cycle phase + GO:meiosis II cell cycle phase + "A meiotic cell cycle phase that occurs after meiosis I (the first meiotic nuclear division)." [GOC:dos] + + + "Any process involved in the maintenance of an internal steady state of inorganic ions within an organism or cell." [GOC:dos] + GO:inorganic ion homeostasis + GO:0098771 + inorganic ion homeostasis + + + Golgi subcompartment + "A compartment that consists of a lumen and an enclosing membrane, and is part of the Golgi Apparatus." [GOC:dos] + GO:Golgi subcompartment + GO:0098791 + + + GO:presynapse + presynapse + "The part of a synapse that is part of the presynaptic cell." [GOC:dos] + GO:0098793 + + + GO:postsynapse + "The part of a synapse that is part of the post-synaptic cell." [GOC:dos] + postsynapse + GO:0098794 + + + GO:0098796 + membrane protein complex + "Any protein complex that is part of a membrane." [GOC:dos] + GO:membrane protein complex + + + plasma membrane protein complex + GO:plasma membrane protein complex + "Any protein complex that is part of the plasma membrane." [GOC:dos] + GO:0098797 + + + "A protein complex that is part of a mitochondrion." [GOC:dos] + mitochondrial protein complex + GO:0098798 + GO:mitochondrial protein complex + + + inner mitochondrial membrane protein complex + GO:0098800 + "Any protein complex that is part of the inner mitochondrial membrane." [GOC:dos] + GO:inner mitochondrial membrane protein complex + + + plasma membrane receptor complex + GO:plasma membrane receptor complex + GO:0098802 + "Any protein complex that is part of the plasma membrane and which functions as a receptor." [GOC:dos] + + + GO:respiratory chain complex + respiratory chain complex + "Any protein complex that is part of a respiratory chain" [GOC:dos] + GO:0098803 + + + whole membrane + GO:whole membrane + GO:0098805 + "Any lipid bilayer that completely encloses some structure, and all the proteins embedded in it or attached to it. Examples include the plasma membrane and most organelle membranes." [GOC:dos] + + + GO:neurotransmitter reuptake + "The directed movement of neurotransmitter molecules from the extrasynaptic space into the presynaptic cytosol." [GOC:dos] + neurotransmitter reuptake + GO:0098810 + + + "The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." [GOC:dos] + GO:nuclear chromosome segregation + nuclear chromosome segregation + GO:0098813 + + + GO:protein transport along microtubule + GO:0098840 + protein transport along microtubule + microtubule-based protein transport + "The directed movement of a protein along a microtubule, mediated by motor proteins." [PMID:25987607] + + + GO:lytic vacuole membrane + GO:0098852 + "The lipid bilayer surrounding a lytic vacuole and separating its contents from the cytoplasm of the cell." [GOC:dos] + lytic vacuole membrane + + + GO:0098856 + intestinal lipid absorption + GO:intestinal lipid absorption + "Any process in which lipids are taken up from the contents of the intestine." [GOC:dos, GOC:sl, PMID:18768481] + + + GO:membrane microdomain + GO:0098857 + "A membrane region with a lipid composition that is distinct from that of the membrane regions that surround it." [PMID:20044567, PMID:26253820] + membrane microdomain + + + actin-based cell projection + GO:actin-based cell projection + GO:0098858 + "A cell projection supported by an assembly of actin filaments, and which lacks microtubules." [PMID:15661519] + + + "A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space." [GOC:dos] + GO:secretory vesicle + secretory vesicle + GO:0099503 + + + GO:0099512 + supramolecular fiber + GO:supramolecular fiber + "A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure." [GOC:dos] + + + "A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits." [GOC:dos] + polymeric cytoskeletal fiber + GO:polymeric cytoskeletal fiber + GO:0099513 + + + "Cell-cell signaling to or from a synapse." [GOC:dos] + GO:0099536 + synaptic signaling + GO:synaptic signaling + + + GO:trans-synaptic signaling + GO:0099537 + trans-synaptic signaling + "Cell-cell signaling in either direction across the synaptic cleft." [GOC:dos] + + + GO:0099568 + "Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm\"" [GOC:dos] + GO:cytoplasmic region + cytoplasmic region + + + GO:postsynaptic specialization + postsynaptic specialization + "A dense network of proteins, adjacent to the postsynaptic membrane, consisting of anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components that spatially and functionally organize the neurotransmitter receptors at the synapse. " [PMID:22046028] + GO:0099572 + + + GO:0099610 + action potential firing + "The initiating cycle of an action potential. In vertebrate neurons this typically occurs at an axon hillock. Not all initiated axon potentials propagate." [ISBN:978-0071390118, PMID:19439602] + action potential initiation + action potential triggering + GO:action potential initiation + + + "Any process that modulates the frequency, rate or extent of hemostasis." [GOC:TermGenie] + GO:1900046 + regulation of hemostasis + GO:regulation of hemostasis + + + downregulation of hemostasis + negative regulation of hemostasis + GO:1900047 + down regulation of hemostasis + down-regulation of hemostasis + GO:negative regulation of hemostasis + "Any process that stops, prevents or reduces the frequency, rate or extent of hemostasis." [GOC:TermGenie] + + + regulation of purine nucleotide metabolic process + regulation of purine nucleotide metabolism + GO:regulation of purine nucleotide metabolic process + "Any process that modulates the frequency, rate or extent of purine nucleotide metabolic process." [GOC:TermGenie] + GO:1900542 + + + GO:1901135 + "The chemical reactions and pathways involving carbohydrate derivative." [GOC:TermGenie] + GO:carbohydrate derivative metabolic process + carbohydrate derivative metabolic process + carbohydrate derivative metabolism + + + GO:1901137 + carbohydrate derivative anabolism + carbohydrate derivative biosynthetic process + carbohydrate derivative synthesis + carbohydrate derivative biosynthesis + carbohydrate derivative formation + GO:carbohydrate derivative biosynthetic process + "The chemical reactions and pathways resulting in the formation of carbohydrate derivative." [GOC:TermGenie] + + + GO:nucleoside phosphate biosynthetic process + nucleoside phosphate biosynthesis + "The chemical reactions and pathways resulting in the formation of a nucleoside phosphate." [GOC:TermGenie] + nucleoside phosphate anabolism + GO:1901293 + nucleoside phosphate synthesis + nucleoside phosphate formation + nucleoside phosphate biosynthetic process + + + "The chemical reactions and pathways involving organic cyclic compound." [GOC:TermGenie] + GO:1901360 + organic cyclic compound metabolic process + GO:organic cyclic compound metabolic process + organic cyclic compound metabolism + + + GO:organic cyclic compound catabolic process + GO:1901361 + organic cyclic compound catabolic process + organic cyclic compound breakdown + organic cyclic compound catabolism + "The chemical reactions and pathways resulting in the breakdown of organic cyclic compound." [GOC:TermGenie] + organic cyclic compound degradation + + + GO:1901362 + organic cyclic compound biosynthetic process + organic cyclic compound biosynthesis + organic cyclic compound formation + "The chemical reactions and pathways resulting in the formation of organic cyclic compound." [GOC:TermGenie] + organic cyclic compound synthesis + GO:organic cyclic compound biosynthetic process + organic cyclic compound anabolism + + + GO:heterocyclic compound binding + heterocyclic compound binding + "Interacting selectively and non-covalently with heterocyclic compound." [GOC:TermGenie] + GO:1901363 + + + GO:organonitrogen compound metabolic process + GO:1901564 + organonitrogen compound metabolism + "The chemical reactions and pathways involving organonitrogen compound." [GOC:pr, GOC:TermGenie] + organonitrogen compound metabolic process + + + organonitrogen compound anabolism + GO:organonitrogen compound biosynthetic process + "The chemical reactions and pathways resulting in the formation of organonitrogen compound." [GOC:pr, GOC:TermGenie] + organonitrogen compound biosynthesis + organonitrogen compound synthesis + organonitrogen compound formation + GO:1901566 + organonitrogen compound biosynthetic process + + + "The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] + organic molecular entity catabolic process + GO:organic substance catabolic process + organic molecular entity catabolism + organic substance degradation + organic substance catabolism + organic molecular entity degradation + GO:1901575 + organic molecular entity breakdown + organic substance breakdown + organic substance catabolic process + + + organic molecular entity formation + organic substance biosynthetic process + organic substance anabolism + organic substance biosynthesis + organic substance synthesis + organic substance formation + "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] + organic molecular entity biosynthetic process + organic molecular entity biosynthesis + GO:organic substance biosynthetic process + organic molecular entity anabolism + organic molecular entity synthesis + GO:1901576 + + + GO:1901605 + "The chemical reactions and pathways involving an alpha-amino acid." [GOC:TermGenie] + alpha-amino acid metabolism + GO:alpha-amino acid metabolic process + alpha-amino acid metabolic process + + + "The chemical reactions and pathways resulting in the formation of an alpha-amino acid." [GOC:TermGenie] + GO:1901607 + alpha-amino acid synthesis + alpha-amino acid formation + alpha-amino acid biosynthesis + GO:alpha-amino acid biosynthetic process + alpha-amino acid biosynthetic process + alpha-amino acid anabolism + + + "The chemical reactions and pathways involving organic hydroxy compound." [GOC:pr, GOC:TermGenie] + organic hydroxy compound metabolism + GO:1901615 + GO:organic hydroxy compound metabolic process + organic hydroxy compound metabolic process + + + organic hydroxy compound formation + organic hydroxy compound biosynthesis + "The chemical reactions and pathways resulting in the formation of organic hydroxy compound." [GOC:pr, GOC:TermGenie] + GO:organic hydroxy compound biosynthetic process + organic hydroxy compound anabolism + organic hydroxy compound biosynthetic process + GO:1901617 + organic hydroxy compound synthesis + + + "The chemical reactions and pathways involving glycosyl compound." [GOC:pr, GOC:TermGenie] + glycosyl compound metabolism + glycosyl compound metabolic process + GO:glycosyl compound metabolic process + GO:1901657 + + + glycosyl compound synthesis + GO:glycosyl compound biosynthetic process + glycosyl compound formation + "The chemical reactions and pathways resulting in the formation of glycosyl compound." [GOC:pr, GOC:TermGenie] + glycosyl compound biosynthesis + glycosyl compound biosynthetic process + glycosyl compound anabolism + GO:1901659 + + + regulation of protein polymer breakdown + regulation of protein depolymerization + regulation of protein polymer catabolism + "Any process that modulates the frequency, rate or extent of protein depolymerization." [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:12032137] + GO:regulation of protein depolymerization + GO:1901879 + regulation of protein polymer catabolic process + regulation of protein polymer degradation + + + "Any process that stops, prevents or reduces the frequency, rate or extent of protein depolymerization." [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:12032137] + down regulation of protein polymer catabolic process + downregulation of protein polymer breakdown + downregulation of protein polymer degradation + GO:negative regulation of protein depolymerization + GO:1901880 + inhibition of protein polymer degradation + downregulation of protein polymer catabolism + down regulation of protein depolymerization + inhibition of protein polymer breakdown + negative regulation of protein polymer catabolism + down-regulation of protein polymer catabolism + negative regulation of protein depolymerization + down regulation of protein polymer breakdown + negative regulation of protein polymer breakdown + down-regulation of protein polymer breakdown + downregulation of protein polymer catabolic process + negative regulation of protein polymer degradation + down-regulation of protein polymer degradation + down regulation of protein polymer catabolism + down-regulation of protein depolymerization + negative regulation of protein polymer catabolic process + down-regulation of protein polymer catabolic process + down regulation of protein polymer degradation + inhibition of protein polymer catabolic process + inhibition of protein polymer catabolism + downregulation of protein depolymerization + + + GO:regulation of beta-amyloid formation + "Any process that modulates the frequency, rate or extent of beta-amyloid formation." [GOC:dph, GOC:TermGenie, PMID:17098871] + regulation of beta-amyloid formation + GO:1902003 + + + enzyme complex + catalytic complex + GO:catalytic complex + "A protein complex which is capable of catalytic activity." [GOC:bhm, GOC:TermGenie, PMID:8077207] + GO:1902494 + + + GO:transmembrane transporter complex + "A transmembrane protein complex which enables the transfer of a substance from one side of a membrane to the other." [GOC:bhm, GOC:TermGenie, PMID:18024586] + transmembrane transporter complex + GO:1902495 + + + regulation of intracellular signaling cascade + regulation of intracellular signal transduction + regulation of signal transduction via intracellular signaling cascade + regulation of intracellular signaling chain + regulation of intracellular signaling pathway + GO:regulation of intracellular signal transduction + GO:1902531 + "Any process that modulates the frequency, rate or extent of intracellular signal transduction." [GOC:dph, GOC:signaling, GOC:tb, GOC:TermGenie] + + + up-regulation of signal transduction via intracellular signaling cascade + positive regulation of intracellular signaling pathway + GO:1902533 + up-regulation of intracellular signal transduction + upregulation of intracellular signal transduction + upregulation of intracellular signaling cascade + "Any process that activates or increases the frequency, rate or extent of intracellular signal transduction." [GOC:BHF, GOC:dph, GOC:signaling, GOC:tb, GOC:TermGenie] + positive regulation of signal transduction via intracellular signaling cascade + positive regulation of intracellular signaling chain + up regulation of intracellular signal transduction + up regulation of intracellular signaling cascade + upregulation of intracellular signaling pathway + up regulation of intracellular signaling pathway + up-regulation of intracellular signaling chain + upregulation of signal transduction via intracellular signaling cascade + activation of intracellular signaling pathway + up-regulation of intracellular signaling cascade + GO:positive regulation of intracellular signal transduction + upregulation of intracellular signaling chain + up regulation of signal transduction via intracellular signaling cascade + up-regulation of intracellular signaling pathway + positive regulation of intracellular signaling cascade + up regulation of intracellular signaling chain + activation of signal transduction via intracellular signaling cascade + positive regulation of intracellular signal transduction + + + PDR16 complex homodimer + serine/threonine protein kinase complex + "A protein complex which is capable of protein serine/threonine kinase activity." [GOC:bhm, GOC:TermGenie, PMID:18191223] + PDR16 complex dimer + GO:1902554 + GO:serine/threonine protein kinase complex + + + single organism localization + "A localization which involves only one organism." [GO_REF:0000089, GOC:jl, PMID:1234] + GO:single-organism localization + GO:1902578 + single-organism localization + + + "A cellular localization which involves only one organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie] + single-organism cellular localization + GO:1902580 + single organism cellular localization + GO:single-organism cellular localization + + + GO:single-organism intracellular transport + "An intracellular transport which involves only one organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie] + single organism intracellular transport + single-organism intracellular transport + GO:1902582 + + + GO:1902589 + "An organelle organization which involves only one organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie] + single organism organelle organization + single-organism organelle organization + GO:single-organism organelle organization + + + GO:secondary alcohol metabolic process + "The chemical reactions and pathways involving secondary alcohol." [GO_REF:0000068, GOC:mengo_curators, GOC:TermGenie, PMID:11288200] + GO:1902652 + secondary alcohol metabolism + secondary alcohol metabolic process + + + secondary alcohol formation + secondary alcohol synthesis + secondary alcohol biosynthetic process + GO:1902653 + "The chemical reactions and pathways resulting in the formation of secondary alcohol." [GO_REF:0000068, GOC:mengo_curators, GOC:TermGenie, PMID:11288200] + GO:secondary alcohol biosynthetic process + secondary alcohol biosynthesis + secondary alcohol anabolism + + + down-regulation of RNA formation + down regulation of RNA biosynthetic process + negative regulation of RNA formation + down regulation of RNA biosynthesis + negative regulation of RNA synthesis + down-regulation of RNA synthesis + downregulation of RNA biosynthetic process + downregulation of RNA biosynthesis + down-regulation of RNA anabolism + negative regulation of RNA anabolism + downregulation of RNA formation + negative regulation of RNA biosynthetic process + down-regulation of RNA biosynthetic process + down regulation of RNA formation + down-regulation of RNA biosynthesis + negative regulation of RNA biosynthesis + downregulation of RNA synthesis + downregulation of RNA anabolism + down regulation of RNA synthesis + "Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process." [GO:jl, GO_REF:0000058, GOC:TermGenie] + down regulation of RNA anabolism + GO:1902679 + GO:negative regulation of RNA biosynthetic process + + + upregulation of RNA biosynthetic process + upregulation of RNA biosynthesis + up-regulation of RNA synthesis + up-regulation of RNA formation + up regulation of RNA biosynthetic process + up regulation of RNA biosynthesis + positive regulation of RNA synthesis + up regulation of RNA formation + positive regulation of RNA formation + up-regulation of RNA anabolism + up regulation of RNA anabolism + positive regulation of RNA biosynthetic process + positive regulation of RNA anabolism + positive regulation of RNA biosynthesis + up regulation of RNA synthesis + GO:1902680 + GO:positive regulation of RNA biosynthetic process + upregulation of RNA anabolism + "Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process." [GO:jl, GO_REF:0000058, GOC:TermGenie] + up-regulation of RNA biosynthesis + up-regulation of RNA biosynthetic process + upregulation of RNA synthesis + upregulation of RNA formation + + + apoptosis activator activity involved in anatomical structure development + induction of apoptosis involved in anatomical structure development + signaling (initiator) caspase activity involved in development of an anatomical structure + induction of apoptosis by p53 involved in development of an anatomical structure + GO:apoptotic process involved in development + programmed cell death by apoptosis involved in anatomical structure development + commitment to apoptosis involved in development of an anatomical structure + apoptotic programmed cell death involved in development of an anatomical structure + apoptotic process involved in development + apoptotic cell death involved in development of an anatomical structure + apoptotic process involved in development of an anatomical structure + programmed cell death by apoptosis involved in development of an anatomical structure + commitment to apoptosis involved in anatomical structure development + GO:1902742 + "Any apoptotic process that is involved in anatomical structure development." [GO_REF:0000060, GOC:mtg_apoptosis, GOC:pg, GOC:TermGenie] + apoptosis activator activity involved in development of an anatomical structure + induction of apoptosis involved in development of an anatomical structure + apoptotic programmed cell death involved in anatomical structure development + apoptotic cell death involved in anatomical structure development + apoptotic process involved in anatomical structure development + signaling (initiator) caspase activity involved in anatomical structure development + induction of apoptosis by p53 involved in anatomical structure development + + + GO:1902850 + GO:microtubule cytoskeleton organization involved in mitosis + "Any microtubule cytoskeleton organization that is involved in mitosis." [GO_REF:0000060, GOC:TermGenie, PMID:18799626] + microtubule cytoskeleton organization involved in mitosis + microtubule dynamics involved in mitosis + microtubule cytoskeleton organization and biogenesis involved in mitosis + microtubule cytoskeleton organisation involved in mitosis + + + GO:1902911 + GO:protein kinase complex + protein kinase complex + "A protein complex which is capable of protein kinase activity." [GO_REF:0000088, GOC:bhm, GOC:TermGenie, PMID:24606918] + + + GO:1902991 + regulation of amyloid precursor protein breakdown + regulation of amyloid precursor protein catabolism + regulation of APP catabolic process + "Any process that modulates the frequency, rate or extent of amyloid precursor protein catabolic process." [GO_REF:0000058, GOC:PARL, GOC:rl, GOC:TermGenie, PMID:24499793] + regulation of amyloid precursor protein degradation + GO:regulation of amyloid precursor protein catabolic process + regulation of amyloid precursor protein catabolic process + regulation of APP catabolism + + + organelle disassembly + "The disaggregation of an organelle into its constituent components." [GO_REF:0000079, GOC:TermGenie] + GO:organelle disassembly + organelle degradation + GO:1903008 + + + "Any process that modulates the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:19164535] + GO:1903034 + regulation of physiological response to wounding + GO:regulation of response to wounding + regulation of response to wounding + + + negative regulation of response to wounding + down-regulation of response to wounding + GO:negative regulation of response to wounding + down-regulation of physiological response to wounding + negative regulation of physiological response to wounding + "Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:19164535] + GO:1903035 + down regulation of physiological response to wounding + down regulation of response to wounding + downregulation of physiological response to wounding + downregulation of response to wounding + + + positive regulation of physiological response to wounding + GO:positive regulation of response to wounding + upregulation of response to wounding + upregulation of physiological response to wounding + positive regulation of response to wounding + up-regulation of physiological response to wounding + "Any process that activates or increases the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:19164535] + GO:1903036 + up regulation of response to wounding + up regulation of physiological response to wounding + up-regulation of response to wounding + + + "A process that is part of the meiotic cell cycle." [GO_REF:0000060, GOC:mtg_cell_cycle, GOC:TermGenie] + GO:1903046 + GO:meiotic cell cycle process + meiotic cell cycle process + + + "A process that is part of the mitotic cell cycle." [GO_REF:0000060, GOC:mtg_cell_cycle, GOC:TermGenie] + GO:mitotic cell cycle process + GO:1903047 + mitotic cell cycle process + + + "The aggregation, arrangement and bonding together of a set of components to form a melanosome, a tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored." [GO_REF:0000079, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:22511774] + melanosome assembly + melanosome formation + GO:melanosome assembly + GO:1903232 + + + phosphatase complex + "A protein complex which is capable of phosphatase activity." [GO_REF:0000088, GOC:bhm, GOC:TermGenie, PMID:24766807] + GO:1903293 + GO:phosphatase complex + + + GO:regulation of protein maturation + regulation of protein maturation + GO:1903317 + "Any process that modulates the frequency, rate or extent of protein maturation." [GO_REF:0000058, GOC:TermGenie, GOC:vw] + + + GO:positive regulation of protein maturation + up-regulation of protein maturation + GO:1903319 + up regulation of protein maturation + upregulation of protein maturation + positive regulation of protein maturation + "Any process that activates or increases the frequency, rate or extent of protein maturation." [GO_REF:0000058, GOC:TermGenie, GOC:vw] + + + reactive oxygen species generation + reactive oxygen species formation + reactive oxygen species synthesis + ROS formation + GO:1903409 + "The chemical reactions and pathways resulting in the formation of reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen." [GO_REF:0000068, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24252804] + GO:reactive oxygen species biosynthetic process + reactive oxygen species biosynthesis + reactive oxygen species biosynthetic process + reactive oxygen species anabolism + ROS generation + + + GO:regulation of cell maturation + GO:1903429 + "Any process that modulates the frequency, rate or extent of cell maturation." [GO_REF:0000058, GOC:TermGenie, PMID:17459944] + regulation of functional differentiation + regulation of cell maturation + + + regulation of nucleic acid-templated transcription + GO:regulation of nucleic acid-templated transcription + GO:1903506 + "Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription." [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:txnOH, GOC:vw] + + + down-regulation of nucleic acid-templated transcription + GO:negative regulation of nucleic acid-templated transcription + "Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription." [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:txnOH, GOC:vw] + downregulation of nucleic acid-templated transcription + negative regulation of nucleic acid-templated transcription + GO:1903507 + down regulation of nucleic acid-templated transcription + + + "Any process that activates or increases the frequency, rate or extent of nucleic acid-templated transcription." [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:txnOH, GOC:vw] + upregulation of nucleic acid-templated transcription + up regulation of nucleic acid-templated transcription + GO:positive regulation of nucleic acid-templated transcription + up-regulation of nucleic acid-templated transcription + positive regulation of nucleic acid-templated transcription + GO:1903508 + + + GO:1903522 + GO:regulation of blood circulation + regulation of hemolymph circulation + regulation of blood circulation + "Any process that modulates the frequency, rate or extent of blood circulation." [GO_REF:0000058, GOC:mr, GOC:TermGenie, PMID:10659969] + + + regulation of cellular secretion + GO:1903530 + regulation of secretion by cell + "Any process that modulates the frequency, rate or extent of secretion by cell." [GO_REF:0000058, GOC:pm, GOC:TermGenie, PMID:12130530] + GO:regulation of secretion by cell + + + GO:extracellular vesicle + extracellular vesicle + microparticle + GO:1903561 + "Any vesicle that is part of the extracellular region." [GO_REF:0000064, GOC:pm, GOC:TermGenie, PMID:24769233] + + + "Any process that modulates the frequency, rate or extent of ATP metabolic process." [GO_REF:0000058, GOC:TermGenie, PMID:20695849] + regulation of ATP metabolism + regulation of ATP metabolic process + GO:regulation of ATP metabolic process + GO:1903578 + + + regulation of cellular response to transforming growth factor beta stimulus + "Any process that modulates the frequency, rate or extent of cellular response to transforming growth factor beta stimulus." [GO_REF:0000058, GOC:BHF, GOC:BHF_miRNA, GOC:rph, GOC:TermGenie, PMID:22269326] + regulation of cellular response to TGFbeta stimulus + GO:regulation of cellular response to transforming growth factor beta stimulus + GO:1903844 + regulation of cellular response to TGF-beta stimulus + + + epithelial cell apoptotic process + GO:1904019 + GO:epithelial cell apoptotic process + epitheliocyte apoptotic process + "Any apoptotic process in an epithelial cell." [GO_REF:0000085, GOC:TermGenie, PMID:19137015] + + + GO:iodide transmembrane transport + "The directed movement of iodide across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:20392814] + iodide transmembrane transport + GO:1904200 + + + induction of retinal programmed cell death + "Any apoptotic process in a retinal cell." [GOC:mtg_apoptosis, PMID:10702418] + GO:1990009 + retinal cell apoptotic process + GO:retinal cell apoptotic process + + + mRNP + mRNP complex + messenger ribonucleoprotein particle + GO:1990124 + "A ribonucleoprotein complex containing both protein and messenger RNA (mRNA) molecules." [GOC:bf, PMID:15574591, PMID:21915786] + GO:messenger ribonucleoprotein complex + mRNA-protein complex + messenger ribonucleoprotein complex + + + epithelial cell apoptotic process involved in palatal shelf morphogenesis + "An apoptotic process in a palatal shelf epithelial cell that contributes to the shaping of the palatal shelf." [GOC:dph, GOC:mtg_apoptosis, PMID:16607638] + GO:1990134 + GO:epithelial cell apoptotic process involved in palatal shelf morphogenesis + + + "Any protein complex that possesses oxidoreductase activity." [GOC:bhm, PMID:18982432] + GO:oxidoreductase complex + oxidation-reduction complex + GO:1990204 + redox complex + oxidoreductase complex + + + GO:transferase complex + GO:1990234 + "A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor)." [GOC:bhm, PMID:16540464] + transferase complex + + + platelet-derived growth factor complex + GO:1990265 + GO:platelet-derived growth factor complex + "A protein complex consisting of two chains of platelet-derived growth factor (PDGF) subunits. PDGF dimers bind to PDGF receptors in the plasma membrane and induce receptor dimerisation and activation. PDGFs are involved in a wide variety of signalling processes. PDGFs are found in all vertebrates where at least 2 different chains (A and B) exist. In human (and other mammals), four types of PDGF chains (A, B, C, and D) are known which form five different dimers (AA, AB, BB, CC and DD)." [GOC:bhm, IntAct:EBI-2881436, IntAct:EBI-2881443, IntAct:EBI-2881451, PMID:11331882] + PDGF complex + + + neutrophil migration + GO:1990266 + "The movement of an neutrophil within or between different tissues and organs of the body." [PMID:1826836] + GO:neutrophil migration + + + transporter complex + GO:1990351 + GO:transporter complex + "A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells." [GOC:bhm, IntAct:EBI-959455, PMID:15449578] + + + GO:1990391 + DNA repair complex + DNA damage repair complex + GO:DNA repair complex + "A protein complex involved in DNA repair processes including direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [GOC:bhm, PMID:22749910] + + + bone regeneration + GO:bone regeneration + GO:1990523 + "The regrowth of bone following its loss or destruction." [PMID:25257467] + + + GO:1990603 + GO:dark adaptation + "The process by which the rods of the retina gradually become fully responsive to dim light when no longer exposed to bright light." [GOC:hjd, http://www.ncbi.nlm.nih.gov/books/NBK11525/, ISBN:0198506732] + dark adaptation + + + GO:microvesicle + extracellular microvesicle + "An extracellular vesicle released from the plasma membrane and ranging in size from about 100 nm to 1000 nm." [GOC:vesicles, PMID:22418571, PMID:24009894, Wikipedia:Microvesicles] + ectosome + microvesicle + GO:1990742 + + + cachectin secretion + "The regulated release of tumor necrosis factor from a cell. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis." [PMID:15560120] + tumor necrosis factor alpha secretion + GO:tumor necrosis factor secretion + tumor necrosis factor ligand superfamily member 2 secretion + TNF superfamily, member 2 secretion + tumor necrosis factor secretion + TNF secretion + TNF-alpha secretion + GO:1990774 + Tnfa secretion + + + "The region of a cell situated by the cell sides which interface adjacent cells and near the base. Often used in reference to animal polarized epithelial cells." [PMID:18495799] + GO:basolateral part of cell + basolateral part of cell + GO:1990794 + + + GO:1990876 + cytoplasmic side of nuclear pore + GO:cytoplasmic side of nuclear pore + cytoplasmic side of NPC + "The side of the nuclear pore complex (NPC) that faces the cytoplasm." [PMID:8422679] + cytoplasmic side of nucleopore + cytoplasmic side of nuclear pore complex + + + GO:1990904 + ribonucleoprotein complex + "A macromolecular complex containing both protein and RNA molecules." [GOC:vesicles] + GO:ribonucleoprotein complex + ribonucleoprotein + RNP + RNA-protein complex + protein-RNA complex + + + "Any process that modulates the frequency, rate or extent of multicellular organismal development." [GOC:obol] + GO:2000026 + GO:regulation of multicellular organismal development + regulation of multicellular organismal development + + + regulation of cellular macromolecule formation + regulation of cellular macromolecule biosynthesis + GO:regulation of cellular macromolecule biosynthetic process + regulation of cellular macromolecule anabolism + regulation of cellular macromolecule biosynthetic process + "Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process." [GOC:obol] + GO:2000112 + regulation of cellular macromolecule synthesis + regulation of cellular biopolymer biosynthetic process + + + GO:negative regulation of cellular macromolecule biosynthetic process + "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process." [GOC:obol] + negative regulation of cellular macromolecule formation + negative regulation of cellular macromolecule biosynthetic process + negative regulation of cellular macromolecule synthesis + negative regulation of cellular biopolymer biosynthetic process + negative regulation of cellular macromolecule anabolism + negative regulation of cellular macromolecule biosynthesis + GO:2000113 + + + "Any process that modulates the frequency, rate or extent of establishment of cell polarity." [GOC:dph] + regulation of cell polarization + GO:regulation of establishment of cell polarity + regulation of establishment of cell polarity + regulation of bud site selection/establishment of cell polarity + GO:2000114 + + + regulation of movement of a cell + GO:regulation of cell motility + regulation of cell motility + GO:2000145 + regulation of cell movement + regulation of cell locomotion + "Any process that modulates the frequency, rate or extent of cell motility." [GOC:mah] + + + GO:regulation of reproductive process + GO:2000241 + regulation of reproductive process + "Any process that modulates the frequency, rate or extent of reproductive process." [GOC:mah] + + + "Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process." [GOC:mah] + GO:2000242 + negative regulation of reproductive process + GO:negative regulation of reproductive process + + + GO:regulation of RNA biosynthetic process + GO:2001141 + regulation of RNA synthesis + regulation of RNA formation + regulation of RNA biosynthetic process + regulation of RNA anabolism + regulation of RNA biosynthesis + "Any process that modulates the frequency, rate or extent of RNA biosynthetic process." [GOC:dph] + + + GO_BP extension classes + + + GO_CC extension classes + + + GO_EXT:0000150 + GO_EXT:bearer of recombinase activity + "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC:elh] + bearer of recombinase activity + recombinase + + + peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase + N-linked-glycopeptide-(N-acetyl-beta-D-glucosaminyl)-L-asparagine amidohydrolase + GO_EXT:bearer of peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity + bearer of peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity + N-oligosaccharide glycopeptidase + "Catalysis of the reaction: 4-N-(N-acetyl-D-glucosaminyl)-protein + H2O = N-acetyl-beta-D-glucosaminylamine + peptide L-aspartate. This reaction is the hydrolysis of an N4-(acetyl-beta-D-glucosaminyl)asparagine residue in which the N-acetyl-D-glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D-glucosaminylamine and the peptide containing an aspartic residue." [EC:3.5.1.52] + N-glycanase + GO_EXT:0000224 + + + sequence-specific DNA binding RNA polymerase II transcription factor + GO_EXT:0000981 + GO_EXT:bearer of RNA polymerase II transcription factor activity, sequence-specific DNA binding + bearer of RNA polymerase II transcription factor activity, sequence-specific DNA binding + "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] + + + bearer of transcription factor activity, protein binding + GO_EXT:bearer of transcription factor activity, protein binding + GO_EXT:0000988 + protein binding transcription factor + "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] + + + "Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] + transcription factor binding transcription factor + GO_EXT:bearer of transcription factor activity, transcription factor binding + GO_EXT:0000989 + bearer of transcription factor activity, transcription factor binding + + + "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] + GO_EXT:bearer of RNA polymerase II activity + RNA polymerase II + bearer of RNA polymerase II activity + GO_EXT:0001055 + + + GO_EXT:0001071 + nucleic acid binding transcription factor + bearer of nucleic acid binding transcription factor activity + "Interacting selectively and non-covalently with a DNA or RNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] + GO_EXT:bearer of nucleic acid binding transcription factor activity + + + G-protein coupled chemoattractant receptor + GO_EXT:bearer of G-protein coupled chemoattractant receptor activity + "Combining with a chemoattractant and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, GOC:mah] + bearer of G-protein coupled chemoattractant receptor activity + GO_EXT:0001637 + G protein chemoattractant receptor + G-protein chemoattractant receptor + + + GO_EXT:bearer of peptide receptor activity + GO_EXT:0001653 + peptide receptor + bearer of peptide receptor activity + "Combining with an extracellular or intracellular peptide to initiate a change in cell activity." [GOC:jl] + + + GO_EXT:0001664 + "Interacting selectively and non-covalently with a G-protein coupled receptor." [GOC:ceb, GOC:dph] + GO_EXT:bearer of G-protein coupled receptor binding + bearer of G-protein coupled receptor binding + + + retinal dehydrogenase + retinal:NAD+ oxidoreductase + cytosolic retinal dehydrogenase + "Catalysis of the reaction: retinal + NAD+ + H2O = retinoate + NADH. Acts on both 11-trans and 13-cis forms of retinal." [EC:1.2.1.36] + GO_EXT:0001758 + bearer of retinal dehydrogenase activity + GO_EXT:bearer of retinal dehydrogenase activity + + + "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators] + GO_EXT:0003674 + bearer of molecular_function + GO_EXT:bearer of molecular_function + + + DNA helicase + GO_EXT:bearer of DNA helicase activity + "Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix." [GOC:jl, GOC:mah] + bearer of DNA helicase activity + GO_EXT:0003678 + + + sequence-specific DNA binding transcription factor + "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:curators, GOC:txnOH] + GO_EXT:0003700 + GO_EXT:bearer of transcription factor activity, sequence-specific DNA binding + bearer of transcription factor activity, sequence-specific DNA binding + + + bearer of retinoic acid receptor activity + "Combining with retinoic acid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. Retinoic acid is one of the forms of vitamin A." [GOC:signaling, PMID:1328967] + GO_EXT:bearer of retinoic acid receptor activity + retinoic acid receptor + GO_EXT:0003708 + + + GO_EXT:0003712 + "Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] + transcription cofactor + transcriptional cofactor + bearer of transcription cofactor activity + GO_EXT:bearer of transcription cofactor activity + + + transcription co-activator + bearer of transcription coactivator activity + GO_EXT:0003713 + transcription coactivator + GO_EXT:bearer of transcription coactivator activity + "Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] + + + "Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] + bearer of transcription corepressor activity + GO_EXT:bearer of transcription corepressor activity + GO_EXT:0003714 + transcription co-repressor + transcription corepressor + + + "Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins." [EC:3.2.1.17] + lysozyme + mucopeptide glucohydrolase + bearer of lysozyme activity + peptidoglycan N-acetylmuramoylhydrolase + 1,4-N-acetylmuramidase + N,O-diacetylmuramidase + GO_EXT:0003796 + GO_EXT:bearer of lysozyme activity + mucopeptide N-acetylmuramoylhydrolase + muramidase + + + protein-glutamine gamma-glutamyltransferase + GO_EXT:bearer of protein-glutamine gamma-glutamyltransferase activity + transglutaminase + "Catalysis of the reaction: protein glutamine + alkylamine = protein N5-alkylglutamine + NH3. This reaction is the formation of the N6-(L-isoglutamyl)-L-lysine isopeptide, resulting in cross-linking polypeptide chains; the gamma-carboxamide groups of peptidyl-glutamine residues act as acyl donors, and the 6-amino-groups of peptidyl-lysine residues act as acceptors, to give intra- and intermolecular N6-(5-glutamyl)lysine cross-links." [EC:2.3.2.13, RESID:AA0124] + glutaminylpeptide gamma-glutamyltransferase + bearer of protein-glutamine gamma-glutamyltransferase activity + polyamine transglutaminase + GO_EXT:0003810 + R-glutaminyl-peptide:amine gamma-glutamyl transferase + fibrinoligase + TGase + + + "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN:0198506732] + GO_EXT:bearer of catalytic activity + catalytic + GO_EXT:0003824 + bearer of catalytic activity + enzyme + + + beta-keto-reductase + GO_EXT:bearer of 3-hydroxyacyl-CoA dehydrogenase activity + L-3-hydroxyacyl coenzyme A dehydrogenase + 3-hydroxyacyl-CoA dehydrogenase + "Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH + H(+)." [EC:1.1.1.35] + L-3-hydroxyacyl CoA dehydrogenase + beta-hydroxyacyl dehydrogenase + 3-oxoacyl-thioester reductase + GO_EXT:0003857 + bearer of 3-hydroxyacyl-CoA dehydrogenase activity + beta-hydroxyacyl-coenzyme A synthetase + beta-hydroxyacylcoenzyme A dehydrogenase + + + nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed) + bearer of DNA-directed RNA polymerase activity + DNA-dependent RNA nucleotidyltransferase + DNA-directed RNA polymerase + GO_EXT:bearer of DNA-directed RNA polymerase activity + DNA-dependent RNA polymerase + "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [EC:2.7.7.6] + RNA nucleotidyltransferase (DNA-directed) + DNA-dependent ribonucleate nucleotidyltransferase + GO_EXT:0003899 + deoxyribonucleic acid-dependent ribonucleic acid polymerase + + + bearer of DNA ligase activity + "Catalysis of the formation of a phosphodiester bond between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of another. This reaction requires an energy source such as ATP or NAD+." [ISBN:0716720094] + GO_EXT:bearer of DNA ligase activity + GO_EXT:0003909 + DNA ligase + + + "Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA." [GOC:mah, PMID:8811192] + GO_EXT:0003916 + DNA topoisomerase + GO_EXT:bearer of DNA topoisomerase activity + bearer of DNA topoisomerase activity + + + bearer of GTPase activity + GO_EXT:0003924 + "Catalysis of the reaction: GTP + H2O = GDP + phosphate." [ISBN:0198547684] + GO_EXT:bearer of GTPase activity + GTPase + + + deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) + revertase + DNA nucleotidyltransferase (RNA-directed) + RNA-dependent deoxyribonucleate nucleotidyltransferase + GO_EXT:0003964 + RNA-directed DNA polymerase + bearer of RNA-directed DNA polymerase activity + reverse transcriptase + RNA revertase + "Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time." [EC:2.7.7.49] + RNA-dependent DNA polymerase + GO_EXT:bearer of RNA-directed DNA polymerase activity + RNA-instructed DNA polymerase + + + bearer of acid phosphatase activity + acid nucleoside diphosphate phosphatase + acid phosphatase + acid monophosphatase + acid phosphomonoester hydrolase + acid phosphohydrolase + GO_EXT:0003993 + GO_EXT:bearer of acid phosphatase activity + "Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum." [EC:3.1.3.2] + acid phosphomonoesterase + + + acyl coenzyme A dehydrogenase + fatty acyl coenzyme A dehydrogenase + acyl dehydrogenase + GO_EXT:bearer of acyl-CoA dehydrogenase activity + "Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor." [EC:1.3.99.3] + acyl-CoA dehydrogenase + acyl-CoA reductase + long-chain acyl coenzyme A dehydrogenase + GO_EXT:0003995 + acyl-CoA:(acceptor) 2,3-oxidoreductase + general acyl CoA dehydrogenase + medium-chain acyl-coenzyme A dehydrogenase + long-chain acyl-CoA dehydrogenase + acyl-CoA:acceptor 2,3-oxidoreductase + bearer of acyl-CoA dehydrogenase activity + fatty-acyl-CoA dehydrogenase + acyl CoA dehydrogenase + + + acyl-CoA oxidase + fatty acyl-CoA oxidase + acyl-CoA:oxygen 2-oxidoreductase + GO_EXT:0003997 + fatty acyl-coenzyme A oxidase + "Catalysis of the reaction: acyl-CoA + O2 = trans-2,3-dehydroacyl-CoA + hydrogen peroxide." [EC:1.3.3.6] + acyl coenzyme A oxidase + bearer of acyl-CoA oxidase activity + GO_EXT:bearer of acyl-CoA oxidase activity + + + GO_EXT:bearer of carbonate dehydratase activity + carboxyanhydrase + carbonate dehydratase + carbonic dehydratase + bearer of carbonate dehydratase activity + anhydrase + carbonate anhydrase + carbonic acid anhydrase + GO_EXT:0004089 + carbonic anhydrase + carbonate hydro-lyase + "Catalysis of the reaction: H2CO3 = CO2 + H2O." [EC:4.2.1.1] + + + GO_EXT:0004095 + outer malonyl-CoA inhibitable carnitine palmitoyltransferase + carnitine O-palmitoyltransferase + L-carnitine palmitoyltransferase + carnitine palmitoyltransferase + "Catalysis of the reaction: palmitoyl-CoA + L-carnitine = CoA + L-palmitoylcarnitine." [EC:2.3.1.21] + palmitoyl-CoA:L-carnitine O-palmitoyltransferase + GO_EXT:bearer of carnitine O-palmitoyltransferase activity + bearer of carnitine O-palmitoyltransferase activity + acylcarnitine transferase + palmitoylcarnitine transferase + + + warburg's respiratory enzyme + cytochrome oxidase + cytochrome c oxidase + GO_EXT:0004129 + "Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O." [EC:1.9.3.1] + cytochrome-c oxidase + complex IV (mitochondrial electron transport) + GO_EXT:bearer of cytochrome-c oxidase activity + bearer of cytochrome-c oxidase activity + + + arachidonoyl-specific diacylglycerol kinase + "Catalysis of the reaction: NTP + 1,2-diacylglycerol = NDP + 1,2-diacylglycerol-3-phosphate." [EC:2.7.1.107, GOC:elh] + DG kinase + diacylglycerol kinase + bearer of diacylglycerol kinase activity + GO_EXT:bearer of diacylglycerol kinase activity + DGK + GO_EXT:0004143 + sn-1,2-diacylglycerol kinase + diglyceride kinase + 1,2-diacylglycerol kinase + + + bearer of endopeptidase activity + elastase + endopeptidase + GO_EXT:0004175 + GO_EXT:bearer of endopeptidase activity + "Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain." [http://merops.sanger.ac.uk/about/glossary.htm#ENDOPEPTIDASE] + + + carboxypeptidase + "Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide." [ISBN:0198506732] + GO_EXT:0004180 + bearer of carboxypeptidase activity + GO_EXT:bearer of carboxypeptidase activity + + + "Catalysis of the hydrolysis of a peptide bond not more than three residues from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine)." [http://merops.sanger.ac.uk/about/glossary.htm#CARBOXYPEPTIDASE, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094] + serine carboxypeptidase + GO_EXT:0004185 + GO_EXT:bearer of serine-type carboxypeptidase activity + bearer of serine-type carboxypeptidase activity + serine-type carboxypeptidase + + + gamma-glutamylcysteinyl synthetase + glutamate-cysteine ligase + "Catalysis of the reaction: L-cysteine + L-glutamate + ATP = L-gamma-glutamyl-L-cysteine + ADP + 2 H(+) + phosphate." [EC:6.3.2.2, RHEA:13288] + L-glutamate:L-cysteine gamma-ligase (ADP-forming) + GO_EXT:0004357 + gamma-glutamyl-L-cysteine synthetase + bearer of glutamate-cysteine ligase activity + gamma-glutamylcysteine synthetase + GO_EXT:bearer of glutamate-cysteine ligase activity + + + bearer of glycerol-3-phosphate O-acyltransferase activity + ACP:sn-glycerol-3-phosphate acyltransferase + glycerol phosphate acyltransferase + glycerol-3-phosphate O-acyltransferase + "Catalysis of the reaction: acyl-CoA + sn-glycerol 3-phosphate = CoA + 1-acyl-sn-glycerol 3-phosphate." [EC:2.3.1.15] + glycerol 3-phosphate acyltransferase + GO_EXT:bearer of glycerol-3-phosphate O-acyltransferase activity + glycerophosphate transacylase + alpha-glycerophosphate acyltransferase + 3-glycerophosphate acyltransferase + sn-glycerol-3-phosphate acyltransferase + glycerol phosphate transacylase + sn-glycerol 3-phosphate acyltransferase + GO_EXT:0004366 + glycerophosphate acyltransferase + acyl-CoA:sn-glycerol-3-phosphate 1-O-acyltransferase + + + helicase + "Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix." [GOC:mah, ISBN:0198506732] + bearer of helicase activity + GO_EXT:bearer of helicase activity + GO_EXT:0004386 + + + GO_EXT:bearer of hexokinase activity + glucose ATP phosphotransferase + "Catalysis of the reaction: ATP + D-hexose = ADP + D-hexose 6-phosphate." [EC:2.7.1.1] + bearer of hexokinase activity + ATP-dependent hexokinase + ATP:D-hexose 6-phosphotransferase + hexokinase + hexokinase type IV glucokinase + GO_EXT:0004396 + + + histone acetyltransferase + bearer of histone acetyltransferase activity + histone acetokinase + histone acetylase + histone transacetylase + GO_EXT:0004402 + nucleosome-histone acetyltransferase + GO_EXT:bearer of histone acetyltransferase activity + "Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone." [EC:2.3.1.48] + histone lysine acetyltransferase + acetyl-CoA:histone acetyltransferase + + + histone deacetylase + bearer of histone deacetylase activity + GO_EXT:bearer of histone deacetylase activity + "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes." [EC:3.5.1.98, PMID:9893272] + GO_EXT:0004407 + + + lactate dehydrogenase + bearer of lactate dehydrogenase activity + GO_EXT:bearer of lactate dehydrogenase activity + GO_EXT:0004457 + "Catalysis of the reaction: lactate + NAD+ = H+ + NADH + pyruvate." [GOC:ai, GOC:bf] + + + GO_EXT:bearer of monooxygenase activity + "Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water." [http://www.onelook.com/, ISBN:0198506732] + GO_EXT:0004497 + monooxygenase + bearer of monooxygenase activity + hydroxylase + + + bearer of nitric-oxide synthase activity + nitric oxide synthetase + endothelium-derived relaxation factor-forming enzyme + NO synthase + nitric-oxide synthase + GO_EXT:0004517 + "Catalysis of the reaction: L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+." [EC:1.14.13.39] + L-arginine,NADPH:oxygen oxidoreductase (nitric-oxide-forming) + nitric oxide synthase + NADPH-diaphorase + endothelium-derived relaxing factor synthase + nitric-oxide synthetase + GO_EXT:bearer of nitric-oxide synthase activity + + + GO_EXT:0004518 + nuclease + bearer of nuclease activity + "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN:0198547684] + GO_EXT:bearer of nuclease activity + + + GO_EXT:bearer of endonuclease activity + endonuclease + bearer of endonuclease activity + "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC:mah, ISBN:0198547684] + GO_EXT:0004519 + + + bearer of endodeoxyribonuclease activity + DNA nicking + endonuclease G + GO_EXT:0004520 + GO_EXT:bearer of endodeoxyribonuclease activity + endodeoxyribonuclease + "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC:mah, ISBN:0198547684] + + + "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GOC:mah, ISBN:0198547684] + GO_EXT:bearer of exonuclease activity + bearer of exonuclease activity + GO_EXT:0004527 + exonuclease + + + "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid." [GOC:mah, ISBN:0198547684] + GO_EXT:0004536 + deoxyribonuclease + bearer of deoxyribonuclease activity + GO_EXT:bearer of deoxyribonuclease activity + + + "Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA." [GOC:mah, ISBN:0198547684] + GO_EXT:0004540 + bearer of ribonuclease activity + GO_EXT:bearer of ribonuclease activity + ribonuclease + + + GO_EXT:0004553 + GO_EXT:bearer of hydrolase activity, hydrolyzing O-glycosyl compounds + O-glucosyl hydrolase + bearer of hydrolase activity, hydrolyzing O-glycosyl compounds + "Catalysis of the hydrolysis of any O-glycosyl bond." [GOC:mah] + + + beta-lactosidase + beta-D-galactanase + trilactase + exo-(1->4)-beta-D-galactanase + GO_EXT:bearer of beta-galactosidase activity + GO_EXT:0004565 + beta-D-lactosidase + beta-D-galactoside galactohydrolase + bearer of beta-galactosidase activity + "Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides." [EC:3.2.1.23] + beta-galactosidase + + + oligosaccharyl transferase + "Catalysis of the transfer of a oligosaccharyl group to an acceptor molecule, typically another carbohydrate or a lipid." [GOC:ai] + GO_EXT:0004576 + oligosaccharide transferase + bearer of oligosaccharyl transferase activity + GO_EXT:bearer of oligosaccharyl transferase activity + + + "Catalysis of the reaction: 2-oxoglutarate + lipoamide = S-succinyldihydrolipoamide + CO2." [EC:1.2.4.2] + alpha-ketoglutarate dehydrogenase + oxoglutarate dehydrogenase (succinyl-transferring) + GO_EXT:bearer of oxoglutarate dehydrogenase (succinyl-transferring) activity + oxoglutarate dehydrogenase + alpha-ketoglutaric dehydrogenase + bearer of oxoglutarate dehydrogenase (succinyl-transferring) activity + 2-oxoglutarate dehydrogenase + AKGDH + 2-ketoglutarate dehydrogenase + oxoglutarate decarboxylase + alpha-ketoglutaric acid dehydrogenase + GO_EXT:0004591 + OGDC + oxoglutarate dehydrogenase (lipoamide) + alpha-oxoglutarate dehydrogenase + 2-oxoglutarate: lipoate oxidoreductase + 2-oxoglutarate:lipoamide 2-oxidoreductase (decarboxylating and acceptor-succinylating) + ketoglutaric dehydrogenase + + + GO_EXT:bearer of peroxidase activity + donor:hydrogen-peroxide oxidoreductase + "Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O." [EC:1.11.1.7] + bearer of peroxidase activity + GO_EXT:0004601 + peroxidase + oxyperoxidase + + + phospholipase + "Catalysis of the hydrolysis of a glycerophospholipid." [ISBN:0198506732] + GO_EXT:0004620 + bearer of phospholipase activity + GO_EXT:bearer of phospholipase activity + + + "Catalysis of the reaction: a phospholipid + H2O = 1,2-diacylglycerol + a phosphatidate." [EC:3.1.4.3, EC:3.1.4.4, GOC:mah] + phospholipase C + lecithinase C + bearer of phospholipase C activity + GO_EXT:0004629 + GO_EXT:bearer of phospholipase C activity + + + propionyl coenzyme A carboxylase + bearer of propionyl-CoA carboxylase activity + PCCase + GO_EXT:bearer of propionyl-CoA carboxylase activity + GO_EXT:0004658 + "Catalysis of the reaction: ATP + propanoyl-CoA + HCO3- = ADP + phosphate + (S)-methylmalonyl-CoA." [EC:6.4.1.3] + propionyl-CoA carboxylase + + + protein kinase + GO_EXT:0004672 + bearer of protein kinase activity + GO_EXT:bearer of protein kinase activity + "Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP." [MetaCyc:PROTEIN-KINASE-RXN] + + + GO_EXT:0004674 + serine/threonine protein kinase + GO_EXT:bearer of protein serine/threonine kinase activity + bearer of protein serine/threonine kinase activity + protein serine/threonine kinase + "Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate." [GOC:bf] + serine(threonine) protein kinase + protein serine-threonine kinase + + + GO_EXT:0004675 + bearer of transmembrane receptor protein serine/threonine kinase activity + receptor serine/threonine protein kinase + transmembrane receptor protein serine/threonine kinase + "Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate." [EC:2.7.11.30] + ATP:receptor-protein phosphotransferase + receptor protein serine/threonine kinase + GO_EXT:bearer of transmembrane receptor protein serine/threonine kinase activity + + + calmodulin-dependent protein kinase + ATP:protein phosphotransferase (Ca2+/calmodulin-dependent) + multifunctional calcium/calmodulin regulated protein kinase + microtubule-associated protein 2 kinase + Ca2+/calmodulin-dependent protein kinase + GO_EXT:bearer of calmodulin-dependent protein kinase activity + "Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin." [GOC:mah, PMID:11264466] + GO_EXT:0004683 + multifunctional calcium- and calmodulin-regulated protein kinase + calmodulin regulated protein kinase + calcium- and calmodulin-dependent protein kinase + CaM-regulated serine/threonine kinase + bearer of calmodulin-dependent protein kinase activity + CaM kinase + Ca2+/CaM-dependent kinase + calcium/calmodulin-dependent protein kinase + + + cyclic nucleotide-dependent protein kinase + bearer of cyclic nucleotide-dependent protein kinase activity + GO_EXT:bearer of cyclic nucleotide-dependent protein kinase activity + GO_EXT:0004690 + "Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of a cyclic nucleotide." [GOC:mah] + + + 3',5' cAMP-dependent protein kinase + ATP:protein phosphotransferase (cAMP-dependent) + GO_EXT:bearer of cAMP-dependent protein kinase activity + cAMP-dependent protein kinase, intrinsic catalyst + bearer of cAMP-dependent protein kinase activity + cyclic AMP-dependent protein kinase + adenosine 3',5'-cyclophosphate-dependent protein kinase + cAMP-dependent protein kinase + 3',5'-cAMP-dependent protein kinase + GO_EXT:0004691 + "Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of cAMP." [EC:2.7.11.11] + + + GO_EXT:bearer of protein kinase C activity + protein kinase C + GO_EXT:0004697 + PKC + diacylglycerol-activated phospholipid-dependent protein kinase C + ATP:protein phosphotransferase (diacylglycerol-dependent) + "Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires diacylglycerol." [EC:2.7.11.13] + bearer of protein kinase C activity + diacylglycerol-activated phospholipid-dependent PKC + + + receptor signalling protein serine/threonine kinase + "Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate." [EC:2.7.11.13, GOC:bf, GOC:mah] + receptor signaling protein serine/threonine kinase + bearer of receptor signaling protein serine/threonine kinase activity + GO_EXT:bearer of receptor signaling protein serine/threonine kinase activity + GO_EXT:0004702 + + + bearer of JUN kinase activity + JUN kinase + GO_EXT:0004705 + GO_EXT:bearer of JUN kinase activity + "Catalysis of the reaction: JUN + ATP = JUN phosphate + ADP. This reaction is the phosphorylation and activation of members of the JUN family, a gene family that encodes nuclear transcription factors." [GOC:bf, ISBN:0198506732] + + + "Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli." [GOC:ma, ISBN:0198547684] + GO_EXT:0004707 + mitogen activated kinase + ATP:protein phosphotransferase (MAPKK-activated) + MAP kinase + GO_EXT:bearer of MAP kinase activity + bearer of MAP kinase activity + mitogen-activated protein kinase + + + MAPK activator + ATP:protein phosphotransferase (MAPKKK-activated) + GO_EXT:0004708 + MAP kinase kinase + MAPKK + GO_EXT:bearer of MAP kinase kinase activity + bearer of MAP kinase kinase activity + mitogen-activated protein kinase kinase + ERK activator kinase + MAP kinase or ERK kinase + "Catalysis of the concomitant phosphorylation of threonine (T) and tyrosine (Y) residues in a Thr-Glu-Tyr (TEY) thiolester sequence in a MAP kinase (MAPK) substrate." [ISBN:0198547684] + + + mitogen-activated protein kinase kinase kinase + MEKK + ATP:protein phosphotransferase (MAPKKKK-activated) + MAP kinase kinase kinase + GO_EXT:0004709 + MAPK/ERK kinase kinase + MEK kinase + MAPKKK + GO_EXT:bearer of MAP kinase kinase kinase activity + "Catalysis of the phosphorylation and activation of a MAP kinase kinase; each MAP kinase kinase can be phosphorylated by any of several MAP kinase kinase kinases." [PMID:9561267] + bearer of MAP kinase kinase kinase activity + + + GO_EXT:bearer of protein serine/threonine/tyrosine kinase activity + "Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine phosphate." [GOC:mah] + protein serine/threonine/tyrosine kinase + bearer of protein serine/threonine/tyrosine kinase activity + ATP:protein phosphotransferase (Ser/Thr- and Tyr-phosphorylating) + GO_EXT:0004712 + + + GO_EXT:0004713 + protein tyrosine kinase + "Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate." [EC:2.7.10] + protein-tyrosine kinase + bearer of protein tyrosine kinase activity + GO_EXT:bearer of protein tyrosine kinase activity + + + GO_EXT:0004714 + ATP:protein-L-tyrosine O-phosphotransferase (receptor-type) + transmembrane receptor protein tyrosine kinase + GO_EXT:bearer of transmembrane receptor protein tyrosine kinase activity + bearer of transmembrane receptor protein tyrosine kinase activity + receptor protein tyrosine kinase + neurotrophin TRKC receptor + sevenless receptor + "Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate." [EC:2.7.10.1, GOC:mah] + receptor protein-tyrosine kinase + neurotrophin TRK receptor + neurotrophin TRKA receptor + neurotrophin TRKB receptor + + + receptor signaling protein tyrosine kinase + GO_EXT:0004716 + bearer of receptor signaling protein tyrosine kinase activity + receptor signalling protein tyrosine kinase + "Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate." [EC:2.7.10.2] + GO_EXT:bearer of receptor signaling protein tyrosine kinase activity + + + protein phosphatase + bearer of phosphoprotein phosphatase activity + GO_EXT:0004721 + GO_EXT:bearer of phosphoprotein phosphatase activity + "Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity." [EC:3.1.3.16, ISBN:0198547684] + phosphoprotein phosphatase + phosphoprotein phosphohydrolase + + + PTPase + phosphotyrosylprotein phosphatase + "Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate." [EC:3.1.3.48] + PTP-phosphatase + tyrosylprotein phosphatase + GO_EXT:bearer of protein tyrosine phosphatase activity + [phosphotyrosine]protein phosphatase + protein-tyrosine-phosphatase + protein tyrosine phosphatase + phosphotyrosine phosphatase + GO_EXT:0004725 + tyrosine O-phosphate phosphatase + phosphoprotein phosphatase (phosphotyrosine) + phosphotyrosine histone phosphatase + phosphotyrosine protein phosphatase + protein phosphotyrosine phosphatase + PPT-phosphatase + protein-tyrosine-phosphate phosphohydrolase + bearer of protein tyrosine phosphatase activity + + + pyruvate dehydrogenase + GO_EXT:bearer of pyruvate dehydrogenase activity + pyruvic acid dehydrogenase + pyruvic dehydrogenase + "Catalysis of the oxidative decarboxylation of pyruvate." [ISBN:0716020094] + GO_EXT:0004738 + bearer of pyruvate dehydrogenase activity + + + phosphoenol transphosphorylase + pyruvate kinase + phosphoenolpyruvate kinase + "Catalysis of the reaction: ATP + pyruvate = ADP + phosphoenolpyruvate." [EC:2.7.1.40] + GO_EXT:0004743 + GO_EXT:bearer of pyruvate kinase activity + ATP:pyruvate 2-O-phosphotransferase + bearer of pyruvate kinase activity + + + superoxide:superoxide oxidoreductase + "Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide." [EC:1.15.1.1, GOC:vw, PMID:15064408] + GO_EXT:bearer of superoxide dismutase activity + GO_EXT:0004784 + superoxide dismutase + bearer of superoxide dismutase activity + + + thioredoxin-disulfide reductase + "Catalysis of the reaction: NADP(+) + thioredoxin = H(+) + NADPH + thioredoxin disulfide." [EC:1.8.1.9, RHEA:20348] + NADP--thioredoxin reductase + NADPH2:oxidized thioredoxin oxidoreductase + NADPH:oxidized thioredoxin oxidoreductase + thioredoxin reductase (NADPH) + GO_EXT:bearer of thioredoxin-disulfide reductase activity + thioredoxin disulfide reductase + GO_EXT:0004791 + thioredoxin-disulphide reductase + NADPH--thioredoxin reductase + thioredoxin:NADP+ oxidoreductase + bearer of thioredoxin-disulfide reductase activity + + + "Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element." [GOC:bm, ISBN:0198506732] + GO_EXT:bearer of transposase activity + GO_EXT:0004803 + bearer of transposase activity + transposase + + + bearer of triglyceride lipase activity + triacylglycerol ester hydrolase + glycerol ester hydrolase + tween hydrolase + GO_EXT:bearer of triglyceride lipase activity + tributyrinase + triglyceride lipase + tween-hydrolyzing esterase + triacylglycerol acylhydrolase + triglyceride hydrolase + triolein hydrolase + cacordase + glycerol-ester hydrolase + tributyrase + butyrinase + triacetinase + triglyceridase + GO_EXT:0004806 + tributyrin esterase + "Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate." [EC:3.1.1.3] + tweenesterase + tweenase + triacylglycerol lipase + + + aminoacyl-tRNA synthetase + aminoacyl-tRNA ligase + GO_EXT:bearer of aminoacyl-tRNA ligase activity + aminoacyl-tRNA synthetase auxiliary protein + "Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP." [ISBN:0198506732] + bearer of aminoacyl-tRNA ligase activity + GO_EXT:0004812 + + + tryptophan translase + tryptophan-tRNA ligase + tryptophanyl-tRNA synthase + tryptophanyl-transfer ribonucleic synthetase + "Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp)." [EC:6.1.1.2] + bearer of tryptophan-tRNA ligase activity + tryptophanyl-transfer ribonucleic acid synthetase + GO_EXT:0004830 + tryptophanyl ribonucleic synthetase + tryptophanyl-tRNA synthetase + tryptophanyl-transfer RNA synthetase + TrpRS + L-tryptophan-tRNA(Trp) ligase (AMP-forming) + GO_EXT:bearer of tryptophan-tRNA ligase activity + tryptophanyl-transfer ribonucleate synthetase + + + bearer of ubiquitin-protein transferase activity + GO_EXT:0004842 + ubiquitin-protein transferase + GO_EXT:bearer of ubiquitin-protein transferase activity + "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages." [GOC:BioGRID, GOC:jh2, PMID:9635407] + + + "Binds to and stops, prevents or reduces the activity of an enzyme." [GOC:ai] + GO_EXT:bearer of enzyme inhibitor activity + GO_EXT:0004857 + enzyme inhibitor + bearer of enzyme inhibitor activity + + + GO_EXT:bearer of signal transducer activity + "Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:go_curators] + GO_EXT:0004871 + bearer of signal transducer activity + signal transducer + + + receptor + "Combining with an extracellular or intracellular messenger to initiate a change in cell activity." [GOC:ceb, ISBN:0198506732] + GO_EXT:bearer of receptor activity + bearer of receptor activity + GO_EXT:0004872 + + + GO_EXT:bearer of complement receptor activity + bearer of complement receptor activity + "Combining with any component or product of the complement cascade and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:signaling, ISBN:0781735149, PMID:11884446] + complement receptor + GO_EXT:0004875 + + + GO_EXT:bearer of RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding + GO_EXT:0004879 + ligand-dependent transcription factor + "Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, GOC:txnOH] + bearer of RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding + ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor + ligand-dependent nuclear receptor + nuclear receptor + + + retinoid-X receptor + 9-cis retinoic acid receptor + GO_EXT:0004886 + GO_EXT:bearer of 9-cis retinoic acid receptor activity + "Combining with 9-cis retinoic acid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, PMID:17132853] + bearer of 9-cis retinoic acid receptor activity + + + GO_EXT:bearer of thyroid hormone receptor activity + "Combining with thyroid hormone and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling] + thyroid hormone receptor + GO_EXT:0004887 + bearer of thyroid hormone receptor activity + + + "Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:go_curators, Wikipedia:Transmembrane_receptor] + transmembrane signaling receptor + transmembrane signalling receptor + GO_EXT:0004888 + bearer of transmembrane signaling receptor activity + GO_EXT:bearer of transmembrane signaling receptor activity + + + bearer of GABA-A receptor activity + ionotropic GABA receptor + "Combining with the amino acid gamma-aminobutyric acid (GABA, 4-aminobutyrate) to initiate a change in cell activity. GABA-A receptors function as chloride channels." [PMID:8974333] + GO_EXT:0004890 + GO_EXT:bearer of GABA-A receptor activity + GABA-A receptor + + + bearer of cytokine receptor activity + "Combining with a cytokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:mah] + cytokine receptor + GO_EXT:0004896 + GO_EXT:bearer of cytokine receptor activity + hematopoietin/interferon-class (D200-domain) cytokine receptor + + + GO_EXT:bearer of G-protein coupled receptor activity + ligand-dependent GPCR + G-protein-coupled receptor + GPCR + GO_EXT:0004930 + bearer of G-protein coupled receptor activity + G-protein linked receptor + "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR] + G protein coupled receptor + G protein linked receptor + G-protein coupled receptor + + + GO_EXT:0004950 + chemokine receptor + GO_EXT:bearer of chemokine receptor activity + "Combining with a chemokine, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Chemokines are a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria." [GOC:BHF, GOC:rl, GOC:signaling, http://en.wikipedia.org/wiki/Chemokine, IUPHAR_GPCR:1280, PMID:12183377, PMID:8662823] + bearer of chemokine receptor activity + + + bearer of dopamine neurotransmitter receptor activity + dopamine neurotransmitter receptor + "Combining with the neurotransmitter dopamine to initiate a change in cell activity." [IUPHAR_GPCR:1282] + GO_EXT:0004952 + GO_EXT:bearer of dopamine neurotransmitter receptor activity + + + GO_EXT:bearer of ionotropic glutamate receptor activity + "Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts." [ISBN:0198506732] + GO_EXT:0004970 + bearer of ionotropic glutamate receptor activity + ionotropic glutamate receptor + + + alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor + GO_EXT:bearer of AMPA glutamate receptor activity + AMPA glutamate receptor + GO_EXT:0004971 + bearer of AMPA glutamate receptor activity + AMPA receptor + "An ionotropic glutamate receptor activity that exhibits fast gating by glutamate and acts by opening a cation channel permeable to sodium, potassium, and, in the absence of a GluR2 subunit, calcium." [GOC:mah, PMID:10049997, PMID:8804111] + + + GO_EXT:0004972 + NMDA glutamate receptor + bearer of NMDA glutamate receptor activity + N-methyl-D-aspartate selective glutamate receptor + "An ionotropic glutamate receptor activity that exhibits slow gating by glutamate, acts by opening a nonselective cation channel, and can be activated by L-aspartate." [GOC:mah, PMID:10049997] + GO_EXT:bearer of NMDA glutamate receptor activity + + + bearer of olfactory receptor activity + olfactory receptor + GO_EXT:0004984 + odorant receptor + "Combining with an odorant and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity in response to detection of smell." [GOC:bf, GOC:dph, GOC:sart, PMID:19135896, PMID:21041441] + GO_EXT:bearer of olfactory receptor activity + + + GO_EXT:bearer of transferrin receptor activity + "Combining selectively with transferrin, and delivering transferrin into the cell via endocytosis. Transferrin is a major iron carrier protein in vertebrates." [GOC:bf, PMID:2678449, PMID:3011819] + bearer of transferrin receptor activity + transferrin receptor + GO_EXT:0004998 + + + bearer of vasopressin receptor activity + GO_EXT:bearer of vasopressin receptor activity + GO_EXT:0005000 + vasopressin receptor + "Combining with vasopressin to initiate a change in cell activity." [GOC:ai] + + + platelet-derived growth factor-activated receptor + PDGF receptor + bearer of platelet-derived growth factor-activated receptor activity + PDGF-activated receptor + GO_EXT:0005017 + PDGFR + platelet-derived growth factor receptor + "Combining with platelet-derived growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:mah] + GO_EXT:bearer of platelet-derived growth factor-activated receptor activity + + + TGF-beta receptor + TGFbeta-activated receptor + transforming growth factor beta-activated receptor + TGFbeta receptor + transforming growth factor beta receptor + bearer of transforming growth factor beta-activated receptor activity + GO_EXT:0005024 + GO_EXT:bearer of transforming growth factor beta-activated receptor activity + "Combining with a transforming growth factor beta (TGFbeta) and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate." [GOC:mah, GOC:signaling] + + + bearer of neurotrophin receptor activity + neurotrophin receptor + GO_EXT:0005030 + "Combining with a neurotrophin, any of a family of growth factors that prevent apoptosis in neurons and promote nerve growth, and transmitting the signal to initiate a change in cell activity." [GOC:jl, GOC:signaling, http://www.mercksource.com/] + GO_EXT:bearer of neurotrophin receptor activity + + + GO_EXT:0005031 + bearer of tumor necrosis factor-activated receptor activity + GO_EXT:bearer of tumor necrosis factor-activated receptor activity + "Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function." [GOC:jl, http://lookwayup.com/] + tumor necrosis factor receptor + TNF receptor + tumor necrosis factor-activated receptor + + + apoptosis-activating receptor + "Combining with an extracellular messenger (called a death ligand), and transmitting the signal from one side of the plasma membrane to the other to initiate apoptotic or necrotic cell death." [GOC:bf, GOC:BHF, GOC:ecd, GOC:mtg_apoptosis, GOC:rl, PMID:10209153] + death receptor + bearer of death receptor activity + GO_EXT:bearer of death receptor activity + GO_EXT:0005035 + + + GO_EXT:0005044 + GO_EXT:bearer of scavenger receptor activity + bearer of scavenger receptor activity + scavenger receptor + "Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, beta-amyloid fibrils, and advanced glycation end products (AGEs)." [GOC:bf, PMID:11790542, PMID:12379907, PMID:12621157, PMID:20981357] + + + GO_EXT:0005057 + GO_EXT:bearer of receptor signaling protein activity + "Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell." [GOC:bf] + intracellular signal transducer + bearer of receptor signaling protein activity + receptor signalling protein + receptor signaling protein + + + GDP-dissociation stimulator + "Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase." [GOC:kd, GOC:mah] + bearer of guanyl-nucleotide exchange factor activity + GO_EXT:bearer of guanyl-nucleotide exchange factor activity + GO_EXT:0005085 + guanyl-nucleotide exchange factor + guanyl-nucleotide release factor + + + receptor-associated protein + GO_EXT:0005102 + GO_EXT:bearer of receptor binding + bearer of receptor binding + "Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:bf, GOC:ceb, ISBN:0198506732] + + + paracrine + autocrine + GO_EXT:0005125 + cytokine + GO_EXT:bearer of cytokine activity + bearer of cytokine activity + "Functions to control the survival, growth, differentiation and effector function of tissues and cells." [ISBN:0198599471] + + + bearer of cytokine receptor binding + GO_EXT:0005126 + GO_EXT:bearer of cytokine receptor binding + "Interacting selectively and non-covalently with a cytokine receptor." [GOC:mah, GOC:vw] + + + bearer of structural molecule activity + GO_EXT:bearer of structural molecule activity + "The action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cell." [GOC:mah] + GO_EXT:0005198 + structural molecule + + + GO_EXT:0005215 + GO_EXT:bearer of transporter activity + "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC:ai, GOC:dgf] + bearer of transporter activity + + + bearer of ion channel activity + GO_EXT:0005216 + GO_EXT:bearer of ion channel activity + ion channel + "Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size)." [GOC:cy, GOC:mtg_transport, GOC:pr, ISBN:0815340729] + + + GO_EXT:0005217 + GO_EXT:bearer of intracellular ligand-gated ion channel activity + bearer of intracellular ligand-gated ion channel activity + intracellular ligand-gated ion channel + "Enables the transmembrane transfer of an ion by a channel that opens when a specific intracellular ligand has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729] + + + GO_EXT:0005218 + intracellular ligand-gated calcium channel + bearer of intracellular ligand-gated calcium channel activity + GO_EXT:bearer of intracellular ligand-gated calcium channel activity + "Enables the transmembrane transfer of a calcium ion by a channel that opens when a specific intracellular ligand has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729] + + + inositol-1,4,5-trisphosphate receptor + inositol 1,4,5-trisphosphate-sensitive calcium-release channel + IP3 receptor + "Enables the transmembrane transfer of a calcium ion by a channel that opens when inositol 1,4,5-trisphosphate (IP3) has been bound by the channel complex or one of its constituent parts." [GOC:mah, GOC:signaling, PMID:8660280, Wikipedia:Inositol_trisphosphate_receptor] + bearer of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity + GO_EXT:0005220 + GO_EXT:bearer of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity + + + GO_EXT:bearer of extracellular ligand-gated ion channel activity + bearer of extracellular ligand-gated ion channel activity + GO_EXT:0005230 + "Enables the transmembrane transfer of an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729] + extracellular ligand-gated ion channel + + + "A wide pore channel activity that enables a direct cytoplasmic connection from one cell to an adjacent cell. The gap junction can pass large solutes as well as electrical signals between cells. Gap junctions consist of two gap junction hemi-channels, or connexons, one contributed by each membrane through which the gap junction passes." [GOC:dgh, GOC:mtg_transport, ISBN:0815340729] + GO_EXT:0005243 + gap junction channel + innexin channel + GO_EXT:bearer of gap junction channel activity + bearer of gap junction channel activity + + + voltage-dependent ion channel + "Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded." [GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729] + GO_EXT:0005244 + voltage gated ion channel + voltage-gated ion channel + bearer of voltage-gated ion channel activity + GO_EXT:bearer of voltage-gated ion channel activity + + + voltage-gated calcium channel + "Enables the transmembrane transfer of a calcium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded." [GOC:mtg_transport, GOC:tb, ISBN:0815340729] + voltage-dependent calcium channel + GO_EXT:0005245 + depolarization-activated voltage gated calcium channel + voltage-gated calcium ion channel + voltage gated calcium channel + GO_EXT:bearer of voltage-gated calcium channel activity + bearer of voltage-gated calcium channel activity + depolarization-activated voltage-gated calcium channel + + + bearer of calcium channel regulator activity + GO_EXT:bearer of calcium channel regulator activity + GO_EXT:0005246 + calcium channel regulator + "Modulates the activity of a calcium channel." [GOC:mah] + + + "Enables the transmembrane transfer of a sodium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded." [GOC:mtg_transport, ISBN:0815340729] + bearer of voltage-gated sodium channel activity + voltage-dependent sodium channel + voltage-gated sodium ion channel + voltage gated sodium channel + GO_EXT:bearer of voltage-gated sodium channel activity + GO_EXT:0005248 + voltage-gated sodium channel + + + bearer of anion channel activity + GO_EXT:0005253 + GO_EXT:bearer of anion channel activity + "Enables the energy-independent passage of anions across a lipid bilayer down a concentration gradient." [GOC:dph, GOC:mtg_transport, GOC:pr, ISBN:0815340729] + anion channel + + + "Enables the facilitated diffusion of a chloride (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:mtg_transport, GOC:pr, ISBN:0815340729] + GO_EXT:0005254 + bearer of chloride channel activity + chloride channel + GO_EXT:bearer of chloride channel activity + + + GO_EXT:bearer of cation channel activity + GO_EXT:0005261 + "Enables the energy-independent passage of cations across a lipid bilayer down a concentration gradient." [GOC:def, GOC:dph, GOC:mtg_transport, GOC:pr, ISBN:0815340729] + cation diffusion facilitator + bearer of cation channel activity + cation channel + + + calcium channel + GO_EXT:0005262 + bearer of calcium channel activity + GO_EXT:bearer of calcium channel activity + "Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:mtg_transport, GOC:pr, ISBN:0815340729] + + + potassium channel + bearer of potassium channel activity + GO_EXT:bearer of potassium channel activity + GO_EXT:0005267 + "Enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:BHF, GOC:mtg_transport, GOC:pr, ISBN:0815340729] + + + GO_EXT:0005272 + bearer of sodium channel activity + sodium channel + GO_EXT:bearer of sodium channel activity + "Enables the facilitated diffusion of a sodium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:BHF, GOC:mtg_transport, GOC:pr, ISBN:0815340729] + + + "Enables the directed movement of lipids into, out of or within a cell, or between cells." [GOC:ai] + GO_EXT:0005319 + lipid transporter + GO_EXT:bearer of lipid transporter activity + bearer of lipid transporter activity + + + GO_EXT:bearer of water transmembrane transporter activity + "Enables the directed movement of water (H2O) from one side of a membrane to the other." [GOC:ai] + bearer of water transmembrane transporter activity + GO_EXT:0005372 + water transmembrane transporter + + + Na(+)/K(+)-ATPase + Na+/K+-ATPase + sodium:potassium exchanging ATPase + Na+,K+-ATPase + sodium/potassium-transporting ATPase + bearer of sodium:potassium-exchanging ATPase activity + (Na+ + K+)-activated ATPase + sodium/potassium-exchanging ATPase + GO_EXT:bearer of sodium:potassium-exchanging ATPase activity + Na(+)/K(+)-exchanging ATPase + Na+/K+-exchanging ATPase + Na,K-activated ATPase + (Na+ + K+)-ATPase + sodium:potassium-exchanging ATPase + "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na+(in) + K+(out) = ADP + phosphate + Na+(out) + K+(in)." [EC:3.6.3.9] + GO_EXT:0005391 + + + GO_EXT:bearer of binding + bearer of binding + GO_EXT:0005488 + "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732] + + + "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC:go_curators] + GO_EXT:bearer of protein binding + protein degradation tagging + alpha-2 macroglobulin receptor-associated protein + protein tagging + GO_EXT:0005515 + bearer of protein binding + + + "The function of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria." [GOC:BHF, GOC:rl, http://en.wikipedia.org/wiki/Chemokine, http://www.copewithcytokines.de/cope.cgi?key=Cytokines, PMID:12183377] + chemokine + GO_EXT:0008009 + bearer of chemokine activity + GO_EXT:bearer of chemokine activity + + + "Binds to and increases the activity of an enzyme." [GOC:mah] + enzyme activator + GO_EXT:0008047 + bearer of enzyme activator activity + GO_EXT:bearer of enzyme activator activity + + + GO_EXT:bearer of glutamate receptor activity + glutamate receptor + "Combining with glutamate and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:ai, GOC:signaling] + GO_EXT:0008066 + bearer of glutamate receptor activity + + + bearer of N-acetyltransferase activity + GO_EXT:bearer of N-acetyltransferase activity + GO_EXT:0008080 + N-acetyltransferase + "Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule." [GOC:ai] + + + endonuclease VIII + "Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group." [EC:3.1.4, GOC:curators] + phosphoric diester hydrolase + bearer of phosphoric diester hydrolase activity + GO_EXT:bearer of phosphoric diester hydrolase activity + GO_EXT:0008081 + + + GO_EXT:bearer of growth factor activity + growth factor + GO_EXT:0008083 + bearer of growth factor activity + "The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation." [ISBN:0815316194] + + + DNA dependent ATPase + "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction." [EC:3.6.1.3, GOC:jl] + GO_EXT:0008094 + GO_EXT:bearer of DNA-dependent ATPase activity + DNA-dependent adenosinetriphosphatase + bearer of DNA-dependent ATPase activity + DNA-dependent ATPase + + + patched + "Combining with a member of the hedgehog protein family and transmitting the signal across the membrane to initiate a change in cell activity." [GOC:bf, GOC:go_curators, PMID:9278137] + GO_EXT:bearer of hedgehog receptor activity + GO_EXT:0008158 + bearer of hedgehog receptor activity + hedgehog receptor + + + "Catalysis of the transfer of a methyl group to an acceptor molecule." [ISBN:0198506732] + methyltransferase + GO_EXT:0008168 + bearer of methyltransferase activity + GO_EXT:bearer of methyltransferase activity + + + GO_EXT:0008200 + GO_EXT:bearer of ion channel inhibitor activity + bearer of ion channel inhibitor activity + ion channel inhibitor + "Stops, prevents, or reduces the activity of an ion channel." [GOC:mah] + + + peptide hydrolase + "Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid." [GOC:jl, ISBN:0815332181] + bearer of peptidase activity + peptidase + GO_EXT:0008233 + GO_EXT:bearer of peptidase activity + + + bearer of cysteine-type peptidase activity + cysteine-type peptidase + GO_EXT:bearer of cysteine-type peptidase activity + "Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile." [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE] + GO_EXT:0008234 + + + "Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine)." [http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, ISBN:0716720094] + GO_EXT:0008236 + bearer of serine-type peptidase activity + GO_EXT:bearer of serine-type peptidase activity + serine-type peptidase + + + GO_EXT:bearer of metallopeptidase activity + GO_EXT:0008237 + "Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions." [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE] + bearer of metallopeptidase activity + metallopeptidase + + + GO_EXT:bearer of exopeptidase activity + GO_EXT:0008238 + exopeptidase + "Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain, in a reaction that requires a free N-terminal amino group, C-terminal carboxyl group or both." [http://merops.sanger.ac.uk/about/glossary.htm#EXOPEPTIDASE] + bearer of exopeptidase activity + + + GO_EXT:bearer of tripeptidyl-peptidase activity + "Catalysis of the release of an N-terminal tripeptide from a polypeptide." [GOC:mah] + GO_EXT:0008240 + tripeptidyl-peptidase + bearer of tripeptidyl-peptidase activity + + + bearer of protein methyltransferase activity + GO_EXT:bearer of protein methyltransferase activity + protein methyltransferase + "Catalysis of the transfer of a methyl group (CH3-) to a protein." [GOC:jl, ISBN:0198506732] + GO_EXT:0008276 + + + cation transmembrane transporter + GO_EXT:bearer of cation transmembrane transporter activity + transmembrane cation transporter + bearer of cation transmembrane transporter activity + GO_EXT:0008324 + "Enables the transfer of cation from one side of the membrane to the other." [GOC:dgf, GOC:mtg_transport, ISBN:0815340729] + + + "Catalysis of the transfer of an acyl group to an oxygen atom on the acceptor molecule." [GOC:ai] + O-acyltransferase + GO_EXT:bearer of O-acyltransferase activity + GO_EXT:0008374 + bearer of O-acyltransferase activity + + + IkappaB kinase + ikappaB kinase + GO_EXT:bearer of IkappaB kinase activity + inhibitor of NFkappaB kinase + bearer of IkappaB kinase activity + "Catalysis of the reaction: ATP + IkappaB protein = ADP + IkappaB phosphoprotein." [EC:2.7.11.10] + GO_EXT:0008384 + ATP:IkappaB protein phosphotransferase + inhibitor of NF-kappaB kinase + + + bearer of ribonuclease inhibitor activity + ribonuclease inhibitor + GO_EXT:bearer of ribonuclease inhibitor activity + "Stops, prevents or reduces the activity of a ribonuclease, any enzyme that catalyzes the hydrolysis of phosphodiester bonds in chains of RNA." [GOC:ai] + GO_EXT:0008428 + + + phosphofructokinase + "Catalysis of the transfer of a phosphate group, usually from ATP, to a fructose substrate molecule." [GOC:jl] + bearer of phosphofructokinase activity + GO_EXT:bearer of phosphofructokinase activity + GO_EXT:0008443 + + + GO_EXT:bearer of sulfuric ester hydrolase activity + sulfatase + GO_EXT:0008484 + bearer of sulfuric ester hydrolase activity + sulphuric ester hydrolase + sulfuric ester hydrolase + "Catalysis of the reaction: RSO-R' + H2O = RSOOH + R'H. This reaction is the hydrolysis of any sulfuric ester bond, any ester formed from sulfuric acid, O=SO(OH)2." [GOC:ai] + + + anion transmembrane transporter + "Enables the transfer of a negatively charged ion from one side of a membrane to the other." [GOC:dgf, GOC:mtg_transport, ISBN:0815340729] + anion transporter + GO_EXT:bearer of anion transmembrane transporter activity + bearer of anion transmembrane transporter activity + GO_EXT:0008509 + + + GO_EXT:bearer of sodium:potassium:chloride symporter activity + GO_EXT:0008511 + bearer of sodium:potassium:chloride symporter activity + "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Na+(out) + K+(out) + Cl-(out) = Na+(in) + K+(in) + Cl-(in)." [TC:2.A.30.1.1] + sodium/potassium/chloride symporter + sodium:potassium:chloride symporter + + + taste receptor + GO_EXT:0008527 + "Combining with soluble compounds to initiate a change in cell activity. These receptors are responsible for the sense of taste." [GOC:dph] + GO_EXT:bearer of taste receptor activity + bearer of taste receptor activity + + + GO_EXT:0008528 + G-protein-coupled peptide receptor + G-protein coupled peptide receptor + bearer of G-protein coupled peptide receptor activity + G protein coupled peptide receptor + GO_EXT:bearer of G-protein coupled peptide receptor activity + "Combining with a peptide and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:dph, GOC:tb] + + + potassium-uptake-ATPase + bearer of potassium-transporting ATPase activity + K(+)-transporting ATPase + K+-translocating Kdp-ATPase + potassium transporting ATPase + GO_EXT:0008556 + GO_EXT:bearer of potassium-transporting ATPase activity + k+-transporting ATPase + K+-transporting ATPase + "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + K+(out) = ADP + phosphate + K+(in)." [EC:3.6.3.12] + K+-importing ATPase + potassium-transporting ATPase + + + chloramphenicol acetyltransferase + bearer of chloramphenicol O-acetyltransferase activity + acetyl-CoA:chloramphenicol 3-O-acetyltransferase + GO_EXT:0008811 + chloramphenicol acetylase + "Catalysis of the reaction: chloramphenicol + acetyl-CoA = chloramphenicol 3-acetate + CoA." [EC:2.3.1.28, RHEA:18424] + chloramphenicol transacetylase + GO_EXT:bearer of chloramphenicol O-acetyltransferase activity + chloramphenicol O-acetyltransferase + + + GO_EXT:bearer of kanamycin kinase activity + GO_EXT:0008910 + APH(3') + "Catalysis of the reaction: ATP + kanamycin = ADP + 2 H(+) + kanamycin 3'-phosphate." [EC:2.7.1.95, RHEA:24259] + kanamycin kinase + neomycin-kanamycin phosphotransferase + bearer of kanamycin kinase activity + aminoglycoside 3'-phosphotransferase + neomycin phosphotransferase + ATP:kanamycin 3'-O-phosphotransferase + + + deoxyribonucleate methylase + deoxyribonucleic acid methylase + DNA transmethylase + GO_EXT:bearer of DNA-methyltransferase activity + GO_EXT:0009008 + DNA methyltransferase + DNA-methyltransferase + deoxyribonucleic acid modification methylase + "Catalysis of the transfer of a methyl group to a DNA molecule." [GOC:jl, ISBN:0198506732] + bearer of DNA-methyltransferase activity + deoxyribonucleate methyltransferase + deoxyribonucleic acid methyltransferase + + + bearer of electron carrier activity + electron carrier + GO_EXT:bearer of electron carrier activity + "Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient." [ISBN:0198506732] + GO_EXT:0009055 + electron transporter + + + "Catalysis of the four-electron reduction of dioxygen (O2) to water, coupled to generation of a proton electrochemical gradient across a membrane." [GOC:kd] + GO_EXT:bearer of heme-copper terminal oxidase activity + haem-copper terminal oxidase + heme-copper terminal oxidase + GO_EXT:0015002 + bearer of heme-copper terminal oxidase activity + + + coreceptor, insoluble ligand + coreceptor + bearer of coreceptor activity + GO_EXT:bearer of coreceptor activity + GO_EXT:0015026 + coreceptor, soluble ligand + "Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity." [GOC:go_curators] + + + bearer of ion transmembrane transporter activity + GO_EXT:bearer of ion transmembrane transporter activity + ion transporter + "Enables the transfer of an ion from one side of a membrane to the other." [GOC:dgf, GOC:mtg_transport, ISBN:0815340729] + GO_EXT:0015075 + ion transmembrane transporter + + + monovalent inorganic cation transmembrane transporter + bearer of monovalent inorganic cation transmembrane transporter activity + "Enables the transfer of a inorganic cations with a valency of one from one side of a membrane to the other. Inorganic cations are atoms or small molecules with a positive charge that do not contain carbon in covalent linkage." [GOC:ai, GOC:mtg_transport, ISBN:0815340729] + GO_EXT:0015077 + GO_EXT:bearer of monovalent inorganic cation transmembrane transporter activity + + + GO_EXT:bearer of hydrogen ion transmembrane transporter activity + proton transporter + GO_EXT:0015078 + bearer of hydrogen ion transmembrane transporter activity + "Enables the transfer of hydrogen ions from one side of a membrane to the other." [GOC:ai] + hydrogen ion transmembrane transporter + + + potassium ion transmembrane transporter + potassium transporter + "Enables the transfer of potassium ions (K+) from one side of a membrane to the other." [GOC:ai] + GO_EXT:bearer of potassium ion transmembrane transporter activity + GO_EXT:0015079 + bearer of potassium ion transmembrane transporter activity + + + sodium transporter + bearer of sodium ion transmembrane transporter activity + GO_EXT:bearer of sodium ion transmembrane transporter activity + sodium ion transmembrane transporter + "Enables the transfer of sodium ions (Na+) from one side of a membrane to the other." [GOC:ai, GOC:BHF] + GO_EXT:0015081 + + + GO_EXT:bearer of calcium ion transmembrane transporter activity + "Enables the transfer of calcium (Ca) ions from one side of a membrane to the other." [GOC:dgf] + calcium ion transmembrane transporter + bearer of calcium ion transmembrane transporter activity + GO_EXT:0015085 + + + bearer of inorganic anion transmembrane transporter activity + inorganic anion transmembrane transporter + GO_EXT:0015103 + GO_EXT:bearer of inorganic anion transmembrane transporter activity + "Enables the transfer of inorganic anions from one side of a membrane to the other. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage." [GOC:ai] + + + GO_EXT:0015108 + GO_EXT:bearer of chloride transmembrane transporter activity + "Enables the transfer of chloride ions from one side of a membrane to the other." [GOC:ai] + chloride ion transmembrane transporter + bearer of chloride transmembrane transporter activity + chloride transmembrane transporter + + + sterol transporter + GO_EXT:bearer of sterol transporter activity + bearer of sterol transporter activity + GO_EXT:0015248 + "Enables the directed movement of sterols into, out of or within a cell, or between cells. Sterol are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC:ai] + + + GO_EXT:bearer of water channel activity + GO_EXT:0015250 + bearer of water channel activity + water channel + "Transport systems of this type enable facilitated diffusion of water (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:mtg_transport, ISBN:0815340729] + + + channel/pore class transporter + alpha-type channel + GO_EXT:bearer of channel activity + pore class transporter + "Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." [GOC:mtg_transport, ISBN:0815340729, TC:1.-.-.-.-] + bearer of channel activity + nonselective channel + channel + GO_EXT:0015267 + channel-forming toxin + + + "Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729] + ligand-gated ion channel + bearer of ligand-gated ion channel activity + GO_EXT:0015276 + GO_EXT:bearer of ligand-gated ion channel activity + + + calcium-release channel + bearer of calcium-release channel activity + GO_EXT:bearer of calcium-release channel activity + "Enables the transmembrane transfer of a calcium ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." [GOC:mah] + GO_EXT:0015278 + + + bearer of porin activity + "Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria." [GOC:mtg_transport, ISBN:0815340729, PMID:10839820, TC:1.B.1.-.-] + porin + GO_EXT:bearer of porin activity + GO_EXT:0015288 + + + "Catalysis of the transfer of a solute from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy, not direct ATP coupling. Chemiosmotic sources of energy include uniport, symport or antiport." [GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729, PMID:10839820] + bearer of secondary active transmembrane transporter activity + GO_EXT:0015291 + galactose/glucose (methylgalactoside) porter + electrochemical potential-driven transporter + GO_EXT:bearer of secondary active transmembrane transporter activity + porter + secondary active transmembrane transporter + + + GO_EXT:0015293 + bearer of symporter activity + GO_EXT:bearer of symporter activity + symporter + "Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy." [GOC:mtg_transport, ISBN:0815340729, PMID:10839820] + + + GO_EXT:0015294 + solute:cation symporter + "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + cation(out) = solute(in) + cation(in)." [GOC:ai] + bearer of solute:cation symporter activity + GO_EXT:bearer of solute:cation symporter activity + + + "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: anion(out) + cation(out) = anion(in) + cation(in)." [TC:2.A.1.14.-] + GO_EXT:bearer of anion:cation symporter activity + GO_EXT:0015296 + anion:cation symporter + bearer of anion:cation symporter activity + + + antiporter + GO_EXT:0015297 + GO_EXT:bearer of antiporter activity + bearer of antiporter activity + solute:solute antiporter + exchange transporter + "Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. The reaction is: solute A(out) + solute B(in) = solute A(in) + solute B(out)." [GOC:mtg_transport, ISBN:0815340729, PMID:10839820] + countertransporter + + + anion exchanger + anion:anion antiporter + bearer of anion:anion antiporter activity + GO_EXT:bearer of anion:anion antiporter activity + GO_EXT:0015301 + "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: anion A(out) + anion B(in) = anion A(in) + anion B(out)." [GOC:ai, GOC:mtg_transport] + + + cation:chloride symporter + GO_EXT:bearer of cation:chloride symporter activity + "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: cation(out) + Cl-(out) = cation(in) + Cl-(in)." [TC:2.A.30.-.-] + bearer of cation:chloride symporter activity + GO_EXT:0015377 + + + bearer of primary active transmembrane transporter activity + "Catalysis of the transfer of a solute from one side of the membrane to the other, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is powered by a primary energy source, directly using ATP. Primary energy sources known to be coupled to transport are chemical, electrical and solar sources." [GOC:mtg_transport, ISBN:0815340729, TC:3.-.-.-.-] + GO_EXT:0015399 + primary active transmembrane transporter + GO_EXT:bearer of primary active transmembrane transporter activity + + + GO_EXT:bearer of P-P-bond-hydrolysis-driven transmembrane transporter activity + P-P-bond-hydrolysis-driven transmembrane transporter + GO_EXT:0015405 + "Primary active transport of a solute across a membrane, driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated. Primary active transport is catalysis of the transport of a solute across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by a primary energy source." [GOC:mtg_transport, ISBN:0815340729, TC:3.A.-.-.-] + bearer of P-P-bond-hydrolysis-driven transmembrane transporter activity + + + efflux permease + bearer of efflux transmembrane transporter activity + "Enables the transfer of a specific substance or related group of substances from the inside of the cell to the outside of the cell across a membrane." [GOC:ai, GOC:mtg_transport, ISBN:0815340729] + GO_EXT:bearer of efflux transmembrane transporter activity + efflux transmembrane transporter + GO_EXT:0015562 + monocarboxylate (lactate, pyruvate, mevalonate) uptake/efflux porter + + + bearer of ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism + "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O = ADP + phosphate, to directly drive the transport of ions across a membrane. The reaction is characterized by the transient formation of a high-energy aspartyl-phosphoryl-enzyme intermediate." [PMID:10322420, PMID:10600683] + GO_EXT:bearer of ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism + GO_EXT:0015662 + P-type ATPase + + + GO_EXT:bearer of restriction endodeoxyribonuclease activity + restriction endodeoxyribonuclease + bearer of restriction endodeoxyribonuclease activity + restriction endonuclease + restriction enzyme + "Catalysis of endonucleolytic cleavage of DNA in a site-specific manner, resulting in double-strand breaks." [GOC:mlg] + GO_EXT:0015666 + + + GO_EXT:0015925 + "Catalysis of the hydrolysis of galactosyl compounds, substances containing a group derived from a cyclic form of galactose or a galactose derivative." [GOC:ai] + bearer of galactosidase activity + galactosidase + GO_EXT:bearer of galactosidase activity + + + GO_EXT:bearer of morphogen activity + GO_EXT:0016015 + "Acts as a trigger for a pattern specification process when present at a specific concentration within a gradient." [GOC:go_curators] + morphogen + bearer of morphogen activity + + + antioxidant + "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage." [ISBN:0198506732] + GO_EXT:0016209 + GO_EXT:bearer of antioxidant activity + bearer of antioxidant activity + + + GO_EXT:bearer of channel regulator activity + GO_EXT:0016247 + channel regulator + "Modulates the activity of a channel. A channel catalyzes energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel." [GOC:mah] + bearer of channel regulator activity + + + bearer of channel inhibitor activity + "Stops, prevents, or reduces the activity of a channel. A channel catalyzes energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel." [GOC:mah] + GO_EXT:0016248 + GO_EXT:bearer of channel inhibitor activity + channel inhibitor + + + GO_EXT:0016298 + lipase + "Catalysis of the hydrolysis of a lipid or phospholipid." [GOC:mah] + bearer of lipase activity + GO_EXT:bearer of lipase activity + + + phosphokinase + GO_EXT:0016301 + "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] + GO_EXT:bearer of kinase activity + kinase + bearer of kinase activity + + + ATP:1-phosphatidyl-1D-myo-inositol 3-phosphotransferase + GO_EXT:bearer of 1-phosphatidylinositol-3-kinase activity + 1-phosphatidylinositol 3-kinase + PtdIns-3-kinase + 1-phosphatidylinositol-3-kinase + GO_EXT:0016303 + PI3-kinase + "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ADP + 2 H(+)." [EC:2.7.1.137, RHEA:12712] + bearer of 1-phosphatidylinositol-3-kinase activity + + + GO_EXT:bearer of carnitine O-acyltransferase activity + carnitine O-acyltransferase + bearer of carnitine O-acyltransferase activity + "Catalysis of the transfer of an acyl group to an oxygen atom on the carnitine molecule." [GOC:ai] + GO_EXT:0016406 + + + bearer of acetyltransferase activity + acetylase + "Catalysis of the transfer of an acetyl group to an acceptor molecule." [GOC:ai] + acetyltransferase + GO_EXT:bearer of acetyltransferase activity + GO_EXT:0016407 + + + "Catalysis of the transfer of a palmitoyl (CH3-[CH2]14-CO-) group to an acceptor molecule." [GOC:ai] + palmitoyltransferase + bearer of palmitoyltransferase activity + GO_EXT:0016409 + GO_EXT:bearer of palmitoyltransferase activity + + + GO_EXT:0016410 + "Catalysis of the transfer of an acyl group to a nitrogen atom on the acceptor molecule." [GOC:ai] + N-acyltransferase + GO_EXT:bearer of N-acyltransferase activity + bearer of N-acyltransferase activity + + + GO_EXT:bearer of O-acetyltransferase activity + GO_EXT:0016413 + "Catalysis of the transfer of an acetyl group to an oxygen atom on the acceptor molecule." [GOC:ai] + O-acetyltransferase + bearer of O-acetyltransferase activity + + + GO_EXT:0016416 + "Catalysis of the transfer of a palmitoyl group to an oxygen atom on the acceptor molecule." [GOC:ai] + O-palmitoyltransferase + GO_EXT:bearer of O-palmitoyltransferase activity + bearer of O-palmitoyltransferase activity + + + CoA carboxylase + GO_EXT:0016421 + GO_EXT:bearer of CoA carboxylase activity + bearer of CoA carboxylase activity + "Catalysis of the joining of a carboxyl group to a molecule that is attached to CoA, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [GOC:mah] + + + GO_EXT:bearer of pyrophosphatase activity + pyrophosphatase + GO_EXT:0016462 + bearer of pyrophosphatase activity + "Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments." [EC:3.6.1.-, GOC:curators] + + + redox + GO_EXT:0016491 + bearer of oxidoreductase activity + GO_EXT:bearer of oxidoreductase activity + oxidoreductase + "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC:go_curators] + + + GO_EXT:0016494 + "Combining with a C-X-C chemokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. A C-X-C chemokine has a single amino acid between the first two cysteines of the characteristic four cysteine motif." [GOC:signaling, PMID:8662823] + GO_EXT:bearer of C-X-C chemokine receptor activity + bearer of C-X-C chemokine receptor activity + C-X-C chemokine receptor + + + GO_EXT:0016530 + "Assists in the delivery of metal ions to target proteins or compartments." [GOC:jl, PMID:11739376] + bearer of metallochaperone activity + metallochaperone + GO_EXT:bearer of metallochaperone activity + + + GO_EXT:bearer of oxidoreductase activity, acting on CH-OH group of donors + "Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor." [GOC:ai] + GO_EXT:0016614 + bearer of oxidoreductase activity, acting on CH-OH group of donors + + + "Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP." [EC:1.1.1.-, GOC:ai] + GO_EXT:0016616 + GO_EXT:bearer of oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor + bearer of oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor + + + GO_EXT:bearer of oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor + "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC:jl] + bearer of oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor + GO_EXT:0016620 + + + bearer of oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor + "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide." [GOC:jl] + GO_EXT:bearer of oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor + GO_EXT:0016624 + + + bearer of oxidoreductase activity, acting on the CH-CH group of donors + GO_EXT:0016627 + GO_EXT:bearer of oxidoreductase activity, acting on the CH-CH group of donors + "Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor." [GOC:ai] + + + GO_EXT:0016634 + "Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces oxygen." [GOC:jl] + GO_EXT:bearer of oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor + bearer of oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor + + + GO_EXT:bearer of oxidoreductase activity, acting on NAD(P)H + GO_EXT:0016651 + bearer of oxidoreductase activity, acting on NAD(P)H + "Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor." [GOC:ai] + + + GO_EXT:0016667 + "Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor." [GOC:ai] + GO_EXT:bearer of oxidoreductase activity, acting on a sulfur group of donors + bearer of oxidoreductase activity, acting on a sulfur group of donors + + + "Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC:jl] + bearer of oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor + GO_EXT:0016668 + GO_EXT:bearer of oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor + + + GO_EXT:bearer of oxidoreductase activity, acting on a heme group of donors + "Catalysis of an oxidation-reduction (redox) reaction in which a heme group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor." [GOC:ai] + GO_EXT:0016675 + bearer of oxidoreductase activity, acting on a heme group of donors + + + "Catalysis of an oxidation-reduction (redox) reaction in which a heme group acts as a hydrogen or electron donor and reduces oxygen." [GOC:jl] + bearer of oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor + GO_EXT:bearer of oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor + GO_EXT:0016676 + + + GO_EXT:0016684 + "Catalysis of an oxidation-reduction (redox) reaction in which the peroxide group acts as a hydrogen or electron acceptor." [GOC:ai] + GO_EXT:bearer of oxidoreductase activity, acting on peroxide as acceptor + bearer of oxidoreductase activity, acting on peroxide as acceptor + + + GO_EXT:0016701 + GO_EXT:bearer of oxidoreductase activity, acting on single donors with incorporation of molecular oxygen + bearer of oxidoreductase activity, acting on single donors with incorporation of molecular oxygen + "Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and molecular oxygen is incorporated into a donor." [GOC:mah] + + + GO_EXT:0016703 + "Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and one oxygen atom is incorporated into a donor." [GOC:mah] + bearer of oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases) + GO_EXT:bearer of oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases) + + + GO_EXT:0016705 + bearer of oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen + "Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor." [GOC:mah] + GO_EXT:bearer of oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen + + + "Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and one atom of oxygen is incorporated into one donor." [GOC:mah] + GO_EXT:0016709 + bearer of oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen + GO_EXT:bearer of oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen + + + bearer of oxidoreductase activity, acting on superoxide radicals as acceptor + "Catalysis of an oxidation-reduction (redox) reaction in which a superoxide radical (O2- or O2.-) acts as a hydrogen or electron acceptor." [GOC:ai] + GO_EXT:bearer of oxidoreductase activity, acting on superoxide radicals as acceptor + GO_EXT:0016721 + + + transferase + bearer of transferase activity + GO_EXT:bearer of transferase activity + GO_EXT:0016740 + "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732] + + + bearer of transferase activity, transferring one-carbon groups + "Catalysis of the transfer of a one-carbon group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] + GO_EXT:0016741 + GO_EXT:bearer of transferase activity, transferring one-carbon groups + + + acyltransferase + GO_EXT:bearer of transferase activity, transferring acyl groups + GO_EXT:0016746 + "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] + bearer of transferase activity, transferring acyl groups + + + GO_EXT:bearer of transferase activity, transferring acyl groups other than amino-acyl groups + GO_EXT:0016747 + bearer of transferase activity, transferring acyl groups other than amino-acyl groups + "Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor)." [GOC:jl] + + + GO_EXT:bearer of transferase activity, transferring amino-acyl groups + bearer of transferase activity, transferring amino-acyl groups + aminoacyltransferase + GO_EXT:0016755 + "Catalysis of the transfer of an amino-acyl group from one compound (donor) to another (acceptor)." [GOC:jl] + + + GO_EXT:bearer of transferase activity, transferring glycosyl groups + glycosyltransferase + transglycosylase + bearer of transferase activity, transferring glycosyl groups + GO_EXT:0016757 + transglycosidase + "Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] + + + hexosyltransferase + "Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor)." [GOC:jl] + bearer of transferase activity, transferring hexosyl groups + GO_EXT:bearer of transferase activity, transferring hexosyl groups + GO_EXT:0016758 + + + bearer of transferase activity, transferring phosphorus-containing groups + GO_EXT:bearer of transferase activity, transferring phosphorus-containing groups + "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] + GO_EXT:0016772 + + + bearer of phosphotransferase activity, alcohol group as acceptor + "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor)." [GOC:jl] + GO_EXT:0016773 + GO_EXT:bearer of phosphotransferase activity, alcohol group as acceptor + + + nucleotidyltransferase + GO_EXT:0016779 + GO_EXT:bearer of nucleotidyltransferase activity + "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN:0198506732] + bearer of nucleotidyltransferase activity + + + hydrolase + GO_EXT:bearer of hydrolase activity + GO_EXT:0016787 + "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732] + bearer of hydrolase activity + + + GO_EXT:bearer of hydrolase activity, acting on ester bonds + "Catalysis of the hydrolysis of any ester bond." [GOC:jl] + bearer of hydrolase activity, acting on ester bonds + GO_EXT:0016788 + esterase + + + GO_EXT:bearer of phosphatase activity + "Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate." [EC:3.1.3, EC:3.1.3.41, GOC:curators, GOC:pg] + phosphoric monoester hydrolase + bearer of phosphatase activity + GO_EXT:0016791 + phosphatase + + + glycosidase + "Catalysis of the hydrolysis of any glycosyl bond." [GOC:jl] + bearer of hydrolase activity, acting on glycosyl bonds + GO_EXT:0016798 + GO_EXT:bearer of hydrolase activity, acting on glycosyl bonds + + + GO_EXT:0016810 + bearer of hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds + GO_EXT:bearer of hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds + "Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds." [GOC:jl] + + + GO_EXT:bearer of hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides + GO_EXT:0016811 + "Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide." [GOC:ai] + bearer of hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides + + + GO_EXT:bearer of hydrolase activity, acting on acid anhydrides + GO_EXT:0016817 + "Catalysis of the hydrolysis of any acid anhydride." [GOC:jl] + bearer of hydrolase activity, acting on acid anhydrides + + + GO_EXT:bearer of hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides + bearer of hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides + GO_EXT:0016818 + "Catalysis of the hydrolysis of any acid anhydride which contains phosphorus." [GOC:jl] + + + bearer of hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances + GO_EXT:0016820 + "Catalysis of the hydrolysis of an acid anhydride to directly drive the transport of a substance across a membrane." [GOC:mah] + GO_EXT:bearer of hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances + + + GO_EXT:bearer of lyase activity + GO_EXT:0016829 + lyase + bearer of lyase activity + "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC:4.-.-.-, ISBN:0198547684] + + + bearer of carbon-carbon lyase activity + carbon-carbon lyase + GO_EXT:0016830 + "Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond." [GOC:jl] + GO_EXT:bearer of carbon-carbon lyase activity + + + "Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound." [http://www.mercksource.com/] + GO_EXT:0016831 + GO_EXT:bearer of carboxy-lyase activity + carboxy-lyase + decarboxylase + bearer of carboxy-lyase activity + + + GO_EXT:0016835 + carbon-oxygen lyase + "Catalysis of the breakage of a carbon-oxygen bond." [EC:4.2.-.-] + bearer of carbon-oxygen lyase activity + GO_EXT:bearer of carbon-oxygen lyase activity + + + GO_EXT:0016836 + bearer of hydro-lyase activity + hydro-lyase + GO_EXT:bearer of hydro-lyase activity + "Catalysis of the cleavage of a carbon-oxygen bond by elimination of water." [EC:4.2.1] + + + isomerase + GO_EXT:bearer of isomerase activity + "Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5." [ISBN:0198506732] + bearer of isomerase activity + GO_EXT:0016853 + + + GO_EXT:bearer of ligase activity + ligase + synthetase + bearer of ligase activity + "Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC:6, GOC:mah] + GO_EXT:0016874 + + + "Catalysis of the joining of two molecules via a carbon-oxygen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC:6.1, GOC:mah] + GO_EXT:0016875 + bearer of ligase activity, forming carbon-oxygen bonds + GO_EXT:bearer of ligase activity, forming carbon-oxygen bonds + + + bearer of ligase activity, forming aminoacyl-tRNA and related compounds + "Catalysis of the joining of an amino acid and a nucleic acid (usually tRNA) or poly(ribitol phosphate), with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. The reaction forms an aminoacyl-tRNA or a related compound." [EC:6.1.1, GOC:mah] + GO_EXT:0016876 + GO_EXT:bearer of ligase activity, forming aminoacyl-tRNA and related compounds + + + bearer of ligase activity, forming carbon-nitrogen bonds + "Catalysis of the joining of two molecules, or two groups within a single molecule, via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC:6.3, GOC:mah] + GO_EXT:0016879 + GO_EXT:bearer of ligase activity, forming carbon-nitrogen bonds + + + bearer of acid-amino acid ligase activity + "Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [GOC:jl, GOC:mah] + peptide synthase + GO_EXT:0016881 + acid-amino acid ligase + GO_EXT:bearer of acid-amino acid ligase activity + + + GO_EXT:bearer of ligase activity, forming carbon-carbon bonds + "Catalysis of the joining of two molecules via a carbon-carbon bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC:6.4, GOC:jl, GOC:mah] + GO_EXT:0016885 + bearer of ligase activity, forming carbon-carbon bonds + + + bearer of ligase activity, forming phosphoric ester bonds + GO_EXT:bearer of ligase activity, forming phosphoric ester bonds + GO_EXT:0016886 + "Catalysis of the joining of two molecules, or two groups within a single molecule, via a phosphoric ester bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC:6.5, GOC:mah] + + + adenosine 5'-triphosphatase + GO_EXT:bearer of ATPase activity + bearer of ATPase activity + ATPase + ATP monophosphatase + ATP hydrolase + "Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction." [EC:3.6.1.3, GOC:jl] + adenosinetriphosphatase + adenosine triphosphatase + GO_EXT:0016887 + ATP phosphohydrolase + + + bearer of oxidoreductase activity, acting on the aldehyde or oxo group of donors + "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor." [GOC:ai] + GO_EXT:0016903 + GO_EXT:bearer of oxidoreductase activity, acting on the aldehyde or oxo group of donors + + + stress-activated kinase + "Catalysis of the phosphorylation of proteins. A family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. Strongly activated by stress signals such as heat or osmotic shock, DNA-damaging agents, inhibitors of protein synthesis and pro-inflammatory cytokines." [GOC:ma] + GO_EXT:0016909 + SAP kinase + GO_EXT:bearer of SAP kinase activity + stress-activated protein kinase + bearer of SAP kinase activity + + + GABA receptor + 4-aminobutanoate receptor + "Combining with gamma-aminobutyric acid (GABA), and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. (GABA, 4-aminobutyrate) is an amino acid which acts as a neurotransmitter in some organisms." [GOC:jl, GOC:signaling, PMID:10637650] + 4-aminobutyrate receptor + bearer of GABA receptor activity + GO_EXT:0016917 + gamma-aminobutyric acid receptor + GO_EXT:bearer of GABA receptor activity + + + GO_EXT:0017080 + bearer of sodium channel regulator activity + sodium channel regulator + GO_EXT:bearer of sodium channel regulator activity + "Modulates the activity of a sodium channel." [GOC:mah] + + + nucleoside-5-triphosphate phosphohydrolase + bearer of nucleoside-triphosphatase activity + unspecific diphosphate phosphohydrolase + nucleoside 5-triphosphatase + NTPase + nucleoside triphosphate hydrolase + nucleoside triphosphate phosphohydrolase + GO_EXT:0017111 + GO_EXT:bearer of nucleoside-triphosphatase activity + nucleoside-triphosphatase + nucleoside triphosphatase + "Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate." [EC:3.6.1.15] + + + NAD-dependent histone deacetylase + "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from a histone." [EC:3.5.1.17, RHEA:24551] + GO_EXT:bearer of NAD-dependent histone deacetylase activity + bearer of NAD-dependent histone deacetylase activity + GO_EXT:0017136 + + + "Catalysis of the hydrolysis of a substrate by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine)." [Wikipedia:Serine_hydrolase] + serine hydrolase + GO_EXT:0017171 + bearer of serine hydrolase activity + GO_EXT:bearer of serine hydrolase activity + + + bearer of transmembrane receptor protein kinase activity + transmembrane receptor protein kinase + GO_EXT:bearer of transmembrane receptor protein kinase activity + GO_EXT:0019199 + "Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: a protein + ATP = a phosphoprotein + ADP." [GOC:mah] + + + GO_EXT:bearer of carbohydrate kinase activity + carbohydrate kinase + "Catalysis of the transfer of a phosphate group, usually from ATP, to a carbohydrate substrate molecule." [GOC:jl] + GO_EXT:0019200 + bearer of carbohydrate kinase activity + + + nucleobase, nucleoside, nucleotide kinase + GO_EXT:0019205 + nucleobase-containing compound kinase + "Catalysis of the transfer of a phosphate group, usually from ATP or GTP, to a nucleobase, nucleoside, nucleotide or polynucleotide substrate." [GOC:jl] + GO_EXT:bearer of nucleobase-containing compound kinase activity + bearer of nucleobase-containing compound kinase activity + + + GO_EXT:bearer of kinase regulator activity + "Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:ai] + kinase regulator + GO_EXT:0019207 + bearer of kinase regulator activity + + + bearer of phosphatase regulator activity + phosphatase regulator + GO_EXT:bearer of phosphatase regulator activity + "Modulates the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule." [GOC:ai] + GO_EXT:0019208 + + + kinase activator + GO_EXT:bearer of kinase activator activity + "Binds to and increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:ai] + bearer of kinase activator activity + GO_EXT:0019209 + + + "Stops, prevents or reduces the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] + bearer of kinase inhibitor activity + kinase inhibitor + GO_EXT:0019210 + GO_EXT:bearer of kinase inhibitor activity + + + phosphatase inhibitor + "Stops, prevents or reduces the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule." [GOC:ai] + GO_EXT:0019212 + bearer of phosphatase inhibitor activity + GO_EXT:bearer of phosphatase inhibitor activity + + + bearer of deacetylase activity + deacetylase + GO_EXT:bearer of deacetylase activity + GO_EXT:0019213 + "Catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule." [GOC:jl] + + + bearer of immunoglobulin receptor activity + GO_EXT:0019763 + immunoglobulin receptor + "Combining with the Fc region of an immunoglobulin protein and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:signaling, ISBN:0198547684] + GO_EXT:bearer of immunoglobulin receptor activity + FC receptor + + + "Catalysis of the transfer of a ubiquitin-like from one protein to another via the reaction X-ULP + Y --> Y-ULP + X, where both X-ULP and Y-ULP are covalent linkages. ULP represents a ubiquitin-like protein." [GOC:mah, GOC:rn, PMID:10806345, PMID:10884686] + GO_EXT:bearer of ubiquitin-like protein transferase activity + small conjugating protein transferase + bearer of ubiquitin-like protein transferase activity + GO_EXT:0019787 + ubiquitin-like protein transferase + + + cation-transporting ATPase + GO_EXT:bearer of cation-transporting ATPase activity + bearer of cation-transporting ATPase activity + "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + cation(out) = ADP + phosphate + cation(in)." [GOC:ai] + GO_EXT:0019829 + + + GO_EXT:bearer of calcium channel inhibitor activity + "Stops, prevents, or reduces the activity of a calcium channel." [GOC:mah] + GO_EXT:0019855 + calcium channel inhibitor + bearer of calcium channel inhibitor activity + + + sodium channel inhibitor + "Stops, prevents, or reduces the activity of a sodium channel." [GOC:mah] + bearer of sodium channel inhibitor activity + GO_EXT:bearer of sodium channel inhibitor activity + GO_EXT:0019871 + + + bearer of protein kinase regulator activity + GO_EXT:bearer of protein kinase regulator activity + GO_EXT:0019887 + "Modulates the activity of a protein kinase, an enzyme which phosphorylates a protein." [GOC:ai] + protein kinase regulator + + + bearer of passive transmembrane transporter activity + GO_EXT:bearer of passive transmembrane transporter activity + "Enables the transfer of a solute from one side of the membrane to the other, down the solute's concentration gradient." [GOC:mtg_transport, ISBN:0815340729] + passive transmembrane transporter + GO_EXT:0022803 + + + GO_EXT:bearer of active transmembrane transporter activity + permease + active carrier + bearer of active transmembrane transporter activity + active transmembrane transporter + GO_EXT:0022804 + pump + carrier + "Catalysis of the transfer of a specific substance or related group of substances from one side of a membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction." [GOC:mtg_transport, ISBN:0815340729] + + + bearer of wide pore channel activity + GO_EXT:0022829 + "Enables the transport of a solute across a membrane via a large pore, un-gated channel. Examples include gap junctions, which transport substances from one cell to another; and porins which transport substances in and out of bacteria, mitochondria and chloroplasts." [GOC:mtg_transport, ISBN:0815340729] + GO_EXT:bearer of wide pore channel activity + wide pore channel + non-gated, wide pore channel + + + bearer of voltage-gated channel activity + voltage-gated channel + GO_EXT:bearer of voltage-gated channel activity + "Enables the transmembrane transfer of a solute by a channel whose open state is dependent on the voltage across the membrane in which it is embedded." [GOC:mtg_transport, ISBN:0815340729] + GO_EXT:0022832 + + + bearer of ligand-gated channel activity + "Enables the transmembrane transfer of a solute by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729] + ligand-gated channel + GO_EXT:0022834 + GO_EXT:bearer of ligand-gated channel activity + + + bearer of gated channel activity + gated channel + GO_EXT:bearer of gated channel activity + "Enables the transmembrane transfer of a solute by a channel that opens in response to a specific stimulus." [GOC:mtg_transport] + GO_EXT:0022836 + + + "Enables the energy-independent facilitated diffusion, mediated by passage of a specific solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." [GOC:mtg_transport] + GO_EXT:0022838 + substrate-specific channel + bearer of substrate-specific channel activity + GO_EXT:bearer of substrate-specific channel activity + + + voltage-gated cation channel + "Enables the transmembrane transfer of a cation by a voltage-gated channel. A cation is a positively charged ion. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded." [GOC:mtg_transport, ISBN:0815340729] + bearer of voltage-gated cation channel activity + GO_EXT:bearer of voltage-gated cation channel activity + GO_EXT:0022843 + + + transmembrane transporter + GO_EXT:bearer of transmembrane transporter activity + GO_EXT:0022857 + "Enables the transfer of a substance from one side of a membrane to the other." [GOC:mtg_transport, ISBN:0815340729] + bearer of transmembrane transporter activity + + + inorganic cation transmembrane transporter + GO_EXT:bearer of inorganic cation transmembrane transporter activity + bearer of inorganic cation transmembrane transporter activity + GO_EXT:0022890 + "Enables the transfer of inorganic cations from one side of a membrane to the other. Inorganic cations are atoms or small molecules with a positive charge that do not contain carbon in covalent linkage." [GOC:ai, GOC:mtg_transport, ISBN:0815340729] + + + "Enables the transfer of a specific substance or group of related substances from one side of a membrane to the other." [GOC:jid, GOC:mtg_transport, ISBN:0815340729] + bearer of substrate-specific transmembrane transporter activity + substrate-specific transmembrane transporter + GO_EXT:bearer of substrate-specific transmembrane transporter activity + GO_EXT:0022891 + + + "Enables the directed movement of a specific substance or group of related substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC:mtg_transport] + substrate-specific transporter + GO_EXT:0022892 + bearer of substrate-specific transporter activity + GO_EXT:bearer of substrate-specific transporter activity + + + bearer of apolipoprotein receptor activity + GO_EXT:0030226 + "Combining with an apolipoprotein to initiate a change in cell activity." [GOC:mah, ISBN:0198506732] + GO_EXT:bearer of apolipoprotein receptor activity + apolipoprotein receptor + + + lipoprotein receptor + GO_EXT:0030228 + lipoprotein particle receptor + bearer of lipoprotein particle receptor activity + GO_EXT:bearer of lipoprotein particle receptor activity + "Combining with a lipoprotein particle and delivering the lipoprotein particle into the cell via endocytosis. A lipoprotein particle, also known as a lipoprotein, is a clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids." [CHEBI:6495, GOC:bf, GOC:mah, PMID:12827279] + plasma lipoprotein particle receptor + + + catalytic regulator + "Binds to and modulates the activity of an enzyme." [GOC:mah] + GO_EXT:0030234 + bearer of enzyme regulator activity + GO_EXT:bearer of enzyme regulator activity + enzyme regulator + + + GO_EXT:0030295 + "Binds to and increases the activity of a protein kinase, an enzyme which phosphorylates a protein." [GOC:ai] + protein kinase activator + bearer of protein kinase activator activity + GO_EXT:bearer of protein kinase activator activity + + + GO_EXT:bearer of receptor regulator activity + "The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed." [GOC:ceb] + receptor regulator + GO_EXT:0030545 + bearer of receptor regulator activity + + + "The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased." [GOC:ceb] + bearer of receptor activator activity + receptor activator + GO_EXT:bearer of receptor activator activity + GO_EXT:0030546 + + + GO_EXT:0030594 + GO_EXT:bearer of neurotransmitter receptor activity + bearer of neurotransmitter receptor activity + neurotransmitter receptor + "Combining with a neurotransmitter and transmitting the signal to initiate a change in cell activity." [GOC:jl, GOC:signaling] + + + GO_EXT:bearer of protein complex scaffold + GO_EXT:0032947 + bearer of protein complex scaffold + "Functions to provide a physical support for the assembly of a multiprotein complex." [GOC:mah] + + + bearer of bitter taste receptor activity + bitter taste receptor + GO_EXT:0033038 + "Combining with soluble bitter compounds to initiate a change in cell activity. These receptors are responsible for the sense of bitter taste." [GOC:mah] + GO_EXT:bearer of bitter taste receptor activity + + + GO_EXT:0033549 + MAPK phosphatase + "Catalysis of the reaction: a phosphorylated MAP kinase + H2O = a MAP kinase + phosphate." [GOC:mah, PMID:12184814, PMID:17208316] + GO_EXT:bearer of MAP kinase phosphatase activity + bearer of MAP kinase phosphatase activity + MAP kinase phosphatase + + + GO_EXT:bearer of protein deacetylase activity + GO_EXT:0033558 + "Catalysis of the hydrolysis of an acetyl group or groups from a protein substrate." [GOC:mah] + protein deacetylase + bearer of protein deacetylase activity + + + deoxyribonucleic acid polymerase + GO_EXT:bearer of DNA polymerase activity + bearer of DNA polymerase activity + deoxyribonucleate nucleotidyltransferase + DNA polymerase + "Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group." [EC:2.7.7.7, GOC:mah] + GO_EXT:0034061 + deoxyribonucleic polymerase + deoxynucleate polymerase + DNA nucleotidyltransferase + + + ribonucleic transcriptase + GO_EXT:0034062 + ribonucleic acid transcriptase + ribonucleic acid polymerase + GO_EXT:bearer of RNA polymerase activity + "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template." [EC:2.7.7.6, GOC:mah] + ribonucleic polymerase + RNA nucleotidyltransferase + bearer of RNA polymerase activity + ribonucleate nucleotidyltransferase + RNA polymerase + RNA transcriptase + ribonucleate polymerase + + + aminoglycoside kinase + GO_EXT:0034071 + bearer of aminoglycoside phosphotransferase activity + GO_EXT:bearer of aminoglycoside phosphotransferase activity + aminoglycoside phosphotransferase + "Catalysis of the reaction: ATP + aminoglycoside = ADP + phosphoaminoglycoside." [GOC:cb, GOC:mah] + + + "Combining with apolipoprotein A-I and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:bf, GOC:BHF, GOC:rl, GOC:signaling, PMID:16443932] + GO_EXT:0034188 + apolipoprotein A-I receptor + GO_EXT:bearer of apolipoprotein A-I receptor activity + bearer of apolipoprotein A-I receptor activity + + + GO_EXT:bearer of peptide N-acetyltransferase activity + bearer of peptide N-acetyltransferase activity + "Catalysis of the acetylation of an amino acid residue of a peptide or protein, according to the reaction: acetyl-CoA + peptide = CoA + N-acetylpeptide." [GOC:mah] + peptide N-acetyltransferase + GO_EXT:0034212 + + + GO_EXT:bearer of NAD-dependent protein deacetylase activity + bearer of NAD-dependent protein deacetylase activity + GO_EXT:0034979 + "Catalysis of the removal of one or more acetyl groups from a protein, requiring NAD." [GOC:BHF, GOC:mah] + NAD-dependent protein deacetylase + + + GO_EXT:bearer of phosphatidylinositol 3-kinase activity + bearer of phosphatidylinositol 3-kinase activity + phosphatidylinositol 3-kinase + "Catalysis of the reaction: ATP + a phosphatidylinositol = ADP + a phosphatidylinositol 3-phosphate. This reaction is the addition of a phosphate group to phosphatidylinositol or one of its phosphorylated derivatives at the 3' position of the inositol ring." [GOC:bf, PMID:10209156, PMID:9255069] + phosphoinositide 3-kinase + GO_EXT:0035004 + + + signalling receptor + "Receiving a signal and transmitting the signal in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:bf, GOC:signaling] + GO_EXT:0038023 + signaling receptor + bearer of signaling receptor activity + GO_EXT:bearer of signaling receptor activity + + + endocytic receptor + transport receptor + GO_EXT:0038024 + "Combining selectively with an extracellular substance and delivering the substance into the cell via endocytosis." [GOC:bf, GOC:signaling, PMID:15239958] + cargo receptor + bearer of cargo receptor activity + GO_EXT:bearer of cargo receptor activity + + + bearer of neuregulin receptor activity + GO_EXT:bearer of neuregulin receptor activity + "Combining with a neuregulin, a member of the EGF family of growth factors, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:bf, GOC:signaling, PMID:16460914, PMID:20672328] + neuregulin receptor + GO_EXT:0038131 + NRG receptor + + + pattern recognition receptor + GO_EXT:0038187 + bearer of pattern recognition receptor activity + "Combining with a pathogen-associated molecular pattern (PAMP), a structure conserved among microbial species, or damage-associated molecular pattern (DAMP), an endogenous molecule released from damaged cells), to initiate a change in cell activity." [GOC:ar, GOC:bf, Wikipedia:Pattern_recognition_receptor] + PRR + GO_EXT:bearer of pattern recognition receptor activity + + + GO_EXT:0042054 + bearer of histone methyltransferase activity + "Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or lysine residue." [EC:2.1.1.43] + GO_EXT:bearer of histone methyltransferase activity + histone methyltransferase + histone methylase + + + GO_EXT:0042056 + chemoattractant + GO_EXT:bearer of chemoattractant activity + "Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal." [GOC:go_curators, ISBN:0198506732] + bearer of chemoattractant activity + + + GO_EXT:0042379 + "Interacting selectively and non-covalently with any chemokine receptor." [GOC:ai] + GO_EXT:bearer of chemokine receptor binding + bearer of chemokine receptor binding + + + bearer of phosphoric ester hydrolase activity + "Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3." [GOC:jl] + GO_EXT:bearer of phosphoric ester hydrolase activity + phosphoric ester hydrolase + GO_EXT:0042578 + + + nucleoplasmin ATPase + non-chaperonin molecular chaperone ATPase + chaperonin ATPase + vesicle-fusing ATPase + GO_EXT:0042623 + "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane." [EC:3.6.1.3, GOC:jl] + bearer of ATPase activity, coupled + peroxisome-assembly ATPase + GO_EXT:bearer of ATPase activity, coupled + + + ATPase coupled ion transmembrane transporter + GO_EXT:0042625 + "Catalysis of the transfer of an ion from one side of a membrane to the other, driven by the reaction: ATP + H2O = ADP + phosphate." [EC:3.6.1.3, GOC:jl, GOC:mtg_transport, ISBN:0815340729] + GO_EXT:bearer of ATPase coupled ion transmembrane transporter activity + bearer of ATPase coupled ion transmembrane transporter activity + + + GO_EXT:0042626 + bearer of ATPase activity, coupled to transmembrane movement of substances + GO_EXT:bearer of ATPase activity, coupled to transmembrane movement of substances + "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane." [EC:3.6.1.3, GOC:jl] + + + GO_EXT:0043492 + "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the transport of a substance." [GOC:jl] + GO_EXT:bearer of ATPase activity, coupled to movement of substances + bearer of ATPase activity, coupled to movement of substances + + + bearer of protein anchor + "Interacting selectively and non-covalently with both a protein or protein complex and a membrane, in order to maintain the localization of the protein at a specific location on the membrane." [GOC:go_curators] + GO_EXT:0043495 + GO_EXT:bearer of protein anchor + + + GO_EXT:bearer of luciferin monooxygenase activity + bearer of luciferin monooxygenase activity + luciferin monooxygenase + luciferase monooxygenase + "Catalysis of the generalized reaction: luciferin + O2 = oxidized luciferin + CO2 + light. There may be additional substrates and reactants involved in the reaction. The reaction results in light emission as luciferin returns to the ground state after enzymatic oxidation." [GOC:bf] + GO_EXT:0045289 + luciferase + + + metal ion transmembrane transporter + bearer of metal ion transmembrane transporter activity + GO_EXT:bearer of metal ion transmembrane transporter activity + "Enables the transfer of metal ions from one side of a membrane to the other." [GOC:ai] + GO_EXT:0046873 + + + GO_EXT:0050248 + Renilla-luciferin 2-monooxygenase + bearer of Renilla-luciferin 2-monooxygenase activity + GO_EXT:bearer of Renilla-luciferin 2-monooxygenase activity + Renilla-type luciferase + "Catalysis of the reaction: Renilla luciferin + O2 = oxidized Renilla luciferin + CO2 + light." [EC:1.13.12.5, MetaCyc:RENILLA-LUCIFERIN-2-MONOOXYGENASE-RXN] + + + GO_EXT:bearer of polynucleotide 5'-hydroxyl-kinase activity + GO_EXT:0051731 + "Catalysis of the reaction: NTP + 5'-dephosphopolynucleotide = NDP + 5'-phosphopolynucleotide. The polynucleotide may be DNA or RNA." [EC:2.7.1.78] + 5'-dephosphopolynucleotide kinase + polynucleotide 5'-hydroxy-kinase + 5'-hydroxyl polynucleotide kinase + polynucleotide 5'-hydroxyl kinase (phosphorylating) + polynucleotide 5'-hydroxyl-kinase + bearer of polynucleotide 5'-hydroxyl-kinase activity + + + carboxylic acid esterase + "Catalysis of the hydrolysis of a carboxylic ester bond." [EC:3.1.1, EC:3.1.1.1, GOC:curators] + carboxyesterase + Ali-esterase + carboxylic ester hydrolase + bearer of carboxylic ester hydrolase activity + carboxylic esterase + carboxylate esterase + carboxyl ester hydrolase + nonspecific carboxylesterase + B-esterase + carboxylic ester hydrolase + carboxylesterase + GO_EXT:0052689 + serine esterase + GO_EXT:bearer of carboxylic ester hydrolase activity + + + "Catalysis of the reaction: ATP + a phosphatidylinositol = ADP + a phosphatidylinositol phosphate." [GOC:ai] + GO_EXT:0052742 + GO_EXT:bearer of phosphatidylinositol kinase activity + phosphatidylinositol kinase + bearer of phosphatidylinositol kinase activity + + + GO_EXT:0055077 + "A wide pore channel activity that enables the transport of a solute across a membrane via a gap junction hemi-channel. Two gap junction hemi-channels coupled together form a complete gap junction." [GOC:dgh] + connexon channel + gap junction hemi-channel + GO_EXT:bearer of gap junction hemi-channel activity + bearer of gap junction hemi-channel activity + + + GO_EXT:0060089 + GO_EXT:bearer of molecular transducer activity + molecular transducer + bearer of molecular transducer activity + "The molecular function that accepts an input of one form and creates an output of a different form." [GOC:mtg_MIT_16mar07] + + + GO_EXT:0060090 + "The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way." [GOC:mtg_MIT_16mar07, GOC:vw] + molecular adaptor + bearer of binding, bridging + GO_EXT:bearer of binding, bridging + + + ubiquitin protein ligase + protein ubiquitination + bearer of ubiquitin protein ligase activity + GO_EXT:bearer of ubiquitin protein ligase activity + "Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S --> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate. Note that this may include the extension of ubiquitin chains." [GOC:BioGRID, GOC:dph] + GO_EXT:0061630 + ubiquitin ligase + + + small conjugating protein ligase + bearer of ubiquitin-like protein ligase activity + GO_EXT:0061659 + GO_EXT:bearer of ubiquitin-like protein ligase activity + "Catalysis of the transfer of a ubiquitin-like protein (ULP) to a substrate protein via the reaction X-ULP + S --> X + S-ULP, where X is either an E2 or E3 enzyme, the X-ULP linkage is a thioester bond, and the S-ULP linkage is an isopeptide bond between the C-terminal glycine of ULP and the epsilon-amino group of lysine residues in the substrate." [GOC:dph] + ubiquitin-like protein ligase + + + GO_EXT:0061733 + "Catalysis of the reaction: acetyl-CoA + lysine in peptide = CoA + N-acetyl-lysine-peptide." [GOC:dph] + bearer of peptide-lysine-N-acetyltransferase activity + GO_EXT:bearer of peptide-lysine-N-acetyltransferase activity + peptide-lysine-N-acetyltransferase + + + "Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine)." [GOC:mah, http://merops.sanger.ac.uk/about/glossary.htm#CATTYPE, http://merops.sanger.ac.uk/about/glossary.htm#EXOPEPTIDASE, ISBN:0716720094] + GO_EXT:0070008 + serine-type exopeptidase + bearer of serine-type exopeptidase activity + GO_EXT:bearer of serine-type exopeptidase activity + + + "Catalysis of the hydrolysis of peptide bonds formed between L-amino acids." [GOC:mah] + GO_EXT:bearer of peptidase activity, acting on L-amino acid peptides + GO_EXT:0070011 + bearer of peptidase activity, acting on L-amino acid peptides + + + high-density lipoprotein particle receptor + high-density lipoprotein receptor + GO_EXT:0070506 + GO_EXT:bearer of high-density lipoprotein particle receptor activity + "Combining with a high-density lipoprotein particle and delivering the high-density lipoprotein into the cell via endocytosis." [GOC:bf, GOC:BHF, GOC:rl, PMID:9211901] + bearer of high-density lipoprotein particle receptor activity + + + divalent inorganic cation transmembrane transporter + GO_EXT:0072509 + "Enables the transfer of inorganic cations with a valency of two from one side of the membrane to the other. Inorganic cations are atoms or small molecules with a positive charge that do not contain carbon in covalent linkage." [GOC:mah] + bearer of divalent inorganic cation transmembrane transporter activity + GO_EXT:bearer of divalent inorganic cation transmembrane transporter activity + + + GO_EXT:0097472 + bearer of cyclin-dependent protein kinase activity + GO_EXT:bearer of cyclin-dependent protein kinase activity + "Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. This reaction requires the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK)." [GOC:pr] + cyclin-dependent protein kinase + + + "A DNA binding transcription factor activity that is directly regulated by binding of a ligand to the protein with this activity. Examples include the lac and trp repressors in E.coli and many steroid hormone receptors." [GOC:dos, http://www.ecocyc.org/ECOLI/NEW-IMAGE?object=BC-3.1.2.3] + bearer of transcription factor activity, direct ligand regulated sequence-specific DNA binding + GO_EXT:0098531 + GO_EXT:bearer of transcription factor activity, direct ligand regulated sequence-specific DNA binding + direct ligand regulated sequence-specific DNA binding transcription factor + + + bearer of molecular function regulator + GO_EXT:bearer of molecular function regulator + GO_EXT:0098772 + "A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators." [GOC:dos, GOC:pt] + + + GO_EXT:bearer of BMP receptor activity + "Combining with a member of the bone morphogenetic protein (BMP) family, and transmitting a signal across the plasma membrane to initiate a change in cell activity." [GOC:BHF, GOC:dos] + bearer of BMP receptor activity + GO_EXT:0098821 + BMP receptor + + + GO_EXT:0099516 + "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ion A(out) + ion B(in) = ion A(in) + ion B(out) where ion A and ion B are different types of ion." [GOC:dos] + ion antiporter + GO_EXT:bearer of ion antiporter activity + bearer of ion antiporter activity + + + GO_EXT:0099528 + bearer of G-protein coupled neurotransmitter receptor activity + GO_EXT:bearer of G-protein coupled neurotransmitter receptor activity + G-protein coupled neurotransmitter receptor + "Combining with a neurotransmitter and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, GOC:fj, GOC:mah] + + + GO_EXT:bearer of serotonin receptor activity + "Combining with the biogenic amine serotonin and transmitting a signal across a membrane by activating some effector activity. Serotonin (5-hydroxytryptamine) is a neurotransmitter and hormone found in vertebrates and invertebrates." [GOC:dos] + serotonin receptor + bearer of serotonin receptor activity + GO_EXT:0099589 + + + GO:'base-excision repair, gap-filling' or GO:'gap filling involved in double-strand break repair via nonhomologous end joining' or GO:'nucleotide-excision repair, DNA gap filling' + gap repair + GO_EXT:DNA_gap_repair + DNA gap repair + GO_EXT:DNA gap repair + For: (DNA) gap repair + + + GO_EXT:DNA_replicator + GO_EXT:DNA replicator + BFO:entity and has_prototype o causally_effects some GO:'DNA replication' + For: (DNA) replicator/replicators + DNA replicator + + + GO_EXT:antibody/immunoglobulin biosynthesis or production + antibody biosynthesis + For: immunoglobulin/antibody/Ab development/generation/production + Ab biosynthesis + GO_EXT:antibody_or_immunoglobulin_biosynthesis_or_production + immunoglobulin biosynthesis + immunoglobulin generation + Ab generation + Ab production + immunoglobulin production + immunoglobulin formation + Ab formation + antibody generation + antibody formation + antibody production + antibody development + antibody/immunoglobulin biosynthesis or production + GO:'immunoglobulin biosynthetic process' or GO:'immunoglobulin production' + immunoglobulin development + Ab development + + + basal body + GO:'bacterial-type flagellum basal body' or GO:'ciliary basal body' + GO_EXT:basal_body + GO_EXT:basal body + For: basal body/bodies + + + behavioral conditioning + GO:'associative learning' or GO:'operant conditioning' + GO_EXT:behavioral_conditioning + GO_EXT:behavioral conditioning + For: condition(v.)/conditioned/conditioning + + + SO_EXT:'fusion' and (has_proper_part some GO_EXT:'bearer of beta-galactosidase activity') and (has_proper_part some GO_EXT:'bearer of kanamycin kinase activity') + betageo + For: beta-geo + GO_EXT:beta_geo + GO_EXT:beta-geo + beta-geo + + + GO_EXT:biogenesis/biosynthesis + For: biogenesis, biosynthesis/biosynthetic, biosynthetic process(es) + biosynthesis + biosynthetic process + biogenesis/biosynthesis + biogenesis + GO:'anatomical structure development' or GO:'biosynthetic process' or GO:'cellular component assembly' + GO_EXT:biogenesis_or_biosynthesis + + + biological direction/guidance + biological direction + GO_EXT:biological_direction_or_guidance + For: direct(v.)/directed/directing/direction/directs, guidance/guide(v.)/guided/guides(v.)/guiding +Not for direction/guidance from humans, experiments, etc. + +(has_causal_agent some (BFO:independent_continuant and + ((causally_effects some (BFO:occurrent or BFO:dependent_continuant or GO_EXT:'biological movement/transport')) or + (causally_influences some BFO:independent_continuant)))) + GO_EXT:biological direction/guidance + GO:'biological regulation' or (BFO:occurrent and causally_effects_or_influences some BFO:entity) or (GO_EXT:biological_movement and causally_effected_or_influenced_by some BFO:entity) + biological guidance + + + GO_EXT:biological_growth_entity_or_process + (BFO:independent_continuant and is_formed_as_result_of some GO:growth) or GO:growth + biological growth + GO_EXT:biological growth entity or process + For: growth/growths + biological growth entity or process + + + GO_EXT:biological_movement_or_translocation_process + biological movement/translocation process + For: migrate/migrated/migrates/migrating/migration, move/moved/movement/movements/moves/moving, pass/passage/passed/passes/passing, relocate/relocated/relocates/relocating/relocation, shuttle/shuttled/shuttles/shuttling, transfer/transferable/transferrable/transfered/transferred/transfering/transferring/transfers, translocate/translocated/translocates/translocating + biological shuttling + biological relocation + biological translocation process + biological movement + GO_EXT:biological movement/translocation process + GO:'establishment of localization' or GO:locomotion or GO:'motor behavior' or GO:'movement of cell or subcellular component' or GO:'multicellular organismal movement' or (BFO:occurrent and results_in_movement_of some BFO:independent_continuant) + biological passage + biological migration + + + biological mover + (BFO:entity and has_prototype o causally_effects some (GO:'establishment of localization' or GO:'movement of cell or subcellular component')) or GO_EXT:bearer_of_transporter_activity + biological transporter + For: carrier/carriers, transporter/transporters + GO_EXT:biological_mover_or_transporter + biological carrier + GO_EXT:biological mover/transporter + biological mover/transporter + + + GO_EXT:biological_recruitment + For: mobilise/mobilised/mobilises/mobilising/mobilize/mobilized/mobilizes/mobilizing, recruit/recruited/recruiting/recruits + biological recruitment + GO:biological_process and causally_effects_or_influences some ((BFO:independent_continuant and causally_effects some GO:biological_process) or GO:'establishment of localization') + biological mobilization + GO_EXT:biological recruitment + biological mobilisation + + + GO_EXT:biological release + GO:secretion or (GO:biological_process and exports some BFO:independent_continuant) or (GO:biological_process and causally_effects some PATO:'detached from') + For: release/released/releasing/releases + biological release + GO_EXT:biological_release + + + biological targeting + GO_EXT:biological routing/transport + biological delivery + GO:'establishment of localization' or GO:'movement of cell or subcellular component' or ((GO:biological_process and (results_in_movement_of some BFO:independent_continuant)) and causally_effected_by some BFO:entity) + biological carrying + biological trafficking + biological routing + biological routing/transport + biological transport + GO_EXT:biological_routing_or_transport + For: carried/carries/carry/carrying, deliver/delivered/delivering/delivers, route(v.)/routed/routes(v.)/routing, target(v.)/targeted/targeting/targets(v.), traffic/trafficked/trafficking/traffics, transport/transported/transporting/transports + + + GO_EXT:biological_movement or GO_SO_EXT:sequence_transposition_entity_or_process + GO_EXT:biological_translocation_entity_or_process + GO_EXT:biological translocation entity or process + biological translocation + biological translocation entity or process + For: translocation/translocations + + + bone development + bone development or ossification + bone formation + bone generation + For: bone development/formation/generation, development/formation/generation of bone, develolopment/formation/generation of bone tissue + GO_EXT:bone development or ossification + GO_EXT:bone_development_or_ossification + GO:'bone development' or GO:ossification + + + GO_EXT:breeder + For: breeder/breeders + GO_EXT:breeder + breeder + (NCBITAXON:Metazoa or UBERON:'multicellular organism') and bearer_of o realized_in some GO_EXT:breeding + + + GO:mating and has_agent some NCBITAXON:'Homo sapiens' + breeding + For: bred/breed(v.)/breeding/breeds(v.) + GO_EXT:breeding + GO_EXT:breeding + + + GO_EXT:cell communication, signaling or signal transduction + biological communication + biological signaling + GO:'cell communication' or GO:signaling or GO:'signal transduction' + cell communication, signaling or signal transduction + biological cascade + For: communicate/communicated/communicates/communicating/communication, signal(v.)/signaled/signalled/signaling/signalling/signals(v.), signal/signaling/signalling pathway/pathways, signal/signaling/signalling cascade/cascades + biological signaling pathway + GO_EXT:cell_communication_or_signaling_or_signal_transduction + + + GO_EXT:chemoattractant or chemoattraction + For: chemoattractant(adj.) + GO_EXT:chemoattractant_or_chemoattraction + GO_EXT:'bearer of chemoattractant activity' or GO:'positive chemotaxis' + chemoattractant or chemoattraction + + + GO_EXT:cytokine biosynthesis or production + For: cytokine generation/production + cytokine development + cytokine generation + GO:'cytokine biosynthetic process' or GO:'cytokine production' + cytokine production + cytokine biosynthesis or production + cytokine biosynthesis + cytokine formation + GO_EXT:cytokine_biosynthesis_or_production + + + nucleocytoplasmic + GO_EXT:cytoplasm or nucleus + cytoplasm or nucleus + For: nucleocytoplasmic + GO_EXT:cytoplasm_or_nucleus + GO:cytoplasm or GO:nucleus + + + GO_EXT:detection/sensing of light stimulus + light sensing + For: detection/sensing of light, light detection/sensing, photosensation/photosensory + light detection + photosensation + photosensory + detection/sensing of light stimulus + GO:'detection of light stimulus' or GO:'sensory perception of light stimulus' + light sensation + GO_EXT:detection_or_sensing_of_light_stimulus + + + mechanosensory + detection/sensing of mechanical stimulus + mechanosensation + GO_EXT:detection_or_sensing_of_mechanical_stimulus + GO_EXT:detection/sensing of mechanical stimulus + GO:'detection of mechanical stimulus' or GO:'sensory perception of mechanical stimulus' + For: mechanosensation/mechanosensory + + + sensing + detection/sensing of stimulus + sensory + stimulus detection + sensation + GO_EXT:detection_or_sensing_of_stimulus + GO_EXT:detection/sensing of stimulus + For: sensation/sense(v.)/sensed/senses(v.)/sensing/sensory + sensory perception + stimulus sensing + GO:'detection of stimulus' or GO:'sensory perception' + + + dimer + GO_EXT:dimeric macromolecular complex + GO_EXT:dimer_macromolecular_complex + dimeric complex + dimeric macromolecular complex + For: dimer(s), dimeric, dimeric complex(es) + GO:'macromolecular complex' and (has_molecular_entity_part exactly 2 CHEBI:macromolecule) and (has_molecular_part only CHEBI:macromolecule) + + + double-hexameric macromolecular complex + GO_EXT:double_hexameric_macromolecular_complex + double hexameric complex + For: double hexamer(s), double hexameric, double hexameric complex(es) + GO:'macromolecular complex' and (has_protein_complex_part exactly 2 GO_EXT:'hexameric macromolecular complex') and (has_protein_complex_part only GO_EXT:'hexameric macromolecular complex') + GO_EXT:double-hexameric macromolecular complex + double hexamer + + + double trimer + GO:'macromolecular complex' and (has_protein_complex_part exactly 2 GO_EXT:'trimeric macromolecular complex') and (has_protein_complex_part only GO_EXT:'trimeric macromolecular complex') + GO_EXT:double_trimer_macromolecular_complex + double trimeric complex + For: double trimer(s), double trimeric, double trimeric complex(es) + double-trimeric macromolecular complex + GO_EXT:double-trimeric macromolecular complex + + + lethality + lethal + fatality/lethality + For: fatal/fatally, lethal/lethality/lethally + fatal + GO:death or (BFO:dependent_continuant and causally_effects some GO:death) + GO_EXT:fatality/lethality + fatality + GO_EXT:fatality_or_lethality + + + flagellum + GO_EXT:flagellum + GO_EXT:flagellum + GO:'archaeal-type flagellum' or GO:'bacterial-type flagellum' or GO:cilium + For: flagellum/flagella, flagellar + + + BFO:entity and has_prototype o causally_effects_or_location_of some GO:'gene expression' + For: (gene) expresser/expressers + gene expresser + GO_EXT:gene_expresser + GO_EXT:gene expresser + + + GO_EXT:glial_cell_development_or_generation + glial cell generation + For: glial cell development/formation/generation, gliogenesis/gliogenic + glial cell development/generation + GO_EXT:glial cell development/generation + gliogenic + gliogenesis + glial cell development + GO:'glial cell development' or GO:gliogenesis + glial cell formation + + + For: haemoglobinisation/haemoglobinization/hemoglobinisation/hemoglobinization, haemoglobinise/haemoglobinize/hemoglobinise/hemoglobinize, haemoglobinises/haemoglobinizes/hemoglobinises/hemoglobinizes, haemoglobinised/haemoglobinized/hemoglobinised/hemoglobinized, haemoglobinising/haemoglobinizing/hemoglobinising/hemoglobinizing + haemoglobinisation + GO:'hemoglobin biosynthetic process' or GO:'hemoglobin import' + hemoglobin biosynthetic process or import + hemoglobinization + GO_EXT:hemoglobin_biosynthetic_process_or_import + GO_EXT:hemoglobin biosynthetic process or import + + + GO_EXT:hexameric macromolecular complex + hexamer + GO_EXT:hexameric_macromolecular_complex + hexameric complex + For: hexamer(s), hexameric, hexameric complex(es) + hexameric macromolecular complex + GO:'macromolecular complex' and (has_molecular_entity_part exactly 6 CHEBI:macromolecule) and (has_molecular_entity_part only CHEBI:macromolecule) + + + GO_EXT:impregnation + BFO:occurrent and causally_effects some GO:'female pregnancy' + GO_EXT:impregnation + For: impregnate/impregnated/impregnates/impregnation/impregnations + impregnation + + + interferon-gamma generation + interferon-gamma production + GO:'interferon-gamma biosynthetic process' or GO:'interferon-gamma production' + interferon-gamma biosythesis + For: interferon-gamma generation/production + interferon-gamma development + interferon-gamma biosynthesis or production + interferon-gamma formation + GO_EXT:interferon-gamma biosynthesis or production + GO_EXT:interferon_gamma_biosynthesis_or_production + + + GO_EXT:killing + BFO:occurrent and causally_effects some GO:death + GO_EXT:killing + For: kill/killed/killing/kills + killing + + + GO_EXT:macromolecule denaturation + For: denature/denatured/denatures/denaturing/denaturation (of macromolecules) + GO_EXT:macromolecule_denaturation + GO:'DNA duplex unwinding' or GO:'protein denaturation' + denaturation + macromolecule denaturation + + + muscularization + myogenesis + muscle structure or tissue development + muscle formation + GO_EXT:muscle_structure_or_tissue_development + For: muscle development/formation, myogenesis/myogenic, muscularisation/muscularise/muscularised/muscularises/muscularising/muscularization/muscularize/muscularized/muscularizes/muscularizing + GO_EXT:muscle structure or tissue development + myogenic + muscle development + GO:'muscle structure development' or GO:'muscle tissue develoment' + muscularisation + + + myelinogenic + myelinogenesis + muscle generation + GO_EXT:myelin_assembly_or_myelination + muscle production + myelin formation + GO:'myelin assembly' or GO:myelination + myelination + myelin assembly/myelination + GO_EXT:myelin assembly/myelination + myelin assembly + For: myelin assembly/formation/generation/production, assembly/formation/generation/production of myelin, myelinate/myelinated/myelinates/myelinating/myelination, myelinogenesis/myelinogenic + + + negative regulation + downregulation + GO_EXT:negative_regulation + GO_EXT:negative regulation + GO:'negative regulation of biological process' or GO:'negative regulation of molecular function' or (GO:biological_process and negatively_regulates some BFO:dependent_continuant) + down-regulation + For: negative regulation/negatively regulate/negatively regulated/negatively regulates/negatively regulating, +down regulate/down regulated/down regulates/down regulating/down regulation, +downregulate/downregulated/downregulates/downregulating/downregulation, +down-regulate/down-regulated/down-regulates/down-regulating/down-regulation + + + GO_EXT:negative regulator + down-regulator + GO_EXT:negative_regulator + negative regulator + For: negative regulator(s) + downregulator + BFO:entity and has_prototype o causally_effects some GO_EXT:negative_regulation + + + neuron production + neuron generation + neuron formation + GO_EXT:neuron development/generation + GO:'generation of neurons' or GO:'neuron development' + GO_EXT:neuron_development_or_generation + neuron development + For: neuron development/formation/generation/production, neurotrophic/neurotrophy + neurotrophy + neuron development/generation + + + For: neurotransmission + GO:'synaptic transmission' or GO:'transmission of nerve impulse' + neurotransmission + GO_EXT:neurotransmission + GO_EXT:neurotransmission + + + GO_EXT:neurotrophin biosynthesis or production + neurotrophin development + (GO:'biosynthetic process' results_in_formation_of some PR:neurotrophin) or GO:'neurotrophin production' + GO_EXT:neurotrophin_biosynthesis_or_production + neurotrophin production + neurotrophin generation + neurotrophin biosynthesis or production + neurotrophin formation + For: neurotrophin formation/formation of neurotrophin(s), neurotrophin production/production of neurotrophin(s), neurotrophin generation/generation of neurotrophin(s) + neurotrophin biosynthesis + + + GO_EXT:nucleotide_exchange_factor + NEF + GO_EXT:'bearer of adenyl-nucleotide exchange factor activity' or GO_EXT:'bearer of guanyl-nucleotide exchange factor activity' + GO_EXT:nucleotide exchange factor + nucleotide exchange factor + + + oligomer + GO_EXT:oligomeric macromolecular complex + oligomeric macromolecular complex + GO:'macromolecular complex' and (has_molecular_entity_part min 2 CHEBI:macromolecule) and (has_molecular_entity_part max 5 CHEBI:macromolecule) and (has_molecular_entity_part only CHEBI:macromolecule) + oligomeric complex + GO_EXT:oligomeric_macromolecular_complex + For: oligomer(s), oligomeric complex(es), oligomeric + + + For: pentamer(s), pentameric complex(es), pentameric + GO_EXT:pentameric_macromolecular_complex + GO_EXT:pentameric macromolecular complex + GO:'macromolecular complex' and (has_molecular_entity_part exactly 5 CHEBI:macromolecule) and (has_molecular_entity_part only CHEBI:macromolecule) + pentameric macromolecular complex + pentameric complex + pentamer + + + GO_EXT:'bearer of 2-phosphoglycerate kinase activity' or GO_EXT:'bearer of phosphoglycerate kinase (GTP) activity' or GO_EXT:'bearer of phosphoglycerate kinase activity' + GO_EXT:phosphoglycerate kinase + GO_EXT:phosphoglycerate_kinase + PGK + For: PGK(s), phosphoglycerate kinase(s) + phosphoglycerate kinase + + + GO_EXT:polymerase + GO_EXT:polymerase + GO_EXT:'bearer of DNA polymerase activity' or GO_EXT:'bearer of RNA polymerase activity' + polymerase + For: polymerase(s) + + + upregulation + GO_EXT:positive regulation + GO:'positive regulation of biological process' or GO:'positive regulation of molecular function' or (GO:biological_process and positively_regulates some BFO:dependent_continuant) + positive regulation + GO_EXT:positive_regulation + For: positive regulation/positively regulate/positively regulated/positively regulates/positively regulating, +up regulate/up regulated/up regulates/up regulating/up regulation, +upregulate/upregulated/upregulates/upregulating/upregulation, +up-regulate/up-regulated/up-regulates/up-regulating/up-regulation + up-regulation + + + For: positive regulator(s) + GO_EXT:positive_regulator + GO_EXT:positive regulator + up-regulator + positive regulator + upregulator + BFO:entity and has_prototype o causally_effects some GO_EXT:positive_regulation + + + biological reaction + GO_EXT:reaction/response + GO_EXT:reaction_or_response + For: react/reacted/reacting/reaction/reactions/reacts, respond/responded/responding/responds/response/responses +Not for chemical reactions. + ((BFO:dependent_continuant or BFO:occurrent) and is_causally_effected_by some BFO:entity) or GO:behavior or GO:'response to stimulus' + reaction/response + biological response + + + GO_EXT:recombinase + GO_EXT:'bearer of recombinase activity' or GO_EXT:'bearer of site-specific recombinase activity' + GO_EXT:recombinase + recombinase + For: recombinase(s) + + + regulator + BFO:entity and has_prototype o causally_effects some GO:'biological regulation' + GO_EXT:regulator + For: regulator/regulators + GO_EXT:regulator + modulator + + + For: responder/responders + BFO:independent_continuant and has_prototype o causally_influenced_in some GO_EXT:reaction_or_response + responder + GO_EXT:responder + GO_EXT:responder + + + GO_EXT:reverse transcription or reverse transcriptase + GO:'reverse transcription' or GO_EXT:'bearer of RNA-directed DNA polymerase activity' + GO_EXT:reverse_transcription_or_reverse_transcriptase + For: RT + RT + reverse transcription or reverse transcriptase + + + secretion entity or process + (BFO:independent_continuant and is_localized_as_result_of some GO:secretion) or GO:secretion or UBERON:'bodily secretion' + secretion + For: secretion/secretions + GO_EXT:secretion entity or process + GO_EXT:secretion_entity_or_process + + + For: secretory pathway(s) + GO_EXT:secretory_pathway + GO_EXT:secretory pathway + GO:'constitutive secretory pathway' or GO:'exosomal secretion' or GO:'regulated exocytosis' + secretory pathway + + + GO:'somite development' or GO:somitogenesis + somite generation + GO_EXT:somite_development_or_somitogenesis + somite development + somitogenesis + somite development/somitogenesis + somite formation + For: somite development/formation/generation, somitogenesis + GO_EXT:somite development/somitogenesis + + + GO_EXT:taster + For: taster/tasters + BFO:entity and has_prototype o agent_in GO:'sensory perception of taste' + GO_EXT:taster + taster + + + GO_EXT:tetrameric macromolecular complex + GO:'macromolecular complex' and (has_molecular_entity_part exactly 4 CHEBI:macromolecule) and (has_molecular_entity_part only CHEBI:macromolecule) + tetramer + tetrameric macromolecular complex + For: tetramer(s), tetrameric complex(es), tetrameric + tetrameric complex + GO_EXT:tetrameric_macromolecular_complex + + + GO:'bicellular tight junction' or GO:'tricellular tight junction' + tight junction + GO_EXT:tight junction + For: tight junction(s), TJ(s) + TJ + GO_EXT:tight_junction + + + For: transcribe/transcribed/transcribes/transcribing/transcription/transcriptional/transcriptionally + GO_EXT:transcription + transcription + GO_EXT:transcription + GO:'nucleic acid-templated transcription' or GO:'reverse transcription' or GO:'viral transcription' + + + GO_EXT:transcription factor + GO_EXT:'bearer of transcription factor activity, protein binding' or GO_EXT:'bearer of nucleic acid binding transcription factor activity' + GO_EXT:transcription_factor + transcription factor + TF + + + CL_GO_EXT:cell and location_of some GO:'DNA mediated transformation' + GO_EXT:transfectant/transformant + transformant + transfectant/transformant + transfectant + For: transfectant/transfectants, transformant/transformants + GO_EXT:transfectant_or_tranformant + + + GO_EXT:trimeric_macromolecular_complex + trimer + For: trimer(s), trimeric complex(es), trimeric + GO:'macromolecular complex' and (has_molecular_entity_part exactly 3 CHEBI:macromolecule) and (has_molecular_entity_part only CHEBI:macromolecule) + trimeric complex + GO_EXT:trimeric macromolecular complex + trimeric macromolecular complex + + + trypsinisation + GO_EXT:trypsinization + GO:proteolysis (GO:GO:0006508) and causally_effected_by some PR_EXT:trypsin (PR_EXT:000027795) + trypsinization + GO_EXT:trypsinization + + + GO_MF extension classes + + + catalysis + GO_MOP_EXT:catalysis + GO_MOP_EXT:catalysis + GO:'catalytic activity' or MOP:catalysis + For: catalysis/catalytic/catalytically + + + GO_MOP_EXT:glycosylation + For: glycosylate/glycosylated/glycosylates/glycosylating/glycosylation + GO_MOP_EXT:glycosylation + GO:glycosylation or MOP:glycosylation + glycosylation + + + GO:'metal chelating activity' or MOP:'metal chelation' + GO_MOP_EXT:metal chelation + GO_MOP_EXT:metal_chelation + metal chelation + chelation + + + GO_MOP_EXT:methylation + GO_MOP_EXT:methylation + For: methylate/methylated/methylates/methylating/methylation/methylations + methylation + GO:methylation or MOP:methylation + + + GO_PATO_EXT:aging_or_agedness + senescent + aged + GO_PATO_EXT:aging or agedess + For: aged, senescent + aging or agedess + GO:aging or PATO:old or PATO:senescent + + + GO_PATO_EXT:apoptotic_process_or_quality + apoptotic process or quality + GO:'apoptotic process' or PATO:apoptotic + For: apoptotic/apoptotically + GO_PATO_EXT:apoptotic process or quality + apoptotically + apoptotic + + + GO:'biological adhesion' or (GO:biological_process and realizes some PATO:adhesive) or (BFO:independent_continuant and is_attached_to min 2 (BFO:independent_continuant and is_attached_as_result_of some (GO:'biological adhesion' or (GO:biological_process and realizes some PATO:adhesive))) + biological adhesion entity or process + For: adhesion/adhesions + GO_PATO_EXT:biological adhesion entity or process + GO_PATO_EXT:biological_adhesion_entity_or_process + + + GO_PATO_EXT:biological adhesion or adhesiveness + GO_PATO_EXT:biological_adhesion_or_adhesiveness + GO:biological_process and realizes some PATO:adhesive) or (BFO:independent_continuant and is_attached_to min 2 (BFO:independent_continuant and is_attached_as_result_of some (GO:'biological adhesion' or (GO:biological_process and realizes some PATO:adhesive)) or PATO:adhesive + For: adhesive + biological adhesion or adhesiveness + + + biological adhesion or attachedness + GO:'biological adhesion' or (BFO:occurrent and realizes some PATO:adhesive) or PATO:attached_to or (BFO:occurrent and causally_effects some PATO:attached_to) + GO_PATO_EXT:biological_adhesion_or_attachedness + For: adhere/adhered/adherent/adheres/adhering, stick/sticking/sticks/stuck + GO_PATO_EXT:biological adhesion or attachedness + + + For: behave/behaved/behaves/behaving/behavior/behavioral/behaviorally/behaviors/behaviour/behavioural/behaviourally/behaviours + GO_PATO_EXT:biological_behavior + (BFO:occurrent and has_participant o bearer_of some (PATO:active or PATO:'behavioural active')) or GO:behavior or GO:'response to stimulus' + GO_PATO_EXT:biological behavior + behaviour + behavior + biological behavior + + + biological localization process or quality + GO_PATO_EXT:biological_localization_process_or_quality + biological localisation + GO_PATO_EXT:biological localization process or quality + GO:localization or (GO:biological_process and causally_effects some PATO:localized) or PATO:localized + biological localization + For: localisation/localise/localised/localises/localising/localization/localize/localized/localizes/localizing + + + GO:'developmental maturation' or GO:'protein maturation' or GO:'RNA processing' or GO:'virus maturation' or (BFO:occurrent and causally_effects some PATO:mature) + biological maturation + For: maturation/mature(v.)/matured/matures/maturing + GO_PATO_EXT:biological_maturation + GO_PATO_EXT:biological maturation + + + GO_PATO_EXT:biological_patterning_process + For: pattern(v.)/patterns(v.) + GO_PATO_EXT:biological patterning process + biological patterning process + GO:'pattern specification process' or (GO:biological_process and causally_effects_or_influences some PATO:'spatial pattern') + + + GO_PATO_EXT:biological_patterning_process or PATO:'spatial pattern' + For: patterned/patterning + biological patterning process or quality + GO_PATO_EXT:biological_patterning_process_or_quality + GO_PATO_EXT:biological patterning process or quality + + + biological pigmentation process or quality + GO_PATO_EXT:biological_pigmentation_process_or_quality + pigmentation + GO:pigmentation or PATO:pigmented or (GO:biological_process and causally_effects some PATO:pigmented) + For: pigmentation/pigmentations + GO_PATO_EXT:biological pigmentation process or quality + + + GO_PATO_EXT:cell proliferation or proliferativity + cell proliferation or proliferativity + GO:'cell proliferation' or PATO:proliferative + For: proliferative + proliferative + GO_PATO_EXT:cell_proliferation_or_proliferativity + + + inflamed + GO:'inflammatory response' or PATO:inflammatory + For: inflamed/inflammation/inflammatory + GO_PATO_EXT:inflammatory_process_or_quality + GO_PATO_EXT:inflammatory process or quality + inflammatory process or quality + inflammatory + inflammation + + + GO_PATO_EXT:necrosis + GO_PATO_EXT:necrosis + For: necrose/necrosed/necroses/necrosing/necrosis + GO:'necrotic cell death' or (BFO:occurrent and causally_effects some PATO:necrotic) + necrosis + + + necrotic + GO_PATO_EXT:necrosis or necrotic quality + GO_PATO_EXT:necrosis_or_necrotic_quality + necrosis or necrotic quality + GO_PATO_EXT:necrosis or PATO:necrotic + For: necrotic + + + GO:phosphorylation or (BFO:occurrent and causally_effects some PATO:phosphorylated) + phosphorylating + GO_PATO_EXT:phosphorylation_process + phosphorylate + GO_PATO_EXT:phosphorylation process + phosphorylates + phosphorylation + phosphorylation process + For: phosphorylate/phosphorylates/phosphorylating/phosphorylation + + + GO_PATO_EXT:phosphorylation_process_or_quality + phosphorylation process or quality + phosphorylated + GO_PATO_EXT:phosphorylation process or quality + GO_PATO_EXT:phosphorylation_process or PATO:phosphorylated + For: phosphorylated + + + physiologic + physiological + For: physiologic/physiological/physiologically/physiology + physiology + GO:biological_process or PATO:'physiological state' + physiological process or quality + GO_PATO_EXT:physiological_process_or_quality + physiologically + GO_PATO_EXT:physiological process or quality + + + GO_PATO_EXT:ubiquitination_process_or_quality + GO:'protein ubiquitination' or PATO:ubiquitinated + GO_PATO_EXT:ubiquitination process or quality + For: ubiquitinated + ubiquitinated + ubiquitination process or quality + + + differentiated + GO_RO_EXT:developmental_differentiation_process or PATO:differentiated + GO_PATO_RO_EXT:developmental_differentiation_process_or_quality + GO_PATO_RO_EXT:developmental differentiation process or quality + For: differentiated + developmental differentiation process or quality + + + trabeculation + GO_PATO_UBERON_EXT:trabeculation_entity_or_process_or_quality + GO_PATO_UBERON_EXT:trabeculation entity, process or quality + For: trabeculation/trabeculations + trabeculation entity, process or quality + PATO_UBERON_EXT:trabeculation_entity_or_quality or GO_EXT:trabeculation_process + + + DHCR7 + sterol delta7-reductase + 7-DHC reductase + GO_PR_EXT:7_dehydrocholesterol_reductase + GO_PR_EXT:7-dehydrocholesterol reductase + GO_EXT:'bearer of 7-dehydrocholesterol reductase activity' or PR_EXT:'7-dehydrocholesterol reductase' + 7-dehydrocholesterol reductase + For: 7-dehydrocholesterol reductase(s), Dhcr7 + sterol delta(7)-reductase + + + GO_PR_EXT:DNA nucleotidylexotransferase + GO_EXT:'bearer of DNA nucleotidylexotransferase activity' or PR_EXT:'DNA nucleotidylexotransferase' + deoxynucleotidyl terminal transferase + terminal deoxynucleotidyltransferase + addase + terminal deoxyribonucleotidyltransferase + GO_PR_EXT:DNA_nucleotidylexotransferase + deoxyribonucleic acid nucleotidyltransferase + terminal addition enzyme + terminal deoxynucleotidyl transferase + DNA nucleotidylexotransferase + terminal deoxynucleotide transferase + terminal transferase + TDT + deoxyribonucleic nucleotidyltransferase + DNTT + + + GO_PR_EXT:G-protein coupled receptor + G protein linked receptor + GO_EXT:'bearer of G-protein coupled receptor activity' or PR_EXT:'G-protein coupled receptor' + GPLR + For: G-protein coupled receptor(s), GPCR(s) + G-protein coupled receptor + GPCR + GO_PR_EXT:G_protein_coupled_receptor + + + mitogen-activated kinase + GO_PR_EXT:MAP kinase + GO_EXT:'bearer of MAP kinase activity' or PR_EXT:'mitogen-activated protein kinase' + mitogen-activated protein kinase + GO_PR_EXT:MAP_kinase + MAPK + MAP kinase + For: MAPK(s), MAP kinase(s), mitogen-activated protein kinase(s) + + + NF-kappaB-inducing kinase + NF-kappa-beta-inducing kinase + For: NF-kappaB-inducing kinase(s), NIK(s), NF-kappa-beta-inducing kinase(s) + NIK + GO_PR_EXT:NF_kappaB_inducing_kinase + GO_PR_EXT:NF-kappaB-inducing kinase + GO_EXT:'bearer of NF-kappaB-inducing kinase activity' or PR_EXT:mitogen-activated protein kinase kinase kinase 14' + serine/threonine-protein kinase NIK + + + PR:'smad protein' or GO:'SMAD protein complex' + For: SMAD(s) + GO_PR_EXT:SMAD + GO_PR_EXT:SMAD + SMAD + + + GO_PR_EXT:acetylcholinesterase + For: acetylcholinesterase(s) + choline esterase I + acetylcholine acetylhydrolase + ACHE + acetylcholinesterase + acetylcholine hydrolase + GO_EXT:'bearer of acetylcholinesterase activity' or PR_EXT:acetylcholinesterase + acetylthiocholinesterase + GO_PR_EXT:acetylcholinesterase + + + GO_PR_EXT:activin receptor type II + GO_PR_EXT:activin_receptor_type_II + For: activin receptor type II + type II activin receptor + activin receptor type II + GO_EXT:'bearer of activin receptor activity, type II' or PR_EXT:'TGF-beta superfamily receptor type-2 with activin receptor domain' + + + alkaline phosphatase + alkaline phenyl phosphatase + GO_PR_EXT:alkaline_phosphatase + GO_PR_EXT:alkaline phosphatase + alkaline phosphomonoesterase + APase + For: alkaline phosphatase(s), AP(s) + alkaline phosphohydrolase + GO_EXT:'bearer of alkaline phosphatase activity' or PR_EXT:'alkaline phosphatase' + + + alpha1-adrenoceptor + alpha-1 adrenoceptor + GO_PR_EXT:alpha1_adrenergic_receptor + alpha1 adrenoceptor + For: alpha1 adrenergic, alpha1 adrenergic receptor(s), alpha1 adrenoceptor(s) + alpha-1 adrenergic receptor + GO_EXT:'bearer of alpha1-adrenergic receptor activity' or PR_EXT:'alpha-1 adrenergic receptor' + alpha1-adrenergic receptor + GO_PR_EXT:alpha1-adrenergic receptor + + + AR + androgen receptor + GO_PR_EXT:androgen_receptor + GO_EXT:'bearer of androgen receptor activity' or PR_EXT:'androgen receptor' + androgen receptor + GO_PR_EXT:androgen receptor + + + N-(L-argininosuccinate) arginine-lyase + ASL + arginine-succinate lyase + argininosuccinase + argininosuccinate lyase + omega-N-(L-arginino)succinate arginine-lyase + For: argininosuccinate lyase(s), ASL(s) + GO_PR_EXT:argininosuccinate lyase + GO_EXT:'bearer of argininosuccinate lyase activity' or PR_EXT:'argininosuccinate lyase' + GO_PR_EXT:argininosuccinate_lyase + argininosuccinic acid lyase + + + GO_PR_EXT:beta1_adrenergic_receptor + ADRB1R + beta-1 adrenergic receptor + BETA1AR + beta1-adrenergic receptor + GO_PR_EXT:beta1-adrenergic receptor + For: beta1 adrenergic, beta1 adrenergic receptor(s), beta1 adrenoceptor(s) + beta1 adrenergic receptor + B1AR + beta1 adrenoceptor + ADRB1 + beta1-adrenoceptor + beta-1 adrenoceptor + GO_EXT:'bearer of beta1-adrenergic receptor activity' or PR_EXT:'beta-1 adrenergic receptor' + + + GO_EXT:'bearer of beta2-adrenergic receptor activity' or PR_EXT:'beta-2 adrenergic receptor' + GO_PR_EXT:beta2_adrenergic_receptor + beta2 adrenoceptor + ADRB2 + ADRB2R + BETA2AR + beta-2 adrenergic receptor + beta2-adrenergic receptor + GO_PR_EXT:beta2-adrenergic receptor + beta2-adrenoceptor + beta-2 adrenoceptor + For: beta2 adrenergic, beta2 adrenergic receptor(s), beta2 adrenoceptor(s) + B2AR + beta2 adrenergic receptor + + + beta3 adrenoceptor + GO_PR_EXT:beta3_adrenergic_receptor + ADRB3 + GO_EXT:'bearer of beta3-adrenergic receptor activity' or PR_EXT:'beta-3 adrenergic receptor' + ADRB3R + BETA3AR + GO_PR_EXT:beta3-adrenergic receptor + beta3-adrenergic receptor + beta-3 adrenergic receptor + beta-3 adrenoceptor + beta3-adrenoceptor + For: beta3 adrenergic, beta3 adrenergic receptor(s), beta3 adrenoceptor(s) + beta3 adrenergic receptor + B3AR + + + GO_PR_EXT:beta-adrenergic receptor + GO_PR_EXT:beta_adrenergic_receptor + beta adrenergic receptor + beta adrenoceptor + For: beta adrenergic receptor(s), beta adrenoceptor(s) + beta-adrenoceptor + beta-adrenergic receptor + GO_EXT:'bearer of beta-adrenergic receptor activity' or PR_EXT:'beta adrenergic receptor' + + + branched-chain-amino-acid aminotransferase + L-branched chain amino acid aminotransferase + GO_PR_EXT:branched-chain-amino-acid aminotransferase + For: BCAT(s), branched-chain-amino-acid aminotransferase(s), branched-chain-amino-acid transaminase(s) + branched-chain amino acid aminotransferase + branched-chain-amino-acid:2-oxoglutarate aminotransferase + transaminase B + GO_EXT:'bearer of branched-chain-amino-acid transaminase activity' or PR_EXT:'branched-chain-amino-acid aminotransferase' + GO_PR_EXT:branched_chain_amino_acid_aminotransferase + glutamate-branched-chain amino acid transaminase + branched-chain amino acid-glutamate transaminase + BCAT + branched-chain-amino-acid transaminase + + + CaN + GO_PR_EXT:calcineurin + GO:'calcineurin complex' or PR:'serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform' or PR:'serine/threonine-protein phosphatase 2B catalytic subunit beta isoform' or PR:'serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform' or PR:'calcineurin subunit B type 1' or PR:'calcineurin subunit B type 2' + calcineurin + GO_PR_EXT:calcineurin + For: calcineurin +GO:0005955 or PR:000003278 or PR:000013148 or PR:000013149 or PR:000013150 or PR:000013151 + + + mu-calpain + calpain-1 complex + calpain-1 + GO_PR_EXT:calpain-1 complex + GO:'macromolecular complex' and (has_molecular_entity_part exactly 1 PR_EXT:'calpain-1 catalytic subunit') and (has_molecular_entity_part exactly 1 PR_EXT:'calpain small subunit 1') and (has_molecular_entity_part only (PR_EXT:'calpain-1 catalytic subunit' or PR_EXT:'calpain small subunit 1') + calcium-activated neutral protease I + GO_PR_EXT:calpain_1_complex + + + calpain-2 complex + milli-calpain + m-calpain + calcium-activated neutral protease II + GO_PR_EXT:calpain-2 complex + GO_PR_EXT:calpain_2_complex + GO:'macromolecular complex' and (has_molecular_entity_part exactly 1 PR_EXT:'calpain-2 catalytic subunit') and (has_molecular_entity_part exactly 1 PR_EXT:'calpain small subunit 1') and (has_molecular_entity_part only PR_EXT:'calpain-2 catalytic subunit' or PR_EXT:'calpain small subunit 1') + calpain-2 + + + GO_PR_EXT:catalase + caperase + optidase + CAT + equilase + GO_EXT:'bearer of catalase activity' or PR_EXT:catalase + For: CAT(s), catalase(s) + catalase + catalase peroxidase + GO_PR_EXT:catalase + + + For: chemokine receptor(s) + chemokine receptor + GO_PR_EXT:chemokine receptor + GO_PR_EXT:chemokine_receptor + GO_EXT:'bearer of chemokine receptor activity' or PR_EXT:'chemokine receptor' + + + GO_PR_EXT:cholesterol_7_alpha_hydroxylase + cholesterol 7alpha-hydroxylase + For: cholesterol 7 alpha-hydroxylase(s), cholesterol 7-alpha-monooxygenase(s) + GO_PR_EXT:cholesterol 7 alpha-hydroxylase + cholesterol 7-alpha-hydroxylase + cholesterol 7 alpha-hydroxylase + GO_EXT:'bearer of cholesterol 7-alpha-monooxygenase activity' or PR_EXT:'cytochrome P450 7A1' + cholesterol 7alpha-monooxygenase + cholesterol 7-alpha-monooxygenase + + + choline O-acetyltransferase + GO_EXT:'bearer of choline O-acetyltransferase activity' or PR_EXT:'choline O-acetyltransferase' + choline acetyltransferase + GO_PR_EXT:choline_O_acetyltransferase + GO_PR_EXT:choline O-acetyltransferase + CHAT + CHOACTase + choline acetylase + + + GO_PR_EXT:citrate synthase + GO_PR_EXT:citrate_synthase + For: citrate synthase(s), CS(s) + GO_EXT:'bearer of citrate synthase activity' or PR_EXT:'citrate synthase, mitochondrial' or PR_EXT:'citrate synthase' + CS + citrate synthase + + + CPK + GO_PR_EXT:creatine kinase + phosphocreatine kinase + GO_EXT:'bearer of creatine kinase activity' or PR_EXT:'creatine kinase' + creatine phosphotransferase + creatine phosphokinase + creatine N-phosphotransferase + CK + creatine kinase + GO_PR_EXT:creatine_kinase + For: CK(s), creatine kinase(s) + + + alkaline deoxyribonuclease + DNASE1 + deoxyribonucleic phosphatase + DNA nuclease + For: deoxyribonuclease I, DNase I + deoxyribonuclease I + DNA depolymerase + DNase I + dornase alfa + GO_PR_EXT:deoxyribonuclease I + GO_EXT:'bearer of deoxyribonuclease I activity' or PR_EXT:'deoxyribonuclease-1' + DNA endonuclease + GO_PR_EXT:deoxyribonuclease_I + alkaline DNase + + + palmitoyl-CoA-sn-1,2-diacylglycerol acyltransferase + GO_EXT:'bearer of diacylglycerol O-acyltransferase activity' or PR_EXT:'diacylglycerol O-acyltransferase 1' + diglyceride O-acyltransferase + DAG acyltransferase + diacylglycerol acyltransferase + diglyceride acyltransferase + 1,2-diacylglycerol acyltransferase + DGAT + For: DGAT(s), diacylglycerol acyltransferas(s), diacylglycerol O-acyltransferase(s), diglyceride acyltransferase(s), diglyceride O-acyltransferase(s) + diacylglycerol O-acyltransferase + GO_PR_EXT:diacylglycerol acyltransferase + GO_PR_EXT:diacylglycerol_acyltransferase + + + lipoic acid dehydrogenase + dehydrolipoate dehydrogenase + GO_EXT:'bearer of dihydrolipoyl dehydrogenase activity' or PR_EXT:'dihydrolipoyl dehydrogenase, mitochondrial' or PR_EXT:'dihydrolipoyl dehydrogenase' + dihydrolipoamide dehydrogenase + DLD + diaphorase + For: dihydrolipoamide dehydrogenase(s) dihydrolipoyl dehydrogenase(s), DLD(s) + LAD + protein-6-N-(dihydrolipoyl)lysine:NAD+ oxidoreductase + dihydrolipoic dehydrogenase + protein-N6-(dihydrolipoyl)lysine:NAD+ oxidoreductase + dihydrolipoamide:NAD+ oxidoreductase + lipoate dehydrogenase + GO_PR_EXT:dihydrolipoamide dehydrogenase + dihydrolipoyl dehydrogenase + DLDH + lipoamide reductase + GO_PR_EXT:dihydrolipoamide_dehydrogenase + lipoyl dehydrogenase + dihydrothioctic dehydrogenase + + + GO_PR_EXT:dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity + 2-methylpropanoyl-CoA:enzyme-N6-(dihydrolipoyl)lysine:S-(2-methylpropanoyl)transferase + GO_PR_EXT:dihydrolipoyllysine_residue_2_methylpropanoyl_transferase + GO_EXT:'bearer of dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity' or PR_EXT:'lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial' + dihydrolipoyl acyltransferase + dihydrolipoamide acetyltransferase + dihydrolipoamide branched chain transacylase + 2-methylpropanoyl-CoA:enzyme-6-N-(dihydrolipoyl)lysine:S-(2-methylpropanoyl)transferase + For: dihydrolipoamide acetyltransferase(s), dihydrolipoyl acyltransferase(s), dihydrolipoyllysine-residue (2-methylpropanoyl)transferase(s) + dihydrolipoyl transacylase + enzyme-dihydrolipoyllysine:2-methylpropanoyl-CoA S-(2-methylpropanoyl)transferase + dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity + + + Eph + ephrin receptor + GO_PR_EXT:ephrin receptor + GO_EXT:'bearer of ephrin receptor activity' or PR_EXT:'ephrin receptor' + erythropoietin-producing human hepatocellular receptor + GO_PR_EXT:ephrin_receptor + For: ephrin receptor(s), Eph(s) + Eph RTK + Eph receptor tyrosine kinase + Eph receptor + + + For: EGFR(s), epidermal growth factor receptor(s) + GO_PR_EXT:epidermal_growth_factor_receptor + EGFR + GO_EXT:'bearer of epidermal growth factor-activated receptor activity' or PR_EXT:'epidermal growth factor receptor' + GO_PR_EXT:epidermal growth factor receptor + epidermal growth factor receptor + transforming growth factor-alpha receptor + EGF receptor + TGF-alpha receptor + + + estrogen receptor + GO_EXT:'bearer of estrogen receptor activity' or PR_EXT:'estrogen receptor' + GO_PR_EXT:estrogen receptor + For: ER(s), estrogen receptor(s) + ER + GO_PR_EXT:estrogen_receptor + + + fMLP receptor + fMet-Leu-Phe receptor + GO_PR_EXT:fMet_Leu_Phe_receptor + For: fMet-Leu-Phe receptor(s), fMLP receptor(s) + N-formyl peptide receptor + FPR + GO_EXT:'bearer of N-formyl peptide receptor activity' or PR_EXT:'fMet-Leu-Phe receptor' + GO_PR_EXT:fMet-Leu-Phe receptor + + + GO_PR_EXT:fatty acid synthase + FAS + GO_PR_EXT:fatty_acid_synthase + FASN + GO_EXT:'bearer of fatty acid synthase activity' or PR_EXT:'fatty acid synthase' + For: FAS(s), FASN(s), fatty acid synthase(s) + fatty acid synthase + + + FGF-activated receptor + fibroblast growth factor receptor + GO_EXT:'bearer of fibroblast growth factor-activated receptor activity' or PR_EXT:'fibroblast growth factor receptor' + FGFR + GO_PR_EXT:fibroblast growth factor receptor + For: FGFR(s), fibroblast growth factor-activated receptor(s), fibroblast growth factor receptor(s) + FGF receptor + GO_PR_EXT:fibroblast_growth_factor_receptor + + + UDP-glucose--hexose-1-phosphate uridylyltransferase + GO_EXT:'bearer of UDP-glucose:hexose-1-phosphate uridylyltransferase activity' or PR_EXT:'galactose-1-phosphate uridylyltransferase' + galactose-1-phosphate uridylyltransferase + hexose-1-phosphate uridylyltransferase + UDPglucose-hexose-1-phosphate uridylyltransferase + UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase + UDP-glucose-hexose-1-phosphate uridylyltransferase + hexose-1-phosphate uridyltransferase + UDPglucose:alpha-D-galactose-1-phosphate uridylyltransferase + GO_PR_EXT:galactose-1-phosphate uridylyltransferase + GO_PR_EXT:galactose_1_phosphate_uridylyltransferase + uridyltransferase + For: galactose-1-phosphate uridylyltransferase(s), GALT(s), UDP-glucose--hexose-1-phosphate uridylyltransferase(s), gal-1-P uridylyltransferase(s) + gal-1-P uridylyltransferase + GALT + + + glucose kinase + GO_PR_EXT:glucokinase + GK + For: glucokinase(s), GCK(s) + GLK + glucokinase + GO_PR_EXT:glucokinase + ATP:D-glucose 6-phosphotransferase + GCK + GO_EXT:'bearer of glucokinase activity' or PR_EXT:glucokinase + ATP:D-hexose 6-phosphotransferase + + + GO_PR_EXT:glucose_6_phosphatase + G-6-Pase + G6PC + glucose-6-phosphate phosphatase + For: glucose 6-phosphatase(s) + glucose 6-phosphatase + GO_PR_EXT:glucose 6-phosphatase + glucose-6-phosphate phosphohydrolase + GO_EXT:'bearer of glucose-6-phosphatase activity' or PR_EXT:'glucose-6-phosphatase' + + + 6-phosphoglucose dehydrogenase + NADP-glucose-6-phosphate dehydrogenase + GO_PR_EXT:glucose_6_phosphate_dehydrogenase + GO_PR_EXT:glucose-6-phosphate dehydrogenase + glucose-6-phosphate 1-dehydrogenase + D-glucose-6-phosphate:NADP+ 1-oxidoreductase + NADP-dependent glucose-6-phosphate dehydrogenase + G6PDH + glucose-6-phosphate dehydrogenase + GO_EXT:'bearer of glucose-6-phosphate dehydrogenase activity' or PR_EXT:'glucose-6-phosphate 1-dehydrogenase' + For: G6PD(s), G6PDH(s), glucose-6-phosphate 1-dehydrogenase(s), glucose-6-phosphate dehydrogenase(s) + G6PD + + + GPI + phosphohexose isomerase + hexose phosphate isomerase + GO_PR_EXT:glucose_6_phosphate_isomerase + D-glucose-6-phosphate aldose-ketose-isomerase + phosphoglucoisomerase + PGI + glucose-6-phosphate isomerase + PHI + phosphoglucose isomerase + GO_EXT:'bearer of glucose-6-phosphate isomerase activity' or PR_EXT:'glucose-6-phosphate isomerase' + GO_PR_EXT:glucose-6-phosphate isomerase + glucose phosphate isomerase + For: GPI(s), glucose-6-phosphate isomerase(s), phosphoglucose isomerase(s) + + + GO_PR_EXT:glutathione S-transferase + glutathione S-alkyltransferase + GO_EXT:'bearer of glutathione transferase activity' or PR_EXT:'glutathione S-transferase' + RX:glutathione R-transferase + GO_PR_EXT:glutathione_S_transferase + GST + For: GST(s), glutathione S-transferase(s), glutathione transferase(s) + glutathione S-alkyl transferase + ligandin + glutathione S-transferase + glutathione transferase + glutathione S-aryltransferase + S-(hydroxyalkyl)glutathione lyase + + + glutathione-disulphide reductase + glutathione reductase + GR + GO_PR_EXT:glutathione-disulfide reductase + GO_EXT:'bearer of glutathione-disulfide reductase activity' or PR_EXT:'glutathione reductase, mitochondrial' + GSR + NADPH-glutathione reductase + GO_PR_EXT:glutathione_disulfide_reductase + NADPH-GSSG reductase + GSSG reductase + GSH reductase + For: glutathione-disulfide reductase(s) + glutathione S-reductase + glutathione:NADP+ oxidoreductase + glutathione-disulfide reductase + NADPH:oxidized-glutathione oxidoreductase + + + GSS + GSH-S + GSH synthetase + GO_EXT:'bearer of glutathione synthase activity' or PR_EXT:'glutathione synthetase' + glutathione synthase + glutathione synthetase + GO_PR_EXT:glutathione_synthase + GSH synthase + GO_PR_EXT:glutathione synthase + + + GAPDH + glyceraldehyde-3-P dehydrogenase + GAPD + glyceraldehyde-3-phosphate dehydrogenase + 3-phosphoglyceraldehyde dehydrogenase + G3PDH + GO_EXT:'bearer of glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity' or PR_EXT:'glyceraldehyde-3-phosphate dehydrogenase' + NAD-dependent glyceraldehyde phosphate dehydrogenase + phosphoglyceraldehyde dehydrogenase + For: GAPD(s), GAPDH(s), glyceraldehyde-3-phosphate dehydrogenase(s) + GO_PR_EXT:glyceraldehyde-3-phosphate dehydrogenase + NAD-dependent glyceraldehyde-3-phosphate dehydrogenase + G3PD + NADH-glyceraldehyde phosphate dehydrogenase + GO_PR_EXT:glyceraldehyde_3_phosphate_dehydrogenase + + + GH receptor + GO_PR_EXT:growth_hormone_receptor + GO_PR_EXT:growth hormone receptor + growth hormone receptor + GO_EXT:'bearer of growth hormone receptor activity' or PR_EXT:'growth hormone receptor' + + + For: GK(s), guanylate kinase(s) + guanosine monophosphate kinase + GMP kinase + ATP:(d)GMP phosphotransferase + GO_EXT:'bearer of guanylate kinase activity' or PR_EXT:'guanylate kinase' + GO_PR_EXT:guanylate_kinase + 5'-GMP kinase + deoxyguanylate kinase + GO_PR_EXT:guanylate kinase + ATP:GMP phosphotransferase + guanylate kinase + + + For: hepatocyte growth factor receptor(s), HGFR(s), MET(s) + SF-activated receptor + scatter factor-activated receptor + SF receptor + GO_PR_EXT:hepatocyte growth factor receptor + GO_PR_EXT:hepatocyte_growth_factor_receptor + HGF/SF receptor + hepatocyte growth factor-activated receptor + HGF receptor + hepatocyte growth factor/scatter factor receptor + hepatocyte growth factor receptor + scatter factor receptor + HGFR + GO_EXT:'bearer of hepatocyte growth factor-activated receptor activity' or PR_EXT:'hepatocyte growth factor receptor' + HGF-activated receptor + + + diacylglycerol acylhydrolase + LIPE + GO_PR_EXT:hormone_sensitive_lipase + GO_PR_EXT:hormone-sensitive lipase + lipase E, hormone-sensitive type + CEH + LHS + hormone-sensitive lipase + GO_EXT:'bearer of hormone-sensitive lipase activity' or PR_EXT:'hormone-sensitive lipase' + HSL + cholesteryl ester hydrolase + + + For: 3-hydroxy-3-methylglutaryl-CoA reductase(s), 3-hydroxy-3-methylglutaryl-coenzyme A reductase(s), hydroxymethylglutaryl-CoA reductase(s), hydroxymethylglutaryl-coenzyme A reductase(s), HMGCR(s) + 3-hydroxy-3-methylglutaryl CoA reductase + HMG-CoA reductase + GO_EXT:'bearer of hydroxymethylglutaryl-CoA reductase activity' or GO_EXT:'bearer of hydroxymethylglutaryl-CoA reductase (NADPH) activity' or PR_EXT:'3-hydroxy-3-methylglutaryl-coenzyme A reductase' + 3-hydroxy-3-methyl-glutaryl-CoA reductase + 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase + GO_PR_EXT:hydroxymethylglutaryl_CoA_reductase + HMGCR + hydroxymethylglutaryl-coenzyme A reductase + GO_PR_EXT:hydroxymethylglutaryl-CoA reductase + hydroxymethylglutaryl-CoA reductase + 3-hydroxy-3-methylglutaryl coenzyme A reductase + + + HGPRTase + hypoxanthine-guanine phosphoribosyltransferase + IMP:diphosphate phospho-D-ribosyltransferase + GO_PR_EXT:hypoxanthine_guanine_phosphoribosyltransferase + HGPRT + GO_EXT:'bearer of hypoxanthine phosphoribosyltransferase activity' or PR_EXT:'hypoxanthine-guanine phosphoribosyltransferase' + GO_PR_EXT:hypoxanthine-guanine phosphoribosyltransferase + For: hypoxanthine-guanine phosphoribosyltransferase(s), HPRT(s) + IMP diphosphorylase + inosine 5'-phosphate pyrophosphorylase + IMP pyrophosphorylase + HPRT + IMP-GMP pyrophosphorylase + inosinic pyrophosphorylase + inosinate pyrophosphorylase + + + GO_EXT:'bearer of insulin-activated receptor activity' or PR_EXT:'insulin receptor' + GO_PR_EXT:insulin receptor + IR + insulin receptor + INSR + insulin receptor + For: insulin receptor(s), IR(s), INSR(s) + GO_PR_EXT:insulin_receptor + + + integrin + GO:'integrin complex' or PR:'integrin alpha' or PR:'integrin beta' + GO_PR_EXT:integrin + GO_PR_EXT:integrin + For: integrin(s) + + + GO_PR_EXT:interleukin_1_receptor_type_I + GO_EXT:'bearer of interleukin-1, Type I, activating receptor activity' or PR_EXT:'interleukin-1 receptor type I' + IL-1 type I receptor + interleukin-1 activating receptor + interleukin-1 receptor type 1 + IL1R + interleukin-1 type 1 receptor + IL-1 type I activating receptor + For: interleukin-1 receptor type I, interleukin-1 activating receptor(s), IL1R1, IL-1R-1, IL-1R-alpha, IL-1RT-1, IL-1RT1, interleukin-1 receptor alpha + interleukin-1 type I receptor + IL1R1 + IL-1R-1 + IL-1 type 1 activating receptor + IL-1 type 1 receptor + IL-1R-alpha + IL1RA + interleukin-1 receptor type I + GO_PR_EXT:interleukin-1 receptor type I + + + LEP-R + LEPR + GO_PR_EXT:leptin_receptor + GO_EXT:'bearer of leptin receptor activity' or PR_EXT:'leptin receptor' + For: leptin receptor(s) + GO_PR_EXT:leptin receptor + leptin receptor + + + For: leukemia inhibitory factor receptor(s), LIFR(s) + LIFR + leukemia inhibitory factor receptor + GO_PR_EXT:leukemia_inhibitory_factor_receptor + LIF-R + GO_PR_EXT:leukemia inhibitory factor receptor + GO_EXT:'bearer of leukemia inhibitory factor receptor activity' or PR_EXT:'leukemia inhibitory factor receptor' + LIF receptor + + + lipoprotein lipase + diacylglycerol lipase + GO_PR_EXT:lipoprotein_lipase + triacylglycero-protein acylhydrolase + GO_PR_EXT:lipoprotein lipase + diacylglycerol hydrolase + diglyceride lipase + postheparin lipase + postheparin esterase + LPL + GO_EXT:'bearer of lipoprotein lipase activity' or PR_EXT:'lipoprotein lipase' + + + palmitoyl-coenzyme A dehydrogenase + ACADL + GO_PR_EXT:long_chain_acyl_CoA_dehydrogenase + long-chain acyl-coenzyme A dehydrogenase + GO_PR_EXT:long-chain acyl-CoA dehydrogenase + long-chain acyl-CoA dehydrogenase + GO_EXT:'bearer of long-chain-acyl-CoA dehydrogenase activity' or PR_EXT:'long-chain specific acyl-CoA dehydrogenase, mitochondrial' + For: LCAD(s), long-chain acyl-CoA dehydrogenase(s) + long-chain-acyl-CoA:acceptor 2,3-oxidoreductase + palmitoyl-CoA dehydrogenase + LCAD + + + LDLR + low-density lipoprotein receptor + LDL receptor + GO_EXT:'bearer of low-density lipoprotein receptor activity' or PR_EXT:'low-density lipoprotein receptor' + GO_PR_EXT:low-density lipoprotein receptor + For: low-density lipoprotein receptor(s) + GO_PR_EXT:low_density_lipoprotein_receptor + + + GO_EXT:'bearer of medium-chain-acyl-CoA dehydrogenase activity' or PR_EXT:'medium-chain specific acyl-CoA dehydrogenase, mitochondrial' + medium-chain acyl-CoA dehydrogenase + medium-chain acyl-coenzyme A dehydrogenase + MCAD + For: MCAD(s), medium-chain acyl-CoA dehydrogenase(s), medium-chain specific acyl-CoA dehydrogenase(s) + GO_PR_EXT:medium-chain acyl-CoA dehydrogenase + ACADM + GO_PR_EXT:medium_chain_acyl_CoA_dehydrogenase + + + N5,10-methylenetetrahydrofolate reductase + GO_PR_EXT:methylenetetrahydrofolate_reductase + For: methylenetetrahydrofolate reductase(s), MTHFR(s) + methylenetetrahydrofolic acid reductase + GO_EXT:'bearer of methylenetetrahydrofolate reductase (NAD(P)H) activity' or GO_EXT:'bearer of methylenetetrahydrofolate reductase (ferredoxin) activity' or PR_EXT:'methylenetetrahydrofolate reductase' + GO_PR_EXT:methylenetetrahydrofolate reductase + 5,10-methylenetetrahydropteroylglutamate reductase + 5,10-methylenetetrahydrofolate reductase + 5,10-CH2-H4folate reductase + MTHFR + methylenetetrahydrofolate reductase + 5,10-CH(2)-H(4)folate reductase + 5-methyltetrahydrofolate:(acceptor) oxidoreductase + N5,N10-methylenetetrahydrofolate reductase + 5,10-methylenetetrahydrofolic acid reductase + + + (R)-2-methyl-3-oxopropanoyl-CoA CoA carbonylmutase + (S)-methylmalonyl-CoA mutase + GO_EXT:'bearer of methylmalonyl-CoA mutase activity' or PR_EXT:'methylmalonyl-CoA mutase, mitochondrial' or PR_EXT:'methylmalonyl-CoA mutase' + methylmalonyl-CoA CoA-carbonyl mutase + GO_PR_EXT:methylmalonyl_CoA_mutase + methylmalonyl coenzyme A mutase + methylmalonyl coenzyme A carbonylmutase + MUT + For: methylmalonyl-CoA isomerase(s), methylmalonyl-CoA mutase(s), MCM(s), MUT(s) + GO_PR_EXT:methylmalonyl-CoA mutase + methylmalonyl-CoA isomerase + MCM + methylmalonyl-CoA mutase + (R)-methylmalonyl-CoA CoA-carbonylmutase + + + For: monophenol monooxygenase(s), tyrosinase(s) + tyrosine-dopa oxidase + polyphenolase + tyrosinase + L-tyrosine monooxygenase + monophenol dihydroxyphenylalanine:oxygen oxidoreductase + N-acetyl-6-hydroxyltryptophan oxidase + polyaromatic oxidase + monophenol oxygenase + GO_PR_EXT:monophenol_monooxygenase_or_tyrosinase + GO_EXT:'bearer of monophenol monooxygenase activity' or PR_EXT:tyrosinase + monophenol monooxidase + TYR + monophenolase + monophenol monooxygenase + GO_PR_EXT:monophenol monooxygenase + + + pancreatic ribonuclease + ribonuclease I + GO_EXT:'bearer of ribonuclease A activity' or PR_EXT:'ribonuclease pancreatic' + alkaline RNase + alkaline ribonuclease + ribonucleic phosphatase + ribonucleate 3'-pyrimidino-oligonucleotidohydrolase + RNase A + endoribonuclease I + GO_PR_EXT:pancreatic ribonuclease + pancreatic RNase + GO_PR_EXT:pancreatic_ribonuclease_or_ribonuclease_A + ribonuclease A + RNase I + + + phosphopyruvate carboxylase + GO_PR_EXT:phosphoenolpyruvate carboxykinase + For: PEPCK(s), phosphoenolpyruvate carboxykinase(s) + GO_PR_EXT:phosphoenolpyruvate_carboxykinase + GO_EXT:'bearer of phosphoenolpyruvate carboxykinase (ATP) activity' or PR_EXT:'phosphoenolpyruvate carboxykinase [ATP]' + PEP carboxykinase + PEPCK + phosphoenolpyruvate carboxykinase + + + GO_EXT:'bearer of phospholipase A2 activity' or PR_EXT:'phospholipase a2' + phosphatidylcholine 2-acylhydrolase + GO_PR_EXT:phospholipase A2 + GO_PR_EXT:phospholipase_A2 + phosphatidolipase + PLA2 + phospholipase A2 + lecithinase A + For: phospholipase(s) A2, PLA2(s) + + + GO_PR_EXT:platelet-activating factor receptor + PAF receptor + platelet-activating factor receptor + GO_EXT:'bearer of platelet activating factor receptor activity' or PR_EXT:'platelet-activating factor receptor' + PAFR + For: PAFR(s), platelet-activating factor receptor(s), PTAFR(s) + GO_PR_EXT:platelet_activating_factor_receptor + PAF-R + PTAFR + + + For: platelet-derived growth factor alpha receptor + PDGF-R alpha + platelet-derived growth factor alpha receptor + PDGFRA + GO_PR_EXT:platelet_derived_growth_factor_alpha_receptor + PDGFR alpha + GO_PR_EXT:platelet-derived growth factor alpha receptor + alphaPDGF receptor + GO_EXT:'bearer of platelet-derived growth factor alpha-receptor activity' or PR_EXT:'alpha-type platelet-derived growth factor receptor' + PDGF alpha receptor + alpha-type platelet-derived growth factor receptor + + + GO_PR_EXT:platelet_derived_growth_factor_beta_receptor + betaPDGF receptor + PDGF-R beta + GO_PR_EXT:platelet-derived growth factor beta receptor + GO_EXT:'bearer of platelet-derived growth factor beta-receptor activity' or PR_EXT:'beta-type platelet-derived growth factor receptor' + For: platelet-derived growth factor beta receptor + beta-type platelet-derived growth factor receptor + PDGFR beta + platelet-derived growth factor beta receptor + PDGFRB + PDGF beta receptor + + + GO_EXT:'bearer of protein disulfide isomerase activity' or PR_EXT:'protein disulfide-isomerase' + protein disulphide isomerase + protein disulfide isomerase + For: protein disulfide isomerase(s), PDI(s) + GO_PR_EXT:protein disulfide isomerase + GO_PR_EXT:protein_disulfide_isomerase + PDI + + + protease-activated receptor + GO_PR_EXT:proteinase-activated receptor + proteinase-activated receptor + PAR + GO_PR_EXT:proteinase_activated_receptor + GO_EXT:'bearer of proteinase activated receptor activity' or PR_EXT:'proteinase-activated receptor' + For: proteinase-activated receptor(s), PAR(s) + + + SCAD + GO_PR_EXT:short_chain_acyl_CoA_dehydrogenase + short-chain acyl-CoA dehydrogenase + GO_PR_EXT:short-chain acyl-CoA dehydrogenase + ACADS + GO_EXT:'bearer of butyryl-CoA dehydrogenase activity' or PR_EXT:'short-chain specific acyl-CoA dehydrogenase, mitochondrial' + short-chain acyl-coenzyme A dehydrogenase + + + SST receptor + somatotropin release inhibiting factor receptor + GO_EXT:'bearer of somatostatin receptor activity' or PR_EXT:'somatostatin receptor' + SRIF receptor + GO_PR_EXT:somatostatin_receptor + GHIH receptor + growth hormone-inhibiting hormone receptor + somatostatin receptor + GO_PR_EXT:somatostatin receptor + + + spectrin + GO_PR_EXT:spectrin + GO_PR_EXT:spectrin + GO:spectrin or PR_EXT:'spectrin alpha chain, erythrocytic 1' or PR_EXT:'spectrin alpha chain, non-erythrocytic 1' or PR_EXT:'spectrin beta subunit' or PR_EXT:'spectrin beta chain, non-erythrocytic' + + + stearoyl-CoA, hydrogen-donor:oxygen oxidoreductase + GO_PR_EXT:stearoyl_CoA_desaturase + GO_PR_EXT:stearoyl-CoA desaturase + stearoyl-CoA desaturase + stearoyl-coenzyme A desaturase + GO_EXT:'bearer of stearoyl-CoA 9-desaturase activity' or PR_EXT:'acyl-CoA desaturase' + For: delta9-desaturase(s), delta(9)-desaturase(s), fatty acid desaturase(s), stearoyl-CoA 9-desaturase(s), stearoyl-CoA desaturase(s), stearoyl-CoA,ferrocytochrome-b5:oxygen oxidoreductase (9,10-dehydrogenating), stearoyl-CoA, hydrogen-donor:oxygen oxidoreductase(s) + + + GO_PR_EXT:thymidine kinase + ATP:thymidine 5'-phosphotransferase + For: thymidine kinase(s), TK(s) + TK + GO_PR_EXT:thymidine_kinase + TDK + GO_EXT:'bearer of thymidine kinase activity' or PR_EXT:'thymidine kinase' or PR_EXT:'thymidine kinase, cytosolic' or PR_EXT:'thymidine kinase 2, mitochondrial' + thymidine kinase + 2'-deoxythymidine kinase + + + For: TGF-beta receptor type-1, transforming growth factor beta receptor activity, type I, TGFBR1(s) + GO_EXT:'bearer of transforming growth factor beta receptor activity, type I' or PR_EXT:'TGF-beta superfamily receptor type-1' + transforming growth factor beta receptor type 1 + transforming growth factor beta receptor type I + type 1 transforming growth factor beta receptor + GO_PR_EXT:transforming_growth_factor_beta_receptor_type_I + type 1 TGF-beta receptor + type I TGFbeta receptor + type I TGF-beta receptor + GO_PR_EXT:transforming growth factor beta receptor type I + type 1 TGFbeta receptor + TGFBR1 + type I transforming growth factor beta receptor + + + type II TGF-beta receptor + type II TGFbeta receptor + transforming growth factor beta receptor type II + GO_PR_EXT:transforming growth factor beta receptor type II + TGFBR2 + type 2 TGFbeta receptor + For: TGF-beta receptor type-2, transforming growth factor beta receptor activity, type II, TGFBR2(s) + GO_PR_EXT:transforming_growth_factor_beta_receptor_type_II + type II transforming growth factor beta receptor + transforming growth factor beta receptor type 2 + type 2 transforming growth factor beta receptor + type 2 TGF-beta receptor + GO_EXT:'bearer of transforming growth factor beta receptor activity, type II' or PR_EXT:'TGF-beta receptor type-2' + + + UDG + GO_PR_EXT:uracil-DNA glycosylase + GO_EXT:'bearer of uracil DNA N-glycosylase activity' or PR_EXT:'uracil-DNA glycosylase' + For: UDG(s), UNG(s), uracil-DNA glycosylase(s), uracil DNA N-glycosylase(s) + GO_PR_EXT:uracil_DNA_glycosylase + uracil DNA N-glycosylase + uracil-DNA glycosylase + UNG + + + GO_PR_EXT:vascular_endothelial_growth_factor_receptor + VEGFR + GO_EXT:'bearer of vascular endothelial growth factor-activated receptor activity' or PR_EXT:'vascular endothelial growth factor receptor' + VEGF-activated receptor + vascular endothelial growth factor activated receptor + VEGF receptor + GO_PR_EXT:vascular endothelial growth factor receptor + vascular endothelial growth factor receptor + + + For: very-long-chain acyl-CoA dehydrogenase(s), VLCAD(s) + VLCAD + ACADVL + GO_EXT:'bearer of very-long-chain-acyl-CoA dehydrogenase activity' or PR_EXT:'very long-chain specific acyl-CoA dehydrogenase, mitochondrial' + GO_PR_EXT:very_long_chain_acyl_CoA_dehydrogenase + very-long-chain acyl-coenzyme A dehydrogenase + GO_PR_EXT:very-long-chain acyl-CoA dehydrogenase + very-long-chain acyl-CoA dehydrogenase + + + GO_RO_EXT:biological_export + GO_RO_EXT:biological export + GO:secretion or (GO:biological_process and exports some BFO:independent_continuant) + biological export + For: export/exported/exporting/exports + + + GO_RO_EXT:developmental differentiation process + GO_RO_EXT:developmental_differentiation_process + developmental differentiation process + (BFO:occurrent and results_in_acquisition_of_features_of some (UBERON:'anatomical entity' or CL:cell or GO:cellular_component)) or GO:'cell differentiation' or GO:'sex differentiation' + For: (developmental) differentiate/differentiates/differentiating/differentiation/differentiative + + + GO_SO_EXT:centromere_or_centromeric_region_or_centromeric_orientation + centromic + centromeric + centromere + centromeric region + GO_SO_EXT:centromere, centromeric region or centromeric orientation + centromere, centromeric region or centromeric orientation + GO:'chromosome, centromeric region' or SO_EXT:centromere or (BFO:dependent_continuant and inheres_in some (bearer_of some PATO:orientation and towards some (GO:'chromosome, centromeric region' or SO_EXT:centromere))) + For: centromere(s), centromeric, centromeric region(s) + + + chromosomal part + chromosome part + chromosome location + chromosomal stretch + chromosomal location + chromosome stretch + GO:'chromosomal part' or SO_EXT:chromosome_part or (PATO:position and inheres_in some (GO:'chromosomal part' or SO_EXT:chromosome_part)) or (BFO:site and site_of some (GO:'chromosomal part' or SO_EXT:chromosome_part)) + For: chromosome/chromosomal domain(s), interval(s), locus/loci, part(s), portion(s), region(s), segment(s), site(s), stretch(es) + chromosome locus + chromosomal locus + GO_SO_EXT:chromosomal_part_or_position_or_region_or_site + chromosome segment + GO_SO_EXT:chromosomal part/position/region/site + chromosomal segment + chromosome domain + chromosomal domain + chromosomal position + chromosome position + chromosomal region + chromosome region + chromosomal portion + chromosome portion + chromosomal part/position/region/site + chromosome interval + chromosomal interval + chromosome site + chromosomal site + + + GO:chromosome or SO_EXT:chromosome + chr + GO_SO_EXT:chromosome + GO_SO_EXT:chromosome + For: chromosome(s), chromosomal(ly) + chromosome + chr. + + + GO_SO_EXT:frameshift entity or process + shift in reading frame + shift of reading frame + frame-shift + For: frameshift/frame shift/frame-shift, frameshifts/frame shifts/frame-shifts, frameshifted/frame shifted/frame-shifted, frameshifting/frame shifting/frame-shifting + GO_SO_EXT:frameshift_entity_or_process + GO:'translational frameshifting' or SO_EXT:frameshift or (BFO:occurrent and results_in_formation_of some SO_EXT:frameshift) + frameshift entity or process + frameshift + + + For: posttranslation/post-translational/post translational modification(s) + posttranslational modification + posttranslational protein modification + post-translational modification + post-translational modification entity or process + GO_SO_EXT:post_translational_modification_entity_or_process + post-translational protein modification + GO_SO_EXT:post-translational modification entity or process + SO_EXT:post_translationally_modified_region or GO:'post-translational protein modification' + + + sequence rearrangement + For: rearrangement/rearrangements + SO_EXT:meiotic_recombination_region or SO_EXT:mitotic_recombination_region or SO_EXT:complex_chromosomal_rearrangement or SO_EXT:rearrangement_region or GO_SO_EXT:sequence_rearrangement_process + sequence rearrangement entity or process + GO_SO_EXT:sequence rearrangement entity or process + GO_SO_EXT:sequence_rearrangement_entity_or_process + + + sequence recombination + GO_SO_EXT:sequence rearrangement process + sequence rearrangement process + GO:'DNA recombination' or (BFO:occurrent and results_in_formation_of some (SO_EXT:meiotic_recombination_region or SO_EXT:mitotic_recombination_region or SO_EXT:complex_chromosomal_rearrangement or SO_EXT:rearrangement_region)) + GO_SO_EXT:sequence_rearrangement_process + For: rearrange/rearranged/rearranges/rearranging, recombination/recombinations/recombine/recombined/recombines/recombining + + + sequence transposition entity or process + sequence transposition + GO_SO_EXT:sequence_transposition_process or SO_EXT:chromosomal_transposition or SO_EXT:translocation + For: transposition/transpositions + GO_SO_EXT:sequence_transposition_entity_or_process + GO_SO_EXT:sequence transposition entity or process + + + sequence transposition process + For: transposable/transpose/transposed/transposes/transposing + GO:transposition or (BFO:occurrent and results_in_formation_of some SO_EXT:chromosomal_transposition) + GO_SO_EXT:sequence_transposition_process + GO_SO_EXT:sequence transposition process + + + telomere + GO:'chromosome, telomeric region' or SO_EXT:telomere or (BFO:dependent_continuant and inheres_in some (bearer_of some PATO:orientation and towards some (GO:'chromosome, telomeric region' or SO_EXT:telomere))) + telomere, telomeric region or telomeric orientation + GO_SO_EXT:telomere, telomeric region or telomeric orientation + telomeric region + GO_SO_EXT:telomere_or_telomeric_region_or_telomeric_orientation + telomeric + For: telomere(s), telomeric region(s), telomeric + + + transcription start + GO_SO_EXT:transcriptional_start_entity_or_process + For: transcription(al) start(s) + GO_SO_EXT:transcriptional start entity or process + GO:'DNA-templated transcription, initiation' or SO_EXT:TSS + transcriptional start entity or process + transcriptional start + + + GO_SO_EXT:transcriptional stop entity or process + transcription stop + For: transcription(al) stop(s) + transcriptional stop + transcriptional stop entity or process + GO:'DNA-templated transcription, termination' or SO_EXT:terminator + GO_SO_EXT:transcriptional_stop_entity_or_process + + + translational start entity or process + translation start + GO_SO_EXT:translational start entity or process + For: translation(al) start(s) + translational start + GO_SO_EXT:translational_start_entity_or_process + GO:'translational initiation' or (SO_EXT:stop_codon and has_prototype o causally_effects some GO:'translational initiation') + + + translational stop + translational stop entity or process + GO_SO_EXT:translational_stop_entity_or_process + GO:'translational termination' or SO_EXT:stop_codon + GO_SO_EXT:translational stop entity or process + For: translation(al) stop(s) + translation stop + + + GO_UBERON_EXT:basal_lamina + GO:'basal lamina' or UBERON:'basal lamina of epithelium' + GO_UBERON_EXT:basal lamina + basement lamina + basal lamina + + + GO_UBERON_EXT:basement_membrane + basement membrane + GO_UBERON_EXT:basement membrane + GO:'basement membrane' or UBERON:'basement membrane of epithelium' + For: basement membrane(s) + basal membrane + + + cell component/part + cell component + cell part + GO_UBERON_EXT:cellular_component_or_cell_part + cellular component + For: cell(ular) part(s), cell(ular) component(s), subcellular(ly) + cellular part + subcellular + GO_UBERON_EXT:cell component/part + GO:cellular_component or UBERON:'cell part' + + + For: innervation/innervations + innervation entity or process + innervation + GO_UBERON_EXT:innervation entity or process + GO:innervation or (UBERON:'anatomical entity' and is_formed_as_result_of some GO:innervation) + GO_UBERON_EXT:innervation_entity_or_process + + + GO_UBERON_EXT:lumen + GO:'membrane-enclosed lumen' or UBERON:'anatomical space' + GO_UBERON_EXT:lumen + lumen + lumen + For: lumen(s) + + + neuron ending + GO_UBERON_EXT:nerve ending or neuron projection terminus + nerve terminal + nerve ending or neuron projection terminus + GO_UBERON_EXT:nerve_ending_or_neuron_projection_terminus + UBERON:'nerve ending' or GO:'neuron projection terminus' + For: (neuron/nerve) ending(s), terminal(s) + neuronal ending + neuron terminal + neuronal terminal + nerve ending + + + GO_UBERON_EXT:nerve_ending_or_neuron_projection_terminus and has_prototype o causally_effects some GO:proprioception + proprioceptor + GO_UBERON_EXT:proprioceptor + GO_UBERON_EXT:proprioceptor + + + villi + GO_UBERON_EXT:villus + villus + GO_UBERON_EXT:villus + villus + For: villus/villi + GO:microvillus or UBERON:'arachnoid villus' or UBERON:'chorionic villus' or UBERON:'cloacal villus' or UBERON:'intestinal villus' + + + univalent carboacylation + MOP:0000029 + univalent carboacylation + "Formation of a covalent bond between a substrate and an univalent carboacyl group." [RSC:xp] + MOP:univalent carboacylation + + + MOP:acetylation + MOP:0000030 + acetylation + acetylation + "Formation of a covalent bond between a substrate and an acetyl group." [RSC:xp] + + + biotinylation + MOP:biotinylation + MOP:0000093 + "Formation of a covalent bond between a substrate and a biotinyl group." [RSC:xp] + biotinylation + + + MOP:fatty-acylation + fatty-acylation + fatty-acylation + MOP:0000104 + "Formation of a covalent bond between a substrate and a fatty-acyl group." [RSC:xp] + + + MOP:myristoylation + "Formation of a covalent bond between a substrate and a myristoyl group." [RSC:xp] + MOP:0000124 + myristoylation + myristoylation + + + MOP:0000162 + MOP:glycosylation + glycosylation + glycosylation + "Formation of a covalent bond between a substrate and a glycosyl group." [RSC:xp] + + + alkylation + MOP:alkylation + alkylation + "Formation of a covalent bond between a substrate and an alkyl group." [RSC:xp] + MOP:0000369 + + + butylation + "Formation of a covalent bond between a substrate and a butyl group." [RSC:xp] + butylation + MOP:butylation + MOP:0000370 + + + hydrocarbylation + "Formation of a covalent bond between a substrate and a hydrocarbyl group." [RSC:xp] + MOP:hydrocarbylation + MOP:0000410 + hydrocarbylation + + + "Formation of a covalent bond between a substrate and an organyl group." [RSC:xp] + MOP:0000458 + organylation + MOP:organylation + organylation + + + MOP:molecular process + molecular process + "A process in which at least one of the participants is a molecule." [RSC:cb] + MOP:0000543 + + + "Formation of a covalent bond between a substrate and a group." [RSC:cb] + MOP:0000566 + MOP:formation of covalent bond with group + formation of covalent bond with group + + + "Breaking of a covalent bond between a substrate and a group." [RSC:cb] + breaking of covalent bond with group + MOP:0000567 + MOP:breaking of covalent bond with group + + + MOP:oxidation + de-electronation + MOP:0000568 + "The complete, net removal of one or mole electrons from a molecular entity, corresponding to an increase in the oxidation number of any atom within any substrate." [AU:O04362] + oxidation + + + MOP:reduction + "The complete transfer of one or more electrons to a molecular entity." [AU:R05222] + MOP:0000569 + reduction + electronation + + + MOP:0000590 + MOP:dehydrogenation + "An oxidation process that involves the removal of adjacent hydrogen atoms, resulting in an increase of bond order." [RSC:cb] + dehydrogenation + + + MOP:electron transfer + "A process where an electron is transferred from one molecular entity or part of a molecular entity to a different molecular entity or part of the same molecular entity." [AU:E02011] + electron transfer + MOP:0000615 + + + MOP:0000618 + MOP:solvolysis + "A molecular process where a molecule is broken up by reaction with a molecule that is part of the solvent material. It may be the primary constituent molecule of the solvent material (for example water, ethanol, ammonia) or its lyonium ion or lyate ion." [AU:S05762, RSC:cb] + solvolysis + + + MOP:hydrolysis + MOP:0000619 + hydrolysis + "A solvolysis reaction where the solvent material is water." [RSC:cb] + + + polymerisation + polymerization + MOP:0000629 + "The process of converting a monomer mixture of monomers into a polymer." [doi:10.1351/goldbook.P04740] + MOP:polymerisation + + + depolymerisation + "The process of converting a polymer into a monomer or mixture of monomers." [doi:10.1351/goldbook.D01600] + MOP:depolymerisation + depolymerization + MOP:0000630 + + + "A reaction in which one or more reactive reaction intermediates (frequently radicals) are continuously regenerated, usually through a repetitive cycle of elementary steps (the 'propagation step')." [doi:10.1351/goldbook.C00960] + MOP:chain reaction + chain reaction + MOP:0000635 + + + MOP:formation of covalent bond + MOP:0000779 + formation of covalent bond + + + breaking of covalent bond + MOP:breaking of covalent bond + MOP:0000780 + + + MOP:isomerisation + "A molecular process where the product is an isomer of the reactant." [doi:10.1359/goldbook.I03295] + MOP:0000789 + isomerisation + + + formation of covalent bond with carbon centre + MOP:formation of covalent bond with carbon centre + "Formation of a covalent bond with a group where the free valence is on a carbon centre." [RSC:cb] + MOP:0000800 + + + "Breaking of a covalent bond between a substrate and a carboacyl group." [RSC:xp] + decarboacylation + MOP:0001028 + MOP:decarboacylation + + + "Breaking of a covalent bond between a substrate and an univalent carboacyl group." [RSC:xp] + MOP:deunivalent carboacylation + MOP:0001029 + deunivalent carboacylation + + + deacetylation + MOP:deacetylation + "Breaking of a covalent bond between a substrate and an acetyl group." [RSC:xp] + MOP:0001030 + + + "Breaking of a covalent bond between a substrate and a glycosyl group." [RSC:xp] + MOP:deglycosylation + deglycosylation + MOP:0001162 + + + MOP:deacylation + "Breaking of a covalent bond between a substrate and an acyl group." [RSC:xp] + MOP:0001479 + deacylation + + + "Formation of a covalent bond between a nitrogen atom in a substrate and a glycosyl group." [RSC:xp] + MOP:0002162 + N-glycosylation + MOP:N-glycosylation + + + MOP extension classes + + + NCBITaxon:1 + NCBITaxon:root + root + + + hamsters + NCBITaxon:Cricetinae + NCBITaxon:10026 + Cricetinae + + + Peromyscus + NCBITaxon:10040 + NCBITaxon:Peromyscus + + + NCBITaxon:10066 + NCBITaxon:Muridae + Muridae + + + NCBITaxon:10088 + mice + NCBITaxon:Mus (genus) + Mus (genus) + + + NCBITaxon:10090 + NCBITaxon:Mus musculus + Mus musculus + house mouse + + + NCBITaxon:Rattus + NCBITaxon:10114 + Rattus + rats + + + NCBITaxon:10116 + Rattus norvegicus + Norway rat + NCBITaxon:Rattus norvegicus + brown rat + + + NCBITaxon:Caviidae + Caviidae + cavies + NCBITaxon:10139 + + + Cavia + guinea pigs + NCBITaxon:Cavia + NCBITaxon:10140 + + + Vira + NCBITaxon:Viruses + Viridae + Viruses + NCBITaxon:10239 + + + NCBITaxon:10292 + Herpesviridae + NCBITaxon:Herpesviridae + + + NCBITaxon:10293 + Alphaherpesvirinae + NCBITaxon:Alphaherpesvirinae + + + NCBITaxon:10294 + NCBITaxon:Simplexvirus + Simplexvirus + + + HSV-1 + herpes simplex virus 1 + Human alphaherpesvirus 1 + human herpesvirus 1 + HSV1 + NCBITaxon:10298 + NCBITaxon:Human alphaherpesvirus 1 + + + NCBITaxon:10357 + NCBITaxon:Betaherpesvirinae + Betaherpesvirinae + + + Cytomegalovirus + NCBITaxon:10358 + NCBITaxon:Cytomegalovirus + + + NCBITaxon:10359 + human herpesvirus 5 + Human betaherpesvirus 5 + NCBITaxon:Human betaherpesvirus 5 + HHV-5 + + + NCBITaxon:Gammaherpesvirinae + Gammaherpesvirinae + NCBITaxon:10374 + lymphoproliferative virus group + + + NCBITaxon:Lymphocryptovirus + NCBITaxon:10375 + Lymphocryptovirus + + + EBV + Human gammaherpesvirus 4 + NCBITaxon:10376 + NCBITaxon:Human gammaherpesvirus 4 + HHV-4 + human herpesvirus type 4 + Epstein Barr virus + + + Baculoviridae + NCBITaxon:Baculoviridae + NCBITaxon:10442 + + + NCBITaxon:10508 + Adenoviridae + NCBITaxon:Adenoviridae + + + simian virus 40 + NCBITaxon:10633 + Macaca mulatta polyomavirus 1 + rhesus polyomavirus + Polyomavirus maccacae + Rhesus macaque polyomavirus + Polyomavirus maccacae 1 + NCBITaxon:Macaca mulatta polyomavirus 1 + SV40 + + + NCBITaxon:Myoviridae + NCBITaxon:10662 + Myoviridae + phages with contractile tails + + + T4-like phages + T4virus + NCBITaxon:10663 + T4 phage group + NCBITaxon:T4virus + T4-like viruses + + + phage T4 + Escherichia virus T4 + coliphage T4 + T4 + NCBITaxon:10665 + NCBITaxon:Escherichia virus T4 + Enterobacteria phage T4 + bacteriophage T4 + + + Enterobacteria phage P1 + NCBITaxon:Escherichia virus P1 + bacteriophage P1 + Escherichia virus P1 + NCBITaxon:10678 + phage P1 + + + Siphoviridae + NCBITaxon:Siphoviridae + Styloviridae + NCBITaxon:10699 + phages with long non-contractile tails + + + coliphage lambda + lambda phage + NCBITaxon:Escherichia virus Lambda + phage lambda + bacteriophage lambda + NCBITaxon:10710 + Enterobacteria phage lambda + Escherichia virus Lambda + + + phages with short tails + NCBITaxon:10744 + NCBITaxon:Podoviridae + Podoviridae + + + Enterobacteria phage T7 + NCBITaxon:10760 + T7 bacteriophage + phage T7 + bacteriophage T7 + NCBITaxon:Enterobacteria phage T7 + T7 + + + NCBITaxon:Microviridae + Microviridae + isometric ssDNA phages + NCBITaxon:10841 + + + NCBITaxon:11018 + Togaviridae + NCBITaxon:Togaviridae + + + Alphaviridae + NCBITaxon:11019 + Alphavirus + arboviruses group A + NCBITaxon:Alphavirus + + + NCBITaxon:Sindbis virus + NCBITaxon:11034 + Sindbis virus + + + NCBITaxon:110456 + T7 phage group + T7-like phages + T7-like viruses + T7virus + NCBITaxon:T7virus + Podovirus + + + NCBITaxon:Coronaviridae + NCBITaxon:11118 + Coronaviridae + + + mouse hepatitis virus + MHV + NCBITaxon:11138 + Murine hepatitis virus + NCBITaxon:Murine hepatitis virus + + + NCBITaxon:Mononegavirales + negative-sense genome single-stranded RNA viruses + NCBITaxon:11157 + Mononegavirales + + + NCBITaxon:11158 + NCBITaxon:Paramyxoviridae + Paramyxoviridae + + + NCBITaxon:Murine respirovirus + Sendai virus + Murine respirovirus + NCBITaxon:11191 + murine parainfluenza virus 1 + + + Pneumoviridae + NCBITaxon:Pneumoviridae + Pneumovirinae + NCBITaxon:11244 + + + NCBITaxon:11263 + PVM + murine pneumonia virus + pneumonia virus of mice + Murine orthopneumovirus + NCBITaxon:Murine orthopneumovirus + + + NCBITaxon:11632 + NCBITaxon:Retroviridae + Retroviridae + + + NCBITaxon:11646 + NCBITaxon:Lentivirus + Lentivirinae + Lentivirus + + + Primate lentivirus group + NCBITaxon:11652 + NCBITaxon:Primate lentivirus group + primate immunodeficiency viruses + + + HIV1 + NCBITaxon:11676 + Human immunodeficiency virus 1 + HIV-1 + human immunodeficiency virus type 1 + NCBITaxon:Human immunodeficiency virus 1 + + + Hyperoartia + NCBITaxon:117569 + NCBITaxon:Hyperoartia + in part: Agnatha, Monorhina, Cephalaspidomorphi + + + NCBITaxon:Mouse mammary tumor virus + MTV + NCBITaxon:11757 + MMT + MMTV + murine mammary tumor provirus + Mouse mammary tumor virus + + + NCBITaxon:Teleostomi + Teleostomi + NCBITaxon:117570 + + + NCBITaxon:117571 + NCBITaxon:Euteleostomi + Euteleostomi + bony vertebrates + + + MuLV + Murine leukemia virus + NCBITaxon:Murine leukemia virus + MLV + NCBITaxon:11786 + + + NCBITaxon:Monoley murine leukemia virus + rat Moloney murine leukeumia virus + MoMLV + MMLV + NCBITaxon:11801 + Monoley murine leukemia virus + MoMuLV + M-MuLV + + + NCBITaxon:Avian myeloblastosis virus + NCBITaxon:11866 + Avian myeloblastosis virus + AMV + + + NCBITaxon:Rous sarcoma virus + RSV + Rous sarcoma virus + NCBITaxon:11886 + + + Adenophorea + NCBITaxon:Chromadorea + Chromadorea + NCBITaxon:119089 + + + NCBITaxon:Gnathostomatidae + Gnathostomatidae + NCBITaxon:119158 + + + Tevenvirinae + NCBITaxon:1198136 + NCBITaxon:Tevenvirinae + + + Mephitidae + NCBITaxon:119825 + NCBITaxon:Mephitidae + skunks + + + NCBITaxon:12058 + NCBITaxon:Picornaviridae + Picornavirus + Picornaviridae + + + NCBITaxon:Ecdysozoa + NCBITaxon:1206794 + Ecdysozoa + + + NCBITaxon:Lophotrochozoa + Lophotrochozoa + NCBITaxon:1206795 + + + NCBITaxon:12103 + cardioviruses + Cardiovirus + NCBITaxon:Cardiovirus + + + NCBITaxon:12104 + Encephalomyocarditis virus + NCBITaxon:Encephalomyocarditis virus + EMCV + + + NCBITaxon:Theiler's encephomyelitis virus + Theiler's encephomyelitis virus + murine poliovirus + TMEV + NCBITaxon:12124 + Theiler's murine encephamyelitis virus + Theiler murine encephalomyelitis virus + + + purple bacteria and relatives + purple non-sulfur bacteria + NCBITaxon:1224 + NCBITaxon:Proteobacteria + purple photosynthetic bacteria + purple photosynthetic bacteria and relatives + purple bacteria + Alphaproteabacteraeota + Proteobacteria + + + NCBITaxon:Neoteleostei + NCBITaxon:123365 + Neoteleostei + + + NCBITaxon:Eurypterygia + NCBITaxon:123366 + Eurypterygia + Eurypterygii + + + NCBITaxon:123367 + Ctenosquamata + NCBITaxon:Ctenosquamata + + + NCBITaxon:123368 + NCBITaxon:Acanthomorphata + Acanthomorpha + Acanthomorphata + + + Euacanthomorphacea + NCBITaxon:123369 + NCBITaxon:Euacanthomorphacea + Euacanthomorpha + + + Gammaproteobacteria + purple bacteria, gamma subdivision + NCBITaxon:1236 + gamma proteobacteria + NCBITaxon:Gammaproteobacteria + g-proteobacteria + + + Clostridium group firmicutes + Firmacutes + Bacillus/Clostridium group + Bacillaeota + low G+C Gram-positive bacteria + NCBITaxon:Firmicutes + low G+C firmicutes + NCBITaxon:1239 + clostridial firmicutes + Firmicutes + + + NCBITaxon:1279 + Aurococcus + NCBITaxon:Staphylococcus + Staphylococcus + + + Staphylococcus aureus + Staphylococcus pyogenes aureus + NCBITaxon:Staphylococcus aureus + Staphylococcus phyogenes citreus + Micrococcus aureus + NCBITaxon:1280 + Micrococcus pyogenes + + + NCBITaxon:Aequoreidae + Aequoreidae + NCBITaxon:128126 + + + NCBITaxon:Leishmaniinae + Leishmaniinae + NCBITaxon:1286322 + + + NCBITaxon:Deinococcus-Thermus + NCBITaxon:1297 + Thermus/Deinococcus group + Deinococcaeota + Deinococcus-Thermus + + + Streptococcaceae + NCBITaxon:1300 + NCBITaxon:Streptococcaceae + + + NCBITaxon:Streptococcus + Streptococcus + NCBITaxon:1301 + + + Charophyta/Embryophyta group + charophyte/embryophyte group + NCBITaxon:Streptophytina + Streptophytina + NCBITaxon:131221 + + + Diplococcus pneumoniae + Streptococcus pneumoniae + NCBITaxon:Streptococcus pneumoniae + Micrococcus pneumoniae + NCBITaxon:1313 + + + cellular organisms + biota + NCBITaxon:131567 + NCBITaxon:cellular organisms + + + NCBITaxon:Archelosauria + Archosauria-Testudines + Testudines+Archosauria group + NCBITaxon:1329799 + Archelosauria + + + Eleutherozoa + NCBITaxon:Eleutherozoa + NCBITaxon:133551 + + + NCBITaxon:1338369 + NCBITaxon:Dipnotetrapodomorpha + Dipnotetrapodomorpha + + + NCBITaxon:Enterococcus + NCBITaxon:1350 + Enterococcus + + + NCBITaxon:135614 + Lysobacterales + NCBITaxon:Xanthomonadales + Xanthomonadales + + + NCBITaxon:135621 + NCBITaxon:Pseudomonadaceae + Pseudomonadaceae + + + NCBITaxon:135622 + NCBITaxon:Alteromonadales + Alteromonadaceae group + Alteromonadales + + + Pasteurellales + NCBITaxon:135625 + NCBITaxon:Pasteurellales + Pasteurellaceae group + + + Pseudomonas aeruginosa group + NCBITaxon:136841 + NCBITaxon:Pseudomonas aeruginosa group + + + Pseudomonas fluorescens group + NCBITaxon:136843 + NCBITaxon:Pseudomonas fluorescens group + fluorescent pseudomonads + + + NCBITaxon:1385 + NCBITaxon:Bacillales + Bacillales + Bacillus/Staphylococcus group + + + NCBITaxon:140052 + NCBITaxon:Betaretrovirus + Betaretrovirus + + + Mycetozoa + NCBITaxon:142796 + NCBITaxon:Mycetozoa + mycetozoans + + + Boreotheria + Boreoeutheria + NCBITaxon:1437010 + NCBITaxon:Boreoeutheria + + + NCBITaxon:Acrogymnospermae + NCBITaxon:1437180 + Acrogymnospermae + + + NCBITaxon:1437183 + NCBITaxon:Mesangiospermae + Mesangiospermae + + + NCBITaxon:Petrosaviidae + Petrosaviidae + NCBITaxon:1437197 + + + NCBITaxon:1437201 + NCBITaxon:Pentapetalae + Pentapetalae + + + NCBITaxon:1446380 + NCBITaxon:Pinales + Pinales + + + NCBITaxon:146277 + Patellacea + NCBITaxon:Patelloidea + Patelloidea + + + true yeasts + Saccharomycotina + NCBITaxon:Saccharomycotina + NCBITaxon:147537 + + + Euascomycota + NCBITaxon:Pezizomycotina + NCBITaxon:147538 + Pezizomycotina + + + NCBITaxon:Sordariomycetes + NCBITaxon:147550 + Sordariomycetes + in part: Pyrenomycetes + + + NCBITaxon:Schizosaccharomycetes + NCBITaxon:147554 + in part: Archiascomycota + Schizosaccharomycetes + + + jawless vertebrates + NCBITaxon:1476529 + NCBITaxon:Cyclostomata + Cyclostomata + Agnatha + + + NCBITaxon:1489341 + Osteoglossocephalai + NCBITaxon:Osteoglossocephalai + + + Euteleosteomorpha + NCBITaxon:Euteleosteomorpha + NCBITaxon:1489388 + + + NCBITaxon:Percomorphaceae + NCBITaxon:1489872 + Percomorphaceae + + + Ovalentaria + Stiassnyiformes + NCBITaxon:Ovalentaria + NCBITaxon:1489908 + + + NCBITaxon:1489913 + Atherinomorphae + NCBITaxon:Atherinomorphae + Atherinomorpha + + + NCBITaxon:Eupercaria + NCBITaxon:1489922 + Percomorpharia + Eupercaria + + + NCBITaxon:Polyomaviridae + NCBITaxon:151341 + Polyomaviridae + + + Alpharetrovirus + ALV-related viruses + avian type C retrovirus group + NCBITaxon:Alpharetrovirus + avian type C retroviruses + NCBITaxon:153057 + avian type C oncoviruses + + + MLV-related viruses + type C oncoviruses + Gammaretrovirus + NCBITaxon:Gammaretrovirus + mammalian type C retrovirus group + mammalian type C retroviruses + mammalian type C oncoviruses + NCBITaxon:153135 + + + NCBITaxon:Galloanserae + ducks, geese, chickens, fowl, quail, currasows and allies + NCBITaxon:1549675 + Galloanseri + Galloanserae + + + Xylella fastiodiosa Dixon + NCBITaxon:Xylella fastiodiosa Dixon + NCBITaxon:155919 + + + NCBITaxon:Lactobacillus + Paralactobacillus + NCBITaxon:1578 + Lactobacillus + + + NCBITaxon:1612408 + NCBITaxon:Aplanulata + Aplanulata + + + Cercideae + NCBITaxon:163092 + NCBITaxon:Cercideae + + + NCBITaxon:163729 + Genisteae + NCBITaxon:Genisteae + + + Phaseoleae + NCBITaxon:Phaseoleae + NCBITaxon:163735 + + + Loteae + NCBITaxon:Loteae + NCBITaxon:163747 + + + Actinobacteria + high G+C Gram-positive bacteria + Actinobacteridae + high GC gram-positive bacteria + NCBITaxon:Actinobacteria + Actinomycetes + NCBITaxon:1760 + + + WEEV complex + NCBITaxon:WEEV complex + NCBITaxon:177874 + + + NCBITaxon:1783272 + NCBITaxon:Terrabacteria group + Terrabacteria group + + + Euamoebida + NCBITaxon:Euamoebida + NCBITaxon:180229 + + + Micropolyspora + Nocardia + NCBITaxon:1817 + NCBITaxon:Nocardia + + + NCBITaxon:1821749 + Cardiovirus A + NCBITaxon:Cardiovirus A + + + NCBITaxon:Cardiovirus B + Cardiovirus B + NCBITaxon:1821750 + + + Actinomyces caviae + NCBITaxon:1823 + NCBITaxon:Nocardia otitidiscaviarum + Nocardia caviae + Nocardia otitidiscaviarum + + + Enterogona + NCBITaxon:183770 + NCBITaxon:Enterogona + + + Streptomyces albus group + NCBITaxon:Streptomyces albus group + NCBITaxon:1852274 + + + NCBITaxon:186623 + Actinopteri + NCBITaxon:Actinopteri + + + Clupeocephala + NCBITaxon:Clupeocephala + NCBITaxon:186625 + + + NCBITaxon:Otophysi + NCBITaxon:186626 + Otophysi + Otophysa + + + Cypriniphysae + NCBITaxon:186627 + NCBITaxon:Cypriniphysae + Cypriniphysi + + + Otocephala + NCBITaxon:186634 + Otomorpha + NCBITaxon:Otomorpha + Ostarioclupeomorpha + + + Lambdavirus + NCBITaxon:186765 + NCBITaxon:Lambdavirus + lambda-like viruses + lambda phage group + + + P4virus + P1-like viruses + NCBITaxon:P4virus + NCBITaxon:186789 + + + NCBITaxon:Orthopneumovirus + Orthopneumovirus + NCBITaxon:1868215 + + + low G+C gram-positive sulfux-oxidizing group + Alicyclobacillaceae + Alicyclobacillus group + NCBITaxon:Alicyclobacillaceae + NCBITaxon:186823 + + + Lactobacillales + NCBITaxon:Lactobacillales + NCBITaxon:186826 + + + NCBITaxon:186938 + NCBITaxon:Respirovirus + Respirovirus + + + Streptomyces + Chainia + NCBITaxon:1883 + NCBITaxon:Streptomyces + + + NCBITaxon:188786 + Thermaceae + NCBITaxon:Thermaceae + + + Hadobacteria + NCBITaxon:188787 + NCBITaxon:Deinococci + Deinococci + + + Streptomyces sp. USC057 + Streptomyces albus + NCBITaxon:Streptomyces albus + Streptomyces griseus subsp. solvifaciens + Streptotrix alba + NCBITaxon:1888 + Streptomyces griseus solvifaciens + + + Betapolyomavirus + NCBITaxon:1891714 + NCBITaxon:Betapolyomavirus + + + NCBITaxon:Bullavirinae + Bullavirinae + NCBITaxon:1910950 + + + Phix174microvirus + NCBITaxon:1910954 + NCBITaxon:Phix174microvirus + + + NCBITaxon:Alicyclobacillus sendaiensis + NCBITaxon:192387 + Alicyclobacillus sendaienensis + Alicyclobacillus sendaiensis + + + Rodentibacter + NCBITaxon:Rodentibacter + NCBITaxon:1960084 + + + NCBITaxon:Myomorpha + NCBITaxon:1963758 + Myomorpha + in part: Sciurognathi + + + NCBITaxon:Pancrustacea + Pancrustacea + NCBITaxon:197562 + + + mandibulates + NCBITaxon:Mandibulata + Mandibulata + NCBITaxon:197563 + + + NCBITaxon:Hippocastanoideae + NCBITaxon:1977916 + Hippocastanoideae + + + NCBITaxon:1977919 + NCBITaxon:Acereae + Acereae + + + Cercidoideae + NCBITaxon:1978181 + NCBITaxon:Cercidoideae + + + NCBITaxon:1985738 + NCBITaxon:Escherichia virus T7 + Escherichia virus T7 + + + eubacteria + NCBITaxon:2 + Bacteria + NCBITaxon:Bacteria + in part: prokaryotes, Prokaryota, Monera + + + Actinobacteraeota + Actinobacteria + NCBITaxon:Actinobacteria + NCBITaxon:201174 + + + ThV + NCBITaxon:204711 + Theilovirus + NCBITaxon:Theilovirus + + + NCBITaxon:2058185 + NCBITaxon:Dictyosteliaceae + Dictyosteliaceae + + + NCBITaxon:2058949 + NCBITaxon:Dictyosteliales + Dictyosteliales + + + Streptomycetaceae + NCBITaxon:Streptomycetaceae + NCBITaxon:2062 + + + Homo/Pan/Gorilla group + NCBITaxon:Homininae + NCBITaxon:207598 + Homininae + + + Paramycetales + Pleuropneumoniales + NCBITaxon:Mycoplasmatales + mycoplasmas + NCBITaxon:2085 + Mycoplasmatales + Mollicutales + Borrelomycetales + + + NCBITaxon:Mycoplasmataceae + Parasitaceae + Mycoplasmataceae + Borrelomycetaceae + Pleuropneumoniaceae + NCBITaxon:2092 + + + Borrelomyces + Asterococcus + Haemobartonella + Pleuropneumonia + Mycoplasma + NCBITaxon:Mycoplasma + Eperythrozoon + Asteromyces + Bovimyces + NCBITaxon:2093 + + + Mycoplasma pulmonis + Asterococcus pulmonis + NCBITaxon:Mycoplasma pulmonis + NCBITaxon:2107 + Murimyces pulmonis + Musculomyces histotropicus + Mycoplasma mergenhagen + Mycoplasma histotropicus + + + Micromyces hominis group II + Asterococcus fermentans + NCBITaxon:2115 + NCBITaxon:Mycoplasma fermentans + Mycoplasma fermentans + Schizoplasma fermentans + + + Archaea + NCBITaxon:2157 + Archaebacteria + Metabacteria + NCBITaxon:Archaea + archaea + Mendosicutes + + + NCBITaxon:Vetigastropoda + NCBITaxon:216275 + Vetigastropoda + + + Fissurelloidea + NCBITaxon:216278 + NCBITaxon:Fissurelloidea + + + Shewanella + NCBITaxon:22 + NCBITaxon:Shewanella + + + Sordariomycetidae + NCBITaxon:Sordariomycetidae + NCBITaxon:222544 + + + Sapindaceae + soapberry family + Xanthoceraceae + NCBITaxon:Sapindaceae + NCBITaxon:23672 + + + NCBITaxon:Xylella + Xylella + NCBITaxon:2370 + + + Xylella fastidiosa + NCBITaxon:2371 + NCBITaxon:Xylella fastidiosa + + + Apioideae + NCBITaxon:241778 + NCBITaxon:Apioideae + + + apioid superclade + NCBITaxon:apioid superclade + NCBITaxon:241780 + + + Apieae + Apium clade + NCBITaxon:Apieae + NCBITaxon:241793 + + + NCBITaxon:Xenopus (subgenus) + Xenopus (subgenus) + NCBITaxon:262014 + + + NCBITaxon:267890 + Shewanellaceae + NCBITaxon:Shewanellaceae + + + NCBITaxon:Thermus + NCBITaxon:270 + Thermus + + + NCBITaxon:Thermus aquaticus + Thermus aquaticus + NCBITaxon:271 + + + Dolichos biflorus + NCBITaxon:Macrotyloma uniflorum + NCBITaxon:271171 + kulthi + Madras gram + Dolichos biflorus sensu auct. + Macrotyloma uniflorum + horse gram + + + eucaryotes + NCBITaxon:2759 + Eukaryota + Eukarya + NCBITaxon:Eukaryota + Eukaryotae + eukaryotes + Eucarya + Eucaryotae + + + NCBITaxon:27592 + Bovinae + NCBITaxon:Bovinae + + + alpha proteobacteria + NCBITaxon:Alphaproteobacteria + Alphaproteobacteria + Alphabacteria + a-proteobacteria + Proteobacteria alpha subdivision + NCBITaxon:28211 + purple bacteria, alpha subdivision + + + Liquidomonas + NCBITaxon:286 + Pseudomonas + NCBITaxon:Pseudomonas + Loefflerella + + + Micrococcus pyocyaneus + Bacterium pyocyaneum + Pseudomonas pyocyanea + Bacterium aeruginosum + NCBITaxon:Pseudomonas aeruginosa + NCBITaxon:287 + Pseudomonas aeruginosa + Bacillus aeruginosus + Pseudomonas polycolor + Bacillus pyocyaneus + + + NCBITaxon:Adrianichthyoidei + NCBITaxon:28781 + Adrianichthyoidei + + + NCBITaxon:Caudovirales + Caudovirales + NCBITaxon:28883 + tailed phages + + + ssDNA viruses + ssDNA nonenveloped viruses + NCBITaxon:29258 + NCBITaxon:ssDNA viruses + + + NCBITaxon:29330 + NCBITaxon:Alicyclobacillus + Alicyclobacillus + + + Liquidomonas fluorescens + NCBITaxon:294 + NCBITaxon:Pseudomonas fluorescens + Bacillus fluorescens + Bacillus fluorescens liquefaciens + Bacterium fluorescen + Pseudomonas fluorescens + + + NCBITaxon:Pipoidea + NCBITaxon:30319 + Pipoidea + + + Ambystomatoidea + NCBITaxon:30367 + Salamandroidea + NCBITaxon:Salamandroidea + + + NCBITaxon:3041 + in part: algae + green algae + Chlorophycota + Chlorophyta + NCBITaxon:Chlorophyta + + + NCBITaxon:Chlamydomonadales + Chlamydomonadales + Chlorococcales + NCBITaxon:3042 + Volvocida + Volvocales + + + NCBITaxon:3051 + NCBITaxon:Chlamydomonadaceae + Chlamydomonadaceae + + + NCBITaxon:3052 + NCBITaxon:Chlamydomonas + Chlamydomonas + + + Cyprinoidea + NCBITaxon:Cyprinoidea + Cyprinoidei + NCBITaxon:30727 + + + NCBITaxon:31022 + NCBITaxon:Tetraodontiformes + Tetraodontiformes + + + NCBITaxon:31028 + NCBITaxon:Tetraodontoidei + Tetraodontoidei + + + puffer fishes + NCBITaxon:Tetraodontidae + NCBITaxon:31031 + Tetraodontidae + puffers + + + NCBITaxon:Takifugu + NCBITaxon:31032 + Takifugu + Fugu + + + torafugu + Takifugu rubripes + Fugu rubripes + NCBITaxon:31033 + NCBITaxon:Takifugu rubripes + tiger puffer + Tetraodon rubripes + Spaeroides rubripes + + + NCBITaxon:Strongylocentrotidae + NCBITaxon:31181 + Strongylocentrotidae + + + Laurasiatheria + NCBITaxon:314145 + NCBITaxon:Laurasiatheria + + + Euarchontoglires + NCBITaxon:314146 + NCBITaxon:Euarchontoglires + + + Glires + NCBITaxon:314147 + NCBITaxon:Glires + rodents and rabbits + + + NCBITaxon:314293 + Simiiformes + NCBITaxon:Simiiformes + Anthropoidea + + + NCBITaxon:Cercopithecoidea + NCBITaxon:314294 + Cercopithecoidea + + + NCBITaxon:314295 + apes + NCBITaxon:Hominoidea + Hominoidea + + + NCBITaxon:3166 + NCBITaxon:Chlorophyceae + Chlorophyceae + + + NCBITaxon:3193 + Embryophyta + higher plants + plants + NCBITaxon:Embryophyta + land plants + + + mycoplasmas + Paramycetes + NCBITaxon:Mollicutes + NCBITaxon:31969 + Mycoplasmas and walled relatives + Mollicutes + + + NCBITaxon:Xanthomonadaceae + Xanthomonadaceae + NCBITaxon:32033 + Xanthomonas group + + + NCBITaxon:Sophophora + NCBITaxon:32341 + Sophophora + + + NCBITaxon:melanogaster group + NCBITaxon:32346 + melanogaster group + + + melanogaster subgroup + NCBITaxon:melanogaster subgroup + NCBITaxon:32351 + + + teleost fishes + NCBITaxon:Teleostei + Teleostei + NCBITaxon:32443 + + + NCBITaxon:32517 + NCBITaxon:Tetradontoidea + Tetradontoidea + + + Ostariophysi + NCBITaxon:Ostariophysi + NCBITaxon:32519 + + + tetrapods + Tetrapoda + NCBITaxon:Tetrapoda + NCBITaxon:32523 + + + Amniota + amniotes + NCBITaxon:32524 + NCBITaxon:Amniota + + + NCBITaxon:32525 + NCBITaxon:Theria + Theria + + + Sauria + NCBITaxon:Sauria + Diapsida + NCBITaxon:32561 + diapsids + + + NCBITaxon:Orthoretrovirinae + Orthoretrovirinae + NCBITaxon:327045 + + + NCBITaxon:33083 + Dictyosteliida + Dictyostelida + cellular slime molds + dictyostelid cellular slime molds + Dictyostelia + Dictyostelids + NCBITaxon:Dictyostelids + + + chlorophyte/embryophyte group + Viridiplantae + NCBITaxon:Viridiplantae + green plants + Chlorobionta + Chlorophyta/Embryophyta group + NCBITaxon:33090 + + + NCBITaxon:Pinidae + Pinidae + Coniferales + NCBITaxon:3313 + + + NCBITaxon:Opisthokonta + Opisthokonta + opisthokonts + Fungi/Metazoa group + NCBITaxon:33154 + + + NCBITaxon:Pinaceae + Pinaceae + pine family + NCBITaxon:3318 + + + metazoans + multicellular animals + Metazoa + NCBITaxon:Metazoa + NCBITaxon:33208 + Animalia + animals + + + NCBITaxon:Bilateria + Bilateria + NCBITaxon:33213 + + + NCBITaxon:33317 + NCBITaxon:Protostomia + Protostomia + + + NCBITaxon:33340 + NCBITaxon:Neoptera + Neoptera + + + NCBITaxon:3337 + Pinus + NCBITaxon:Pinus + + + NCBITaxon:33392 + NCBITaxon:Holometabola + Endopterygota + Holometabola + + + deuterostomes + NCBITaxon:Deuterostomia + Deuterostomia + NCBITaxon:33511 + + + NCBITaxon:Hystricomorpha + Hystricognathi + NCBITaxon:33550 + Hystricomorpha + + + Sciuromorpha + NCBITaxon:33553 + in part: Sciurognathi + NCBITaxon:Sciuromorpha + + + NCBITaxon:Carnivora + carnivores + NCBITaxon:33554 + Carnivora + + + Euglenozoa + NCBITaxon:Euglenozoa + euglenozoans + NCBITaxon:33682 + + + NCBITaxon:337677 + NCBITaxon:Cricetidae + Cricetidae + + + NCBITaxon:Muroidea + Muroidea + NCBITaxon:337687 + + + NCBITaxon:337963 + NCBITaxon:Neotominae + Neotominae + + + Felinae + NCBITaxon:Felinae + NCBITaxon:338152 + + + NCBITaxon:Lactobacillaceae + NCBITaxon:33958 + Lactobacillaceae + + + Angiospermae + NCBITaxon:3398 + angiosperms + flowering plants + NCBITaxon:Magnoliophyta + Magnoliophyta + + + NCBITaxon:Schizosaccharomycetales + Schizosaccharomycetales + NCBITaxon:34346 + + + NCBITaxon:35218 + Amoebidae + NCBITaxon:Amoebidae + + + NCBITaxon:dsDNA viruses, no RNA stage + NCBITaxon:35237 + dsDNA viruses, no RNA stage + + + NCBITaxon:Retro-transcribing viruses + retroid viruses + NCBITaxon:35268 + Retro-transcribing viruses + + + NCBITaxon:35278 + ssRNA positive-strand viruses, no DNA stage + NCBITaxon:ssRNA positive-strand viruses, no DNA stage + + + ssRNA negative-strand viruses + NCBITaxon:35301 + NCBITaxon:ssRNA negative-strand viruses + + + Replication competent viruses + NCBITaxon:Replication competent viruses + NCBITaxon:353210 + + + NCBITaxon:Mammalian gammaretrovirus group + NCBITaxon:353212 + Mammalian gammaretrovirus group + + + NCBITaxon:Streptophyta + Streptophyta + NCBITaxon:35493 + + + NCBITaxon:Pecora + Pecora + NCBITaxon:35500 + + + Equus subg. Asinus + Asinus + NCBITaxon:Asinus + NCBITaxon:35508 + + + NCBITaxon:Equus + NCBITaxon:35510 + Equus + Equus subg. Equus + + + NCBITaxon:Rhizobiales + in part: alpha-2 proteobacteria + NCBITaxon:356 + Rhizobiaceae group + Rhizobiales + rhizobacteria + + + Apiineae + NCBITaxon:364270 + NCBITaxon:Apiineae + + + NCBITaxon:Brassicales + Capparales + Brassicales + NCBITaxon:3699 + + + Cruciferae + mustard family + NCBITaxon:Brassicaceae + Brassicaceae + NCBITaxon:3700 + + + NCBITaxon:Arabidopsis + Arabidopsis + Cardaminopsis + NCBITaxon:3701 + + + mouse-ear cress + NCBITaxon:Arabidopsis thaliana + NCBITaxon:3702 + thale cress + Arabidopsis thaliana + + + Armoracia + NCBITaxon:3703 + NCBITaxon:Armoracia + + + Armoracia lapathifolia + Armoracia rusticana + NCBITaxon:3704 + horseradish + NCBITaxon:Armoracia rusticana + Armoracia rustica + + + NCBITaxon:Nakaseomyces + Nakaseomyces + NCBITaxon:374468 + + + Renillidae + NCBITaxon:Renillidae + NCBITaxon:37509 + + + NCBITaxon:37516 + Hydroidolina + NCBITaxon:Hydroidolina + Hydroidomedusae + Hydroida + + + Haplorrhini + NCBITaxon:Haplorrhini + NCBITaxon:376913 + + + Feliformia + NCBITaxon:379583 + NCBITaxon:Feliformia + + + NCBITaxon:379584 + Caniformia + NCBITaxon:Caniformia + + + pea family + NCBITaxon:3803 + Fabaceae + NCBITaxon:Fabaceae + Leguminosae + + + NCBITaxon:3814 + Faboideae + Papilionoideae + NCBITaxon:Papilionoideae + + + Rochalimaea henselae + NCBITaxon:Bartonella henselae + Bartonella henselae + NCBITaxon:38323 + + + NCBITaxon:3849 + Griffonia + NCBITaxon:Griffonia + + + NCBITaxon:Griffonia simplicifolia + Griffonia simplicifolia + NCBITaxon:3850 + + + Lotus + NCBITaxon:3867 + NCBITaxon:Lotus + + + NCBITaxon:Lotus tetragonolobus + Lotus tetragonolobus + NCBITaxon:3868 + winged pea + Tetragonolobus purpureus + + + NCBITaxon:Macrotyloma + NCBITaxon:3875 + Macrotyloma + + + Ulex + NCBITaxon:3901 + NCBITaxon:Ulex + + + gorse + NCBITaxon:Ulex europaeus + furze + Ulex europaeus + NCBITaxon:3902 + Ulex europeus + + + NCBITaxon:Murinae + includes: Otomyinae + NCBITaxon:39107 + Murinae + + + Acer + NCBITaxon:Acer + NCBITaxon:4022 + maple trees + + + NCBITaxon:4036 + NCBITaxon:Apiales + Apiales + Araliales + + + Umbelliferae + NCBITaxon:4037 + NCBITaxon:Apiaceae + Apiaceae + carrot family + + + onion family + Alliaceae + NCBITaxon:Allioideae + Allioideae + NCBITaxon:40553 + + + Gymnoblastea + Athecata + Anthoathecata + Anthoathecatae + NCBITaxon:406427 + Anthomedusae + NCBITaxon:Anthoathecata + + + NCBITaxon:Mammalia + mammals + Mammalia + NCBITaxon:40674 + + + NCBITaxon:Solanales + Solanales + Solananae + NCBITaxon:4069 + + + NCBITaxon:Solanaceae + NCBITaxon:4070 + Solanaceae + nightshade family + + + NCBITaxon:4085 + NCBITaxon:Nicotiana + Nicotiana + + + NCBITaxon:Anethum + Anethum + NCBITaxon:40921 + + + Anethum graveolens + dill + NCBITaxon:Anethum graveolens + NCBITaxon:40922 + + + NCBITaxon:Nicotiana tabacum + NCBITaxon:4097 + American tobacco + Nicotiana tabacum + tobacco + common tobacco + + + NCBITaxon:Polyphaga + NCBITaxon:41084 + Polyphaga + + + NCBITaxon:Elateriformia + Elateriformia + NCBITaxon:41087 + + + NCBITaxon:Neopterygii + Neopterygii + NCBITaxon:41665 + Neopterygi + + + NCBITaxon:Batrachia + NCBITaxon:41666 + Batrachia + + + Protacanthopterygii + NCBITaxon:41705 + NCBITaxon:Protacanthopterygii + + + Culicoidea + NCBITaxon:41827 + NCBITaxon:Culicoidea + + + in part: Rutanae + NCBITaxon:Sapindales + Sapindales + NCBITaxon:41937 + + + Peromyscus polionotus + NCBITaxon:42413 + NCBITaxon:Peromyscus polionotus + oldfield mouse + + + Nicotianoideae + NCBITaxon:424554 + NCBITaxon:Nicotianoideae + + + NCBITaxon:Nicotianeae + Nicotianeae + NCBITaxon:424562 + + + NCBITaxon:Dinosauria + NCBITaxon:436486 + Dinosauria + dinosaurs + + + NCBITaxon:436489 + NCBITaxon:Saurischia + Saurischia + + + Theropoda + NCBITaxon:436491 + NCBITaxon:Theropoda + + + NCBITaxon:Coelurosauria + Coelurosauria + NCBITaxon:436492 + + + Muscomorpha + Asilomorpha + NCBITaxon:Muscomorpha + NCBITaxon:43733 + + + NCBITaxon:Schizophora + NCBITaxon:43738 + Schizophora + + + NCBITaxon:Acalyptratae + Acalyptratae + NCBITaxon:43741 + + + NCBITaxon:Ephydroidea + NCBITaxon:43746 + Ephydroidea + + + NCBITaxon:43786 + Culicomorpha + NCBITaxon:Culicomorpha + + + NCBITaxon:Anophelinae + NCBITaxon:43816 + Anophelinae + + + NCBITaxon:43845 + NCBITaxon:Drosophilinae + Drosophilinae + + + NCBITaxon:ssRNA viruses + NCBITaxon:439488 + ssRNA viruses + + + NCBITaxon:44295 + coral anemones + jewel anemones + coral-like anemones + false anemones + NCBITaxon:Corallimorpharia + mushroom anemones + Corallimorpharia + + + NCBITaxon:4447 + monocotyledons + monocots + NCBITaxon:Liliopsida + Liliopsida + Monocotyledoneae + + + Cellia + NCBITaxon:Cellia + NCBITaxon:44534 + + + NCBITaxon:Pyretophorus + Pyretophorus + NCBITaxon:44537 + + + gambiae species complex + NCBITaxon:gambiae species complex + NCBITaxon:44542 + + + NCBITaxon:Dictyostelium discoideum + Dictyostelium discoideum + NCBITaxon:44689 + + + NCBITaxon:Dikarya + Dikarya + NCBITaxon:451864 + + + Taphrinomycotina + NCBITaxon:451866 + NCBITaxon:Taphrinomycotina + + + NCBITaxon:464095 + NCBITaxon:Picornavirales + Picornavirales + + + NCBITaxon:466544 + Perdicinae + NCBITaxon:Perdicinae + + + Amaryllidaceae + NCBITaxon:4668 + NCBITaxon:Amaryllidaceae + amaryllis family + + + Allium + NCBITaxon:4678 + NCBITaxon:Allium + + + NCBITaxon:Allium cepa + NCBITaxon:4679 + onion + Allium cepa + + + NCBITaxon:46877 + Drosophilini + NCBITaxon:Drosophilini + + + NCBITaxon:46909 + Crithidia luciliae + NCBITaxon:Crithidia luciliae + + + Tetraodon + NCBITaxon:47144 + NCBITaxon:Tetraodon + + + NCBITaxon:Fungi + NCBITaxon:4751 + Fungi + fungi + + + NCBITaxon:47757 + NCBITaxon:Adrianichthyidae + Adrianichthyidae + + + NCBITaxon:480117 + Cyclorrhapha + NCBITaxon:Cyclorrhapha + + + Eremoneura + NCBITaxon:480118 + NCBITaxon:Eremoneura + + + NCBITaxon:Ascomycota + Ascomycota + sac fungi + ascomycetes + NCBITaxon:4890 + + + NCBITaxon:Saccharomycetes + NCBITaxon:4891 + Saccharomycetes + Hermiascomycetes + + + Saccharomycetales + NCBITaxon:4892 + Endomycetales + budding yeasts + NCBITaxon:Saccharomycetales + + + NCBITaxon:4893 + Saccharomycetaceae + NCBITaxon:Saccharomycetaceae + + + Schizosaccharomycetaceae + NCBITaxon:Schizosaccharomycetaceae + fission yeasts + Schizosaccharomycetoideae + NCBITaxon:4894 + + + NCBITaxon:Schizosaccharomyces + NCBITaxon:4895 + Schizosaccharomyces + + + fission yeast + Schizosaccharomyces malidevorans + NCBITaxon:Schizosaccharomyces pombe + NCBITaxon:4896 + Schizosaccharomyces pombe + + + NCBITaxon:Saccharomyces + Saccharomyces + Pachytichospora + NCBITaxon:4930 + + + Saccharomyces cerevisiae + NCBITaxon:Saccharomyces cerevisiae + Saccharomyces oviformis + brewer's yeast + Saccharomyces capensis + Saccharomyces uvarum var. melibiosus + NCBITaxon:4932 + Saccharomyces italicus + baker's yeast + + + Leptothecatae + Thecata + Leptomedusae + NCBITaxon:Leptothecata + Leptothecata + Calyptoblastea + NCBITaxon:500008 + + + NCBITaxon:50557 + Insecta + NCBITaxon:Insecta + true insects + + + NCBITaxon:51025 + Oxyuroidea + NCBITaxon:Oxyuroidea + + + NCBITaxon:51026 + NCBITaxon:Oxyuridae + Oxyuridae + + + NCBITaxon:Enterobius + NCBITaxon:51027 + Enterobius + + + NCBITaxon:Sordariales + Sordariales + NCBITaxon:5139 + + + Neurospora + NCBITaxon:Neurospora + NCBITaxon:5140 + + + NCBITaxon:Neurospora crassa + Neurospora crassa + NCBITaxon:5141 + + + Sordariaceae + NCBITaxon:Sordariaceae + NCBITaxon:5148 + + + NCBITaxon:542835 + NCBITaxon:Autographivirinae + Autographivirinae + + + Enterobacteraceae + NCBITaxon:543 + NCBITaxon:Enterobacteriaceae + Enterobacteriaceae + in part: gamma-3 proteobacteria + + + NCBITaxon:Tenericutes + NCBITaxon:544448 + Mollicutaeota + Tenericutes + + + NCBITaxon:5478 + NCBITaxon:Candida glabrata + Torulopsis glabrata + Candida glabrata + Cryptococcus glabratus + + + NCBITaxon:Herpesvirales + Herpesvirales + NCBITaxon:548681 + + + NCBITaxon:54986 + NCBITaxon:Fissurellidae + Fissurellidae + + + Sciuridae + NCBITaxon:55153 + NCBITaxon:Sciuridae + + + NCBITaxon:554915 + NCBITaxon:Amoebozoa + Amoebozoa + + + Tubulinea + NCBITaxon:555369 + NCBITaxon:Tubulinea + Lobosea + + + Tubulinida + NCBITaxon:555370 + NCBITaxon:Tubulinida + + + NCBITaxon:Rhabditoidea + NCBITaxon:55879 + Rhabditoidea + + + Peloderinae + NCBITaxon:55885 + NCBITaxon:Peloderinae + + + NCBITaxon:Escherichia + NCBITaxon:561 + Escherichia + + + Escherichia coli + Escherichia/Shigella coli + NCBITaxon:Escherichia coli + Bacterium coli + Bacterium coli commune + Bacillus coli + NCBITaxon:562 + Enterococcus coli + + + Kinetoplastida + kinetoplasts + NCBITaxon:Kinetoplastida + NCBITaxon:5653 + Kinetoplastea + kinetoplastids + Protomonadida + + + Trypanosomatidae + NCBITaxon:5654 + NCBITaxon:Trypanosomatidae + + + Crithidia + NCBITaxon:5655 + NCBITaxon:Crithidia + + + NCBITaxon:5690 + NCBITaxon:Trypanosoma + Trypanosoma + + + NCBITaxon:57486 + Japanese wild mouse + NCBITaxon:Mus musculus molossinus + Mus molossinus + Mus musculus molossinus + + + Amoeba + NCBITaxon:5774 + NCBITaxon:Amoeba + + + Dictyostelium + NCBITaxon:5782 + NCBITaxon:Dictyostelium + + + Tracheophyta + NCBITaxon:Tracheophyta + NCBITaxon:58023 + vascular plants + + + seed plants + NCBITaxon:Spermatophyta + Spermatophyta + NCBITaxon:58024 + + + NCBITaxon:600669 + Nakaseomyces/Candida clade + NCBITaxon:Nakaseomyces/Candida clade + + + sponges + NCBITaxon:6040 + Parazoa + NCBITaxon:Porifera + Porifera + + + NCBITaxon:6072 + Eumetazoa + NCBITaxon:Eumetazoa + + + NCBITaxon:6073 + cnidarians + coelenterates + in part: Coelenterata + NCBITaxon:Cnidaria + Cnidaria + + + NCBITaxon:6074 + Hydrozoa + NCBITaxon:Hydrozoa + hydrozoans + + + NCBITaxon:Hydridae + NCBITaxon:6080 + Hydridae + hydras + + + NCBITaxon:Hydra + Pelmatohydra + Chlorohydra + Hydra + NCBITaxon:6083 + + + NCBITaxon:6099 + NCBITaxon:Aequorea + Aequorea + + + NCBITaxon:6100 + Aequorea victoria + NCBITaxon:Aequorea victoria + + + NCBITaxon:6101 + anthozoans + Anthozoa + NCBITaxon:Anthozoa + + + Zoantharia + NCBITaxon:6102 + NCBITaxon:Hexacorallia + Hexacorallia + + + NCBITaxon:6132 + NCBITaxon:Octocorallia + Octocorallia + Alcyonaria + + + Pennatulacea + sea pansies + sea pens + NCBITaxon:6133 + NCBITaxon:Pennatulacea + + + NCBITaxon:6134 + Renilla + NCBITaxon:Renilla + + + NCBITaxon:Scyphozoa + jellyfishes + Scyphozoa + NCBITaxon:6142 + + + NCBITaxon:61462 + NCBITaxon:Gnathostomatoidea + Gnathostomatoidea + + + NCBITaxon:61463 + Gnathostoma + NCBITaxon:Gnathostoma + + + NCBITaxon:6231 + Nemata + Nematoda + roundworms + NCBITaxon:Nematoda + nematodes + + + Rhabditida + NCBITaxon:6236 + NCBITaxon:Rhabditida + + + Caenorhabditis + NCBITaxon:Caenorhabditis + NCBITaxon:6237 + + + NCBITaxon:Caenorhabditis elegans + Rhabditis elegans + NCBITaxon:6239 + Caenorhabditis elegans + + + NCBITaxon:6243 + Rhabditidae + NCBITaxon:Rhabditidae + + + Spirurida + NCBITaxon:6274 + NCBITaxon:Spirurida + + + NCBITaxon:Mollusca + mollusks + NCBITaxon:6447 + Mollusca + molluscs + + + Gastropoda + gastropods + NCBITaxon:6448 + NCBITaxon:Gastropoda + + + NCBITaxon:Patellidae + NCBITaxon:6462 + Patellidae + limpets + + + NCBITaxon:6656 + arthropods + Arthropoda + NCBITaxon:Arthropoda + + + Thermus group + NCBITaxon:Thermales + NCBITaxon:68933 + Thermales + + + NCBITaxon:693995 + Coronavirinae + NCBITaxon:Coronavirinae + + + Coronavirus group 2 + group 2 species + NCBITaxon:694002 + in part: Coronavirus + Betacoronavirus + NCBITaxon:Betacoronavirus + + + NCBITaxon:Murine coronavirus + NCBITaxon:694005 + Murine coronavirus + + + insects + NCBITaxon:Hexapoda + NCBITaxon:6960 + Hexapoda + in part: Uniramia, Tracheata, Atelocerata + + + NCBITaxon:Patellogastropoda + NCBITaxon:69675 + Patellogastropoda + Docoglossa + + + NCBITaxon:Allieae + Allieae + NCBITaxon:703248 + + + Coleoptera + NCBITaxon:Coleoptera + beetles + NCBITaxon:7041 + + + NCBITaxon:70426 + Oxyurida + NCBITaxon:Oxyurida + + + NCBITaxon:Lampyridae + fireflies + Lampyridae + firefly beetles + NCBITaxon:7049 + + + NCBITaxon:70863 + NCBITaxon:Shewanella oneidensis + Shewanella oneidensis + + + NCBITaxon:Elateroidea + NCBITaxon:71193 + Elateroidea + + + NCBITaxon:Pasteurellaceae + NCBITaxon:712 + Pasteurellaceae + + + eudicotyledons + eudicots + in part: dicotyledons, dicots, Magnoliopsida, Dicotyledoneae + NCBITaxon:71240 + NCBITaxon:eudicotyledons + + + Asteridae + asterids + NCBITaxon:71274 + NCBITaxon:asterids + + + NCBITaxon:71275 + in part: Rosidae + rosids + NCBITaxon:rosids + + + NCBITaxon:Diptera + NCBITaxon:7147 + flies + Diptera + + + Nematocera + NCBITaxon:7148 + NCBITaxon:Nematocera + + + NCBITaxon:7157 + Culicidae + mosquitos + NCBITaxon:Culicidae + + + NCBITaxon:715989 + NCBITaxon:Sordariomyceta + Sordariomyceta + + + Anopheles + NCBITaxon:7164 + NCBITaxon:Anopheles + + + Anopheles gambiae + NCBITaxon:Anopheles gambiae + NCBITaxon:7165 + Anopheles gambiae S + Anopheles gambiae sensu stricto + African malaria mosquito + + + NCBITaxon:Saccharomyceta + NCBITaxon:716545 + Saccharomyceta + + + NCBITaxon:716546 + NCBITaxon:Leotiomyceta + Leotiomyceta + + + Fabales + NCBITaxon:Fabales + NCBITaxon:72025 + + + NCBITaxon:Brachycera + NCBITaxon:7203 + Brachycera + + + NCBITaxon:Drosophilidae + Drosophilidae + NCBITaxon:7214 + pomace flies + + + NCBITaxon:7215 + Drosophila + NCBITaxon:Drosophila + fruit flies + + + NCBITaxon:7227 + Sophophora melanogaster + Drosophila melanogaster + NCBITaxon:Drosophila melanogaster + + + Pseudomonaceae/Moraxellaceae group + NCBITaxon:Pseudomonadales + NCBITaxon:72274 + in part: gamma-3 proteobacteria + Pseudomonadales + + + NCBITaxon:Haemophilus + Haemophilus + NCBITaxon:724 + + + Haemophilus influenzae + Coccobacillus pfeifferi + Bacterium influenzae + Influenza bacillus + NCBITaxon:727 + Haemophilus meningitidis + NCBITaxon:Haemophilus influenzae + Mycobacterium influenzae + + + in part: Liliiflorae, Liliales/Asparagales group + NCBITaxon:Asparagales + Asparagales + NCBITaxon:73496 + + + NCBITaxon:Pterygota + Pterygota + NCBITaxon:7496 + winged insects + + + Pasteurella pneumotropica + NCBITaxon:Rodentibacter pneumotropicus + Rodentibacter pneumotropicus + NCBITaxon:758 + + + echinoderms + Echinodermata + NCBITaxon:Echinodermata + NCBITaxon:7586 + + + Beloniformes + NCBITaxon:76071 + NCBITaxon:Beloniformes + + + NCBITaxon:Echinozoa + NCBITaxon:7624 + Echinozoa + + + Echinoidea + sea urchins + NCBITaxon:7625 + NCBITaxon:Echinoidea + + + Euechinoidea + NCBITaxon:Euechinoidea + NCBITaxon:7638 + + + Paracentrotus + NCBITaxon:7655 + NCBITaxon:Paracentrotus + + + Paracentrotus lividus + common urchin + NCBITaxon:7656 + common sea urchin + NCBITaxon:Paracentrotus lividus + + + Strongylocentrotus + NCBITaxon:Strongylocentrotus + NCBITaxon:7664 + + + purple urchin + NCBITaxon:7668 + purple sea urchin + Strongylocentrotus purpuratus + NCBITaxon:Strongylocentrotus purpuratus + + + NCBITaxon:Echinacea + NCBITaxon:7674 + Echinacea + + + Echinoida + NCBITaxon:7675 + NCBITaxon:Echinoida + + + NCBITaxon:Echinidae + NCBITaxon:7676 + Echinidae + + + NCBITaxon:76804 + NCBITaxon:Nidovirales + Nidovirales + + + NCBITaxon:Chordata + Chordata + chordates + NCBITaxon:7711 + + + NCBITaxon:Tunicata + Urochordata + tunicates + NCBITaxon:7712 + Tunicata + + + Ascidiacea + NCBITaxon:7713 + sea squirts + NCBITaxon:Ascidiacea + + + NCBITaxon:7716 + Phlebobranchia + NCBITaxon:Phlebobranchia + + + NCBITaxon:Cionidae + NCBITaxon:7717 + Cionidae + + + NCBITaxon:Ciona + Ciona + NCBITaxon:7718 + + + Ascidia intestinalis + Ciona intestinalis + NCBITaxon:Ciona intestinalis + yellow sea squirt + sea vase + vase tunicate + NCBITaxon:7719 + + + NCBITaxon:772 + Bartonellaceae + NCBITaxon:Bartonellaceae + Bartonella group + + + NCBITaxon:7720 + Stolidobranchia + NCBITaxon:Stolidobranchia + + + NCBITaxon:7727 + Pyuridae + NCBITaxon:Pyuridae + + + NCBITaxon:7728 + NCBITaxon:Halocynthia + Halocynthia + + + NCBITaxon:Halocynthia roretzi + Halocynthia roretzi + NCBITaxon:7729 + + + NCBITaxon:Bartonella + Grahamella + Rocha-Limae + NCBITaxon:773 + Grahmia + Rochalimaea + Bartonella + + + NCBITaxon:7735 + NCBITaxon:Cephalochordata + lancelets + Cephalochordata + + + lancelets + NCBITaxon:Branchiostomidae + NCBITaxon:7736 + amphioxi + amphioxius + Branchiostomatidae + Branchiostomidae + + + NCBITaxon:7737 + Branchiostoma + NCBITaxon:Branchiostoma + + + common lancelet + Branchiostoma lanceolatum + NCBITaxon:Branchiostoma lanceolatum + NCBITaxon:7740 + amphioxus + + + Vertebrata + vertebrates + NCBITaxon:7742 + NCBITaxon:Vertebrata + + + Petromyzontiformes + NCBITaxon:7745 + Petromyozoniformes + lampreys + NCBITaxon:Petromyzontiformes + + + Gnathostomata + NCBITaxon:7776 + jawed vertebrates + NCBITaxon:Gnathostomata + + + euphyllophytes + NCBITaxon:78536 + Euphyllophyta + NCBITaxon:Euphyllophyta + + + bony fishes + Actinopterygii + in part: Osteichthyes + NCBITaxon:7898 + NCBITaxon:Actinopterygii + ray-finned fishes + + + NCBITaxon:Cypriniformes + NCBITaxon:7952 + Cypriniformes + + + Cyprinidae + NCBITaxon:Cyprinidae + NCBITaxon:7953 + + + Brachydanio + Danio + Celestichthys + NCBITaxon:7954 + NCBITaxon:Danio + + + Danio rerio + Brachydanio rerio + NCBITaxon:Danio rerio + Cyprinus rerio + leopard danio + Brachydanio rerio frankei + zebra fish + Danio rerio frankei + NCBITaxon:7955 + zebrafish + zebra danio + + + Salmoniformes + NCBITaxon:Salmoniformes + NCBITaxon:8006 + + + Salmonidae + NCBITaxon:Salmonidae + NCBITaxon:8015 + salmonids + + + Oryziatinae + Oryziinae + medakas + NCBITaxon:8088 + NCBITaxon:Oryziinae + ricefishes + + + NCBITaxon:Enterococcaceae + Enterococcaceae + NCBITaxon:81852 + + + Sarcopterygii + NCBITaxon:8287 + NCBITaxon:Sarcopterygii + + + NCBITaxon:Amphibia + NCBITaxon:8292 + amphibians + Amphibia + + + NCBITaxon:8293 + salamanders + Caudata + Urodela + NCBITaxon:Caudata + + + NCBITaxon:8294 + NCBITaxon:Ambystomatidae + mole salamanders + Ambystomatidae + + + Ambystoma + NCBITaxon:8295 + big salamanders + mole salamanders + NCBITaxon:Ambystoma + + + Ambystoma mexicanum + NCBITaxon:Ambystoma mexicanum + axolotl + NCBITaxon:8296 + + + Escherichia coli K12 + Escherichia coli K-12 + NCBITaxon:Escherichia coli K-12 + NCBITaxon:83333 + + + NCBITaxon:8342 + Salientia + NCBITaxon:Anura + frogs and toads + Anura + anurans + frogs + + + NCBITaxon:8352 + tongueless frogs + Pipidae + NCBITaxon:Pipidae + pipid frogs + + + NCBITaxon:Xenopus (genus) + NCBITaxon:8353 + Xenopus (genus) + + + African clawed frog + NCBITaxon:8355 + Xenopus laevis + clawed frog + common platanna + Bufo laevis + platanna + NCBITaxon:Xenopus laevis + + + NCBITaxon:Xenopodinae + Siluraninae + Xenopodinae + NCBITaxon:8360 + + + NCBITaxon:8363 + Silurana + NCBITaxon:Silurana + Xenopus tropicalis group + + + Xenopus tropicalis + western clawed frog + NCBITaxon:8364 + Silurana tropicalis + Xenopus laevis tropicalis + NCBITaxon:Xenopus tropicalis + tropical clawed frog + + + NCBITaxon:8457 + NCBITaxon:Sauropsida + Sauropsida + sauropsids + + + NCBITaxon:Archosauria + NCBITaxon:8492 + Archosauria + + + Corynebacterineae + NCBITaxon:Corynebacteriales + NCBITaxon:85007 + Corynebacteriales + + + NCBITaxon:85011 + Streptomycetes + Streptomycetales + Streptomycineae + NCBITaxon:Streptomycetales + Streptomycetineae + + + NCBITaxon:85025 + Nocardiaceae + NCBITaxon:Nocardiaceae + + + NCBITaxon:85512 + NCBITaxon:Dicondylia + Dicondylia + + + NCBITaxon:862507 + Mus (subgenus) + NCBITaxon:Mus (subgenus) + + + NCBITaxon:Sessiliflorae + NCBITaxon:86567 + Sessiliflorae + + + NCBITaxon:86598 + Discosomatidae + NCBITaxon:Discosomatidae + + + NCBITaxon:86599 + Actinodiscus + Discosoma + NCBITaxon:Discosoma + + + NCBITaxon:8782 + NCBITaxon:Aves + avian + Aves + birds + + + NCBITaxon:8825 + Neognathae + NCBITaxon:Neognathae + + + NCBITaxon:Panarthropoda + NCBITaxon:88770 + Panarthropoda + + + Craniata + NCBITaxon:Craniata + NCBITaxon:89593 + + + Galliformes + NCBITaxon:Galliformes + NCBITaxon:8976 + fowls + + + NCBITaxon:9005 + NCBITaxon:Phasianidae + turkeys + Phasianidae + + + NCBITaxon:9030 + NCBITaxon:Gallus + Gallus + + + Gallus gallus + bantam + NCBITaxon:Gallus gallus + chicken + NCBITaxon:9031 + Gallus gallus domesticus + + + NCBITaxon:9072 + NCBITaxon:Phasianinae + Phasianinae + + + NCBITaxon:Coturnix + Coturnix + NCBITaxon:9090 + + + Staphylococcus group + NCBITaxon:Staphylococcaceae + NCBITaxon:90964 + Staphylococcaceae + Staphylococceae + + + NCBITaxon:Bacilli + NCBITaxon:91061 + Bacilli + Bacillus/Lactobacillus/Streptococcus group + + + NCBITaxon:Enterobacterales + Enterobacterales + Enterobacteriaceae group + NCBITaxon:91347 + Enterobacteriales + enterobacteria + Enterobacteriaceae and related endosymbionts + in part: gamma-3 proteobacteria + + + Cetartiodactyla + NCBITaxon:91561 + whales, hippos, ruminants, pigs, camels, etc. + NCBITaxon:Cetartiodactyla + even-toed ungulates + + + NCBITaxon:91827 + NCBITaxon:Gunneridae + Gunneridae + core eudicots + core eudicotyledons + + + NCBITaxon:91835 + fabids + eurosids I + NCBITaxon:fabids + + + NCBITaxon:91836 + NCBITaxon:malvids + malvids + + + NCBITaxon:91882 + euasterids II + campanulids + NCBITaxon:campanulids + + + NCBITaxon:lamiids + NCBITaxon:91888 + euasterids I + lamiids + + + NCBITaxon:9254 + Prototheria + NCBITaxon:Prototheria + + + NCBITaxon:Monotremata + egg-laying mammals + NCBITaxon:9255 + monotremes + Monotremata + + + NCBITaxon:9256 + NCBITaxon:Ornithorhynchidae + Ornithorhynchidae + + + NCBITaxon:9257 + Ornithorhynchus + NCBITaxon:Ornithorhynchus + + + duck-billed platypus + NCBITaxon:Ornithorhynchus anatinus + NCBITaxon:9258 + duckbill platypus + platypus + Ornithorhynchus anatinus + + + NCBITaxon:Metatheria + Marsupialia + Metatheria + marsupials + NCBITaxon:9263 + + + NCBITaxon:Eutheria + eutherian mammals + placentals + Eutheria + placental mammals + NCBITaxon:9347 + Placentalia + + + Coturnix japonica japonica + Coturnix japonica + NCBITaxon:Coturnix japonica + Coturnix coturnix Japonicus + NCBITaxon:93934 + Coturnix coturnix japonica + Coturnix coturnix japanica + Japanese quail + + + primates + NCBITaxon:Primates + NCBITaxon:9443 + Primata + Primates + + + NCBITaxon:Catarrhini + Catarrhini + NCBITaxon:9526 + + + Old World monkeys + monkeys + Cercopithecidae + NCBITaxon:Cercopithecidae + NCBITaxon:9527 + + + Cercopithecinae + NCBITaxon:Cercopithecinae + NCBITaxon:9528 + + + macaques + Macaca + NCBITaxon:9539 + NCBITaxon:Macaca + + + NCBITaxon:Pan + chimpanzees + Pan + NCBITaxon:9596 + + + Pan troglodytes + NCBITaxon:9598 + chimpanzee + NCBITaxon:Pan troglodytes + + + NCBITaxon:Hominidae + great apes + Hominidae + NCBITaxon:9604 + Pongidae + + + NCBITaxon:9605 + Homo + humans + NCBITaxon:Homo + + + NCBITaxon:9606 + human + NCBITaxon:Homo sapiens + man + Homo sapiens + + + NCBITaxon:Canidae + NCBITaxon:9608 + dogs, coyotes, wolves and foxes + Canidae + + + Canis + NCBITaxon:Canis + NCBITaxon:9611 + + + Canis lupus + gray wolf + NCBITaxon:9612 + grey wolf + NCBITaxon:Canis lupus + + + NCBITaxon:Canis lupus familiaris + NCBITaxon:9615 + Canis canis + Canis familiaris + dogs + Canis domesticus + Canis lupus familiaris + + + Procyonidae + NCBITaxon:Procyonidae + NCBITaxon:9647 + raccoons, coatis and olingos + + + Procyon + NCBITaxon:9653 + NCBITaxon:Procyon + + + Procyon lotor + raccoon + Northern raccoon + NCBITaxon:9654 + NCBITaxon:Procyon lotor + + + NCBITaxon:Felidae + cat family + NCBITaxon:9681 + Felidae + + + Felis + NCBITaxon:9682 + NCBITaxon:Felis + + + domestic cat + Felis silvestris catus + NCBITaxon:9685 + Felis domesticus + NCBITaxon:Felis catus + Felis catus + cats + + + NCBITaxon:9787 + NCBITaxon:Perissodactyla + odd-toed ungulates + Perissodactyla + + + Equidae + horses + NCBITaxon:9788 + NCBITaxon:Equidae + + + Equus (genus) + NCBITaxon:9789 + NCBITaxon:Equus (genus) + + + NCBITaxon:9793 + African wild ass + NCBITaxon:Equus asinus + African ass + donkey + domestic ass + Somali wild ass + Equus asinus + ass + + + horse + Equus przewalskii forma caballus + domestic horse + NCBITaxon:9796 + Equus przewalskii f. caballus + equine + Equus caballus + NCBITaxon:Equus caballus + + + NCBITaxon:Camelineae + NCBITaxon:980083 + Camelineae + + + NCBITaxon:Cardamineae + Cardamineae + NCBITaxon:980193 + + + NCBITaxon:9845 + NCBITaxon:Ruminantia + Ruminantia + in part: Artiodactyla + + + NCBITaxon:Bovidae + Bovidae + NCBITaxon:9895 + + + oxen and cattle + NCBITaxon:Bos + Bos + NCBITaxon:9903 + + + cow + Bos taurus + cattle + bovine + Bos bovis + domestic cow + domestic cattle + Bos primigenius taurus + NCBITaxon:9913 + NCBITaxon:Bos taurus + + + Capra + NCBITaxon:Capra + NCBITaxon:9922 + + + goat + NCBITaxon:Capra hircus + Capra aegagrus hircus + Capra hircus + NCBITaxon:9925 + domestic goat + + + Ovis + NCBITaxon:Ovis + NCBITaxon:9935 + + + Ovis aries + sheep + domestic sheep + NCBITaxon:Ovis aries + lambs + NCBITaxon:9940 + Ovis ammon aries + wild sheep + Ovis ovis + Ovis orientalis aries + + + NCBITaxon:9963 + NCBITaxon:Caprinae + Caprinae + + + NCBITaxon:Lagomorpha + rabbits and hares + Lagomorpha + NCBITaxon:9975 + + + Leporidae + NCBITaxon:9979 + NCBITaxon:Leporidae + rabbits and hares + + + NCBITaxon:Oryctolagus + Oryctolagus + NCBITaxon:9984 + + + European rabbit + Oryctolagus cuniculus + rabbit + domestic rabbit + Japanese white rabbit + NCBITaxon:Oryctolagus cuniculus + NCBITaxon:9986 + + + Tetraodon nigroviridis + spotted green pufferfish + NCBITaxon:99883 + NCBITaxon:Tetraodon nigroviridis + + + rodents + NCBITaxon:9989 + Rodentia + NCBITaxon:Rodentia + + + NCBITaxon:'Human immunodeficiency virus 1' or NCBITaxon:'Human immunodeficiency virus 2' or NCBITaxon:'Human immunodeficiency virus' + NCBITaxon_EXT:HIV + HIV + NCBITaxon_EXT:HIV + human immunodeficiency virus + + + NCBITaxon_EXT:HSV + NCBITaxon_EXT:HSV + NCBITaxon:'Human alphaherpesvirus 1' or NCBITaxon:'Human alphaherpesvirus 2' + HSV + herpes simplex virus + + + NCBITaxon:7959 or NCBITaxon:7962 or NCBITaxon:7965 or NCBITaxon:13095 or NCBITaxon:52617 or NCBITaxon:52657 or NCBITaxon:75348 or NCBITaxon:76593 or NCBITaxon:76932 or NCBITaxon:101364 or NCBITaxon:101840 or NCBITaxon:138676 or NCBITaxon:145527 or NCBITaxon:160766 or NCBITaxon:172907 or NCBITaxon:182801 or NCBITaxon:205124 or NCBITaxon:210633 or NCBITaxon:217509 or NCBITaxon:227286 or NCBITaxon:238031 or NCBITaxon:263515 or NCBITaxon:327762 or NCBITaxon:329116 or NCBITaxon:367866 or NCBITaxon:564874 or NCBITaxon:643345 or NCBITaxon:643366 or NCBITaxon:643380 or NCBITaxon:657186 or NCBITaxon:670200 or NCBITaxon:763460 or NCBITaxon:932675 or NCBITaxon:999361 or NCBITaxon:1211648 or NCBITaxon:1217998 or NCBITaxon:1218010 or NCBITaxon:1240730 or NCBITaxon:1752860 + NCBITaxon_EXT:carp + carp + NCBITaxon_EXT:carp + + + NCBITaxon_EXT:fish + NCBITaxon_EXT:fish + fish + NCBITaxon:Chondrichthyes or NCBITaxon:Dipnoi or NCBITaxon:Actinopterygii or NCBITaxon:Hyperoartia or NCBITaxon:Hyperotreti or NCBITaxon:Coelicanthimorpha + + + NCBITaxon_EXT:ground squirrel + ground squirrel + NCBITaxon_EXT:ground_squirrel + NCBITaxon:'Atlantoxerus getulus' or NCBITaxon:Callospermophilus or NCBITaxon:'Dremomys pernyi' or NCBITaxon:Ictidomys or NCBITaxon:'Lariscus insignis' or NCBITaxon:'Lariscus niobe' or NCBITaxon:'Menetes berdmorei' or NCBITaxon:Notocitellus or NCBITaxon:Otospermophilus or NCBITaxon:'Poliocitellus franklinii' or NCBITaxon:'Rheithrosciurus macrotis' or NCBITaxon:Spermophilus or NCBITaxon:Urocitellus or NCBITaxon:Xerospermophilus or NCBITaxon:Xerus + + + NCBITaxon:Metazoa and not NCBITaxon:Vertebrata + NCBITaxon_EXT:invertebrate + NCBITaxon_EXT:invertebrate + invertebrate + + + monkey + NCBITaxon_EXT:monkey + NCBITaxon_EXT:monkey + NCBITaxon:Cercopithecidae or NCBITaxon:Platyrrhini + + + NCBITaxon_EXT:quail + quail + NCBITaxon:'Coturnix chinensis' or NCBITaxon:'Coturnix coturnix' or NCBITaxon:'Coturnix delegorguei' or NCBITaxon:'Coturnix japonica' or NCBITaxon:'Coturnix pectoralis' or NCBITaxon:'Coturnix ypsilophora' or NCBITaxon:'Crex crex' or NCBITaxon:Odontophoridae or NCBITaxon:'Perdicula asiatica' or NCBITaxon:'Perdicula erythrorhyncha' or NCBITaxon:'Synoicus australis' + NCBITaxon_EXT:quail + + + NCBITaxon:Crocodylia or NCBITaxon:Lepidosauria or NCBITaxon:Testudines + reptile + NCBITaxon_EXT:reptile + NCBITaxon_EXT:reptile + + + NCBITaxon_EXT:ungulate + NCBITaxon_EXT:ungulate + ungulate + NCBITaxon:Cetartiodactyla or NCBITaxon:Perissodactyla + + + NCBITaxon:Acanthocephala or NCBITaxon:Annelida or NCBITaxon:Chaetognatha or NCBITaxon:Enteropneusta or NCBITaxon:Entoprocta or NCBITaxon:Nematoda or NCBITaxon:Nematomorpha or NCBITaxon:Nemertea or NCBITaxon:Onychophora or NCBITaxon:Pentastomida or NCBITaxon:Phorononiformea or NCBITaxon:Platyhelminthes or NCBITaxon:Priapulida or NCBITaxon:Teredinidae + NCBITaxon_EXT:worm + worm + NCBITaxon_EXT:worm + + + yeast + NCBITaxon_EXT:yeast + NCBITaxon:Chaetothyriales or NCBITaxon:'Cystobasidium sp. BG02-6-15-006A-1' or NCBITaxon:'Cystobasidium sp. CBS 8913' or NCBITaxon:'Cystobasidium sp. CBS 8923' or NCBITaxon:'Galactomyces sp. HIT-BY2' or NCBITaxon:Saccharomycotina or NCBITaxon:Schizosaccharomycetaceae or NCBITaxon:'Takashimella tepidaria' + NCBITaxon_EXT:yeast + + + (NCBITaxon:Bovidae or NCBITaxon:Camelus or NCBITaxon:Cervidae or NCBITaxon:Emetopias or NCBITaxon:Giraffidae or NCBITaxon:Hippopotamidae or NCBITaxon:Mirounga or NCBITaxon:Neophoca or NCBITaxon:Odobenidae or NCBITaxon:Otaria or NCBITaxon:Phocarctos or NCBITaxon:Proboscidea or NCBITaxon:Rhinocerotidae or NCBITaxon:Sirenia or NCBITaxon:Tapiridae or NCBITaxon:'Varanus komodoensis' or NCBITaxon:'Vicugna vicugna' or NCBITaxon:Zalophus) and (UBERON:'sexually immature organism' or bearer_of some (PATO:juvenile or PATO:young)) + For: calf/calves + calf + NCBITaxon_UBERON_EXT:calf + NCBITaxon_UBERON_EXT:calf + + + chick + NCBITaxon:Aves and (UBERON:'sexually immature organism' or bearer_of some (PATO:juvenile or PATO:young)) + For: chick/chicks + NCBITaxon_UBERON_EXT:chick + NCBITaxon_UBERON_EXT:chick + + + NCBITaxon_UBERON_EXT:child + child + NCBITaxon_UBERON_EXT:child + For: child/children + NCBITaxon:'Homo sapiens' and (UBERON:'sexually immature organism' or bearer_of some (PATO:juvenile or PATO:young)) + + + NCBITaxon_UBERON_EXT:girl + girl + For: girl/girls + NCBITaxon:'Homo sapiens' and PATO_UBERON_EXT:female_or_bearer_of_femaleness and (UBERON:'sexually immature organism' or bearer_of some (PATO:juvenile or PATO:young)) + NCBITaxon_UBERON_EXT:girl + + + For: man/men (male human(s)) +Not for: man (human) + NCBITaxon_UBERON_EXT:man + NCBITaxon:'Homo sapiens' and PATO_UBERON_EXT:male_or_bearer_of_maleness and (UBERON:'adult organism' or bearer_of some PATO:mature) + man + NCBITaxon_UBERON_EXT:man + male human + + + mare + For: mare/mares + NCBITaxon_UBERON_EXT:mare + NCBITaxon_UBERON_EXT:mare + NCBITaxon:Equidae and PATO_UBERON_EXT:female_or_bearer_of_femaleness + + + pup + For: pup(s) + NCBITaxon_UBERON_EXT:pup + NCBITaxon_UBERON_EXT:pup + (NCBITaxon:Canidae or NCBITaxon:Castoridae or NCBITaxon:Cavia or NCBITaxon:Chiroptera or NCBITaxon:Cingulata or NCBITaxon:Cricetinae or NCBITaxon:Cynomys or NCBITaxon:Delphinidae or NCBITaxon:Erethizontidae or NCBITaxon:Erinaceidae or NCBITaxon:Folivora or NCBITaxon:Gerbilliinae or NCBITaxon:Herpestidae or NCBITaxon:Hyaenidae or NCBITaxon:Hystricidae or NCBITaxon:Lutrinae or NCBITaxon:Mus or NCBITaxon:Nasua or NCBITaxon:Nasuella or NCBITaxon:Otariidae or NCBITaxon:Phocidae or NCBITaxon:Platanistidae or NCBITaxon:Pontoporiidae or NCBITaxon:Potos or NCBITaxon:Rattus or NCBITaxon:Sciuridae or NCBITaxon:Selachii or NCBITaxon:Talpidae) and (UBERON:'sexually immature organism' or bearer_of some (PATO:juvenile or PATO:young)) + + + NCBITaxon_UBERON_EXT:woman + For: woman/women + woman + NCBITaxon:'Homo sapiens' and PATO_UBERON_EXT:female_or_bearer_of_femaleness and (UBERON:'adult organism' or bearer_of some PATO:mature) + NCBITaxon_UBERON_EXT:woman + + + NCBITaxon extension classes + + + NCBITaxon:kingdom + kingdom + NCBITaxon:kingdom + + + NCBITaxon:phylum + NCBITaxon:phylum + phylum + + + NCBITaxon:species + species + NCBITaxon:species + + + NCBITaxon:subspecies + NCBITaxon:subspecies + subspecies + + + taxonomic_rank + NCBITaxon:taxonomic_rank + NCBITaxon:taxonomic_rank + + + For: genetics + (OBI:investigation and achieves_planned_objective o is_about some SO_EXT:gene) or (GO:biological_process and has_participant some SO_EXT:gene) + OBI_SO_EXT:genetic investigation or process + OBI_SO_EXT:gene_or_genetic_investigation_or_genetic_process + genetic investigation or process + genetics + + + aneuploid + aneuploidy + PATO_SO_EXT:aneuploidy + For: aneuploid(y) + PATO:aneuploid or SO_EXT:aneuploid + PATO_SO_EXT:aneuploidy + + + PATO_UBERON_EXT:bone or boniness + bony + osseous + PATO_UBERON_EXT:bone_or_boniness + PATO:osseous or UBERON:'bone tissue' + For: bony, osseous + bone or boniness + + + female + UBERON:'female organism' or bearer_of some PATO:female + For: female/females + PATO_UBERON_EXT:female organism/bearer of femaleness + PATO_UBERON_EXT:female_or_bearer_of_femaleness + female organism/bearer of femaleness + + + (UBERON:'multicellular organism' and bearer_of some PATO:juvenile) or UBERON:'sexually immature organism' + PATO_UBERON_EXT:juvenile_organism + For: juvenile/juveniles + juvenile organism + juvenile + PATO_UBERON_EXT:juvenile organism + + + PATO_UBERON_EXT:male_or_bearer_of_maleness + PATO_UBERON_EXT:male organism/bearer of maleness + UBERON:'male organism' or bearer_of some PATO:male + male + male organism/bearer of maleness + For: male/males + + + neonate + For: neonate(s), neonatal(ly), newborn(s), newly born + neonatal/newborn organism + newborn + PATO_UBERON_EXT:neonate_or_newborn + PATO_UBERON_EXT:neonatal/newborn organism + neonatal + (UBERON:'multicellular organism' and existence_starts_with some UBERON:'neonate stage' and existence_ends_with some UBERON:'neonate stage') or bearer_of some PATO:neonatal + + + trabecular + PATO_UBERON_EXT:trabeculation entity or quality + trabeculated + PATO:trabecular or UBERON:trabecula + trabeculation entity or quality + PATO_UBERON_EXT:trabeculation_entity_or_quality + For: trabecular/trabeculated + + + PR:000025402 + T cell receptor co-receptor CD8 + CD8alphabeta + TCR co-receptor CD8 + PR:T cell receptor co-receptor CD8 + "A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction." [PMID:18275828, PMID:3264320, PRO:DAN] + + + PR:000026878 + active caspase-3 + caspase-3 complex + PR:caspase-3 complex + "A caspase complex that is composed of p12 and p17 subunits of caspase-3." [PMID:9045680, PMID:9202418] + + + PR_EXT:000000001 + protein + "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA." [PRO:DAN, PRO:WCB] + PR_EXT:protein + + + TRANSFORMING GROWTH FACTOR-BETA RECEPTOR TYPE I (PTHR23255:SF15) + "A protein that is a translation product of an evolutionary-related gene with core domain composition consisting of an extracellular Activin types I and II receptor domain (Pfam:PF01064), a transmembrane domain, a Transforming growth factor beta type I GS-motif (Pfam:PF08515) and a Protein kinase domain (Pfam:PF00069). The transforming growth factor-beta (TGF-beta) superfamily of receptors comprises two groups of transmembrane serine-threonine kinase receptors, so called type-1, and type-2 receptors, that are activated following engagement by members of the TGF-beta superfamily of ligands. These events specify diverse downstream responses that are differentially regulated by controlling access and activation of the ligands, their receptors and downstream substrates in different cell types. The type 1 receptors are characterized by the presence of a glycine-serine rich juxta-membrane domain (the GS-motif) that is critical for their activation." [PRO:CNA] + PR_EXT:000000006 + TGF-beta superfamily receptor type-1 + PR_EXT:TGF-beta superfamily receptor type-1 + + + TGF-beta superfamily receptor type-2 with activin receptor domain + "A protein that is a translation product of an evolutionary-related gene with core domain composition consisting of an extracellular Activin types I and II receptor domain (Pfam:PF01064), a transmembrane domain, and a Protein kinase domain (Pfam:PF00069). The transforming growth factor-beta (TGF-beta) superfamily of receptors comprises two groups of transmembrane serine-threonine kinase receptors, so called type-1, and type-2 receptors, that are activated following engagement by members of the TGF-beta superfamily of ligands. These events specify diverse downstream responses that are differentially regulated by controlling access and activation of the ligands, their receptors and downstream substrates in different cell types." [PRO:CNA] + PR_EXT:000000007 + PR_EXT:TGF-beta superfamily receptor type-2 with activin receptor domain + + + PR_EXT:TGF-beta-like cystine-knot cytokine + TGF-beta-like cystine-knot cytokine + PR_EXT:000000008 + "A protein with a core domain composition consisting of a signal peptide, a variable propeptide region and a Transforming growth factor beta like domain (Pfam:PF00019), which is a cystine-knot domain containing four conserved beta strands, S1-S4, which form two antiparallel beta sheets (SI-S2 and S3-S4) interconnected by three disulfide bridges in a knot-like topology. Cystines [II-V] and [III-VI] form a ring through which the remaining disulfide bond (Cys[I-IV]) penetrates. Insertion of different variable regions into this common motif has given rise to various subclasses of the growth factor cystine-knot domain." [PRO:CNA] + TGF-beta superfamily + + + PR_EXT:chordin + PR_EXT:000000010 + CHRD + "A protein that is a translation product of the human CHRD gene or a 1:1 ortholog thereof. Chordin regulates signaling by BMP pathway." [PRO:CNA] + chordin + + + "A protein with a core domain composition consisting of eight to ten tandem leucine-rich repeat sequences that are flanked at either end by cysteine rich disulfide loops." [PMID:14562268] + PR_EXT:class 1 small leucine-rich proteoglycan + PR_EXT:000000011 + class 1 small leucine-rich proteoglycan + + + cyclin-dependent kinase inhibitor + "A protein with a core domain composition consisting of four ankyrin repeats, and that functions as negative regulator of cyclin-dependent kinases." [PRO:CNA] + PR_EXT:000000014 + PR_EXT:cyclin-dependent kinase inhibitor + + + "A type II interferon that is a translation product of the human IFNG gene or a 1:1 ortholog thereof. The core domain structure consists of an Interferon gamma domain (Pfam:PF00714) that is four-helical cytokine domain with an additional helix in one of the crossover connections. It is a cytokine produced by lymphocytes activated by specific antigens or mitogens that has important immunoregulatory functions." [PRO:CNA] + IFN-gamma + IFNG + PR_EXT:interferon gamma + immune interferon + interferon gamma + PR_EXT:000000017 + + + mitogen-activated protein kinase + "A protein that is a serine/threonine-specific protein kinase that responds to extracellular stimuli (mitogens) and regulates cellular activities such as gene expression, mitosis, differentiation, and cell survival/apoptosis. The activated form phosphorylates target substrates on Ser or Thr residues followed by a proline. A distinguishing feature is the conserved sequence TxY." [PRO:CNA, Wikipedia:Mitogen-activated_protein_kinase] + PR_EXT:000000019 + PR_EXT:mitogen-activated protein kinase + kinase-related transforming protein + MAPK + + + PR_EXT:000000020 + "A protein that belongs to the clade B of the bHLH proteins (see PMID:20219281) with a core domain composition consisting of a Myc amino-terminal region (Pfam:PF01056) regulatory domain (known as TAD domain), a helix-loop-helix DNA-binding domain (Pfam:PF00010). Some members such as c-Myc contains an addition C-terminal Myc leucine zipper domain (Pfam:PF02344). Myc proteins participate in the regulation of cell proliferation, cell differentiation, and apoptosis." [PMID:16113099, PMID:16537894, PMID:16543245, PRO:CNA] + myc protein + PR_EXT:myc protein + + + "A protein that is a translation product of the human NOG gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:noggin + PR_EXT:000000021 + noggin + NOG + + + "A protein with a core domain composition consisting of a Retinoblastoma-associated protein A domain (Pfam:PF01858) followed by a Retinoblastoma-associated protein B domain (Pfam:PF01857). The retinoblastoma-like proteins are key regulators of entry into cell division. They are directly involved in heterochromatin formation by maintaining overall chromatin structure and, in particular, that of constitutive heterochromatin by stabilizing histone methylation." [PRO:CNA] + PR_EXT:000000023 + retinoblastoma-like protein + PR_EXT:retinoblastoma-like protein + + + "A protein with core domain composition consisting of one MH1 domain (Pfam:PF03165) at the N terminus and one MH2 domain (Pfam:PF03166) at the C-terminus, separated by a non-conserved linker region. Smad proteins are mediators of signal transduction in transforming growth factor beta (TGF-beta) superfamily pathways." [PRO:CNA] + PR_EXT:smad protein + smad protein + PR_EXT:000000027 + + + PR_EXT:000000031 + "A protein with a core domain composition consisting of a TAZ zinc finger (Pfam:PF02135) domain, a KIX domain (Pfam:PF02172), a Bromodomain (Pfam:PF00439), a dystrophin zinc finger domain, and a second copy of the TAZ zinc finger (Pfam:PF02135) domain." [PRO:CNA] + fam:CBP-p300 + PR_EXT:transcription adapter with TAZ, KIX and bromo-domains + transcription adapter with TAZ, KIX and bromo-domains + + + PR_EXT:000000032 + PR_EXT:transcription factor Sp + transcription factor Sp + "A protein that is a translation product of an evolutionary-related gene with core domain composition consisting of N-terminal serine/threonine stretches adjacent to one or two glutamine-rich domains, which constitute the activation domains, and three copies of the Zinc finger, C2H2 type (Pfam:PF00096) domain at the C-terminus that are involved in binding GC/GT-rich promoter elements." [PMID:16209919] + + + PR_EXT:000000033 + tumor necrosis factor, TNF-like + PR_EXT:tumor necrosis factor, TNF-like + "A protein with a core domain composition consisting of an N-terminal cytosolic domain, a type II transmembrane domain and a C-terminal TNF domain (Pfam:PF00229)." [PRO:CNA] + + + PR_EXT:BMP + BMP + "A TGF-beta-like cystine-knot cytokine that is related to the transforming growth factor-beta, anti-Muellerian hormone, and activin/inhibin protein families, which are all involved in the regulation of cell growth and differentiation. These are produced as dimeric precursors and undergo post-translational processing for activation, requiring cleavage to release bioactive the C-terminal peptide. BMP is involved in body patterning and morphogenesis. BMP signals are transmitted through specific type 2 and type 1 receptors." [PIRSF:PIRSF037272] + PR_EXT:000000034 + + + PR_EXT:000000035 + BMPR-1A + PR_EXT:BMP receptor type-1A + BMP-2/BMP-4 receptor + BMP type-1A receptor + SKR5 + BMPR1A + ALK3 + ACVRLK3 + BMP receptor type-1A + "A TGF-beta superfamily receptor type-1 that is a translation product of the human BMPR1A gene or a 1:1 ortholog thereof. Bone morphogenetic protein (BMP) signals are transmitted by type 2 and type 1 serine/threonine kinase receptors. Type 2 receptors phosphorylate and activate type 1 receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. Receptor for BMP2 and BMP4." [PRO:CNA] + Bmpr + ALK-3 + serine/threonine-protein kinase receptor R5 + CD292 + activin receptor-like kinase 3 + + + BMP type-1B receptor + PR_EXT:BMP receptor type-1B + BMPR-1B + CDw293 + Acvrlk6 + BMPR1B + PR_EXT:000000036 + BMP receptor type-1B + SKR6 + "A TGF-beta superfamily receptor type-1 that is a translation product of the human BMPR1B gene or a 1:1 ortholog thereof. Bone morphogenetic protein (BMP) signals are transmitted by type 2 and type 1 serine/threonine kinase receptors. Type 2 receptors phosphorylate and activate type 1 receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. Receptor for BMPS/OP-1." [PRO:CNA] + serine/threonine-protein kinase receptor R6 + ALK-6 + activin receptor-like kinase 6 + + + BMP type-2 receptor + BMPR-2 + BRK-3 + BMP type II receptor + "A TGF-beta superfamily receptor type-2 with activin receptor domain that is a translation product of the human BMPR2 gene or a 1:1 ortholog thereof. Bone morphogenetic protein (BMP) signals are transmitted by type 2 and type 1 serine/threonine kinase receptors. Type 2 receptors phosphorylate and activate type 1 receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators." [PRO:CNA] + PR_EXT:BMP receptor type-2 + BMPR2 + PPH1 + bone morphogenetic protein receptor type II + BMPR-II + BMP receptor type-2 + PR_EXT:000000037 + + + PR_EXT:BMP receptor-regulated smad protein + R-SMAD(BMP) + "A smad protein that mediates signal transduction through activation of bone morphogenetic protein (BMP) or anti-Mullerian hormone pathways." [PMID:11532220] + PR_EXT:000000038 + BMP receptor-regulated smad protein + + + PR_EXT:TGF-beta + PR_EXT:000000046 + TGF-beta + "A TGF-beta-like cystine-knot cytokine whose propeptide region is a latent associated peptide (LAP) that remains associated to the mature TGF-beta after cleavage and secretion, keeping TGF-beta inactive. TGF-beta is the founding member of the cystine-knot cytokine family, and is related to the activin/inhibin, anti-Muellerian hormone, and bone morphogenic protein families, which are all involved in the regulation of cell growth and differentiation." [PIRSF:PIRSF001787] + transforming growth factor beta + + + transforming growth factor-beta receptor type I + TGFR-1 + TGF-beta type I receptor + PR_EXT:TGF-beta receptor type-1 + "A TGF-beta superfamily receptor type-1 that is a translation product of the human TGFBR1 gene or a 1:1 ortholog thereof." [PRO:CNA] + TbetaR-I + serine/threonine-protein kinase receptor R4 + ALK-5 + TGF-beta receptor type-1 + TGFBR1 + activin receptor-like kinase 5 + PR_EXT:000000047 + TGF-beta receptor type I + ESK2 + SKR4 + + + R-SMAD(TGFB) + TGF-beta receptor-regulated smad protein + PR_EXT:TGF-beta receptor-regulated smad protein + PR_EXT:000000066 + "A smad protein that mediates signal transduction through activation of transforming growth factor beta (TGF-beta) or activin pathways." [PMID:11532220] + + + ACTR-I + "A TGF-beta superfamily receptor type-1 that is a translation product of the human ACVR1 gene or a 1:1 ortholog thereof." [PRO:CNA] + TGF-B superfamily receptor type I + ALK-2 + serine/threonine-protein kinase receptor R1 + activin receptor type-1 + activin receptor-like kinase 2 + Tgfb1 + activin receptor type I + PR_EXT:activin receptor type-1 + ACVR1 + ACVRLK2 + TSK-7L + SKR1 + TSR-I + PR_EXT:000000067 + + + PR_EXT:activin receptor type-2A + ACTRIIA + activin receptor type IIA + ACTR-IIA + PR_EXT:000000070 + "A TGF-beta superfamily receptor type-2 with activin receptor domain that is a translation product of the human ACVR2A gene or a 1:1 ortholog thereof." [PRO:CNA] + ACVR2 + ACVR2A + activin receptor type-2A + + + PR_EXT:activin receptor type-2B + "A TGF-beta superfamily receptor type-2 with activin receptor domain that is a translation product of the human ACVR2B gene or a 1:1 ortholog thereof." [PRO:CNA] + ACVR2B + ACTR-IIB + activin receptor type IIB + PR_EXT:000000071 + activin receptor type-2B + + + PR_EXT:activin/inhibin beta subunit + "A TGF-beta-like cystine-knot cytokine that is the beta subunit of inhibin and activin complexes. Related to the transforming growth factor-beta, anti-Muellerian hormone, and bone morphogenic protein families which are all involved in the regulation of cell growth and differentiation." [PRO:CNA] + PR_EXT:000000072 + activin/inhibin beta subunit + + + "A TGF-beta-like cystine-knot cytokine that is a translation product of the human AMH gene or a 1:1 ortholog thereof. Related to the transforming growth factor-beta, activin/inhibin, and bone morphogenic protein families which are all involved in the regulation of cell growth and differentiation." [PRO:CNA] + anti-Muellerian hormone + PR_EXT:anti-Muellerian hormone + MIF + PR_EXT:000000073 + MIS + AMH + muellerian-inhibiting substance + + + "A myc protein that is a translation product of the human MYC gene or a 1:1 ortholog thereof. The gene has 3 exons, with exon 1 lacking ATG codons." [PRO:CNA] + proto-oncogene c-Myc + bHLHe39 + c-myc protein + PR_EXT:c-myc protein + MYC + PR_EXT:000000084 + transcription factor p64 + class E basic helix-loop-helix protein 39 + + + "A class 1 small leucine-rich proteoglycan that is a translation product of the human DCN gene or a 1:1 ortholog thereof." [PRO:CNA] + DCN + PG40 + SLRR1B + bone proteoglycan II + PR_EXT:decorin + PR_EXT:000000094 + PG-S2 + decorin + + + "A TGF-beta-like cystine-knot cytokine that is closely related to the BMP family. These are produced as dimeric precursors and undergo post-translational processing for activation, requiring cleavage to release the bioactive C-terminal peptide. GDFs act as signaling molecules during embryonic tendon/ligament formation." [PRO:CNA] + PR_EXT:growth/differentiation factor + growth/differentiation factor + PR_EXT:000000098 + + + "A TGF-beta-like cystine-knot cytokine that is an antagonist of nodal signaling. The nodal and lefty genes form positive and negative regulatory loops that resemble the reaction-diffusion system. As a pair, these genes control various events of vertebrate embryonic patterning, including left-right specification and mesoderm formation." [PRO:CNA] + PR_EXT:lefty protein + PR_EXT:000000102 + lefty protein + + + mitogen-activated protein kinase 1 + MAPK 2 + MAPK 1 + MAP kinase isoform p42 + "A mitogen-activated protein kinase that is a translation product of the human MAPK1 gene or a 1:1 ortholog thereof." [PRO:CNA] + ERK-2 + MAPK1 + ERT1 + PR_EXT:mitogen-activated protein kinase 1 + p42-MAPK + PR_EXT:000000103 + mitogen-activated protein kinase 2 + ERK2 + MAP kinase 2 + Mapk + MAP kinase 1 + PRKM2 + extracellular signal-regulated kinase 2 + PRKM1 + + + insulin-stimulated MAP2 kinase + MAP kinase isoform p44 + PRKM3 + mitogen-activated protein kinase 3 + MAP kinase 3 + "A mitogen-activated protein kinase that is a translation product of the human MAPK3 gene or a 1:1 ortholog thereof." [PRO:CNA] + ERK1 + mitogen-activated protein kinase 1 + MNK1 + MAP kinase 1 + ERK-1 + MAPK 3 + MAPK3 + p44-ERK1 + MAPK 1 + ERT2 + PR_EXT:000000104 + PR_EXT:mitogen-activated protein kinase 3 + p44-MAPK + microtubule-associated protein 2 kinase + extracellular signal-regulated kinase 1 + + + NODAL + PR_EXT:000000105 + "A TGF-beta-like cystine-knot cytokine that is a translation product of the human NODAL gene or a 1:1 ortholog thereof. The nodal and lefty genes form positive and negative regulatory loops that resemble the reaction-diffusion system. As a pair, these genes control various events of vertebrate embryonic patterning, including left-right specification and mesoderm formation." [PRO:CNA] + PR_EXT:nodal protein + nodal protein + + + pRb1 + retinoblastoma-like protein 1 + "A retinoblastoma-like protein that is a translation product of the human RBL1 gene or a 1:1 ortholog thereof." [PRO:CNA] + RBL1 + PR_EXT:retinoblastoma-like protein 1 + 107 kDa retinoblastoma-associated protein + PR_EXT:000000118 + + + SP1 + PR_EXT:transcription factor Sp1 + PR_EXT:000000133 + "A transcription factor Sp that is a translation product of the human SP1 gene or a 1:1 ortholog thereof. It comprises the exons that code for an N-terminal inhibitory domain, two serine/threonine stretches adjacent to activation domains and three zinc fingers." [PRO:CNA] + TSFP1 + transcription factor Sp1 + + + TNFA + tumor necrosis factor alpha + cachectin + PR_EXT:000000134 + TNFSF2 + tumor necrosis factor ligand superfamily member 2 + TNF-alpha + TNF + "A tumor necrosis factor, TNF-like that is a translation product of the human TNF gene or a 1:1 ortholog thereof. Tumour necrosis factor alpha (TNF) is a pleiotropic cytokine that mediates apoptosis, cell proliferation, immunomodulation, inflammation, viral replication, allergy, arthritis, septic shock, insulin resistance, autoimmune diseases, and other pathological conditions. TNF transduces these cellular responses through two distinct receptors: type I, which are expressed on all cell types, and type II, which are expressed only on cells of the immune system and endothelial cells." [PMID:11053079, PRO:CNA] + TNF-a + PR_EXT:tumor necrosis factor alpha + + + BMP2 + PR_EXT:000000164 + BMP-2 + BMP-2A + BMP2A + bone morphogenetic protein 2A + PR_EXT:BMP2 + "A BMP that is a translation product of the human BMP2 gene or a 1:1 ortholog thereof." [PRO:CNA] + BMP2 + + + PR_EXT:000000165 + BMP-4 + "A BMP that is a translation product of the human BMP4 gene or a 1:1 ortholog thereof." [PRO:CNA] + BMP-2B + bone morphogenetic protein 2B + PR_EXT:BMP4 + BMP2B + DVR4 + BMP4 + Dvr-4 + BMP4 + + + "A BMP that is a translation product of the human BMP5 gene or a 1:1 ortholog thereof." [PRO:CNA] + BMP5 + PR_EXT:000000166 + PR_EXT:BMP5 + BMP5 + BMP-5 + + + Vgr1 + BMP6 + PR_EXT:000000167 + VGR + VGR-1 + "A BMP that is a translation product of the human BMP6 gene or a 1:1 ortholog thereof." [PRO:CNA] + VG-1-related protein + BMP6 + PR_EXT:BMP6 + VG-1-R + BMP-6 + + + BMP7 + OP1 + "A BMP that is a translation product of the human BMP7 gene or a 1:1 ortholog thereof." [PRO:CNA] + osteogenic protein 1 + OP-1 + BMP7 + PR_EXT:BMP7 + eptotermin alfa + BMP-7 + PR_EXT:000000168 + + + TGF-beta 1 + TGFB1 + PR_EXT:TGF-beta 1 + TGFB + PR_EXT:000000182 + "A TGF-beta that is a translation product of the human TGFB1 gene or a 1:1 ortholog thereof." [PRO:CNA] + TGF-beta-1 + + + TGF-beta 2 + BSC-1 cell growth inhibitor + cetermin + polyergin + TGFB2 + "A TGF-beta that is a translation product of the human TGFB2 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:000000183 + PR_EXT:TGF-beta 2 + glioblastoma-derived T-cell suppressor factor + G-TSF + TGF-beta-2 + + + PR_EXT:000000216 + PR_EXT:activin/inhibin beta A chain + INHBA + erythroid differentiation protein + activin beta-A chain + activin/inhibin beta A chain + "An activin/inhibin beta subunit that is a translation product of the human INHBA gene or a 1:1 ortholog thereof." [PRO:CNA] + EDF + + + PR_EXT:000000281 + CDMP-1 + "A growth/differentiation factor that is a translation product of the human GDF5 gene or a 1:1 ortholog thereof." [PRO:CNA] + GDF5 + radotermin + growth/differentiation factor 5 + GDF-5 + Bp + CDMP1 + cartilage-derived morphogenetic protein 1 + PR_EXT:growth/differentiation factor 5 + + + PR_EXT:000000282 + GDF7 + growth/differentiation factor 7 + PR_EXT:growth/differentiation factor 7 + "A growth/differentiation factor that is a translation product of the human GDF7 gene or a 1:1 ortholog thereof." [PRO:CNA] + GDF-7 + + + LEFTYB + TGF-beta-4 + Lefty + stimulated by retinoic acid gene 3 protein + protein lefty-B + PR_EXT:lefty 1 + Tgfb4 + "A lefty protein that is a translation product of the human LEFTY1 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:000000287 + Ebaf + Stra3 + lefty 1 + Left-right determination factor B + protein lefty-1 + transforming growth factor beta-4 + LEFTB + LEFTY1 + + + SMAD1 + "A BMP receptor-regulated smad protein that is a translation product of the human SMAD1 gene or a 1:1 ortholog thereof." [PMID:10708949, PRO:CNA] + PR_EXT:smad1 + mMad1 + SMAD 1 + JV4-1 + mothers-against-DPP-related 1 + Dwf-A + SMAD family member 1 + BSP-1 + Mad-related protein 1 + MADH1 + mothers against DPP homolog 1 + transforming growth factor-beta-signaling protein 1 + PR_EXT:000000363 + MAD homolog 1 + BSP1 + dwarfin-A + smad1 + MADR1 + + + MAD homolog 2 + PR_EXT:smad2 + mothers against DPP homolog 2 + Mad-related protein 2 + SMAD family member 2 + MADH2 + hMAD-2 + mMad2 + SMAD 2 + MADR2 + PR_EXT:000000364 + SMAD2 + "A TGF-beta receptor-regulated smad protein that is a translation product of the human SMAD2 gene or a 1:1 ortholog thereof." [PMID:9311995] + smad2 + JV18-1 + + + MAD homolog 3 + PR_EXT:smad3 + mothers against DPP homolog 3 + mad3 + SMAD family member 3 + MADH3 + hMAD-3 + mMad3 + SMAD 3 + PR_EXT:000000365 + smad3 + SMAD3 + JV15-2 + "A TGF-beta receptor-regulated smad protein that is a translation product of the human SMAD3 gene or a 1:1 ortholog thereof." [PMID:9311995] + + + PR_EXT:smad5 + smad5 + dwarfin-C + MAD homolog 5 + "A BMP receptor-regulated smad protein that is a translation product of the human SMAD5 gene or a 1:1 ortholog thereof." [PMID:10708949] + Smad5 + SMAD5 + PR_EXT:000000372 + SMAD 5 + JV5-1 + Dwf-C + mothers against DPP homolog 5 + MADH5 + SMAD family member 5 + + + "A BMP receptor-regulated smad protein that is a translation product of the human SMAD9 gene or a 1:1 ortholog thereof." [PMID:10708948] + PR_EXT:smad9 + mothers against DPP homolog 9 + SMAD family member 9 + smad9 + PR_EXT:000000375 + SMAD 9 + smad8 + SMAD9 + Madh6 + Madh8 + MADH9 + MAD homolog 9 + + + "A protein with amino- and carboxyl-terminal intracellular domains separated by a domain (common with other ion channels) containing six transmembrane helices (S1-S6) in which the last two helices (S5 and S6) flank a loop, called the pore loop, which determines ion selectivity. The carboxy-terminal region contains the Cyclic nucleotide-binding domain (Pfam:PF00027) (CNBD) and a region connecting the CNBD to the S6 segment (C-linker), which is important for modulation by transition metals. In addition, CNG alpha has a carboxy-terminal leucine zipper that seems to be involved in inter-subunit interaction. CNG alpha subunits combine with the beta subunits to form the cyclic nucleotide-gated ion channels, which mediate sensory transduction in photoreceptors and olfactory sensory neurons. These channels are likely composed of four subunits around a centrally located ion-permeable pore that opens in response to the direct binding of intracellular cyclic nucleotides. CNG channels are non-selective cation channels. They are not gated by membrane voltage although their structure includes the transmembrane S4 motif known to function as the membrane voltage sensor in all voltage-gated ion channels, but it has been shown to be important for proper folding and processing. Alpha and beta subunits of the CNG channel are very similar, however only alpha subunits are able to homooligomerize and form functional channels." [PMID:12432397, PRO:CNA] + cyclic nucleotide-gated channel alpha subunit + PR_EXT:000000673 + PR_EXT:cyclic nucleotide-gated channel alpha subunit + + + PR_EXT:000000681 + PR_EXT:transient receptor potential cation channel TRPV + "A protein that is a member of the subfamily V of the transient receptor potential cation channels (TRPs), with amino- and carboxyl-terminal intracellular domains separated by a domain (common with other ion channels) containing six transmembrane helices (S1-S6) in which the last two helices (S5 and S6) flank a loop, called the pore loop, which determines ion selectivity. The amino terminal domain contains up to 6 copies of detectable ankyrin repeat (Pfam:PF00023). Most TRPs are relatively non-selective. They may be modulated by voltage changes but channel gating is generally effected by other means." [PMID:16382100, PMID:16460286, PMID:17579562, PRO:WCB] + transient receptor potential cation channel TRPV + + + PR_EXT:000000684 + fam:Kchan_sub-KQT + voltage-gated potassium channel subunit KQT + "A protein with a core domain composition consisting of six transmembrane domains (S1-S6), arranged in a voltage sensor (S1-S4) and pore modules (S5-P-S6), and with both N and C termini on the intracellular side of the membrane. The charged S4 segment with a basic amino acid at every third position confers their voltage sensitivity. Unlike other voltage-gated potassium channels, these proteins lack the N-terminal tetramerization domain (T1), which encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. Also, unique to this class is the presence of a carboxyl terminal domain called the KCNQ voltage-gated potassium channel domain (Pfam:PF03520) or A-domain. Voltage-gated potassium channels are composed of tetramers of alpha subunits, with each alpha subunit containing a voltage sensor and contributing to the central pore. This pore is formed by these subunits that encircle a central ion conduction pathway. KQT channels are responsible for M-type potassium currents in the nervous and auditory systems and slow delayed rectifier K+ currents in the heart." [PRO:CNA] + PR_EXT:voltage-gated potassium channel subunit KQT + + + fam:Kchan_sub-a + PR_EXT:voltage-gated potassium channel alpha subunit + voltage-gated potassium channel alpha subunit + PR_EXT:000000685 + "A protein with a core domain composition consisting of six transmembrane domains (S1-S6), arranged in a voltage sensor (S1-S4) and pore modules (S5-P-S6), and with both N and C termini on the intracellular side of the membrane. The charged S4 segment with a basic amino acid at every third position confers their voltage sensitivity. A hallmark of this class is the presence of an N-terminal K+ channel tetramerisation domain (Pfam:PF02214) (T1), which encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. Carbonyl oxygen atoms from the potassium channel signature sequence (TTxGYGD) line the selectivity filter, where they preferentially coordinate potassium. Voltage-gated potassium channels are composed of tetramers of alpha subunits with each alpha subunit containing a voltage sensor and contributing to the central pore. This pore is formed by these subunits that encircle a central ion conduction pathway." [PMID:16382097, PMID:17606609, PMID:9886290] + + + CNG1 + cyclic nucleotide-gated channel, photoreceptor + CNCG1 + rod photoreceptor cGMP-gated channel subunit alpha + cyclic nucleotide-gated cation channel 1 + PR_EXT:000000686 + CNG channel alpha-1 + "A cyclic nucleotide-gated channel alpha subunit that is a translation product of the human CNGA1 gene or a 1:1 ortholog thereof. In the retina, these proteins can be activated by cyclic GMP which leads to an opening of the cation channel and thereby causing a depolarization of rod photoreceptors." [PRO:CNA] + CNG-1 + cGMP-gated cation channel alpha-1 + CNCG + cyclic nucleotide-gated channel alpha-1 + CNGA1 + PR_EXT:cGMP-gated cation channel alpha-1 + + + CNCG3 + CNG-3 + CNG channel alpha-3 + "A cyclic nucleotide-gated channel alpha subunit that is a translation product of the human CNGA3 gene or a 1:1 ortholog thereof. These proteins are the alpha subunits of the cone cyclic nucleotide-gated cation channel. This channel generates the light-evoked electrical responses of cone photoreceptors." [PRO:CNA] + cyclic nucleotide-gated cation channel alpha-3 + cone photoreceptor cGMP-gated channel subunit alpha + CNG3 + PR_EXT:cyclic nucleotide-gated cation channel alpha-3 + cyclic nucleotide-gated channel alpha-3 + PR_EXT:000000696 + CNGA3 + + + fam:Kchan_shaw_sub-a + "A voltage-gated potassium channel alpha subunit that is a constituent of Kv3 channels. These proteins are characterized by the high sequence conservation in the S5 segment which seems to determine the gating properties of the Kv3 channels: rightward shifted voltage dependence and fast deactivation rates. They also contain an ATM motif at the lysine-rich C-terminal region that is unique to this group. Kv3 channels are necessary for high-frequency, repetitive firing of action potentials. High activation threshold is a hallmark of Kv3 channels. They regulate rapid spiking, transmitter release and dendritic integration of many central neurons. In common with Kv2 and Kv4 channels, the tetramerization domain at the N terminus contains a zinc-binding site." [PMID:11506885] + Kv3 channel + PR_EXT:shaw-related voltage-gated potassium channel alpha subunit + PR_EXT:000000711 + shaw-related voltage-gated potassium channel alpha subunit + + + voltage-gated potassium channel subunit KCNQ1 + PR_EXT:000000728 + voltage-gated potassium channel subunit Kv7.1 + KVLQT1 + KCNA8 + KCNQ1 + IKs producing slow voltage-gated potassium channel subunit alpha KvLQT1 + KCNA9 + KQT-like 1 + PR_EXT:voltage-gated potassium channel subunit KCNQ1 + "A voltage-gated potassium channel subunit KQT that is a translation product of the human KCNQ1 gene or a 1:1 ortholog thereof." [PRO:CNA] + + + potassium channel subunit alpha KvLQT4 + PR_EXT:000000731 + voltage-gated potassium channel subunit KCNQ4 + "A voltage-gated potassium channel subunit KQT that is a translation product of the human KCNQ4 gene or a 1:1 ortholog thereof." [PRO:CNA] + voltage-gated potassium channel subunit Kv7.4 + KCNQ4 + KQT-like 4 + PR_EXT:voltage-gated potassium channel subunit KCNQ4 + + + KCNC1 + "A shaw-related voltage-gated potassium channel alpha subunit that is a translation product of the human KCNC1 gene or a 1:1 ortholog thereof. They contain an ATM motif at the C-terminus, following the S6 segment that allows interaction with axonal targeting machinery when exposed." [PRO:CNA] + voltage-gated potassium channel subunit Kv3.1 + NGK2 + voltage-gated potassium channel subunit Kv4 + PR_EXT:000000781 + PR_EXT:voltage-gated potassium channel KCNC1 + voltage-gated potassium channel KCNC1 + RAW2 + + + KSHIIIA + voltage-gated potassium channel Kv3.2 + PR_EXT:000000782 + PR_EXT:voltage-gated potassium channel KCNC2 + voltage-gated potassium channel KCNC2 + voltage-gated potassium channel subunit Kv3.2 + "A shaw-related voltage-gated potassium channel alpha subunit that is a translation product of the human KCNC2 gene or a 1:1 ortholog thereof." [PRO:CNA] + KCNC2 + + + KCNC1/iso:Long + Kv3.1b + PR_EXT:voltage-gated potassium channel KCNC1 isoform Long + PR_EXT:000000940 + voltage-gated potassium channel KCNC1 isoform Long + "A voltage-gated potassium channel KCNC1 that is a translation product of a mature transcript of the KCNC1 gene, and that includes the core domains and the longest C-terminal tail compare to isoform 1. Example: UniProtKB:P25122-1." [PRO:CNA] + voltage-gated potassium channel KCNC1 isoform 2 + KCNC1/iso:2 + + + T-cell surface antigen T4/Leu-3 + T-cell surface glycoprotein CD4 + CD4 molecule + PR_EXT:000001004 + "A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence." [PMID:15326605] + CD4 + T-cell differentiation antigen L3T4 + PR_EXT:CD4 molecule + + + PR_EXT:000001005 + PR_EXT:integrin alpha with A domain + integrin alpha with A domain + "An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage." [PIRSF:PIRSF002497] + integrin alpha with I domain + + + lymphocyte antigen 5 + receptor-type tyrosine-protein phosphatase C + leukocyte common antigen + CD45 + "A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule." [PMID:1351092, PRO:CNA] + PTPRC + PR_EXT:000001006 + PR_EXT:receptor-type tyrosine-protein phosphatase C + L-CA + ly-5 + + + integrin alpha-X + leukocyte adhesion receptor p150,95 + Leu M5 + CD11 antigen-like family member C + leukocyte adhesion glycoprotein p150,95 alpha chain + CD11c + PR_EXT:000001013 + ITGAX + PR_EXT:integrin alpha-X + "An integrin alpha with A domain that is a translation product of the human ITGAX gene or a 1:1 ortholog thereof. Integrin alpha-X complexed with beta-2 is a receptor for fibrinogen. It recognizes the sequence GPR in fibrinogen. It mediates cell-cell interaction during inflammatory responses. It is especially important in monocyte adhesion and chemotaxis." [UniProtKB:P20702] + + + receptor-type tyrosine-protein phosphatase C isoform CD45R + PTPRC/iso:CD45R + "A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that includes the region encoded by the variable exons 4(A), 5(B), and 6(C). Example: UniProtKB:P08575-1." [PMID:1351092, PRO:CNA] + CD45R + CD45RABC + PR_EXT:000001014 + B220 + PR_EXT:receptor-type tyrosine-protein phosphatase C isoform CD45R + + + "A receptor-type tyrosine-protein phosphatase C that is a translation product of a mature transcript of the PTPRC gene, that includes the region encoded by the variable exon 5(B), and lacks the region encoded by exons 4(A) and 6(C)." [PMID:1351092, PRO:CNA] + PR_EXT:000001016 + PR_EXT:receptor-type tyrosine-protein phosphatase C isoform CD45RB + receptor-type tyrosine-protein phosphatase C isoform CD45RB + PTPRC/iso:CD45RB + + + PR_EXT:000001018 + CD3 subunit with Ig-like domain + "A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response." [PMID:16473826, PMID:1724736] + PR_EXT:CD3 subunit with immunoglobulin domain + CD3 subunit with immunoglobulin domain + + + PR_EXT:neural cell adhesion molecule + PR_EXT:000001022 + "A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain." [PRO:CNA] + neural cell adhesion molecule + + + neural cell adhesion molecule NCAM + "A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration." [PMID:17975827] + PR_EXT:000001023 + PR_EXT:neural cell adhesion molecule NCAM + + + cAMP-dependent chloride channel + CFTR + ABCC7 + ATP-binding cassette transporter sub-family C member 7 + channel conductance-controlling ATPase + PR_EXT:cystic fibrosis transmembrane conductance regulator + cystic fibrosis transmembrane conductance regulator + PR_EXT:000001044 + "A protein that is a translation product of the human CFTR gene or a 1:1 ortholog thereof. Involved in the transport of chloride ions. The characteristic domain composition of the functional isoform consists of two modules of a membrane-spanning domain (ABC transporter transmembrane region) followed by a nucleotide-binding domain (ABC transporter domains), separated by an intracellular regulatory domain (R-domain). It also contains a C-terminal PDZ-binding region. The R-domain is an inhibitory domain of CFTR,and phosphorylation of the R-domain removes this inhibition, allowing activation of chloride flux." [PMID:9922375, PRO:CNA] + + + secretin receptor-like G-protein coupled receptor + adhesion G-protein coupled receptor + PR_EXT:000001087 + "A G-protein coupled receptor with a 7 transmembrane (secretin family) domain (Pfam:PF00002) preceded by an amino-terminal region containing one or more functional domains with adhesion-like motifs." [PMID:12761335, PRO:DAN, PRO:WCB] + fam:adhesion + PR_EXT:adhesion G-protein coupled receptor + subfamily B2 G-protein coupled receptor + + + PR_EXT:interleukin-1 + interleukin-1 + "A protein with a core domain composition consisting of a propeptide region and an Interleukin-1 / 18 domain." [PMID:8001745, PRO:CNA] + PR_EXT:000001091 + + + class 1 G-protein coupled receptor + fam:rhodopsin + rhodopsin-like G-protein coupled receptor + "A G-protein coupled receptor that contains the 7 transmembrane receptor (rhodopsin family) domain (Pfam:PF00001), which includes 7 transmembrane helices (TMI-TM7) with 3 intracellular loops (IL1-IL3) and 3 extracellular loops (EL1-EL3) between the helices. The amino-terminal region is extracellular and the carboxyl-terminal region is intracellular. Rhodopsin-like G-protein coupled receptors (GPCRs) are unique among the several classes of GPCRs in that most have a very short amino-terminal segment and several characteristic sequence motifs, particularly NSxxNPxxY in TM7 and D/E-R-Y/F between TM3 and loop IL2. Most bind their ligands within a cavity between the TM regions." [PMID:12761335, PRO:DAN, PRO:WCB] + PR_EXT:000001094 + PR_EXT:rhodopsin-like G-protein coupled receptor + + + PR_EXT:Toll-like receptor + PR_EXT:000001096 + Toll-like receptor + fam:TLR + "A protein with a core domain composition consisting of a signal peptide, an extracellular domain with multiple Leucine rich repeat (Pfam:PF13855) domain (LRR), a cysteine-rich region, a single-pass transmembrane domain and a C-terminal cytoplasmic tail containing a TIR domain (Pfam:PF01582)." [PMID:11022119] + + + 5-hydroxytryptamine receptor 2 + "A rhodopsin-like G-protein coupled receptor that is a translation product of genes HTR2A, HTR2B, or HTR2C. The preferred ligand is 5-hydroxytryptamine (serotonin)." [PRO:WCB] + PR_EXT:000001099 + PR_EXT:5-hydroxytryptamine receptor 2 + + + PR_EXT:000001107 + D(1)-like dopamine receptor + PR_EXT:D(1)-like dopamine receptor + "A rhodopsin-like G-protein coupled receptor that is a product of the DRD1 or DRD5 gene. The active form binds dopamine and its activity is mediated by G proteins that cause activation of adenylate cyclase." [PRO:WCB, Wikipedia:Dopamine_receptor] + + + "A rhodopsin-like G-protein coupled receptor that is a product of the DRD2, DRD3, or DRD4 gene. The active form binds dopamine and its activity is mediated by G proteins that cause inhibition of adenylate cyclase." [PRO:WCB, Wikipedia:Dopamine_receptor] + PR_EXT:000001108 + PR_EXT:D(2)-like dopamine receptor + D(2)-like dopamine receptor + + + PR_EXT:animal opsin + PR_EXT:000001119 + "A rhodopsin-like G-protein coupled receptor that is a translation product of some metazoan gene and that binds a vitamin A-based retinaldehyde chromophore through a Schiff base linkage to a Lys residue in the seventh transmembrane alpha helix." [PRO:WCB, Wikipedia:Opsin] + animal opsin + + + PR_EXT:000001128 + PR_EXT:chemokine receptor + "A rhodopsin-like G-protein coupled receptor that in active form binds to one or more chemokines. Only those that have been unequivocally shown to activate a G-protein coupled signaling pathway appear on the official IUPHAR list." [PMID:12037138, PRO:WCB] + chemokine receptor + + + Dfy + ACKR1 + glycoprotein D + GPD + duffy antigen/chemokine receptor + GpFy + FY + PR_EXT:000001132 + "A rhodopsin-like G-protein coupled receptor that is a translation product of the human ACKR1 gene or a 1:1 ortholog thereof. This is a non-specific, non-signaling chemokine receptor." [PRO:WCB] + plasmodium vivax receptor + CD234 + PR_EXT:atypical chemokine receptor 1 + Fy glycoprotein + DARC + duffy antigen chemokine receptor + atypical chemokine receptor 1 + + + "An interleukin-1 that is a translation product of the human IL1B gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:000001136 + PR_EXT:interleukin-1 beta + IL1F2 + interleukin-1 beta + IL1B + catabolin + IL-1 beta + + + tachykinin receptor + "A rhodopsin-like G-protein coupled receptor that binds tachykinin peptides--neuropeptides of 10-12 amino acids derived from the translation products of the TAC1 and TAC3 genes. Tachykinin receptors are not specific but have different affinities for the various peptides." [PRO:WCB, Wikipedia:Tachykinin_peptides] + PR_EXT:000001150 + PR_EXT:tachykinin receptor + + + Toll/interleukin-1 receptor-like protein 4 + "A Toll-like receptor that is a translation product of the human TLR2 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:000001153 + PR_EXT:Toll-like receptor 2 + CD282 + TIL4 + TLR2 + Toll-like receptor 2 + + + hToll + "A Toll-like receptor that is a translation product of the human TLR4 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:Toll-like receptor 4 + CD284 + PR_EXT:000001155 + Toll-like receptor 4 + TLR4 + Lps + + + TLR5 + "A Toll-like receptor that is a translation product of the human TLR5 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:Toll-like receptor 5 + Toll/interleukin-1 receptor-like protein 3 + Toll-like receptor 5 + PR_EXT:000001156 + TIL3 + + + HTR2A + PR_EXT:5-hydroxytryptamine receptor 2A + HTR2 + "A 5-hydroxytryptamine receptor 2 that is a translation product of the human HTR2A gene or a 1:1 ortholog thereof." [PRO:WCB] + serotonin receptor 2A + PR_EXT:000001166 + 5-HT-2 + 5-HT-2A + 5-hydroxytryptamine receptor 2A + + + HTR2C + 5-HT-2C + 5-HT-1C + serotonin receptor 2C + 5-HTR2C + 5-hydroxytryptamine receptor 1C + 5-hydroxytryptamine receptor 2C + HTR1C + 5ht1c + PR_EXT:5-hydroxytryptamine receptor 2C + PR_EXT:000001168 + 5-HT1C + "A 5-hydroxytryptamine receptor 2 that is a translation product of the human HTR2C gene or a 1:1 ortholog thereof." [PRO:WCB] + 5-HT2C + + + "A D(1)-like dopamine receptor that is a translation product of the human DRD1 gene or a 1:1 ortholog thereof." [PRO:WCB] + DRD1 + Drd1a + dopamine D1 receptor + PR_EXT:D(1A) dopamine receptor + Gpcr15 + PR_EXT:000001175 + D(1A) dopamine receptor + + + DRD1L2 + "A D(1)-like dopamine receptor that is a translation product of the human DRD5 gene or a 1:1 ortholog thereof." [PRO:WCB] + DRD5 + PR_EXT:D(1B) dopamine receptor + D1beta dopamine receptor + dopamine D5 receptor + D(1B) dopamine receptor + DRD1B + PR_EXT:000001176 + D(5) dopamine receptor + + + D(2) dopamine receptor + dopamine D2 receptor + "A D(2)-like dopamine receptor that is a translation product of the human DRD2 gene or a 1:1 ortholog thereof." [PRO:WCB] + DRD2 + PR_EXT:000001177 + PR_EXT:D(2) dopamine receptor + + + "A D(2)-like dopamine receptor that is a translation product of the human DRD3 gene or a 1:1 ortholog thereof." [PRO:WCB] + D(3) dopamine receptor + PR_EXT:000001178 + dopamine D3 receptor + PR_EXT:D(3) dopamine receptor + DRD3 + + + "A D(2)-like dopamine receptor that is a translation product of the human DRD4 gene or a 1:1 ortholog thereof." [PRO:WCB] + dopamine D4 receptor + PR_EXT:000001179 + DRD4 + D(4) dopamine receptor + PR_EXT:D(4) dopamine receptor + D(2C) dopamine receptor + + + S opsin + blue-sensitive opsin + PR_EXT:000001195 + OPN1SW + short wavelength-sensitive cone opsin + BOP + short-wave-sensitive opsin 1 + BCP + "An animal opsin that is a translation product of the human OPN1SW gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:short-wave-sensitive opsin 1 + blue cone photoreceptor pigment + + + CXC-R4 + SDF-1 receptor + HM89 + Sdf1r + PR_EXT:C-X-C chemokine receptor type 4 + PR_EXT:000001208 + leukocyte-derived seven transmembrane domain receptor + LESTR + FB22 + pre-B-cell-derived chemokine receptor + PB-CKR + CXCR4 + NPYRL + stromal cell-derived factor 1 receptor + chemokine receptor CXCR4 + LCR1 + C-X-C chemokine receptor type 4 + "A chemokine receptor that is a translation product of the human CXCR4 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL12." [PMID:12037138, PRO:WCB] + fusin + Cmkar4 + CXCR-4 + CD184 + + + OPN1MW2 + "An animal opsin that is a translation product of the human OPN1MW or OPN1MW2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." [PRO:DAN, PRO:WCB] + medium-wave-sensitive opsin 1 + green cone photoreceptor pigment + PR_EXT:000001224 + green-sensitive opsin + M opsin + Gcp + medium wavelength-sensitive cone opsin + GOP + Opn1mw + OPN1MW + PR_EXT:medium-wave-sensitive opsin 1 + + + NK-3 receptor + PR_EXT:000001242 + TACR3 + NKR + "A tachykinin receptor that is a translation product of the human TACR3 gene or a 1:1 ortholog thereof. The preferred ligand is neurokinin B, also known as neuromedin-K." [PRO:WCB, Wikipedia:Tachykinin_peptides, Wikipedia:Tachykinin_receptor] + NK3R + PR_EXT:neuromedin-K receptor + neuromedin-K receptor + tachykinin receptor 3 + NK-3R + neurokinin B receptor + TAC3R + + + PR_EXT:000001244 + OPN1LW + RCP + red-sensitive opsin + ROP + PR_EXT:long-wave-sensitive opsin 1 + long-wave-sensitive opsin 1 + "An animal opsin that is a translation product of the human OPN1LW gene or a 1:1 ortholog thereof." [PRO:WCB] + red cone photoreceptor pigment + + + "An animal opsin that is a translation product of the human RHO gene or a 1:1 ortholog thereof." [PRO:WCB] + OPN2 + RHO + rhodopsin + PR_EXT:rhodopsin + opsin-2 + PR_EXT:000001245 + + + ADAM 10 endopeptidase + mammalian disintegrin-metalloprotease + CDw156 + MADM + disintegrin and metalloproteinase domain-containing protein 10 + ADAM10 + ADAM 10 + CD156c + "A protein that is a translation product of the human ADAM10 gene or a 1:1 ortholog thereof." [PRO:WCB] + kuzbanian protein homolog + PR_EXT:000001278 + KUZ + PR_EXT:disintegrin and metalloproteinase domain-containing protein 10 + + + PR_EXT:ADAM 17 endopeptidase + "A protein that is a translation product of the human ADAM17 gene or a 1:1 ortholog thereof." [PRO:WCB] + ADAM 17 endopeptidase + CSVP + CD156b + PR_EXT:000001279 + TNF-alpha-converting enzyme + snake venom-like protease + ADAM17 + TNF-alpha convertase + TACE + ADAM 17 + + + MS2 + CD156a + macrophage cysteine-rich glycoprotein + "A protein that is a translation product of the human ADAM8 gene or a 1:1 ortholog thereof." [PRO:WCB] + ADAM 8 endopeptidase + PR_EXT:000001280 + PR_EXT:disintegrin and metalloproteinase domain-containing protein 8 + ADAM 8 + disintegrin and metalloproteinase domain-containing protein 8 + ADAM8 + cell surface antigen MS2 + + + PR_EXT:E/P-selectin + E/P-selectin + "A protein with core domain structure consisting of one lectin C-type domain (Pfam:PF00059), followed by one EGF domain (Pfam:PF00008), followed by 4-9 sushi domains (Pfam:PF00084), with the P-selectins generally being longer." [PRO:WCB] + PR_EXT:000001313 + + + frizzled-like G-protein coupled receptor + PR_EXT:frizzled-like G-protein coupled receptor + PR_EXT:000001315 + fam:frizzled + "A G-protein coupled receptor with core architecture consisting of an Fz domain (Pfam:PF01392), also known as Frizzled CRD (cysteine rich domain), followed by a Frizzled/Smoothened family membrane region (Pfam:PF01534), which includes 7 transmembrane helices, and a cytoplasmic domain containing the motif Lys-Thr-x-x-x-Trp. They generally function as cell-surface receptors for Wnts." [InterPro:IPR015526, PRO:DAN, PRO:WCB] + + + IL-7 + interleukin-7 + PR_EXT:interleukin-7 + "A protein that is a translation product of the human IL7 gene or a 1:1 ortholog thereof." [PRO:JAN] + IL7 + PR_EXT:000001317 + + + leukocyte-endothelial cell adhesion molecule 1 + Ly22 + gp90-MEL + leukocyte surface antigen Leu-8 + leukocyte adhesion molecule 1 + LECAM1 + CD62 antigen-like family member L + LAM-1 + L-selectin + lymphocyte surface MEL-14 antigen + PR_EXT:000001318 + ly-22 + LYAM1 + "A protein that is a translation product of the human SELL gene or a 1:1 ortholog thereof. It is a leukocyte adhesion receptor that play an important role in regulating the inflammatory response by mediating leukocyte tethering and rolling on adherent leukocytes." [PMID:12403782, PRO:JAN] + SELL + lymphocyte antigen 22 + TQ1 + PR_EXT:L-selectin + lymph node homing receptor + LNHR + CD62L + + + cadherin + PR_EXT:cadherin + "A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues." [PRO:WCB] + PR_EXT:000001327 + + + IGF-II receptor + PR_EXT:000001333 + "A protein that is a translation product of the human IGF2R gene or a 1:1 ortholog thereof." [PRO:WCB] + insulin-like growth factor II receptor + M6P/IGF2R + MPRI + MPR 300 + PR_EXT:cation-independent mannose-6-phosphate receptor + insulin-like growth factor 2 receptor + IGF2R + CI-MPR + cation-independent mannose-6-phosphate receptor + M6P/IGF2 receptor + 300 kDa mannose 6-phosphate receptor + CD222 + CI Man-6-P receptor + + + class 2 cytokine, IL-10 type + "A protein with a core domain architecture consisting of an N-terminal Interleukin 10 (Pfam:PF00726) domain." [PRO:CNA] + PR_EXT:class 2 cytokine, IL-10 type + PR_EXT:000001335 + + + CD55-like protein + complement decay-accelerating factor like protein + PR_EXT:000001336 + PR_EXT:CD55-like protein + "A protein that is a translation product of the human CD55 or CD55B genes, 1:1 orthologs thereof, or a semi-ortholog thereof. In human, alternative splicing of CD55 transcript produces either a single-pass type 1 membrane protein or a GPI-anchored form. In mouse, the single-pass transmembrane form is encoded by the closely related gene CD55B, which was produced by a recent lineage-specific duplication." [PRO:DAN, PRO:WCB] + + + PR_EXT:complement receptor type 1 + complement receptor type 1 + C3BR + C3b/C4b receptor + CD35 + CR1 + "A protein that is a translation product of the human CR1 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:000001337 + + + PR_EXT:complement receptor type 2 + "A protein that is a translation product of the human CR2 gene or a 1:1 ortholog thereof." [PRO:WCB] + complement receptor type 2 + C3DR + PR_EXT:000001338 + complement C3d receptor + CR2 + EBV receptor + Cr2 + CD21 + epstein-Barr virus receptor + + + PR_EXT:fibroblast growth factor receptor + fibroblast growth factor receptor + PR_EXT:000001349 + "A protein with an extracellular region containing three copies of the Immunoglobulin domain (Pfam:PF00047), a single transmembrane region, and an intracellular region containing a Protein tyrosine kinase domain (Pfam:PF07714). Its active form binds fibroblast growth factor (FGF). FGFs and its receptor comprise a signaling system that is conserved throughout metazoan evolution." [PMID:15475116] + + + immunoglobulin gamma Fc receptor II/III/IV + PR_EXT:000001355 + "A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III." [PRO:WCB] + PR_EXT:immunoglobulin gamma Fc receptor II/III/IV + + + "A protein with a core domain architecture consisting of an Intercellular adhesion molecule (ICAM), N-terminal domain (Pfam:PF03921), a type of Ig-like domain, and four copies of the Immunoglobulin domain (Pfam:PF00047), most of which are not detected by Pfam." [PRO:WCB] + intercellular adhesion molecule 1/3 + PR_EXT:intercellular adhesion molecule 1/3 + ICAM + PR_EXT:000001357 + + + interleukin-2 receptor subunit alpha + CD25 + Il2r + TAC antigen + IL-2-RA + IL-2 receptor subunit alpha + IL-2R subunit alpha + PR_EXT:000001380 + IL2RA + IL2-RA + PR_EXT:interleukin-2 receptor subunit alpha + "A protein that is a translation product of the human IL2RA gene or a 1:1 ortholog thereof." [PRO:CNA] + + + IL-22a + cytokine Zcyto18 + IL-10-related T-cell-derived-inducible factor + PR_EXT:interleukin-22 + Il22a + "A protein that is a translation product of the human IL22 gene or a 1:1 ortholog thereof." [PRO:CNA] + IL-22 + interleukin-22 + IL-TIF + PR_EXT:000001383 + IL22 + interleukin-22a + IL-TIF alpha + ILTIF + ZCYTO18 + Iltifa + + + interleukin-4 + PR_EXT:interleukin-4 + IGG1 induction factor + B-cell growth factor 1 + BSF-1 + lymphocyte stimulatory factor 1 + "A protein that is a translation product of the human IL4 gene or a 1:1 ortholog thereof." [PRO:JAN] + IL4 + B-cell IgG differentiation factor + pitrakinra + PR_EXT:000001391 + IL-4 + B-cell stimulatory factor 1 + binetrakin + + + PR_EXT:000001393 + CDF + PR_EXT:interleukin-6 + BSF-2 + "A protein that is a translation product of the human IL6 gene or a 1:1 ortholog thereof." [PRO:JAN] + interferon beta-2 + B-cell hybridoma growth factor + interleukin HP-1 + interleukin-6 + IL6 + IFN-beta-2 + IFNB2 + CTL differentiation factor + hybridoma growth factor + B-cell stimulatory factor 2 + IL-6 + + + GCP-1 + interleukin-8 + emoctakin + PR_EXT:interleukin-8 + CXCL8 + C-X-C motif chemokine 8 + monocyte-derived neutrophil chemotactic factor + NAP-1 + neutrophil-activating protein 1 + "A protein that is a translation product of the human IL8 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:000001395 + monocyte-derived neutrophil-activating peptide + T-cell chemotactic factor + MDNCF + MONAP + granulocyte chemotactic protein 1 + IL8 + IL-8 + protein 3-10C + + + NGFR + gp80-LNGFR + PR_EXT:000001405 + low affinity neurotrophin receptor p75NTR + NGF receptor + tumor necrosis factor receptor superfamily member 16 + TNFRSF16 + CD271 + PR_EXT:tumor necrosis factor receptor superfamily member 16 + low-affinity nerve growth factor receptor + p75 ICD + "A death receptor that is a translation product of the human NGFR gene or a 1:1 ortholog thereof. This receptor contains an extracellular domain containing four repeats (about 40 residues long) with 6 cysteine residues at conserved positions followed by a serine/threonine-rich region, a single transmembrane domain, and a cytoplasmic domain. The cysteine-rich region contains the nerve growth factor binding domain." [PRO:JAN, RefSeq:NP_002498] + + + PR_EXT:000001415 + E-selectin + CD62 antigen-like family member E + PR_EXT:E-selectin + endothelial leukocyte adhesion molecule 1 + SELE + LECAM2 + ELAM-1 + "An E/P-selectin that is a translation product of the human SELE gene or a 1:1 ortholog thereof." [PRO:WCB] + CD62E + leukocyte-endothelial cell adhesion molecule 2 + ELAM1 + + + P-selectin + GMP-140 + granule membrane protein 140 + PR_EXT:000001432 + CD62P + GRMP + PR_EXT:P-selectin + SELP + LECAM3 + PADGEM + GMRP + CD62 antigen-like family member P + "An E/P-selectin that is a translation product of the human SELP gene or a 1:1 ortholog thereof." [PRO:WCB] + platelet activation dependent granule-external membrane protein + leukocyte-endothelial cell adhesion molecule 3 + + + CDHN + NCAD + CDH2 + "A cadherin that is a translation product of the human CDH2 gene or a 1:1 ortholog thereof." [PRO:WCB] + cadherin-2 + CDw325 + PR_EXT:000001443 + PR_EXT:cadherin-2 + N-cadherin + CD325 + neural cadherin + + + E-cadherin + uvomorulin + UVO + epithelial cadherin + cadherin-1 + PR_EXT:000001447 + PR_EXT:cadherin-1 + CDHE + CAM 120/80 + CDH1 + CD324 + "A cadherin that is a translation product of the human CDH1 gene or a 1:1 ortholog thereof." [PRO:WCB] + ARC-1 + + + Fms-like tyrosine kinase 2 + MFR + FGFBR + "A fibroblast growth factor receptor that is a translation product of the human FGFR1 gene or a 1:1 ortholog thereof." [PRO:CNA] + FGFR1 + PR_EXT:000001448 + CD331 + bFGF-R-1 + fibroblast growth factor receptor 1 + FLG + FLT2 + FLT-2 + PR_EXT:fibroblast growth factor receptor 1 + FGFR-1 + + + CD333 + fibroblast growth factor receptor 3 + Sam3 + JTK4 + "A fibroblast growth factor receptor that is a translation product of the human FGFR3 gene or a 1:1 ortholog thereof." [PRO:CNA] + Mfr3 + PR_EXT:fibroblast growth factor receptor 3 + PR_EXT:000001450 + heparin-binding growth factor receptor + FGFR-3 + FGFR3 + + + JTK2 + CD334 + protein-tyrosine kinase receptor MPK-11 + "A fibroblast growth factor receptor that is a translation product of the human FGFR4 gene or a 1:1 ortholog thereof." [PRO:CNA] + TKF + Mpk-11 + fibroblast growth factor receptor 4 + PR_EXT:000001451 + PR_EXT:fibroblast growth factor receptor 4 + FGFR4 + FGFR-4 + + + MyD10 + major group rhinovirus receptor + ICAM1 + ICAM-1 + CD54 + "An intercellular adhesion molecule 1/3 that is a translation product of the human ICAM1 gene or a 1:1 ortholog thereof." [PRO:WCB] + intercellular adhesion molecule 1 + PR_EXT:000001467 + MALA-2 + PR_EXT:intercellular adhesion molecule 1 + + + CSIF + PR_EXT:000001471 + IL-10 + cytokine synthesis inhibitory factor + interleukin-10 + "A class 2 cytokine, IL-10 type that is a translation product of the human IL10 gene or a 1:1 ortholog thereof. Active interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells. Structurally, IL-10 is a protein of about 160 amino acids that contains four conserved cysteines involved in disulfide bonds." [PANTHER:PTHR11585\:SF1, PRO:JAN] + IL10 + PR_EXT:interleukin-10 + + + Fcgr2b + Fc-gamma RII + Fcgr2 + Fc-gamma-RIIB + ly-17 + IgG Fc receptor II beta + Fc gamma receptor IIB + lymphocyte antigen 17 + PR_EXT:low affinity immunoglobulin gamma Fc region receptor II + "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof." [PRO:CNA] + low affinity immunoglobulin gamma Fc region receptor II + FcRII + PR_EXT:000001479 + + + PR_EXT:000001481 + FCGR2B + FCG2 + IGFR2 + Fc-gamma-RIIb + IgG Fc receptor II-b + low affinity immunoglobulin gamma Fc region receptor II-b + FcRII-b + "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCGR2B gene or a 1:1 ortholog thereof." [PRO:CNA] + Fc-gamma RII-b + PR_EXT:low affinity immunoglobulin gamma Fc region receptor II-b + + + PR_EXT:000001483 + Fcgr3 + FcRIII + CD16 + low affinity immunoglobulin gamma Fc region receptor III + "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof." [PRO:CNA] + Fc-gamma RIII + PR_EXT:low affinity immunoglobulin gamma Fc region receptor III + IgG Fc receptor III + + + PR_EXT:proteinase-activated receptor + "A rhodopsin-like G-protein coupled receptor whose active form binds trypsin-related proteinases. The proteinase cleaves the mature peptide, exposing a new amino end. The new N-terminal residues act as a tethered ligand that induces activity." [PRO:WCB] + proteinase-activated receptor + PR_EXT:000001550 + + + "A rhodopsin-like G-protein coupled receptor whose active form binds somatostatin." [PRO:WCB] + PR_EXT:000001555 + somatostatin receptor + PR_EXT:somatostatin receptor + + + PR_EXT:vasopressin/oxytocin receptor + PR_EXT:000001562 + vasopressin/oxytocin receptor + "A rhodopsin-like G-protein coupled receptor that binds vasopressin or oxytocin or related nonapeptides." [PRO:WCB, Wikipedia:Vasopressin, Wikipedia:Vasopressin_receptor] + + + PR_EXT:000001664 + F2RL3 + "A proteinase-activated receptor that is a translation product of the human F2RL3 gene or a 1:1 ortholog thereof. It is activated by thrombin and cathepsin G, which cleave the mature peptide, exposing a new amino end. The six new N-terminal residues act as a tethered ligand that induces activity." [PMID:10702240, PMID:9618465, PRO:WCB] + PAR-4 + coagulation factor II receptor-like 3 + PR_EXT:proteinase-activated receptor 4 + proteinase-activated receptor 4 + thrombin receptor-like 3 + PAR4 + + + PR_EXT:000001669 + SSTR2 + PR_EXT:somatostatin receptor type 2 + SS2R + "A somatostatin receptor that is a translation product of the human SSTR2 gene or a 1:1 ortholog thereof." [PRO:WCB] + SRIF-1 + Sst2 + Smstr2 + somatostatin receptor 2 + SS-2-R + SS2-R + somatostatin receptor type 2 + + + SSTR5 + PR_EXT:somatostatin receptor type 5 + "A somatostatin receptor that is a translation product of the human SSTR5 gene or a 1:1 ortholog thereof." [PRO:WCB] + Smstr5 + PR_EXT:000001672 + SS5R + SS-5-R + somatostatin receptor 5 + somatostatin receptor type 5 + SS5-R + + + DIR3 + renal-type arginine vasopressin receptor + V2R + vasopressin receptor 2 + antidiuretic hormone receptor + vasopressin V2 receptor + "A vasopressin/oxytocin receptor that is a translation product of the human AVPR2 gene or a 1:1 ortholog thereof. The preferred ligand is vasopressin. The receptor is expressed in kidney tubule, fetal lung, lung cancer, and liver." [PRO:WCB, Wikipedia:Vasopressin_receptor] + AVPR V2 + PR_EXT:vasopressin V2 receptor + DIR + ADHR + AVPR2 + PR_EXT:000001683 + + + PR_EXT:myeloid differentiation primary response protein MyD88 + "A protein that is a translation product of the human MYD88 gene or a 1:1 ortholog thereof. This protein is an adapter involved in the Toll-like receptor and IL-1 receptor signaling pathway in the innate immune response." [PMID:9575168, PRO:CNA] + PR_EXT:000001740 + MYD88 + myeloid differentiation primary response protein MyD88 + + + inhibitor of nuclear factor kappa-B kinase complex alpha/beta subunits + "A protein with core domain architecture consisting of an N-terminal Protein kinase domain (Pfam:PF00069), and a C-terminus that is involved in the interaction with NEMO (PR:000001752). In response to a large variety of stimuli, among them pro-inflammatory cytokines, growth factors and microbial pathogens, signals emanating from cell surface receptors converge at the IkappaB kinase (IKK) complex. This complex is composed of four subunits, IKKalpha, IKKbeta, ELK, and NEMO. IKKbeta and NEMO subunits are known to be essential for activating NF-kappaB. Activation of NF-kappaB dimers is the result of IKK-mediated, phosphorylation-induced degradation of the IkappaB inhibitor, which enables the NF-kappaB dimers to enter the nucleus and activate specific target gene expression." [PIRSF:PIRSF000581, PMID:10359587, PMID:18462684, PRO:CNA] + PR_EXT:000001774 + PR_EXT:inhibitor of nuclear factor kappa-B kinase complex alpha/beta subunits + + + IkappaB kinase + I-kappa-B kinase alpha + transcription factor 16 + IKK1 + conserved helix-loop-helix ubiquitous kinase + inhibitor of nuclear factor kappa-B kinase subunit alpha + NFKBIKA + IkBKA + nuclear factor NF-kappa-B inhibitor kinase alpha + TCF16 + CHUK + TCF-16 + IKK-alpha + IKKA + PR_EXT:inhibitor of nuclear factor kappa-B kinase subunit alpha + I-kappa-B kinase 1 + PR_EXT:000001775 + IKK-A + "An inhibitor of nuclear factor kappa-B kinase complex alpha/beta subunits that is a translation product of the human CHUK gene or a 1:1 ortholog thereof." [PRO:CNA] + + + IKKB + PR_EXT:inhibitor of nuclear factor kappa-B kinase subunit beta + inhibitor of nuclear factor kappa-B kinase subunit beta + IKK2 + "An inhibitor of nuclear factor kappa-B kinase complex alpha/beta subunits that is a translation product of the human IKBKB gene or a 1:1 ortholog thereof." [PRO:CNA] + IKBKB + IkBKB + PR_EXT:000001776 + NFKBIKB + IKK-beta + IKK-B + I-kappa-B kinase 2 + nuclear factor NF-kappa-B inhibitor kinase beta + I-kappa-B-kinase beta + + + PR_EXT:000001781 + PR_EXT:interleukin-1 receptor-associated kinase IRAK1/3 + "A protein with core domain architecture consisting of an N-terminal Death domain (Pfam:PF00531) followed by a Protein kinase domain (Pfam:PF00069). This class is closely related to IRAK-4 (PR:000001780), but it contains an extra C-terminal region of about 200 residues." [PMID:12620219] + interleukin-1 receptor-associated kinase IRAK1/3 + + + pelle-like protein kinase + "An interleukin-1 receptor-associated kinase IRAK1/3 that is a translation product of the human IRAK1 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:000001782 + PR_EXT:interleukin-1 receptor-associated kinase 1 + IRAK-1 + Il1rak + IRAK + mPLK + interleukin-1 receptor-associated kinase 1 + IRAK1 + + + C/C-C motif small inducible chemokine + "A protein with core architecture consisting of a Small cytokines (intecrine/chemokine), interleukin-8 like (Pfam:PF00048) domain." [PRO:WCB] + PR_EXT:000001808 + PR_EXT:C/C-C motif small inducible chemokine + + + PR_EXT:000001810 + "A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (Pfam:PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. Pfam:PF00047 is most common, but other members of the Ig domain clan, Pfam:PF07679 and Pfam:PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines." [PRO:WCB] + CSF-1/PDGF receptor-type tyrosine-protein kinase + PR_EXT:CSF-1/PDGF receptor-type tyrosine-protein kinase + + + PR_EXT:000001811 + ikaros family zinc finger protein 1 + ZNFN1A1 + IKZF1 + LYF1 + Zfpn1a1 + IKAROS + PR_EXT:DNA-binding protein Ikaros + "An Ikaros-like zinc finger transcription factor that is a translation product of the human IKZF1 gene or a 1:1 ortholog thereof." [PRO:WCB] + DNA-binding protein Ikaros + lymphoid transcription factor LyF-1 + IK1 + + + PR_EXT:000001812 + "A protein with core architecture consisting of a signal sequence, a Receptor L domain (Pfam:PF01030), a Furin-like cysteine rich region (Pfam:PF00757), another Receptor L domain, a transmembrane domain, and a Protein tyrosine kinase domain (Pfam:PF07714), that may be followed by up to two YLP motifs (Pfam:PF02757)." [PRO:WCB] + EGF receptor type tyrosine-protein kinase + PR_EXT:EGF receptor type tyrosine-protein kinase + + + "An adhesion G-protein coupled receptor that is a translation product of the human ADGRE1 gene or a 1:1 ortholog thereof." [PRO:DAN, PRO:WCB] + ADGRE1 + PR_EXT:000001813 + PR_EXT:adhesion G protein-coupled receptor E1 + TM7LN3 + cell surface glycoprotein F4/80 + Gpf480 + EGF-like module receptor 1 + adhesion G protein-coupled receptor E1 + EMR1 hormone receptor + EGF-like module-containing mucin-like hormone receptor-like 1 + EMR1 + + + G protein-activated inward rectifier potassium channel + PR_EXT:000001814 + "A protein with core architecture consisting of an Inward rectifier potassium channel domain (Pfam:PF01007), which may be preceeded by an Inward rectifier potassium channel N-terminal domain (Pfam:PF08466)." [PRO:WCB] + PR_EXT:G protein-activated inward rectifier potassium channel + + + PR_EXT:HGF/MSP receptor type tyrosine-protein kinase + "A protein with core architecture consisting of a signal sequence, followed by a Sema domain (Pfam:PF01403), three IPT/TIG domains (Pfam:PF01833), a transmembrane region, and a Protein tyrosine kinase domain (Pfam:PF07714)." [PRO:WCB] + HGF/MSP receptor type tyrosine-protein kinase + PR_EXT:000001816 + + + PR_EXT:LDL receptor-related protein + LDL receptor-related protein + "A protein with core architecture containing 31-36 copies of Low-density lipoprotein receptor domain class A (Pfam:PF00057), 34-37 copies of Low-density lipoprotein receptor repeat class B (Pfam:PF00058), and 14-22 copies EGF-like domains (Pfam:PF07974, Pfam:PF00008, or Pfam:PF07645)." [PRO:WCB] + PR_EXT:000001817 + + + "A protein with core architecture consisting of a signal sequence, a Class II histocompatibility antigen, beta domain (Pfam:PF00969) and an Immunoglobulin C1-set domain (Pfam:PF07654); these form the extracellular domain and are followed by a single-pass transmembrane region and a small cytoplasmic region. There are three major and two minor class II MHC (major histocompatability complex) beta chain genes in human. Designations for the MHC complex loci are species specific: HLA (human leukocyte antigen) in human, H-2 in mouse. MHC class II loci are characterized by large numbers of allelic variants." [PRO:WCB, Wikipedia:Human_leukocyte_antigen] + PR_EXT:000001821 + MHC class II histocompatibility antigen beta chain + PR_EXT:MHC class II histocompatibility antigen beta chain + + + BLIMP1 + PRDI-binding factor 1 + beta-interferon gene positive regulatory domain I-binding factor + PR domain-containing protein 1 + PR domain zinc finger protein 1 + PR_EXT:000001831 + PRDI-BF1 + positive regulatory domain I-binding factor 1 + PR_EXT:PR domain zinc finger protein 1 + "A protein that is a translation product of the human PRDM1 gene or a 1:1 ortholog thereof." [PRO:WCB] + PRDM1 + BLIMP-1 + + + "A protein with core architecture consisting of a signal sequence, one Immunoglobulin V-set domain (Pfam:PF07686), two Immunoglobulin C1-set domains (Pfam:PF07654), a single-pass transmembrane region and a very small cytoplasmic region." [PRO:WCB] + PR_EXT:000001832 + SIRP/SHPS-1 family protein + PR_EXT:SIRP/SHPS-1 family protein + + + PR_EXT:SLAM family member 1 + "A protein that is a translation product of the human SLAMF1 gene or a 1:1 ortholog thereof." [PRO:WCB] + SLAMF1 + PR_EXT:000001833 + SLAM + IPO-3 + SLAM family member 1 + CD150 + CDw150 + + + PR_EXT:000001843 + CDw90 + Thy-1 membrane glycoprotein + THY1 + Thy-1 antigen + "A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof." [PRO:WCB] + Thy-1 + CD90 + PR_EXT:Thy-1 membrane glycoprotein + + + PR_EXT:cytotoxic T-lymphocyte protein 4 + CTLA4 + CD152 + CTLA-4 + cytotoxic T-lymphocyte protein 4 + PR_EXT:000001852 + "A protein that is a translation product of the human CTLA4 gene or a 1:1 ortholog thereof." [PRO:WCB] + cytotoxic T-lymphocyte-associated antigen 4 + + + IHABP + intracellular hyaluronic acid-binding protein + receptor for hyaluronan-mediated motility + PR_EXT:hyaluronan mediated motility receptor + HMMR + RHAMM + hyaluronan mediated motility receptor + CD168 + "A protein that is a translation product of the human HMMR gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:000001856 + + + integrin beta + "A protein with core architecture consisting of a large extracellular region containing one Integrin, beta chain domain (Pfam:PF00362), up to four EGF-like domains (Pfam:PF07974), and an Integrin beta tail domain (Pfam:PF07965), followed by a single-pass transmembrane region and a small cytoplasmic region often containing an Integrin beta cytoplasmic domain (Pfam:PF08725)." [PRO:WCB] + PR_EXT:000001861 + PR_EXT:integrin beta + + + PR_EXT:000001883 + PR_EXT:lysosome-associated membrane protein + lysosome-associated membrane protein + "A protein with core architecture consisting of a Lysosome-associated membrane glycoprotein (Pfam:PF01299) domain. It is a single-pass type I membrane protein that shuttles between lysosomes, endosomes, and the plasma membrane." [PRO:WCB] + + + scavenger receptor type A + MSR1 + CD204 + SR-A + macrophage acetylated LDL receptor I and II + SCARA1 + "A protein that is a translation product of the human MSR1 gene or a 1:1 ortholog thereof." [PRO:WCB] + Scvr + scavenger receptor class A member 1 + PR_EXT:macrophage scavenger receptor types I and II + PR_EXT:000001885 + macrophage scavenger receptor types I and II + + + PRIP + PRNP + major prion protein + PrP27-30 + "A protein that is a translation product of the human PRNP gene or a 1:1 ortholog thereof." [PRO:WCB] + Prn-p + ASCR + PrP33-35C + PR_EXT:major prion protein + PrP + CD230 + PR_EXT:000001886 + + + PR_EXT:CD14 molecule + "A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof." [PRO:WCB] + myeloid cell-specific leucine-rich glycoprotein + monocyte differentiation antigen CD14 + CD14 molecule + CD14 + PR_EXT:000001889 + + + atriopeptidase + NEP + CD10 + neprilysin + PR_EXT:000001898 + neutral endopeptidase 24.11 + enkephalinase + CALLA + MME + PR_EXT:neprilysin + "A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof." [PRO:WCB] + neutral endopeptidase + EPN + common acute lymphocytic leukemia antigen + + + paired box protein PAX-5 + BSAP + Pax-5 + PR_EXT:000001903 + PAX5 + PR_EXT:paired box protein PAX-5 + B-cell-specific transcription factor + "A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof." [PRO:WCB] + + + platelet endothelial cell adhesion molecule + PR_EXT:platelet endothelial cell adhesion molecule + CD31 + GPIIA' + Pecam + "A protein that is a translation product of the human PECAM1 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:000001904 + PECAM1 + PECA1 + PECAM-1 + EndoCAM + + + GPIV + glycoprotein IIIb + platelet glycoprotein IV + PAS IV + "A protein that is a translation product of the human CD36 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:000001905 + PAS-4 + leukocyte differentiation antigen CD36 + CD36 + platelet collagen receptor + GP3B + GPIIIB + platelet glycoprotein 4 + GP4 + PR_EXT:platelet glycoprotein 4 + thrombospondin receptor + FAT + fatty acid translocase + + + CD339 + JAGL1 + PR_EXT:000001921 + protein jagged-1 + "A protein that is a translation product of the human JAG1 gene or a 1:1 ortholog thereof." [PRO:WCB] + JAG1 + hJ1 + PR_EXT:protein jagged-1 + Jagged1 + + + "A protein with core architecture consisting of an extracellular region containing an Ig-like domain (Pfam:PF00047 or Pfam:PF10430), followed by 3 EGF-like domains (Pfam:PF07947 or Pfam:PF00053), another Ig-like domain, and 3 Fibronectin type III domains (Pfam:PF00041), and a cytoplasmic region containing the Protein tyrosine kinase domain (Pfam:PF07714)." [PRO:WCB] + PR_EXT:000001923 + PR_EXT:receptor-type tyrosine-protein kinase Tie + receptor-type tyrosine-protein kinase Tie + + + semaphorin + PR_EXT:semaphorin + "A protein with core architecture consisting of a signal sequence,a Sema domain (Pfam:PF01403), a Plexin repeat (Pfam:PF01437), and an Ig-like domain (Pfam:PF00047, Pfam:PF07686, or Pfam:PF07679)." [PRO:WCB] + PR_EXT:000001926 + + + PR_EXT:signal transducer and transcription activator STAT + PR_EXT:000001933 + signal transducer and transcription activator STAT + "A protein with core architecture consisting of a STAT protein, protein interaction domain (Pfam:PF02865), an SH2 domain (Pfam:PF01017), a STAT protein, DNA binding domain (Pfam:PF02864), and a second SH2 domain." [PRO:WCB] + + + TR-AP + Trap + tartrate-resistant acid phosphatase type 5 + PR_EXT:tartrate-resistant acid phosphatase type 5 + TrATPase + "A protein that is a translation product of the human ACP5 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:000001937 + type 5 acid phosphatase + T5ap + tartrate-resistant acid ATPase + ACP5 + + + Cf3 + "A protein that is a translation product of the human F3 gene or a 1:1 ortholog thereof." [PRO:WCB] + tissue factor + PR_EXT:000001940 + CD142 + PR_EXT:tissue factor + thromboplastin + Cf-3 + F3 + coagulation factor III + TF + + + Sfpi1 + PR_EXT:000001944 + SPI1 + SFFV proviral integration 1 protein + 31 kDa-transforming protein + transcription factor PU.1 + PR_EXT:transcription factor PU.1 + "A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof." [PRO:WCB] + Sfpi-1 + + + PR_EXT:000001946 + tumor necrosis factor ligand superfamily member 10/11 + PR_EXT:tumor necrosis factor ligand superfamily member 10/11 + "A protein with core architecture consisting of a fairly small cytoplasmic region, a transmembrane domain, and an extracellular domain containing a TNF(Tumour Necrosis Factor) family domain (Pfam:PF00229)." [PRO:WCB] + + + CD252 + TAX transcriptionally-activated glycoprotein 1 + TXGP1 + tumor necrosis factor ligand superfamily member 4 + PR_EXT:tumor necrosis factor ligand superfamily member 4 + OX40L + glycoprotein Gp34 + OX40 ligand + Txgp1l + PR_EXT:000001949 + "A protein that is a translation product of the human TNFSF4 gene or a 1:1 ortholog thereof." [PRO:WCB] + TNFSF4 + + + PR_EXT:tumor necrosis factor receptor superfamily member 11A + tumor necrosis factor receptor superfamily member 11A + PR_EXT:000001954 + ODFR + osteoclast differentiation factor receptor + receptor activator of NF-KB + CD265 + "A protein that is a translation product of the human TNFRSF11A gene or a 1:1 ortholog thereof." [PRO:WCB] + RANK + TNFRSF11A + + + TNFRSF6 + CD95 + APT1 + apo-1 antigen + FAS1 + PR_EXT:000001962 + tumor necrosis factor receptor superfamily member 6 + PR_EXT:tumor necrosis factor receptor superfamily member 6 + apoptosis-mediating surface antigen FAS + FASLG receptor + "A protein that is a translation product of the human FAS gene or a 1:1 ortholog thereof." [PRO:WCB] + FAS + + + Sirp-alpha-1 + SIRP + Sirp-alpha-3 + mSIRP-alpha1 + signal-regulatory protein alpha-2 + CD172a + SHPS-1 + SHP substrate 1 + brain Ig-like molecule with tyrosine-based activation motifs + "A SIRP/SHPS-1 family protein that is a translation product of the human SIRPA gene or a 1:1 ortholog thereof." [PRO:WCB] + MyD-1 antigen + Sirp-alpha-2 + PTPNS1 + signal-regulatory protein alpha-1 + tyrosine-protein phosphatase non-receptor type substrate 1 + CD172 antigen-like family member A + SHPS1 + MYD1 + MFR + signal-regulatory protein alpha-3 + PR_EXT:000001968 + PR_EXT:tyrosine-protein phosphatase non-receptor type substrate 1 + Bit + SIRPA + inhibitory receptor SHPS-1 + macrophage fusion receptor + + + vascular endothelial growth factor receptor + "A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain." [PRO:WCB] + PR_EXT:000001971 + PR_EXT:vascular endothelial growth factor receptor + + + inward rectifier K(+) channel Kir1.2 + inward rectifier K(+) channel Kir4.1 + "A G protein-activated inward rectifier potassium channel that is a translation product of the human KCNJ10 gene or a 1:1 ortholog thereof." [PRO:WCB] + ATP-sensitive inward rectifier potassium channel 10 + PR_EXT:ATP-sensitive inward rectifier potassium channel 10 + ATP-dependent inwardly rectifying potassium channel Kir4.1 + PR_EXT:000001979 + KCNJ10 + potassium channel, inwardly rectifying subfamily J member 10 + + + KCNJ11 + potassium channel, inwardly rectifying subfamily J member 11 + ATP-sensitive inward rectifier potassium channel 11 + inward rectifier K(+) channel Kir6.2 + "A G protein-activated inward rectifier potassium channel that is a translation product of the human KCNJ11 gene or a 1:1 ortholog thereof." [PRO:WCB] + IKATP + PR_EXT:000001980 + PR_EXT:ATP-sensitive inward rectifier potassium channel 11 + + + macrophage inflammatory protein 3 alpha + SCYA20 + CCL20 + MIP-3-alpha + small-inducible cytokine A20 + CC chemokine ST38 + "A C/C-C motif small inducible chemokine that is a translation product of the human CCL20 gene or a 1:1 ortholog thereof." [PRO:WCB] + CC chemokine LARC + PR_EXT:C-C motif chemokine 20 + LARC + PR_EXT:000001992 + MIP3A + liver and activation-regulated chemokine + C-C motif chemokine 20 + beta chemokine exodus-1 + + + KCNJ9 + potassium channel, inwardly rectifying subfamily J member 9 + PR_EXT:000002004 + "A G protein-activated inward rectifier potassium channel that is a translation product of the human KCNJ9 gene or a 1:1 ortholog thereof." [PRO:WCB] + G protein-activated inward rectifier potassium channel 3 + PR_EXT:G protein-activated inward rectifier potassium channel 3 + inward rectifier K(+) channel Kir3.3 + GIRK3 + GIRK-3 + + + KATP-1 + inward rectifier K(+) channel Kir3.4 + cardiac inward rectifier + PR_EXT:000002005 + KCNJ5 + GIRK4 + GIRK-4 + "A G protein-activated inward rectifier potassium channel that is a translation product of the human KCNJ5 gene or a 1:1 ortholog thereof." [PRO:WCB] + IRK-4 + G protein-activated inward rectifier potassium channel 4 + PR_EXT:G protein-activated inward rectifier potassium channel 4 + potassium channel, inwardly rectifying subfamily J member 5 + heart KATP channel + + + PR_EXT:MHC class II histocompatibility antigen beta chain HLA-DRB4 + MHC class II histocompatibility antigen beta chain HLA-DRB4 + PR_EXT:000002021 + HLA-DRB4 + "An MHC class II histocompatibility antigen beta chain that is a translation product of the human HLA-DRB4 gene or a 1:1 ortholog thereof." [PRO:WCB] + + + p140 TEK + STK1 + tyrosine-protein kinase receptor TEK + HYK + TEK + tyrosine-protein kinase receptor TIE-2 + tunica interna endothelial cell kinase + CD202b + "A receptor-type tyrosine-protein kinase Tie that is a translation product of the human TEK gene or a 1:1 ortholog thereof." [PRO:WCB] + TIE2 + PR_EXT:000002032 + PR_EXT:angiopoietin-1 receptor + angiopoietin-1 receptor + Tie-2 + + + PR_EXT:000002038 + "A C/C-C motif small inducible chemokine that is a member of a subfamily that includes eotaxin." [PRO:WCB] + PR_EXT:eotaxin-like cytokine + eotaxin-like cytokine + + + "An integrin beta that is a translation product of the human ITGB1 gene or a 1:1 ortholog thereof." [PRO:WCB] + MDF2 + fibronectin receptor subunit beta + CD29 + FNRB + PR_EXT:000002040 + integrin beta-1 + ITGB1 + PR_EXT:integrin beta-1 + VLA-4 subunit beta + MSK12 + + + platelet membrane glycoprotein IIIa + GPIIIa + integrin beta-3 + PR_EXT:000002042 + CD61 + "An integrin beta that is a translation product of the human ITGB3 gene or a 1:1 ortholog thereof." [PRO:WCB] + GP3A + PR_EXT:integrin beta-3 + ITGB3 + + + APOER + LRP-1 + PR_EXT:low-density lipoprotein receptor-related protein 1 + apolipoprotein E receptor + "An LDL receptor-related protein that is a translation product of the human LRP1 gene or a 1:1 ortholog thereof." [PRO:WCB] + low-density lipoprotein receptor-related protein 1 + APR + A2MR + alpha-2-macroglobulin receptor + PR_EXT:000002058 + LRP1 + CD91 + + + "A C/C-C motif small inducible chemokine that is a translation product of the human XCL1 or XCL2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." [PRO:DAN, PRO:WCB] + PR_EXT:lymphotactin-like chemokine + lymphotactin-like chemokine + PR_EXT:000002059 + + + 120 kDa lysosomal membrane glycoprotein + LAMP1 + LGP-120 + CD107 antigen-like family member A + PR_EXT:lysosome-associated membrane glycoprotein 1 + P2B + lysosome-associated membrane glycoprotein 1 + LAMP-1 + CD107a + LGP-A + "A lysosome-associated membrane protein that is a translation product of the human LAMP1 gene or a 1:1 ortholog thereof." [PRO:WCB] + lysosomal membrane glycoprotein A + PR_EXT:000002060 + lysosome-associated membrane protein 1 + + + LAMP-2 + lysosome-associated membrane protein 2 + "A lysosome-associated membrane protein that is a translation product of the human LAMP2 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:000002061 + PR_EXT:lysosome-associated membrane glycoprotein 2 + CD107 antigen-like family member B + lysosomal membrane glycoprotein type B + lysosome-associated membrane glycoprotein 2 + LAMP2 + LGP-B + CD107b + + + CD68 + PR_EXT:000002064 + macrosialin + gp110 + PR_EXT:macrosialin + "A lysosome-associated membrane protein that is a translation product of the human CD68 gene or a 1:1 ortholog thereof." [PRO:WCB] + + + tyrosine-protein kinase Kit + CD117 + KIT + PR_EXT:mast/stem cell growth factor receptor + proto-oncogene c-Kit + Sl + PR_EXT:000002065 + SCFR + "A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof." [PRO:WCB] + mast/stem cell growth factor receptor + + + proto-oncogene c-ErbB-2 + receptor tyrosine-protein kinase erbB-2 + tyrosine kinase-type cell surface receptor HER2 + NGL + MLN 19 + MLN19 + p185erbB2 + "An EGF receptor type tyrosine-protein kinase that is a translation product of the human ERBB2 gene or a 1:1 ortholog thereof." [PRO:WCB] + ERBB2 + Kiaa3023 + proto-oncogene Neu + PR_EXT:000002082 + PR_EXT:receptor tyrosine-protein kinase erbB-2 + NEU + CD340 + metastatic lymph node gene 19 protein + HER2 + + + STAT1 + Signal transducer and activator of transcription 1-alpha/beta + signal transducer and activator of transcription 1 + transcription factor ISGF-3 components p91/p84 + "A signal transducer and transcription activator STAT that is a translation product of the human STAT1 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:signal transducer and activator of transcription 1 + PR_EXT:000002087 + + + STAT2 + signal transducer and activator of transcription 2 + PR_EXT:signal transducer and activator of transcription 2 + "A signal transducer and transcription activator STAT that is a translation product of the human STAT2 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:000002088 + + + APRF + STAT3 + acute-phase response factor + signal transducer and activator of transcription 3 + "A signal transducer and transcription activator STAT that is a translation product of the human STAT3 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:000002089 + PR_EXT:signal transducer and activator of transcription 3 + + + PR_EXT:000002090 + STAT4 + "A signal transducer and transcription activator STAT that is a translation product of the human STAT4 gene or a 1:1 ortholog thereof." [PRO:WCB] + signal transducer and activator of transcription 4 + PR_EXT:signal transducer and activator of transcription 4 + + + Mpf + PR_EXT:000002091 + STAT5A + signal transducer and activator of transcription 5a + Mgf + "A signal transducer and transcription activator STAT that is a translation product of the human STAT5A gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:signal transducer and activator of transcription 5a + mammary gland factor + STAT5 + + + signal transducer and activator of transcription 5b + STAT5B + PR_EXT:000002092 + "A signal transducer and transcription activator STAT that is a translation product of the human STAT5B gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:signal transducer and activator of transcription 5b + + + TRANCE + tumor necrosis factor ligand superfamily member 11 + osteoclast differentiation factor + receptor activator of nuclear factor kappa-B ligand + "A tumor necrosis factor ligand superfamily member 10/11 that is a translation product of the human TNFSF11 gene or a 1:1 ortholog thereof." [PRO:WCB] + ODF + CD254 + PR_EXT:tumor necrosis factor ligand superfamily member 11 + TNFSF11 + osteoprotegerin ligand + TNF-related activation-induced cytokine + PR_EXT:000002107 + OPGL + RANKL + + + "A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:000002112 + fetal liver kinase 1 + kinase insert domain receptor + FLK-1 + VEGFR-2 + vascular endothelial growth factor receptor 2 + kinase NYK + PR_EXT:vascular endothelial growth factor receptor 2 + CD309 + protein-tyrosine kinase receptor flk-1 + KDR + FLK1 + + + MCP-1 + PR_EXT:C-C motif chemokine 2 + monocyte chemotactic and activating factor + MCAF + HC11 + monocyte chemotactic protein 1 + "An eotaxin-like cytokine that is a translation product of the human CCL2 gene or a 1:1 ortholog thereof." [PRO:WCB] + C-C motif chemokine 2 + PR_EXT:000002122 + monocyte secretory protein JE + MCP1 + platelet-derived growth factor-inducible protein JE + CCL2 + monocyte chemoattractant protein 1 + Je + small-inducible cytokine A2 + SCYA2 + + + LTN + ATAC + "A lymphotactin-like chemokine that is a translation product of the human XCL1 gene or a 1:1 ortholog thereof." [PRO:WCB] + XC chemokine ligand 1 + lymphotaxin + C motif chemokine 1 + XCL1 + PR_EXT:lymphotactin + SCM-1-alpha + cytokine SCM-1 + SCYC1 + PR_EXT:000002140 + lymphotactin + Lptn + small-inducible cytokine C1 + + + bcl2-L-8 + bcl-XL/Bcl-2-associated death promoter + PR_EXT:Bcl2 antagonist of cell death + bcl-2-like protein 8 + Bcl2 antagonist of cell death + "A protein that is a translation product of the human BAD gene or a 1:1 ortholog thereof." [PRO:WCB] + BAD + PR_EXT:000002184 + BBC6 + bcl-2-binding component 6 + BCL2L8 + + + PR_EXT:Bcl-2-like apoptosis inhibitor + Bcl-2-like apoptosis inhibitor + PR_EXT:000002186 + "A protein that is a translation product of the human BCL2, BCL2L1, or BCL2L2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. The core domain architecture consists of an amino-terminal BH4 domain (Pfam:PF02180), which confers apoptosis inhibitory activity, and a Bcl-2 domain (Pfam:PF02180) common to many apoptosis regulator proteins." [PRO:DAN, PRO:WCB] + + + AKT1 + Akt + proto-oncogene c-Akt + RAC-PK-alpha + RAC-alpha serine/threonine-protein kinase + PR_EXT:RAC-alpha serine/threonine-protein kinase + thymoma viral proto-oncogene + protein kinase B + AKT1 kinase + RAC + PR_EXT:000002190 + "An AKT kinase that is a translation product of the human AKT1 gene or a 1:1 ortholog thereof." [PRO:WCB] + + + PR_EXT:TNF receptor-associated factor + TRAF + PR_EXT:000002191 + TNF receptor-associated factor + "A protein that is a translation product of a family of genes including the six human genes, TRAF1 to TRAF6. The core architectures of this protein consists of a zinc finger C3HC4 type (Ring finger) (Pfam:PF00097), a TRAF-type zinc finger (Pfam:PF02176) and a MATH domain (Pfam:PF00917)." [PRO:WCB] + + + bcl2-L-4 + BCL2L4 + PR_EXT:000002193 + "A protein that is a translation product of the human BAX gene or a 1:1 ortholog thereof. In this class the Bcl-2 domain is characterized by the presence of the BH3, BH1, and BH2 motifs." [PRO:SY, PRO:WCB] + apoptosis regulator BAX + PR_EXT:apoptosis regulator BAX + BAX + bcl-2-like protein 4 + + + apoptotic protease-activating factor 1 + APAF1 + PR_EXT:000002194 + "A protein that is a translation product of the human APAF1 gene or a 1:1 ortholog thereof." [PRO:WCB] + APAF-1 + PR_EXT:apoptotic protease-activating factor 1 + KIAA0413 + + + "A protein that is a translation product of a gene family that includes CASP3, CASP6, and CASP7 genes. The core architecture consists of a Caspase domain (Pfam:PF00656). Encoded as zymogens, the activated proteins are cysteine proteases typically involved in apoptosis." [PRO:WCB] + caspase-3-like protease + PR_EXT:000002196 + PR_EXT:caspase-3-like protease + + + CTNNB1 + catenin beta-1 + Catnb + PR_EXT:000002198 + "A protein that is a translation product of the human CTNNB1 gene or a 1:1 ortholog thereof." [PRO:WCB] + beta-catenin + PR_EXT:catenin beta-1 + CTNNB + + + "A protein that is a translation product of the CYC, CYCS or closely related CYCT gene (mouse and rat) with core architecture consisting of a Cytochrome c (Pfam:PF00034) domain." [PRO:WCB] + cytochrome c protein + PR_EXT:000002199 + PR_EXT:cytochrome c protein + + + "A protein that is a translation product of the human DYNLL1 or DYNLL2 genes, or 1:1 orthologs thereof. The protein is small (89 residues in human and mouse) with core architecture consisting of a Dynein light chain type 1 domain (Pfam:PF01221)." [PRO:WCB] + PR_EXT:dynein light chain + dynein light chain + PR_EXT:000002201 + + + stress-activated protein kinase JNK1 + PRKM8 + MAP kinase 8 + mitogen-activated protein kinase 8 + MAPK8 + "A protein that is a translation product of the human MAPK8 gene or a 1:1 ortholog thereof." [PRO:WCB] + JNK-46 + MAPK 8 + PR_EXT:mitogen-activated protein kinase 8 + c-Jun N-terminal kinase 1 + PR_EXT:000002206 + stress-activated protein kinase 1 + SAPK1 + JNK1 + + + PR_EXT:000002207 + "A protein that is a translation product of the human OCLN gene or a 1:1 ortholog thereof." [PRO:WCB] + occludin + Ocl + PR_EXT:occludin + OCLN + + + RING finger protein 84 + "A TNF receptor-associated factor that is a translation product of the human TRAF5 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:TNF receptor-associated factor 5 + RNF84 + TNF receptor-associated factor 5 + PR_EXT:000002291 + TRAF5 + + + RING finger protein 85 + TRAF6 + interleukin-1 signal transducer + E3 ubiquitin-protein ligase TRAF6 + PR_EXT:TNF receptor-associated factor 6 + "A TNF receptor-associated factor that is a translation product of the human TRAF6 gene or a 1:1 ortholog thereof." [PRO:WCB] + TNF receptor-associated factor 6 + PR_EXT:000002292 + RNF85 + + + BCL2 + "A Bcl-2-like apoptosis inhibitor that is a translation product of the human BCL2 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:apoptosis regulator Bcl-2 + PR_EXT:000002307 + Bcl-2 + apoptosis regulator Bcl-2 + + + bcl2-L-1 + BCL2L1 + "A Bcl-2-like apoptosis inhibitor that is a translation product of the human BCL2L1 gene or a 1:1 ortholog thereof." [PRO:WCB] + PR_EXT:bcl-2-like protein 1 + BCL2L + PR_EXT:000002308 + bcl-2-like protein 1 + BCLX + apoptosis regulator Bcl-X + + + LICE + CASP-3 + SREBP cleavage activity 1 + cysteine protease CPP32 + PR_EXT:caspase-3 + CPP32 + CPP-32 + apopain + "A caspase-3-like protease that is a translation product of the human CASP3 gene or a 1:1 ortholog thereof." [PRO:JAN] + SCA-1 + caspase-3 + CASP3 + protein Yama + PR_EXT:000002312 + + + HDLC1 + dynein light chain LC8-type 1 + DNCL1 + PR_EXT:000002325 + DYNLL1 + protein inhibitor of neuronal nitric oxide synthase + DLC1 + PIN + "A dynein light chain that is a translation product of the human DYNLL1 gene or a 1:1 ortholog thereof. Dynein light chain 1 is a component of the dynein motor complex." [PRO:WCB] + dynein light chain 1, cytoplasmic + 8 kDa dynein light chain + PR_EXT:dynein light chain 1, cytoplasmic + DNCLC1 + + + "A bcl-2-like protein 1 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:Q64373-1 or a 1:1 ortholog thereof." [PRO:JAN] + PR_EXT:000002385 + BCL2L1/iso:1 + apoptosis regulator Bcl-X isoform 1 + isoform Bcl-X(L) + PR_EXT:bcl-2-like protein 1 isoform 1 + bcl-2-like protein 1 isoform 1 + + + PR_EXT:000002976 + ly-6-like protein + PR_EXT:ly-6-like protein + "A protein that is the translation product of any of the LY6 genes (LY6A-LY6I)." [PRO:CNA] + + + ly-6G.1 + PR_EXT:lymphocyte antigen 6G + PR_EXT:000002978 + ly-6G + Ly6g + "A ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof." [PRO:CNA] + lymphocyte antigen 6G + + + PR_EXT:000002986 + Ikaros family of zinc finger transcription factors + Ikaros-like zinc finger transcription factor + PR_EXT:Ikaros-like zinc finger transcription factor + "A protein that is the translation product of some gene evolved from the last common ancestor of human IKZF1 and human IKZF5 gene. The canonical protein sequence has a core domain architecture consisting of two copies of the Zinc finger, C2H2 type (Pfam:PF00096) domains, an N-terminal domain important for DNA recognition, and a C-terminal domain that mediates homo- and heterotypic associations between family members." [PMID:10978333, PMID:19342657] + + + PR_EXT:000002997 + Src family tyrosine kinase + PR_EXT:proto-oncogene SRC-like tyrosine-protein kinase + proto-oncogene SRC-like tyrosine-protein kinase + "A protein that contains one copy of the SH3 domain (Pfam:PF00018), a copy of the SH2 domain (Pfam:PF00017), and a copy of the Protein tyrosine kinase (Pfam:PF07714) domain. Members of this class are cytoplasmic protein-tyrosine kinases believed to be involved in signal transduction." [PMID:7545532, PRO:CNA] + SFK + + + Trp53 + P53 + cellular tumor antigen p53 + PR_EXT:000003035 + PR_EXT:cellular tumor antigen p53 + TP53 + tumor suppressor p53 + "A protein that is a translation product of the human TP53 gene or a 1:1 ortholog thereof." [PRO:CNA] + phosphoprotein p53 + antigen NY-CO-13 + + + PR_EXT:000003041 + FRAP2 + FRAP1 + MTOR + mTOR + rapamycin target protein 1 + "A protein that is a translation product of the human MTOR gene or a 1:1 ortholog thereof." [PRO:CL] + serine/threonine-protein kinase mTOR + PR_EXT:serine/threonine-protein kinase mTOR + FRAP + FKBP12-rapamycin complex-associated protein + FK506-binding protein 12-rapamycin complex-associated protein 1 + mammalian target of rapamycin + RAPT1 + + + "A protein that is a member of the conventional phorbol ester (and diacylglycerol) receptor/protein kinase class. The canonical protein sequence has a core domain architecture consisting of two copies of the Phorbol esters/diacylglycerol binding domain (C1 domain) (Pfam:PF00130), followed by a C2 domain (Pfam:PF00168), a Protein kinase domain (Pfam:PF00069) and a Protein kinase C terminal domain (Pfam:PF00433)." [PMID:1877391] + conventional protein kinase C + protein kinase C, alpha/beta/gamma types + PR_EXT:000003057 + Calcium-dependent PKC + cPKC + PR_EXT:conventional protein kinase C + + + PKC-A + protein kinase C alpha type + PR_EXT:protein kinase C alpha type + protein kinase Calpha + PKC-alpha + PR_EXT:000003058 + PRKCA + PRKACA + "A conventional protein kinase C that is a translation product of the human PRKCA gene or a 1:1 ortholog thereof." [PRO:CL] + PKCA + + + CDKN1B + cyclin-dependent kinase inhibitor p27 + "A protein that is a translation product of the human CDKN1B gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:cyclin-dependent kinase inhibitor 1B + KIP1 + PR_EXT:000003090 + cyclin-dependent kinase inhibitor 1B + p27Kip1 + + + PR_EXT:map kinase p38 + PR_EXT:000003106 + fam:MAPKp38 + "A protein that is a serine/threonine-specific protein kinase that responds to extracellular stimuli (environmental stress, pro-inflammatory cytokines and lipopolysaccharide) and regulates cellular activities such as gene expression, mitosis, differentiation, and cell survival/apoptosis. The activated form phosphorylates target substrates on Ser or Thr residues followed by a proline. A distinguishing feature is the conserved sequence TxY." [PRO:CNA] + map kinase p38 + + + MAPK14 + PR_EXT:000003107 + "A map kinase p38 that is a translation product of the human MAPK14 gene or a 1:1 ortholog thereof." [PRO:CNA] + MAPK 14 + CRK1 + MAP kinase p38 alpha + cytokine suppressive anti-inflammatory drug-binding protein + MAP kinase 14 + mitogen-activated protein kinase p38 alpha + CSPB1 + SAPK2A + MAX-interacting protein 2 + CSBP1 + CSBP2 + MXI2 + CSBP + PR_EXT:mitogen-activated protein kinase 14 + mitogen-activated protein kinase 14 + MAP kinase MXI2 + CSAID-binding protein + + + subtilisin/kexin-type proprotein convertase + PR_EXT:000003136 + PR_EXT:subtilisin/kexin-type proprotein convertase + + + dibasic-processing enzyme + FURIN + PCSK3 + PR_EXT:furin + furin + FUR + PACE + "A subtilisin/kexin-type proprotein convertase that is a translation product of the human FURIN gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:000003137 + paired basic amino acid residue-cleaving enzyme + prohormone convertase 3 + + + TGF-beta-activated kinase 1 + PR_EXT:000003158 + mitogen-activated protein kinase kinase kinase 7 + TAK1 + "A protein that is a translation product of the human MAP3K7 gene or a 1:1 ortholog thereof." [PRO:CNA] + transforming growth factor-beta-activated kinase 1 + PR_EXT:mitogen-activated protein kinase kinase kinase 7 + MAP3K7 + + + PR_EXT:000003171 + IGFBP-related protein + PR_EXT:IGFBP-related protein + + + PR_EXT:000003172 + connective tissue growth factor + PR_EXT:connective tissue growth factor + Fisp12 + IGFBP-8 + HCS24 + IBP-8 + CCN family member 2 + IGFBP8 + IGF-binding protein 8 + hypertrophic chondrocyte-specific protein 24 + CCN2 + Fisp-12 + "An IGFBP-related protein that is a translation product of the human CTGF gene or a 1:1 ortholog thereof." [PRO:CNA] + CTGF + protein FISP-12 + insulin-like growth factor-binding protein 8 + + + PR_EXT:shc-transforming protein + SHC + PR_EXT:000003177 + shc-transforming protein + "A protein that is a translation product of the human SHC1, SHC2, SHC3 or SHC4 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. The canonical protein sequence has a core domain architecture consisting of a copy of the Phosphotyrosine interaction domain (PTB/PID) (Pfam:PF00640) and a copy of the SH2 domain (Pfam:PF00017) towards the C-terminus." [PRO:CNA, PRO:DAN] + + + PR_EXT:000003197 + calcium/calmodulin-dependent protein kinase type II chain + CAMKII + "A protein with a core domain architecture consisting of a Protein kinase domain (Pfam:PF00069) and a C terminal Calcium/calmodulin dependent protein kinase II Association (Pfam:PF08332) domain." [PRO:CNA] + PR_EXT:calcium/calmodulin-dependent protein kinase type II chain + + + CAV1 + PR_EXT:000003198 + PR_EXT:caveolin-1 + "A protein that is a translation product of the human CAV1 gene or a 1:1 ortholog thereof." [PRO:CNA] + caveolin-1 + CAV + + + CAMK2A + calcium/calmodulin-dependent protein kinase type II subunit alpha + KIAA0968 + PR_EXT:000003199 + CaMK-II subunit alpha + "A calcium/calmodulin-dependent protein kinase type II chain that is a translation product of the human CAMK2A gene or a 1:1 ortholog thereof." [PRO:CNA] + CAMKA + CaM kinase II subunit alpha + PR_EXT:calcium/calmodulin-dependent protein kinase type II subunit alpha + calcium/calmodulin-dependent protein kinase type II alpha chain + + + "A protein that is a translation product of the FMRP, FXR1 or FXR2." [PMID:15968590] + PR_EXT:000003222 + PR_EXT:fragile X-related protein + fragile X-related protein + FXR + + + PR_EXT:envelope glycoprotein gp160 + PR_EXT:000003225 + envelope glycoprotein gp160 + "A protein that is a translation product of the HIV env gene or a 1:1 ortholog thereof." [PRO:CNA] + Env polyprotein + env + + + RAF + "A protein that is a translation product of the human RAF1 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:RAF proto-oncogene serine/threonine-protein kinase + cRaf + proto-oncogene c-RAF + RAF proto-oncogene serine/threonine-protein kinase + PR_EXT:000003244 + RAF1 + Raf-1 + + + "A protein that is a component of collagen. Collagens are trimeric molecules in which each chain comprises a repeating Gly-X-Y triplet, in which X and Y can be any residue but are usually proline and hydroxyproline, respectively. This results in a left-handed helix that combines with other two to form a triple-helical structure." [Pfam:PF01391, PMID:15788652, PMID:1639194] + PR_EXT:collagen alpha chain + PR_EXT:000003262 + collagen alpha chain + + + collagen type I alpha chain + PR_EXT:collagen type I alpha chain + "A collagen alpha chain that is a translation product of the human COL1A1 or COL1A2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." [PRO:CNA, PRO:DAN] + PR_EXT:000003263 + + + collagen alpha-1(I) chain + COL1A1 + alpha-1 type I collagen + PR_EXT:000003264 + "A collagen type I alpha chain that is a translation product of the human COL1A1 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:collagen alpha-1(I) chain + Cola1 + + + alpha-1 type II collagen + collagen type II alpha chain + COL2A1 + "A collagen alpha chain that is a translation product of the human COL2A1 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:000003266 + PR_EXT:collagen type II alpha chain + + + kinase-related transforming protein + PR_EXT:000003270 + CDK2-related kinase + "A protein that is cyclin-dependent kinase. The activated form phosphorylates target substrates on Ser or Thr residues followed by a proline. The core domain architecture consists of a copy of the Protein kinase domain (Pfam:PF00069)." [PRO:CNA] + PR_EXT:CDK2-related kinase + CDK + + + PR_EXT:000003272 + insulin receptor family + insulin receptor-related receptor + "A protein with a core domain composition consisting of a Receptor L domain (Pfam:PF01030) followed by a Furin-like cysteine rich region (Pfam:PF00757) and a second copy of the Receptor L domain (Pfam:PF01030), two to four copies of the Fibronectin type 3 domain (Pfam:PF00041) and a copy of the Protein tyrosine kinase (Pfam:PF07714) domain at the C-terminus." [PRO:JAN] + PR_EXT:insulin receptor-related receptor + + + CD221 + insulin-like growth factor I receptor + PR_EXT:insulin-like growth factor 1 receptor + PR_EXT:000003273 + insulin-like growth factor 1 receptor + "An insulin receptor-related receptor that is a translation product of the human IGF1R gene or a 1:1 ortholog thereof." [PRO:JAN] + IGF-I receptor + IGF1R + + + PR_EXT:000003292 + "A protein that is a translation product of the human NFKBIA, NFKBIB, or NFKBIE genes, 1:1 orthologs thereof, or a semi-ortholog thereof. It contains multiple copies of the Ankyrin repeats (Pfam:PF00023 or Pfam:PF12796)." [PRO:CNA, PRO:DAN] + PR_EXT:NF-kappa-B inhibitor + NF-kappa-B inhibitor + IKB + + + MAD3 + major histocompatibility complex enhancer-binding protein MAD3 + IKBalpha + IkappaBalpha + IkB-alpha + "An NF-kappa-B inhibitor that is a translation product of the human NFKBIA gene or a 1:1 ortholog thereof." [PMID:19302050, TLR:AMM] + NF-kappa-B inhibitor alpha + NFKBI + PR_EXT:NF-kappa-B inhibitor alpha + PR_EXT:000003293 + I-kappa-B-alpha + IKBA + NFKBIA + + + TR-interacting protein 9 + thyroid receptor-interacting protein 9 + IkB-beta + TRIP-9 + IKBbeta + IkappaBbeta + IkB-B + "An NF-kappa-B inhibitor that is a translation product of the human NFKBIB gene or a 1:1 ortholog thereof." [PMID:19302050, TLR:AMM] + NFKBIB + PR_EXT:000003294 + TRIP9 + NF-kappa-B inhibitor beta + I-kappa-B-beta + IKBB + NF-kappa-BIB + PR_EXT:NF-kappa-B inhibitor beta + + + NFKBIE + I-kappa-B-epsilon + IKBepsilon + NF-kappa-B inhibitor epsilon + IkappaBepsilon + IkB-epsilon + IKBE + "An NF-kappa-B inhibitor that is a translation product of the human NFKBIE gene or a 1:1 ortholog thereof." [PMID:19302050, TLR:AMM] + NF-kappa-BIE + IkB-E + PR_EXT:NF-kappa-B inhibitor epsilon + PR_EXT:000003295 + + + PR_EXT:collagen alpha-1(III) chain + COL3A1 + collagen alpha-1(III) chain + "A collagen alpha chain that is a translation product of the human COL3A1 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:000003328 + + + "A fragile X-related protein that is a translation product of the human FMR1 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:synaptic functional regulator FMR1 + synaptic functional regulator FMR1 + FMR1 + PR_EXT:000003389 + fragile X mental retardation protein 1 + fragile X mental retardation 1 protein + + + fragile X mental retardation syndrome-related protein 1 + PR_EXT:fragile X mental retardation syndrome-related protein 1 + hFXR1p + Fxr1h + "A fragile X-related protein that is a translation product of the human FXR1 gene or a 1:1 ortholog thereof." [MGI:104860, PRO:HJD] + FXR1 + mFxr1p + PR_EXT:000003390 + + + PR_EXT:000003391 + fragile X mental retardation syndrome-related protein 2 + "A fragile X-related protein that is a translation product of the human FXR2 gene or a 1:1 ortholog thereof." [PRO:CNA] + FMR1L2 + FXR2 + Fxr2h + PR_EXT:fragile X mental retardation syndrome-related protein 2 + + + hsp70 family chaperone + PR_EXT:000003425 + "A protein that is a stand alone version of the Hsp70 protein (Pfam:PF00012) domain, which comprises two major regions: an N-terminal ATP-binding domain and a C-terminal substrate-binding domain." [Pfam:PF00012, PRO:CNA] + PR_EXT:hsp70 family chaperone + + + "An hsp70 family chaperone that has its ATP-binding and substrate-binding domains separated by a linker domain of fewer than 25 amino acids." [PMID:18663603] + PR_EXT:HSPA protein + PR_EXT:000003426 + HSPA protein + typical hsp70 protein + + + "A protein that is a translation product of the human CUGBP1 gene or a 1:1 ortholog thereof." [MGI:1342295, PRO:HJD] + PR_EXT:CUGBP Elav-like family member 1 + brain protein F41 + BRUNOL2 + CUGBP Elav-like family member 1 + CELF1 + CELF-1 + CUG triplet repeat RNA-binding protein 1 + PR_EXT:000003439 + CUGBP1 + EDEN-BP homolog + deadenylation factor CUG-BP + deadenylation factor EDEN-BP + RNA-binding protein BRUNOL-2 + CUG-BP1 + CUGBP + 50 kDa nuclear polyadenylated RNA-binding protein + embryo deadenylation element-binding protein homolog + NAB50 + bruno-like protein 2 + + + RAG1 + PR_EXT:V(D)J recombination-activating protein 1 + V(D)J recombination-activating protein 1 + RAG-1 + PR_EXT:000003457 + RING finger protein 74 + "A protein that is a translation product of the human RAG1 gene or a 1:1 ortholog thereof." [PRO:CNA] + RNF74 + + + PR_EXT:000003463 + TBR2 + T-box brain protein 2 + TBR-2 + PR_EXT:eomesodermin + "A T-brain transcription factor that is a translation product of the human EOMES gene or a 1:1 ortholog thereof." [PMID:10407135, PRO:CNA] + eomesodermin + T-brain-2 + EOMES + + + "A protein that contains one copy of the T-box domain (Pfam:PF00907) and it is involved in the anterior neural specification." [PMID:10750050, PMID:12210112] + T-brain transcription factor + PR_EXT:000003506 + Eomes/Tbr1/Tbx21 family protein + PR_EXT:T-brain transcription factor + + + CERP + ABC1 + ATP-binding cassette transporter 1 + ABCA1 + PR_EXT:000003537 + cholesterol efflux regulatory protein + "A protein that is a translation product of the human ABCA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:ATP-binding cassette sub-family A member 1 + ATP-binding cassette 1 + ATP-binding cassette sub-family A member 1 + ABC-1 + + + ATP-binding cassette sub-family B member 11 + ABCB11 + sister of P-glycoprotein + bile salt export pump + "A protein that is a translation product of the human ABCB11 gene or a 1:1 ortholog thereof." [PRO:DNx] + Spgp + BSEP + PR_EXT:000003549 + PR_EXT:bile salt export pump + + + SUR + ATP-binding cassette sub-family C member 8 + SUR1 + PR_EXT:ATP-binding cassette sub-family C member 8 + HRINS + "A protein that is a translation product of the human ABCC8 gene or a 1:1 ortholog thereof." [PRO:DNx] + ATP-binding cassette transporter sub-family C member 8 + PR_EXT:000003563 + sulfonylurea receptor 1 + ABCC8 + + + ABCG5 + PR_EXT:ATP-binding cassette sub-family G member 5 + PR_EXT:000003572 + ATP-binding cassette sub-family G member 5 + sterolin-1 + "A protein that is a translation product of the human ABCG5 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:ATP-binding cassette sub-family G member 8 + "A protein that is a translation product of the human ABCG8 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000003573 + ABCG8 + ATP-binding cassette sub-family G member 8 + sterolin-2 + + + "A protein that is a translation product of the human ACAN gene or a 1:1 ortholog thereof." [PRO:DNx] + MSK16 + CSPG1 + PR_EXT:000003606 + cartilage-specific proteoglycan core protein + chondroitin sulfate proteoglycan 1 + AGC1 + Agc + ACAN + PR_EXT:aggrecan core protein + aggrecan core protein + chondroitin sulfate proteoglycan core protein 1 + CSPCP + + + palmitoyl-CoA oxidase + straight-chain acyl-CoA oxidase + peroxisomal acyl-coenzyme A oxidase 1 + Paox + ACOX + ACOX1 + "A protein that is a translation product of the human ACOX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + SCOX + PR_EXT:peroxisomal acyl-coenzyme A oxidase 1 + PR_EXT:000003642 + AOX + + + "A protein that is a translation product of the human ACTA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + ACTA1 + actin, alpha skeletal muscle + PR_EXT:000003674 + PR_EXT:actin, alpha skeletal muscle + alpha-actin-1 + ACTA + + + "A protein that is a translation product of the human ACTA2 gene or a 1:1 ortholog thereof." [PRO:DNx] + alpha-actin-2 + ACTVS + ACTSA + PR_EXT:actin, aortic smooth muscle + cell growth-inhibiting gene 46 protein + ACTA2 + PR_EXT:000003675 + actin, aortic smooth muscle + + + "A protein that is a translation product of the human ACTB gene or a 1:1 ortholog thereof." [PRO:DNx] + actin, cytoplasmic 1 + beta-actin + ACTB + PR_EXT:000003676 + PR_EXT:actin, cytoplasmic 1 + + + PR_EXT:disintegrin and metalloproteinase domain-containing protein 11 + MDC + ADAM 11 + PR_EXT:000003710 + metalloproteinase-like, disintegrin-like, and cysteine-rich protein + ADAM11 + "A protein that is a translation product of the human ADAM11 gene or a 1:1 ortholog thereof." [PRO:DNx] + disintegrin and metalloproteinase domain-containing protein 11 + + + "A protein that is a translation product of the human ADAM12 gene or a 1:1 ortholog thereof." [PRO:DNx] + MLTN + Mltna + meltrin-alpha + disintegrin and metalloproteinase domain-containing protein 12 + PR_EXT:disintegrin and metalloproteinase domain-containing protein 12 + PR_EXT:000003711 + ADAM12 + ADAM 12 + + + PR_EXT:disintegrin and metalloproteinase domain-containing protein 15 + disintegrin and metalloproteinase domain-containing protein 15 + MDC15 + metargidin + PR_EXT:000003712 + ADAM15 + AD56 + MDC-15 + ADAM 15 + metalloproteinase-like, disintegrin-like, and cysteine-rich protein 15 + metalloprotease RGD disintegrin protein + "A protein that is a translation product of the human ADAM15 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A protein that is a translation product of the human ADAM19 gene or a 1:1 ortholog thereof." [PRO:DNx] + disintegrin and metalloproteinase domain-containing protein 19 + ADAM 19 + meltrin-beta + ADAM19 + MLTNB + metalloprotease and disintegrin dendritic antigen marker + MADDAM + PR_EXT:disintegrin and metalloproteinase domain-containing protein 19 + PR_EXT:000003714 + + + PR_EXT:disintegrin and metalloproteinase domain-containing protein 2 + fertilin subunit beta + ADAM2 + ADAM 2 + PR_EXT:000003715 + cancer/testis antigen 15 + FTNB + PH30-beta + "A protein that is a translation product of the human ADAM2 gene or a 1:1 ortholog thereof." [PRO:DNx] + CT15 + PH30 + disintegrin and metalloproteinase domain-containing protein 2 + PH-30 + + + metalloproteinase-disintegrin ADAM22-3 + PR_EXT:000003718 + PR_EXT:disintegrin and metalloproteinase domain-containing protein 22 + disintegrin and metalloproteinase domain-containing protein 22 + "A protein that is a translation product of the human ADAM22 gene or a 1:1 ortholog thereof." [PRO:DNx] + metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2 + ADAM 22 + MDC2 + ADAM22 + + + metalloproteinase-like, disintegrin-like, and cysteine-rich protein 3 + PR_EXT:disintegrin and metalloproteinase domain-containing protein 23 + ADAM 23 + MDC-3 + "A protein that is a translation product of the human ADAM23 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000003719 + disintegrin and metalloproteinase domain-containing protein 23 + ADAM23 + MDC3 + + + myeloma cell metalloproteinase + KIAA0021 + ADAM9 + ADAM 9 + metalloprotease/disintegrin/cysteine-rich protein 9 + "A protein that is a translation product of the human ADAM9 gene or a 1:1 ortholog thereof." [PRO:DNx] + meltrin-gamma + MDC9 + MLTNG + PR_EXT:000003725 + PR_EXT:disintegrin and metalloproteinase domain-containing protein 9 + disintegrin and metalloproteinase domain-containing protein 9 + MCMP + cellular disintegrin-related protein + + + ADAMTS3 + ADAM-TS3 + ADAMTS-3 + PR_EXT:a disintegrin and metalloproteinase with thrombospondin motifs 3 + KIAA0366 + procollagen II N-proteinase + procollagen II amino propeptide-processing enzyme + a disintegrin and metalloproteinase with thrombospondin motifs 3 + PR_EXT:000003732 + PC II-NP + "A protein that is a translation product of the human ADAMTS3 gene or a 1:1 ortholog thereof." [PRO:DNx] + ADAM-TS 3 + + + alpha-1-fetoprotein + alpha-fetoglobulin + PR_EXT:000003809 + alpha-fetoprotein + HPAFP + "A protein that is a translation product of the human AFP gene or a 1:1 ortholog thereof." [PRO:DNx] + AFP + PR_EXT:alpha-fetoprotein + + + aryl-hydrocarbon-interacting protein-like 1 + AIPL1 + "A protein that is a translation product of the human AIPL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:aryl-hydrocarbon-interacting protein-like 1 + PR_EXT:000003876 + + + AKT2 + RAC-beta serine/threonine-protein kinase + PR_EXT:RAC-beta serine/threonine-protein kinase + PR_EXT:000003912 + protein kinase Akt-2 + protein kinase B beta + "An AKT kinase that is a translation product of the human AKT2 gene or a 1:1 ortholog thereof." [PRO:CNA] + PKB beta + RAC-PK-beta + + + RAC-gamma serine/threonine-protein kinase + PR_EXT:RAC-gamma serine/threonine-protein kinase + PR_EXT:000003913 + "An AKT kinase that is a translation product of the human AKT3 gene or a 1:1 ortholog thereof." [PRO:CNA] + protein kinase Akt-3 + PKBG + STK-2 + PKB gamma + RAC-PK-gamma + protein kinase B gamma + AKT3 + + + serum albumin + "A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof." [PRO:DNx] + ALB + Alb1 + Alb-1 + PR_EXT:serum albumin + PR_EXT:000003918 + + + PR_EXT:000003921 + RALDH(II) + RALDH 2 + ALDH1A2 + retinaldehyde-specific dehydrogenase type 2 + "A protein that is a translation product of the human ALDH1A2 gene or a 1:1 ortholog thereof." [PRO:DNx] + Aldh1a7 + PR_EXT:retinal dehydrogenase 2 + RalDH2 + aldehyde dehydrogenase family 1 member A2 + retinal dehydrogenase 2 + + + ALMS1 + PR_EXT:Alstrom syndrome protein 1 + KIAA0328 + PR_EXT:000003956 + "A protein that is a translation product of the human ALMS1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Alstrom syndrome protein 1 + + + "A protein that is a translation product of the human ALPP gene or a 1:1 ortholog thereof." [PRO:DNx] + alkaline phosphatase, placental type + placental alkaline phosphatase 1 + ALPP + PLAP + PR_EXT:alkaline phosphatase, placental type + alkaline phosphatase Regan isozyme + PR_EXT:000003969 + PLAP-1 + + + homeobox protein aristaless-like 3 + ALX3 + PR_EXT:homeobox protein aristaless-like 3 + "A protein that is a translation product of the human ALX3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000003979 + proline-rich transcription factor ALX3 + + + homeobox protein aristaless-like 4 + PR_EXT:homeobox protein aristaless-like 4 + "A protein that is a translation product of the human ALX4 gene or a 1:1 ortholog thereof." [PRO:DNx] + KIAA1788 + ALX4 + PR_EXT:000003980 + ALX-4 + + + protein amnionless + PR_EXT:protein amnionless + PR_EXT:000003996 + "A protein that is a translation product of the human AMN gene or a 1:1 ortholog thereof." [PRO:DNx] + AMN + + + "A protein that is a translation product of the human ANGPT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:angiopoietin-1 + Agpt + ANGPT1 + PR_EXT:000004023 + angiopoietin-1 + ANG-1 + KIAA0003 + + + Lpc-1 + ANX1 + chromobindin-9 + phospholipase A2 inhibitory protein + ANXA1 + annexin-1 + lipocortin I + annexin A1 + "A protein that is a translation product of the human ANXA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + calpactin-2 + LPC1 + PR_EXT:000004071 + annexin I + PR_EXT:annexin A1 + calpactin II + + + ANXA11 + CAP-50 + annexin-11 + annexin A11 + ANX11 + "A protein that is a translation product of the human ANXA11 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000004073 + calcyclin-associated annexin 50 + PR_EXT:annexin A11 + 56 kDa autoantigen + annexin XI + + + ANXA2 + PAP-IV + annexin-2 + CAL1H + ANX2 + LPC2D + lipocortin II + chromobindin-8 + annexin A2 + placental anticoagulant protein IV + "A protein that is a translation product of the human ANXA2 gene or a 1:1 ortholog thereof." [PRO:DNx] + ANX2L4 + protein I + PR_EXT:000004075 + PR_EXT:annexin A2 + calpactin-1 heavy chain + calpactin I heavy chain + annexin II + + + protein II + carbohydrate-binding protein p33/p41 + endonexin I + ANX4 + annexin-4 + PP4-X + annexin A4 + ANXA4 + lipocortin IV + annexin IV + PR_EXT:000004077 + P32.5 + PAP-II + "A protein that is a translation product of the human ANXA4 gene or a 1:1 ortholog thereof." [PRO:DNx] + chromobindin-4 + PR_EXT:annexin A4 + 35-beta calcimedin + placental anticoagulant protein II + + + ANXA5 + placental anticoagulant protein I + annexin-5 + anchorin CII + annexin A5 + PR_EXT:000004078 + ANX5 + calphobindin I + PP4 + "A protein that is a translation product of the human ANXA5 gene or a 1:1 ortholog thereof." [PRO:DNx] + annexin V + vascular anticoagulant-alpha + PR_EXT:annexin A5 + placental anticoagulant protein 4 + thromboplastin inhibitor + ENX2 + CBP-I + endonexin II + VAC-alpha + PAP-I + lipocortin V + + + synexin + annexin VII + PR_EXT:000004080 + SNX + ANX7 + PR_EXT:annexin A7 + annexin-7 + annexin A7 + ANXA7 + "A protein that is a translation product of the human ANXA7 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000004122 + DP2.5 + protein APC + deleted in polyposis 2.5 + APC + adenomatous polyposis coli protein + PR_EXT:adenomatous polyposis coli protein + "A protein that is a translation product of the human APC gene or a 1:1 ortholog thereof." [PRO:DNx] + + + SAP + PR_EXT:000004126 + serum amyloid P-component + PTX2 + "A protein that is a translation product of the human APCS gene or a 1:1 ortholog thereof." [PRO:DNx] + 9.5S alpha-1-glycoprotein + PR_EXT:serum amyloid P-component + APCS + + + APLP2 + PR_EXT:000004137 + CDEBP + "A protein that is a translation product of the human APLP2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:amyloid-like protein 2 + APPH + APPL2 + amyloid protein homolog + amyloid-like protein 2 + CDEI box-binding protein + + + apo-AI + apolipoprotein A-I + PR_EXT:apolipoprotein A-I + apolipoprotein A1 + "A protein that is a translation product of the human APOA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + ApoA-I + PR_EXT:000004140 + APOA1 + + + apo-AII + PR_EXT:000004142 + apolipoprotein A-II + ApoA-II + apolipoprotein A2 + "A protein that is a translation product of the human APOA2 gene or a 1:1 ortholog thereof." [PRO:DNx] + APOA2 + PR_EXT:apolipoprotein A-II + + + "A protein that is a translation product of the human APOA4 gene or a 1:1 ortholog thereof." [PRO:DNx] + APOA4 + PR_EXT:000004143 + apolipoprotein A-IV + ApoA-IV + apolipoprotein A4 + apo-AIV + PR_EXT:apolipoprotein A-IV + + + "A protein that is a translation product of the human APOB gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000004145 + PR_EXT:apolipoprotein B-100 + apo B-100 + APOB + apolipoprotein B-100 + + + apolipoprotein E + apo-E + PR_EXT:apolipoprotein E + PR_EXT:000004155 + APOE + "A protein that is a translation product of the human APOE gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:beta-2-glycoprotein 1 + beta(2)GPI + "A protein that is a translation product of the human APOH gene or a 1:1 ortholog thereof." [PRO:DNx] + activated protein C-binding protein + apolipoprotein H + B2GPI + beta-2-glycoprotein 1 + B2gp1 + APOH + B2G1 + beta-2-glycoprotein I + PR_EXT:000004157 + APC inhibitor + apo-H + anticardiolipin cofactor + + + alzheimer disease amyloid protein + APPI + AG + "A protein that is a translation product of the human APP gene or a 1:1 ortholog thereof." [PRO:DNx] + ABPP + APP + CVAP + amyloidogenic glycoprotein + AD1 + A4 + PR_EXT:000004168 + PR_EXT:amyloid beta A4 protein + PreA4 + amyloid beta A4 protein + protease nexin-II + PN-II + cerebral vascular amyloid peptide + alzheimer disease amyloid A4 protein homolog + + + CHIP28 + AQP-1 + water channel protein for red blood cells and kidney proximal tubule + delayed early response protein 2 + aquaporin-1 + AQP1 + DER2 + "A protein that is a translation product of the human AQP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000004177 + PR_EXT:aquaporin-1 + aquaporin-CHIP + urine water channel + + + "A protein that is a translation product of the human AQP2 gene or a 1:1 ortholog thereof." [PRO:DNx] + collecting duct water channel protein + AQP-2 + PR_EXT:000004182 + water channel protein for renal collecting duct + aquaporin-2 + WCH-CD + AQP2 + aquaporin-CD + ADH water channel + AQP-CD + PR_EXT:aquaporin-2 + + + aquaporin-3 + PR_EXT:aquaporin-3 + "A protein that is a translation product of the human AQP3 gene or a 1:1 ortholog thereof." [PRO:DNx] + AQP-3 + PR_EXT:000004183 + AQP3 + + + aquaporin-5 + PR_EXT:aquaporin-5 + PR_EXT:000004185 + AQP5 + "A protein that is a translation product of the human AQP5 gene or a 1:1 ortholog thereof." [PRO:DNx] + AQP-5 + + + PR_EXT:000004192 + PKS + ARAF1 + PKS2 + proto-oncogene A-Raf + serine/threonine-protein kinase A-Raf + ARAF + PR_EXT:serine/threonine-protein kinase A-Raf + A-raf + proto-oncogene A-Raf-1 + proto-oncogene Pks + "A protein that is a translation product of the human ARAF gene or a 1:1 ortholog thereof." [PRO:DNx] + A-Raf proto-oncogene serine/threonine-protein kinase + + + AREG + amphiregulin + AR + PR_EXT:amphiregulin + CRDGF + Areg + colorectum cell-derived growth factor + SDGF + "A protein that is a translation product of the human AREG gene or a 1:1 ortholog thereof." [PRO:DNx] + schwannoma-derived growth factor + PR_EXT:000004200 + AREGB + + + PR_EXT:000004257 + rho guanine nucleotide exchange factor 4 + KIAA1112 + PR_EXT:rho guanine nucleotide exchange factor 4 + "A protein that is a translation product of the human ARHGEF4 gene or a 1:1 ortholog thereof." [PRO:DNx] + Asef + ARHGEF4 + APC-stimulated guanine nucleotide exchange factor + + + hypoxia-inducible factor 1-beta + bHLHe2 + class E basic helix-loop-helix protein 2 + HIF1-beta + dioxin receptor, nuclear translocator + aryl hydrocarbon receptor nuclear translocator + HIF-1-beta + PR_EXT:aryl hydrocarbon receptor nuclear translocator + ARNT + "A protein that is a translation product of the human ARNT gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000004303 + ARNT protein + + + ASH-1 + PR_EXT:achaete-scute homolog 1 + achaete-scute homolog 1 + ASH1 + "A protein that is a translation product of the human ASCL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + class A basic helix-loop-helix protein 46 + bHLHa46 + ASCL1 + PR_EXT:000004362 + + + PR_EXT:000004372 + agouti switch protein + ASIP + PR_EXT:agouti-signaling protein + "A protein that is a translation product of the human ASIP gene or a 1:1 ortholog thereof." [PRO:DNx] + ASP + AGTIL + a + AGTI + agouti-signaling protein + agouti coat color protein + + + PR_EXT:000004427 + A-T mutated + PR_EXT:serine-protein kinase ATM + A-T mutated homolog + ataxia telangiectasia mutated + ataxia telangiectasia mutated homolog + "A protein that is a translation product of the human ATM gene or a 1:1 ortholog thereof." [PRO:DNx] + serine-protein kinase ATM + ATM + + + "A protein that is a translation product of the human ATOH1 gene or a 1:1 ortholog thereof." [PRO:DNx] + bHLHa14 + PR_EXT:000004430 + class A basic helix-loop-helix protein 14 + helix-loop-helix protein mATH-1 + ATH1 + ATOH1 + protein atonal homolog 1 + helix-loop-helix protein hATH-1 + PR_EXT:protein atonal homolog 1 + + + "A protein that is a translation product of the human ATP2B1 gene or a 1:1 ortholog thereof." [PRO:DNx] + plasma membrane calcium-transporting ATPase 1 + plasma membrane calcium ATPase isoform 1 + ATP2B1 + plasma membrane calcium pump isoform 1 + PMCA1 + PR_EXT:000004445 + PR_EXT:plasma membrane calcium-transporting ATPase 1 + + + PR_EXT:ATP synthase subunit alpha, mitochondrial + ATP synthase subunit alpha, mitochondrial + ATP5A + PR_EXT:000004453 + ATP5A1 + ATPM + ATP5AL2 + "A protein that is a translation product of the human ATP5A1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + ATP synthase subunit beta, mitochondrial + ATPSB + PR_EXT:ATP synthase subunit beta, mitochondrial + ATP5B + ATPMB + "A protein that is a translation product of the human ATP5B gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000004454 + + + ATR + PR_EXT:000004499 + FRAP-related protein 1 + serine/threonine-protein kinase ATR + PR_EXT:serine/threonine-protein kinase ATR + "A protein that is a translation product of the human ATR gene or a 1:1 ortholog thereof." [PRO:DNx] + FRP1 + Kiaa4069 + ataxia telangiectasia and Rad3-related protein + + + HP1 alpha-interacting protein + RAD54L + heterochromatin protein 2 + Znf-HX + "A protein that is a translation product of the human ATRX gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:transcriptional regulator ATRX + ATRX + X-linked nuclear protein + XH2 + HP1-BP38 protein + XNP + ATP-dependent helicase ATRX + transcriptional regulator ATRX + PR_EXT:000004503 + X-linked helicase II + Hp1bp2 + + + aurora/IPL1-related kinase 1 + serine/threonine-protein kinase Ayk1 + STK6 + aurora-related kinase 1 + STK15 + serine/threonine-protein kinase 6 + serine/threonine-protein kinase 15 + ARK-1 + PR_EXT:000004515 + ARK1 + BTAK + aurora kinase A + Ayk1 + Iak1 + breast tumor-amplified kinase + serine/threonine-protein kinase aurora-A + AURKA + AURA + AIK + ipl1- and aurora-related kinase 1 + "An aurora kinase that is a translation product of the human AURKA gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:aurora kinase A + aurora family kinase 1 + + + aurora/Ipl1-related kinase 3 + STK13 + aurora-related kinase 3 + AIK3 + AURKC + AIE2 + PR_EXT:000004518 + Aie1 + ARK3 + serine/threonine-protein kinase 13 + ARK-3 + aurora kinase C + PR_EXT:aurora kinase C + "An aurora kinase that is a translation product of the human AURKC gene or a 1:1 ortholog thereof." [PRO:DNx] + serine/threonine-protein kinase aurora-C + aurora/Ipl1/Eg2 protein 2 + aurora/Ipl1/Eg2 protein 1 + + + conductin + axin-2 + PR_EXT:axin-2 + Axin-like protein + Axil + axis inhibition protein 2 + AXIN2 + "An axin that is a translation product of the human AXIN2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000004527 + + + Aldh1a7 + ALDH class 1 + ALHDII + aldehyde dehydrogenase phenobarbital-inducible + "A protein that is a translation product of the mouse Aldh1a7 gene or a 1:1 ortholog thereof." [PRO:DNx] + ALDH-E1 + aldehyde dehydrogenase family 1 member A7 + Aldh-pb + PR_EXT:aldehyde dehydrogenase, cytosolic 1 + aldehyde dehydrogenase, cytosolic 1 + PR_EXT:000004564 + + + aspartyl protease 2 + PR_EXT:beta-secretase 1 + BACE1 + Asp 2 + beta-site amyloid precursor protein cleaving enzyme 1 + BACE + KIAA1149 + memapsin-2 + ASP2 + beta-secretase 1 + membrane-associated aspartic protease 2 + PR_EXT:000004615 + "A protein that is a translation product of the human BACE1 gene or a 1:1 ortholog thereof." [PRO:DNx] + beta-site APP cleaving enzyme 1 + + + BAG1 + PR_EXT:BAG family molecular chaperone regulator 1 + "A protein that is a translation product of the human BAG1 gene or a 1:1 ortholog thereof." [PRO:DNx] + BAG family molecular chaperone regulator 1 + BAG-1 + PR_EXT:000004619 + HAP + bcl-2-associated athanogene 1 + + + bcl-2-binding protein Bis + docking protein CAIR-1 + BAG3 + PR_EXT:BAG family molecular chaperone regulator 3 + BAG family molecular chaperone regulator 3 + BAG-3 + "A protein that is a translation product of the human BAG3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000004621 + bcl-2-associated athanogene 3 + BIS + + + BRCA1-associated RING domain protein 1 + BARD1 + PR_EXT:000004642 + "A protein that is a translation product of the human BARD1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:BRCA1-associated RING domain protein 1 + BARD-1 + + + BBS4 + PR_EXT:Bardet-Biedl syndrome 4 protein + "A protein that is a translation product of the human BBS4 gene or a 1:1 ortholog thereof." [PRO:DNx] + Bardet-Biedl syndrome 4 protein + PR_EXT:000004667 + + + PP18 + BCATM + branched-chain-amino-acid aminotransferase, mitochondrial + "A protein that is a translation product of the human BCAT2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000004683 + BCT2 + ECA40 + BCAT(m) + placental protein 18 + PR_EXT:branched-chain-amino-acid aminotransferase, mitochondrial + BCAT2 + + + BCKDE1A + PR_EXT:000004686 + 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial + PR_EXT:2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial + branched-chain alpha-keto acid dehydrogenase E1 component alpha chain + BCKDHA + "A protein that is a translation product of the human BCKDHA gene or a 1:1 ortholog thereof." [PRO:DNx] + BCKDH E1-alpha + + + PR_EXT:000004687 + BCKDH E1-beta + PR_EXT:2-oxoisovalerate dehydrogenase subunit beta, mitochondrial + BCKDHB + "A protein that is a translation product of the human BCKDHB gene or a 1:1 ortholog thereof." [PRO:DNx] + 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial + branched-chain alpha-keto acid dehydrogenase E1 component beta chain + BCKDE1B + + + PR_EXT:000004716 + brain-derived neurotrophic factor + PR_EXT:brain-derived neurotrophic factor + abrineurin + BDNF + "A neurotrophin that is a translation product of the human BDNF gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:filensin + "A protein that is a translation product of the human BFSP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + BFSP1 + lens intermediate filament-like heavy + beaded filament structural protein 1 + PR_EXT:000004733 + LIFL-H + CP115 + lens fiber cell beaded-filament structural protein CP 115 + CP95 + filensin + lens fiber cell beaded-filament structural protein CP 95 + + + beaded filament structural protein 2 + 49 kDa cytoskeletal protein + lens intermediate filament-like light + lens fiber cell beaded filament protein CP 49 + lens fiber cell beaded filament protein CP 47 + LIFL-L + "A protein that is a translation product of the human BFSP2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:phakinin + BFSP2 + PR_EXT:000004734 + CP47 + phakinin + CP49 + + + DNA helicase, RecQ-like type 2 + PR_EXT:bloom syndrome protein + BLM + RecQ protein-like 3 + bloom syndrome protein + PR_EXT:000004759 + RECQL3 + RecQ2 + "A protein that is a translation product of the human BLM gene or a 1:1 ortholog thereof." [PRO:DNx] + + + polycomb group RING finger protein 4 + PR_EXT:polycomb complex protein BMI-1 + RING finger protein 51 + RNF51 + Bmi-1 + PCGF4 + BMI1 + "A protein that is a translation product of the human BMI1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000004770 + polycomb complex protein BMI-1 + + + PR_EXT:protein boule-like + protein boule-like + BOULE + "A protein that is a translation product of the human BOLL gene or a 1:1 ortholog thereof." [PRO:DNx] + BOLL + PR_EXT:000004789 + + + v-Raf murine sarcoma viral oncogene homolog B1 + BRAF1 + B-raf + BRAF + proto-oncogene B-Raf + PR_EXT:B-Raf proto-oncogene serine/threonine-protein kinase + "A protein that is a translation product of the human BRAF gene or a 1:1 ortholog thereof." [PRO:DNx] + RAFB1 + PR_EXT:000004801 + B-Raf proto-oncogene serine/threonine-protein kinase + + + RNF53 + "A protein that is a translation product of the human BRCA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + RING finger protein 53 + BRCA1 + PR_EXT:000004803 + breast cancer type 1 susceptibility protein + PR_EXT:breast cancer type 1 susceptibility protein + + + breast cancer type 2 susceptibility protein + PR_EXT:breast cancer type 2 susceptibility protein + Fanconi anemia group D1 protein homolog + FANCD1 + FACD + BRCA2 + PR_EXT:000004804 + "A protein that is a translation product of the human BRCA2 gene or a 1:1 ortholog thereof." [PRO:DNx] + Fanconi anemia group D1 protein + + + CELF4 + bruno-like protein 4 + CELF-4 + PR_EXT:000004825 + CUGBP Elav-like family member 4 + PR_EXT:CUGBP Elav-like family member 4 + RNA-binding protein BRUNOL-4 + Brul4 + BRUNOL4 + "A protein that is a translation product of the human CELF4 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A protein that is a translation product of the human BTC gene or a 1:1 ortholog thereof." [PRO:DNx] + probetacellulin + BTC + PR_EXT:000004837 + Bcn + PR_EXT:probetacellulin + + + BUBR1 + "A BUB1/BUB1B protein that is a translation product of the human BUB1B gene or a 1:1 ortholog thereof." [PMID:22698286, PRO:CNA] + BubR1 + protein SSK1 + MAD3L + PR_EXT:000004855 + BUB1B + PR_EXT:mitotic checkpoint serine/threonine-protein kinase BUB1 beta + SSK1 + mitotic checkpoint serine/threonine-protein kinase BUB1 beta + MAD3/BUB1-related protein kinase + mitotic checkpoint kinase MAD3L + + + C5 + hemolytic complement + PR_EXT:complement C5 + CPAMD4 + C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4 + Hc + complement C5 + PR_EXT:000004904 + "A protein that is a translation product of the human C5 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A single domain alpha-type carbonic anhydrase that is a translation product of the human CA12 gene or a 1:1 ortholog thereof." [PRO:DNx] + carbonic anhydrase 12 + carbonic anhydrase XII + tumor antigen HOM-RCC-3.1.3 + CA-XII + PR_EXT:000004915 + carbonate dehydratase XII + Car12 + CA12 + PR_EXT:carbonic anhydrase 12 + + + CA4 + "A single domain alpha-type carbonic anhydrase that is a translation product of the human CA4 gene or a 1:1 ortholog thereof." [PRO:DNx] + Car4 + carbonate dehydratase IV + PR_EXT:carbonic anhydrase 4 + carbonic anhydrase IV + CA-IV + carbonic anhydrase 4 + PR_EXT:000004920 + + + calcium-binding protein 5 + PR_EXT:calcium-binding protein 5 + PR_EXT:000004937 + CaBP5 + CABP5 + "A protein that is a translation product of the human CABP5 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000004967 + calbindin + PCD-29 + spot 35 protein + CAB27 + CALB1 + D-28K + "A protein that is a translation product of the human CALB1 gene or a 1:1 ortholog thereof." [PRO:DNx] + vitamin D-dependent calcium-binding protein, avian-type + PR_EXT:calbindin + calbindin D28 + + + calretinin + PR_EXT:calretinin + CAB29 + PR_EXT:000004968 + CALB2 + 29 kDa calbindin + CR + "A protein that is a translation product of the human CALB2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000004978 + "A protein that is a translation product of the human CALM1, CALM2, or CALM3 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." [PRO:DAN] + CALML2 + CAMC + CaM + CALM + CAMIII + calmodulin + PR_EXT:calmodulin + + + ERp60 + endoplasmic reticulum resident protein 60 + PR_EXT:calreticulin + "A protein that is a translation product of the human CALR gene or a 1:1 ortholog thereof." [PRO:DNx] + grp60 + CRP55 + calreticulin + calregulin + CALR + CRTC + PR_EXT:000004984 + HACBP + + + major histocompatibility complex class I antigen-binding protein p88 + "A protein that is a translation product of the human CANX gene or a 1:1 ortholog thereof." [PRO:DNx] + calnexin + IP90 + PR_EXT:000005005 + PR_EXT:calnexin + CANX + + + calcium-activated neutral proteinase 1 + calpain-1 catalytic subunit + PR_EXT:calpain-1 catalytic subunit + muCANP + calpain-1 large subunit + micromolar-calpain + Canp1 + CANP 1 + CAPN1 + CANPL1 + Capa1 + PR_EXT:000005009 + cell proliferation-inducing gene 30 protein + "A protein that is a translation product of the human CAPN1 gene or a 1:1 ortholog thereof." [PRO:DNx] + calpain mu-type + + + CANP 2 + PR_EXT:calpain-2 catalytic subunit + PR_EXT:000005015 + "A protein that is a translation product of the human CAPN2 gene or a 1:1 ortholog thereof." [PRO:DNx] + calcium-activated neutral proteinase 2 + 80 kDa M-calpain subunit + calpain-2 large subunit + millimolar-calpain + calpain-2 catalytic subunit + M-calpain + calpain large polypeptide L2 + CALP80 + CANPL2 + calpain M-type + CAPN2 + + + CAPNS1 + calpain regulatory subunit + calcium-dependent protease small subunit 1 + "A protein that is a translation product of the human CAPNS1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000005022 + calpain small subunit 1 + PR_EXT:calpain small subunit 1 + CANP small subunit + CAPNS + CAPN4 + CSS1 + calcium-dependent protease small subunit + CDPS + calcium-activated neutral proteinase small subunit + + + "A protein that is a translation product of the human CAST gene or a 1:1 ortholog thereof." [PRO:DNx] + calpain inhibitor + calpastatin + PR_EXT:000005060 + PR_EXT:calpastatin + CAST + sperm BS-17 component + + + CBX + heterochromatin protein 1 homolog beta + M31 + modifier 1 protein + HP1Hsbeta + HP1 beta + heterochromatin protein p25 + PR_EXT:000005082 + CBX1 + PR_EXT:chromobox protein homolog 1 + chromobox protein homolog 1 + "A protein that is a translation product of the human CBX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + p25beta + + + "A protein that is a translation product of the human CBX5 gene or a 1:1 ortholog thereof." [PRO:DNx] + antigen p25 + PR_EXT:chromobox protein homolog 5 + heterochromatin protein 1 homolog alpha + HP1 alpha + PR_EXT:000005086 + HP1A + CBX5 + chromobox protein homolog 5 + + + cholecystokinin + PR_EXT:000005110 + CCK + PR_EXT:cholecystokinin + "A protein that is a translation product of the human CCK gene or a 1:1 ortholog thereof." [PRO:DNx] + + + Cyca + CCN1 + cyclin-A2 + CCNA2 + PR_EXT:000005115 + "A cyclin-A that is a translation product of the human CCNA2 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:cyclin-A2 + + + BCL-1 + PRAD1 + "A cell cycle-related cyclin that is a translation product of the human CCND1 gene or a 1:1 ortholog thereof." [PRO:DNx] + B-cell lymphoma 1 protein + PR_EXT:G1/S-specific cyclin-D1 + Cyl-1 + BCL-1 oncogene + BCL1 + PRAD1 oncogene + PR_EXT:000005121 + CCND1 + G1/S-specific cyclin-D1 + + + CCNH + cyclin-H + PR_EXT:000005130 + MO15-associated protein + PR_EXT:cyclin-H + "A protein that is a translation product of the human CCNH gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:M-phase inducer phosphatase 3 + M-phase inducer phosphatase 3 + CDC25C + "A protein that is a translation product of the human CDC25C gene or a 1:1 ortholog thereof." [PRO:DNx] + dual specificity phosphatase Cdc25C + PR_EXT:000005193 + Cdc25m1 + + + CDC45-related protein + PR_EXT:CDC45-related protein + CDC45L2 + CDC45L + "A protein that is a translation product of the human CDC45 gene or a 1:1 ortholog thereof." [PRO:DNx] + cdc45 + CDC45 + PORC-PI-1 + PR_EXT:000005215 + + + CDC7-related kinase + cell division cycle 7-related protein kinase + PR_EXT:000005218 + "A protein that is a translation product of the human CDC7 gene or a 1:1 ortholog thereof." [PRO:DNx] + Cdc7 + CDC7 + CDC7L1 + PR_EXT:cell division cycle 7-related protein kinase + uCdc7 + + + cadherin-3 + PR_EXT:cadherin-3 + CDHP + P-cadherin + CDH3 + placental cadherin + PR_EXT:000005245 + "A cadherin that is a translation product of the human CDH3 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + cell division protein kinase 4 + cyclin-dependent kinase 4 + PR_EXT:cell division protein kinase 4 + PSK-J3 + "A CDK2-related kinase that is a translation product of the human CDK4 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000005257 + CDK4 + CRK3 + + + CDK5R + CDK5R1 + NCK5A + cyclin-dependent kinase 5 regulatory subunit 1 + TPKII regulatory subunit + "A protein that is a translation product of the human CDK5R1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000005259 + CDK5 activator 1 + cyclin-dependent kinase 5 activator 1 + PR_EXT:cyclin-dependent kinase 5 activator 1 + + + protein-tyrosine kinase MPK-7 + CR4 protein kinase + "A CDK2-related kinase that is a translation product of the human CDK7 gene or a 1:1 ortholog thereof." [PRO:DNx] + STK1 + MO15 + Cdkn7 + Mpk-7 + PR_EXT:000005265 + CRK4 + CDK7 + CAK + 39 kDa protein kinase + p39 Mo15 + cell division protein kinase 7 + TFIIH basal transcription factor complex kinase subunit + PR_EXT:cell division protein kinase 7 + + + SDI1 + PR_EXT:000005274 + WAF1 + melanoma differentiation-associated protein + cyclin-dependent kinase inhibitor 1 + melanoma differentiation-associated protein 6 + CDK-interacting protein 1 + PIC1 + CIP1 + "A protein that is a translation product of the human CDKN1A gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:cyclin-dependent kinase inhibitor 1 + CAP20 + CDKN1A + MDA-6 + CDKN1 + MDA6 + + + p19-INK4d + "A cyclin-dependent kinase inhibitor that is a translation product of the human CDKN2D gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000005279 + PR_EXT:cyclin-dependent kinase 4 inhibitor D + cyclin-dependent kinase 4 inhibitor D + CDKN2D + + + CDX2 + homeobox protein CDX-2 + CDX-3 + PR_EXT:homeobox protein CDX-2 + caudal-type homeobox protein 2 + "A protein that is a translation product of the human CDX2 gene or a 1:1 ortholog thereof." [PRO:DNx] + Cdx-2 + CDX3 + PR_EXT:000005296 + + + "A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof." [PRO:DNx] + C/EBP alpha + CEBPA + CCAAT/enhancer-binding protein alpha + PR_EXT:CCAAT/enhancer-binding protein alpha + PR_EXT:000005307 + + + C/EBP beta + LAP + IL-6DBP + interleukin-6-dependent-binding protein + TCF5 + transcription factor 5 + CEBPB + AGP/EBP + "A protein that is a translation product of the human CEBPB gene or a 1:1 ortholog thereof." [PRO:DNx] + nuclear factor NF-IL6 + PR_EXT:CCAAT/enhancer-binding protein beta + CCAAT/enhancer-binding protein beta + liver activator protein + liver-enriched transcriptional activator + PR_EXT:000005308 + TCF-5 + + + C/EBP-related protein 3 + CCAAT/enhancer-binding protein delta + PR_EXT:CCAAT/enhancer-binding protein delta + nuclear factor NF-IL6-beta + CEBPD + PR_EXT:000005309 + Crp3 + C/EBP delta + "A protein that is a translation product of the human CEBPD gene or a 1:1 ortholog thereof." [PRO:DNx] + NF-IL6-beta + + + PR_EXT:CCAAT/enhancer-binding protein epsilon + CCAAT/enhancer-binding protein epsilon + PR_EXT:000005310 + CEBPE + Gm294 + "A protein that is a translation product of the human CEBPE gene or a 1:1 ortholog thereof." [PRO:DNx] + C/EBP epsilon + + + PR_EXT:000005311 + immunoglobulin enhancer-binding protein 1 + CCAAT/enhancer-binding protein gamma + C/EBP gamma + PR_EXT:CCAAT/enhancer-binding protein gamma + granulocyte colony-stimulating factor promoter element 1-binding protein + CEBPG + GPE1-BP + "A protein that is a translation product of the human CEBPG gene or a 1:1 ortholog thereof." [PRO:DNx] + IG/EBP-1 + GPE1-binding protein + + + DF + C3 convertase activator + complement factor D + adipsin + CFD + "A protein that is a translation product of the human CFD gene or a 1:1 ortholog thereof." [PRO:DNx] + properdin factor D + PR_EXT:000005376 + Adn + 28 kDa adipocyte protein + PR_EXT:complement factor D + PFD + + + CFL + cofilin, non-muscle isoform + PR_EXT:cofilin-1 + PR_EXT:000005385 + "A protein that is a translation product of the human CFL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + CFL1 + 18 kDa phosphoprotein + cofilin-1 + + + Caip150 + CAF-I p150 + CAF + CHAF1A + CAF-I 150 kDa subunit + CAF1P150 + chromatin assembly factor 1 subunit A + hp150 + chromatin assembly factor I p150 subunit + PR_EXT:chromatin assembly factor 1 subunit A + "A protein that is a translation product of the human CHAF1A gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000005402 + CAF-1 subunit A + + + MPP7 + CHAF1B + CAF-I 60 kDa subunit + CAF1P60 + M-phase phosphoprotein 7 + chromatin assembly factor 1 subunit B + chromatin assembly factor I p60 subunit + CAF1A + PR_EXT:chromatin assembly factor 1 subunit B + CAF-I p60 + MPHOSPH7 + PR_EXT:000005403 + CAF-1 subunit B + "A protein that is a translation product of the human CHAF1B gene or a 1:1 ortholog thereof." [PRO:DNx] + + + rab proteins geranylgeranyltransferase component A 1 + CHM + TCD protein + TCD + rab escort protein 1 + PR_EXT:rab proteins geranylgeranyltransferase component A 1 + REP1 + "A protein that is a translation product of the human CHM gene or a 1:1 ortholog thereof." [PRO:DNx] + REP-1 + choroideraemia protein homolog + choroideraemia protein + PR_EXT:000005430 + + + MSG1 + CITED1 + "A protein that is a translation product of the human CITED1 gene or a 1:1 ortholog thereof." [PRO:DNx] + melanocyte-specific protein 1 + PR_EXT:000005505 + Cbp/p300-interacting transactivator 1 + PR_EXT:Cbp/p300-interacting transactivator 1 + + + Msg2 + MSG-related protein 1 + "A protein that is a translation product of the human CITED2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000005506 + P35srj + PR_EXT:Cbp/p300-interacting transactivator 2 + Cbp/p300-interacting transactivator 2 + MRG-1 + CITED2 + MRG1 + + + KIAA0097 + cytoskeleton-associated protein 5 + CKAP5 + colonic and hepatic tumor over-expressed gene protein + Ch-TOG + PR_EXT:000005512 + "A protein that is a translation product of the human CKAP5 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:cytoskeleton-associated protein 5 + + + "A creatine kinase that is a translation product of the human CKM gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000005515 + creatine kinase, muscle + CKMM + MM-CK + CKM + creatine kinase M-type + creatine kinase M chain + PR_EXT:creatine kinase M-type + M-CK + + + PR_EXT:000005573 + PR_EXT:calmegin + A2/6 + MEG 1 antigen + calmegin + Meg1 + CLGN + calnexin-T + "A protein that is a translation product of the human CLGN gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:battenin + CLN3 + protein CLN3 + BTS + batten disease protein + "A protein that is a translation product of the human CLN3 gene or a 1:1 ortholog thereof." [PRO:DNx] + battenin + PR_EXT:000005591 + + + CNNM1 + cyclin-like protein 1 + "A protein that is a translation product of the human CNNM1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:metal transporter CNNM1 + cyclin-M1 + CLP-1 + metal transporter CNNM1 + ACDP1 + ancient conserved domain-containing protein 1 + PR_EXT:000005643 + + + ancient conserved domain-containing protein 2 + cyclin-M2 + PR_EXT:metal transporter CNNM2 + "A protein that is a translation product of the human CNNM2 gene or a 1:1 ortholog thereof." [PRO:DNx] + ACDP2 + metal transporter CNNM2 + PR_EXT:000005644 + CNNM2 + + + ancient conserved domain-containing protein 3 + cyclin-M3 + PR_EXT:metal transporter CNNM3 + ACDP3 + "A protein that is a translation product of the human CNNM3 gene or a 1:1 ortholog thereof." [PRO:DNx] + metal transporter CNNM3 + PR_EXT:000005645 + CNNM3 + + + ancient conserved domain-containing protein 4 + KIAA1592 + PR_EXT:metal transporter CNNM4 + PR_EXT:000005646 + ACDP4 + cyclin-M4 + metal transporter CNNM4 + "A protein that is a translation product of the human CNNM4 gene or a 1:1 ortholog thereof." [PRO:DNx] + CNNM4 + + + PR_EXT:collagen alpha-1(X) chain + collagen alpha-1(X) chain + COL10A1 + "A protein that is a translation product of the human COL10A1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000005693 + + + "A protein that is a translation product of the human COL8A1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:collagen alpha-1(VIII) chain + PR_EXT:000005720 + COL8A1 + collagen alpha-1(VIII) chain + + + "A protein that is a translation product of the human COX11 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:cytochrome c oxidase assembly protein COX11, mitochondrial + PR_EXT:000005770 + cytochrome c oxidase assembly protein COX11, mitochondrial + COX11 + + + Cox4a + cytochrome c oxidase polypeptide IV + "A protein that is a translation product of the human COX4I1 gene or a 1:1 ortholog thereof." [PRO:DNx] + COX4I1 + COX4 + PR_EXT:cytochrome c oxidase subunit 4 isoform 1, mitochondrial + cytochrome c oxidase subunit 4 isoform 1, mitochondrial + COX IV-1 + cytochrome c oxidase subunit IV isoform 1 + PR_EXT:000005776 + + + PR_EXT:cytoplasmic polyadenylation element-binding protein 1 + cytoplasmic polyadenylation element-binding protein 1 + "A protein that is a translation product of the human CPEB1 gene or a 1:1 ortholog thereof." [PRO:DNx] + CPEB-1 + CPE-BP1 + CPEB + CPEB1 + PR_EXT:000005805 + h-CEBP + CPE-binding protein 1 + + + CPT1 + carnitine O-palmitoyltransferase I, liver isoform + Cpt-1 + CPT1A + carnitine O-palmitoyltransferase 1, liver isoform + carnitine palmitoyltransferase 1A + CPT1-L + PR_EXT:000005835 + "A protein that is a translation product of the human CPT1A gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:carnitine O-palmitoyltransferase 1, liver isoform + CPTI-L + + + PR_EXT:carnitine O-palmitoyltransferase 1, muscle isoform + CPT1-M + carnitine O-palmitoyltransferase I, muscle isoform + KIAA1670 + carnitine palmitoyltransferase I-like protein + carnitine palmitoyltransferase 1B + CPT1B + carnitine O-palmitoyltransferase 1, muscle isoform + "A protein that is a translation product of the human CPT1B gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000005836 + CPTI-M + + + "A protein that is a translation product of the human CPT2 gene or a 1:1 ortholog thereof." [PRO:DNx] + Cpt-2 + CPT2 + CPT II + carnitine palmitoyltransferase II + PR_EXT:000005838 + carnitine O-palmitoyltransferase 2, mitochondrial + PR_EXT:carnitine O-palmitoyltransferase 2, mitochondrial + CPT1 + + + CPZ + PR_EXT:000005841 + "A protein that is a translation product of the human CPZ gene or a 1:1 ortholog thereof." [PRO:DNx] + carboxypeptidase Z + PR_EXT:carboxypeptidase Z + + + RIP-associated protein with a death domain + death domain-containing protein CRADD + "A protein that is a translation product of the human CRADD gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:death domain-containing protein CRADD + RAIDD + CRADD + PR_EXT:000005845 + caspase and RIP adapter with death domain + + + "A protein that is a translation product of the human CRB1 gene or a 1:1 ortholog thereof." [PRO:DNx] + protein crumbs homolog 1 + PR_EXT:protein crumbs homolog 1 + PR_EXT:000005848 + CRB1 + + + PR_EXT:000005850 + crumbs protein 3 + protein crumbs homolog 3 + PR_EXT:protein crumbs homolog 3 + "A protein that is a translation product of the human CRB3 gene or a 1:1 ortholog thereof." [PRO:DNx] + CRB3 + + + cysteine-rich PDZ-binding protein + "A protein that is a translation product of the human CRIPT gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:cysteine-rich PDZ-binding protein + cysteine-rich interactor of PDZ three + cysteine-rich interactor of PDZ3 + CRIPT + PR_EXT:000005877 + + + proto-oncogene C-crk + proto-oncogene c-Crk + PR_EXT:adapter molecule crk + PR_EXT:000005882 + adapter molecule crk + "A protein that is a translation product of the human CRK gene or a 1:1 ortholog thereof." [PRO:DNx] + CRK + Crko + + + "A protein that is a translation product of the human CRKL gene or a 1:1 ortholog thereof." [PRO:DNx] + Crkol + PR_EXT:000005883 + PR_EXT:Crk-like protein + CRKL + Crk-like protein + + + "A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof." [PRO:DNx] + PTX1 + PR_EXT:C-reactive protein + CRP + C-reactive protein + PR_EXT:000005897 + + + PR_EXT:000005904 + CORD2 + cone-rod homeobox protein + PR_EXT:cone-rod homeobox protein + "A protein that is a translation product of the human CRX gene or a 1:1 ortholog thereof." [PRO:DNx] + CRX + + + CRYAA + CRYA1 + alpha-crystallin A chain + PR_EXT:alpha-crystallin A chain + "A protein that is a translation product of the human CRYAA gene or a 1:1 ortholog thereof." [PRO:DNx] + heat shock protein beta-4 + hspB4 + PR_EXT:000005907 + + + CRYA2 + renal carcinoma antigen NY-REN-27 + CRYAB + "A protein that is a translation product of the human CRYAB gene or a 1:1 ortholog thereof." [PRO:DNx] + P23 + alpha-crystallin B chain + heat shock protein beta-5 + hspB5 + PR_EXT:alpha-crystallin B chain + alpha(B)-crystallin + rosenthal fiber component + PR_EXT:000005908 + + + MCSF + CSF-1 + CSF1 + macrophage colony-stimulating factor 1 + Csfm + PR_EXT:macrophage colony-stimulating factor 1 + PR_EXT:000005930 + M-CSF + "A protein that is a translation product of the human CSF1 gene or a 1:1 ortholog thereof." [PRO:DNx] + lanimostim + + + CSRP + PR_EXT:cysteine and glycine-rich protein 1 + cysteine and glycine-rich protein 1 + CYRP + CSRP1 + CRP1 + "A protein that is a translation product of the human CSRP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000005958 + + + PR_EXT:000005997 + transcriptional repressor CTCF + CCCTC-binding factor + CTCF + PR_EXT:transcriptional repressor CTCF + 11-zinc finger protein + "A protein that is a translation product of the human CTCF gene or a 1:1 ortholog thereof." [PRO:DNx] + CTCFL paralog + + + CTSB + "A cathepsin-like protease that is a translation product of the human CTSB gene or a 1:1 ortholog thereof." [PRO:DNx] + CPSB + APP secretase + cathepsin B1 + APPS + PR_EXT:000006023 + PR_EXT:cathepsin B + cathepsin B + + + cathepsin D + CTSD + CPSD + PR_EXT:000006025 + "A cathepsin-like protease that is a translation product of the human CTSD gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:cathepsin D + + + intrinsic factor-vitamin B12 receptor + IFCR + intrinsic factor-cobalamin receptor + "A protein that is a translation product of the human CUBN gene or a 1:1 ortholog thereof." [PRO:DNx] + CUBN + PR_EXT:000006043 + cubilin + PR_EXT:cubilin + 460 kDa receptor + intestinal intrinsic factor receptor + + + interferon-inducible T-cell alpha chemoattractant + beta-R1 + CXCL11 + C-X-C motif chemokine 11 + I-TAC + IP-9 + "A protein that is a translation product of the human CXCL11 gene or a 1:1 ortholog thereof." [PRO:DNx] + ITAC + SCYB11 + PR_EXT:000006065 + interferon gamma-inducible protein 9 + PR_EXT:C-X-C motif chemokine 11 + small-inducible cytokine B11 + SCYB9B + H174 + + + CXC chemokine BLC + C-X-C motif chemokine 13 + small-inducible cytokine B13 + BCA1 + B cell-attracting chemokine 1 + angie + PR_EXT:000006067 + SCYB13 + "A protein that is a translation product of the human CXCL13 gene or a 1:1 ortholog thereof." [PRO:DNx] + BLC + PR_EXT:C-X-C motif chemokine 13 + CXCL13 + B lymphocyte chemoattractant + BCA-1 + + + PR_EXT:cytochrome P450 7A1 + cytochrome P450 7A1 + "A protein that is a translation product of the human CYP7A1 gene or a 1:1 ortholog thereof." [PRO:DNx] + cholesterol 7-alpha-hydroxylase + CYP7 + CYPVII + PR_EXT:000006148 + CYP7A1 + + + PSCD1 + CLM1 + SEC7 homolog A + PH, SEC7 and coiled-coil domain-containing protein 1 + SEC7 homolog B2-1 + D17S811E + PR_EXT:000006153 + "A protein that is a translation product of the human CYTH1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:cytohesin-1 + mSec7-1 + cytohesin-1 + CYTH1 + + + RBFOX3 + Fox-1 C + PR_EXT:RNA binding protein fox-1 homolog 3 + D11Bwg0517e + "A protein that is a translation product of the human RBFOX3 gene or a 1:1 ortholog thereof." [PMID:16141072, PRO:HJD] + PR_EXT:000006252 + RNA binding protein fox-1 homolog 3 + Fox-1 homolog C + + + "A protein that is a translation product of the human DAB2 gene or a 1:1 ortholog thereof." [PRO:DNx] + DOC2 + PR_EXT:000006259 + PR_EXT:disabled homolog 2 + mitogen-responsive phosphoprotein + differentially-expressed protein 2 + disabled homolog 2 + DAB2 + DOC-2 + + + DAG1 + PR_EXT:dystroglycan + dystroglycan + PR_EXT:000006267 + Dag-1 + dystrophin-associated glycoprotein 1 + "A protein that is a translation product of the human DAG1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + ETS1-associated protein 1 + PR_EXT:death domain-associated protein 6 + "A protein that is a translation product of the human DAXX gene or a 1:1 ortholog thereof." [PRO:DNx] + BING2 + DAP6 + PR_EXT:000006283 + Fas death domain-associated protein + death domain-associated protein 6 + DAXX + Daxx + + + DAZ + deleted in azoospermia protein 1 + DAZ1 + "A protein that is a translation product of the human DAZ1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000006284 + PR_EXT:deleted in azoospermia protein 1 + + + DAZ-associated protein 1 + "A protein that is a translation product of the human DAZAP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + DAZAP1 + PR_EXT:DAZ-associated protein 1 + PR_EXT:000006288 + deleted in azoospermia-associated protein 1 + + + DAZLA + PR_EXT:deleted in azoospermia-like + deleted in azoospermia-like 1 + deleted in azoospermia-like + DAZH + DAZL + PR_EXT:000006290 + DAZ-like autosomal + SPGYLA + DAZL1 + DAZ homolog + SPGY-like-autosomal + "A protein that is a translation product of the human DAZL gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial + lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial + "A protein that is a translation product of the human DBT gene or a 1:1 ortholog thereof." [PRO:DNx] + DBT + branched-chain alpha-keto acid dehydrogenase complex component E2 + dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex + dihydrolipoamide branched chain transacylase + dihydrolipoyllysine-residue (2-methylpropanoyl)transferase + BCKAD-E2 + PR_EXT:000006300 + BCATE2 + BCKADE2 + + + DDX19 + DEAD box protein 19B + DBP5 + PR_EXT:ATP-dependent RNA helicase DDX19B + PR_EXT:000006358 + ATP-dependent RNA helicase DDX19B + DDX19B + "A protein that is a translation product of the human DDX19B gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000006427 + "A protein that is a translation product of the human DES gene or a 1:1 ortholog thereof." [PRO:DNx] + desmin + DES + PR_EXT:desmin + + + diacylglycerol O-acyltransferase 2 + PR_EXT:diacylglycerol O-acyltransferase 2 + DGAT2 + PR_EXT:000006433 + diglyceride acyltransferase 2 + "A protein that is a translation product of the human DGAT2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + 3-beta-hydroxysterol delta-24-reductase + "A protein that is a translation product of the human DHCR24 gene or a 1:1 ortholog thereof." [PRO:DNx] + seladin-1 + KIAA0018 + diminuto/dwarf1 homolog + delta(24)-sterol reductase + DHCR24 + PR_EXT:000006453 + PR_EXT:delta(24)-sterol reductase + 24-dehydrocholesterol reductase + + + "A protein that is a translation product of the human DHH gene or a 1:1 ortholog thereof." [PRO:DNx] + HHG-3 + desert hedgehog protein + PR_EXT:000006459 + DHH + PR_EXT:desert hedgehog protein + + + PR_EXT:000006498 + Nopp140-associated protein of 57 kDa + NOLA4 + H/ACA ribonucleoprotein complex subunit 4 + CBF5 homolog + DKC1 + nucleolar protein NAP57 + "A protein that is a translation product of the human DKC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:H/ACA ribonucleoprotein complex subunit 4 + dyskerin + nucleolar protein family A member 4 + snoRNP protein DKC1 + + + "A protein that is a translation product of the human DKK1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000006499 + dickkopf-1 + DKK1 + Dkk-1 + SK + dickkopf-related protein 1 + PR_EXT:dickkopf-related protein 1 + + + LAD + "A protein that is a translation product of the human DLD gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:dihydrolipoyl dehydrogenase, mitochondrial + DLD + GCSL + PR_EXT:000006506 + PHE3 + dihydrolipoyl dehydrogenase, mitochondrial + + + SAP-97 + hDlg + PR_EXT:000006511 + PR_EXT:disks large homolog 1 + E-dlg/SAP97 + synapse-associated protein 97 + embryo-dlg/synapse-associated protein 97 + DLG1 + "A protein that is a translation product of the human DLG1 gene or a 1:1 ortholog thereof." [PRO:DNx] + disks large homolog 1 + SAP97 + Dlgh1 + + + "A protein that is a translation product of the human DLGAP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + GKAP + DLGAP1 + SAP90/PSD-95-associated protein 1 + PR_EXT:disks large-associated protein 1 + guanylate kinase-associated protein + DAP1 + disks large-associated protein 1 + Kiaa4162 + SAPAP1 + DAP-1 + PR_EXT:000006516 + PSD-95/SAP90-binding protein 1 + + + DLL1 + PR_EXT:000006523 + drosophila Delta homolog 1 + delta1 + delta-like protein 1 + H-Delta-1 + "A protein that is a translation product of the human DLL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:delta-like protein 1 + + + PR_EXT:000006524 + drosophila Delta homolog 3 + DLL3 + delta-like protein 3 + "A protein that is a translation product of the human DLL3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:delta-like protein 3 + delta3 + M-Delta-3 + + + DLL4 + drosophila Delta homolog 4 + PR_EXT:000006525 + delta-like protein 4 + PR_EXT:delta-like protein 4 + "A protein that is a translation product of the human DLL4 gene or a 1:1 ortholog thereof." [PRO:DNx] + delta4 + + + DLX1 + "A protein that is a translation product of the human DLX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + homeobox protein DLX-1 + PR_EXT:homeobox protein DLX-1 + PR_EXT:000006527 + + + salivary agglutinin + muclin + DMBT1 + glycoprotein 300 + Crpd + CRP-ductin + glycoprotein 340 + deleted in malignant brain tumors 1 protein + GP340 + Gp-340 + gp300 + PR_EXT:000006534 + vomeroglandin + apactin + hensin + PR_EXT:deleted in malignant brain tumors 1 protein + surfactant pulmonary-associated D-binding protein + "A protein that is a translation product of the human DMBT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + mucin-like glycoprotein + + + PR_EXT:meiotic recombination protein DMC1/LIM15 + DMC1 + meiotic recombination protein DMC1/LIM15 + DMC1H + LIM15 + PR_EXT:000006536 + "A protein that is a translation product of the human DMC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + DMT1 + DMRT1 + doublesex- and mab-3-related transcription factor 1 + "A protein that is a translation product of the human DMRT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:doublesex- and mab-3-related transcription factor 1 + PR_EXT:000006542 + DM domain expressed in testis protein 1 + + + DSXL-2 + PR_EXT:doublesex- and mab-3-related transcription factor 2 + doublesex- and mab-3-related transcription factor 2 + DMRT2 + doublesex-like 2 protein + PR_EXT:000006543 + DSXL2 + "A protein that is a translation product of the human DMRT2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + DMRTA1 + Dmrt4 + "A protein that is a translation product of the human DMRTA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + doublesex- and mab-3-related transcription factor A1 + doublesex- and mab-3-related transcription factor 4 + DMO + PR_EXT:000006545 + PR_EXT:doublesex- and mab-3-related transcription factor A1 + + + PR_EXT:000006549 + Dmrt7 + doublesex- and mab-3-related transcription factor 7 + PR_EXT:doublesex- and mab-3-related transcription factor C2 + doublesex- and mab-3-related transcription factor C2 + DMRTC2 + "A protein that is a translation product of the human DMRTC2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + DNA MTase HsaI + "A protein that is a translation product of the human DNMT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + AIM + M.MmuI + DNA MTase MmuI + DNA (cytosine-5)-methyltransferase 1 + DNA methyltransferase MmuI + M.HsaI + DNA methyltransferase HsaI + MCMT + Dnmt1 + met-1 + DNMT1 + DNMT + Met1 + PR_EXT:DNA (cytosine-5)-methyltransferase 1 + CXXC-type zinc finger protein 9 + PR_EXT:000006606 + CXXC9 + Uim + + + DNMT3A + Dnmt3a + DNA MTase MmuIIIA + M.HsaIIIA + DNA methyltransferase MmuIIIA + DNA methyltransferase HsaIIIA + M.MmuIIIA + PR_EXT:DNA (cytosine-5)-methyltransferase 3A + DNA (cytosine-5)-methyltransferase 3A + "A protein that is a translation product of the human DNMT3A gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000006607 + DNA MTase HsaIIIA + + + DNMT3B + Dnmt3b + DNA methyltransferase HsaIIIB + DNA methyltransferase MmuIIIB + M.HsaIIIB + M.MmuIIIB + DNA (cytosine-5)-methyltransferase 3B + PR_EXT:DNA (cytosine-5)-methyltransferase 3B + "A protein that is a translation product of the human DNMT3B gene or a 1:1 ortholog thereof." [PRO:DNx] + DNA MTase HsaIIIB + PR_EXT:000006608 + DNA MTase MmuIIIB + + + "A protein that is a translation product of the human DOCK1 gene or a 1:1 ortholog thereof." [PRO:DNx] + DOCK1 + PR_EXT:000006616 + PR_EXT:dedicator of cytokinesis protein 1 + 180 kDa protein downstream of CRK + DOCK180 + dedicator of cytokinesis protein 1 + + + primordial germ cell protein 7 + Pgc7 + PR_EXT:000006666 + Crg1 + DPPA3 + developmental pluripotency-associated protein 3 + PR_EXT:developmental pluripotency-associated protein 3 + "A protein that is a translation product of the human DPPA3 gene or a 1:1 ortholog thereof." [PRO:DNx] + compaction-associated protein 1 + Cap1p + stella-related protein + STELLAR + + + 3ch134 + PR_EXT:dual specificity protein phosphatase 1 + protein-tyrosine phosphatase ERP + protein-tyrosine phosphatase CL100 + dual specificity protein phosphatase hVH1 + "A protein that is a translation product of the human DUSP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + MKP-1 + protein-tyrosine phosphatase 3CH134 + CL100 + Ptpn16 + dual specificity protein phosphatase 1 + DUSP1 + PR_EXT:000006736 + PTPN10 + VH1 + mitogen-activated protein kinase phosphatase 1 + MKP1 + MAP kinase phosphatase 1 + + + "A protein that is a translation product of the human DVL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + dishevelled-1 + PR_EXT:segment polarity protein dishevelled homolog DVL-1 + PR_EXT:000006765 + DVL1 + segment polarity protein dishevelled DVL-1 + segment polarity protein dishevelled homolog DVL-1 + DSH homolog 1 + Dvl + + + Ecat2 + PR_EXT:000006847 + PR_EXT:developmental pluripotency-associated protein 5A + ES cell-associated transcript 2 protein + protein pH 34 + developmental pluripotency-associated protein 5A + embryonal stem cell-specific gene 1 protein + Dppa5 + Esg1 + Ph34 + Dppa5a + "A protein that is a translation product of the mouse Dppa5a gene or a 1:1 ortholog thereof." [PRO:DNx] + ESG-1 + + + PBR3 + retinoblastoma-associated protein 1 + PR_EXT:transcription factor E2F1 + RBBP3 + transcription factor E2F1 + RBAP-1 + RBBP-3 + retinoblastoma-binding protein 3 + PR_EXT:000006852 + E2F-1 + "A protein that is a translation product of the human E2F1 gene or a 1:1 ortholog thereof." [PRO:DNx] + E2F1 + PRB-binding protein E2F-1 + + + transcription factor E2F2 + E2F-2 + PR_EXT:000006853 + "A protein that is a translation product of the human E2F2 gene or a 1:1 ortholog thereof." [PRO:DNx] + E2F2 + PR_EXT:transcription factor E2F2 + + + PR_EXT:transcription factor E2F3 + E2F3 + transcription factor E2F3 + E2F-3 + "A protein that is a translation product of the human E2F3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000006854 + KIAA0075 + + + E2F4 + transcription factor E2F4 + PR_EXT:transcription factor E2F4 + E2F-4 + PR_EXT:000006855 + "A protein that is a translation product of the human E2F4 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + E2F5 + PR_EXT:transcription factor E2F5 + transcription factor E2F5 + PR_EXT:000006856 + E2F-5 + "A protein that is a translation product of the human E2F5 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A protein that is a translation product of the human E2F6 gene or a 1:1 ortholog thereof." [PRO:DNx] + EMA + PR_EXT:transcription factor E2F6 + E2F6 + PR_EXT:000006857 + E2F-6 + transcription factor E2F6 + E2F-binding site-modulating activity protein + + + E2F7 + PR_EXT:000006858 + PR_EXT:transcription factor E2F7 + E2F-7 + "A protein that is a translation product of the human E2F7 gene or a 1:1 ortholog thereof." [PRO:DNx] + transcription factor E2F7 + + + endothelin-converting enzyme 1 + "A protein that is a translation product of the human ECE1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:endothelin-converting enzyme 1 + ECE1 + ECE-1 + PR_EXT:000006874 + + + ZFYVE2 + "A protein that is a translation product of the human EEA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:early endosome antigen 1 + early endosome antigen 1 + zinc finger FYVE domain-containing protein 2 + EEA1 + endosome-associated protein p162 + PR_EXT:000006901 + + + WAIT-1 + PR_EXT:polycomb protein EED + polycomb protein EED + WD protein associating with integrin cytoplasmic tails 1 + PR_EXT:000006902 + EED + "A protein that is a translation product of the human EED gene or a 1:1 ortholog thereof." [PRO:DNx] + + + EFHC1 + myoclonin-1 + PR_EXT:000006915 + EF-hand domain-containing protein 1 + PR_EXT:EF-hand domain-containing protein 1 + "A protein that is a translation product of the human EFHC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + Epl2 + ELK-L + stimulated by retinoic acid gene 1 protein + EPLG2 + EPH-related receptor tyrosine kinase ligand 2 + EFL3 + ELK ligand + CEK5-L + PR_EXT:ephrin-B1 + Stra1 + EFL-3 + LERK2 + PR_EXT:000006921 + LERK-2 + ephrin-B1 + EFNB1 + "An ephrin that is a translation product of the human EFNB1 gene or a 1:1 ortholog thereof." [PRO:DNx] + CEK5 receptor ligand + + + Elf2 + Epl5 + ELF-2 + EPLG5 + HTKL + EPH-related receptor tyrosine kinase ligand 5 + PR_EXT:ephrin-B2 + HTK ligand + LERK5 + ephrin-B2 + LERK-5 + "An ephrin that is a translation product of the human EFNB2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000006922 + EFNB2 + HTK-L + + + "A protein that is a translation product of the human EGF gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000006928 + EGF + pro-epidermal growth factor + PR_EXT:pro-epidermal growth factor + + + transcription factor ETR103 + EGR-1 + PR_EXT:000006937 + nerve growth factor-induced protein A + early growth response protein 1 + transcription factor Zif268 + EGR1 + PR_EXT:early growth response protein 1 + KROX24 + "A protein that is a translation product of the human EGR1 gene or a 1:1 ortholog thereof." [PRO:DNx] + zinc finger protein Krox-24 + AT225 + NGFI-A + Krox-24 + zinc finger protein 225 + ZNF225 + + + PR_EXT:early growth response protein 3 + early growth response protein 3 + PR_EXT:000006939 + "A protein that is a translation product of the human EGR3 gene or a 1:1 ortholog thereof." [PRO:DNx] + zinc finger protein pilot + PILOT + EGR3 + EGR-3 + + + eIF-4E + eukaryotic translation initiation factor 4E + PR_EXT:eukaryotic translation initiation factor 4E + EIF4EL1 + "A protein that is a translation product of the human EIF4E gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000006990 + eIF-4F 25 kDa subunit + EIF4F + EIF4E + eIF4E + mRNA cap-binding protein + + + PR_EXT:000007004 + PR_EXT:eukaryotic translation initiation factor 5A-2 + eIF-5A2 + eIF-5A-2 + "A protein that is a translation product of the human EIF5A2 gene or a 1:1 ortholog thereof." [PRO:DNx] + eukaryotic initiation factor 5A isoform 2 + eukaryotic translation initiation factor 5A-2 + EIF5A2 + + + elongation of very long chain fatty acids protein 2 + ELOVL2 + PR_EXT:000007037 + SSC2 + PR_EXT:elongation of very long chain fatty acids protein 2 + "A protein that is a translation product of the human ELOVL2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + EDMD + EMD + "A protein that is a translation product of the human EMD gene or a 1:1 ortholog thereof." [PRO:DNx] + STA + emerin + PR_EXT:000007050 + PR_EXT:emerin + + + "A protein that is a translation product of the human EN1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000007070 + PR_EXT:homeobox protein engrailed-1 + En-1 + EN1 + Mo-En-1 + homeobox protein engrailed-1 + Hu-En-1 + homeobox protein en-1 + + + "A protein that is a translation product of the human ENAH gene or a 1:1 ortholog thereof." [PRO:DNx] + protein enabled + PR_EXT:protein enabled + NPC-derived proline-rich protein 1 + MENA + Ndpp1 + NDPP-1 + PR_EXT:000007072 + ENAH + + + PR_EXT:cytosolic endo-beta-N-acetylglucosaminidase + cytosolic endo-beta-N-acetylglucosaminidase + PR_EXT:000007078 + ENGASE + ENGase + "A protein that is a translation product of the human ENGASE gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:histone acetyltransferase p300 + p300 HAT + histone acetyltransferase p300 + E1A-associated protein p300 + EP300 + PR_EXT:000007102 + P300 + "A transcription adapter with TAZ, KIX and bromo-domains that is a translation product of the human EP300 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + neuronal protein 4.1 + 4.1N + EPB41L1 + band 4.1-like protein 1 + "A protein that is a translation product of the human EPB41L1 gene or a 1:1 ortholog thereof." [PRO:DNx] + KIAA0338 + Epb4.1l1 + PR_EXT:000007108 + PR_EXT:band 4.1-like protein 1 + Epb4 + + + tyrosine-protein kinase receptor SEK-1 + EPH-like kinase 8 + EK8 + TYRO1 + PR_EXT:ephrin type-A receptor 4 + "An ephrin receptor that is a translation product of the human EPHA4 gene or a 1:1 ortholog thereof." [PRO:DNx] + tyrosine-protein kinase receptor SEK + PR_EXT:000007124 + tyrosine-protein kinase TYRO1 + tyrosine-protein kinase receptor MPK-3 + SEK + Sek1 + EPHA4 + ephrin type-A receptor 4 + + + EPTH3 + neural kinase + PR_EXT:000007130 + ephrin type-B receptor 2 + TYRO5 + tyrosine-protein kinase receptor EPH-3 + ERK + EPHT3 + Nuk receptor tyrosine kinase + EPHB2 + Sek3 + DRT + Nuk + tyrosine-protein kinase TYRO5 + EPH-like kinase 5 + PR_EXT:ephrin type-B receptor 2 + EK5 + tyrosine-protein kinase receptor SEK-3 + renal carcinoma antigen NY-REN-47 + "An ephrin receptor that is a translation product of the human EPHB2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000007131 + TYRO6 + ephrin type-B receptor 3 + ETK2 + EPHB3 + EPH-like kinase 2 + EK2 + Sek4 + Mdk5 + tyrosine-protein kinase TYRO6 + developmental kinase 5 + tyrosine-protein kinase receptor SEK-4 + PR_EXT:ephrin type-B receptor 3 + mDK-5 + "An ephrin receptor that is a translation product of the human EPHB3 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + proto-oncogene-like protein c-ErbB-3 + PR_EXT:000007159 + ERBB3 + HER3 + glial growth factor receptor + receptor tyrosine-protein kinase erbB-3 + "An EGF receptor type tyrosine-protein kinase that is a translation product of the human ERBB3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:receptor tyrosine-protein kinase erbB-3 + tyrosine kinase-type cell surface receptor HER3 + + + PR_EXT:DNA excision repair protein ERCC-1 + Ercc-1 + DNA excision repair protein ERCC-1 + "A protein that is a translation product of the human ERCC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + ERCC1 + PR_EXT:000007163 + + + TFIIH 80 kDa subunit + TFIIH basal transcription factor complex 80 kDa subunit + DNA repair protein complementing XP-D cells + DNA excision repair protein ERCC-2 + xeroderma pigmentosum group D-complementing protein + PR_EXT:TFIIH basal transcription factor complex helicase XPD subunit + TFIIH basal transcription factor complex helicase subunit + PR_EXT:000007164 + XPD + "A protein that is a translation product of the human ERCC2 gene or a 1:1 ortholog thereof." [PRO:DNx] + TFIIH p80 + CXPD + XPDC + TFIIH basal transcription factor complex helicase XPD subunit + BTF2 p80 + ERCC2 + basic transcription factor 2 80 kDa subunit + + + TFIIH basal transcription factor complex 89 kDa subunit + xeroderma pigmentosum group B-complementing protein + TFIIH 89 kDa subunit + DNA excision repair protein ERCC-3 + XPB + PR_EXT:TFIIH basal transcription factor complex helicase XPB subunit + basic transcription factor 2 89 kDa subunit + PR_EXT:000007165 + BTF2 p89 + "A protein that is a translation product of the human ERCC3 gene or a 1:1 ortholog thereof." [PRO:DNx] + ERCC3 + TFIIH p89 + DNA repair protein complementing XP-B cells + TFIIH basal transcription factor complex helicase XPB subunit + XPBC + + + PR_EXT:DNA repair endonuclease XPF + "A protein that is a translation product of the human ERCC4 gene or a 1:1 ortholog thereof." [PRO:DNx] + DNA repair endonuclease XPF + ERCC4 + xeroderma pigmentosum group F-complementing protein + DNA excision repair protein ERCC-4 + XPF + DNA repair protein complementing XP-F cells + ERCC11 + PR_EXT:000007166 + + + Ercc-5 + xeroderma pigmentosum group G-complementing protein homolog + "A protein that is a translation product of the human ERCC5 gene or a 1:1 ortholog thereof." [PRO:DNx] + XPGC + PR_EXT:000007167 + xeroderma pigmentosum group G-complementing protein + PR_EXT:DNA repair protein complementing XP-G cells + ERCC5 + XPG + ERCM2 + DNA excision repair protein ERCC-5 + DNA repair protein complementing XP-G cells + + + estrogen receptor + PR_EXT:estrogen receptor + "A protein that is a translation product of the human ESR1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Estr + NR3A1 + ESR + ER + ESR1 + estradiol receptor + ER-alpha + nuclear receptor subfamily 3 group A member 1 + PR_EXT:000007204 + Estra + + + ERR1 + nuclear receptor subfamily 3 group B member 1 + steroid hormone receptor ERR1 + "A protein that is a translation product of the human ESRRA gene or a 1:1 ortholog thereof." [PRO:DNx] + ESRL1 + estrogen receptor-like 1 + NR3B1 + estrogen-related receptor alpha + PR_EXT:000007208 + ESRRA + Estrra + ERR-alpha + PR_EXT:steroid hormone receptor ERR1 + + + PR_EXT:ETS translocation variant 1 + ETS protein ER81 + Ets-related protein 81 + Etsrp81 + PR_EXT:000007223 + ER81 + "A protein that is a translation product of the human ETV1 gene or a 1:1 ortholog thereof." [PRO:DNx] + ETS translocation variant 1 + ETV1 + + + polyomavirus enhancer activator 3 + protein PEA3 + ETS translocation variant 4 + Pea3 + adenovirus E1A enhancer-binding protein + E1A-F + PR_EXT:000007227 + ETV4 + Pea-3 + PR_EXT:ETS translocation variant 4 + E1AF + "A protein that is a translation product of the human ETV4 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + ETS translocation variant 5 + ETV5 + ERM + PR_EXT:000007228 + PR_EXT:ETS translocation variant 5 + "A protein that is a translation product of the human ETV5 gene or a 1:1 ortholog thereof." [PRO:DNx] + Ets-related protein ERM + + + "A protein that is a translation product of the human ETV6 gene or a 1:1 ortholog thereof." [PRO:DNx] + transcription factor ETV6 + ETS translocation variant 6 + Tel + PR_EXT:transcription factor ETV6 + TEL1 + ETV6 + ETS-related protein Tel1 + PR_EXT:000007229 + + + ellis-van Creveld syndrome protein + "A protein that is a translation product of the human EVC gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000007232 + EVC + DWF-1 + PR_EXT:ellis-van Creveld syndrome protein + + + homeobox even-skipped protein 1 + PR_EXT:homeobox even-skipped homolog protein 1 + homeobox even-skipped homolog protein 1 + PR_EXT:000007241 + EVX-1 + EVX1 + "A protein that is a translation product of the human EVX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + ewing sarcoma breakpoint region 1 protein + "A protein that is a translation product of the human EWSR1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:RNA-binding protein EWS + RNA-binding protein EWS + PR_EXT:000007243 + Ewsh + EWS oncogene + EWSR1 + EWS + + + PTA + PR_EXT:coagulation factor XI + coagulation factor XI + F11 + "A protein that is a translation product of the human F11 gene or a 1:1 ortholog thereof." [PRO:DNx] + FXI + plasma thromboplastin antecedent + PR_EXT:000007295 + + + PR_EXT:coagulation factor XII + coagulation factor XII + "A protein that is a translation product of the human F12 gene or a 1:1 ortholog thereof." [PRO:DNx] + HAF + hageman factor + F12 + PR_EXT:000007296 + + + PR_EXT:000007301 + SPCA + proconvertin + coagulation factor VII + eptacog alfa + Cf7 + "A protein that is a translation product of the human F7 gene or a 1:1 ortholog thereof." [PRO:DNx] + serum prothrombin conversion accelerator + F7 + PR_EXT:coagulation factor VII + + + PR_EXT:000007302 + PR_EXT:coagulation factor VIII + coagulation factor VIII + F8C + antihemophilic factor + F8 + Cf8 + "A protein that is a translation product of the human F8 gene or a 1:1 ortholog thereof." [PRO:DNx] + AHF + procoagulant component + + + PR_EXT:000007303 + christmas factor + plasma thromboplastin component + PTC + PR_EXT:coagulation factor IX + coagulation factor IX + F9 + Cf9 + "A protein that is a translation product of the human F9 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A fatty acid-binding protein that is a translation product of the human FABP4 gene or a 1:1 ortholog thereof." [PRO:DNx] + P15 + adipocyte lipid-binding protein + A-FABP + protein 422 + P2 adipocyte protein + Ap2 + fatty acid-binding protein 4 + myelin P2 protein homolog + fatty acid-binding protein, adipocyte + PR_EXT:fatty acid-binding protein, adipocyte + 3T3-L1 lipid-binding protein + ALBP + AFABP + FABP4 + PR_EXT:000007312 + adipocyte-type fatty acid-binding protein + + + BLBP + mammary-derived growth inhibitor related + B-FABP + MRG + fatty acid-binding protein, brain + fatty acid-binding protein 7 + FABP7 + FABPB + PR_EXT:000007315 + brain-type fatty acid-binding protein + PR_EXT:fatty acid-binding protein, brain + "A fatty acid-binding protein that is a translation product of the human FABP7 gene or a 1:1 ortholog thereof." [PRO:DNx] + brain lipid-binding protein + + + "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000007431 + IgE Fc receptor subunit alpha + FCE1A + high affinity immunoglobulin epsilon receptor subunit alpha + FCER1A + FcERI + Fc-epsilon RI-alpha + PR_EXT:high affinity immunoglobulin epsilon receptor subunit alpha + + + "A protein that is a translation product of the human FCER1G gene or a 1:1 ortholog thereof." [PRO:DNx] + Fc-epsilon RI-gamma + FceRI gamma + PR_EXT:000007432 + PR_EXT:high affinity immunoglobulin epsilon receptor subunit gamma + high affinity immunoglobulin epsilon receptor subunit gamma + IgE Fc receptor subunit gamma + FCER1G + Fce1g + + + SPAP2 + IFGP family protein 3 + "A protein that is a translation product of the human FCRL3 gene or a 1:1 ortholog thereof." [PRO:DNx] + IFGP3 + Fc receptor homolog 3 + immune receptor translocation-associated protein 3 + PR_EXT:Fc receptor-like protein 3 + Fc receptor-like protein 3 + PR_EXT:000007442 + FcR-like protein 3 + SH2 domain-containing phosphatase anchor protein 2 + CD307c + IRTA3 + FcRL3 + FCRL3 + FcRH3 + + + aFGF + FGFA + beta-endothelial cell growth factor + fibroblast growth factor 1 + ECGF-beta + HBGF-1 + PR_EXT:000007479 + heparin-binding growth factor 1 + Fgf-1 + acidic fibroblast growth factor + "A protein that is a translation product of the human FGF1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:fibroblast growth factor 1 + FGF1 + + + "A protein that is a translation product of the human FGF10 gene or a 1:1 ortholog thereof." [PRO:DNx] + FGF-10 + FGF10 + PR_EXT:fibroblast growth factor 10 + keratinocyte growth factor 2 + fibroblast growth factor 10 + PR_EXT:000007480 + + + heparin-binding growth factor 8 + androgen-induced growth factor + FGF8 + PR_EXT:fibroblast growth factor 8 + HBGF-8 + fibroblast growth factor 8 + "A protein that is a translation product of the human FGF8 gene or a 1:1 ortholog thereof." [PRO:DNx] + FGF-8 + PR_EXT:000007499 + AIGF + + + FGF9 + "A protein that is a translation product of the human FGF9 gene or a 1:1 ortholog thereof." [PRO:DNx] + HBGF-9 + PR_EXT:fibroblast growth factor 9 + glia-activating factor + heparin-binding growth factor 9 + fibroblast growth factor 9 + FGF-9 + GAF + PR_EXT:000007500 + + + fibroblast growth factor receptor 5 + FGFR-like protein + FGF homologous factor receptor + FGFR5 + FGF receptor-like protein 1 + PR_EXT:000007506 + FGFR-5 + fibroblast growth factor receptor-like 1 + "A protein that is a translation product of the human FGFRL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + FGFRL1 + PR_EXT:fibroblast growth factor receptor-like 1 + FHFR + + + PR_EXT:000007551 + filaggrin + PR_EXT:filaggrin + FLG + "A protein that is a translation product of the human FLG gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:vascular endothelial growth factor receptor 1 + PR_EXT:000007563 + vascular endothelial growth factor receptor 1 + VEGFR-1 + tyrosine-protein kinase FRT + tyrosine-protein kinase receptor FLT + Emrk2 + vascular permeability factor receptor + "A vascular endothelial growth factor receptor that is a translation product of the human FLT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Fms-like tyrosine kinase 1 + FLT1 + FRT + FLT + embryonic receptor kinase 2 + FLT-1 + + + cold-insoluble globulin + "A protein that is a translation product of the human FN1 gene or a 1:1 ortholog thereof." [PRO:DNx] + fibronectin + FN + FN1 + PR_EXT:fibronectin + PR_EXT:000007581 + CIG + + + proto-oncogene protein c-fos + G0S7 + PR_EXT:000007597 + FOS + proto-oncogene c-Fos + cellular oncogene fos + "A protein that is a translation product of the human FOS gene or a 1:1 ortholog thereof." [PRO:DNx] + G0/G1 switch regulatory protein 7 + PR_EXT:proto-oncogene c-Fos + + + FOSB + G0S3 + PR_EXT:000007598 + protein fosB + G0/G1 switch regulatory protein 3 + "A protein that is a translation product of the human FOSB gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:protein fosB + + + FOXA2 + HNF3B + hepatocyte nuclear factor 3-beta + transcription factor 3B + "A protein that is a translation product of the human FOXA2 gene or a 1:1 ortholog thereof." [PRO:DNx] + forkhead box protein A2 + TCF3B + PR_EXT:hepatocyte nuclear factor 3-beta + TCF-3B + HNF-3-beta + HNF-3B + PR_EXT:000007603 + + + forkhead box protein G1C + forkhead box protein G1B + BF-1 + forkhead box protein G1A + HFK3 + HFK2 + HFK1 + "A protein that is a translation product of the human FOXG1 gene or a 1:1 ortholog thereof." [PRO:DNx] + forkhead box protein G1 + PR_EXT:000007623 + FOXG1 + Fkhl1 + FoxG1 + brain factor 2 + BF-2 + Foxg1b + PR_EXT:forkhead box protein G1 + BF2 + BF1 + forkhead-related protein FKHL3 + Hfhbf1 + forkhead-related protein FKHL2 + forkhead-related protein FKHL1 + brain factor 1 + + + FOXO3A + FOXO3 + AF6q21 protein + PR_EXT:forkhead box protein O3 + "A protein that is a translation product of the human FOXO3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000007641 + FKHRL1 + forkhead in rhabdomyosarcoma-like 1 + forkhead box protein O3 + + + PR_EXT:000007680 + fibronectin type III and SPRY domain-containing protein 1 + GLFND + MID1-related protein 1 + microtubule-associated protein GLFND + MIR1 + PR_EXT:fibronectin type III and SPRY domain-containing protein 1 + FSD1 + "A protein that is a translation product of the human FSD1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:gamma-aminobutyric acid receptor subunit alpha-1 + gamma-aminobutyric acid receptor subunit alpha-1 + Gabra-1 + "A protein that is a translation product of the human GABRA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + GABA(A) receptor subunit alpha-1 + GABRA1 + PR_EXT:000007766 + + + PR_EXT:gamma-aminobutyric acid receptor subunit alpha-2 + GABRA2 + GABA(A) receptor subunit alpha-2 + PR_EXT:000007767 + Gabra-2 + gamma-aminobutyric acid receptor subunit alpha-2 + "A protein that is a translation product of the human GABRA2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + GABRA3 + PR_EXT:gamma-aminobutyric acid receptor subunit alpha-3 + GABA(A) receptor subunit alpha-3 + PR_EXT:000007768 + Gabra-3 + gamma-aminobutyric acid receptor subunit alpha-3 + "A protein that is a translation product of the human GABRA3 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + GABRA4 + PR_EXT:gamma-aminobutyric acid receptor subunit alpha-4 + PR_EXT:000007769 + GABA(A) receptor subunit alpha-4 + gamma-aminobutyric acid receptor subunit alpha-4 + "A protein that is a translation product of the human GABRA4 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + GABRA6 + PR_EXT:gamma-aminobutyric acid receptor subunit alpha-6 + GABA(A) receptor subunit alpha-6 + PR_EXT:000007771 + "A protein that is a translation product of the human GABRA6 gene or a 1:1 ortholog thereof." [PRO:DNx] + Gabra-6 + gamma-aminobutyric acid receptor subunit alpha-6 + + + gamma-aminobutyric acid receptor subunit beta-1 + PR_EXT:gamma-aminobutyric acid receptor subunit beta-1 + PR_EXT:000007772 + GABA(A) receptor subunit beta-1 + "A protein that is a translation product of the human GABRB1 gene or a 1:1 ortholog thereof." [PRO:DNx] + GABRB1 + + + PR_EXT:gamma-aminobutyric acid receptor subunit beta-2 + Gabrb-2 + PR_EXT:000007773 + GABA(A) receptor subunit beta-2 + GABRB2 + gamma-aminobutyric acid receptor subunit beta-2 + "A protein that is a translation product of the human GABRB2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + gamma-aminobutyric acid receptor subunit beta-3 + PR_EXT:gamma-aminobutyric acid receptor subunit beta-3 + GABA(A) receptor subunit beta-3 + PR_EXT:000007774 + GABRB3 + Gabrb-3 + "A protein that is a translation product of the human GABRB3 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A protein that is a translation product of the human GABRD gene or a 1:1 ortholog thereof." [PRO:DNx] + GABA(A) receptor subunit delta + PR_EXT:gamma-aminobutyric acid receptor subunit delta + GABRD + gamma-aminobutyric acid receptor subunit delta + PR_EXT:000007775 + + + gamma-aminobutyric acid receptor subunit epsilon + GABA(A) receptor subunit epsilon + PR_EXT:gamma-aminobutyric acid receptor subunit epsilon + PR_EXT:000007776 + GABRE + "A protein that is a translation product of the human GABRE gene or a 1:1 ortholog thereof." [PRO:DNx] + + + GABRG1 + GABA(A) receptor subunit gamma-1 + gamma-aminobutyric acid receptor subunit gamma-1 + "A protein that is a translation product of the human GABRG1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000007777 + PR_EXT:gamma-aminobutyric acid receptor subunit gamma-1 + + + gamma-aminobutyric acid receptor subunit gamma-2 + "A protein that is a translation product of the human GABRG2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:gamma-aminobutyric acid receptor subunit gamma-2 + PR_EXT:000007778 + GABRG2 + GABA(A) receptor subunit gamma-2 + + + GABRP + "A protein that is a translation product of the human GABRP gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000007780 + GABA(A) receptor subunit pi + PR_EXT:gamma-aminobutyric acid receptor subunit pi + gamma-aminobutyric acid receptor subunit pi + + + gamma-aminobutyric acid receptor subunit theta + PR_EXT:000007781 + "A protein that is a translation product of the human GABRQ gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:gamma-aminobutyric acid receptor subunit theta + GABRQ + GABA(A) receptor subunit theta + + + "A protein that is a translation product of the human GAD2 gene or a 1:1 ortholog thereof." [PRO:DNx] + GAD-65 + 65 kDa glutamic acid decarboxylase + glutamate decarboxylase 2 + GAD65 + GAD2 + PR_EXT:glutamate decarboxylase 2 + PR_EXT:000007786 + glutamate decarboxylase 65 kDa isoform + + + CR6 + DDIT2 + growth arrest and DNA damage-inducible protein GADD45 gamma + GADD45G + PR_EXT:000007789 + DDIT-2 + "A protein that is a translation product of the human GADD45G gene or a 1:1 ortholog thereof." [PRO:DNx] + DNA damage-inducible transcript 2 protein + PR_EXT:growth arrest and DNA damage-inducible protein GADD45 gamma + cytokine-responsive protein CR6 + + + "A protein that is a translation product of the human GAS6 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000007853 + GAS6 + AXLLG + growth arrest-specific protein 6 + AXL receptor tyrosine kinase ligand + GAS-6 + PR_EXT:growth arrest-specific protein 6 + + + "A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + GATA-binding factor 1 + GF1 + erythroid transcription factor + NF-E1 DNA-binding protein + GATA1 + Eryf1 + GATA-1 + GF-1 + PR_EXT:000007857 + PR_EXT:erythroid transcription factor + + + PR_EXT:000007858 + GATA-binding protein 2 + GATA2 + endothelial transcription factor GATA-2 + PR_EXT:endothelial transcription factor GATA-2 + "A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + GATA-binding factor 4 + PR_EXT:000007859 + transcription factor GATA-4 + PR_EXT:transcription factor GATA-4 + GATA4 + Gata-4 + "A protein that is a translation product of the human GATA4 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + GATA-binding factor 6 + PR_EXT:000007861 + transcription factor GATA-6 + "A protein that is a translation product of the human GATA6 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:transcription factor GATA-6 + GATA6 + + + DBP + Gc-globulin + vitamin D-binding protein + VDB + PR_EXT:vitamin D-binding protein + PR_EXT:000007883 + "A protein that is a translation product of the human GC gene or a 1:1 ortholog thereof." [PRO:DNx] + group-specific component + GC + + + GCKR + glucokinase regulatory protein + PR_EXT:glucokinase regulatory protein + glucokinase regulator + "A protein that is a translation product of the human GCKR gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000007896 + + + "A protein that is a translation product of the human GCLC gene or a 1:1 ortholog thereof." [PRO:DNx] + GLCLC + PR_EXT:glutamate--cysteine ligase catalytic subunit + GCLC + glutamate--cysteine ligase catalytic subunit + gamma-glutamylcysteine synthetase + GLCL + GCS heavy chain + gamma-ECS + PR_EXT:000007897 + + + "A protein that is a translation product of the human GCM1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:chorion-specific transcription factor GCMa + GCM1 + GCMa + GCMA + glial cells missing homolog 1 + PR_EXT:000007899 + GCM motif protein 1 + chorion-specific transcription factor GCMa + + + "A protein that is a translation product of the human KAT2A gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:histone acetyltransferase KAT2A + histone acetyltransferase KAT2A + KAT2A + general control of amino acid synthesis protein 5-like 2 + HGCN5 + histone acetyltransferase GCN5 + lysine acetyltransferase 2A + PR_EXT:000007902 + GCN5L2 + STAF97 + GCN5 + + + BMP11 + growth/differentiation factor 11 + PR_EXT:growth/differentiation factor 11 + BMP-11 + bone morphogenetic protein 11 + "A protein that is a translation product of the human GDF11 gene or a 1:1 ortholog thereof." [PRO:DNx] + GDF11 + PR_EXT:000007919 + GDF-11 + + + prostate differentiation factor + PR_EXT:growth/differentiation factor 15 + PDF + macrophage inhibitory cytokine 1 + NSAID-regulated gene 1 protein + placental bone morphogenetic protein + Sbf + PR_EXT:000007920 + MIC1 + growth/differentiation factor 15 + NAG-1 + placental TGF-beta + PLAB + "A protein that is a translation product of the human GDF15 gene or a 1:1 ortholog thereof." [PRO:DNx] + NSAID-activated gene 1 protein + GDF15 + MIC-1 + GDF-15 + PTGFB + NRG-1 + + + growth/differentiation factor 6 + PR_EXT:000007924 + GDF6 + growth/differentiation factor 16 + GDF-6 + GDF16 + PR_EXT:growth/differentiation factor 6 + "A BMP that is a translation product of the human GDF6 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + GDF9 + PR_EXT:growth/differentiation factor 9 + GDF-9 + growth/differentiation factor 9 + PR_EXT:000007925 + "A protein that is a translation product of the human GDF9 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:glial cell line-derived neurotrophic factor + glial cell line-derived neurotrophic factor + "A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof." [PRO:DNx] + astrocyte-derived trophic factor + PR_EXT:000007928 + GDNF + ATF + + + glial fibrillary acidic protein + PR_EXT:glial fibrillary acidic protein + GFAP + "A protein that is a translation product of the human GFAP gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000007939 + + + somatotropin + GH + pituitary growth hormone + PR_EXT:somatotropin + growth hormone 1 + growth hormone + PR_EXT:000007968 + GH-N + "A somatotropin hormone family member that is a translation product of the human GH1 gene or a 1:1 ortholog thereof." [PRO:DNx] + GH1 + + + connexin-26 + Cxn-26 + GJB2 + PR_EXT:gap junction beta-2 protein + "A protein that is a translation product of the human GJB2 gene or a 1:1 ortholog thereof." [PRO:DNx] + Cx26 + gap junction beta-2 protein + PR_EXT:000007998 + + + GLI1 + glioma-associated oncogene + PR_EXT:zinc finger protein GLI1 + glioma-associated oncogene homolog + PR_EXT:000008026 + oncogene GLI + GLI + "A protein that is a translation product of the human GLI1 gene or a 1:1 ortholog thereof." [PRO:DNx] + zinc finger protein GLI1 + + + zinc finger protein GLI2 + GLI2 + PR_EXT:zinc finger protein GLI2 + "A protein that is a translation product of the human GLI2 gene or a 1:1 ortholog thereof." [PRO:DNx] + THP + Tax helper protein + PR_EXT:000008027 + + + PR_EXT:transcriptional activator GLI3 + transcriptional activator GLI3 + GLI3 + "A protein that is a translation product of the human GLI3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000008028 + zinc finger protein GLI3 + + + PR_EXT:lactoylglutathione lyase + lactoylglutathione lyase + aldoketomutase + "A protein that is a translation product of the human GLO1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Glx I + S-D-lactoylglutathione methylglyoxal lyase + glyoxalase I + GLO1 + gloA + ketone-aldehyde mutase + methylglyoxalase + PR_EXT:000008038 + + + PR_EXT:000008043 + "A protein that is a translation product of the human GLRA2 gene or a 1:1 ortholog thereof." [PRO:DNx] + GLRA2 + glycine receptor subunit alpha-2 + PR_EXT:glycine receptor subunit alpha-2 + + + G alpha-12 + GNA12 + Gna-12 + PR_EXT:000008081 + G-protein subunit alpha-12 + "A protein that is a translation product of the human GNA12 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:guanine nucleotide-binding protein subunit alpha-12 + guanine nucleotide-binding protein subunit alpha-12 + + + guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-3 + "A protein that is a translation product of the human GNB3 gene or a 1:1 ortholog thereof." [PRO:DNx] + GNB3 + transducin beta chain 3 + PR_EXT:000008099 + PR_EXT:guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-3 + + + PR_EXT:golgin subfamily A member 2 + golgin subfamily A member 2 + GM130 autoantigen + GM130 + 130 kDa cis-Golgi matrix protein + GOLGA2 + PR_EXT:000008131 + golgin-95 + "A protein that is a translation product of the human GOLGA2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000008174 + GPHN + KIAA1385 + PR_EXT:gephyrin + "A protein that is a translation product of the human GPHN gene or a 1:1 ortholog thereof." [PRO:DNx] + GPH + gephyrin + + + "A protein that is a translation product of the human GPX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + GSHPx-1 + cellular glutathione peroxidase + PR_EXT:glutathione peroxidase 1 + glutathione peroxidase 1 + GPX1 + GPx-1 + PR_EXT:000008210 + + + PR_EXT:000008212 + "A protein that is a translation product of the human GPX3 gene or a 1:1 ortholog thereof." [PRO:DNx] + GSHPx-P + GSHPx-3 + GPXP + extracellular glutathione peroxidase + glutathione peroxidase 3 + PR_EXT:glutathione peroxidase 3 + GPX3 + GPx-3 + GPx-P + plasma glutathione peroxidase + + + ASH + PR_EXT:000008224 + GRB2 + "A protein that is a translation product of the human GRB2 gene or a 1:1 ortholog thereof." [PRO:DNx] + adapter protein GRB2 + protein Ash + PR_EXT:growth factor receptor-bound protein 2 + SH2/SH3 adapter GRB2 + growth factor receptor-bound protein 2 + + + "A protein that is a translation product of the human GRB7 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000008225 + growth factor receptor-bound protein 7 + B47 + PR_EXT:growth factor receptor-bound protein 7 + GRB7 adapter protein + GRB7 + epidermal growth factor receptor GRB-7 + + + DAN domain family member 2 + Down-regulated in Mos-transformed cells protein + cell proliferation-inducing gene 2 protein + PR_EXT:gremlin-1 + PR_EXT:000008227 + gremlin-1 + IHG-2 + CKTSF1B1 + "A protein that is a translation product of the human GREM1 gene or a 1:1 ortholog thereof." [PRO:DNx] + DRM + DAND2 + cysteine knot superfamily 1, BMP antagonist 1 + increased in high glucose protein 2 + GREM1 + + + glutamate receptor 1 + GLUR1 + GluR-1 + GluR-A + "A protein that is a translation product of the human GRIA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + glutamate receptor ionotropic, AMPA 1 + PR_EXT:000008233 + AMPA-selective glutamate receptor 1 + GRIA1 + PR_EXT:glutamate receptor 1 + GLUH1 + GluR-K1 + + + glutamate receptor 2 + PR_EXT:glutamate receptor 2 + PR_EXT:000008234 + glutamate receptor ionotropic, AMPA 2 + GLUR2 + GluR-B + GluR-2 + "A protein that is a translation product of the human GRIA2 gene or a 1:1 ortholog thereof." [PRO:DNx] + GluR-K2 + GRIA2 + AMPA-selective glutamate receptor 2 + + + glutamate receptor 4 + GluR-D + GluR-4 + "A protein that is a translation product of the human GRIA4 gene or a 1:1 ortholog thereof." [PRO:DNx] + glutamate receptor ionotropic, AMPA 4 + PR_EXT:glutamate receptor 4 + PR_EXT:000008236 + GRIA4 + GluR4 + AMPA-selective glutamate receptor 4 + + + EAA4 + glutamate receptor beta-2 + GluR-6 + excitatory amino acid receptor 4 + "A protein that is a translation product of the human GRIK2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:glutamate receptor ionotropic, kainate 2 + GluR6 + GRIK2 + glutamate receptor ionotropic, kainate 2 + GluR beta-2 + glutamate receptor 6 + PR_EXT:000008241 + + + NMDAR2A + NR2A + "A protein that is a translation product of the human GRIN2A gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000008246 + N-methyl D-aspartate receptor subtype 2A + PR_EXT:glutamate receptor ionotropic, NMDA 2A + glutamate [NMDA] receptor subunit epsilon-1 + glutamate receptor ionotropic, NMDA 2A + GRIN2A + + + "A protein that is a translation product of the human GRIN2C gene or a 1:1 ortholog thereof." [PRO:DNx] + NMDAR2C + PR_EXT:000008248 + NR2C + PR_EXT:glutamate receptor ionotropic, NMDA 2C + GRIN2C + glutamate [NMDA] receptor subunit epsilon-3 + glutamate receptor ionotropic, NMDA 2C + N-methyl D-aspartate receptor subtype 2C + + + "A protein that is a translation product of the human GRK4 gene or a 1:1 ortholog thereof." [PRO:DNx] + G protein-coupled receptor kinase 4 + PR_EXT:G protein-coupled receptor kinase 4 + ITI1 + GRK4 + GPRK2L + PR_EXT:000008258 + GPRK4 + G-protein coupled receptor kinase 4 + G-protein coupled receptor kinase GRK4 + + + GRK6 + PR_EXT:G protein-coupled receptor kinase 6 + G protein-coupled receptor kinase 6 + GPRK6 + G-protein coupled receptor kinase 6 + G-protein coupled receptor kinase GRK6 + PR_EXT:000008260 + "A protein that is a translation product of the human GRK6 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + homeobox protein goosecoid + GSC + PR_EXT:000008278 + PR_EXT:homeobox protein goosecoid + "A protein that is a translation product of the human GSC gene or a 1:1 ortholog thereof." [PRO:DNx] + + + GSK-3 beta + GSK3B + "A GSK3-like glycogen synthase kinase that is a translation product of the human GSK3B gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000008288 + glycogen synthase kinase-3 beta + PR_EXT:glycogen synthase kinase-3 beta + + + PR_EXT:glutathione reductase, mitochondrial + PR_EXT:000008292 + GSR + GR + GRD1 + Gr1 + glutathione reductase, mitochondrial + "A protein that is a translation product of the human GSR gene or a 1:1 ortholog thereof." [PRO:DNx] + GLUR + + + GSTM1 + glutathione S-transferase GT8.7 + GSTM1-1 + "A glutathione S-transferase mu that is a translation product of the human GSTM1 gene or a 1:1 ortholog thereof." [PRO:DAN] + GST class-mu 1 + GST HB subunit 4 + GSTM1b-1b + GSTM1a-1a + pmGT10 + GST 1-1 + GST1 + glutathione S-transferase mu 1 + PR_EXT:000008300 + PR_EXT:glutathione S-transferase mu 1 + GTH4 + + + PR_EXT:maleylacetoacetate isomerase + MAAI + glutathione S-transferase zeta 1 + PR_EXT:000008307 + GSTZ1 + "A protein that is a translation product of the human GSTZ1 gene or a 1:1 ortholog thereof." [PRO:DNx] + GSTZ1-1 + maleylacetoacetate isomerase + + + GS homeobox 1 + PR_EXT:GS homeobox 1 + GSH1 + homeobox protein GSH-1 + "A protein that is a translation product of the human GSX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000008308 + Gsh-1 + GSX1 + + + PR_EXT:GS homeobox 2 + homeobox protein GSH-2 + GSH2 + "A protein that is a translation product of the human GSX2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000008309 + Gsh-2 + GSX2 + GS homeobox 2 + + + TFIIB + PR_EXT:transcription initiation factor IIB + RNA polymerase II alpha initiation factor + transcription initiation factor IIB + TF2B + "A protein that is a translation product of the human GTF2B gene or a 1:1 ortholog thereof." [PRO:DNx] + S300-II + GTF2B + general transcription factor TFIIB + PR_EXT:000008313 + + + basic transcription factor 2 62 kDa subunit + "A protein that is a translation product of the human GTF2H1 gene or a 1:1 ortholog thereof." [PRO:DNx] + TFIIH basal transcription factor complex p62 subunit + BTF2 p62 + PR_EXT:general transcription factor IIH subunit 1 + PR_EXT:000008317 + BTF2 + GTF2H1 + general transcription factor IIH polypeptide 1 + general transcription factor IIH subunit 1 + + + "A protein that is a translation product of the human GTF2H2 gene or a 1:1 ortholog thereof." [PRO:DNx] + BTF2P44 + TFIIH basal transcription factor complex p44 subunit + PR_EXT:general transcription factor IIH subunit 2 + PR_EXT:000008318 + basic transcription factor 2 44 kDa subunit + BTF2 p44 + general transcription factor IIH subunit 2 + general transcription factor IIH polypeptide 2 + GTF2H2 + + + "A protein that is a translation product of the human GTF2H3 gene or a 1:1 ortholog thereof." [PRO:DNx] + basic transcription factor 2 34 kDa subunit + TFIIH basal transcription factor complex p34 subunit + PR_EXT:general transcription factor IIH subunit 3 + PR_EXT:000008319 + BTF2 p34 + general transcription factor IIH subunit 3 + GTF2H3 + general transcription factor IIH polypeptide 3 + + + basic transcription factor 2 52 kDa subunit + TFIIH basal transcription factor complex p52 subunit + PR_EXT:000008320 + BTF2 p52 + "A protein that is a translation product of the human GTF2H4 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:general transcription factor IIH subunit 4 + GTF2H4 + general transcription factor IIH polypeptide 4 + general transcription factor IIH subunit 4 + + + PR_EXT:000008321 + PR_EXT:general transcription factor IIH subunit 5 + "A protein that is a translation product of the human GTF2H5 gene or a 1:1 ortholog thereof." [PRO:DNx] + D17Wsu155e + general transcription factor IIH subunit 5 + TTDA + TFIIH basal transcription factor complex TTD-A subunit + general transcription factor IIH polypeptide 5 + TFB5 ortholog + C6orf175 + GTF2H5 + + + "A protein that is a translation product of the human GUCY2D gene or a 1:1 ortholog thereof." [PRO:DNx] + rod outer segment membrane guanylate cyclase + GUCY2D + guanylate cyclase 2E + PR_EXT:retinal guanylyl cyclase 1 + GUC2D + Guc2e + PR_EXT:000008353 + ROS-GC + RETGC1 + GUC1A4 + retinal guanylyl cyclase 1 + RETGC + guanylyl cyclase GC-E + Gucy2e + CORD6 + RETGC-1 + guanylate cyclase 2D, retinal + + + gap junction alpha-1 protein + PR_EXT:gap junction alpha-1 protein + connexin-43 + "A protein that is a translation product of the human GJA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Cxn-43 + Cx43 + gap junction 43 kDa heart protein + GJA1 + PR_EXT:000008373 + + + PR_EXT:H-2 class I histocompatibility antigen, Q10 alpha chain + H-2 class I histocompatibility antigen, Q10 alpha chain + H2-Q10 + "A protein that is a translation product of the mouse H2-Q10 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000008409 + + + "A histone H2A that is a translation product of the human H2AFX gene or a 1:1 ortholog thereof." [PRO:DNx] + H2a/x + PR_EXT:000008418 + PR_EXT:histone H2A.x + H2a.x + H2AFX + H2AX + histone H2A.x + Hist5-2ax + + + histone H3.3 + H3.3B + PR_EXT:histone H3.3 + "A histone H3 that is a translation product of the human H3F3B gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000008425 + H3F3B + + + Thing1 + Th1 + Hxt + HAND1 + bHLHa27 + PR_EXT:heart- and neural crest derivatives-expressed protein 1 + class A basic helix-loop-helix protein 27 + helix-loop-helix transcription factor expressed in extraembryonic mesoderm and trophoblast + extraembryonic tissues, heart, autonomic nervous system and neural crest derivatives-expressed protein 1 + heart- and neural crest derivatives-expressed protein 1 + PR_EXT:000008439 + "A basic helix-loop-helix transcription factor HAND that is a translation product of the human HAND1 gene or a 1:1 ortholog thereof." [PRO:DNx] + thing-1 + eHAND + + + PR_EXT:hydroxyacid oxidase 2 + HAO2 + hydroxyacid oxidase 2 + (S)-2-hydroxy-acid oxidase, peroxisomal + medium chain alpha-hydroxy acid oxidase + cell growth-inhibiting gene 16 protein + "A protein that is a translation product of the human HAO2 gene or a 1:1 ortholog thereof." [PRO:DNx] + long chain alpha-hydroxy acid oxidase + PR_EXT:000008442 + medium-chain L-2-hydroxy acid oxidase + HAOX2 + long-chain L-2-hydroxy acid oxidase + Hao3 + + + "A protein that is a translation product of the human HBB gene or a 1:1 ortholog thereof." [PRO:DNx] + beta-globin + PR_EXT:hemoglobin subunit beta + HBB + PR_EXT:000008457 + hemoglobin beta chain + hemoglobin subunit beta + + + DTR + HEGFL + PR_EXT:000008459 + "A protein that is a translation product of the human HBEGF gene or a 1:1 ortholog thereof." [PRO:DNx] + DTS + HBEGF + proheparin-binding EGF-like growth factor + PR_EXT:proheparin-binding EGF-like growth factor + + + "A protein that is a translation product of the human HES1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:transcription factor HES-1 + PR_EXT:000008515 + hairy-like protein + hairy homolog + Hes-1 + HES1 + HRY + transcription factor HES-1 + bHLHb39 + class B basic helix-loop-helix protein 39 + hairy and enhancer of split 1 + HL + + + bHLHb38 + class B basic helix-loop-helix protein 38 + PR_EXT:000008519 + transcription factor HES-5 + hairy and enhancer of split 5 + "A protein that is a translation product of the human HES5 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:transcription factor HES-5 + HES5 + Hes-5 + + + homeobox protein ANF + PR_EXT:000008523 + "A protein that is a translation product of the human HESX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Hes-1 + rathke pouch homeo box + Rpx + HESX1 + homeobox expressed in ES cells 1 + hAnf + anterior-restricted homeobox protein + PR_EXT:homeobox expressed in ES cells 1 + + + HPTA + "A protein that is a translation product of the human HGF gene or a 1:1 ortholog thereof." [PRO:DNx] + HGF + hepatopoeitin-A + scatter factor + SF + PR_EXT:hepatocyte growth factor + PR_EXT:000008534 + hepatocyte growth factor + + + Hrs + hepatocyte growth factor-regulated tyrosine kinase substrate + HGS + "A protein that is a translation product of the human HGS gene or a 1:1 ortholog thereof." [PRO:DNx] + protein pp110 + PR_EXT:hepatocyte growth factor-regulated tyrosine kinase substrate + PR_EXT:000008536 + + + bHLHe78 + class E basic helix-loop-helix protein 78 + PASD8 + hypoxia-inducible factor 1-alpha + ARNT-interacting protein + HIF-1-alpha + PR_EXT:000008555 + HIF1-alpha + PR_EXT:hypoxia-inducible factor 1-alpha + member of PAS protein 1 + MOP1 + PAS domain-containing protein 8 + HIF1A + "A protein that is a translation product of the human HIF1A gene or a 1:1 ortholog thereof." [PRO:DNx] + basic-helix-loop-helix-PAS protein MOP1 + + + PR_EXT:000008570 + protein HIRA + PR_EXT:protein HIRA + "A protein that is a translation product of the human HIRA gene or a 1:1 ortholog thereof." [PRO:DNx] + TUPLE1 + HIRA + TUP1-like enhancer of split protein 1 + DGCR1 + HIR + + + "A core histone that is a translation product of any of the human HIST4H4 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." [PRO:DAN] + histone H4 + PR_EXT:000008603 + PR_EXT:histone H4 + HIST4H4 + + + HK I + hexokinase type I + "A protein that is a translation product of the human HK1 gene or a 1:1 ortholog thereof." [PRO:DNx] + brain form hexokinase + hexokinase-1 + PR_EXT:hexokinase-1 + HK1 + PR_EXT:000008608 + hexokinase, tumor isozyme + + + "A protein that is a translation product of the human HK2 gene or a 1:1 ortholog thereof." [PRO:DNx] + HK II + hexokinase type II + muscle form hexokinase + PR_EXT:000008609 + PR_EXT:hexokinase-2 + hexokinase-2 + HK2 + + + HK III + hexokinase type III + "A protein that is a translation product of the human HK3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000008610 + hexokinase-3 + HK3 + PR_EXT:hexokinase-3 + + + PR_EXT:000008649 + MT-RNR2 + humanin + "A protein that is a translation product of the human MT-RNR2 gene or a 1:1 ortholog thereof." [PRO:DNx] + HN + PR_EXT:humanin + + + Hnf-4 + HNF-4-alpha + TCF-14 + "A protein that is a translation product of the human HNF4A gene or a 1:1 ortholog thereof." [PRO:DNx] + NR2A1 + HNF4A + hepatocyte nuclear factor 4-alpha + PR_EXT:hepatocyte nuclear factor 4-alpha + TCF14 + PR_EXT:000008654 + transcription factor HNF-4 + transcription factor 14 + nuclear receptor subfamily 2 group A member 1 + HNF4 + + + "A protein that is a translation product of the human HOMER3 gene or a 1:1 ortholog thereof." [PRO:DNx] + homer-3 + homer protein homolog 3 + HOMER3 + PR_EXT:homer protein homolog 3 + PR_EXT:000008680 + + + homeobox protein Hox-2.2 + Hox-2.2 + Hoxb-6 + "A protein that is a translation product of the human HOXB6 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:homeobox protein Hox-B6 + homeobox protein Hox-2B + HOX2B + homeobox protein MH-22A + PR_EXT:000008703 + HOXB6 + homeobox protein Hu-2 + homeobox protein Hox-B6 + + + "A protein that is a translation product of the human HPRT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:hypoxanthine-guanine phosphoribosyltransferase + HPRT1 + PR_EXT:000008735 + HPRT B + HGPRTase + hypoxanthine-guanine phosphoribosyltransferase + HPRT + HGPRT + + + PR_EXT:000008785 + HSD3B1 + trophoblast antigen FDO161G + PR_EXT:3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 1 + "A protein that is a translation product of the human HSD3B1 gene or a 1:1 ortholog thereof." [PRO:DNx] + 3BH + 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type I + Hsd3b + 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 1 + 3-beta-HSD I + HSDB3A + + + 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type II + HSDB3B + HSD3B2 + 3-beta-HSD II + PR_EXT:000008786 + "A protein that is a translation product of the human HSD3B2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 2 + 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 2 + + + HSPA8 + HSPA10 + heat shock cognate 71 kDa protein + "An HSPA protein that is a translation product of the human HSPA8 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:heat shock cognate 71 kDa protein + Hsc73 + PR_EXT:000008812 + heat shock 70 kDa protein 8 + HSP73 + HSC70 + + + heat shock 70 kDa protein 9 + stress-70 protein, mitochondrial + MOT + peptide-binding protein 74 + mortalin + PR_EXT:000008813 + PR_EXT:stress-70 protein, mitochondrial + "An HSPA protein that is a translation product of the human HSPA9 gene or a 1:1 ortholog thereof." [PRO:DNx] + PBP74 + HSPA9 + p66 MOT + Hspa9a + GRP75 + GRP-75 + HSPA9B + 75 kDa glucose-regulated protein + Hsp74 + + + "An HSPB protein that is a translation product of the human HSPB2 gene or a 1:1 ortholog thereof." [PRO:DNx] + DMPK-binding protein + PR_EXT:000008816 + heat shock protein beta-2 + PR_EXT:heat shock protein beta-2 + MKBP + HSPB2 + HspB2 + + + HD protein + IT15 + PR_EXT:huntingtin + huntington disease protein homolog + Hdh + HD + huntingtin + "A protein that is a translation product of the human HTT gene or a 1:1 ortholog thereof." [PRO:DNx] + huntington disease protein + PR_EXT:000008840 + HD protein homolog + HTT + + + "A protein that is a translation product of the mouse Hsd3b3 gene or a 1:1 ortholog thereof." [PRO:DNx] + 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 3 + Hsd3b3 + PR_EXT:000008867 + 3-beta-HSD III + 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type III + PR_EXT:3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 3 + + + PR_EXT:000008870 + 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 6 + "A protein that is a translation product of the mouse Hsd3b6 gene or a 1:1 ortholog thereof." [PRO:DNx] + 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type VI + 3-beta-HSD VI + Hsd3b6 + PR_EXT:3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 6 + + + PR_EXT:000008871 + hsp68 + heat shock 70 kDa protein 1A + Hsp70-3 + HSPA1A + PR_EXT:heat shock 70 kDa protein 1A + "An HSPA protein that is a translation product of the human HSPA1A gene or a 1:1 ortholog thereof." [PRO:DAN] + HSP70.3 + Hsp70A1 + heat shock 70 kDa protein 3 + + + TgN737Rpw + PR_EXT:000008940 + recessive polycystic kidney disease protein Tg737 homolog + Tg737Rpw + "A protein that is a translation product of the human IFT88 gene or a 1:1 ortholog thereof." [PRO:DNx] + IFT88 + TPR repeat protein 10 + TG737 + TgN(Imorpk)737Rpw + PR_EXT:intraflagellar transport protein 88 + tetratricopeptide repeat protein 10 + recessive polycystic kidney disease protein Tg737 + intraflagellar transport protein 88 + TTC10 + + + protein alpha-4 + "A protein that is a translation product of the human IGBP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + IBP1 + PR_EXT:immunoglobulin-binding protein 1 + IGBP1 + lymphocyte signal transduction molecule alpha 4 + Pc52 + PR_EXT:000008941 + renal carcinoma antigen NY-REN-16 + immunoglobulin-binding protein 1 + alpha4 phosphoprotein + B-cell signal transduction molecule alpha 4 + CD79a-binding protein 1 + + + PR_EXT:000008947 + IBP1 + PP12 + insulin-like growth factor-binding protein 1 + placental protein 12 + IGF-binding protein 1 + PR_EXT:insulin-like growth factor-binding protein 1 + IGFBP1 + IBP-1 + IGFBP-1 + "A protein that is a translation product of the human IGFBP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + DNA-binding protein SMUBP-2 + CATF1 + IGHMBP2 + Smbp-2 + ATP-dependent helicase IGHMBP2 + "A protein that is a translation product of the human IGHMBP2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000008964 + GF-1 + cardiac transcription factor 1 + immunoglobulin mu-binding protein 2 + SMUBP2 + glial factor 1 + SMBP2 + PR_EXT:DNA-binding protein SMUBP-2 + + + "A protein that is a translation product of the human IHH gene or a 1:1 ortholog thereof." [PRO:DNx] + indian hedgehog protein + PR_EXT:indian hedgehog protein + IHH + HHG-2 + PR_EXT:000008974 + + + IRR + insulin receptor-related protein + IR-related receptor + INSRR + "A protein that is a translation product of the human INSRR gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000009065 + PR_EXT:insulin receptor-related protein + + + inversion of embryo turning homolog + nephrocystin-2 + PR_EXT:000009079 + PR_EXT:inversin + NPHP2 + "A protein that is a translation product of the human INVS gene or a 1:1 ortholog thereof." [PRO:DNx] + INVS + inversion of embryo turning protein + inversin + INV + + + IRS-2 + PR_EXT:000009108 + "A protein that is a translation product of the human IRS2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:insulin receptor substrate 2 + insulin receptor substrate 2 + IRS2 + 4PS + + + PR_EXT:insulin gene enhancer protein ISL-1 + ISL1 + islet-1 + PR_EXT:000009116 + insulin gene enhancer protein ISL-1 + "A protein that is a translation product of the human ISL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + CD49f + "An integrin alpha lacking A domain that is a translation product of the human ITGA6 gene or a 1:1 ortholog thereof." [PRO:DNx] + ITGA6 + PR_EXT:000009131 + CD49 antigen-like family member F + integrin alpha-6 + VLA-6 + PR_EXT:integrin alpha-6 + + + "A protein that is a translation product of the human ITGB4 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000009140 + ITGB4 + PR_EXT:integrin beta-4 + CD104 + GP150 + integrin beta-4 + + + inositol 1,4,5-trisphosphate receptor type 1 + Pcd6 + Purkinje cell protein 1 + Insp3r + IP3R 1 + inositol 1,4,5-trisphosphate-binding protein P400 + IP3 receptor isoform 1 + type 1 inositol 1,4,5-trisphosphate receptor + InsP3R1 + "A protein that is a translation product of the human ITPR1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Pcp1 + ITPR1 + PR_EXT:000009158 + protein PCD-6 + type 1 InsP3 receptor + PR_EXT:inositol 1,4,5-trisphosphate receptor type 1 + + + "A protein that is a translation product of the human ITPR2 gene or a 1:1 ortholog thereof." [PRO:DNx] + ITPR2 + PR_EXT:inositol 1,4,5-trisphosphate receptor type 2 + PR_EXT:000009159 + inositol 1,4,5-trisphosphate type V receptor + IP3R 2 + type 2 inositol 1,4,5-trisphosphate receptor + IP3 receptor isoform 2 + InsP3R2 + Itpr5 + inositol 1,4,5-trisphosphate receptor type 2 + type 2 InsP3 receptor + + + PR_EXT:involucrin + "A protein that is a translation product of the human IVL gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000009167 + involucrin + IVL + + + protein jagged-2 + JAG2 + Jagged2 + "A protein that is a translation product of the human JAG2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:protein jagged-2 + hJ2 + PR_EXT:000009194 + + + "A protein that is a translation product of the human JMJD6 gene or a 1:1 ortholog thereof." [PRO:DNx] + jumonji domain-containing protein 6 + histone arginine demethylase JMJD6 + JmjC domain-containing protein 6 + bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 + KIAA0585 + PTDSR + phosphatidylserine receptor + peptide-lysine 5-dioxygenase JMJD6 + protein PTDSR + PR_EXT:bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 + PR_EXT:000009218 + lysyl-hydroxylase JMJD6 + JMJD6 + + + PR_EXT:jerky protein + jerky protein + JRK + "A protein that is a translation product of the human JRK gene or a 1:1 ortholog thereof." [PRO:DNx] + JH8 + PR_EXT:000009226 + + + JUB + protein ajuba + PR_EXT:000009231 + AJUBA + "A protein that is a translation product of the human AJUBA gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:protein ajuba + + + "A protein that is a translation product of the human JUN gene or a 1:1 ortholog thereof." [PRO:DNx] + jun A + JUN + V-jun avian sarcoma virus 17 oncogene homolog + AP1 + AH119 + PR_EXT:000009232 + PR_EXT:transcription factor AP-1 + transcription factor AP-1 + proto-oncogene c-Jun + activator protein 1 + + + catenin gamma + PR_EXT:junction plakoglobin + DP3 + "A protein that is a translation product of the human JUP gene or a 1:1 ortholog thereof." [PRO:DNx] + CTNNG + junction plakoglobin + JUP + desmoplakin-3 + desmoplakin III + PR_EXT:000009235 + + + PR_EXT:potassium voltage-gated channel subfamily E member 1 + PR_EXT:000009255 + minimal potassium channel + IKs producing slow voltage-gated potassium channel subunit beta Mink + KCNE1 + "A protein that is a translation product of the human KCNE1 gene or a 1:1 ortholog thereof." [PRO:DNx] + potassium voltage-gated channel subfamily E member 1 + mISK + delayed rectifier potassium channel subunit IsK + + + KDEL receptor 2 + KDEL endoplasmic reticulum protein retention receptor 2 + KDELR2 + ERD2.2 + PR_EXT:ER lumen protein-retaining receptor 2 + ERD2-like protein 1 + ELP-1 + PR_EXT:000009274 + ER lumen protein-retaining receptor 2 + "A protein that is a translation product of the human KDELR2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A protein that is a translation product of the human KHDRBS1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:KH domain-containing, RNA-binding, signal transduction-associated protein 1 + PR_EXT:000009279 + KH domain-containing, RNA-binding, signal transduction-associated protein 1 + KHDRBS1 + p21 Ras GTPase-activating protein-associated p62 + GAP-associated tyrosine phosphoprotein p62 + src-associated in mitosis 68 kDa protein + sam68 + + + KHDRBS2 + PR_EXT:KH domain-containing, RNA-binding, signal transduction-associated protein 2 + "A protein that is a translation product of the human KHDRBS2 gene or a 1:1 ortholog thereof." [PRO:DNx] + SLM-1 + KH domain-containing, RNA-binding, signal transduction-associated protein 2 + SLM1 + sam68-like mammalian protein 1 + PR_EXT:000009280 + + + KHDRBS3 + PR_EXT:KH domain-containing, RNA-binding, signal transduction-associated protein 3 + SLM-2 + KH domain-containing, RNA-binding, signal transduction-associated protein 3 + RNA-binding protein T-Star + "A protein that is a translation product of the human KHDRBS3 gene or a 1:1 ortholog thereof." [PRO:DNx] + SALP + sam68-like mammalian protein 2 + PR_EXT:000009281 + SLM2 + sam68-like phosphotyrosine protein + RNA-binding protein Etoile + + + KLP2 + "A protein that is a translation product of the human KIF15 gene or a 1:1 ortholog thereof." [PRO:DNx] + serologically defined breast cancer antigen NY-BR-62 + PR_EXT:kinesin-like protein KIF15 + kinesin-like protein 7 + kinesin-like protein KIF15 + PR_EXT:000009289 + KIF15 + KNSL7 + + + PR_EXT:kinesin-like protein KIF3A + microtubule plus end-directed kinesin motor 3A + KIF3A + PR_EXT:000009311 + KIF3 + "A protein that is a translation product of the human KIF3A gene or a 1:1 ortholog thereof." [PRO:DNx] + kinesin-like protein KIF3A + + + HH0048 + PR_EXT:kinesin-like protein KIF3B + KIF3B + PR_EXT:000009312 + microtubule plus end-directed kinesin motor 3B + kinesin-like protein KIF3B + KIAA0359 + "A protein that is a translation product of the human KIF3B gene or a 1:1 ortholog thereof." [PRO:DNx] + + + kinesin-like protein KIF3C + KIF3C + PR_EXT:kinesin-like protein KIF3C + PR_EXT:000009313 + "A protein that is a translation product of the human KIF3C gene or a 1:1 ortholog thereof." [PRO:DNx] + + + conventional kinesin heavy chain + "A protein that is a translation product of the human KIF5B gene or a 1:1 ortholog thereof." [PRO:DNx] + Khcs + KIF5B + kinesin-1 heavy chain + KNS1 + UKHC + KNS + PR_EXT:000009317 + ubiquitous kinesin heavy chain + PR_EXT:kinesin-1 heavy chain + + + PR_EXT:kinesin heavy chain isoform 5C + NKHC2 + kinesin heavy chain isoform 5C + KIF5C + "A protein that is a translation product of the human KIF5C gene or a 1:1 ortholog thereof." [PRO:DNx] + kinesin heavy chain neuron-specific 2 + KIAA0531 + PR_EXT:000009318 + + + KAP-3 + kinesin-associated protein 3 + "A protein that is a translation product of the human KIFAP3 gene or a 1:1 ortholog thereof." [PRO:DNx] + Smg GDS-associated protein + PR_EXT:000009322 + KIF3AP + KAP3 + SMAP + PR_EXT:kinesin-associated protein 3 + KIFAP3 + + + PR_EXT:kit ligand + KITLG + Sl + hematopoietic growth factor KL + Slf + "A protein that is a translation product of the human KITLG gene or a 1:1 ortholog thereof." [PRO:DNx] + steel factor + c-Kit ligand + Kitl + PR_EXT:000009345 + mast cell growth factor + SCF + stem cell factor + kit ligand + + + basic transcription element-binding protein 2 + colon krueppel-like factor + PR_EXT:000009365 + krueppel-like factor 5 + KLF5 + CKLF + BTEB2 + IKLF + GC-box-binding protein 2 + "A protein that is a translation product of the human KLF5 gene or a 1:1 ortholog thereof." [PRO:DNx] + intestinal-enriched krueppel-like factor + transcription factor BTEB2 + BTE-binding protein 2 + PR_EXT:krueppel-like factor 5 + + + KLK5 + kallikrein-like protein 2 + SCTE + kallikrein-5 + KLK-L2 + "A protein that is a translation product of the human KLK5 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000009415 + stratum corneum tryptic enzyme + PR_EXT:kallikrein-5 + + + neurosin + "A protein that is a translation product of the human KLK6 gene or a 1:1 ortholog thereof." [PRO:DNx] + Zyme + PRSS18 + serine protease 18 + PR_EXT:kallikrein-6 + serine protease 9 + PR_EXT:000009416 + KLK6 + kallikrein-6 + protease M + SP59 + PRSS9 + + + PTAC97 + NTF97 + PR_EXT:000009439 + importin subunit beta-1 + Impnb + PR_EXT:importin subunit beta-1 + karyopherin subunit beta-1 + SCG + nuclear factor p97 + pore targeting complex 97 kDa subunit + KPNB1 + importin-90 + "A protein that is a translation product of the human KPNB1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + CK-1 + K1 + 67 kDa cytokeratin + keratin-1 + "A protein that is a translation product of the human KRT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000009450 + Krt2-1 + keratin, type II cytoskeletal 1 + PR_EXT:keratin, type II cytoskeletal 1 + KRTA + KRT1 + cytokeratin-1 + hair alpha protein + type-II keratin Kb1 + + + KRT14 + keratin-14 + cytokeratin-14 + Krt1-14 + "A protein that is a translation product of the human KRT14 gene or a 1:1 ortholog thereof." [PRO:DNx] + CK-14 + keratin, type I cytoskeletal 14 + PR_EXT:000009454 + K14 + PR_EXT:keratin, type I cytoskeletal 14 + + + "A protein that is a translation product of the human KRT18 gene or a 1:1 ortholog thereof." [PRO:DNx] + cytokeratin-18 + cytokeratin endo B + K18 + keratin D + KRT18 + PR_EXT:keratin, type I cytoskeletal 18 + CYK18 + keratin, type I cytoskeletal 18 + CK-18 + cell proliferation-inducing gene 46 protein + keratin-18 + Kerd + PR_EXT:000009458 + Krt1-18 + + + PR_EXT:000009481 + type-II keratin Kb5 + keratin, type II cytoskeletal 5 + CK-5 + cytokeratin-5 + Krt2-5 + K5 + 58 kDa cytokeratin + keratin-5 + KRT5 + PR_EXT:keratin, type II cytoskeletal 5 + "A protein that is a translation product of the human KRT5 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + type-II keratin Kb8 + keratin, type II cytoskeletal 8 + PR_EXT:000009495 + "A protein that is a translation product of the human KRT8 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:keratin, type II cytoskeletal 8 + cytokeratin-8 + KRT8 + cytokeratin endo A + CYK8 + CK-8 + K8 + keratin-8 + Krt2-8 + + + L3MBT + H-l(3)mbt protein + PR_EXT:000009640 + L(3)mbt protein homolog + L3MBTL + lethal(3)malignant brain tumor-like protein 1 + KIAA0681 + H-l(3)mbt + lethal(3)malignant brain tumor-like protein + L3MBTL1 + PR_EXT:lethal(3)malignant brain tumor-like protein 1 + L(3)mbt-like + "A protein that is a translation product of the human L3MBTL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + laminin-15 subunit beta + laminin-14 subunit beta + laminin-9 subunit beta + laminin-7 subunit beta + "A protein that is a translation product of the human LAMB2 gene or a 1:1 ortholog thereof." [PRO:DNx] + laminin subunit beta-2 + PR_EXT:000009655 + S-LAM beta + PR_EXT:laminin subunit beta-2 + laminin B1s chain + LAMB2 + laminin-11 subunit beta + LAMS + laminin-4 subunit beta + S-laminin subunit beta + laminin-3 subunit beta + + + Lamb-2 + Lamc-1 + "A protein that is a translation product of the human LAMC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + LAMB2 + laminin subunit gamma-1 + laminin-9 subunit gamma + laminin-8 subunit gamma + laminin-7 subunit gamma + laminin-6 subunit gamma + laminin-11 subunit gamma + laminin-10 subunit gamma + laminin-4 subunit gamma + laminin-3 subunit gamma + S-laminin subunit gamma + laminin-2 subunit gamma + laminin-1 subunit gamma + laminin B2 chain + PR_EXT:000009658 + PR_EXT:laminin subunit gamma-1 + LAMC1 + S-LAM gamma + + + PR_EXT:000009739 + LDHA + LDH-M + L-lactate dehydrogenase A chain + "A protein that is a translation product of the human LDHA gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:L-lactate dehydrogenase A chain + LDH muscle subunit + Ldh-1 + LDH-A + renal carcinoma antigen NY-REN-59 + cell proliferation-inducing gene 19 protein + Ldh1 + + + PR_EXT:lymphoid enhancer-binding factor 1 + T cell-specific transcription factor 1-alpha + LEF-1 + PR_EXT:000009751 + "A protein that is a translation product of the human LEF1 gene or a 1:1 ortholog thereof." [PRO:DNx] + LEF1 + lymphoid enhancer-binding factor 1 + TCF1-alpha + + + LGALS3 + 35 kDa lectin + galactose-specific lectin 3 + "A protein that is a translation product of the human LGALS3 gene or a 1:1 ortholog thereof." [PRO:DNx] + Mac-2 antigen + IgE-binding protein + galactoside-binding protein + PR_EXT:000009771 + GALBP + L-34 galactoside-binding lectin + MAC2 + PR_EXT:galectin-3 + galectin-3 + carbohydrate-binding protein 35 + CBP 35 + L-31 + laminin-binding protein + lectin L-29 + gal-3 + + + LGI1 + "A protein that is a translation product of the human LGI1 gene or a 1:1 ortholog thereof." [PRO:DNx] + epitempin-1 + leucine-rich glioma-inactivated protein 1 + PR_EXT:leucine-rich glioma-inactivated protein 1 + EPT + PR_EXT:000009779 + + + homeobox protein Lim-1 + LIM1 + LIM/homeobox protein Lhx1 + PR_EXT:LIM/homeobox protein Lhx1 + LIM-1 + "A protein that is a translation product of the human LHX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000009791 + LIM homeobox protein 1 + hLim-1 + LHX1 + + + PR_EXT:000009799 + MLPLI + LIF + "A protein that is a translation product of the human LIF gene or a 1:1 ortholog thereof." [PRO:DNx] + D factor + PR_EXT:leukemia inhibitory factor + emfilermin + differentiation-stimulating factor + melanoma-derived LPL inhibitor + HILDA + leukemia inhibitory factor + + + PR_EXT:000009822 + LIN37 + antolefinine + PR_EXT:protein lin-37 + antolefinin + "A protein that is a translation product of the human LIN37 gene or a 1:1 ortholog thereof." [PRO:DNx] + protein lin-37 + + + "A protein that is a translation product of the human LMNB2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000009861 + lamin-B2 + PR_EXT:lamin-B2 + LMN2 + LMNB2 + + + LMO-2 + RHOM2 + TTG2 + RBTN2 + PR_EXT:rhombotin-2 + T-cell translocation protein 2 + LIM domain only protein 2 + "A protein that is a translation product of the human LMO2 gene or a 1:1 ortholog thereof." [PRO:DNx] + rhombotin-2 + Rbtn-2 + RBTNL1 + cysteine-rich protein TTG-2 + PR_EXT:000009863 + LMO2 + Rhom-2 + + + LMX-1.2 + PR_EXT:LIM homeobox transcription factor 1-beta + LIM/homeobox protein 1.2 + LIM/homeobox protein LMX1B + PR_EXT:000009871 + LMX1B + LIM homeobox transcription factor 1-beta + "A protein that is a translation product of the human LMX1B gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A protein that is a translation product of the human LOR gene or a 1:1 ortholog thereof." [PRO:DNx] + LOR + loricrin + LRN + PR_EXT:000009882 + PR_EXT:loricrin + + + PR_EXT:lysyl oxidase homolog 1 + lysyl oxidase-like protein 1 + lysyl oxidase homolog 1 + Lox2 + lysyl oxidase 2 + LOXL + PR_EXT:000009884 + "A protein that is a translation product of the human LOXL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + LOL + LOXL1 + + + leucine-rich alpha-2-glycoprotein + PR_EXT:leucine-rich alpha-2-glycoprotein + PR_EXT:000009913 + LRG + LRG1 + "A protein that is a translation product of the human LRG1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + glycoprotein 330 + PR_EXT:low-density lipoprotein receptor-related protein 2 + LRP-2 + megalin + low-density lipoprotein receptor-related protein 2 + "An LDL receptor-related protein that is a translation product of the human LRP2 gene or a 1:1 ortholog thereof." [PRO:DNx] + LRP2 + PR_EXT:000009921 + gp330 + + + PR_EXT:000009965 + PR_EXT:U6 snRNA-associated Sm-like protein LSm7 + "A protein that is a translation product of the human LSM7 gene or a 1:1 ortholog thereof." [PRO:DNx] + LSM7 + U6 snRNA-associated Sm-like protein LSm7 + + + "A protein that is a translation product of the mouse Lyz2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000010030 + Lyz + lysozyme C-2 + lysozyme C type M + Lyz2 + Lyzs + PR_EXT:lysozyme C-2 + + + MAGOHA + protein mago nashi + PR_EXT:protein mago nashi + MAGOH + PR_EXT:000010086 + "A protein that is a translation product of the human MAGOH gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:microtubule-associated protein 2 + microtubule-associated protein 2 + MAP-2 + PR_EXT:000010124 + "A protein that is a translation product of the human MAP2 gene or a 1:1 ortholog thereof." [PRO:DNx] + MAP2 + Mtap2 + + + MAP2K1 + MAP kinase kinase 1 + MAPKK 1 + "A protein that is a translation product of the human MAP2K1 gene or a 1:1 ortholog thereof." [PRO:DNx] + MEK1 + dual specificity mitogen-activated protein kinase kinase 1 + MEK 1 + MAPK/ERK kinase 1 + PR_EXT:000010125 + ERK activator kinase 1 + PR_EXT:dual specificity mitogen-activated protein kinase kinase 1 + PRKMK1 + + + PRKMK5 + MAP2K5 + MEK5 + MAPK/ERK kinase 5 + dual specificity mitogen-activated protein kinase kinase 5 + MEK 5 + PR_EXT:dual specificity mitogen-activated protein kinase kinase 5 + MAPKK 5 + MKK5 + "A protein that is a translation product of the human MAP2K5 gene or a 1:1 ortholog thereof." [PRO:DNx] + MAP kinase kinase 5 + PR_EXT:000010127 + + + NF-kappa-beta-inducing kinase + "A protein that is a translation product of the human MAP3K14 gene or a 1:1 ortholog thereof." [PRO:DNx] + MAP3K14 + PR_EXT:mitogen-activated protein kinase kinase kinase 14 + NIK + PR_EXT:000010133 + serine/threonine-protein kinase NIK + mitogen-activated protein kinase kinase kinase 14 + + + PR_EXT:mitogen-activated protein kinase kinase kinase 2 + "A protein that is a translation product of the human MAP3K2 gene or a 1:1 ortholog thereof." [PRO:DNx] + mitogen-activated protein kinase kinase kinase 2 + MAPKKK2 + MEKK 2 + MAPK/ERK kinase kinase 2 + MAP3K2 + PR_EXT:000010135 + MEKK2 + MEK kinase 2 + + + "A protein that is a translation product of the human MAP3K3 gene or a 1:1 ortholog thereof." [PRO:DNx] + MEKK 3 + MEKK3 + PR_EXT:mitogen-activated protein kinase kinase kinase 3 + mitogen-activated protein kinase kinase kinase 3 + PR_EXT:000010136 + MEK kinase 3 + MAPKKK3 + MAP3K3 + MAPK/ERK kinase kinase 3 + + + microtubule-associated protein 4 + Mtap4 + PR_EXT:000010142 + "A protein that is a translation product of the human MAP4 gene or a 1:1 ortholog thereof." [PRO:DNx] + MAP4 + PR_EXT:microtubule-associated protein 4 + MAP-4 + + + "A map kinase p38 that is a translation product of the human MAPK11 gene or a 1:1 ortholog thereof." [PRO:DNx] + MAP kinase 11 + stress-activated protein kinase 2 + p38-2 + mitogen-activated protein kinase p38 beta + PRKM11 + MAP kinase p38 beta + MAPK 11 + SAPK2 + MAPK11 + p38b + PR_EXT:000010152 + PR_EXT:mitogen-activated protein kinase 11 + mitogen-activated protein kinase 11 + + + mitogen-activated protein kinase p38 gamma + extracellular signal-regulated kinase 6 + stress-activated protein kinase 3 + MAP kinase 12 + "A map kinase p38 that is a translation product of the human MAPK12 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:mitogen-activated protein kinase 12 + MAPK 12 + SAPK3 + MAPK12 + PR_EXT:000010153 + ERK6 + ERK-6 + MAP kinase p38 gamma + mitogen-activated protein kinase 12 + + + "A map kinase p38 that is a translation product of the human MAPK13 gene or a 1:1 ortholog thereof." [PRO:DNx] + Serk4 + PR_EXT:mitogen-activated protein kinase 13 + SAPK4 + PRKM13 + mitogen-activated protein kinase p38 delta + MAPK13 + MAPK 13 + MAP kinase p38 delta + PR_EXT:000010154 + MAP kinase 13 + mitogen-activated protein kinase 13 + stress-activated protein kinase 4 + + + ERK-8 + ERK-7 + PR_EXT:mitogen-activated protein kinase 15 + MAPK15 + MAPK 15 + PR_EXT:000010155 + ERK8 + extracellular signal-regulated kinase 8 + MAP kinase 15 + extracellular signal-regulated kinase 7 + mitogen-activated protein kinase 15 + ERK7 + "A protein that is a translation product of the human MAPK15 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + MAPK6 + ERK-3 + MAPK 6 + PR_EXT:mitogen-activated protein kinase 6 + p97-MAPK + "A protein that is a translation product of the human MAPK6 gene or a 1:1 ortholog thereof." [PRO:DNx] + extracellular signal-regulated kinase 3 + Prkm4 + PRKM6 + mitogen-activated protein kinase 6 + MAP kinase 6 + ERK3 + MAP kinase isoform p97 + PR_EXT:000010158 + + + ERK5 + MAPK7 + BMK-1 + MAPK 7 + ERK-5 + PR_EXT:mitogen-activated protein kinase 7 + "A protein that is a translation product of the human MAPK7 gene or a 1:1 ortholog thereof." [PRO:DNx] + Big MAP kinase 1 + extracellular signal-regulated kinase 5 + BMK1 + PR_EXT:000010159 + PRKM7 + mitogen-activated protein kinase 7 + MAP kinase 7 + + + JNK MAP kinase scaffold protein 3 + PR_EXT:000010162 + KIAA1066 + sunday driver 2 + MAPK8IP3 + C-Jun-amino-terminal kinase-interacting protein 3 + Syd2 + PR_EXT:C-Jun-amino-terminal kinase-interacting protein 3 + JNK-interacting protein 3 + JIP-3 + JSAP1 + JIP3 + JNK/SAPK-associated protein 1 + mitogen-activated protein kinase 8-interacting protein 3 + "A protein that is a translation product of the human MAPK8IP3 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + End-binding protein 1 + PR_EXT:000010170 + microtubule-associated protein RP/EB family member 1 + MAPRE1 + APC-binding protein EB1 + PR_EXT:microtubule-associated protein RP/EB family member 1 + "A protein that is a translation product of the human MAPRE1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PHF-tau + Mtapt + neurofibrillary tangle protein + MAPT + PR_EXT:000010173 + PR_EXT:microtubule-associated protein tau + MAPTL + paired helical filament-tau + "A protein that is a translation product of the human MAPT gene or a 1:1 ortholog thereof." [PRO:DNx] + microtubule-associated protein tau + TAU + MTBT1 + + + protein kinase C substrate, 80 kDa protein, light chain + PR_EXT:myristoylated alanine-rich C-kinase substrate + 80K-L protein + PR_EXT:000010184 + "A protein that is a translation product of the human MARCKS gene or a 1:1 ortholog thereof." [PRO:DNx] + PKCSL + MARCKS + MACS + myristoylated alanine-rich C-kinase substrate + PRKCSL + + + MARCKS-like protein 1 + MRP + macrophage myristoylated alanine-rich C kinase substrate + Mac-MARCKS + PR_EXT:000010185 + "A protein that is a translation product of the human MARCKSL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + MARCKS-related protein + PR_EXT:MARCKS-related protein + MARCKSL1 + MLP + MacMARCKS + brain protein F52 + + + matrilin-4 + "A protein that is a translation product of the human MATN4 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:matrilin-4 + PR_EXT:000010208 + MATN4 + MAT-4 + + + CXXC3 + PR_EXT:000010214 + CXXC-type zinc finger protein 3 + MBD1 + PCM1 + "A protein that is a translation product of the human MBD1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:methyl-CpG-binding domain protein 1 + methyl-CpG-binding protein MBD1 + protein containing methyl-CpG-binding domain 1 + methyl-CpG-binding domain protein 1 + + + PR_EXT:000010228 + myelin basic protein + myelin A1 protein + MBP + myelin membrane encephalitogenic protein + Shi + "A protein that is a translation product of the human MBP gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:myelin basic protein + + + CDCL1 + DNA replication licensing factor MCM2 + nuclear protein BM28 + PR_EXT:DNA replication licensing factor MCM2 + CCNL1 + MCM2 + Mcmd2 + "A protein that is a translation product of the human MCM2 gene or a 1:1 ortholog thereof." [PRO:DNx] + BM28 + minichromosome maintenance protein 2 homolog + PR_EXT:000010242 + KIAA0030 + + + DNA polymerase alpha holoenzyme-associated protein P1 + P1-MCM3 + DNA replication licensing factor MCM3 + PR_EXT:DNA replication licensing factor MCM3 + MCM3 + Mcmd3 + RLF subunit beta + PR_EXT:000010243 + "A protein that is a translation product of the human MCM3 gene or a 1:1 ortholog thereof." [PRO:DNx] + Mcmd + + + MCM4 + "A protein that is a translation product of the human MCM4 gene or a 1:1 ortholog thereof." [PRO:DNx] + CDC21 + PR_EXT:DNA replication licensing factor MCM4 + PR_EXT:000010246 + CDC21 homolog + P1-CDC21 + Mcmd4 + DNA replication licensing factor MCM4 + + + p105MCM + Mis5 + MCM6 + PR_EXT:DNA replication licensing factor MCM6 + Mcmd6 + mis5 homolog + PR_EXT:000010248 + "A protein that is a translation product of the human MCM6 gene or a 1:1 ortholog thereof." [PRO:DNx] + DNA replication licensing factor MCM6 + + + MCM7 + CDC47 homolog + CDC47 + DNA replication licensing factor MCM7 + PR_EXT:DNA replication licensing factor MCM7 + PR_EXT:000010249 + P1.1-MCM3 + MCM2 + Mcmd7 + "A protein that is a translation product of the human MCM7 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + MCM8 + DNA replication licensing factor MCM8 + minichromosome maintenance 8 + DNA helicase MCM8 + PR_EXT:DNA helicase MCM8 + "A protein that is a translation product of the human MCM8 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000010250 + C20orf154 + + + mucolipin-1 + MG-2 + "A protein that is a translation product of the human MCOLN1 gene or a 1:1 ortholog thereof." [PRO:DNx] + mucolipidin + ML4 + PR_EXT:000010252 + PR_EXT:mucolipin-1 + MCOLN1 + + + methyl-CpG-binding protein 2 + "A protein that is a translation product of the human MECP2 gene or a 1:1 ortholog thereof." [PRO:DNx] + MeCp-2 protein + MeCp2 + PR_EXT:000010277 + MECP2 + PR_EXT:methyl-CpG-binding protein 2 + + + MED31 + PR_EXT:mediator of RNA polymerase II transcription subunit 31 + mediator complex subunit 31 + mediator of RNA polymerase II transcription subunit 31 + "A protein that is a translation product of the human MED31 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000010303 + mediator complex subunit SOH1 + SOH1 + + + myocyte-specific enhancer factor 2C + "A protein that is a translation product of the human MEF2C gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:myocyte-specific enhancer factor 2C + MEF2C + PR_EXT:000010311 + + + proto-oncogene tyrosine-protein kinase MER + "A protein that is a translation product of the human MERTK gene or a 1:1 ortholog thereof." [PRO:DNx] + receptor tyrosine kinase MerTK + PR_EXT:tyrosine-protein kinase Mer + MERTK + MER + proto-oncogene c-Mer + PR_EXT:000010329 + tyrosine-protein kinase Mer + + + HGF receptor + PR_EXT:000010335 + proto-oncogene c-Met + HGF/SF receptor + "An HGF/MSP receptor type tyrosine-protein kinase that is a translation product of the human MET gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:hepatocyte growth factor receptor + MET + hepatocyte growth factor receptor + SF receptor + scatter factor receptor + tyrosine-protein kinase Met + + + MFGM + SED1 + MFGE8 + PR_EXT:lactadherin + breast epithelial antigen BA46 + MP47 + HMFG + milk fat globule-EGF factor 8 + MFG-E8 + PR_EXT:000010367 + sperm surface protein SP47 + "A protein that is a translation product of the human MFGE8 gene or a 1:1 ortholog thereof." [PRO:DNx] + lactadherin + + + putative transcription factor XPRF + midline 1 RING finger protein + MID1 + "A protein that is a translation product of the human MID1 gene or a 1:1 ortholog thereof." [PRO:DNx] + RNF59 + E3 ubiquitin-protein ligase Midline-1 + RING finger protein 59 + PR_EXT:E3 ubiquitin-protein ligase Midline-1 + midline-1 + tripartite motif-containing protein 18 + PR_EXT:000010406 + midin + XPRF + TRIM18 + FXY + + + "A protein that is a translation product of the human MID1IP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:mid1-interacting protein 1 + PR_EXT:000010407 + protein STRAIT11499 homolog + gastrulation-specific G12-like protein + mid1-interacting G12-like protein + protein STRAIT11499 + MIG12 + MID1IP1 + mid1-interacting protein 1 + + + MKI67 + "A protein that is a translation product of the human MKI67 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000010425 + PR_EXT:antigen KI-67 + antigen KI-67 + + + "A protein that is a translation product of the human MLH1 gene or a 1:1 ortholog thereof." [PRO:DNx] + MLH1 + PR_EXT:DNA mismatch repair protein Mlh1 + DNA mismatch repair protein Mlh1 + MutL protein homolog 1 + COCA2 + PR_EXT:000010442 + + + PR_EXT:DNA mismatch repair protein Mlh3 + DNA mismatch repair protein Mlh3 + "A protein that is a translation product of the human MLH3 gene or a 1:1 ortholog thereof." [PRO:DNx] + MLH3 + MutL protein homolog 3 + PR_EXT:000010443 + + + zinc finger protein HRX + MLL + HRX + KMT2A + ALL1 + PR_EXT:000010445 + HTRX + histone-lysine N-methyltransferase HRX + TRX1 + CXXC7 + histone-lysine N-methyltransferase 2A + CXXC-type zinc finger protein 7 + ALL-1 + "A protein that is a translation product of the human KMT2A gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:histone-lysine N-methyltransferase 2A + trithorax-like protein + MLL1 + + + MMP-13 + MMP13 + "A protein that is a translation product of the human MMP13 gene or a 1:1 ortholog thereof." [PRO:DNx] + matrix metalloproteinase-13 + collagenase 3 + PR_EXT:collagenase 3 + PR_EXT:000010473 + + + EMS-2 + transin-1 + matrix metalloproteinase-3 + stromelysin-1 + MMP3 + STMY1 + SL-1 + "A protein that is a translation product of the human MMP3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000010488 + PR_EXT:stromelysin-1 + MMP-3 + + + "A protein that is a translation product of the human MMP7 gene or a 1:1 ortholog thereof." [PRO:DNx] + uterine metalloproteinase + MPSL1 + PR_EXT:000010489 + PR_EXT:matrilysin + MMP-7 + PUMP1 + Pump-1 protease + matrix metalloproteinase-7 + matrin + matrilysin + MMP7 + + + GELB + gelatinase B + MMP-9 + 92 kDa type IV collagenase + 92 kDa gelatinase + CLG4B + PR_EXT:matrix metalloproteinase-9 + PR_EXT:000010491 + MMP9 + "A protein that is a translation product of the human MMP9 gene or a 1:1 ortholog thereof." [PRO:DNx] + matrix metalloproteinase-9 + + + RNF66 + MNAT1 + RING finger protein 66 + menage a trois + CDK7/cyclin-H assembly factor + PR_EXT:CDK-activating kinase assembly factor MAT1 + MAT1 + CAP35 + PR_EXT:000010496 + CDK-activating kinase assembly factor MAT1 + "A protein that is a translation product of the human MNAT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + cyclin-G1-interacting protein + RING finger protein MAT1 + + + motor neuron and pancreas homeobox protein 1 + PR_EXT:000010501 + PR_EXT:motor neuron and pancreas homeobox protein 1 + homeobox protein HB9 + HLXB9 + MNX1 + "A protein that is a translation product of the human MNX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + MOG + "A protein that is a translation product of the human MOG gene or a 1:1 ortholog thereof." [PRO:DNx] + myelin-oligodendrocyte glycoprotein + PR_EXT:myelin-oligodendrocyte glycoprotein + PR_EXT:000010514 + + + PR_EXT:000010562 + HNGS1 + MRE11 + double-strand break repair protein MRE11A + PR_EXT:double-strand break repair protein MRE11A + MRE11 homolog 1 + MRE11 homolog A + "A protein that is a translation product of the human MRE11A gene or a 1:1 ortholog thereof." [PRO:DNx] + MmMRE11A + MRE11A + meiotic recombination 11 homolog A + meiotic recombination 11 homolog 1 + + + MutS protein homolog 4 + MSH4 + PR_EXT:000010668 + mMsh4 + PR_EXT:MutS protein homolog 4 + "A protein that is a translation product of the human MSH4 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + MSH5 + MutS protein homolog 5 + PR_EXT:000010669 + PR_EXT:MutS protein homolog 5 + "A protein that is a translation product of the human MSH5 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:growth/differentiation factor 8 + GDF-8 + growth/differentiation factor 8 + GDF8 + PR_EXT:000010684 + myostatin + "A protein that is a translation product of the human MSTN gene or a 1:1 ortholog thereof." [PRO:DNx] + MSTN + + + Hox7.1 + homeobox protein Hox-7 + "A protein that is a translation product of the human MSX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:homeobox protein MSX-1 + homeobox protein MSX-1 + Msh homeobox 1-like protein + Hox-7.1 + HOX7 + PR_EXT:000010686 + MSX1 + + + homeobox protein Hox-8 + PR_EXT:homeobox protein MSX-2 + "A protein that is a translation product of the human MSX2 gene or a 1:1 ortholog thereof." [PRO:DNx] + homeobox protein MSX-2 + Hox-8.1 + homeobox protein Hox-8-1 + MSX2 + HOX8 + PR_EXT:000010687 + Msx-2 + + + PR_EXT:000010690 + cytochrome b-c1 complex subunit 3 + cytochrome b + CYTB + "A protein that is a translation product of the human MT-CYB gene or a 1:1 ortholog thereof." [PRO:DNx] + ubiquinol-cytochrome-c reductase complex cytochrome b subunit + MT-CYB + complex III subunit III + COB + complex III subunit 3 + PR_EXT:cytochrome b + mt-Cytb + + + "A protein that is a translation product of the human MT2A gene or a 1:1 ortholog thereof." [PRO:DNx] + CES1 + PR_EXT:metallothionein-2 + MT2A + PR_EXT:000010704 + MT2 + metallothionein-2 + metallothionein-2A + + + MT-IV + PR_EXT:metallothionein-4 + MT-4 + "A protein that is a translation product of the human MT4 gene or a 1:1 ortholog thereof." [PRO:DNx] + MT4 + PR_EXT:000010706 + metallothionein-IV + metallothionein-4 + + + MTA1 + metastasis-associated protein MTA1 + PR_EXT:000010707 + "A protein that is a translation product of the human MTA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:metastasis-associated protein MTA1 + + + MRE-binding transcription factor + Mtf-1 + metal regulatory transcription factor 1 + transcription factor MTF-1 + "A protein that is a translation product of the human MTF1 gene or a 1:1 ortholog thereof." [PRO:DNx] + MTF1 + PR_EXT:000010717 + PR_EXT:metal regulatory transcription factor 1 + + + "A protein that is a translation product of the human MUC2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:mucin-2 + MUC-2 + MCM + PR_EXT:000010764 + colonic mucin + SMUC + intestinal mucin-2 + mucin-2 + secreted gel-forming mucin + MUC2 + + + interferon-induced GTP-binding protein Mx1 + influenza resistance protein + "A protein that is a translation product of the human MX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + IFI-78K + interferon-induced protein p78 + interferon-regulated resistance GTP-binding protein MxA + MX1 + PR_EXT:000010788 + PR_EXT:interferon-induced GTP-binding protein Mx1 + myxovirus resistance protein 1 + + + PR_EXT:myb proto-oncogene protein + MYB + myb proto-oncogene protein + "A protein that is a translation product of the human MYB gene or a 1:1 ortholog thereof." [PRO:DNx] + proto-oncogene c-Myb + PR_EXT:000010799 + + + MYCN + bHLHe37 + PR_EXT:N-myc proto-oncogene protein + class E basic helix-loop-helix protein 37 + "A myc protein that is a translation product of the human MYCN gene or a 1:1 ortholog thereof." [PRO:DNx] + N-myc proto-oncogene protein + PR_EXT:000010812 + NMYC + Nmyc1 + + + myosin-12 + "A protein that is a translation product of the human MYO5A gene or a 1:1 ortholog thereof." [PRO:DNx] + myosin-Va + MYH12 + PR_EXT:000010865 + PR_EXT:myosin-Va + myosin heavy chain 12 + dilute myosin heavy chain, non-muscle + Dilute + MYO5A + myoxin + + + "A protein that is a translation product of the human MYO6 gene or a 1:1 ortholog thereof." [PRO:DNx] + myosin-VI + PR_EXT:myosin-VI + MYO6 + Sv + PR_EXT:000010868 + unconventional myosin-6 + KIAA0389 + + + MYO7A + USH1B + PR_EXT:myosin-VIIa + Myo7 + myosin-VIIa + PR_EXT:000010869 + "A protein that is a translation product of the human MYO7A gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000010873 + trabecular meshwork-induced glucocorticoid response protein + MYOC + "A protein that is a translation product of the human MYOC gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:myocilin + GLC1A + TIGR + myocilin + + + myoblast determination protein 1 + PR_EXT:myoblast determination protein 1 + bHLHc1 + MYOD1 + Myf-3 + PR_EXT:000010875 + MYF3 + class C basic helix-loop-helix protein 1 + "A protein that is a translation product of the human MYOD1 gene or a 1:1 ortholog thereof." [PRO:DNx] + myogenic factor 3 + MYOD + + + PR_EXT:myogenin + MYF4 + myogenin + myogenic factor 4 + "A protein that is a translation product of the human MYOG gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000010877 + Myf-4 + class C basic helix-loop-helix protein 3 + MYOD1-related protein + bHLHc3 + MYOG + + + PR_EXT:mast cell protease 2 + mast cell protease 2 + Mcpt2 + mMCP-2 + PR_EXT:000010903 + "A protein that is a translation product of the mouse Mcpt2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A protein that is a translation product of the mouse Ms4a6c gene or a 1:1 ortholog thereof." [PRO:DNx] + membrane-spanning 4-domains subfamily A member 6C + Ms4a6c + PR_EXT:membrane-spanning 4-domains subfamily A member 6C + PR_EXT:000010921 + + + PR_EXT:000010925 + MT-1 + metallothionein-I + metallothionein-1 + Mt1 + MT-I + PR_EXT:metallothionein-1 + "A protein that is a translation product of the mouse Mt1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + early embryo specific expression NK-type homeobox protein + Ecat4 + NANOG + Enk + PR_EXT:homeobox protein NANOG + "A protein that is a translation product of the human NANOG gene or a 1:1 ortholog thereof." [PRO:DNx] + ES cell-associated protein 4 + homeobox transcription factor Nanog + PR_EXT:000010968 + homeobox protein NANOG + hNanog + + + PR_EXT:cytoplasmic protein NCK1 + NCK adaptor protein 1 + NCK + PR_EXT:000011033 + "A protein that is a translation product of the human NCK1 gene or a 1:1 ortholog thereof." [PRO:DNx] + NCK1 + SH2/SH3 adaptor protein NCK-alpha + Nck-1 + cytoplasmic protein NCK1 + + + rit42 + Tdd5 + reducing agents and tunicamycin-responsive protein + DRG-1 + PR_EXT:000011059 + DRG1 + NDRG1 + differentiation-related gene 1 protein + Ndr1 + nickel-specific induction protein Cap43 + CAP43 + Ndrl + N-myc downstream-regulated gene 1 protein + PR_EXT:protein NDRG1 + RTP + protein NDRG1 + "A protein that is a translation product of the human NDRG1 gene or a 1:1 ortholog thereof." [PRO:DNx] + protein Ndr1 + + + NF-M + PR_EXT:000011120 + neurofilament triplet M protein + 160 kDa neurofilament protein + neurofilament 3 + "A protein that is a translation product of the human NEFM gene or a 1:1 ortholog thereof." [PRO:DNx] + neurofilament medium polypeptide + PR_EXT:neurofilament medium polypeptide + NEFM + NFM + NEF3 + + + nestin + PR_EXT:nestin + NES + PR_EXT:000011141 + "A protein that is a translation product of the human NES gene or a 1:1 ortholog thereof." [PRO:DNx] + + + protein atonal homolog 4 + neurogenin-2 + PR_EXT:000011157 + "A protein that is a translation product of the human NEUROG2 gene or a 1:1 ortholog thereof." [PRO:DNx] + class A basic helix-loop-helix protein 8 + PR_EXT:neurogenin-2 + mATH4A + helix-loop-helix protein mATH-4A + bHLHa8 + NGN-2 + ATOH4 + Ath4a + NGN2 + NEUROG2 + + + PR_EXT:beta-nerve growth factor + beta-nerve growth factor + "A neurotrophin that is a translation product of the human NGF gene or a 1:1 ortholog thereof." [PRO:DNx] + NGFB + NGF + beta-NGF + PR_EXT:000011194 + + + PR_EXT:000011196 + peptide:N-glycanase + PNGase + N-glycanase 1 + "A protein that is a translation product of the human NGLY1 gene or a 1:1 ortholog thereof." [PRO:DNx] + NGLY1 + PR_EXT:peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase + PNG1 + peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase + + + "A protein that is a translation product of the human NKX2-2 gene or a 1:1 ortholog thereof." [PRO:DNx] + NKX2.2 + NKX2B + NKX2-2 + PR_EXT:000011242 + homeobox protein Nkx-2.2 + Nkx-2.2 + PR_EXT:homeobox protein Nkx-2.2 + homeobox protein NK-2 homolog B + + + NKX2-5 + homeobox protein Nkx-2.5 + NKX2.5 + homeobox protein CSX + NKX2E + homeobox protein NK-2 homolog E + "A protein that is a translation product of the human NKX2-5 gene or a 1:1 ortholog thereof." [PRO:DNx] + Nkx-2.5 + cardiac-specific homeobox + CSX + PR_EXT:homeobox protein Nkx-2.5 + PR_EXT:000011245 + + + Nkx-3.1 + PR_EXT:000011248 + NKX3A + homeobox protein NK-3 homolog A + NKX3.1 + "A protein that is a translation product of the human NKX3-1 gene or a 1:1 ortholog thereof." [PRO:DNx] + NKX3-1 + homeobox protein Nkx-3.1 + PR_EXT:homeobox protein Nkx-3.1 + + + "A protein that is a translation product of the human NKX6-2 gene or a 1:1 ortholog thereof." [PRO:DNx] + NKX6B + GTX + PR_EXT:000011251 + homeobox protein NK-6 homolog B + NKX6-2 + homeobox protein Nkx-6.2 + PR_EXT:homeobox protein Nkx-6.2 + + + CARD15 + caspase recruitment domain-containing protein 15 + IBD1 + PR_EXT:nucleotide-binding oligomerization domain-containing protein 2 + nucleotide-binding oligomerization domain-containing protein 2 + inflammatory bowel disease protein 1 + NOD2 + "A protein that is a translation product of the human NOD2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000011306 + + + NOS1 + NC-NOS + PR_EXT:nitric oxide synthase, brain + nNOS + "A protein that is a translation product of the human NOS1 gene or a 1:1 ortholog thereof." [PRO:DNx] + N-NOS + bNOS + PR_EXT:000011326 + neuronal NOS + nitric oxide synthase, brain + NOS type I + + + NOS type III + NOS3 + EC-NOS + Ecnos + PR_EXT:nitric oxide synthase, endothelial + endothelial NOS + NOSIII + "A protein that is a translation product of the human NOS3 gene or a 1:1 ortholog thereof." [PRO:DNx] + eNOS + PR_EXT:000011328 + nitric oxide synthase, endothelial + cNOS + + + translocation-associated notch protein TAN-1 + "A protein that is a translation product of the human NOTCH1 gene or a 1:1 ortholog thereof." [PRO:DNx] + motch A + NOTCH1 + neurogenic locus notch protein 1 + PR_EXT:000011331 + Motch + notch 1 + TAN1 + PR_EXT:neurogenic locus notch homolog protein 1 + mT14 + hN1 + neurogenic locus notch homolog protein 1 + + + notch 4 + NOTCH4 + neurogenic locus notch protein 4 + "A protein that is a translation product of the human NOTCH4 gene or a 1:1 ortholog thereof." [PRO:DNx] + neurogenic locus notch homolog protein 4 + PR_EXT:000011335 + hNotch4 + INT3 + Int-3 + PR_EXT:neurogenic locus notch homolog protein 4 + + + NOTO + "A protein that is a translation product of the human NOTO gene or a 1:1 ortholog thereof." [PRO:DNx] + Not + PR_EXT:000011336 + PR_EXT:homeobox protein notochord + homeobox protein notochord + + + onconeural ventral antigen 1 + neuro-oncological ventral antigen 1 + NOVA1 + PR_EXT:RNA-binding protein Nova-1 + ventral neuron-specific protein 1 + RNA-binding protein Nova-1 + PR_EXT:000011339 + paraneoplastic Ri antigen + "A protein that is a translation product of the human NOVA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + NPHS2 + PR_EXT:podocin + podocin + "A protein that is a translation product of the human NPHS2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000011366 + + + "A protein that is a translation product of the human NR0B1 gene or a 1:1 ortholog thereof." [PRO:DNx] + nuclear receptor DAX-1 + AHC + Ahch + nuclear receptor subfamily 0 group B member 1 + PR_EXT:nuclear receptor subfamily 0 group B member 1 + NR0B1 + PR_EXT:000011390 + DSS-AHC critical region on the X chromosome protein 1 + DAX1 + + + NR1H3 + PR_EXT:oxysterols receptor LXR-alpha + LXRA + oxysterols receptor LXR-alpha + liver X receptor alpha + PR_EXT:000011395 + "A protein that is a translation product of the human NR1H3 gene or a 1:1 ortholog thereof." [PRO:DNx] + nuclear receptor subfamily 1 group H member 3 + + + farnesol receptor HRR-1 + RIP14 + bile acid receptor + "A protein that is a translation product of the human NR1H4 gene or a 1:1 ortholog thereof." [PRO:DNx] + retinoid X receptor-interacting protein 14 + PR_EXT:bile acid receptor + PR_EXT:000011396 + nuclear receptor subfamily 1 group H member 4 + BAR + farnesoid X-activated receptor + HRR1 + NR1H4 + RXR-interacting protein 14 + FXR + + + RNR + PNR + retina-specific nuclear receptor + PR_EXT:photoreceptor-specific nuclear receptor + PR_EXT:000011403 + nuclear receptor subfamily 2 group E member 3 + NR2E3 + "A protein that is a translation product of the human NR2E3 gene or a 1:1 ortholog thereof." [PRO:DNx] + photoreceptor-specific nuclear receptor + + + COUP-TF II + TFCOUP2 + COUP transcription factor II + apolipoprotein AI regulatory protein 1 + ARP-1 + COUP transcription factor 2 + NR2F2 + PR_EXT:000011405 + COUP-TF2 + nuclear receptor subfamily 2 group F member 2 + ARP1 + Aporp1 + PR_EXT:COUP transcription factor 2 + "A protein that is a translation product of the human NR2F2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + retinoid receptor-related testis-specific receptor + NR6A1 + GCNF + nuclear receptor subfamily 6 group A member 1 + PR_EXT:000011413 + germ cell nuclear factor + RTR + "A protein that is a translation product of the human NR6A1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:nuclear receptor subfamily 6 group A member 1 + + + PR_EXT:000011416 + "A protein that is a translation product of the human NRAS gene or a 1:1 ortholog thereof." [PRO:DNx] + transforming protein N-Ras + HRAS1 + GTPase NRas + PR_EXT:GTPase NRas + NRAS + + + alpha-pal + PR_EXT:000011422 + NRF1 + alpha palindromic-binding protein + PR_EXT:nuclear respiratory factor 1 + NRF-1 + nuclear respiratory factor 1 + "A protein that is a translation product of the human NRF1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + D14S46E + PR_EXT:000011432 + PR_EXT:neural retina-specific leucine zipper protein + "A protein that is a translation product of the human NRL gene or a 1:1 ortholog thereof." [PRO:DNx] + NRL + neural retina-specific leucine zipper protein + + + "A protein that is a translation product of the human NSD1 gene or a 1:1 ortholog thereof." [PRO:DNx] + histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific + NR-binding SET domain-containing protein + nuclear receptor-binding SET domain-containing protein 1 + androgen receptor-associated protein of 267 kDa + ARA267 + KMT3B + H3-K36-HMTase + PR_EXT:histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific + androgen receptor coactivator 267 kDa protein + H4-K20-HMTase + lysine N-methyltransferase 3B + PR_EXT:000011441 + NSD1 + + + "A protein that is a translation product of the human NSF gene or a 1:1 ortholog thereof." [PRO:DNx] + NEM-sensitive fusion protein + vesicular-fusion protein NSF + Skd2 + PR_EXT:vesicle-fusing ATPase + protein SKD2 + PR_EXT:000011443 + N-ethylmaleimide-sensitive fusion protein + NSF + suppressor of K(+) transport growth defect 2 + vesicle-fusing ATPase + + + neurotrophin-3 + NT-3 + Ntf-3 + neurotrophic factor + HDNF + "A neurotrophin that is a translation product of the human NTF3 gene or a 1:1 ortholog thereof." [PRO:DNx] + nerve growth factor 2 + NTF3 + NGF-2 + PR_EXT:000011459 + PR_EXT:neurotrophin-3 + + + high affinity nerve growth factor receptor + TRK + neurotrophic tyrosine kinase receptor type 1 + PR_EXT:high affinity nerve growth factor receptor + PR_EXT:000011469 + TRK1-transforming tyrosine kinase protein + p140-TrkA + Trk-A + NTRK1 + "A TRK receptor that is a translation product of the human NTRK1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:BDNF/NT-3 growth factors receptor + PR_EXT:000011470 + TrkB tyrosine kinase + GP145-TrkB + neurotrophic tyrosine kinase receptor type 2 + TRKB + GP145-TrkB/GP95-TrkB + "A TRK receptor that is a translation product of the human NTRK2 gene or a 1:1 ortholog thereof." [PRO:DNx] + Trk-B + BDNF/NT-3 growth factors receptor + NTRK2 + + + neurotrophic tyrosine kinase receptor type 3 + PR_EXT:000011471 + GP145-TrkC + TrkC tyrosine kinase + NT-3 growth factor receptor + TRKC + "A TRK receptor that is a translation product of the human NTRK3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:NT-3 growth factor receptor + NTRK3 + Trk-C + + + NUMA + PR_EXT:nuclear mitotic apparatus protein 1 + nuclear mitotic apparatus protein 1 + SP-H antigen + NUMA1 + PR_EXT:000011503 + "A protein that is a translation product of the human NUMA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + NuMA protein + + + nucleoporin Nup107 + 107 kDa nucleoporin + NUP107 + "A protein that is a translation product of the human NUP107 gene or a 1:1 ortholog thereof." [PRO:DNx] + nuclear pore complex protein Nup107 + PR_EXT:000011506 + PR_EXT:nuclear pore complex protein Nup107 + + + "A protein that is a translation product of the human NUP153 gene or a 1:1 ortholog thereof." [PRO:DNx] + 153 kDa nucleoporin + NUP153 + PR_EXT:nuclear pore complex protein Nup153 + PR_EXT:000011508 + nucleoporin Nup153 + nuclear pore complex protein Nup153 + + + nucleoporin Nup160 + NUP160 + 160 kDa nucleoporin + "A protein that is a translation product of the human NUP160 gene or a 1:1 ortholog thereof." [PRO:DNx] + Gtl1-13 + KIAA0197 + nuclear pore complex protein Nup160 + PR_EXT:nuclear pore complex protein Nup160 + gene trap locus 1-13 protein + GTL-13 + NUP120 + PR_EXT:000011510 + + + nucleoporin Nup62 + 62 kDa nucleoporin + PR_EXT:000011521 + "A protein that is a translation product of the human NUP62 gene or a 1:1 ortholog thereof." [PRO:DNx] + NUP62 + PR_EXT:nuclear pore glycoprotein p62 + nuclear pore glycoprotein p62 + + + nuclear pore complex protein Nup98-Nup96 + PR_EXT:000011526 + "A protein that is a translation product of the human NUP98 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:nuclear pore complex protein Nup98-Nup96 + ADAR2 + NUP98 + + + PR_EXT:000011533 + NTF2 + "A protein that is a translation product of the human NUTF2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PP15 + NTF-2 + nuclear transport factor 2 + NUTF2 + placental protein 15 + PR_EXT:nuclear transport factor 2 + + + mRNA export factor TAP + "A protein that is a translation product of the human NXF1 gene or a 1:1 ortholog thereof." [PRO:DNx] + TAP + NXF1 + PR_EXT:nuclear RNA export factor 1 + PR_EXT:000011535 + Tip-associating protein + nuclear RNA export factor 1 + Tip-associated protein + + + CT39 + PR_EXT:000011536 + TAP-like protein 2 + NXF2 + "A protein that is a translation product of the human NXF2 or NXF2B genes, 1:1 orthologs thereof, or a semi-ortholog thereof." [PRO:DAN] + TAPL-2 + cancer/testis antigen 39 + nuclear RNA export factor 2 + NXF2B + PR_EXT:nuclear RNA export factor 2 + + + TAPL3 + PR_EXT:000011537 + TAPL-3 + nuclear RNA export factor 3 + PR_EXT:nuclear RNA export factor 3 + "A protein that is a translation product of the human NXF3 gene or a 1:1 ortholog thereof." [PRO:DNx] + TAP-like protein 3 + NXF3 + + + TAPL1 + NXF5 + PR_EXT:000011538 + TAPL-1 + nuclear RNA export factor 5 + "A protein that is a translation product of the human NXF5 gene or a 1:1 ortholog thereof." [PRO:DNx] + TAP-like protein 1 + PR_EXT:nuclear RNA export factor 5 + + + PR_EXT:000011546 + "A protein that is a translation product of the human NXT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:NTF2-related export protein 1 + NTF2-related export protein 1 + NXT1 + protein p15 + + + lectin-like oxidized LDL receptor 1 + C-type lectin domain family 8 member A + LOX-1 + CLEC8A + PR_EXT:000011634 + OLR1 + Ox-LDL receptor 1 + lectin-type oxidized LDL receptor 1 + "A protein that is a translation product of the human OLR1 gene or a 1:1 ortholog thereof." [PRO:DNx] + oxidized low-density lipoprotein receptor 1 + LOX1 + PR_EXT:oxidized low-density lipoprotein receptor 1 + lectin-like oxLDL receptor 1 + + + otopetrin-3 + PR_EXT:otopetrin-3 + PR_EXT:000012076 + OTOP3 + "A protein that is a translation product of the human OTOP3 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + orthodenticle homolog 2 + OTX2 + Otx-2 + "A protein that is a translation product of the human OTX2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:homeobox protein OTX2 + homeobox protein OTX2 + PR_EXT:000012086 + + + (2-5')oligo(A) synthetase 1A + "A protein that is a translation product of the mouse Oas1a gene or a 1:1 ortholog thereof." [PRO:DNx] + 2'-5'-oligoadenylate synthetase 1A + Oias1 + PR_EXT:000012101 + p42 OAS + 2-5A synthetase 1A + PR_EXT:2'-5'-oligoadenylate synthetase 1A + Oas1a + + + peptidylarginine deiminase IV + protein-arginine deiminase type IV + PADI4 + PADI5 + Pdi4 + PDI5 + protein-arginine deiminase type-4 + PR_EXT:000012222 + PR_EXT:protein-arginine deiminase type-4 + HL-60 PAD + "A protein that is a translation product of the human PADI4 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + parkinson juvenile disease protein 2 + PR_EXT:000012285 + PARK2 + "A protein that is a translation product of the human PARK2 gene or a 1:1 ortholog thereof." [PRO:DNx] + E3 ubiquitin-protein ligase parkin + parkinson disease protein 2 + PR_EXT:E3 ubiquitin-protein ligase parkin + PRKN + + + PR_EXT:000012286 + PARK7 + oncogene DJ1 + protein DJ-1 + parkinson disease protein 7 + "A protein that is a translation product of the human PARK7 gene or a 1:1 ortholog thereof." [PRO:DNx] + parkinson disease protein 7 homolog + PR_EXT:protein DJ-1 + + + PR_EXT:000012289 + Adprt1 + PARP-1 + msPARP + PPOL + ADPRT 1 + ADPRT + PARP1 + NAD(+) ADP-ribosyltransferase 1 + poly [ADP-ribose] polymerase 1 + poly[ADP-ribose] synthetase 1 + Adprp + "A protein that is a translation product of the human PARP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:poly [ADP-ribose] polymerase 1 + + + PR_EXT:000012315 + Pax-2 + "A paired box protein PAX group II that is a translation product of the human PAX2 gene or a 1:1 ortholog thereof." [PRO:DNx] + paired box protein Pax-2 + PR_EXT:paired box protein Pax-2 + PAX2 + + + "A paired box protein PAX group III that is a translation product of the human PAX3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000012316 + paired box protein Pax-3 + HuP2 + PAX3 + Pax-3 + PR_EXT:paired box protein Pax-3 + + + PR_EXT:paired box protein Pax-6 + AN2 + PR_EXT:000012318 + Sey + oculorhombin + PAX6 + aniridia type II protein + paired box protein Pax-6 + "A paired box protein PAX group IV that is a translation product of the human PAX6 gene or a 1:1 ortholog thereof." [PRO:DNx] + Pax-6 + + + "A protein that is a translation product of the human KAT2B gene or a 1:1 ortholog thereof." [PRO:DNx] + KAT2B + histone acetyltransferase PCAF + PCAF + P300/CBP-associated factor + lysine acetyltransferase 2B + PR_EXT:histone acetyltransferase KAT2B + histone acetylase PCAF + PR_EXT:000012332 + P/CAF + histone acetyltransferase KAT2B + + + KIAA1775 + prCAD + cadherin-related family member 1 + PCDH21 + "A protein that is a translation product of the human CDHR1 gene or a 1:1 ortholog thereof." [PRO:DNx] + protocadherin-21 + PR_EXT:cadherin-related family member 1 + PR_EXT:000012351 + photoreceptor cadherin + CDHR1 + + + PCK1 + PEPCK-C + PR_EXT:phosphoenolpyruvate carboxykinase, cytosolic [GTP] + PEPCK1 + phosphoenolpyruvate carboxykinase, cytosolic [GTP] + Pepck + PR_EXT:000012416 + "A protein that is a translation product of the human PCK1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A protein that is a translation product of the human PCNA gene or a 1:1 ortholog thereof." [PRO:DNx] + cyclin + PR_EXT:000012421 + PCNA + PR_EXT:proliferating cell nuclear antigen + proliferating cell nuclear antigen + + + "A protein that is a translation product of the human PDE6A gene or a 1:1 ortholog thereof." [PRO:DNx] + GMP-PDE alpha + PDE6A + PR_EXT:000012478 + PDE V-B1 + rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha + PDEA + PR_EXT:rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha + Mpa + + + Mpb + "A protein that is a translation product of the human PDE6B gene or a 1:1 ortholog thereof." [PRO:DNx] + PDEB + GMP-PDE beta + rd + PDE6B + PR_EXT:000012479 + PR_EXT:rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta + rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta + + + "A protein that is a translation product of the human PDGFB gene or a 1:1 ortholog thereof." [PRO:DNx] + platelet-derived growth factor B chain + PR_EXT:000012491 + PR_EXT:platelet-derived growth factor subunit B + PDGF-2 + proto-oncogene c-Sis + platelet-derived growth factor beta polypeptide + PDGF subunit B + SIS + platelet-derived growth factor subunit B + PDGFB + PDGF2 + becaplermin + + + PDPN + OTS-8 + Ots8 + gp36 + transmembrane glycoprotein E11 + gp38 + PR_EXT:podoplanin + T1-alpha + aggrus + glycoprotein 38 + podoplanin + T1A + PR_EXT:000012516 + PA2.26 antigen + glycoprotein 36 + "A protein that is a translation product of the human PDPN gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:pancreas/duodenum homeobox protein 1 + "A protein that is a translation product of the human PDX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + IUF-1 + glucose-sensitive factor + insulin promoter factor 1 + islet/duodenum homeobox-1 + GSF + IPF-1 + PR_EXT:000012523 + IPF1 + IDX-1 + pancreas/duodenum homeobox protein 1 + PDX1 + islet/duodenum homeobox 1 + PDX-1 + insulin upstream factor 1 + somatostatin-transactivating factor 1 + STF-1 + + + "A protein that is a translation product of the human PENK gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:proenkephalin-A + Penk1 + PENK + PR_EXT:000012544 + proenkephalin-A + + + PFK-A + phosphofructo-1-kinase isozyme A + PFKM + PR_EXT:000012583 + phosphofructokinase-M + Pfka + "A protein that is a translation product of the human PFKM gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:ATP-dependent 6-phosphofructokinase, muscle type + Pfk-m + PFKX + ATP-dependent 6-phosphofructokinase, muscle type + + + PlGF + PR_EXT:000012605 + placenta growth factor + PGF + PR_EXT:placenta growth factor + PGFL + "A protein that is a translation product of the human PGF gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A protein that is a translation product of the human PGK1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Pgk-1 + PRP 2 + primer recognition protein 2 + cell migration-inducing gene 10 protein + phosphoglycerate kinase 1 + PGK1 + PR_EXT:000012607 + PR_EXT:phosphoglycerate kinase 1 + PGKA + + + early development regulatory protein 1 + EDR1 + PR_EXT:000012633 + Edr + RAE-28 + "A protein that is a translation product of the human PHC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PHC1 + PR_EXT:polyhomeotic-like protein 1 + polyhomeotic-like protein 1 + PH1 + Rae28 + + + polycystin-1 + PKD1 + "A protein that is a translation product of the human PKD1 gene or a 1:1 ortholog thereof." [PRO:DNx] + autosomal dominant polycystic kidney disease 1 protein homolog + PR_EXT:polycystin-1 + autosomal dominant polycystic kidney disease 1 protein + PR_EXT:000012769 + + + autosomal dominant polycystic kidney disease type II protein + polycystin-2 + PKD2 + polycystwin + R48321 + polycystic kidney disease 2 protein homolog + polycystic kidney disease 2 protein + "A protein that is a translation product of the human PKD2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000012773 + PR_EXT:polycystin-2 + + + tigmin + PKHD1 + fibrocystin + "A protein that is a translation product of the human PKHD1 gene or a 1:1 ortholog thereof." [PRO:DNx] + polycystic kidney and hepatic disease 1 protein + PR_EXT:000012777 + TIGM1 + PR_EXT:fibrocystin + FCYT + polyductin + + + PLAT + t-plasminogen activator + reteplase + tPA + "A protein that is a translation product of the human PLAT gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000012825 + tissue-type plasminogen activator + PR_EXT:tissue-type plasminogen activator + alteplase + t-PA + + + U-plasminogen activator + PLAU + uPA + PR_EXT:urokinase-type plasminogen activator + PR_EXT:000012826 + "A protein that is a translation product of the human PLAU gene or a 1:1 ortholog thereof." [PRO:DNx] + urokinase-type plasminogen activator + + + PR_EXT:000012867 + plasminogen + PR_EXT:plasminogen + "A protein that is a translation product of the human PLG gene or a 1:1 ortholog thereof." [PRO:DNx] + PLG + + + PR_EXT:000012879 + myelin proteolipid protein + PLP + lipophilin + PLP1 + PR_EXT:myelin proteolipid protein + "A protein that is a translation product of the human PLP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PNKP + bifunctional polynucleotide phosphatase/kinase + polynucleotide kinase-3'-phosphatase + PR_EXT:bifunctional polynucleotide phosphatase/kinase + DNA 5'-kinase/3'-phosphatase + PR_EXT:000012924 + "A protein that is a translation product of the human PNKP gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PNPLA2 + transport-secretion protein 2 + PR_EXT:patatin-like phospholipase domain-containing protein 2 + pigment epithelium-derived factor + adipose triglyceride lipase + IPLA2-zeta + patatin-like phospholipase domain-containing protein 2 + calcium-independent phospholipase A2 + desnutrin + "A protein that is a translation product of the human PNPLA2 gene or a 1:1 ortholog thereof." [PRO:DNx] + TTS2.2 + TTS2 + ATGL + PR_EXT:000012942 + + + NTE + neuropathy target esterase + patatin-like phospholipase domain-containing protein 6 + PR_EXT:000012946 + "A protein that is a translation product of the human PNPLA6 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:neuropathy target esterase + PNPLA6 + + + "A protein that is a translation product of the human POLR2A gene or a 1:1 ortholog thereof." [PRO:DNx] + POLR2A + PR_EXT:DNA-directed RNA polymerase II subunit RPB1 + DNA-directed RNA polymerase II subunit RPB1 + Rpo2-1 + DNA-directed RNA polymerase III largest subunit + DNA-directed RNA polymerase II subunit A + Rpii215 + PR_EXT:000012987 + POLR2 + RNA polymerase II subunit B1 + RNA-directed RNA polymerase II subunit RPB1 + + + OTF9 + PR_EXT:000013040 + POU3F4 + octamer-binding protein 9 + OTF-9 + Oct-9 + BRN4 + brain-specific homeobox/POU domain protein 4 + Brn-4 + octamer-binding transcription factor 9 + "A protein that is a translation product of the human POU3F4 gene or a 1:1 ortholog thereof." [PRO:DNx] + POU domain, class 3, transcription factor 4 + PR_EXT:POU domain, class 3, transcription factor 4 + brain-4 + + + Oct-T1 + POU4F1 + Brn3 + "A protein that is a translation product of the human POU4F1 gene or a 1:1 ortholog thereof." [PRO:DNx] + brain-specific homeobox/POU domain protein 3A + RDC1 + Brn-3.0 + brain-3A + homeobox/POU domain protein RDC-1 + POU domain, class 4, transcription factor 1 + Brn-3A + Brn-3 + PR_EXT:POU domain, class 4, transcription factor 1 + PR_EXT:000013041 + BRN3A + + + POU4F2 + Brn-3.2 + "A protein that is a translation product of the human POU4F2 gene or a 1:1 ortholog thereof." [PRO:DNx] + Brn-3B + brain-specific homeobox/POU domain protein 3B + PR_EXT:POU domain, class 4, transcription factor 2 + POU domain, class 4, transcription factor 2 + brain-3B + BRN3B + PR_EXT:000013042 + + + PR_EXT:000013043 + BRN3C + Brn-3C + "A protein that is a translation product of the human POU4F3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:POU domain, class 4, transcription factor 3 + POU4F3 + POU domain, class 4, transcription factor 3 + brain-3C + brain-specific homeobox/POU domain protein 3C + + + PR_EXT:000013044 + POU5F1 + Oct-3 + octamer-binding protein 4 + octamer-binding protein 3 + NF-A3 + OTF-3 + Oct-4 + "A protein that is a translation product of the human POU5F1 gene or a 1:1 ortholog thereof." [PRO:DNx] + octamer-binding transcription factor 3 + OTF3 + OCT4 + OCT3 + POU domain, class 5, transcription factor 1 + PR_EXT:POU domain, class 5, transcription factor 1 + + + nuclear receptor subfamily 1 group C member 1 + "A protein that is a translation product of the human PPARA gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000013056 + PPAR + PR_EXT:peroxisome proliferator-activated receptor alpha + PPAR-alpha + NR1C1 + PPARA + peroxisome proliferator-activated receptor alpha + + + peroxisome proliferator-activated receptor beta + nuclear receptor subfamily 1 group C member 2 + PPAR-delta + PPARB + NUC1 + PPARD + peroxisome proliferator-activated receptor delta + NR1C2 + NUCI + PPAR-beta + PR_EXT:000013057 + "A protein that is a translation product of the human PPARD gene or a 1:1 ortholog thereof." [PRO:DNx] + nuclear hormone receptor 1 + PR_EXT:peroxisome proliferator-activated receptor delta + + + peroxisome proliferator-activated receptor gamma + NR1C3 + PPARG + PR_EXT:000013058 + PPAR-gamma + "A protein that is a translation product of the human PPARG gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:peroxisome proliferator-activated receptor gamma + nuclear receptor subfamily 1 group C member 3 + + + PPARGC-1-alpha + ligand effect modulator 6 + "A protein that is a translation product of the human PPARGC1A gene or a 1:1 ortholog thereof." [PRO:DNx] + PGC1 + LEM6 + PPARGC1 + PR_EXT:000013059 + PR_EXT:peroxisome proliferator-activated receptor gamma coactivator 1-alpha + PPAR-gamma coactivator 1-alpha + peroxisome proliferator-activated receptor gamma coactivator 1-alpha + PGC1A + PPARGC1A + PGC-1-alpha + + + PPARGC1B + PGC1B + PGC-1-related estrogen receptor alpha coactivator + peroxisome proliferator-activated receptor gamma coactivator 1-beta + PR_EXT:peroxisome proliferator-activated receptor gamma coactivator 1-beta + PERC + PGC1 + PGC-1-beta + PPARGC1 + PPARGC-1-beta + "A protein that is a translation product of the human PPARGC1B gene or a 1:1 ortholog thereof." [PRO:DNx] + Errl1 + ERR ligand 1 + PPAR-gamma coactivator 1-beta + PR_EXT:000013060 + + + dopamine- and cAMP-regulated neuronal phosphoprotein + DARPP32 + DARPP-32 + PPP1R1B + "A protein that is a translation product of the human PPP1R1B gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:protein phosphatase 1 regulatory subunit 1B + protein phosphatase 1 regulatory subunit 1B + PR_EXT:000013121 + + + PR_EXT:peroxisome proliferator-activated receptor gamma coactivator-related protein 1 + PGC-1-related coactivator + PRC + PR_EXT:000013159 + PPRC1 + KIAA0595 + peroxisome proliferator-activated receptor gamma coactivator-related protein 1 + "A protein that is a translation product of the human PPRC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PRC1 + PR_EXT:000013176 + protein regulator of cytokinesis 1 + PR_EXT:protein regulator of cytokinesis 1 + "A protein that is a translation product of the human PRC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000013249 + "A protein that is a translation product of the human PRM1 gene or a 1:1 ortholog thereof." [PRO:DNx] + cysteine-rich protamine + sperm protamine P1 + PRM1 + Prm-1 + PR_EXT:sperm protamine P1 + + + PROS1 + PR_EXT:vitamin K-dependent protein S + PR_EXT:000013269 + PROS + "A protein that is a translation product of the human PROS1 gene or a 1:1 ortholog thereof." [PRO:DNx] + vitamin K-dependent protein S + + + peripherin-2 + "A protein that is a translation product of the human PRPH2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:peripherin-2 + PRPH + PR_EXT:000013290 + TSPAN22 + tspan-22 + tetraspanin-22 + retinal degeneration slow protein + RDS + PRPH2 + + + Pmx + homeobox protein K-2 + homeobox protein PHOX1 + paired-related homeobox protein 1 + PRX-1 + PRRX1 + PR_EXT:000013316 + paired mesoderm homeobox protein 1 + homeobox protein mHox + "A protein that is a translation product of the human PRRX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PMX1 + PR_EXT:paired mesoderm homeobox protein 1 + + + PSNL1 + AD3 + PR_EXT:000013344 + protein S182 + PSEN1 + presenilin-1 + PS1 + PS-1 + Ad3h + PR_EXT:presenilin-1 + "A protein that is a translation product of the human PSEN1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + STM-2 + PR_EXT:000013345 + presenilin-2 + AD5 + E5-1 + AD3LP + Ad4h + PR_EXT:presenilin-2 + Alg3 + AD4 + PSNL2 + PS2 + PSEN2 + PS-2 + "A protein that is a translation product of the human PSEN2 gene or a 1:1 ortholog thereof." [PRO:DNx] + STM2 + + + PR_EXT:polypyrimidine tract-binding protein 2 + brain-enriched PTB + PTBP2 + PTBLP + PTB + polypyrimidine tract-binding protein 2 + RRM-type RNA-binding protein brPTB + PTB-like protein + "A protein that is a translation product of the human PTBP2 gene or a 1:1 ortholog thereof." [PRO:DNx] + neural polypyrimidine tract-binding protein + PR_EXT:000013411 + Brptb + neurally-enriched homolog of PTB + brain-enriched polypyrimidine tract-binding protein + NPTB + + + PTCH + PR_EXT:protein patched homolog 1 + PR_EXT:000013412 + "A protein that is a translation product of the human PTCH1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PTC1 + protein patched homolog 1 + PTC + PTCH1 + + + COX-2 + glucocorticoid-regulated inflammatory cyclooxygenase + prostaglandin G/H synthase 2 + "A protein that is a translation product of the human PTGS2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PGH synthase 2 + COX2 + gripghs + TIS10 protein + macrophage activation-associated marker protein P71/73 + prostaglandin-endoperoxide synthase 2 + PR_EXT:prostaglandin G/H synthase 2 + cyclooxygenase-2 + Pghs-b + PGHS-2 + Tis10 + PHS II + PR_EXT:000013428 + PES-2 + prostaglandin H2 synthase 2 + PTGS2 + + + PTH-rP + parathyroid hormone-like protein + PR_EXT:parathyroid hormone-related protein + PLP + PR_EXT:000013433 + PTHLH + parathyroid hormone-related protein + "A protein that is a translation product of the human PTHLH gene or a 1:1 ortholog thereof." [PRO:DNx] + PTHrP + + + tyrosine-protein kinase BRK + breast tumor kinase + SRC-related intestinal kinase + "A proto-oncogene SRC-like tyrosine-protein kinase that is a translation product of the human PTK6 gene or a 1:1 ortholog thereof." [PRO:DNx] + Sik + PR_EXT:protein-tyrosine kinase 6 + PR_EXT:000013434 + PTK6 + BRK + tyrosine-protein kinase 6 + protein-tyrosine kinase 6 + + + PTP2C + protein-tyrosine phosphatase 1D + SHPTP2 + protein-tyrosine phosphatase 2C + PTP-1D + PTP-2C + protein-tyrosine phosphatase SYP + "A protein that is a translation product of the human PTPN11 gene or a 1:1 ortholog thereof." [PRO:DNx] + SH-PTP2 + PR_EXT:tyrosine-protein phosphatase non-receptor type 11 + tyrosine-protein phosphatase non-receptor type 11 + shp2 + PR_EXT:000013449 + PTPN11 + SH-PTP3 + SHP-2 + + + "A protein that is a translation product of the human PTPN22 gene or a 1:1 ortholog thereof." [PRO:DNx] + PTPN8 + tyrosine-protein phosphatase non-receptor type 22 + hematopoietic cell protein-tyrosine phosphatase 70Z-PEP + lymphoid phosphatase + PR_EXT:000013457 + PR_EXT:tyrosine-protein phosphatase non-receptor type 22 + LyP + PTPN22 + + + parvalbumin alpha + PR_EXT:000013502 + PR_EXT:parvalbumin alpha + PVALB + "A protein that is a translation product of the human PVALB gene or a 1:1 ortholog thereof." [PRO:DNx] + Pva + + + PYGM + PR_EXT:000013522 + "A protein that is a translation product of the human PYGM gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:glycogen phosphorylase, muscle form + myophosphorylase + glycogen phosphorylase, muscle form + + + PYGO1 + PR_EXT:000013523 + pygopus homolog 1 + PR_EXT:pygopus homolog 1 + "A protein that is a translation product of the human PYGO1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PYGO2 + PR_EXT:000013524 + pygopus homolog 2 + PR_EXT:pygopus homolog 2 + "A protein that is a translation product of the human PYGO2 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + probasin + PB + PR_EXT:probasin + "A protein that is a translation product of the mouse Pbsn gene or a 1:1 ortholog thereof." [PRO:DNx] + Pbsn + Prbs + PR_EXT:000013530 + + + Csh1 + Pl1 + prolactin-3D1 + "A somatotropin hormone family member that is a translation product of the mouse Prl3d1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000013543 + chorionic somatomammotropin hormone 1 + Prl3d1 + placental lactogen I + Pl-1 + PL-I + PR_EXT:prolactin-3D1 + + + Prh1 + proline-rich protein 2 + proline-rich protein MP-3 + PR_EXT:000013555 + Prp + "A protein that is a translation product of the mouse Prp2 gene or a 1:1 ortholog thereof." [PRO:DNx] + Prp2 + PR_EXT:proline-rich protein 2 + + + MqkI + Hqk + Qk + PR_EXT:protein quaking + "A protein that is a translation product of the human QKI gene or a 1:1 ortholog thereof." [PRO:DNx] + HqkI + Qk1 + PR_EXT:000013564 + HKQ + qkI + QKI + protein quaking + Qka1 + + + RAB7A + PR_EXT:000013639 + ras-related protein Rab-7a + PR_EXT:ras-related protein Rab-7a + RAB7 + "A protein that is a translation product of the human RAB7A gene or a 1:1 ortholog thereof." [PRO:DNx] + + + ras-related C3 botulinum toxin substrate 1 + PR_EXT:ras-related C3 botulinum toxin substrate 1 + RAC1 + PR_EXT:000013660 + "A protein that is a translation product of the human RAC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + ras-like protein TC25 + p21-Rac1 + cell migration-inducing gene 5 protein + TC25 + + + "A protein that is a translation product of the human RAC3 gene or a 1:1 ortholog thereof." [PRO:DNx] + ras-related C3 botulinum toxin substrate 3 + RAC3 + PR_EXT:ras-related C3 botulinum toxin substrate 3 + p21-Rac3 + PR_EXT:000013662 + + + RAD17 + RF-C/activator 1 homolog + PR_EXT:000013665 + cell cycle checkpoint protein RAD17 + R24L + hRad17 + "A protein that is a translation product of the human RAD17 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:cell cycle checkpoint protein RAD17 + + + XP-C repair-complementing complex 58 kDa protein + PR_EXT:000013670 + RAD23B + "A protein that is a translation product of the human RAD23B gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:UV excision repair protein RAD23 homolog B + UV excision repair protein RAD23 homolog B + HR23B + + + "A protein that is a translation product of the human RAD51 gene or a 1:1 ortholog thereof." [PRO:DNx] + RAD51 + PR_EXT:DNA repair protein RAD51 homolog 1 + RAD51 homolog A + RECA + DNA repair protein RAD51 homolog 1 + PR_EXT:000013672 + RAD51A + + + PR_EXT:DNA repair protein RAD51 homolog 3 + "A protein that is a translation product of the human RAD51C gene or a 1:1 ortholog thereof." [PRO:DNx] + RAD51L2 + RAD51 homolog C + RAD51C + DNA repair protein RAD51 homolog 3 + PR_EXT:000013675 + RAD51-like protein 2 + + + "A protein that is a translation product of the human RAD51B gene or a 1:1 ortholog thereof." [PRO:DNx] + Rad51B + RAD51B + PR_EXT:000013676 + RAD51 homolog B + PR_EXT:DNA repair protein RAD51 homolog 2 + RAD51L1 + DNA repair protein RAD51 homolog 2 + REC2 + R51H2 + RAD51-like protein 1 + + + PR_EXT:DNA repair protein RAD51 homolog 4 + PR_EXT:000013677 + TRAD + DNA repair protein RAD51 homolog 4 + RAD51L3 + RAD51 homolog D + "A protein that is a translation product of the human RAD51D gene or a 1:1 ortholog thereof." [PRO:DNx] + RAD51D + RAD51-like protein 3 + + + RAD54 homolog + "A protein that is a translation product of the human RAD54L gene or a 1:1 ortholog thereof." [PRO:DNx] + RAD54A + RAD54 + PR_EXT:DNA repair and recombination protein RAD54-like + RAD54L + PR_EXT:000013680 + Rad54 + DNA repair and recombination protein RAD54-like + HR54 + + + ras-related nuclear protein + androgen receptor-associated protein 24 + GTP-binding nuclear protein Ran + "A protein that is a translation product of the human RAN gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000013708 + ras-like protein TC4 + ARA24 + PR_EXT:GTP-binding nuclear protein Ran + Rasl2-8 + GTPase Ran + RAN + + + ran-binding protein 1 + ran-specific GTPase-activating protein + PR_EXT:ran-specific GTPase-activating protein + PR_EXT:000013709 + Htf9a + RanBP1 + RANBP1 + Htf9-a + HpaII tiny fragments locus 9a protein + "A protein that is a translation product of the human RANBP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + NUP358 + 358 kDa nucleoporin + ran-binding protein 2 + nucleoporin Nup358 + nuclear pore complex protein Nup358 + E3 SUMO-protein ligase RanBP2 + RANBP2 + RanBP2 + PR_EXT:000013712 + "A protein that is a translation product of the human RANBP2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:E3 SUMO-protein ligase RanBP2 + + + "A protein that is a translation product of the human RANGAP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000013717 + SD + RANGAP1 + RanGAP1 + ran GTPase-activating protein 1 + PR_EXT:ran GTPase-activating protein 1 + Fug1 + KIAA1835 + + + "A protein that is a translation product of the human RASA1 gene or a 1:1 ortholog thereof." [PRO:DNx] + RASA1 + p120GAP + RASA + ras GTPase-activating protein 1 + PR_EXT:ras GTPase-activating protein 1 + ras p21 protein activator + PR_EXT:000013743 + RasGAP + GTPase-activating protein + + + PR_EXT:000013771 + RAX + retina and anterior neural fold homeobox protein + PR_EXT:retinal homeobox protein Rx + "A protein that is a translation product of the human RAX gene or a 1:1 ortholog thereof." [PRO:DNx] + retinal homeobox protein Rx + RX + + + PR_EXT:000013773 + PR_EXT:retinoblastoma-associated protein + pRb + Rb + pp110 + RB1 + retinoblastoma-associated protein + "A protein that is a translation product of the human RB1 gene or a 1:1 ortholog thereof." [PRO:DNx] + pp105 + p105-Rb + Rb-1 + + + PR_EXT:000013776 + "A protein that is a translation product of the human RBBP4 gene or a 1:1 ortholog thereof." [PRO:DNx] + CAF-1 subunit C + CAF-I p48 + RBBP4 + histone-binding protein RBBP4 + nucleosome-remodeling factor subunit RBAP48 + RBBP-4 + chromatin assembly factor 1 subunit C + PR_EXT:histone-binding protein RBBP4 + retinoblastoma-binding protein 4 + retinoblastoma-binding protein p48 + chromatin assembly factor I p48 subunit + CAF-I 48 kDa subunit + RBAP48 + + + PR_EXT:RNA-binding protein 8A + PR_EXT:000013809 + RNA-binding protein Y14 + binder of OVCA1-1 + BOV-1 + RNA-binding motif protein 8A + RNA-binding protein 8A + ribonucleoprotein RBM8A + RBM8A + "A protein that is a translation product of the human RBM8A gene or a 1:1 ortholog thereof." [PRO:DNx] + RBM8 + + + interphotoreceptor retinoid-binding protein + interstitial retinol-binding protein + PR_EXT:000013820 + PR_EXT:retinol-binding protein 3 + "A protein that is a translation product of the human RBP3 gene or a 1:1 ortholog thereof." [PRO:DNx] + RBP3 + retinol-binding protein 3 + IRBP + + + DSC1 + myocyte-enriched calcineurin-interacting protein 1 + Adapt78 + DSCR1 + calcipressin-1 + "A protein that is a translation product of the human RCAN1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000013829 + Down syndrome critical region protein 1 + CSP1 + RCAN1 + Down syndrome critical region protein 1 homolog + regulator of calcineurin 1 + MCIP1 + PR_EXT:calcipressin-1 + + + RCV1 + recoverin + protein CAR + 23 kDa photoreceptor cell-specific protein + PR_EXT:recoverin + "A protein that is a translation product of the human RCVRN gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000013845 + cancer-associated retinopathy protein + RCVRN + + + PR_EXT:meiotic recombination protein REC8 + meiotic recombination protein REC8 + "A protein that is a translation product of the human REC8 gene or a 1:1 ortholog thereof." [PRO:DNx] + REC8L1 + cohesin Rec8p + REC8 + PR_EXT:000013858 + Mei8 + + + "A protein that is a translation product of the human REN gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000013883 + angiotensinogenase + PR_EXT:renin + renin + REN + + + PR_EXT:000013894 + REST + PR_EXT:RE1-silencing transcription factor + NRSF + X2 box repressor + XBR + RE1-silencing transcription factor + neural-restrictive silencer factor + "A protein that is a translation product of the human REST gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000013947 + RGS12 + regulator of G-protein signaling 12 + PR_EXT:regulator of G-protein signaling 12 + "A protein that is a translation product of the human RGS12 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + regulator of G-protein signaling 9 + "A protein that is a translation product of the human RGS9 gene or a 1:1 ortholog thereof." [PRO:DNx] + RGS9 + PR_EXT:regulator of G-protein signaling 9 + PR_EXT:000013965 + + + receptor-interacting serine/threonine-protein kinase 2 + RICK + receptor-interacting protein 2 + CARD-containing IL-1 beta ICE-kinase + CARDIAK + RIP2 + PR_EXT:000014023 + PR_EXT:receptor-interacting serine/threonine-protein kinase 2 + RIP-like-interacting CLARP kinase + CARD-containing interleukin-1 beta-converting enzyme-associated kinase + "A protein that is a translation product of the human RIPK2 gene or a 1:1 ortholog thereof." [PRO:DNx] + RIPK2 + RIP-2 + + + rod outer segment membrane protein 1 + ROSP1 + "A protein that is a translation product of the human ROM1 gene or a 1:1 ortholog thereof." [PRO:DNx] + ROM1 + TSPAN23 + tspan-23 + PR_EXT:000014157 + PR_EXT:rod outer segment membrane protein 1 + Rom-1 + tetraspanin-23 + + + all-trans-retinyl-palmitate hydrolase + RPE65 + PR_EXT:retinal pigment epithelium-specific 65 kDa protein + "A protein that is a translation product of the human RPE65 gene or a 1:1 ortholog thereof." [PRO:DNx] + retinol isomerase + PR_EXT:000014179 + retinal pigment epithelium-specific 65 kDa protein + + + PR_EXT:000014182 + PR_EXT:X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 + "A protein that is a translation product of the human RPGRIP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + RPGRIP1 + X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 + RPGR-interacting protein 1 + + + 60S ribosomal protein L10E + 60S acidic ribosomal protein P0 + Arbp + "A protein that is a translation product of the human RPLP0 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000014237 + RPLP0 + PR_EXT:60S acidic ribosomal protein P0 + + + 40S ribosomal protein S16 + "A protein that is a translation product of the human RPS16 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000014258 + PR_EXT:40S ribosomal protein S16 + RPS16 + + + osteoblast-specific transcription factor 2 + polyomavirus enhancer-binding protein 2 alpha A subunit + acute myeloid leukemia 3 protein + runt-related transcription factor 2 + CBFA1 + oncogene AML-3 + RUNX2 + SL3-3 enhancer factor 1 alpha A subunit + core-binding factor subunit alpha-1 + PEBP2-alpha A + OSF2 + AML3 + PEBP2A + CBF-alpha-1 + OSF-2 + PEA2-alpha A + "A protein that is a translation product of the human RUNX2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000014364 + SL3/AKV core-binding factor alpha A subunit + PR_EXT:runt-related transcription factor 2 + + + PEBP2A3 + polyomavirus enhancer-binding protein 2 alpha C subunit + PR_EXT:000014365 + runt-related transcription factor 3 + acute myeloid leukemia 2 protein + CBFA3 + oncogene AML-2 + RUNX3 + PEBP2-alpha C + SL3-3 enhancer factor 1 alpha C subunit + core-binding factor subunit alpha-3 + "A protein that is a translation product of the human RUNX3 gene or a 1:1 ortholog thereof." [PRO:DNx] + CBF-alpha-3 + AML2 + PEA2-alpha C + PR_EXT:runt-related transcription factor 3 + SL3/AKV core-binding factor alpha C subunit + + + PR_EXT:000014373 + nuclear receptor subfamily 2 group B member 2 + PR_EXT:retinoic acid receptor RXR-beta + MHC class I regulatory element-binding protein H-2RIIBP + "A protein that is a translation product of the human RXRB gene or a 1:1 ortholog thereof." [PRO:DNx] + retinoid X receptor beta + NR2B2 + RXRB + retinoic acid receptor RXR-beta + + + Refbp2 + Ref2 + Alyref2 + PR_EXT:Aly/REF export factor 2 + Aly/REF export factor 2 + "A protein that is a translation product of the mouse Alyref2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000014390 + RNA and export factor-binding protein 2 + + + PR_EXT:000014394 + Ren1 + kidney renin + PR_EXT:renin-1 + Ren-1 + renin-1 + "A protein that is a translation product of the mouse Ren1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Ren + + + Ren2 + "A protein that is a translation product of the mouse Ren2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000014395 + renin-2 + Ren-2 + submandibular gland renin + PR_EXT:renin-2 + + + PR_EXT:homeobox protein Rhox5 + placenta and embryonic expression protein + homeobox protein Pem + Rhox5 + "A protein that is a translation product of the mouse Rhox5 gene or a 1:1 ortholog thereof." [PRO:DNx] + homeobox protein Rhox5 + PR_EXT:000014397 + reproductive homeobox on chromosome X 5 + Pem + + + S100A + S-100 protein alpha chain + S-100 protein subunit alpha + PR_EXT:protein S100-A1 + "A protein that is a translation product of the human S100A1 gene or a 1:1 ortholog thereof." [PRO:DNx] + protein S100-A1 + S100 calcium-binding protein A1 + PR_EXT:000014402 + S100A1 + + + calpactin I light chain + cellular ligand of annexin II + protein S100-A10 + ANX2LG + p10 protein + PR_EXT:000014403 + S100 calcium-binding protein A10 + S100A10 + "A protein that is a translation product of the human S100A10 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:protein S100-A10 + CAL1L + calpactin-1 light chain + CLP11 + + + MLN 4 + growth factor-inducible protein 2A9 + 5B10 + calcyclin + prolactin receptor-associated protein + S100A6 + PR_EXT:protein S100-A6 + protein S100-A6 + S100 calcium-binding protein A6 + "A protein that is a translation product of the human S100A6 gene or a 1:1 ortholog thereof." [PRO:DNx] + PRA + CACY + PR_EXT:000014413 + + + S-AG + 48 kDa protein + S-arrestin + retinal S-antigen + rod photoreceptor arrestin + PR_EXT:S-arrestin + "A protein that is a translation product of the human SAG gene or a 1:1 ortholog thereof." [PRO:DNx] + SAG + PR_EXT:000014434 + + + SAM domain-containing protein 11 + major retinal SAM domain-containing protein + SAMD11 + sterile alpha motif domain-containing protein 11 + PR_EXT:000014441 + Mr-s + PR_EXT:sterile alpha motif domain-containing protein 11 + "A protein that is a translation product of the human SAMD11 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:lathosterol oxidase + "A protein that is a translation product of the human SC5D gene or a 1:1 ortholog thereof." [PRO:DNx] + sterol-C5-desaturase + lathosterol oxidase + SC5D + PR_EXT:000014480 + C-5 sterol desaturase + delta(7)-sterol 5-desaturase + SC5DL + lathosterol 5-desaturase + Sc5d + + + CCSP + PCB-binding protein + PR_EXT:uteroglobin + UP1 + clara cell 17 kDa protein + SCGB1A1 + urine protein 1 + clara cell phospholipid-binding protein + Utg + CCPBP + CC10 + UP-1 + urinary protein 1 + clara cells 10 kDa secretory protein + UGB + "A protein that is a translation product of the human SCGB1A1 gene or a 1:1 ortholog thereof." [PRO:DNx] + uteroglobin + secretoglobin family 1A member 1 + PR_EXT:000014505 + + + "A semaphorin that is a translation product of the human SEMA3A gene or a 1:1 ortholog thereof." [PRO:DNx] + SEMAD + PR_EXT:semaphorin-3A + semaphorin III + Sema III + semaphorin-3A + semaphorin-D + Sema D + SemD + PR_EXT:000014615 + SEMA3A + + + SelW + PR_EXT:selenoprotein W + SEPW1 + PR_EXT:000014662 + "A protein that is a translation product of the human SEPW1 gene or a 1:1 ortholog thereof." [PRO:DNx] + selenoprotein W + + + serpin E1 + PR_EXT:000014702 + PAI1 + SERPINE1 + PR_EXT:plasminogen activator inhibitor 1 + Mr1 + PAI-1 + plasminogen activator inhibitor 1 + "A serpin that is a translation product of the human SERPINE1 gene or a 1:1 ortholog thereof." [PRO:CNA] + endothelial plasminogen activator inhibitor + PAI + PLANH1 + + + "A serpin that is a translation product of the human SERPINF2 gene or a 1:1 ortholog thereof." [PRO:CNA] + PLI + PR_EXT:000014706 + SERPINF2 + alpha-2-PI + alpha-2-antiplasmin + alpha-2-plasmin inhibitor + PR_EXT:alpha-2-antiplasmin + serpin F2 + alpha-2-AP + AAP + + + SP-B + 6 kDa protein + PR_EXT:000014773 + pulmonary surfactant-associated proteolipid SPL(Phe) + SFTP3 + PR_EXT:pulmonary surfactant-associated protein B + 18 kDa pulmonary-surfactant protein + "A protein that is a translation product of the human SFTPB gene or a 1:1 ortholog thereof." [PRO:DNx] + pulmonary surfactant-associated protein B + SFTPB + + + SFTPC + SFTP2 + pulmonary surfactant-associated proteolipid SPL(Val) + PR_EXT:000014774 + PR_EXT:pulmonary surfactant-associated protein C + "A protein that is a translation product of the human SFTPC gene or a 1:1 ortholog thereof." [PRO:DNx] + pulmonary surfactant-associated protein C + SP-C + + + SFTPD + SFTP4 + "A protein that is a translation product of the human SFTPD gene or a 1:1 ortholog thereof." [PRO:DNx] + SP-D + PSP-D + PSPD + collectin-7 + PR_EXT:000014775 + pulmonary surfactant-associated protein D + PR_EXT:pulmonary surfactant-associated protein D + COLEC7 + lung surfactant protein D + + + sonic hedgehog protein + "A protein that is a translation product of the human SHH gene or a 1:1 ortholog thereof." [PRO:DNx] + Hhg1 + SHH + PR_EXT:000014841 + PR_EXT:sonic hedgehog protein + HHG-1 + + + mSIR2a + hSIR2 + SIRT1 + "A protein that is a translation product of the human SIRT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:NAD-dependent protein deacetylase sirtuin-1 + sir2 + NAD-dependent protein deacetylase sirtuin-1 + NAD-dependent deacetylase sirtuin-1 + PR_EXT:000014888 + SIR2alpha + SIR2-like protein 1 + SIR2L1 + + + SIR2L6 + NAD-dependent deacetylase sirtuin-6 + SIRT6 + PR_EXT:NAD-dependent protein deacetylase sirtuin-6 + mono-ADP-ribosyltransferase sirtuin-6 + NAD-dependent protein deacetylase sirtuin-6 + "A protein that is a translation product of the human SIRT6 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000014892 + SIR2-like protein 6 + + + homeobox protein SIX3 + PR_EXT:homeobox protein SIX3 + PR_EXT:000014898 + SIX3 + sine oculis homeobox homolog 3 + "A protein that is a translation product of the human SIX3 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + SNO + SKIL + Skir + PR_EXT:000014906 + "A protein that is a translation product of the human SKIL gene or a 1:1 ortholog thereof." [PRO:DNx] + ski-like protein + PR_EXT:ski-like protein + ski-related protein + ski-related oncogene + + + "A protein that is a translation product of the human SLC12A2 gene or a 1:1 ortholog thereof." [PRO:DNx] + solute carrier family 12 member 2 + basolateral Na-K-Cl symporter + PR_EXT:000014925 + SLC12A2 + PR_EXT:solute carrier family 12 member 2 + NKCC1 + bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1 + + + PR_EXT:000014963 + solute carrier family 17 member 7 + SLC17A7 + PR_EXT:vesicular glutamate transporter 1 + vesicular glutamate transporter 1 + VGluT1 + "A protein that is a translation product of the human SLC17A7 gene or a 1:1 ortholog thereof." [PRO:DNx] + BNPI + brain-specific Na(+)-dependent inorganic phosphate cotransporter + + + "A protein that is a translation product of the human SLC18A3 gene or a 1:1 ortholog thereof." [PRO:DNx] + VAChT + SLC18A3 + PR_EXT:000014968 + PR_EXT:vesicular acetylcholine transporter + solute carrier family 18 member 3 + vesicular acetylcholine transporter + + + GC1 + "A protein that is a translation product of the human SLC25A22 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:mitochondrial glutamate carrier 1 + mitochondrial glutamate carrier 1 + GC-1 + PR_EXT:000015018 + solute carrier family 25 member 22 + SLC25A22 + glutamate/H(+) symporter 1 + + + PR_EXT:000015039 + sodium-independent chloride/iodide transporter + PDS + PR_EXT:pendrin + "A protein that is a translation product of the human SLC26A4 gene or a 1:1 ortholog thereof." [PRO:DNx] + pendrin + SLC26A4 + solute carrier family 26 member 4 + + + SPNT + Na(+)/nucleoside cotransporter 2 + sodium-coupled nucleoside transporter 2 + CNT 2 + solute carrier family 28 member 2 + concentrative nucleoside transporter 2 + sodium/nucleoside cotransporter 2 + SLC28A2 + "A protein that is a translation product of the human SLC28A2 gene or a 1:1 ortholog thereof." [PRO:DNx] + sodium/purine nucleoside co-transporter + PR_EXT:sodium/nucleoside cotransporter 2 + PR_EXT:000015052 + CNT2 + sodium/purine nucleoside cotransporter + + + GLUT2 + "A protein that is a translation product of the human SLC2A2 gene or a 1:1 ortholog thereof." [PRO:DNx] + SLC2A2 + GLUT-2 + PR_EXT:solute carrier family 2, facilitated glucose transporter member 2 + glucose transporter type 2, liver + PR_EXT:000015064 + solute carrier family 2, facilitated glucose transporter member 2 + + + solute carrier family 2, facilitated glucose transporter member 4 + glucose transporter type 4, insulin-responsive + GT2 + PR_EXT:solute carrier family 2, facilitated glucose transporter member 4 + PR_EXT:000015066 + GLUT4 + "A protein that is a translation product of the human SLC2A4 gene or a 1:1 ortholog thereof." [PRO:DNx] + GLUT-4 + SLC2A4 + + + PR_EXT:zinc transporter 1 + ZNT1 + SLC30A1 + PR_EXT:000015073 + solute carrier family 30 member 1 + ZnT-1 + "A protein that is a translation product of the human SLC30A1 gene or a 1:1 ortholog thereof." [PRO:DNx] + zinc transporter 1 + + + PR_EXT:zinc transporter 2 + "A protein that is a translation product of the human SLC30A2 gene or a 1:1 ortholog thereof." [PRO:DNx] + ZNT2 + ZnT-2 + solute carrier family 30 member 2 + SLC30A2 + PR_EXT:000015075 + zinc transporter 2 + + + PR_EXT:zinc transporter 3 + ZNT3 + "A protein that is a translation product of the human SLC30A3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000015076 + solute carrier family 30 member 3 + ZnT-3 + SLC30A3 + zinc transporter 3 + + + solute carrier family 39 member 10 + zinc transporter ZIP10 + SLC39A10 + PR_EXT:zinc transporter ZIP10 + PR_EXT:000015124 + "A protein that is a translation product of the human SLC39A10 gene or a 1:1 ortholog thereof." [PRO:DNx] + Zrt- and Irt-like protein 10 + ZIP-10 + ZIP10 + KIAA1265 + + + low affinity sodium-glucose cotransporter + Na(+)/glucose cotransporter 2 + SLC5A2 + sodium/glucose cotransporter 2 + "A protein that is a translation product of the human SLC5A2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000015169 + SGLT2 + PR_EXT:sodium/glucose cotransporter 2 + solute carrier family 5 member 2 + + + slit-2 + slit 2 protein + SLIL3 + PR_EXT:slit homolog 2 protein + SLIT2 + "A protein that is a translation product of the human SLIT2 gene or a 1:1 ortholog thereof." [PRO:DNx] + slit homolog 2 protein + PR_EXT:000015235 + + + integrase interactor 1 protein + INI1 + BRG1-associated factor 47 + PR_EXT:SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 + PR_EXT:000015262 + "A protein that is a translation product of the human SMARCB1 gene or a 1:1 ortholog thereof." [PRO:DNx] + SNF5L1 + SMARCB1 + SNF5 + BAF47 + SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 + + + smoothened + protein Gx + PR_EXT:000015288 + PR_EXT:smoothened + SMOH + "A frizzled-like G-protein coupled receptor that is a translation product of the human SMO gene or a 1:1 ortholog thereof." [PRO:DAN] + SMO + + + SMUG1 + PR_EXT:single-strand selective monofunctional uracil DNA glycosylase + single-strand selective monofunctional uracil DNA glycosylase + PR_EXT:000015305 + "A protein that is a translation product of the human SMUG1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + protein snail homolog 1 + protein sna + zinc finger protein SNAI1 + "A protein that is a translation product of the human SNAI1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000015308 + SNAH + PR_EXT:zinc finger protein SNAI1 + SNAI1 + Sna + + + SLUGH + SLUG + zinc finger protein SNAI2 + PR_EXT:zinc finger protein SNAI2 + protein snail homolog 2 + "A protein that is a translation product of the human SNAI2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000015309 + neural crest transcription factor Slug + SNAI2 + + + synaptosomal-associated protein 25 + SUP + super protein + SNAP25 + "A protein that is a translation product of the human SNAP25 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000015312 + SNAP-25 + synaptosomal-associated 25 kDa protein + PR_EXT:synaptosomal-associated protein 25 + SNAP + + + non-A4 component of amyloid precursor + SNCA + "A protein that is a translation product of the human SNCA gene or a 1:1 ortholog thereof." [PRO:DNx] + alpha-synuclein + PR_EXT:000015322 + non-A beta component of AD amyloid + PARK1 + NACP + PR_EXT:alpha-synuclein + Syn + + + PR_EXT:000015348 + SNRPG + "A protein that is a translation product of the human SNRPG gene or a 1:1 ortholog thereof." [PRO:DNx] + Sm protein G + Sm-G + PR_EXT:small nuclear ribonucleoprotein G + snRNP-G + PBSCG + SmG + small nuclear ribonucleoprotein G + + + suppressor of cytokine signaling 2 + STAT-induced STAT inhibitor 2 + SSI2 + CIS-2 + cytokine-inducible SH2 protein 2 + STATI2 + SSI-2 + PR_EXT:000015393 + Cish2 + "A protein that is a translation product of the human SOCS2 gene or a 1:1 ortholog thereof." [PRO:DNx] + SOCS-2 + CIS2 + SOCS2 + PR_EXT:suppressor of cytokine signaling 2 + + + SSI3 + suppressor of cytokine signaling 3 + STAT-induced STAT inhibitor 3 + CIS3 + CIS-3 + cytokine-inducible SH2 protein 3 + PR_EXT:suppressor of cytokine signaling 3 + protein EF-10 + PR_EXT:000015394 + SSI-3 + SOCS-3 + Cish3 + "A protein that is a translation product of the human SOCS3 gene or a 1:1 ortholog thereof." [PRO:DNx] + SOCS3 + + + "A SODC domain protein that is a translation product of the human SOD1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:superoxide dismutase [Cu-Zn] + PR_EXT:000015399 + SOD1 + superoxide dismutase [Cu-Zn] + + + EC-SOD + SOD3 + extracellular superoxide dismutase [Cu-Zn] + "A SODC domain protein that is a translation product of the human SOD3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:extracellular superoxide dismutase [Cu-Zn] + PR_EXT:000015401 + + + SOS-1 + SOS1 + PR_EXT:son of sevenless homolog 1 + PR_EXT:000015413 + "A protein that is a translation product of the human SOS1 gene or a 1:1 ortholog thereof." [PRO:DNx] + son of sevenless homolog 1 + + + Sox-1 + SOX1 + transcription factor SOX-1 + PR_EXT:000015417 + "A protein that is a translation product of the human SOX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:transcription factor SOX-1 + + + SOX2 + Sox-2 + "A protein that is a translation product of the human SOX2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:transcription factor SOX-2 + PR_EXT:000015426 + transcription factor SOX-2 + + + SOX3 + PR_EXT:000015428 + Sox-3 + PR_EXT:transcription factor SOX-3 + "A protein that is a translation product of the human SOX3 gene or a 1:1 ortholog thereof." [PRO:DNx] + transcription factor SOX-3 + + + "A protein that is a translation product of the human SOX5 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000015431 + Sox-5 + PR_EXT:transcription factor SOX-5 + SOX5 + transcription factor SOX-5 + + + "A protein that is a translation product of the human SOX6 gene or a 1:1 ortholog thereof." [PRO:DNx] + SOX-LZ + PR_EXT:000015432 + Sox-6 + SOX6 + PR_EXT:transcription factor SOX-6 + transcription factor SOX-6 + + + PR_EXT:000015435 + transcription factor SOX-9 + SOX9 + PR_EXT:transcription factor SOX-9 + "A protein that is a translation product of the human SOX9 gene or a 1:1 ortholog thereof." [PRO:DNx] + Sox-9 + + + "A protein that is a translation product of the human SP7 gene or a 1:1 ortholog thereof." [PRO:DNx] + C22 + transcription factor Sp7 + zinc finger protein osterix + OSX + PR_EXT:000015445 + SP7 + PR_EXT:transcription factor Sp7 + + + "A protein that is a translation product of the human SPAG17 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000015456 + PR_EXT:sperm-associated antigen 17 + sperm-associated antigen 17 + SPAG17 + projection protein PF6 homolog + + + SPG4 + ADPSP + PR_EXT:000015477 + KIAA1083 + FSP2 + SPAST + PR_EXT:spastin + "A protein that is a translation product of the human SPAST gene or a 1:1 ortholog thereof." [PRO:DNx] + spastic paraplegia 4 protein + spastin + + + SPO11 + CT35 + PR_EXT:meiotic recombination protein SPO11 + meiotic recombination protein SPO11 + "A protein that is a translation product of the human SPO11 gene or a 1:1 ortholog thereof." [PRO:DNx] + cancer/testis antigen 35 + PR_EXT:000015553 + + + uropontin + BNSP + SPP1 + calcium oxalate crystal growth inhibitor protein + SPP-1 + OPN + nephropontin + early T-lymphocyte activation 1 protein + PR_EXT:000015561 + "A protein that is a translation product of the human SPP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + osteopontin + PR_EXT:osteopontin + secreted phosphoprotein 1 + Eta-1 + urinary stone protein + 2AR + bone sialoprotein 1 + Op + minopontin + + + PR_EXT:sterol regulatory element-binding protein 2 + bHLHd2 + sterol regulatory element-binding protein 2 + SREBP2 + "A sterol regulatory element-binding protein that is a translation product of the human SREBF2 gene or a 1:1 ortholog thereof." [PRO:CNA] + SREBF2 + SREBP-2 + sterol regulatory element-binding transcription factor 2 + class D basic helix-loop-helix protein 2 + PR_EXT:000015612 + + + 22 kDa protein + V19 + sorcin + PR_EXT:000015619 + CP-22 + PR_EXT:sorcin + "A protein that is a translation product of the human SRI gene or a 1:1 ortholog thereof." [PRO:DNx] + SRI + + + SRY + PR_EXT:sex-determining region Y protein + TDF + testis-determining factor + Tdy + "A protein that is a translation product of the human SRY gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000015643 + sex-determining region Y protein + + + "A protein that is a translation product of the human STAG3 gene or a 1:1 ortholog thereof." [PRO:DNx] + stromalin-3 + PR_EXT:cohesin subunit SA-3 + PR_EXT:000015706 + cohesin subunit SA-3 + stromal antigen 3 + STAG3 + SCC3 homolog 3 + + + "A protein that is a translation product of the human STOM gene or a 1:1 ortholog thereof." [PRO:DNx] + erythrocyte band 7 integral membrane protein + stomatin + protein 7.2b + EPB72 + STOM + BND7 + PR_EXT:erythrocyte band 7 integral membrane protein + PR_EXT:000015763 + Epb7.2 + + + "A protein that is a translation product of the human STX18 gene or a 1:1 ortholog thereof." [PRO:DNx] + STX18 + cell growth-inhibiting gene 9 protein + PR_EXT:000015790 + syntaxin-18 + PR_EXT:syntaxin-18 + + + C-alpha-formylglycine-generating enzyme 1 + FGE + SUMF1 + PR_EXT:sulfatase-modifying factor 1 + sulfatase-modifying factor 1 + PR_EXT:000015827 + "A protein that is a translation product of the human SUMF1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + SMT3H3 + PR_EXT:000015829 + SUMO1 + small ubiquitin-related modifier 1 + SMT3C + GAP-modifying protein 1 + UBL1 + PR_EXT:small ubiquitin-related modifier 1 + GMP1 + SMT3 homolog 3 + "A protein that is a translation product of the human SUMO1 gene or a 1:1 ortholog thereof." [PRO:DNx] + SUMO-1 + ubiquitin-like protein UBL1 + ubiquitin-homology domain protein PIC1 + ubiquitin-like protein SMT3C + sentrin + + + Sv2 + SV2A + PR_EXT:synaptic vesicle glycoprotein 2A + synaptic vesicle protein 2 + calcium regulator SV2A + "A protein that is a translation product of the human SV2A gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000015849 + KIAA0736 + synaptic vesicle glycoprotein 2A + synaptic vesicle protein 2A + + + synaptic vesicle protein 2C + PR_EXT:synaptic vesicle glycoprotein 2C + PR_EXT:000015851 + KIAA1054 + SV2C + "A protein that is a translation product of the human SV2C gene or a 1:1 ortholog thereof." [PRO:DNx] + synaptic vesicle glycoprotein 2C + + + PR_EXT:000015862 + SYCP1 + synaptonemal complex protein 1 + SCP1 + "A protein that is a translation product of the human SYCP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + CT8 + PR_EXT:synaptonemal complex protein 1 + SCP-1 + cancer/testis antigen 8 + + + SCP3 + synaptonemal complex protein 3 + SCP-3 + "A protein that is a translation product of the human SYCP3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:synaptonemal complex protein 3 + PR_EXT:000015865 + SYCP3 + + + SYN2 + PR_EXT:synapsin-2 + "A protein that is a translation product of the human SYN2 gene or a 1:1 ortholog thereof." [PRO:DNx] + synapsin-2 + PR_EXT:000015871 + synapsin II + + + synaptojanin-1 + PR_EXT:000015882 + PR_EXT:synaptojanin-1 + "A protein that is a translation product of the human SYNJ1 gene or a 1:1 ortholog thereof." [PRO:DNx] + synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 + SYNJ1 + KIAA0910 + + + PR_EXT:synaptophysin + synaptophysin + "A protein that is a translation product of the human SYP gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000015890 + BM89 antigen + SYP + major synaptic vesicle protein p38 + + + PR_EXT:synaptotagmin-1 + synaptotagmin-1 + "A protein that is a translation product of the human SYT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000015894 + SYT + synaptotagmin I + SYT1 + SVP65 + SytI + + + PR_EXT:synaptotagmin-4 + synaptotagmin-4 + SytIV + Syt3 + "A protein that is a translation product of the human SYT4 gene or a 1:1 ortholog thereof." [PRO:DNx] + synaptotagmin IV + PR_EXT:000015906 + SYT4 + KIAA1342 + + + Saa3 + "A protein that is a translation product of the mouse Saa3 gene or a 1:1 ortholog thereof." [PRO:DNx] + murine-type serum amyloid A-3 protein + PR_EXT:murine-type serum amyloid A-3 protein + PR_EXT:000015919 + + + delta(9)-desaturase 1 + PR_EXT:acyl-CoA desaturase 1 + Scd1 + stearoyl-CoA desaturase 1 + PR_EXT:000015921 + "A protein that is a translation product of the mouse Scd1 gene or a 1:1 ortholog thereof." [PRO:DNx] + acyl-CoA desaturase 1 + + + Sftpa1 + SP-A + PSP-A + Sftp1 + Sftpa + PR_EXT:pulmonary surfactant-associated protein A + Sftp-1 + "A protein that is a translation product of the mouse Sftpa1 gene or a 1:1 ortholog thereof." [PRO:DNx] + pulmonary surfactant-associated protein A + PR_EXT:000015945 + + + PR_EXT:solute carrier organic anion transporter family member 1A4 + Slc21a5 + solute carrier organic anion transporter family member 1A4 + sodium-independent organic anion-transporting polypeptide 2 + PR_EXT:000015966 + "A solute carrier organic anion transporter family member that is a translation product of the mouse Slco1a4 gene or a 1:1 ortholog thereof." [PRO:DNx] + Oatp2 + solute carrier family 21 member 5 + Slco1a4 + + + PR_EXT:brachyury protein + brachyury protein + T + "A protein that is a translation product of the human T gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000016001 + protein T + + + gastric cancer antigen Ga55 + TACC1 + transforming acidic coiled-coil-containing protein 1 + taxin-1 + "A protein that is a translation product of the human TACC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:transforming acidic coiled-coil-containing protein 1 + KIAA1103 + PR_EXT:000016006 + + + AZU-1 + transforming acidic coiled-coil-containing protein 2 + anti-Zuai-1 + "A protein that is a translation product of the human TACC2 gene or a 1:1 ortholog thereof." [PRO:DNx] + TACC2 + PR_EXT:transforming acidic coiled-coil-containing protein 2 + PR_EXT:000016007 + + + PR_EXT:000016008 + Aint + transforming acidic coiled-coil-containing protein 3 + ARNT-interacting protein + ERIC1 + PR_EXT:transforming acidic coiled-coil-containing protein 3 + TACC3 + "A protein that is a translation product of the human TACC3 gene or a 1:1 ortholog thereof." [PRO:DNx] + ERIC-1 + + + T-cell acute lymphocytic leukemia protein 1 + PR_EXT:T-cell acute lymphocytic leukemia protein 1 + SCL + stem cell protein + T-cell leukemia/lymphoma protein 5 + TCL5 + PR_EXT:000016043 + "A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + TAL-1 + TAL1 + bHLHa17 + class A basic helix-loop-helix protein 17 + + + TDP43 + TAR DNA-binding protein 43 + TDP-43 + TARDBP + PR_EXT:TAR DNA-binding protein 43 + "A protein that is a translation product of the human TARDBP gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000016057 + + + Sac + TR3 + PR_EXT:000016062 + T1R3 + PR_EXT:taste receptor type 1 member 3 + saccharin preference protein + TAS1R3 + "A taste receptor type 1 that is a translation product of the human TAS1R3 gene or a 1:1 ortholog thereof." [PRO:DNx] + sweet taste receptor T1R3 + taste receptor type 1 member 3 + + + "A protein that is a translation product of the human TBX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + T-box protein 1 + TBX1 + PR_EXT:T-box transcription factor TBX1 + PR_EXT:000016143 + testis-specific T-box protein + T-box transcription factor TBX1 + + + T-box transcription factor TBX14 + PR_EXT:000016145 + TBX14 + "A protein that is a translation product of the human TBX15 gene or a 1:1 ortholog thereof." [PRO:DNx] + TBX15 + Tbx8 + T-box protein 14 + MmTBx8 + T-box protein 15 + PR_EXT:T-box transcription factor TBX15 + T-box transcription factor TBX15 + + + T-box transcription factor TBX18 + T-box protein 18 + "A protein that is a translation product of the human TBX18 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:T-box transcription factor TBX18 + TBX18 + PR_EXT:000016146 + + + PR_EXT:T-box transcription factor TBX22 + T-box protein 22 + TBX22 + T-box transcription factor TBX22 + PR_EXT:000016150 + "A protein that is a translation product of the human TBX22 gene or a 1:1 ortholog thereof." [PRO:DNx] + TBOX22 + + + "A protein that is a translation product of the human TBX6 gene or a 1:1 ortholog thereof." [PRO:DNx] + T-box transcription factor TBX6 + PR_EXT:000016154 + PR_EXT:T-box transcription factor TBX6 + T-box protein 6 + TBX6 + + + T-cell leukemia translocation-altered gene protein + T-cell leukemia translocation-associated gene protein + TCTA + PR_EXT:000016206 + "A protein that is a translation product of the human TCTA gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:T-cell leukemia translocation-altered gene protein + + + TERF2 + PR_EXT:000016236 + "A protein that is a translation product of the human TERF2 gene or a 1:1 ortholog thereof." [PRO:DNx] + TRBF2 + telomeric repeat-binding factor 2 + PR_EXT:telomeric repeat-binding factor 2 + TTAGGG repeat-binding factor 2 + TRF2 + telomeric DNA-binding protein + + + transferrin + PR_EXT:serotransferrin + siderophilin + TF + PR_EXT:000016261 + Trf + serotransferrin + beta-1 metal-binding globulin + "A protein that is a translation product of the human TF gene or a 1:1 ortholog thereof." [PRO:DNx] + + + mitochondrial transcription factor 1 + PR_EXT:transcription factor A, mitochondrial + transcription factor 6-like 2 + transcription factor A, mitochondrial + mtTFA + TFAM + TCF-6 + Hmgts + transcription factor 6 + TS-HMG + TCF6 + MtTF1 + "A protein that is a translation product of the human TFAM gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000016262 + TCF6L2 + testis-specific high mobility group protein + + + transcription factor Dp-1 + DRTF1-polypeptide 1 + PR_EXT:transcription factor Dp-1 + PR_EXT:000016269 + "A protein that is a translation product of the human TFDP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + TFDP1 + DRTF1 + E2F dimerization partner 1 + DP1 + + + "A protein that is a translation product of the human TGFA gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:protransforming growth factor alpha + PR_EXT:000016285 + TGFA + protransforming growth factor alpha + + + TGase H + TGase-2 + TGC + PR_EXT:000016293 + tissue transglutaminase + TG(C) + transglutaminase-2 + TGM2 + transglutaminase C + TGase C + PR_EXT:protein-glutamine gamma-glutamyltransferase 2 + protein-glutamine gamma-glutamyltransferase 2 + "A protein-glutamine gamma-glutamyltransferase that is a translation product of the human TGM2 gene or a 1:1 ortholog thereof." [PRO:DNx] + transglutaminase H + + + bZIP-enhancing factor BEF + BEF + Ref1 + Ally of AML-1 and LEF-1 + THO complex subunit 4 + ALYREF + RNA and export factor-binding protein 1 + "A protein that is a translation product of the human ALYREF gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:THO complex subunit 4 + ALY + PR_EXT:000016313 + THOC4 + REF1-I + tho4 + Refbp1 + transcriptional coactivator Aly/REF + + + nuclear receptor subfamily 1 group A member 2 + THR1 + THRB + "A protein that is a translation product of the human THRB gene or a 1:1 ortholog thereof." [PRO:DNx] + ERBA2 + PR_EXT:thyroid hormone receptor beta + PR_EXT:000016321 + c-erbA-2 + NR1A2 + c-erbA-beta + thyroid hormone receptor beta + + + "A protein that is a translation product of the human THRSP gene or a 1:1 ortholog thereof." [PRO:DNx] + SPOT14 + spot 14 protein + PR_EXT:thyroid hormone-inducible hepatic protein + THRSP + S14 + thyroid hormone-inducible hepatic protein + PR_EXT:000016322 + + + TIM1 + TIM + TIMELESS1 + PR_EXT:000016340 + mTim + PR_EXT:protein timeless + "A protein that is a translation product of the human TIMELESS gene or a 1:1 ortholog thereof." [PRO:DNx] + TIMELESS + protein timeless + + + PR_EXT:000016364 + zona occludens protein 1 + tight junction protein 1 + PR_EXT:tight junction protein ZO-1 + TJP1 + "A protein that is a translation product of the human TJP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + ZO1 + zonula occludens protein 1 + tight junction protein ZO-1 + + + zona occludens protein 2 + PR_EXT:tight junction protein ZO-2 + tight junction protein 2 + tight junction protein ZO-2 + X104 + ZO2 + PR_EXT:000016365 + TJP2 + "A protein that is a translation product of the human TJP2 gene or a 1:1 ortholog thereof." [PRO:DNx] + zonula occludens protein 2 + + + hexabrachion + GP 150-225 + JI + TN-C + HXB + tenascin + cytotactin + neuronectin + TNC + TN + PR_EXT:000016471 + myotendinous antigen + PR_EXT:tenascin + glioma-associated-extracellular matrix antigen + GMEM + tenascin-C + "A protein that is a translation product of the human TNC gene or a 1:1 ortholog thereof." [PRO:DNx] + + + troponin I, slow-twitch isoform + PR_EXT:troponin I, slow skeletal muscle + "A protein that is a translation product of the human TNNI1 gene or a 1:1 ortholog thereof." [PRO:DNx] + troponin I, slow skeletal muscle + TNNI1 + PR_EXT:000016504 + + + PR_EXT:troponin I, fast skeletal muscle + "A protein that is a translation product of the human TNNI2 gene or a 1:1 ortholog thereof." [PRO:DNx] + troponin I, fast skeletal muscle + troponin I, fast-twitch isoform + TNNI2 + PR_EXT:000016505 + + + ETR-1 + RNA-binding protein BRUNOL-1 + CAG repeat protein 4 + expanded repeat domain protein CAG/CTG 4 + bruno-like protein 1 + trinucleotide repeat-containing gene 4 protein + CELF3 + ERDA4 + TNRC4 + BRUNOL1 + CUGBP Elav-like family member 3 + CELF-3 + ELAV-type RNA-binding protein 1 + "A protein that is a translation product of the human CELF3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:CUGBP Elav-like family member 3 + PR_EXT:000016517 + CAGH4 + + + PR_EXT:000016548 + DNA topoisomerase II-binding protein 1 + DNA topoisomerase 2-binding protein 1 + PR_EXT:DNA topoisomerase 2-binding protein 1 + TOPBP1 + TopBP1 + DNA topoisomerase II-beta-binding protein 1 + "A protein that is a translation product of the human TOPBP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + KIAA0259 + + + KET + P73H + CUSP + keratinocyte transcription factor KET + transformation-related protein 63 + TP73L + PR_EXT:000016567 + Trp63 + "A protein that is a translation product of the human TP63 gene or a 1:1 ortholog thereof." [PRO:DNx] + TP63 + p73L + PR_EXT:tumor protein 63 + tumor protein 63 + chronic ulcerative stomatitis protein + tumor protein p73-like + + + P73 + tumor protein p73 + p53-related protein + "A protein that is a translation product of the human TP73 gene or a 1:1 ortholog thereof." [PRO:DNx] + p53-like transcription factor + PR_EXT:tumor protein p73 + PR_EXT:000016568 + Trp73 + TP73 + + + tropomyosin-1 + "A protein that is a translation product of the human TPM1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Tpm-1 + TMSA + TPM1 + PR_EXT:tropomyosin alpha-1 chain + Tpma + PR_EXT:000016579 + tropomyosin alpha-1 chain + alpha-tropomyosin + C15orf13 + + + tripeptidyl-peptidase I + TPP1 + LPIC + PR_EXT:tripeptidyl-peptidase 1 + TPP-I + lysosomal pepstatin-insensitive protease + PR_EXT:000016585 + CLN2 + "A protein that is a translation product of the human TPP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + cell growth-inhibiting gene 1 protein + tripeptidyl-peptidase 1 + TPP-1 + + + RING finger protein 92 + tripartite motif-containing protein 11 + RNF92 + PR_EXT:000016642 + E3 ubiquitin-protein ligase TRIM11 + protein BIA1 + PR_EXT:E3 ubiquitin-protein ligase TRIM11 + TRIM11 + "A protein that is a translation product of the human TRIM11 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + TRIM24 + transcription intermediary factor 1-alpha + TIF1 + tripartite motif-containing protein 24 + TIF1A + TIF1-alpha + RNF82 + PR_EXT:000016649 + PR_EXT:transcription intermediary factor 1-alpha + "A protein that is a translation product of the human TRIM24 gene or a 1:1 ortholog thereof." [PRO:DNx] + RING finger protein 82 + + + PR_EXT:000016650 + TRIM25 + PR_EXT:E3 ubiquitin/ISG15 ligase TRIM25 + estrogen-responsive finger protein + zinc finger protein 147 + ZNF147 + RING finger protein 147 + tripartite motif-containing protein 25 + Zfp147 + EFP + ubiquitin/ISG15-conjugating enzyme TRIM25 + "A protein that is a translation product of the human TRIM25 gene or a 1:1 ortholog thereof." [PRO:DNx] + E3 ubiquitin/ISG15 ligase TRIM25 + RNF147 + + + RNF76 + ret finger protein + PR_EXT:000016651 + RFP + zinc finger protein RFP + TRIM27 + "A protein that is a translation product of the human TRIM27 gene or a 1:1 ortholog thereof." [PRO:DNx] + tripartite motif-containing protein 27 + RING finger protein 76 + PR_EXT:zinc finger protein RFP + + + nuclear corepressor KAP-1 + PR_EXT:000016652 + TRIM28 + transcription intermediary factor 1-beta + KAP1 + KRAB-associated protein 1 + KAP-1 + KRAB-A-interacting protein + RING finger protein 96 + KRAB-interacting protein 1 + TIF1-beta + tripartite motif-containing protein 28 + Krip1 + KRIP-1 + TIF1B + "A protein that is a translation product of the human TRIM28 gene or a 1:1 ortholog thereof." [PRO:DNx] + RNF96 + PR_EXT:transcription intermediary factor 1-beta + + + PR_EXT:000016653 + tripartite motif-containing protein 29 + PR_EXT:tripartite motif-containing protein 29 + TRIM29 + "A protein that is a translation product of the human TRIM29 gene or a 1:1 ortholog thereof." [PRO:DNx] + ATDC + ataxia telangiectasia group D-associated protein + + + KIAA1113 + PR_EXT:000016655 + ectodermin homolog + RET-fused gene 7 protein + TIF1-gamma + transcription intermediary factor 1-gamma + protein Rfg7 + TRIM33 + PR_EXT:E3 ubiquitin-protein ligase TRIM33 + TIF1G + "A protein that is a translation product of the human TRIM33 gene or a 1:1 ortholog thereof." [PRO:DNx] + tripartite motif-containing protein 33 + RFG7 + E3 ubiquitin-protein ligase TRIM33 + + + RING finger protein 88 + PR_EXT:000016660 + tripartite motif-containing protein 5 + PR_EXT:tripartite motif-containing protein 5 + "A protein that is a translation product of the human TRIM5 gene or a 1:1 ortholog thereof." [PRO:DNx] + RNF88 + TRIM5 + + + thyroid hormone receptor interactor 13 + 16E1-BP + PR_EXT:000016672 + TRIP-13 + thyroid receptor-interacting protein 13 + human papillomavirus type 16 E1 protein-binding protein + TRIP13 + HPV16 E1 protein-binding protein + TR-interacting protein 13 + PR_EXT:thyroid receptor-interacting protein 13 + "A protein that is a translation product of the human TRIP13 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + TTR + ATTR + prealbumin + "A protein that is a translation product of the human TTR gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:transthyretin + PALB + transthyretin + PR_EXT:000016801 + + + tubulin beta-4 chain + TUBB3 + PR_EXT:tubulin beta-3 chain + tubulin beta-III + tubulin beta-3 chain + "A tubulin that is a translation product of the human TUBB3 gene or a 1:1 ortholog thereof." [PRO:DNx] + TUBB4 + PR_EXT:000016819 + + + gene associated with retinoic and IFN-induced mortality 12 protein + "A protein that is a translation product of the human TXNRD1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Trxr1 + thioredoxin reductase 1, cytoplasmic + TR + GRIM12 + KM-102-derived reductase-like factor + GRIM-12 + gene associated with retinoic and interferon-induced mortality 12 protein + TXNRD1 + PR_EXT:thioredoxin reductase 1, cytoplasmic + thioredoxin reductase TR1 + KDRF + PR_EXT:000016871 + + + PR_EXT:000016890 + PR_EXT:taste receptor type 2 member 103 + T2R10 + Tas2r103 + "A protein that is a translation product of the mouse Tas2r103 gene or a 1:1 ortholog thereof." [PRO:DNx] + Tas2r10 + taste receptor type 2 member 103 + T2R103 + taste receptor type 2 member 10 + taste receptor family B member 2 + TRB2 + + + PR_EXT:taste receptor type 2 member 104 + T2r45 + Tas2r104 + "A protein that is a translation product of the mouse Tas2r104 gene or a 1:1 ortholog thereof." [PRO:DNx] + taste receptor type 2 member 104 + T2R104 + PR_EXT:000016891 + + + PR_EXT:taste receptor type 2 member 105 + taste receptor type 2 member 5 + T2R9 + "A protein that is a translation product of the mouse Tas2r105 gene or a 1:1 ortholog thereof." [PRO:DNx] + taste receptor type 2 member 105 + Tas2r9 + T2R105 + T2R5 + Tas2r105 + Tas2r5 + PR_EXT:000016892 + taste receptor type 2 member 9 + + + PR_EXT:000016893 + "A protein that is a translation product of the mouse Tas2r106 gene or a 1:1 ortholog thereof." [PRO:DNx] + taste receptor type 2 member 106 + T2r44 + Tas2r106 + PR_EXT:taste receptor type 2 member 106 + T2R106 + + + STC 9-1 + PR_EXT:000016896 + T2R110 + Tas2r110 + PR_EXT:taste receptor type 2 member 110 + taste receptor type 2 member 110 + "A protein that is a translation product of the mouse Tas2r110 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + T2r46 + "A protein that is a translation product of the mouse Tas2r114 gene or a 1:1 ortholog thereof." [PRO:DNx] + taste receptor type 2 member 114 + PR_EXT:000016898 + PR_EXT:taste receptor type 2 member 114 + Tas2r114 + T2R114 + + + T2r56 + taste receptor type 2 member 116 + "A protein that is a translation product of the mouse Tas2r116 gene or a 1:1 ortholog thereof." [PRO:DNx] + TRB4 + TRB1 + PR_EXT:000016899 + T2R116 + Tas2r116 + PR_EXT:taste receptor type 2 member 116 + + + T2r54 + "A protein that is a translation product of the mouse Tas2r117 gene or a 1:1 ortholog thereof." [PRO:DNx] + taste receptor type 2 member 117 + PR_EXT:000016900 + T2R117 + Tas2r117 + PR_EXT:taste receptor type 2 member 117 + + + T2R120 + taste receptor type 2 member 120 + PR_EXT:taste receptor type 2 member 120 + Tas2r120 + PR_EXT:000016902 + T2r47 + "A protein that is a translation product of the mouse Tas2r120 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + Tas2r124 + taste receptor type 2 member 124 + T2r50 + PR_EXT:000016904 + PR_EXT:taste receptor type 2 member 124 + "A protein that is a translation product of the mouse Tas2r124 gene or a 1:1 ortholog thereof." [PRO:DNx] + T2R124 + + + Tpbpa + trophoblast-specific protein alpha + Tpbp + PR_EXT:trophoblast-specific protein alpha + "A protein that is a translation product of the mouse Tpbpa gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000016934 + + + U2 auxiliary factor 35 kDa subunit + PR_EXT:000016944 + U2AFBP + PR_EXT:splicing factor U2AF 35 kDa subunit + splicing factor U2AF 35 kDa subunit + "A protein that is a translation product of the human U2AF1 gene or a 1:1 ortholog thereof." [PRO:DNx] + U2AF1 + U2 snRNP auxiliary factor small subunit + U2AF35 + + + ubiquitin-conjugating enzyme E2 I + ubiquitin-protein ligase I + PR_EXT:000016977 + UBE2I + SUMO-protein ligase + SUMO-conjugating enzyme UBC9 + ubiquitin carrier protein I + UBCE9 + Ubce2i + ubiquitin carrier protein 9 + UBC9 + "A protein that is a translation product of the human UBE2I gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:SUMO-conjugating enzyme UBC9 + + + KIAA0860 + RNF37 + PR_EXT:RING finger protein 37 + UBOX5 + PR_EXT:000017005 + RING finger protein 37 + Uip5 + UBCE7IP5 + ubiquitin-conjugating enzyme 7-interacting protein 5 + "A protein that is a translation product of the human UBOX5 gene or a 1:1 ortholog thereof." [PRO:DNx] + UbcM4-interacting protein 5 + U-box domain-containing protein 5 + + + ubiquitin-protein ligase E3-alpha-I + PR_EXT:E3 ubiquitin-protein ligase UBR1 + N-recognin-1 + UBR1 + E3 ubiquitin-protein ligase UBR1 + ubiquitin-protein ligase E3-alpha-1 + "A protein that is a translation product of the human UBR1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000017012 + + + PR_EXT:000017035 + mitochondrial brown fat uncoupling protein 1 + "A protein that is a translation product of the human UCP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + SLC25A7 + UCP + PR_EXT:mitochondrial brown fat uncoupling protein 1 + UCP1 + solute carrier family 25 member 7 + UCP 1 + thermogenin + + + mitochondrial uncoupling protein 2 + "A protein that is a translation product of the human UCP2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000017036 + solute carrier family 25 member 8 + UCPH + PR_EXT:mitochondrial uncoupling protein 2 + UCP 2 + SLC25A8 + UCP2 + + + retinal protein 4 + Unc119h + "A protein that is a translation product of the human UNC119 gene or a 1:1 ortholog thereof." [PRO:DNx] + RG4 + UNC119 + PR_EXT:protein unc-119 homolog A + protein unc-119 homolog A + PR_EXT:000017084 + + + PR_EXT:000017268 + "A protein that is a translation product of the human VAX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + ventral anterior homeobox 1 + PR_EXT:ventral anterior homeobox 1 + VAX1 + + + VEGFA + VEGF-A + PR_EXT:000017284 + PR_EXT:vascular endothelial growth factor A + vascular permeability factor + VPF + "A protein that is a translation product of the human VEGFA gene or a 1:1 ortholog thereof." [PRO:DNx] + VEGF + vascular endothelial growth factor A + + + villin-1 + VIL1 + "A protein that is a translation product of the human VIL1 gene or a 1:1 ortholog thereof." [PRO:DNx] + VIL + PR_EXT:villin-1 + PR_EXT:000017296 + + + PR_EXT:000017298 + VIM + "A protein that is a translation product of the human VIM gene or a 1:1 ortholog thereof." [PRO:DNx] + vimentin + PR_EXT:vimentin + + + RINX + "A protein that is a translation product of the human VSX1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:visual system homeobox 1 + retinal inner nuclear layer homeobox protein + VSX1 + visual system homeobox 1 + homeodomain protein RINX + PR_EXT:000017354 + transcription factor VSX1 + + + PR_EXT:visual system homeobox 2 + "A protein that is a translation product of the human VSX2 gene or a 1:1 ortholog thereof." [PRO:DNx] + visual system homeobox 2 + homeobox protein CHX10 + Ceh-10 homeodomain-containing homolog + PR_EXT:000017355 + VSX2 + HOX10 + CHX10 + + + von Willebrand factor + "A protein that is a translation product of the human VWF gene or a 1:1 ortholog thereof." [PRO:DNx] + VWF + PR_EXT:000017364 + vWF + PR_EXT:von Willebrand factor + F8VWF + + + tryptophanyl-tRNA synthetase, mitochondrial + "A protein that is a translation product of the human WARS2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000017370 + WARS2 + tryptophan--tRNA ligase, mitochondrial + (Mt)TrpRS + PR_EXT:tryptophan--tRNA ligase, mitochondrial + + + NORI-1 + WDR1 + PR_EXT:WD repeat-containing protein 1 + actin-interacting protein 1 + PR_EXT:000017387 + WD repeat-containing protein 1 + AIP1 + "A protein that is a translation product of the human WDR1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + WISP-1 + Wnt-1-induced secreted protein + WISP1 + PR_EXT:000017426 + "An IGFBP-related protein that is a translation product of the human WISP1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:WNT1-inducible-signaling pathway protein 1 + CCN family member 4 + Elm1 + ELM-1 + WNT1-inducible-signaling pathway protein 1 + CCN4 + + + proto-oncogene Wnt-1 + Int-1 + INT1 + Wnt-1 + PR_EXT:000017435 + proto-oncogene protein Wnt-1 + proto-oncogene Int-1 + WNT1 + proto-oncogene Int-1 homolog + PR_EXT:proto-oncogene Wnt-1 + "A protein that is a translation product of the human WNT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:protein Wnt-11 + Wnt-11 + "A protein that is a translation product of the human WNT11 gene or a 1:1 ortholog thereof." [PRO:DNx] + protein Wnt-11 + PR_EXT:000017438 + WNT11 + + + Int-4 + WNT3 + proto-oncogene Int-4 homolog + PR_EXT:000017442 + INT4 + Wnt-3 + proto-oncogene protein Wnt-3 + proto-oncogene Int-4 + proto-oncogene Wnt-3 + "A protein that is a translation product of the human WNT3 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:proto-oncogene Wnt-3 + + + PR_EXT:000017443 + WNT3A + Wnt-3a + PR_EXT:protein Wnt-3a + "A protein that is a translation product of the human WNT3A gene or a 1:1 ortholog thereof." [PRO:DNx] + protein Wnt-3a + + + WNT4 + PR_EXT:000017444 + PR_EXT:protein Wnt-4 + Wnt-4 + protein Wnt-4 + "A protein that is a translation product of the human WNT4 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + protein Wnt-7a + PR_EXT:000017448 + WNT7A + Wnt-7a + PR_EXT:protein Wnt-7a + "A protein that is a translation product of the human WNT7A gene or a 1:1 ortholog thereof." [PRO:DNx] + + + protein Wnt-7b + Wnt-7b + WNT7B + PR_EXT:protein Wnt-7b + "A protein that is a translation product of the human WNT7B gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000017449 + + + WNT9A + WNT14 + PR_EXT:000017452 + protein Wnt-9a + PR_EXT:protein Wnt-9a + protein Wnt-14 + "A protein that is a translation product of the human WNT9A gene or a 1:1 ortholog thereof." [PRO:DNx] + + + WNT9B + WNT14B + WNT15 + PR_EXT:000017453 + protein Wnt-9b + protein Wnt-14b + protein Wnt-15 + PR_EXT:protein Wnt-9b + "A protein that is a translation product of the human WNT9B gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000017459 + Wt-1 + Wilms tumor protein + WT1 + "A protein that is a translation product of the human WT1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:Wilms tumor protein + WT33 + + + XPAC + XPA + PR_EXT:000017493 + xeroderma pigmentosum group A-complementing protein + PR_EXT:DNA repair protein complementing XP-A cells + xeroderma pigmentosum group A-complementing protein homolog + DNA repair protein complementing XP-A cells + "A protein that is a translation product of the human XPA gene or a 1:1 ortholog thereof." [PRO:DNx] + + + XPCC + xeroderma pigmentosum group C-complementing protein homolog + PR_EXT:000017494 + PR_EXT:DNA repair protein complementing XP-C cells + DNA repair protein complementing XP-C cells + xeroderma pigmentosum group C-complementing protein + "A protein that is a translation product of the human XPC gene or a 1:1 ortholog thereof." [PRO:DNx] + XPC + + + PR_EXT:exportin-1 + chromosome region maintenance 1 protein homolog + exp1 + exportin-1 + PR_EXT:000017497 + CRM1 + XPO1 + "A protein that is a translation product of the human XPO1 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + X-ray repair cross-complementing protein 1 + DNA repair protein XRCC1 + PR_EXT:000017504 + "A protein that is a translation product of the human XRCC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + Xrcc-1 + PR_EXT:DNA repair protein XRCC1 + XRCC1 + + + X-ray repair cross-complementing protein 2 + PR_EXT:000017505 + "A protein that is a translation product of the human XRCC2 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:DNA repair protein XRCC2 + DNA repair protein XRCC2 + XRCC2 + + + "A protein that is a translation product of the human XRCC3 gene or a 1:1 ortholog thereof." [PRO:DNx] + X-ray repair cross-complementing protein 3 + PR_EXT:000017506 + XRCC3 + PR_EXT:DNA repair protein XRCC3 + DNA repair protein XRCC3 + + + Ku70 + CTCBF + thyroid-lupus autoantigen + XRCC6 + ATP-dependent DNA helicase II 70 kDa subunit + TLAA + 70 kDa subunit of Ku antigen + X-ray repair cross-complementing protein 6 + PR_EXT:X-ray repair cross-complementing protein 6 + PR_EXT:000017509 + CTC75 + CTC box-binding factor 75 kDa subunit + lupus Ku autoantigen protein p70 + Ku autoantigen protein p70 homolog + "A protein that is a translation product of the human XRCC6 gene or a 1:1 ortholog thereof." [PRO:DNx] + G22P1 + DNA repair protein XRCC6 + + + YEATS domain-containing protein 4 + PR_EXT:YEATS domain-containing protein 4 + NuBI1 + NuBI-1 + PR_EXT:000017527 + glioma-amplified sequence 41 + YEATS4 + NuMA-binding protein 1 + gas41 + "A protein that is a translation product of the human YEATS4 gene or a 1:1 ortholog thereof." [PRO:DNx] + + + "A protein that is a translation product of the human ZFPM2 gene or a 1:1 ortholog thereof." [PRO:DNx] + friend of GATA protein 2 + FOG-2 + zinc finger protein multitype 2 + FOG2 + friend of GATA 2 + zinc finger protein ZFPM2 + PR_EXT:zinc finger protein ZFPM2 + ZFPM2 + PR_EXT:000017653 + + + PR_EXT:zinc finger Y-chromosomal protein + zinc finger Y-chromosomal protein + ZFY + PR_EXT:000017657 + "A protein that is a translation product of the human ZFY gene or a 1:1 ortholog thereof." [PRO:DNx] + + + ZBP89 + zinc finger DNA-binding protein 89 + transcription factor ZBP-89 + transcription factor BFCOL1 + G-rich box-binding protein + PR_EXT:000017718 + ZNF148 + Zfp148 + "A protein that is a translation product of the human ZNF148 gene or a 1:1 ortholog thereof." [PRO:DNx] + beta enolase repressor factor 1 + zinc finger protein 148 + PR_EXT:zinc finger protein 148 + + + PR_EXT:000018212 + "A protein that is a translation product of the human ZP3 gene or a 1:1 ortholog thereof." [PRO:DNx] + zona pellucida glycoprotein 3 + zona pellucida sperm-binding protein 3 + sperm receptor + ZP3B + ZP3 + Zp-3 + ZP3A + PR_EXT:zona pellucida sperm-binding protein 3 + zona pellucida protein C + ZP3A/ZP3B + ZPC + + + zyxin-2 + "A protein that is a translation product of the human ZYX gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:zyxin + ZYX + PR_EXT:000018242 + zyxin + + + amino acid chain + "An organic amino compound that is a polymer of amino acid chain components (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds." [PRO:DAN, PRO:JSG] + PR_EXT:amino acid chain + PR_EXT:000018263 + + + "An amino acid chain that is produced as the result of peptide bond cleavage of a longer amino acid chain." [PRO:DAN] + PR_EXT:proteolytic cleavage product + proteolytic cleavage product + PR_EXT:000018264 + + + PR_EXT:000018762 + PR_EXT:caspase-3 proteolytic cleavage product + CASP3/ClvPrd + "A proteolytic cleavage product that is derived from caspase-3." [PRO:DNx] + caspase-3 proteolytic cleavage product + + + SHH/Full + PR_EXT:sonic hedgehog protein, full-length form + sonic hedgehog protein, full-length form + PR_EXT:000021466 + "A sonic hedgehog protein that contains all the amino acids specified by its template mRNA." [PRO:DNx] + + + PR_EXT:TRK receptor + TRK receptor + "A protein that is a tyrosine kinase receptor that is activated by dimerization, resulting in autophosphorylation of intracellular tyrosine residues and triggering of the signal transduction cascade." [PMID:10388563] + PR_EXT:000021997 + + + "A protein that is a neurotrophic polypeptide factor that regulates neuronal differentiation and is essential for neuronal survival, neurite growth and plasticity. It contains a signal peptide, a propeptide, and a C-terminal Nerve growth factor family (Pfam:PF00243) domain." [PMID:10388563] + PR_EXT:neurotrophin + neurotrophin + PR_EXT:000021998 + + + "A protein that contains multiple TNFR/NGFR cysteine-rich region (Pfam:PF00020) within the extracellular ligand-binding domain, a type I (single pass) transmembrane domain, and a cytoplasmic Death domain (Pfam:PF00531) required for intracellular signaling." [PMID:12655292] + death receptor + PR_EXT:000021999 + PR_EXT:death receptor + + + uncE + ATP synthase F(0) sector subunit c + F-type ATPase subunit c + papH + lipid-binding protein + ATP synthase subunit c + atpE + F-ATPase subunit c + PR_EXT:ATP synthase subunit c + PR_EXT:000022190 + "A protein that is a translation product of the Escherichia coli K-12 atpE gene or a 1:1 ortholog thereof." [PRO:DNx] + dicyclohexylcarbodiimide-binding protein + + + PR_EXT:ATP-dependent Clp protease ATP-binding subunit ClpA + ATP-dependent Clp protease ATP-binding subunit ClpA + PR_EXT:000022296 + clpA + "A protein that is a translation product of the Escherichia coli K-12 clpA gene or a 1:1 ortholog thereof." [PRO:DNx] + lopD + + + PR_EXT:magnesium transport protein CorA + "A protein that is a translation product of the Escherichia coli K-12 corA gene or a 1:1 ortholog thereof." [PRO:DNx] + magnesium transport protein CorA + PR_EXT:000022320 + corA + + + corC + "A protein that is a translation product of the Escherichia coli K-12 corC gene or a 1:1 ortholog thereof." [PRO:DNx] + magnesium and cobalt efflux protein CorC + ybeX + PR_EXT:magnesium and cobalt efflux protein CorC + PR_EXT:000022321 + + + PR_EXT:000022460 + grpA + groP + replicative DNA helicase + PR_EXT:replicative DNA helicase + dnaB + "A protein that is a translation product of the Escherichia coli K-12 dnaB gene or a 1:1 ortholog thereof." [PRO:DNx] + + + flaF + hag + flagellin FliC + "A protein that is a translation product of the Escherichia coli K-12 fliC gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:flagellin FliC + PR_EXT:000022655 + fliC + + + PR_EXT:LexA repressor + "A protein that is a translation product of the Escherichia coli K-12 lexA gene or a 1:1 ortholog thereof." [PRO:DNx] + tsl + LexA repressor + PR_EXT:000023087 + lexA + exrA + spr + umuA + + + ompC + par + PR_EXT:000023451 + porin ompC + outer membrane protein C + PR_EXT:outer membrane protein C + outer membrane protein 1B + meoA + "A protein that is a translation product of the Escherichia coli K-12 ompC gene or a 1:1 ortholog thereof." [PRO:DNx] + + + primosomal protein N' + priA + PR_EXT:000023591 + PR_EXT:primosomal protein N' + ATP-dependent helicase priA + replication factor Y + "A protein that is a translation product of the Escherichia coli K-12 priA gene or a 1:1 ortholog thereof." [PRO:DNx] + + + protein RecA + recH + lexB + recombinase A + umuB + PR_EXT:000023696 + rnmB + tif + recA + zab + PR_EXT:protein RecA + "A protein that is a translation product of the Escherichia coli K-12 recA gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000024938 + interferon alpha + fam:IFNA + PR_EXT:interferon alpha + + + interferon beta + PR_EXT:interferon beta + IFNB + PR_EXT:000024939 + + + PR_EXT:type II interferon + IFN type II + "A protein that binds to a specific cell surface receptor complex known as the IFN-gamma receptor (IFNGR), a complex of two IFNGR1 and two IFNGR2 chains." [PMID:9607096, PRO:DAN, PRO:MSY] + type II interferon + interferon gamma + PR_EXT:000024990 + interferon type II + + + PR_EXT:HSPB protein + PR_EXT:000025349 + sHSP + HSPB protein + "An hsp70 family chaperone that contains a crystallin domain." [PMID:18663603, PRO:DAN] + small heat shock protein + + + PR_EXT:HSPC protein + PR_EXT:000025350 + "An hsp70 family chaperone that contains an ATPase and HSP90 domains." [PMID:18663603, PRO:DAN] + HSP90 + HSPC protein + + + cytochrome c oxidase subunit 2 + MT-CO2 + MTCO2 + PR_EXT:000025365 + PR_EXT:cytochrome c oxidase subunit 2 + "A protein that is a translation product of the human MT-CO2 gene or a 1:1 ortholog thereof." [PRO:CNA] + + + PR_EXT:000025471 + PR_EXT:nuclease S1 + nucS + deoxyribonuclease S1 + "A protein that is a translation product of the Aspergillus oryzae nucS gene or a 1:1 ortholog thereof." [PRO:DAN] + endonuclease S1 + nuclease S1 + single-stranded-nucleate endonuclease + + + "A CD55-like protein that is a translation product of the human CD55 gene or a 1:1 ortholog thereof." [PRO:DAN] + DAF + Daf2 + CD55 + CD55 antigen + Daf1 + PR_EXT:complement decay-accelerating factor + complement decay-accelerating factor + CR + Complement decay-accelerating factor + Cd55a + PR_EXT:000025662 + + + "A protein with core domain composition consisting of an N-termianl FERM domain, followed by a copy of the SH2 domain (Pfam:PF00017), and two copies of the Protein tyrosine kinase (Pfam:PF07714) domain. Janus kinase is a non-receptor tyrosine kinase." [PMID:15575979] + PR_EXT:000025748 + Janus kinase + PR_EXT:Janus kinase + + + PR_EXT:integrin alpha + "A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif." [PMID:19693543] + PR_EXT:000025796 + integrin alpha + + + "An integrin alpha that lacks an A domain. This type of integrin is often cleaved into heavy and light chains." [PRO:DAN] + integrin alpha lacking A domain + PR_EXT:000025797 + PR_EXT:integrin alpha lacking A domain + + + PR_EXT:solute carrier organic anion transporter family member + PR_EXT:000025823 + "A protein that contains an OATP domain (Pfam:PF03137) and a Kazal-type serine protease inhibitor domain (Pfam:PF07648)." [PRO:DAN] + solute carrier organic anion transporter family member + + + "A protein that contains a copy of the Regulator of G protein signaling domain (Pfam:PF00615), followed by a copy of the Axin beta-catenin binding domain (Pfam:PF08833) and a C-terminal copy of the DIX domain (Pfam:PF00778). Axins play key roles in WNT signalling." [PMID:15067197, PMID:17404597, PMID:19909509, PRO:CNA] + axin + fam:axin + PR_EXT:000025824 + PR_EXT:axin + axis inhibition protein + + + PR_EXT:single domain alpha-type carbonic anhydrase + PR_EXT:000025841 + "A protein that contains a single copy of the Eukaryotic-type carbonic anhydrase domain (Pfam:PF00194) with no other conserved domains." [PRO:DAN] + single domain alpha-type carbonic anhydrase + + + PR_EXT:000025844 + ephrin + PR_EXT:ephrin + "A protein that consists solely of the Ephrin domain (Pfam:PF00812) near the N terminus followed by about 70 amino acids." [PRO:DAN] + + + ephrin receptor + PR_EXT:ephrin receptor + PR_EXT:000025845 + "A protein that consists of an Ephrin receptor ligand binding domain (Pfam:PF01404), two copies of the Fibronectin type III domain (Pfam:PF00041), and a copy of either type of SAM domain (Sterile alpha motif) (Pfam:PF00536 or Pfam:PF07647)." [PRO:DAN] + + + "A protein that consists solely of the Lipocalin / cytosolic fatty-acid binding protein family domain (Pfam:PF00061)." [PRO:DAN] + PR_EXT:000025846 + fatty acid-binding protein + PR_EXT:fatty acid-binding protein + + + IFN type I + "A protein that consists solely of an Interferon alpha/beta domain (Pfam:PF00143) and which binds to a specific cell surface receptor complex known as the IFN-alpha receptor (IFNAR), a heterodimer of IFNAR1 and IFNAR2 chains." [PMID:15233997, PMID:9607096, PRO:DAN, PRO:MSY] + type I interferon + PR_EXT:000025848 + interferon type I + PR_EXT:type I interferon + + + BAG1/iso:BAG-1L + "A BAG family molecular chaperone regulator 1 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:Q60739-1 or a 1:1 ortholog thereof." [PMID:9679980, PRO:CNA] + BAG family molecular chaperone regulator 1 isoform BAG-1L + BAG-1 p50 + PR_EXT:000025855 + PR_EXT:BAG family molecular chaperone regulator 1 isoform BAG-1L + + + BAG-1 p32 + "A BAG family molecular chaperone regulator 1 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:Q60739-2 or a 1:1 ortholog thereof." [PMID:9679980, PRO:CNA] + BAG1/iso:BAG-1 + BAG family molecular chaperone regulator 1 isoform BAG-1 + PR_EXT:BAG family molecular chaperone regulator 1 isoform BAG-1 + PR_EXT:000025856 + + + serpin + PR_EXT:serpin + "A protein that is primarily known as an irreversible serine protease inhibitor active against S1, S8 and C14 peptidases. There are both extra- and intra-cellular serpins, which are found in all groups of organisms with the notable exception of fungi. Serpin contains a copy of the Serpin (Pfam:PF00079) domain." [InterPro:IPR000215, PRO:CNA] + PR_EXT:000025875 + + + PML + MYL + transcription factor PML + RNF71 + RING finger protein 71 + "A protein that is a translation product of the human PML gene or a 1:1 ortholog thereof." [PMID:20832753, PRO:CNA] + TRIM19 + PR_EXT:000026474 + PR_EXT:transcription factor PML + Tripartite motif-containing protein 19 + + + PR_EXT:000026780 + transcription factor SOX-5 isoform 2 + SOX5/iso:2 + "A transcription factor SOX-5 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P35710-2 or a 1:1 ortholog thereof." [PRO:HJD] + PR_EXT:transcription factor SOX-5 isoform 2 + + + PR_EXT:000027209 + CAV1/iso:1 + PR_EXT:caveolin-1 isoform 1 + caveolin-1 isoform 1 + "A caveolin-1 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:Q03135-1 or a 1:1 ortholog thereof." [PRO:PD] + + + SRC + "A proto-oncogene SRC-like tyrosine-protein kinase that is a translation product of the human SRC gene or a 1:1 ortholog thereof." [PMID:18789131, PRO:CNA] + pp60c-src + Proto-oncogene c-Src + PR_EXT:proto-oncogene tyrosine-protein kinase Src + PR_EXT:000027234 + SRC1 + proto-oncogene tyrosine-protein kinase Src + + + MIH1 + CDC25 + "A protein that is a translation product of the Schizosaccharomyces pombe 972h- cdc25 gene or a 1:1 ortholog thereof." [PRO:CNA] + PR_EXT:M-phase inducer phosphatase + PR_EXT:000027506 + Mitosis initiation protein + M-phase inducer phosphatase + P80 + cdc25 + + + PR_EXT:histone H2A + histone H2A + PR_EXT:000027547 + "A core histone that is a translation product of one of the H2A gene variants. It is a core histone and contains a copy of the Histone (Pfam:PF00125) domain." [PMID:18443735, PMID:19234519, PRO:CNA] + + + histone H3 + PR_EXT:000027594 + H3(any) + "A core histone that is a translation product of one of the H3 gene variants. It is a core histone and contains a copy of the Histone (Pfam:PF00125) domain at its C-terminus." [PMID:18443735, PMID:19234519, PRO:CNA] + PR_EXT:histone H3 + + + PRSS + PR_EXT:trypsin + "A protein that in active form is a serine protease that cleaves peptide bonds on the carboxyl side of lysine or arginine amino acids within amino acid chains." [PRO:DAN, Wikipedia:Trypsin] + PR_EXT:000027795 + trypsin + + + "A protein that belongs to the clade A of the bHLH proteins (see PMID:20219281) with with a C-terminal copy of the helix-loop-helix DNA-binding domain (Pfam:PF00010), and it is the translation product of the human HAND1 or HAND2 genes, or 1:1 orthologs thereof." [PMID:12909338, PMID:20219281, PRO:CNA] + PR_EXT:basic helix-loop-helix transcription factor HAND + HAND + basic helix-loop-helix transcription factor HAND + PR_EXT:000027804 + + + "A protein that belongs to the clade A of the bHLH proteins (see PMID:20219281) with with a C-terminal copy of the helix-loop-helix DNA-binding domain (Pfam:PF00010), and it is the translation product of any of the TWIST genes." [PMID:12909338, PMID:20219281, PRO:CNA] + TWIST + PR_EXT:000027825 + PR_EXT:twist-related protein + twist-related protein + + + PR_EXT:phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN + TEP1 + "A protein that is a translation product of the human PTEN gene or a 1:1 ortholog thereof." [PMID:18757404, PRO:PD] + MMAC1 + PR_EXT:000028746 + Mutated in multiple advanced cancers 1 + PTEN + Phosphatase and tensin homolog + phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN + + + PR_EXT:000028775 + transcription factor E2F3 isoform 1 + "A transcription factor E2F3 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:O00716-1 or a 1:1 ortholog thereof." [PMID:10753885, PRO:PD] + E2F3/iso:1 + PR_EXT:transcription factor E2F3 isoform 1 + + + "A protein with a core domain composition consisting of a Tubulin/FtsZ family, GTPase domain (Pfam:PF00091) at the N terminus, and a Tubulin C-terminal domain (Pfam:PF03953). Tubulins possess GTPase activity, and are the principle components of microtubules." [Pfam:PF03953, PRO:DAN] + PR_EXT:tubulin + tubulin + fam:TUB + PR_EXT:000028799 + + + SREBF + PR_EXT:sterol regulatory element-binding protein + SRE + sterol regulatory element-binding transcription factor + PR_EXT:000028988 + SREBP + "A protein that is a transmembrane protein where the N- and C-termini are both cytosolic, and the N terminus contains a basic helix-loop-helix domain (Pfam:PF00010) and functions as a transcription factor when cleaved off." [PMID:17303406] + sterol regulatory element-binding protein + + + Mus musculus protein + mouse protein + PR_EXT:Mus musculus protein + PR_EXT:000029032 + "A protein that is encoded in the genome of Mus musculus." [PRO:DAN] + + + "A protein that is encoded in the genome of Rattus norvegicus." [PRO:DAN] + Rattus norvegicus protein + rat protein + PR_EXT:000029033 + PR_EXT:Rattus norvegicus protein + + + "A protein that is encoded in the genome of Schizosaccharomyces pombe 972h-." [PRO:DAN] + Schizosaccharomyces pombe 972h- protein + PR_EXT:Schizosaccharomyces pombe 972h- protein + PR_EXT:000029043 + Spom972h- protein + + + Athal protein + "A protein that is encoded in the genome of Arabidopsis thaliana." [PRO:DAN] + PR_EXT:Arabidopsis thaliana protein + PR_EXT:000029045 + Arabidopsis thaliana protein + + + Saccharomyces cerevisiae protein + PR_EXT:000029055 + "A protein that is encoded in the genome of Saccharomyces cerevisiae." [PRO:DAN] + yeast protein + PR_EXT:Saccharomyces cerevisiae protein + + + fruit fly protein + Drosophila melanogaster protein + PR_EXT:Drosophila melanogaster protein + PR_EXT:000029060 + "A protein that is encoded in the genome of Drosophila melanogaster." [PRO:DAN] + + + "A protein that is encoded in the genome of Danio rerio." [PRO:DAN] + Danio rerio protein + PR_EXT:Danio rerio protein + PR_EXT:000029061 + zebrafish protein + + + "A protein that is encoded in the genome of Gallus gallus." [PRO:DAN] + chicken protein + Gallus gallus protein + PR_EXT:Gallus gallus protein + PR_EXT:000029063 + + + human protein + Homo sapiens protein + PR_EXT:000029067 + PR_EXT:Homo sapiens protein + "A protein that is encoded in the genome of Homo sapiens." [PRO:DAN] + + + "A protein that is a translation product of the human CDKN2A gene or a 1:1 ortholog thereof." [PRO:DNx] + MTS1 + CDKN2A + MTS-1 + p16INK4A + CDK4I + CDKN2 + p16-INK4a + cyclin-dependent kinase inhibitor 2A + p16-INK4 + PR_EXT:000029097 + PR_EXT:CDKN2A gene translation product + cyclin-dependent kinase 4 inhibitor A + CDKN2A gene translation product + multiple tumor suppressor 1 + + + PR_EXT:immunoglobulin G-binding protein A + "A protein that is a translation product of the Staphylococcus aureus spa gene or a 1:1 ortholog thereof." [PRO:DNx] + immunoglobulin G-binding protein A + IgG-binding protein A + PR_EXT:000029158 + surface protein A + spa + staphylococcal protein A + + + PR_EXT:AKT kinase + serine-threonine kinase Akt + PR_EXT:000029189 + AKT + "A protein that has a core domain composition consisting of a PH domain (Pfam:PF00169), Protein kinase domain (Pfam:PF00069) and a Protein kinase C terminal domain (Pfam:PF00433). Mammals have three genes encoding AKT1, AKT2 and AKT3. The second messenger phosphatidylinositol-3,4,5-trisphosphate [PIP(3)], product of phosphatidylinositol 3-kinase, acts largely through its role as an kinase activator. Binding of the pleckstrin domain to PIP(3) results in its targeting to the plasma membrane. Full activity is gained only after phosphorylation at two sites." [PMID:9736715, PRO:CNA] + AKT kinase + + + PR_EXT:000029191 + "A protein that consists of a copy of the Cyclin, N-terminal domain (Pfam:PF00134) and a copy of the Cyclin, C-terminal domain (Pfam:PF02984). This class includes the G1/S cyclins, essential for the control of the cell cycle at the G1/S transition, and the G2/M cyclins, essential for the control of the cell cycle at the G2/M transition." [PRO:CNA, Wikipedia:Cyclin] + PR_EXT:cell cycle-related cyclin + cell cycle-related cyclin + cyclin, A/B/D/E types + + + PR_EXT:lamina-associated polypeptide 2 + lamina-associated polypeptide 2 + thymopoietin + TMPO + "A protein that is a translation product of the human TMPO gene or a 1:1 ortholog thereof." [PRO:DAN] + PR_EXT:000029585 + thymopoietin-related peptide + TPRP + TP alpha + LAP2 + + + PR_EXT:000029674 + PICALM + "A protein that is a translation product of the human PICALM gene or a 1:1 ortholog thereof." [PRO:DNx] + clathrin assembly lymphoid myeloid leukemia + Fit1 + phosphatidylinositol-binding clathrin assembly protein + CALM + clathrin assembly lymphoid myeloid leukemia protein + PR_EXT:phosphatidylinositol-binding clathrin assembly protein + + + Trap + tudor domain-containing protein 7 + PCTAIRE2-binding protein + tudor repeat associator with PCTAIRE 2 + TDRD7 + "A protein that is a translation product of the human TDRD7 gene or a 1:1 ortholog thereof." [PRO:DNx] + PCTAIRE2BP + PR_EXT:tudor domain-containing protein 7 + PR_EXT:000029784 + + + PR_EXT:glutathione S-transferase + glutathione S-transferase + PR_EXT:000029945 + fam:GST + + + PR_EXT:glutathione S-transferase mu + fam:GSTM + glutathione S-transferase mu + PR_EXT:000029948 + + + PR_EXT:000029950 + PR_EXT:glutathione S-transferase pi + glutathione S-transferase pi + fam:GSTP + + + fam:GH1 + PR_EXT:somatotropin hormone family member + "A protein that is a standalone version of the Hormone_1 domain (Pfam:PF00103). In the immature form, the domain is preceded by a signal peptide." [PRO:DAN] + somatotropin hormone family member + PR_EXT:000029968 + + + PR_EXT:000029971 + PR_EXT:creatine kinase + "A protein that contains a single ATP:guanido phosphotransferase N-terminal domain (Pfam:PF02807) followed by a single ATP:guanido phosphotransferase C-terminal catalytic domain (Pfam:PF00217)." [PRO:DAN] + creatine kinase + fam:CK + + + PR_EXT:000029983 + protein-glutamine gamma-glutamyltransferase + PR_EXT:protein-glutamine gamma-glutamyltransferase + fam:TGM + + + fam:GPCR + PR_EXT:G-protein coupled receptor + PR_EXT:000030035 + G-protein coupled receptor + + + fam:glutamate + PR_EXT:glutamate G-protein coupled receptor + PR_EXT:000030038 + glutamate G-protein coupled receptor + + + GSTM4 + "A glutathione S-transferase mu that is a translation product of the human GSTM4 gene or a 1:1 ortholog thereof." [PRO:DNx] + GST class-mu 4 + PR_EXT:glutathione S-transferase mu 4 + GSTM4-4 + PR_EXT:000030257 + GST-Mu2 + glutathione S-transferase mu 4 + + + NSD2 + Wolf-Hirschhorn syndrome candidate 1 protein + protein trithorax-5 + KIAA1090 + "A protein that is a translation product of the human WHSC1 gene or a 1:1 ortholog thereof." [PRO:DNx] + TRX5 + multiple myeloma SET domain-containing protein + nuclear SET domain-containing protein 2 + PR_EXT:histone-lysine N-methyltransferase NSD2 + MMSET + histone-lysine N-methyltransferase NSD2 + PR_EXT:000030426 + WHSC1 + + + BGP + BGLAP + gamma-carboxyglutamic acid-containing protein + osteocalcin + bone Gla protein + PR_EXT:000030444 + PR_EXT:osteocalcin + "A protein that is a translation product of the human BGLAP gene or a 1:1 ortholog thereof." [PRO:DNx] + + + PR_EXT:000030954 + YRRM2 + PR_EXT:RNA-binding motif protein, Y chromosome, family 1 member A1 + "A protein that is a translation product of the human RBMY1A1 gene or a 1:1 ortholog thereof." [PRO:DNx] + RBMY1A1 + RBM1 + RBM2 + hRBMY + Rbm + YRRM1 + Y chromosome RNA recognition motif 1 + RNA-binding motif protein, Y chromosome, family 1 member A1 + RNA-binding motif protein 2 + + + MEI1 + "A protein that is a translation product of the human MEI1 gene or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000031227 + meiosis inhibitor protein 1 + PR_EXT:meiosis inhibitor protein 1 + meiosis defective protein 1 + + + ATP11B + PR_EXT:phospholipid-transporting ATPase IF + ATPase IR + PR_EXT:000031229 + ATPIF + ATPase class VI type 11B + KIAA0956 + "A protein that is a translation product of the human ATP11B gene or a 1:1 ortholog thereof." [PRO:DNx] + ATPIR + phospholipid-transporting ATPase IF + + + MUC-5AC + "A protein that is a translation product of the human MUC5AC gene or a 1:1 ortholog thereof." [PRO:DNx] + LeB + PR_EXT:mucin-5AC + mucin-5AC + gastric mucin + lewis B blood group antigen + major airway glycoprotein + MUC5AC + TBM + PR_EXT:000031343 + mucin-5 subtype AC, tracheobronchial + MUC5 + + + PR_EXT:000031436 + KIAA0465 + "A protein that is a translation product of the human MACF1 gene or a 1:1 ortholog thereof." [PRO:DNx] + MACF1 + microtubule-actin cross-linking factor 1 + macrophin-1 + 620 kDa actin-binding protein + ABP620 + Macf + Aclp7 + trabeculin-alpha + ACF7 + actin cross-linking family protein 7 + PR_EXT:microtubule-actin cross-linking factor 1 + KIAA1251 + + + bacterial-type beta-galactosidase + PR_EXT:bacterial-type beta-galactosidase + lacZ + "A protein that is a translation product of the Escherichia coli K-12 lacZ gene or a 1:1 ortholog thereof in bacteria. The bacterial-type beta-galactosidase contains a Glycosyl hydrolases family 2 (Pfam:PF00703) domain instead of the Glycosyl hydrolases family 35 (Pfam:PF01301) domain typical of the eukaryotic-type." [PRO:DNx] + PR_EXT:000033987 + + + aurora kinase + PR_EXT:aurora kinase + "A protein that is a serine-threonine protein kinase that controls several aspects of cell division. It contains a copy of the Protein kinase domain (Pfam:PF00069)." [PIRSF:PIRSF501130, PMID:18662747, PRO:CNA] + PR_EXT:000035365 + AURK + + + PR_EXT:BUB1/BUB1B protein + PR_EXT:000035665 + "A protein that consists of a core domain composition consisting of a the Mad3/BUB1 homology region 1 (Pfam:PF00831) and a C-terminal Protein kinase domain (Pfam:PF00069). Members of this class are related to MAD3." [PMID:22698286, PRO:CNA] + BUB1/BUB1B protein + + + "A protein that is a translation product of the human MECOM gene or a 1:1 ortholog thereof." [PRO:DAN] + PR_EXT:000035849 + MECOM + PR_EXT:MDS1 and EVI1 complex locus protein + MDS1 and EVI1 complex locus protein + + + GSK3-like glycogen synthase kinase + PR_EXT:000035899 + "A protein that contains a copy of the Protein kinase (Pfam:PF00069) domain and normally functions as a non-receptor serine/threonine protein kinase that is involved in a variety of biological processes, such as developmental signalling pathways and also regulation of the cytoskeleton." [PMID:16504046, PMID:22051150] + PR_EXT:GSK3-like glycogen synthase kinase + + + PR_EXT:000036194 + eukaryotic protein + "A protein that is encoded in the genome of some Eukaryota." [PRO:DAN] + Eukaryota protein + PR_EXT:eukaryotic protein + + + Bacteria <prokaryote> protein + PR_EXT:000036195 + bacterial protein + PR_EXT:bacterial protein + "A protein that is encoded in the genome of some Bacteria <prokaryote>." [PRO:DAN] + + + virus protein + "A protein that is encoded in the genome of some virus." [PRO:DAN] + viral protein + PR_EXT:viral protein + PR_EXT:000036197 + + + fam:Tas1r + PR_EXT:000036336 + PR_EXT:taste receptor type 1 + taste receptor type 1 + + + taste receptor type 2 + fam:Tas2r + PR_EXT:000036337 + PR_EXT:taste receptor type 2 + "A G-protein coupled receptor that is a standalone Taste receptor protein (Pfam:PF05296) domain." [PRO:DAN] + + + PR_EXT:histone H2B + PR_EXT:000036509 + "A core histone that is a translation product of one of the H2B gene variants. It is a core histone and contains a copy of the Histone (Pfam:PF00125) domain." [PRO:DAN] + histone H2B + H2B(any) + + + PR_EXT:000037206 + TMPO/iso:alpha + lamina-associated polypeptide 2 isoform alpha + Tmpo alpha + "A lamina-associated polypeptide 2 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:Q61033-1 or a 1:1 ortholog thereof." [PMID:8743987, PRO:HJD] + PR_EXT:lamina-associated polypeptide 2 isoform alpha + + + paired box protein PAX + PR_EXT:000037797 + "A protein that contains a copy of the 'Paired box' domain (Pfam:PF00292), a conserved amino acid motif with DNA-binding activity. Members of this class are transcription factors involved in pattern formation during embryogenesis, possibly by determining the time and place of organ initiation or morphogenesis." [PIRSF:PIRSF038195, PMID:9297966, PRO:CNA] + PR_EXT:paired box protein PAX + + + paired box protein PAX group IV + "A paired box protein PAX that contains, in addition to the 'Paired box' domain (Pfam:PF00292), a C-terminal Homeobox domain (Pfam:PF00046)." [PIRSF:PIRSF500778, PMID:11750700, PMID:24951566, PRO:CNA] + PR_EXT:paired box protein PAX group IV + paired box protein, PAX6-type + PR_EXT:000037798 + + + paired box protein, PAX-3/PAX-7 types + PR_EXT:paired box protein PAX group III + PR_EXT:000037799 + paired box protein PAX group III + "A paired box protein PAX that contains, in addition to the 'Paired box' domain (Pfam:PF00292), an octapeptide motif ([HY]S[IV][NS]G[IL]LG), a Homeobox domain (Pfam:PF00046), and a Paired box protein 7 (Pfam:PF12360) domain." [PIRSF:PIRSF500779, PMID:11750700, PMID:24951566, PRO:CNA] + + + paired box protein PAX group II + PR_EXT:paired box protein PAX group II + PR_EXT:000037800 + paired box protein, PAX-2/PAX-8 types + "A paired box protein PAX that contains, in addition to the 'Paired box' domain (Pfam:PF00292), an octapeptide motif ([HY]S[IV][NS]G[IL]LG) and a Paired box protein 7 C terminal (Pfam:PF12403) domain." [PIRSF:PIRSF500780, PMID:11750700, PRO:CNA] + + + "A peroxisome proliferator-activated receptor gamma that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P37231-1 or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:peroxisome proliferator-activated receptor gamma isoform 1 + PPARG/iso:1 + PR_EXT:000039376 + peroxisome proliferator-activated receptor gamma isoform 1 + + + PR_EXT:adapter molecule crk isoform 1 + adapter molecule crk isoform 1 + PR_EXT:000039485 + "An adapter molecule crk that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P46108-1 or a 1:1 ortholog thereof." [PRO:DNx] + CRK/iso:1 + + + SODC domain protein + PR_EXT:SODC domain protein + fam:SODC + PR_EXT:000039980 + "A protein that is a standalone Copper/zinc superoxide dismutase (Pfam:PF00080) domain." [PRO:DAN] + + + "A protein that is a translation product of some metazoan gene that encodes a signal peptide followed by a single Cathepsin propeptide inhibitor domain (Pfam:PF08246) followed by a single Papain family cysteine protease (Pfam:PF00112) domain at the C terminus." [PRO:DAN] + PR_EXT:000040662 + PR_EXT:cathepsin-like protease + fam:CTS + cathepsin-like protease + + + SYN2/iso:1 + PR_EXT:synapsin-2 isoform 1 + "A synapsin-2 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:Q64332-1 or a 1:1 ortholog thereof." [PRO:DNx] + synapsin-2 isoform 1 + PR_EXT:000041110 + + + PR_EXT:synapsin-2 isoform 2 + SYN2/iso:2 + synapsin-2 isoform 2 + "A synapsin-2 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:Q64332-2 or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000041111 + + + CCNA + cyclin-A + "A cell cycle-related cyclin that is a translation product of the human CCNA1 or CCNA2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." [PRO:DAN] + PR_EXT:000041205 + PR_EXT:cyclin-A + + + PR_EXT:mucolipin-1 isoform 1 + "A mucolipin-1 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:Q9GZU1-1 or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000043184 + mucolipin-1 isoform 1 + MCOLN1/iso:1 + + + "A protein that contains a single copy of the Histone (Pfam:PF00125) domain, optionally followed by a C-terminus of histone H2A (Pfam:PF16211) domain (for histone H2A) with or without a Macro domain (Pfam:PF01661)." [PRO:DAN] + PR_EXT:core histone + PR_EXT:000043452 + fam:coreHistone + core histone + + + zinc finger protein 148 isoform 1 + ZNF148/iso:1 + PR_EXT:zinc finger protein 148 isoform 1 + "A zinc finger protein 148 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:Q9UQR1-1 or a 1:1 ortholog thereof." [PRO:DNx] + PR_EXT:000044061 + + + PR_EXT:insulin family protein + fam:INS + insulin family protein + PR_EXT:000045358 + "A protein that is a translation product of a gene that encodes a standalone Insulin (Pfam:PF00049) domain preceded by a signal peptide." [PRO:DAN] + + + CNNM + PR_EXT:ACDP_or_CNNM + ACDP/CNNM + ACDP + PR_EXT:'metal transporter CNNM1' (PR_EXT:000005643) or PR_EXT:'metal transporter CNNM2' (PR_EXT:000005644) or PR_EXT:'metal transporter CNNM3' (PR_EXT:000005645) or PR_EXT:'metal transporter CNNM4' (PR_EXT:000005646) + ancient conserved domain protein + PR_EXT:ACDP/CNNM + + + APLP + amyloid-like protein + PR_EXT:APLP + PR_EXT:'amyloid-like protein 1' (PR_EXT:000004136) or PR_EXT:'amyloid-like protein 2' (PR_EXT:000004137) + amyloid beta precursor-like protein + PR_EXT:APLP + + + BMP receptor type 1 + BMP type 1 receptor + PR_EXT:BMP_type_1_receptor + bone morphogenetic protein receptor type I + BMP type I receptor + bone morphogenetic protein type I receptor + BMP receptor type I + PR_EXT:'activin receptor type-1' or PR_EXT:'BMP receptor type-1A' or PR_EXT:'BMP receptor type-1B' + bone morphogenetic protein receptor type 1 + PR_EXT:BMP type I receptor + bone morphogenetic protein type 1 receptor + + + PR_EXT:BRCA + PR_EXT:BRCA + BRCA + PR_EXT:'breast cancer type 1 susceptibility protein' (PR_EXT:000004803) or PR_EXT:'breast cancer type 2 susceptibility protein' (PR_EXT:000004804) + + + PR_EXT:'CCAAT/enhancer-binding protein alpha' (PR_EXT:000005307) or PR_EXT:'CCAAT/enhancer-binding protein beta' (PR_EXT:000005308) or PR_EXT:'CCAAT/enhancer-binding protein delta' (PR_EXT:000005309) or PR_EXT:'CCAAT/enhancer-binding protein epsilon' (PR_EXT:000005310) or PR_EXT:'CCAAT/enhancer-binding protein gamma' (PR_EXT:000005311) or PR_EXT:'CCAAT/enhancer-binding protein zeta' (PR_EXT:000005312) + CCAAT/enhancer-binding protein + CEBP + PR_EXT:CEBP + C/EBP + CCAAT-enhancer-binding protein + PR_EXT:CEBP + + + PR_EXT:CLASP + PR_EXT:CLASP + PR_EXT:'CLIP-associating protein 1' (PR_EXT:000005520) or PR_EXT:'CLIP-associating protein 2' (PR_EXT:000005521) + CLIP-associating protein + CLASP + + + PR_EXT:CREB + PR_EXT:'cyclic AMP-responsive element-binding protein 1' (PR_EXT:000005854) or PR_EXT:'cyclic AMP-dependent transcription factor ATF-2' (PR_EXT:000004398) or PR_EXT:'cyclic AMP-dependent transcription factor ATF-4' (PR_EXT:000004400) or PR_EXT:'cyclic AMP-responsive element-binding protein 3' (PR_EXT:000005855) or PR_EXT:'cyclic AMP-responsive element-binding protein 3-like protein 4' (PR_EXT:000005859) or PR_EXT:'cyclic AMP-responsive element-binding protein 5' (PR_EXT:000005860) + cAMP-responsive element-binding protein + PR_EXT:CREB + CREB + + + DLL + PR_EXT:'delta-like protein 1' (PR_EXT:000006523) or PR_EXT:'delta-like protein 3' (PR_EXT:000006524) or PR_EXT:'delta-like protein 4' (PR_EXT:000006525) + delta-like protein + delta-like + PR_EXT:DLL + PR_EXT:DLL + + + PR_EXT:'transcription factor E2F1' (PR_EXT:000006852) or PR_EXT:'transcription factor E2F2' (PR_EXT:000006853) or PR_EXT:'transcription factor E2F3' (PR_EXT:000006854) or PR_EXT:'transcription factor E2F4' (PR_EXT:000006855) or PR_EXT:'transcription factor E2F5' (PR_EXT:000006856) or PR_EXT:'transcription factor E2F6' (PR_EXT:000006857) or PR_EXT:'transcription factor E2F7' (PR_EXT:000006858) or PR_EXT:'transcription factor E2F8' (PR_EXT:000006859) + PR_EXT:E2F + PR_EXT:E2F + E2F + + + ELMO + engulgment and cell motility protein + PR_EXT:ELMO + PR_EXT:ELMO + PR_EXT:'engulfment and cell motility protein 1' (PR_EXT:000007031) or PR_EXT:'engulfment and cell motility protein 2' (PR_EXT:000007032) or PR_EXT:'engulfment and cell motility protein 3' (PR_EXT:000007033) + + + PR_EXT:EMX + EMX + PR_EXT:EMX + PR_EXT:'homeobox protein EMX1' (PR:000007068) or PR_EXT:'homeobox protein EMX2' (PR:000007069) + + + PR_EXT:ERK + extracellular signal-regulated kinase + PR_EXT:ERK + PR_EXT:'mitogen-activated protein kinase 1' or PR_EXT:'mitogen-activated protein kinase 3' + ERK + + + PR_EXT:'zinc finger protein GLI1' (PR_EXT:000008026) or PR_EXT:'zinc finger protein GLI2' (PR_EXT:000008027) or PR_EXT:'transcriptional activator GLI3' (PR_EXT:000008028) + PR_EXT:Gli + Gli + PR_EXT:Gli + + + PR_EXT:HOMER + PR_EXT:'homer protein homolog 1' (PR_EXT:000008678) or PR_EXT:'homer protein homolog 2' (PR_EXT:000008679) or PR_EXT:'homer protein homolog 3' (PR_EXT:000008680) + HOMER + PR_EXT:HOMER + + + PR_EXT:JNK + c-Jun N-terminal kinase + PR_EXT:JNK + JNK + PR_EXT:'mitogen-activated protein kinase 8' (PR_EXT:000002206) or PR_EXT:'mitogen-activated protein kinase 9' (PR_EXT:000010163) or PR_EXT:'mitogen-activated protein kinase 10' (PR_EXT:000010151) + + + PR_EXT:'protein jagged-1' (PR_EXT:000001921) or PR_EXT:'protein jagged-2' (PR_EXT:000009194) or PR_EXT:'zinc finger protein JAGGED (Arabidopsis thaliana)' (PR_EXT:Q6S591) + Jagged + PR_EXT:Jagged + PR_EXT:Jagged + + + PR_EXT:'RNA-binding protein Nova-1' (PR_EXT:000011339) or PR_EXT:'RNA-binding protein Nova-2' (PR_EXT:000011340) + NOVA + PR_EXT:NOVA + PR_EXT:NOVA + + + PR_EXT:NXF + PR_EXT:NXF + nuclear export factor + PR_EXT:'nuclear RNA export factor 1' (PR_EXT:000011535) or PR_EXT:'nuclear RNA export factor 2' (PR_EXT:000011536) or PR_EXT:'nuclear RNA export factor 3' (PR_EXT:000011537) or PR_EXT:'nuclear RNA export factor 5' (PR_EXT:000011538) + NXF + + + PR_EXT:Notch + PR_EXT:'neurogenic locus notch homolog protein 1' (PR_EXT:000011331) or PR_EXT:'neurogenic locus notch homolog protein 2' (PR_EXT:000011332) or PR_EXT:'neurogenic locus notch homolog protein 3 ' (PR_EXT:000011334) or PR_EXT:'neurogenic locus notch homolog protein 4' (PR_EXT:000011335) + Notch + PR_EXT:Notch + + + who + PR_EXT:O01367 + "A protein that is a translation product of the how gene in fruit fly." [PRO:DNx, UniProtKB:O01367] + fly-how + PR_EXT:protein held out wings (fruit fly) + quaking-related 93F (fruit fly) + CG10293 + RNA-binding protein (fruit fly) + stru + KH93F + protein wings held out (fruit fly) + KH domain protein KH93F (fruit fly) + protein struthio (fruit fly) + protein held out wings (fruit fly) + protein muscle-specific (fruit fly) + qkr93F + + + "A kinesin-like protein KIF3C that is encoded in the genome of human." [PRO:DNx, UniProtKB:O14782] + PR_EXT:kinesin-like protein KIF3C (human) + hKIF3C + PR_EXT:O14782 + kinesin-like protein KIF3C (human) + + + "A kinesin-like protein KIF3B that is encoded in the genome of human." [PRO:DNx, UniProtKB:O15066] + PR_EXT:O15066 + PR_EXT:kinesin-like protein KIF3B (human) + kinesin-like protein KIF3B (human) + hKIF3B + + + PR_EXT:O18214 + Y53C12B.5 + "A protein that is a translation product of the mab-3 gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:O18214] + worm-mab-3 + protein male abnormal 3 (Caenorhabditis elegans) + PR_EXT:protein male abnormal 3 (Caenorhabditis elegans) + + + "A kinesin-like protein KIF3C that is encoded in the genome of mouse." [OMA:MOUSE04571, PRO:DNx] + PR_EXT:O35066 + mKIF3C + kinesin-like protein KIF3C (mouse) + PR_EXT:kinesin-like protein KIF3C (mouse) + + + PR_EXT:O54908 + Dkk-1 (mouse) + dickkopf-related protein 1 (mouse) + mDkk-1 (mouse) + dickkopf-1 (mouse) + mDKK1 + "A dickkopf-related protein 1 that is encoded in the genome of mouse." [OMA:MOUSE11388, PRO:DNx] + PR_EXT:dickkopf-related protein 1 (mouse) + + + kinesin-like protein KIF3C (rat) + PR_EXT:kinesin-like protein KIF3C (rat) + "A kinesin-like protein KIF3C that is encoded in the genome of rat." [OMA:RATNO17519, PRO:DNx] + PR_EXT:O55165 + rKIF3C + + + hHMMR + PR_EXT:O75330 + PR_EXT:hyaluronan mediated motility receptor (human) + hyaluronan mediated motility receptor (human) + "A hyaluronan mediated motility receptor that is encoded in the genome of human." [PRO:WCB, UniProtKB:O75330] + + + hTACC1 + PR_EXT:O75410 + PR_EXT:transforming acidic coiled-coil-containing protein 1 (human) + "A transforming acidic coiled-coil-containing protein 1 that is encoded in the genome of human." [PRO:DNx, UniProtKB:O75410] + transforming acidic coiled-coil-containing protein 1 (human) + + + hTACC1/iso:h1 + PR_EXT:O75410-1 + PR_EXT:transforming acidic coiled-coil-containing protein 1 isoform h1 (human) + transforming acidic coiled-coil-containing protein 1 isoform h1 (human) + transforming acidic coiled-coil-containing protein 1 isoform A (human) + "A transforming acidic coiled-coil-containing protein 1 (human) that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:O75410-1." [PRO:DNx, UniProtKB:O75410] + transforming acidic coiled-coil-containing protein 1 isoform Long (human) + + + "A transforming acidic coiled-coil-containing protein 2 that is encoded in the genome of human." [PRO:DNx, UniProtKB:O95359] + transforming acidic coiled-coil-containing protein 2 (human) + hTACC2 + PR_EXT:O95359 + PR_EXT:transforming acidic coiled-coil-containing protein 2 (human) + + + "A transforming acidic coiled-coil-containing protein 2 (human) that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:O95359-1." [PRO:DNx, UniProtKB:O95359] + hTACC2/iso:h1 + PR_EXT:transforming acidic coiled-coil-containing protein 2 isoform h1 (human) + PR_EXT:O95359-1 + transforming acidic coiled-coil-containing protein 2 isoform Short (human) + transforming acidic coiled-coil-containing protein 2 isoform h1 (human) + + + transforming acidic coiled-coil-containing protein 2 isoform Long (human) + transforming acidic coiled-coil-containing protein 2 isoform TACC2s (human) + "A transforming acidic coiled-coil-containing protein 2 (human) that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:O95359-4." [PRO:DNx, UniProtKB:O95359] + PR_EXT:O95359-4 + PR_EXT:transforming acidic coiled-coil-containing protein 2 isoform h4 (human) + transforming acidic coiled-coil-containing protein 2 isoform h4 (human) + hTACC2/iso:h4 + + + OTX + PR_EXT:OTX + PR_EXT:'homeobox protein OTX1' (PR_EXT:000012085) or PR_EXT:'homeobox protein OTX2' (PR_EXT:000012086) + PR_EXT:OTX + + + hSOD1 + superoxide dismutase [Cu-Zn] (human) + PR_EXT:superoxide dismutase [Cu-Zn] (human) + PR_EXT:P00441 + "A superoxide dismutase [Cu-Zn] that is encoded in the genome of human." [PRO:DNx, UniProtKB:P00441] + + + 1 (BPT7) + PR_EXT:T7 RNA polymerase (Enterobacteria phage T7) + T7 RNA polymerase (Enterobacteria phage T7) + PR_EXT:P00573 + "A protein that is a translation product of the 1 gene in Enterobacteria phage T7." [PRO:DNx, UniProtKB:P00573] + DNA-directed RNA polymerase (Enterobacteria phage T7) + + + site-specific recombinase Flp (yeast) + PR_EXT:site-specific recombinase Flp (yeast) + protein Able (yeast) + yFLP1 + R0010W + FLP (yeast) + "A protein that is a translation product of the FLP1 gene in yeast." [PRO:DNx, UniProtKB:P03870] + PR_EXT:P03870 + + + 21S rRNA intron maturase (yeast) + intron-encoded endonuclease I-SceI (yeast) + OMEGA + PR_EXT:intron-encoded endonuclease I-SceI (yeast) + ySCEI + "A protein that is a translation product of the SCEI gene in yeast." [PRO:DNx, UniProtKB:P03882] + SECY + homing endonuclease omega (yeast) + PR_EXT:P03882 + Q0160 + + + YEL021W + yURA3 + "A protein that is a translation product of the URA3 gene in yeast." [PRO:DNx, UniProtKB:P03962] + PR_EXT:P03962 + OMP decarboxylase (yeast) + PR_EXT:orotidine 5'-phosphate decarboxylase (yeast) + orotidine 5'-phosphate decarboxylase (yeast) + OMPdecase (yeast) + OMPDCase (yeast) + uridine 5'-monophosphate synthase (yeast) + UMP synthase (yeast) + + + regulatory protein GAL4 (yeast) + PR_EXT:regulatory protein GAL4 (yeast) + yGAL4 + "A protein that is a translation product of the GAL4 gene in yeast." [PRO:DNx, UniProtKB:P04386] + PR_EXT:P04386 + + + tetracycline repressor protein class B from transposon Tn10 (Escherichia coli) + tetR (ECOLX) + PR_EXT:P04483 + "A protein that is a translation product of the tetR gene in Escherichia coli." [PRO:DNx, UniProtKB:P04483] + PR_EXT:tetracycline repressor protein class B from transposon Tn10 (Escherichia coli) + + + PR_EXT:P04692 + tropomyosin-1 (rat) + Tpma + "A protein that is a translation product of the Tpm1 gene in rat." [PRO:DNx, UniProtKB:P04692] + tropomyosin alpha-1 chain (rat) + PR_EXT:tropomyosin alpha-1 chain (rat) + Alpha-tm + alpha-tropomyosin (rat) + rTpm1 + + + Prp + PrP33-35C (mouse) + mPRNP + Prn-p + PrP (mouse) + PR_EXT:P04925 + CD230 (mouse) + PR_EXT:major prion protein (mouse) + major prion protein (mouse) + "A major prion protein that is encoded in the genome of mouse." [OMA:MOUSE13086, PRO:DNx] + PrP27-30 (mouse) + + + PR_EXT:P05084 + CG9786 + "A protein that is a translation product of the hb gene in fruit fly." [PRO:DNx, UniProtKB:P05084] + fly-hb + protein hunchback (fruit fly) + PR_EXT:protein hunchback (fruit fly) + + + PR_EXT:P05187 + "An alkaline phosphatase, placental type that is encoded in the genome of human." [PRO:DNx, UniProtKB:P05187] + alkaline phosphatase, placental type (human) + PR_EXT:alkaline phosphatase, placental type (human) + hALPP + + + non-histone chromosomal protein C1A9 antigen (fruit fly) + PR_EXT:P05205 + heterochromatin protein 1 (fruit fly) + fly-Su(var)205 + "A protein that is a translation product of the Su(var)205 gene in fruit fly." [PRO:DNx, UniProtKB:P05205] + HP1 (fruit fly) + PR_EXT:heterochromatin protein 1 (fruit fly) + HP1 + CG8409 + + + PR_EXT:P06002 + PR_EXT:opsin Rh1 (fruit fly) + opsin Rh1 (fruit fly) + CG4550 + neither inactivation nor afterpotential E protein (fruit fly) + "A protein that is a translation product of the ninaE gene in fruit fly." [PRO:DNx, UniProtKB:P06002] + fly-ninaE + outer R1-R6 photoreceptor cells opsin (fruit fly) + Rh1 + + + alpha-TIF (Herpes simplex virus type 1 strain 17) + Vmw65 (Herpes simplex virus type 1 strain 17) + alpha trans-inducing protein (Herpes simplex virus type 1 strain 17) + tegument protein VP16 (Herpes simplex virus type 1 strain 17) + PR_EXT:tegument protein VP16 (Herpes simplex virus type 1 strain 17) + "A protein that is a translation product of the UL48 gene in Herpes simplex virus type 1 strain 17." [PRO:DNx, UniProtKB:P06492] + HSV1(17)-UL48 + PR_EXT:P06492 + ICP25 (Herpes simplex virus type 1 strain 17) + + + PR_EXT:imidazoleglycerol-phosphate dehydratase (yeast) + IGPD (yeast) + yHIS3 + PR_EXT:P06633 + imidazoleglycerol-phosphate dehydratase (yeast) + "A protein that is a translation product of the HIS3 gene in yeast." [PRO:DNx, UniProtKB:P06633] + YOR202W + + + yERCC4 + PR_EXT:P06777 + PR_EXT:DNA repair protein RAD1 (yeast) + DNA repair protein RAD1 (yeast) + "A DNA repair endonuclease XPF that is encoded in the genome of yeast." [OMA:YEAST06121, PANTHER:PTHR10150\:SF0, PRO:DNx] + YPL022W + + + worm-mec-3 + "A protein that is a translation product of the mec-3 gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:P09088] + PR_EXT:mechanosensory protein 3 (Caenorhabditis elegans) + F01D4.6 + PR_EXT:P09088 + mechanosensory protein 3 (Caenorhabditis elegans) + + + hTPM1 + "A tropomyosin alpha-1 chain that is encoded in the genome of human." [PRO:DNx, UniProtKB:P09493] + PR_EXT:tropomyosin alpha-1 chain (human) + PR_EXT:P09493 + tropomyosin alpha-1 chain (human) + + + PR_EXT:P09615 + dInt-1 (fruit fly) + CG4889 + dWnt-1 (fruit fly) + "A proto-oncogene Wnt-1 that is encoded in the genome of fruit fly." [OMA:DROME00946, PANTHER:PTHR12027\:SF15, PRO:DNx] + PR_EXT:protein wingless (fruit fly) + protein int-1 (fruit fly) + protein Wnt-1 (fruit fly) + fly-WNT1 + protein wingless (fruit fly) + + + "A protein that is a translation product of the crb gene in fruit fly." [PRO:DNx, UniProtKB:P10040] + protein crumbs (fruit fly) + fly-crb + PR_EXT:P10040 + PR_EXT:protein crumbs (fruit fly) + CG6383 + 95F (fruit fly) + + + neurogenic locus protein delta (fruit fly) + PR_EXT:neurogenic locus protein delta (fruit fly) + fly-Dl + PR_EXT:P10041 + CG3619 + "A protein that is a translation product of the Dl gene in fruit fly." [PRO:DNx, UniProtKB:P10041] + + + T5 + achaete-scute complex protein T5 (fruit fly) + protein achaete (fruit fly) + PR_EXT:achaete-scute complex protein T5 (fruit fly) + fly-ac + CG3796 + PR_EXT:P10083 + "A protein that is a translation product of the ac gene in fruit fly." [PRO:DNx, UniProtKB:P10083] + + + PR_EXT:P10084 + "A protein that is a translation product of the sc gene in fruit fly." [PRO:DNx, UniProtKB:P10084] + sis-b + protein scute (fruit fly) + T4 + PR_EXT:achaete-scute complex protein T4 (fruit fly) + CG3827 + achaete-scute complex protein T4 (fruit fly) + fly-sc + + + ski-like protein (human) + PR_EXT:P12757 + hSKIL + PR_EXT:ski-like protein (human) + "A ski-like protein that is encoded in the genome of human." [PRO:DNx, UniProtKB:P12757] + + + PR_EXT:ski-like protein isoform SNON (human) + hSKIL/iso:SNON + "A ski-like protein (human) that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P12757-1." [PRO:DNx, UniProtKB:P12757] + ski-like protein isoform SNON (human) + PR_EXT:P12757-1 + + + "A protein that is a translation product of the tpma gene in zebrafish." [PRO:DNx, UniProtKB:P13104] + PR_EXT:tropomyosin alpha-1 chain (zebrafish) + PR_EXT:P13104 + tpm1 + alpha-tropomyosin (zebrafish) + ztpma + tropomyosin-1 (zebrafish) + tropomyosin alpha-1 chain (zebrafish) + + + PR_EXT:tropomyosin-1 (yeast) + YNL079C + N2332 + PR_EXT:P17536 + "A protein that is a translation product of the TPM1 gene in yeast." [PRO:DNx, UniProtKB:P17536] + tropomyosin-1 (yeast) + yTPM1 + + + fly-Ser + PR_EXT:P18168 + protein serrate (fruit fly) + "A protein that is a translation product of the Ser gene in fruit fly." [PRO:DNx, UniProtKB:P18168] + PR_EXT:protein serrate (fruit fly) + protein beaded (fruit fly) + Bd + CG6127 + + + armadillo segment polarity protein (fruit fly) + PR_EXT:P18824 + "A catenin beta-1 that is encoded in the genome of fruit fly." [OMA:DROME12396, PRO:DNx] + PR_EXT:armadillo segment polarity protein (fruit fly) + fly-CTNNB1 + CG11579 + + + abnormal cell lineage protein 11 (Caenorhabditis elegans) + worm-LHX1 + PR_EXT:protein lin-11 (Caenorhabditis elegans) + "A LIM/homeobox protein Lhx1 that is encoded in the genome of Caenorhabditis elegans." [OMA:CAEEL02022, PRO:DNx] + ZC247.3 + protein lin-11 (Caenorhabditis elegans) + PR_EXT:P20154 + + + mAbcb4 + PR_EXT:P21440 + Mdr2 + multidrug resistance protein 2 (mouse) + multidrug resistance protein 3 (mouse) + P-glycoprotein 3 (mouse) + ATP-binding cassette sub-family B member 4 (mouse) + phosphatidylcholine translocator ABCB4 (mouse) + "A protein that is a translation product of the Abcb4 gene in mouse." [PRO:DNx, UniProtKB:P21440] + P-glycoprotein 2 (mouse) + PR_EXT:phosphatidylcholine translocator ABCB4 (mouse) + + + GAM1 + regulatory protein SWI2 (yeast) + ATP-dependent helicase SNF2 (yeast) + YOR290C + TYE3 + transcription regulatory protein SNF2 (yeast) + ySNF2 + regulatory protein GAM1 (yeast) + SWI2 + PR_EXT:transcription regulatory protein SNF2 (yeast) + "A protein that is a translation product of the SNF2 gene in yeast." [PRO:DNx, UniProtKB:P22082] + RIC1 + SWI/SNF complex component SNF2 (yeast) + transcription factor TYE3 (yeast) + PR_EXT:P22082 + + + fly-oc + Otd + protein orthodenticle (fruit fly) + PR_EXT:P22810 + homeotic protein ocelliless (fruit fly) + CG12154 + "A protein that is a translation product of the oc gene in fruit fly." [PRO:DNx, UniProtKB:P22810] + PR_EXT:homeotic protein ocelliless (fruit fly) + + + CG11094 + protein doublesex (fruit fly) + PR_EXT:P23023 + PR_EXT:protein doublesex (fruit fly) + "A protein that is a translation product of the dsx gene in fruit fly." [PRO:DNx, UniProtKB:P23023] + fly-dsx + + + protein doublesex isoform A (fruit fly) + PR_EXT:protein doublesex isoform Male (fruit fly) + fly-dsx/iso:Male + "A protein doublesex (fruit fly) that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P23023-1." [PRO:DNx, UniProtKB:P23023] + PR_EXT:P23023-1 + protein doublesex isoform Male (fruit fly) + + + type-2 restriction enzyme BamHI (Bacillus amyloliquefaciens) + PR_EXT:P23940 + "A protein that is a translation product of the bamHIR gene in Bacillus amyloliquefaciens." [PRO:DNx, UniProtKB:P23940] + bamHIR (BACAM) + R.BamHI (Bacillus amyloliquefaciens) + endonuclease BamHI (Bacillus amyloliquefaciens) + type II restriction enzyme BamHI (Bacillus amyloliquefaciens) + PR_EXT:type-2 restriction enzyme BamHI (Bacillus amyloliquefaciens) + + + Spom972h-ERCC2 + rad5 + DNA repair helicase RAD3 homolog (Schizosaccharomyces pombe 972h-) + DNA repair helicase rad15 (Schizosaccharomyces pombe 972h-) + PR_EXT:P26659 + "A TFIIH basal transcription factor complex helicase XPD subunit that is encoded in the genome of Schizosaccharomyces pombe 972h-." [OMA:SCHPO00261, PANTHER:PTHR11472\:SF1, PRO:DNx] + PR_EXT:DNA repair helicase rad15 (Schizosaccharomyces pombe 972h-) + SPAC1D4.12 + protein rhp3 (Schizosaccharomyces pombe 972h-) + + + fly-Sos + protein son of sevenless (fruit fly) + CG7793 + PR_EXT:protein son of sevenless (fruit fly) + PR_EXT:P26675 + "A protein that is a translation product of the Sos gene in fruit fly." [PRO:DNx, UniProtKB:P26675] + + + microtubule plus end-directed kinesin motor 3A (mouse) + Kif3 + mKIF3A + PR_EXT:P28741 + "A kinesin-like protein KIF3A that is encoded in the genome of mouse." [OMA:MOUSE03076, PRO:DNx] + PR_EXT:kinesin-like protein KIF3A (mouse) + kinesin-like protein KIF3A (mouse) + + + protein apterous (fruit fly) + PR_EXT:P29673 + "A protein that is a translation product of the ap gene in fruit fly." [PRO:DNx, UniProtKB:P29673] + CG8376 + PR_EXT:protein apterous (fruit fly) + fly-ap + + + PR_EXT:synaptonemal complex protein ZIP1 (yeast) + yZIP1 + synaptonemal complex protein ZIP1 (yeast) + "A protein that is a translation product of the ZIP1 gene in yeast." [PRO:DNx, UniProtKB:P31111] + PR_EXT:P31111 + + + yRAD24 + PR_EXT:P32641 + SYGP-ORF60 + PR_EXT:checkpoint protein RAD24 (yeast) + "A protein that is a translation product of the RAD24 gene in yeast." [PRO:DNx, UniProtKB:P32641] + checkpoint protein RAD24 (yeast) + YER173W + + + PR_EXT:aquaporin-2 (rat) + AQP-CD (rat) + ADH water channel (rat) + rAQP2 + "An aquaporin-2 that is encoded in the genome of rat." [PANTHER:PTHR19139\:SF37, PRO:DNx] + PR_EXT:P34080 + AQP-2 (rat) + water channel protein for renal collecting duct (rat) + collecting duct water channel protein (rat) + aquaporin-2 (rat) + aquaporin-CD (rat) + WCH-CD (rat) + + + "A protein that is a translation product of the lin-36 gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:P34427] + PR_EXT:protein lin-36 (Caenorhabditis elegans) + worm-lin-36 + PR_EXT:P34427 + protein lin-36 (Caenorhabditis elegans) + abnormal cell lineage protein 36 (Caenorhabditis elegans) + F44B9.6 + + + C15F1.3 + "A protein that is a translation product of the tra-2 gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:P34709] + PR_EXT:P34709 + Ce-Tra-2 (Caenorhabditis elegans) + worm-tra-2 + sex-determining transformer protein 2 (Caenorhabditis elegans) + PR_EXT:sex-determining transformer protein 2 (Caenorhabditis elegans) + + + PR_EXT:P34766 + ceh-3 + homeobox protein ceh-3 (Caenorhabditis elegans) + homeobox protein pal-1 (Caenorhabditis elegans) + caudal homolog 1 (Caenorhabditis elegans) + worm-pal-1 + "A protein that is a translation product of the pal-1 gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:P34766] + posterior alae in males protein 1 (Caenorhabditis elegans) + PR_EXT:homeobox protein pal-1 (Caenorhabditis elegans) + C38D4.6 + + + "A protein that is a translation product of the PCH2 gene in yeast." [PRO:DNx, UniProtKB:P38126] + PR_EXT:P38126 + YBR186W + YBR1308 + pachytene checkpoint protein 2 (yeast) + PR_EXT:pachytene checkpoint protein 2 (yeast) + yPCH2 + + + "A protein that is a translation product of the SPC72 gene in yeast." [PRO:DNx, UniProtKB:P39723] + FUN42 + YAL047C + PR_EXT:P39723 + spindle pole component SPC72 (yeast) + ySPC72 + PR_EXT:spindle pole component SPC72 (yeast) + SPI6 + LDB4 + + + PR_EXT:aquaporin-2 (human) + "An aquaporin-2 that is encoded in the genome of human." [PRO:DNx, UniProtKB:P41181] + aquaporin-2 (human) + PR_EXT:P41181 + hAQP2 + + + RANBP1 (yeast) + HTN1 + perinuclear array-localized protein (yeast) + chromosome stability protein 20 (yeast) + YDR002W + YD8119.08 + PR_EXT:ran-specific GTPase-activating protein 1 (yeast) + "A protein that is a translation product of the YRB1 gene in yeast." [PRO:DNx, UniProtKB:P41920] + CST20 + ran-binding protein 1 (yeast) + SFO1 + PR_EXT:P41920 + ran-specific GTPase-activating protein 1 (yeast) + yYRB1 + + + "A protein that is a translation product of the hindIIIR gene in Haemophilus influenzae Rd KW20." [PRO:DNx, UniProtKB:P43870] + type-2 restriction enzyme HindIII (Haemophilus influenzae Rd KW20) + type II restriction enzyme HindIII (Haemophilus influenzae Rd KW20) + Hinf-hindIIIR + HI_1393 + endonuclease HindIII (Haemophilus influenzae Rd KW20) + R.HindIII (Haemophilus influenzae Rd KW20) + PR_EXT:type-2 restriction enzyme HindIII (Haemophilus influenzae Rd KW20) + PR_EXT:P43870 + + + protein lag-2 (Caenorhabditis elegans) + "A protein that is a translation product of the lag-2 gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:P45442] + lethal protein 461 (Caenorhabditis elegans) + let-461 + worm-lag-2 + Y73C8B.4 + PR_EXT:P45442 + PR_EXT:protein lag-2 (Caenorhabditis elegans) + + + YLR045C + protein STU2 (yeast) + L2108 + "A protein that is a translation product of the STU2 gene in yeast." [PRO:DNx, UniProtKB:P46675] + suppressor of tubulin 2 (yeast) + PR_EXT:P46675 + PR_EXT:protein STU2 (yeast) + ySTU2 + + + bipolar kinesin KRP-130 (fruit fly) + PR_EXT:P46863 + "A protein that is a translation product of the Klp61F gene in fruit fly." [PRO:DNx, UniProtKB:P46863] + kinesin-like protein Klp61F (fruit fly) + fly-Klp61F + KLP2 + PR_EXT:kinesin-like protein Klp61F (fruit fly) + CG9191 + + + PR_EXT:kinesin-like protein Klp68D (fruit fly) + kinesin-like protein Klp68D (fruit fly) + KLP5 + CG7293 + fly-KIF3B + "A kinesin-like protein KIF3B that is encoded in the genome of fruit fly." [OMA:DROME07090, PRO:DNx] + PR_EXT:P46867 + + + "A protein that is a translation product of the SAE2 gene in yeast." [PRO:DNx, UniProtKB:P46946] + DNA endonuclease SAE2 (yeast) + completion of meiotic recombination protein 1 (yeast) + PR_EXT:DNA endonuclease SAE2 (yeast) + ySAE2 + sporulation in the absence of SPO11 protein 2 (yeast) + PR_EXT:P46946 + + + "A protein that is a translation product of the ZAP1 gene in yeast." [PRO:DNx, UniProtKB:P47043] + J1145 + PR_EXT:P47043 + PR_EXT:zinc-responsive transcriptional regulator ZAP1 (yeast) + zinc-responsive transcriptional regulator ZAP1 (yeast) + yZAP1 + YJL056C + + + gastrulation-specific protein G12 (zebrafish) + g12 + PR_EXT:P47805 + mid1-interacting protein 1A (zebrafish) + PR_EXT:mid1-interacting protein 1A (zebrafish) + "A protein that is a translation product of the mid1ip1a gene in zebrafish." [PRO:DNx, UniProtKB:P47805] + zmid1ip1a + + + PR_EXT:P48987 + protein atonal (fruit fly) + fly-ato + "A protein that is a translation product of the ato gene in fruit fly." [PRO:DNx, UniProtKB:P48987] + CG7508 + PR_EXT:protein atonal (fruit fly) + + + YGL249W + NRC704 + zipping up meiotic chromosomes protein 2 (yeast) + PR_EXT:protein ZIP2 (yeast) + PR_EXT:P53061 + "A protein that is a translation product of the ZIP2 gene in yeast." [PRO:DNx, UniProtKB:P53061] + yZIP2 + protein ZIP2 (yeast) + + + PR_EXT:aquaporin-2 (mouse) + aquaporin-2 (mouse) + PR_EXT:P56402 + AQP-CD (mouse) + ADH water channel (mouse) + "An aquaporin-2 that is encoded in the genome of mouse." [OMA:MOUSE08261, PRO:DNx] + AQP-2 (mouse) + aquaporin-CD (mouse) + WCH-CD (mouse) + mAQP2 + water channel protein for renal collecting duct (mouse) + collecting duct water channel protein (mouse) + + + mTPM1 + alpha-tropomyosin (mouse) + PR_EXT:tropomyosin alpha-1 chain (mouse) + "A tropomyosin alpha-1 chain that is encoded in the genome of mouse." [OMA:MOUSE23764, PRO:DNx] + tropomyosin-1 (mouse) + Tpm-1 + PR_EXT:P58771 + Tpma + tropomyosin alpha-1 chain (mouse) + + + "A protein that is a translation product of the lin-53 gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:P90916] + abnormal cell lineage protein 53 (Caenorhabditis elegans) + worm-lin-53 + PR_EXT:P90916 + rba-2 + PR_EXT:histone-binding protein lin-53 (Caenorhabditis elegans) + histone-binding protein lin-53 (Caenorhabditis elegans) + K07A1.12 + synthetic multivulva protein p48 (Caenorhabditis elegans) + + + CD168 (rat) + PR_EXT:hyaluronan-mediated motility receptor (rat) + hyaluronan-mediated motility receptor (rat) + Ihabp + Rhamm + PR_EXT:P97779 + receptor for hyaluronan-mediated motility (rat) + intracellular hyaluronic acid-binding protein (rat) + "A hyaluronan mediated motility receptor that is encoded in the genome of rat." [PANTHER:PTHR18956\:SF1, PRO:DNx] + rHMMR + + + PPAR + PR_EXT:PPAR + PR_EXT:PPAR + PR_EXT:'peroxisome proliferator-activated receptor alpha' (PR_EXT:000013056) or PR_EXT:'peroxisome proliferator-activated receptor delta' (PR_EXT:000013057) or PR_EXT:'peroxisome proliferator-activated receptor gamma' (PR_EXT:000013058) + peroxisome proliferator-activated receptor + + + PTC + PR_EXT:'protein patched homolog 1' (PR_EXT:000013412) or PR_EXT:'protein patched homolog 2' (PR_EXT:000013413) + Patched + PTCH + PR_EXT:Patched + PR_EXT:Patched + + + PR_EXT:Pygo + PR_EXT:Pygo + PR_EXT:'protein pygopus (fruit fly)' (PR_EXT:Q9V9W8) or PR_EXT:'pygopus homolog 1' (PR_EXT:000013523) or PR_EXT:'pygopus homolog 2' (PR_EXT:000013524) + Pygo + + + PR_EXT:hyaluronan mediated motility receptor (mouse) + hyaluronan mediated motility receptor (mouse) + PR_EXT:Q00547 + Rhamm + "A hyaluronan mediated motility receptor that is encoded in the genome of mouse." [OMA:MOUSE02916, PRO:DNx] + CD168 (mouse) + mHMMR + receptor for hyaluronan-mediated motility (mouse) + Ihabp + intracellular hyaluronic acid-binding protein (mouse) + + + aquaporin-1 (mouse) + AQP-1 (mouse) + water channel protein for red blood cells and kidney proximal tubule (mouse) + PR_EXT:Q02013 + delayed early response protein 2 (mouse) + DER2 (mouse) + mAQP1 + "An aquaporin-1 that is encoded in the genome of mouse." [OMA:MOUSE18525, PRO:DNx] + PR_EXT:aquaporin-1 (mouse) + aquaporin-CHIP (mouse) + + + "A protein that is a translation product of the twe gene in fruit fly." [PRO:DNx, UniProtKB:Q03019] + PR_EXT:Q03019 + cdc25-like protein phosphatase twine (fruit fly) + CG4965 + fly-twe + PR_EXT:cdc25-like protein phosphatase twine (fruit fly) + + + CErac1 (Caenorhabditis elegans) + cell-corpse engulfment protein ced-10 (Caenorhabditis elegans) + ras-related protein rac-1 (Caenorhabditis elegans) + PR_EXT:ras-related protein ced-10 (Caenorhabditis elegans) + C09G12.8 + "A ras-related C3 botulinum toxin substrate 3 that is encoded in the genome of Caenorhabditis elegans." [OMA:CAEEL09885, PRO:DNx] + rac-1 + cell death protein 10 (Caenorhabditis elegans) + worm-RAC3 + PR_EXT:Q03206 + ras-related protein ced-10 (Caenorhabditis elegans) + + + H3-K79-HMTase (yeast) + yDOT1 + YDR440W + histone H3-K79 methyltransferase (yeast) + PR_EXT:Q04089 + histone-lysine N-methyltransferase, H3 lysine-79 specific (yeast) + KMT4 + lysine N-methyltransferase 4 (yeast) + PR_EXT:histone-lysine N-methyltransferase, H3 lysine-79 specific (yeast) + PCH1 + disrupter of telomere silencing protein 1 (yeast) + "A protein that is a translation product of the DOT1 gene in yeast." [PRO:DNx, UniProtKB:Q04089] + D9461.26 + + + PR_EXT:protein unc-119 (Caenorhabditis elegans) + protein unc-119 (Caenorhabditis elegans) + "A protein that is a translation product of the unc-119 gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:Q10658] + PR_EXT:Q10658 + M142.1 + uncoordinated protein 119 (Caenorhabditis elegans) + worm-unc-119 + + + PR_EXT:Q12436 + yZRT2 + L3120 + PR_EXT:zinc-regulated transporter 2 (yeast) + YLR130C + low-affinity zinc transport protein ZRT2 (yeast) + zinc-regulated transporter 2 (yeast) + "A protein that is a translation product of the ZRT2 gene in yeast." [PRO:DNx, UniProtKB:Q12436] + + + female germline-specific tumor suppressor gld-1 (Caenorhabditis elegans) + defective in germ line development protein 1 (Caenorhabditis elegans) + T23G11.3 + PR_EXT:Q17339 + worm-gld-1 + PR_EXT:female germline-specific tumor suppressor gld-1 (Caenorhabditis elegans) + "A protein that is a translation product of the gld-1 gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:Q17339] + + + "A meiotic recombination protein SPO11 that is encoded in the genome of Caenorhabditis elegans." [OMA:CAEEL11634, PANTHER:PTHR10848\:SF0, PRO:DNx] + T05E11.4 + PR_EXT:Q22236 + worm-SPO11 + PR_EXT:meiotic recombination protein spo-11 (Caenorhabditis elegans) + meiotic recombination protein spo-11 (Caenorhabditis elegans) + + + "A protein that is a translation product of the smg gene in fruit fly." [PRO:DNx, UniProtKB:Q23972] + CG5263 + protein Smaug (fruit fly) + PR_EXT:protein Smaug (fruit fly) + PR_EXT:Q23972 + fly-smg + + + PR_EXT:SOX domain-containing protein dichaete (fruit fly) + fish + PR_EXT:Q24533 + SOX domain-containing protein dichaete (fruit fly) + "A protein that is a translation product of the D gene in fruit fly." [PRO:DNx, UniProtKB:Q24533] + protein fish-hook (fruit fly) + CG5893 + Sox70D + fly-D + + + worm-lin-15A + PR_EXT:Q27365 + ZK678.1 + PR_EXT:protein lin-15A (Caenorhabditis elegans) + "A protein that is a translation product of the lin-15A gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:Q27365] + protein lin-15A (Caenorhabditis elegans) + abnormal cell lineage protein 15A (Caenorhabditis elegans) + + + PR_EXT:kinesin-like protein KIF3B (mouse) + microtubule plus end-directed kinesin motor 3B (mouse) + "A kinesin-like protein KIF3B that is encoded in the genome of mouse." [OMA:MOUSE13356, PRO:DNx] + kinesin-like protein KIF3B (mouse) + mKIF3B + PR_EXT:Q61771 + + + Edr1 + polyhomeotic-like protein 1 (mouse) + Edr + PR_EXT:Q64028 + mPH1 (mouse) + "A polyhomeotic-like protein 1 that is encoded in the genome of mouse." [OMA:MOUSE19144, PRO:DNx] + RAE-28 (mouse) + early development regulatory protein 1 (mouse) + mPHC1 + Rae28 + PR_EXT:polyhomeotic-like protein 1 (mouse) + + + zTRIM33 + TIF1-gamma (zebrafish) + mon + "An E3 ubiquitin-protein ligase TRIM33 that is encoded in the genome of zebrafish." [OMA:DANRE25172, PRO:DNx] + PR_EXT:E3 ubiquitin-protein ligase TRIM33 (zebrafish) + ectodermin homolog (zebrafish) + PR_EXT:Q6E2N3 + RING-type E3 ubiquitin transferase TRIM33 (zebrafish) + transcription intermediary factor 1-gamma (zebrafish) + protein moonshine (zebrafish) + tripartite motif-containing protein 33 (zebrafish) + E3 ubiquitin-protein ligase TRIM33 (zebrafish) + + + PR_EXT:cytochrome c oxidase assembly protein COX11, mitochondrial (mouse) + "A cytochrome c oxidase assembly protein COX11, mitochondrial that is encoded in the genome of mouse." [OMA:MOUSE03827, PRO:DNx] + cytochrome c oxidase assembly protein COX11, mitochondrial (mouse) + PR_EXT:Q6P8I6 + mCOX11 + + + kinesin-like protein KIF15 (rat) + "A protein that is a translation product of the Kif15 gene in rat." [PRO:DNx, UniProtKB:Q7TSP2] + kinesin-like protein 2 (rat) + PR_EXT:kinesin-like protein KIF15 (rat) + rKif15 + Klp2 + PR_EXT:Q7TSP2 + + + Y106G6E.5 + cell death abnormality protein 12 (Caenorhabditis elegans) + "A protein that is a translation product of the ced-12 gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:Q8STE5] + worm-ced-12 + PR_EXT:Q8STE5 + PR_EXT:cell death abnormality protein 12 (Caenorhabditis elegans) + + + SHH (chicken) + "A sonic hedgehog protein that is encoded in the genome of chicken." [OMA:CHICK05349, PANTHER:PTHR11889\:SF16, PRO:DNx] + PR_EXT:sonic hedgehog protein (chicken) + PR_EXT:Q91035 + chick-SHH + sonic hedgehog protein (chicken) + + + "A histone acetyltransferase KAT2A that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q92830] + PR_EXT:histone acetyltransferase KAT2A (human) + PR_EXT:Q92830 + histone acetyltransferase KAT2A (human) + hKAT2A + + + "A protein that is a translation product of the lgs gene in fruit fly." [PRO:DNx, UniProtKB:Q961D9] + PR_EXT:Q961D9 + protein legless (fruit fly) + fly-lgs + protein BCL9 homolog (fruit fly) + BCL9 + PR_EXT:protein BCL9 homolog (fruit fly) + CG2041 + + + nuclear hormone receptor family member nhr-86 (Caenorhabditis elegans) + Y40B10A.8 + PR_EXT:nuclear hormone receptor family member nhr-86 (Caenorhabditis elegans) + worm-nhr-86 + PR_EXT:Q965W2 + "A protein that is a translation product of the nhr-86 gene in Caenorhabditis elegans." [PRO:DNx, UniProtKB:Q965W2] + + + Tip-associating protein (mouse) + Tip-associated protein (mouse) + nuclear RNA export factor 1 (mouse) + mRNA export factor TAP (mouse) + mNXF1 + Tap + PR_EXT:nuclear RNA export factor 1 (mouse) + PR_EXT:Q99JX7 + "A nuclear RNA export factor 1 that is encoded in the genome of mouse." [OMA:MOUSE11130, PRO:DNx] + + + PR_EXT:Q9BRQ0 + pygopus homolog 2 (human) + PR_EXT:pygopus homolog 2 (human) + hPYGO2 + "A pygopus homolog 2 that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q9BRQ0] + + + "A pygopus homolog 1 that is encoded in the genome of mouse." [OMA:MOUSE23818, PRO:DNx] + pygopus homolog 1 (mouse) + mPYGO1 + PR_EXT:Q9D0P5 + PR_EXT:pygopus homolog 1 (mouse) + + + worm-JMJD6 + PR_EXT:bifunctional arginine demethylase and lysyl-hydroxylase psr-1 (Caenorhabditis elegans) + phosphatidylserine receptor 1 (Caenorhabditis elegans) + F29B9.4 + bifunctional arginine demethylase and lysyl-hydroxylase psr-1 (Caenorhabditis elegans) + "A bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 that is encoded in the genome of Caenorhabditis elegans." [OMA:CAEEL10144, PANTHER:PTHR12480\:SF5, PRO:DNx] + PR_EXT:Q9GYI4 + + + cancer/testis antigen 39 (human) + hNXF2 + PR_EXT:nuclear RNA export factor 2 (human) + CT39 (human) + "A nuclear RNA export factor 2 that is encoded in the genome of human." [PRO:DAN, UniProtKB:Q9GZY0] + TAP-like protein 2 (human) + PR_EXT:Q9GZY0 + nuclear RNA export factor 2 (human) + hNXF2B + TAPL-2 (human) + + + "A nuclear RNA export factor 5 that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q9H1B4] + hNXF5 + PR_EXT:Q9H1B4 + nuclear RNA export factor 5 (human) + PR_EXT:nuclear RNA export factor 5 (human) + + + PR_EXT:Q9H4D5 + nuclear RNA export factor 3 (human) + hNXF3 + "A nuclear RNA export factor 3 that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q9H4D5] + PR_EXT:nuclear RNA export factor 3 (human) + + + mTACC3 + transforming acidic coiled-coil-containing protein 3 (mouse) + ARNT-interacting protein (mouse) + "A transforming acidic coiled-coil-containing protein 3 that is encoded in the genome of mouse." [OMA:MOUSE16779, PRO:DNx] + Aint + PR_EXT:transforming acidic coiled-coil-containing protein 3 (mouse) + PR_EXT:Q9JJ11 + + + cell death abnormality protein 2 (Caenorhabditis elegans) + PR_EXT:cell death abnormality protein 2 (Caenorhabditis elegans) + Y41D4B.13 + PR_EXT:Q9NHC3 + worm-CRKL + cell-corpse engulfment protein CED-2 (Caenorhabditis elegans) + "A Crk-like protein that is encoded in the genome of Caenorhabditis elegans." [PRO:DNx] + + + PR_EXT:Q9NPA3 + PR_EXT:mid1-interacting protein 1 (human) + hMID1IP1 + "A mid1-interacting protein 1 that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q9NPA3] + mid1-interacting protein 1 (human) + + + PR_EXT:Q9NS87 + "A kinesin-like protein KIF15 that is encoded in the genome of human." [PRO:CNx, Reactome:R-HSA-984825] + PR_EXT:kinesin-like protein KIF15 (human) + kinesin-like protein KIF15 (human) + hKIF15 + + + glycine-rich protein DOT1 (Arabidopsis thaliana) + PR_EXT:glycine-rich protein DOT1 (Arabidopsis thaliana) + At-DOT1 + protein DEFECTIVELY ORGANIZED TRIBUTARIES 1 (Arabidopsis thaliana) + At2g36120 + PR_EXT:Q9SIH2 + "A protein that is a translation product of the DOT1 gene in Arabidopsis thaliana." [PRO:DNx, UniProtKB:Q9SIH2] + + + CG1664 + DmNXF1 (fruit fly) + nxf1 + PR_EXT:Q9U1H9 + PR_EXT:nuclear RNA export factor 1 (fruit fly) + fly-NXF1 + protein small bristles (fruit fly) + "A nuclear RNA export factor 1 that is encoded in the genome of fruit fly." [OMA:DROME13273, PRO:DNx] + protein tip-associating (fruit fly) + nuclear RNA export factor 1 (fruit fly) + + + PR_EXT:nuclear RNA export factor 1 (human) + nuclear RNA export factor 1 (human) + PR_EXT:Q9UBU9 + hNXF1 + "A nuclear RNA export factor 1 that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q9UBU9] + + + protein btn1 (Schizosaccharomyces pombe 972h-) + SPAC607.09c + PR_EXT:protein btn1 (Schizosaccharomyces pombe 972h-) + PR_EXT:Q9US09 + "A battenin that is encoded in the genome of Schizosaccharomyces pombe 972h-." [OMA:SCHPO00846, PANTHER:PTHR10981\:SF0, PRO:DNx] + Spom972h-CLN3 + + + fly-COL8A1 + PR_EXT:protein pygopus (fruit fly) + CG11518 + "A collagen alpha-1(VIII) chain that is encoded in the genome of fruit fly." [PRO:DNx] + PR_EXT:Q9V9W8 + gam + protein pygopus (fruit fly) + protein gammy legs (fruit fly) + + + fly-sqz + "A protein that is a translation product of the sqz gene in fruit fly." [PRO:DNx, UniProtKB:Q9VDZ3] + CG5557 + PR_EXT:zinc finger protein squeeze (fruit fly) + PR_EXT:Q9VDZ3 + zinc finger protein squeeze (fruit fly) + + + PR_EXT:protein mini spindles (fruit fly) + protein mini spindles (fruit fly) + PR_EXT:Q9VEZ3 + "A protein that is a translation product of the msps gene in fruit fly." [PRO:DNx, UniProtKB:Q9VEZ3] + fly-msps + CG5000 + + + PR_EXT:polycomb protein Scm (fruit fly) + CG9495 + polycomb protein Scm (fruit fly) + fly-Scm + "A protein that is a translation product of the Scm gene in fruit fly." [PRO:DNx, UniProtKB:Q9VHA0] + PR_EXT:Q9VHA0 + sex comb on midleg protein (fruit fly) + + + CG4557 protein (fruit fly) + PR_EXT:Q9W3V2 + FI19713p1 (fruit fly) + PR_EXT:CG4557 protein (fruit fly) + "A hyaluronan mediated motility receptor that is encoded in the genome of fruit fly." [PRO:WCB] + fly-HMMR + CG4557 + + + nuclear RNA export factor 1 (Caenorhabditis elegans) + C15H11.3 + PR_EXT:nuclear RNA export factor 1 (Caenorhabditis elegans) + "A nuclear RNA export factor 1 that is encoded in the genome of Caenorhabditis elegans." [PRO:DNx] + PR_EXT:Q9XVS7 + worm-NXF1 + + + kinesin-like protein KIF3A (human) + PR_EXT:kinesin-like protein KIF3A (human) + PR_EXT:Q9Y496 + hKIF3A + "A kinesin-like protein KIF3A that is encoded in the genome of human." [PRO:DNx] + + + PR_EXT:Q9Y6A5 + "A transforming acidic coiled-coil-containing protein 3 that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q9Y6A5] + transforming acidic coiled-coil-containing protein 3 (human) + hTACC3 + PR_EXT:transforming acidic coiled-coil-containing protein 3 (human) + + + PR_EXT:'UV excision repair protein RAD23 (yeast)' (PR_EXT:P32628) or PR_EXT:'UV excision repair protein RAD23 homolog A' (PR_EXT:000013669) or PR_EXT:'UV excision repair protein RAD23 homolog B' (PR_EXT:000013670) + PR_EXT:RAD23 + RAD23 + PR_EXT:RAD23 + + + PR_EXT:'roundabout homolog 1' (PR_EXT:000014151) or PR_EXT:'roundabout homolog 2' (PR_EXT:000014152) or PR_EXT:'roundabout homolog 3' (PR_EXT:000014153) or PR_EXT:'roundabout homolog 4' (PR_EXT:000014154) + PR_EXT:ROBO + ROBO + PR_EXT:ROBO + + + PR_EXT:SLIT + SLIT + PR_EXT:SLIT + PR_EXT:'slit homolog 1 protein' (PR_EXT:000015234) or PR_EXT:'slit homolog 2 protein' (PR_EXT:000015235) or PR_EXT:'slit homolog 3 protein' (PR_EXT:000015236) + + + PR_EXT:SOXB1 + PR_EXT:SOXB1 + PR_EXT:'transcription factor SOX-1' (PR_EXT:000015417) or PR_EXT:'transcription factor SOX-2' (PR_EXT:000015426) or PR_EXT:'transcription factor SOX-3' (PR_EXT:000015428) + SOXB1 + + + transcription factor Dp + PR_EXT:TFDP + PR_EXT:'transcription factor Dp-1' (PR_EXT:000016269) or PR_EXT:'transcription factor Dp-2' (PR_EXT:000016270) or PR_EXT:'transcription factor Dp family member 3' (PR_EXT:000032577) + TFDP + PR_EXT:TFDP + + + PR_EXT:TIF1 + TIF1 + PR_EXT:'transcription intermediary factor 1-alpha' (PR_EXT:000016649) or PR_EXT:'transcription intermediary factor 1-beta' (PR_EXT:000016652) or PR_EXT:'E3 ubiquitin-protein ligase TRIM33' (PR_EXT:000016655) + PR_EXT:TIF1 + transcription intermediary factor 1 + TIF 1 + TIF-1 + transcriptional intermediary factor 1 + + + PR_EXT:'catenin alpha-1' (PR_EXT:000006006) or PR_EXT:'catenin alpha-2' (PR_EXT:000006007) or PR_EXT:'catenin alpha-3' (PR_EXT:000006008) + CTNNA + PR_EXT:alpha_catenin + PR_EXT:alpha-catenin + alpha-catenin + + + PR_EXT:alpha-crystallin + PR_EXT:'alpha-crystallin A chain' (PR_EXT:000005907) or PR_EXT:'alpha-crystallin B chain' (PR_EXT:000005908) + PR_EXT:alpha_crystallin + alpha-crystallin + + + PR_EXT:annexin + annexin + PR_EXT:annexin + PR_EXT:'annexin A1' (PR_EXT:000004071) or PR_EXT:'annexin A2' (PR_EXT:000004075) or PR_EXT:'annexin A3' (PR_EXT:000004076) or PR_EXT:'annexin A4' (PR_EXT:000004077) or PR_EXT:'annexin A5' (PR_EXT:000004078) or PR_EXT:'annexin A6' (PR_EXT:000004079) or PR_EXT:'annexin A7' (PR_EXT:000004080) or PR_EXT:'annexin A8' (PR_EXT:000004081) or PR_EXT:'annexin A9' (PR_EXT:000004084) or PR_EXT:'annexin A10' (PR_EXT:000004072) or PR_EXT:'annexin A11' (PR_EXT:000004073) or PR_EXT:'annexin A13' (PR_EXT:000004074) + + + PR_EXT:'S-arrestin' (PR_EXT:000014434) or PR_EXT:'beta-arrestin-1' (PR_EXT:0000043190 or PR_EXT:'beta-arrestin-2' (PR_EXT:000004320) or PR_EXT:'arrestin-C' (PR_EXT:000004318) + PR_EXT:arrestin + arrestin + PR_EXT:arrestin + + + carbonic anhydrase 2 + CA2 + carbonic anhydrase II + CA-II + Car2 + CAII + PR_EXT:carbonic_anhydrase_2 + PR_EXT:'carbonic anhydrase 2' (PR_EXT:000034449) or PR_EXT:'carbonic anhydrase 2' (PR:000004918) + PR_EXT:carbonic anhydrase 2 + + + PR_EXT:clathrin + clathrin + PR_EXT:'clathrin light chain A' (PR_EXT:000005612) or PR_EXT:'clathrin light chain B' (PR_EXT:000005613) or PR_EXT:'clathrin heavy chain 1' (PR_EXT:000030907) or PR_EXT:'clathrin heavy chain 2' (PR_EXT:000005614) + PR_EXT:clathrin + + + PR_EXT:cyclin_D + cyclin D + PR_EXT:cyclin D + PR_EXT:'G1/S-specific cyclin-D1' (PR_EXT:000005121) or PR_EXT:'G1/S-specific cyclin-D2' (PR_EXT:000005122) or PR_EXT:'G1/S-specific cyclin-D3' (PR_EXT:000005123) + CCND + + + PR_EXT:'flotillin-1' (PR_EXT:000007558) or PR_EXT:'flotillin-2' (PR_EXT:000007559) + flotillin + PR_EXT:flotillin + PR_EXT:flotillin + + + PR_EXT:glycogen synthase kinase-3 + PR_EXT:'glycogen synthase kinase-3 alpha' (PR_EXT:000008287) or PR_EXT:'glycogen synthase kinase-3 beta' (PR_EXT:000008288) + GSK3 + PR_EXT:glycogen_synthase_kinase_3 + glycogen synthase kinase-3 + + + PR_EXT:hedgehog + hedgehog + Hh + PR_EXT:hedgehog + PR_EXT:'desert hedgehog protein' (PR_EXT:000006459) or PR_EXT:'indian hedgehog protein' (PR_EXT:000008974) or PR_EXT:'sonic hedgehog protein' (PR_EXT:000014841) or PR_EXT:'tiggy-winkle hedgehog protein (zebrafish)' (PR_EXT:Q90419) + + + PR_EXT:keratin_6 + PR_EXT:'keratin, type II cytoskeletal 6A' (PR_EXT:000009482) or PR_EXT:'keratin, type II cytoskeletal 6B' (PR_EXT:000009483) or PR_EXT:'keratin, type II cytoskeletal 6C' (PR_EXT:000009484) + PR_EXT:keratin 6 + K6 + keratin-6 + KRT6 + keratin 6 + + + PR_EXT:'oxysterols receptor LXR-alpha' (PR_EXT:000011395) or PR_EXT:'oxysterols receptor LXR-beta' (PR_EXT:000011394) + PR_EXT:liver X receptor + liver X receptor + LXR + PR_EXT:liver_X_receptor + + + PR_EXT:'lymphotoxin-alpha' (PR_EXT:000002204) or PR_EXT:'lymphotoxin-beta' (PR_EXT:000002205) + PR_EXT:lymphotoxin + PR_EXT:lymphotoxin + lymphotoxin + + + MYOVII + myosin VII + PR_EXT:myosin VII + MYO7 + myosin 7 + myosin-7 + PR_EXT:myosin_VII + myosin-VII + PR_EXT:'myosin-VIIa' or PR_EXT:'myosin-VIIb' + + + PR_EXT:'parvalbumin alpha' (PR_EXT:000013502) or PR_EXT:'oncomodulin-1' (PR_EXT:000011592) + PVALB + parvalbumin + PR_EXT:parvalbumin + PR_EXT:parvalbumin + + + peripherin + PR_EXT:peripherin + PR_EXT:peripherin + PRPH + PR_EXT:peripherin (PR_EXT:000013289) or PR_EXT:'peripherin-2' (PR_EXT:000013290) + + + phosphoinositide phospholipase C gamma + PLCG + PR_EXT:phospholipase Cgamma + PLC-gamma + phospholipase Cgamma + PR_EXT:'1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1' (PR_EXT:000012836) or PR_EXT:'1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2' (PR_EXT:000012837) + PR_EXT:phospholipase_Cgamma + phospholipase C gamma + + + PR:'profilin-1' (PR:000012585) or PR:'profilin-2' (PR:000012586) or PR:'profilin-3' (PR:000012587) or PR:'profilin-4' (PR:000012588) + PR_EXT:profilin + PFN + PR_EXT:profilin + profilin + + + PR_EXT:selectin + PR_EXT:selectin + PR_EXT:'E/P-selectin' (PR_EXT:000001313) or PR_EXT:'L-selectin' (PR_EXT:000001318) + selectin + + + PR_EXT:'ATP-binding cassette sub-family G member 5' (PR_EXT:000003572) or PR_EXT:'ATP-binding cassette sub-family G member 8' (PR_EXT:000003573) + sterolin + PR_EXT:sterolin + PR_EXT:sterolin + + + PR_EXT:'syndecan (Caenorhabditis elegans)' (PR_EXT:P50605) or PR_EXT:'syndecan (fruit fly)' (PR_EXT:P49415) or PR_EXT:'syndecan-1' (PR_EXT:000001935) or PR_EXT:'syndecan-2' (PR_EXT:000014552) or PR_EXT:'syndecan-3' (PR_EXT:000001936) or PR_EXT:'syndecan-4' (PR_EXT:000014553) + PR_EXT:syndecan + syndecan + PR_EXT:syndecan + + + PR_EXT:'tumor necrosis factor, TNF-like' (PR_EXT:000000033) or PR_EXT:'tumor necrosis factor ligand superfamily member 4' (PR_EXT:000001949) or PR_EXT:'tumor necrosis factor ligand superfamily member 5' (PR_EXT:000001950) or PR_EXT:'CD70 molecule' (PR_EXT:000001309) or PR_EXT:'tumor necrosis factor ligand superfamily member 8' (PR_EXT:000001404) or PR_EXT:'tumor necrosis factor ligand superfamily member 9' (PR_EXT:000016489) or PR_EXT:'tumor necrosis factor ligand superfamily member 10/11' (PR_EXT:000001946) or PR_EXT:'tumor necrosis factor ligand superfamily member 12' (PR_EXT:000016487) or PR_EXT:'tumor necrosis factor ligand superfamily member 13' (PR_EXT:000001947) or PR_EXT:'tumor necrosis factor ligand superfamily member 13B' (PR_EXT:000001948) or PR_EXT:'tumor necrosis factor ligand superfamily member 18' (PR_EXT:000016488) or PR_EXT:'ectodysplasin-A' (PR_EXT:000006886) + TNF + tumour necrosis factor + PR_EXT:tumor_necrosis_factor + PR_EXT:tumor necrosis factor + tumor necrosis factor + + + PR_EXT:ubiquitin (PR_EXT:000035728) or PR_EXT:'ubiquitin (UBB)' (PR_EXT:000035726) or PR_EXT:'ubiquitin (UBC)' (PR_EXT:000035720) or PR_EXT:'ubiquitin (UBA52)' (PR_EXT:000035722) or PR_EXT:'ubiquitin (RPS27A)' (PR_EXT:000035716) + ubiquitin + PR_EXT:ubiquitin protein + PR_EXT:ubiquitin + ubiquitin protein + + + VEGF + PR_EXT:'vascular endothelial growth factor A' (PR_EXT:000017284) or PR_EXT:'vascular endothelial growth factor B' (PR_EXT:000003096) or PR_EXT:'vascular endothelial growth factor C' (PR_EXT:000017285) or PR_EXT:'vascular endothelial growth factor D' (PR_EXT:000007520) + vascular endothelial growth factor + PR_EXT:vascular endothelial growth factor + PR_EXT:vascuar_endothelial_growth_factor + + + PR extension classes + + + protein_coding + SO:protein_coding + protein-coding + SO:0000010 + + + SO:0000067 + gene to gene feature + SO:gene_to_gene_feature + gene_to_gene_feature + + + SO:overlapping + SO:0000068 + overlapping + "An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke] + + + SO:0000077 + antisense + SO:antisense + "A region sequence that is complementary to a sequence of messenger RNA." [SO:ke] + + + SO:0000237 + transcript_attribute + SO:transcript_attribute + transcript attribute + + + nucleic acid + SO:nucleic_acid + nucleic_acid + "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb] + SO:0000348 + + + synthetic_sequence + SO:0000351 + synthetic sequence + "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma] + SO:synthetic_sequence + + + "An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke] + SO:flanked + flanked + SO:0000357 + + + "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke] + SO:0000359 + SO:floxed + floxed + + + SO:FRT_flanked + "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke] + SO:0000361 + FRT flanked + FRT_flanked + + + sequence_attribute + SO:0000400 + "An attribute describes a quality of sequence." [SO:ke] + sequence attribute + SO:sequence_attribute + + + gene_attribute + SO:0000401 + gene attribute + SO:gene_attribute + + + SO:polymer_attribute + SO:0000443 + polymer_attribute + polymer attribute + "An attribute to describe the kind of biological sequence." [SO:ke] + + + predicted + "An attribute describing an unverified region." [SO:ke] + SO:0000732 + SO:predicted + + + SO:feature_attribute + feature attribute + feature_attribute + SO:0000733 + "An attribute describing a located_sequence_feature." [SO:ke] + + + SO:0000735 + sequence location + sequence_location + SO:sequence_location + + + organelle_sequence + SO:organelle_sequence + organelle sequence + SO:0000736 + + + SO:0000737 + SO:mitochondrial_sequence + mitochondrial_sequence + mitochondrial sequence + + + SO:conserved + conserved + SO:0000856 + + + homologous + SO:homologous + "Similarity due to common ancestry." [SO:ke] + SO:0000857 + + + orthologous + SO:0000858 + SO:orthologous + "An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke] + + + "An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke] + SO:0000859 + paralogous + SO:paralogous + + + SO:syntenic + "Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke] + SO:0000860 + syntenic + + + "An attribute describing an mRNA feature." [SO:ke] + mRNA attribute + SO:mRNA_attribute + SO:0000863 + mRNA_attribute + + + dicistronic + "An attribute describing a sequence that contains the code for two gene products." [SO:ke] + SO:0000879 + SO:dicistronic + + + SO:polycistronic + SO:0000880 + polycistronic + "An attribute describing a sequence that contains the code for more than one gene product." [SO:ke] + + + status + SO:0000905 + SO:status + "An attribute describing the status of a feature, based on the available evidence." [SO:ke] + + + SO:0000910 + SO:orphan + orphan + + + SO:cryptic + "A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke] + cryptic + SO:0000976 + + + strand attribute + SO:strand_attribute + SO:0000983 + strand_attribute + + + SO:0000984 + SO:single + single + + + SO:double + SO:0000985 + double + + + topology_attribute + SO:topology_attribute + topology attribute + SO:0000986 + + + two-ended + "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb] + SO:linear + SO:0000987 + linear + + + circular + SO:circular + zero-ended + SO:0000988 + "A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb] + + + SO:0000993 + SO:consensus + consensus + + + SO:direction_attribute + SO:0001029 + direction attribute + direction_attribute + + + forward + SO:0001030 + "Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke] + SO:forward + + + "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke] + SO:0001031 + SO:reverse + reverse + + + mtDNA + SO:0001032 + mitochondrial DNA + SO:mitochondrial_DNA + mitochondrial_DNA + + + SO:morpholino_backbone + morpholino backbone + "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb] + SO:0001183 + morpholino_backbone + + + variant_quality + variant quality + "A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke] + SO:0001761 + SO:variant_quality + + + SO:0001814 + coding variant quality + SO:coding_variant_quality + coding_variant_quality + + + non_synonymous + non synonymous + SO:non_synonymous + SO:0001816 + + + "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke] + inframe + SO:inframe + SO:0001817 + + + SO_EXT:0000001 + region + sequence + "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke] + SO_EXT:region + + + SO_EXT:0000002 + sequence secondary structure + SO_EXT:sequence_secondary_structure + "A folded sequence." [SO:ke] + sequence_secondary_structure + + + "A region amplified by a PCR reaction." [SO:ke] + SO_EXT:0000006 + PCR_product + SO_EXT:PCR_product + amplicon + PCR product + + + "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046] + linkage_group + linkage group + SO_EXT:linkage_group + SO_EXT:0000018 + + + base pair + SO_EXT:base_pair + base_pair + SO_EXT:0000028 + + + "A clone of a DNA region of a genome." [SO:ma] + genomic clone + genomic_clone + SO_EXT:0000040 + SO_EXT:genomic_clone + + + "A pseudogene created via retrotranposition of the mRNA of a functional protein-coding parent gene followed by accumulation of deleterious mutations lacking introns and promoters, often including a polyA tail." [GENCODE:http\://www.gencodegenes.org/gencode_biotypes.html] + processed_pseudogene + R psi G + pseudogene by reverse transcription + retropseudogene + SO_EXT:processed_pseudogene + SO_EXT:0000043 + processed pseudogene + + + nuclease binding site + "A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb] + nuclease_binding_site + SO_EXT:nuclease_binding_site + SO_EXT:0000059 + + + "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb] + SO_EXT:0000061 + restriction_enzyme_binding_site + SO_EXT:restriction_enzyme_binding_site + restriction endonuclease binding site + restriction enzyme binding site + + + SO_EXT:polycistronic_transcript + "A transcript that is polycistronic." [SO:xp] + polycistronic_transcript + polycistronic transcript + SO_EXT:0000078 + + + "A transcript that is dicistronic." [SO:ke] + dicistronic_transcript + dicistronic transcript + SO_EXT:dicistronic_transcript + SO_EXT:0000079 + + + SO_EXT:0000087 + nuclear_gene + SO_EXT:nuclear_gene + nuclear gene + "A gene from nuclear sequence." [SO:xp] + + + SO_EXT:0000088 + mitochondrial gene + mt_gene + mt gene + SO_EXT:mt_gene + "A gene located in mitochondrial sequence." [SO:xp] + + + transposon + SO_EXT:0000101 + transposable_element + transposable element + SO_EXT:transposable_element + "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html] + + + SO_EXT:chromosome_arm + chromosome_arm + SO_EXT:0000105 + "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152] + chromosome arm + + + sequence feature + located sequence feature + sequence_feature + SO_EXT:sequence_feature + "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke] + located_sequence_feature + SO_EXT:0000110 + + + SO_EXT:0000112 + primer polynucleotide + primer oligonucleotide + primer + DNA primer + "An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke] + primer sequence + SO_EXT:primer + + + pre mRNA + protein_coding_primary_transcript + "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke] + protein coding primary transcript + SO_EXT:protein_coding_primary_transcript + SO_EXT:0000120 + + + forward_primer + DNA forward primer + forward DNA primer + SO_EXT:forward_primer + forward primer polynucleotide + forward primer + forward primer sequence + SO_EXT:0000121 + "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] + forward primer oligo + forward primer oligonucleotide + + + SO_EXT:0000122 + "A folded RNA sequence." [SO:ke] + RNA_sequence_secondary_structure + RNA sequence secondary structure + SO_EXT:RNA_sequence_secondary_structure + + + reverse primer oligonucleotide + reverse primer oligo + DNA reverse primer + reverse DNA primer + SO_EXT:reverse_primer + reverse_primer + SO_EXT:0000132 + reverse primer sequence + reverse primer + "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] + + + SO_EXT:0000139 + SO_EXT:ribosome_entry_site + "Region in mRNA where ribosome assembles." [SO:ke] + ribosome_entry_site + ribosome entry site + + + terminator + SO_EXT:terminator + terminator sequence + "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + SO_EXT:0000141 + + + SO_EXT:assembly_component + assembly component + "A region of known length which may be used to manufacture a longer region." [SO:ke] + assembly_component + SO_EXT:0000143 + + + SO_EXT:0000147 + "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke] + exon + SO_EXT:exon + + + SO_EXT:contig + "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls] + contig + SO_EXT:0000149 + + + read + "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd] + SO_EXT:read + SO_EXT:0000150 + + + "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke] + SO_EXT:0000151 + SO_EXT:clone + clone + + + bacterial artificial chromosome + BAC + "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma] + SO_EXT:0000153 + SO_EXT:BAC + + + P1 + SO_EXT:PAC + PAC + SO_EXT:0000154 + P1 artificial chromosome + "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome] + + + plasmid sequence + SO_EXT:0000155 + "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma] + SO_EXT:plasmid + plasmid + + + "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma] + cosmid vector + SO_EXT:0000156 + cosmid + SO_EXT:cosmid + + + splice site + "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke] + splice_site + SO_EXT:0000162 + SO_EXT:splice_site + + + SO_EXT:enhancer + enhancer + SO_EXT:0000165 + "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + + + promoter sequence + SO_EXT:promoter + "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative] + promoter + SO_EXT:0000167 + + + CAAT signal + "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + CAAT-box + CAAT_signal + SO_EXT:0000172 + CAAT box + SO_EXT:CAAT_signal + + + primary_transcript + SO_EXT:0000185 + primary transcript + SO_EXT:primary_transcript + precursor RNA + "A transcript that in its initial state requires modification to be functional." [SO:ma] + + + SO_EXT:intron + intron + "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + SO_EXT:0000188 + + + SO_EXT:0000190 + five prime intron + 5' intron sequence + 5' intron + SO_EXT:five_prime_intron + five_prime_intron + + + restriction fragment length polymorphism + SO_EXT:0000193 + SO_EXT:RFLP_fragment + "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj] + RFLP fragment + RFLP + RFLP_fragment + + + coding exon + "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke] + SO_EXT:0000195 + SO_EXT:coding_exon + coding_exon + + + noncoding exon + SO_EXT:0000198 + "An exon that does not contain any codons." [SO:ke] + noncoding_exon + SO_EXT:noncoding_exon + + + five_prime_coding_exon + SO_EXT:0000200 + "The 5' most coding exon." [SO:ke] + 5' coding exon + five prime coding exon + SO_EXT:five_prime_coding_exon + + + untranslated region + "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke] + SO_EXT:0000203 + SO_EXT:UTR + UTR + + + 5' UTR + five prime UTR + SO_EXT:0000204 + "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + five_prime_UTR + SO_EXT:five_prime_UTR + five_prime_untranslated_region + + + SO_EXT:three_prime_UTR + "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + SO_EXT:0000205 + three prime UTR + three prime untranslated region + three_prime_UTR + + + simple sequence length variation + SO_EXT:simple_sequence_length_variation + simple_sequence_length_variation + SSLP + SO_EXT:0000207 + simple sequence length polymorphism + "SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ." [SO:ke] + + + SO_EXT:0000233 + mature transcript + "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke] + mature_transcript + SO_EXT:mature_transcript + + + SO_EXT:0000234 + "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma] + protein_coding_transcript + messenger RNA + mRNA + SO_EXT:mRNA + + + SO_EXT:0000235 + TF binding site + "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke] + TF_binding_site + transcription factor binding site + SO_EXT:TF_binding_site + + + "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma] + ORF + SO_EXT:0000236 + SO_EXT:ORF + open reading frame + + + "The sequences extending on either side of a specific region." [SO:ke] + flanking_region + SO_EXT:0000239 + flanking region + SO_EXT:flanking_region + + + SO_EXT:0000243 + IRES + SO_EXT:internal_ribosome_entry_site + internal ribosome entry sequence + internal_ribosome_entry_site + internal ribosomal entry sequence + internal ribosome entry site + internal ribosomal entry site + "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke] + + + "A kind of kind of sequence alteration where the copies of a region present varies across a population." [SO:ke] + sequence length alteration + SO_EXT:sequence_length_alteration + SO_EXT:0000248 + sequence_length_alteration + + + ribosomal ribonucleic acid + ribosomal RNA + "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732] + rRNA + SO_EXT:rRNA + SO_EXT:0000252 + + + "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + SO_EXT:origin_of_replication + ori + origin_of_replication + SO_EXT:0000296 + origin of replication + + + displacement loop + "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + SO_EXT:0000297 + D_loop + D-loop + SO_EXT:D_loop + + + recombination feature + recombination_feature + SO_EXT:0000298 + SO_EXT:recombination_feature + + + specific recombination site + SO_EXT:0000299 + SO_EXT:specific_recombination_site + specific_recombination_site + + + stem-loop + stem_loop + SO_EXT:stem_loop + "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + stem loop + SO_EXT:0000313 + RNA_hairpin_loop + + + "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke] + transcription_start_site + transcription start site + TSS + SO_EXT:0000315 + SO_EXT:TSS + + + CDS + SO_EXT:0000316 + coding sequence + "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma] + coding_sequence + SO_EXT:CDS + + + cDNA_clone + SO_EXT:0000317 + cDNA clone + SO_EXT:cDNA_clone + "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] + + + SO_EXT:start_codon + SO_EXT:0000318 + start_codon + initiation codon + start codon + "First codon to be translated by a ribosome." [SO:ke] + + + stop_codon + "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke] + SO_EXT:0000319 + stop codon + SO_EXT:stop_codon + + + translation start + coding_start + coding start + SO_EXT:0000323 + translation initiation site + "The first base to be translated into protein." [SO:ke] + SO_EXT:coding_start + + + "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke] + tag + SO_EXT:tag + SO_EXT:0000324 + + + conserved region + "Region of sequence similarity by descent from a common ancestor." [SO:ke] + SO_EXT:0000330 + conserved_region + SO_EXT:conserved_region + + + sequence tag site + STS + "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com] + SO_EXT:STS + SO_EXT:0000331 + + + exon junction + "The boundary between two exons in a processed transcript." [SO:ke] + exon_junction + SO_EXT:exon_junction + SO_EXT:0000333 + + + SO_EXT:0000336 + SO_EXT:pseudogene + "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] + pseudogene + + + SO_EXT:0000340 + chromosome + "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma] + SO_EXT:chromosome + + + site specific recombination target region + SO_EXT:site_specific_recombination_target_region + site_specific_recombination_target_region + SO_EXT:0000342 + + + match + "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke] + SO_EXT:match + SO_EXT:0000343 + + + EST + expressed sequence tag + "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke] + SO_EXT:EST + SO_EXT:0000345 + + + SO_EXT:loxP_site + loxP site + loxP_site + SO_EXT:0000346 + Cre-recombination target region + + + FRT_site + SO_EXT:0000350 + SO_EXT:FRT_site + "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma] + FRT site + FLP recombination target region + + + SO_EXT:sequence_assembly + "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma] + sequence_assembly + SO_EXT:0000353 + sequence assembly + + + SO_EXT:0000360 + codon + SO_EXT:codon + "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [SO:ke] + + + SO_EXT:0000363 + floxed gene + "A transgene that is floxed." [SO:xp] + SO_EXT:floxed_gene + floxed_gene + + + SO_EXT:0000366 + insertion site + insertion_site + "The junction where an insertion occurred." [SO:ke] + SO_EXT:insertion_site + + + 18S rRNA + rRNA_18S + "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke] + SO_EXT:rRNA_18S + rRNA 18S + 18S ribosomal RNA + SO_EXT:0000407 + + + binding_or_interaction_site + site + SO_EXT:0000409 + binding_site + "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke] + SO_EXT:binding_site + + + SO_EXT:protein_binding_site + "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke] + SO_EXT:0000410 + protein_binding_site + protein binding site + + + SO_EXT:0000412 + restriction_fragment + restriction fragment + "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke] + SO_EXT:restriction_fragment + + + SO_EXT:0000417 + polypeptide domain + "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR] + polypeptide_domain + SO_EXT:polypeptide_domain + polypeptide_structural_domain + + + vector_replicon + vector + vector replicon + SO_EXT:vector_replicon + SO_EXT:0000440 + "A replicon that has been modified to act as a vector for foreign sequence." [SO:ma] + + + SO_EXT:ss_oligo + single stranded oligonucleotide + single strand oligonucleotide + single strand oligo + ss_oligo + ss oligonucleotide + ss oligo + SO_EXT:0000441 + "A single stranded oligonucleotide." [SO:ke] + + + ds-oligonucleotide + SO_EXT:ds_oligo + ds oligo + "A double stranded oligonucleotide." [SO:ke] + SO_EXT:0000442 + double stranded oligonucleotide + ds_oligo + + + 5' non coding exon + "Non-coding exon in the 5' UTR." [SO:ke] + 5' nc exon + SO_EXT:five_prime_noncoding_exon + SO_EXT:0000445 + five_prime_noncoding_exon + five prime noncoding exon + + + SO_EXT:0000484 + "The sequence of the 3' exon that is not coding." [SO:ke] + SO_EXT:three_prime_coding_exon_noncoding_region + three_prime_coding_exon_noncoding_region + three_prime_exon_noncoding_region + three prime coding exon noncoding region + + + five_prime_exon_noncoding_region + five prime coding exon noncoding region + SO_EXT:five_prime_coding_exon_noncoding_region + "The sequence of the 5' exon preceding the start codon." [SO:ke] + five_prime_coding_exon_noncoding_region + SO_EXT:0000486 + + + poly(A) signal + SO_EXT:polyA_signal_sequence + SO_EXT:0000551 + polyadenylation termination signal + "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + polyA_signal_sequence + polyA signal sequence + + + SO_EXT:0000553 + polyA_site + polyadenylation site + polyA junction + polyA site + SO_EXT:polyA_site + "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + polyA_junction + polyA cleavage site + + + SO_EXT:bidirectional_promoter + bidirectional_promoter + bidirectional promoter + SO_EXT:0000568 + "An unregulated promoter that allows continuous expression." [SO:ke] + + + cap + SO_EXT:0000581 + "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] + SO_EXT:cap + + + intergenic_region + "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm] + SO_EXT:intergenic_region + SO_EXT:0000605 + intergenic region + + + polyA_sequence + "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke] + polyA sequence + SO_EXT:0000610 + SO_EXT:polyA_sequence + + + branch site + branch_point + "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke] + SO_EXT:branch_site + branch point + SO_EXT:0000611 + branch_site + + + polypyrimidine tract + polypyrimidine_tract + "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888] + SO_EXT:0000612 + SO_EXT:polypyrimidine_tract + + + "The base where transcription ends." [SO:ke] + transcription end site + transcription_end_site + SO_EXT:transcription_end_site + SO_EXT:0000616 + + + "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke] + SO_EXT:0000625 + SO_EXT:silencer + silencer + + + polycistronic processed transcript + SO_EXT:0000634 + "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd] + SO_EXT:polycistronic_mRNA + polycistronic_mRNA + polycistronic mRNA + + + antisense RNA + SO_EXT:antisense_RNA + SO_EXT:0000644 + antisense_RNA + "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke] + + + "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000] + SO_EXT:siRNA + SO_EXT:0000646 + small interfering RNA + siRNA + + + small subunit rRNA + SO_EXT:0000650 + "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke] + SSU RNA + small_subunit_rRNA + SSU rRNA + SO_EXT:small_subunit_rRNA + + + SO_EXT:0000651 + large_subunit_rRNA + SO_EXT:large_subunit_rRNA + "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke] + LSU rRNA + large subunit rRNA + LSU RNA + + + SO_EXT:rRNA_28S + SO_EXT:0000653 + rRNA_28S + 28S LSU rRNA + 28S ribosomal RNA + 28S rRNA + rRNA 28S + "A component of the large ribosomal subunit." [SO:ke] + + + noncoding RNA + SO_EXT:ncRNA + SO_EXT:0000655 + "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] + ncRNA + known_ncrna + + + repeat_region + SO_EXT:0000657 + repeat region + SO_EXT:repeat_region + "A region of sequence containing one or more repeat units." [SO:ke] + + + nucleotide insertion + insertion + "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke] + nucleotide_insertion + SO_EXT:0000667 + SO_EXT:insertion + insertion + + + sequence_rearrangement_feature + sequence rearrangement feature + SO_EXT:0000669 + SO_EXT:sequence_rearrangement_feature + + + "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma] + SO_EXT:0000673 + transcript + SO_EXT:transcript + + + SO_EXT:deletion_junction + "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke] + SO_EXT:0000687 + deletion junction + deletion_junction + + + SNP + SO_EXT:0000694 + SO_EXT:SNP + "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb] + single nucleotide polymorphism + + + "A sequence used in experiment." [SO:ke] + SO_EXT:reagent + SO_EXT:0000695 + reagent + + + SO_EXT:0000696 + oligonucleotide + oligo + SO_EXT:oligo + "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma] + + + boundary + SO_EXT:junction + breakpoint + SO_EXT:0000699 + junction + "A sequence_feature with an extent of zero." [SO:ke] + + + SO_EXT:remark + "A comment about the sequence." [SO:ke] + remark + SO_EXT:0000700 + + + experimental result region + SO_EXT:0000703 + experimental_result_region + SO_EXT:experimental_result_region + "A region of sequence implicated in an experimental result." [SO:ke] + + + SO_EXT:0000704 + SO_EXT:gene + gene + "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop] + + + SO_EXT:0000713 + SO_EXT:DNA_motif + "A motif that is active in the DNA form of the sequence." [SO:ke] + DNA motif + DNA_motif + + + nucleotide motif + SO_EXT:0000714 + SO_EXT:nucleotide_motif + nucleotide_motif + "A region of nucleotide sequence corresponding to a known motif." [SO:ke] + + + SO_EXT:dicistronic_mRNA + dicistronic_mRNA + SO_EXT:0000716 + "An mRNA that has the quality dicistronic." [SO:ke] + dicistronic processed transcript + dicistronic mRNA + + + reading_frame + SO_EXT:0000717 + SO_EXT:reading_frame + "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb] + reading frame + + + cis regulatory module + SO_EXT:CRM + SO_EXT:0000727 + transcription factor module + CRM + TF module + "A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG] + + + SO_EXT:0000730 + "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke] + SO_EXT:gap + gap + + + "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke] + clone_insert + clone insert + SO_EXT:0000753 + SO_EXT:clone_insert + + + lambda_vector + "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8] + lambda vector + SO_EXT:0000754 + SO_EXT:lambda_vector + + + SO_EXT:plasmid_vector + plasmid vector + plasmid_vector + SO_EXT:0000755 + + + SO_EXT:QTL + QTL + quantitative trait locus + "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/] + SO_EXT:0000771 + + + SO_EXT:engineered_region + construct + engineered sequence + engineered region + "A region that is engineered." [SO:xp] + engineered_region + SO_EXT:0000804 + + + SO_EXT:invalidated_cDNA_clone + invalidated cDNA clone + SO_EXT:0000809 + invalidated_cDNA_clone + "A cDNA clone that is invalid." [SO:xp] + + + chimeric cDNA clone + SO_EXT:0000810 + chimeric_cDNA_clone + SO_EXT:chimeric_cDNA_clone + "A cDNA clone invalidated because it is chimeric." [SO:xp] + + + "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143] + mini_gene + SO_EXT:0000815 + SO_EXT:mini_gene + mini gene + + + chromosome part + "A region of a chromosome." [SO:ke] + SO_EXT:0000830 + SO_EXT:chromosome_part + chromosome_part + + + SO_EXT:gene_member_region + SO_EXT:0000831 + gene_member_region + "A region of a gene." [SO:ke] + gene member region + + + transcript region + SO_EXT:transcript_region + transcript_region + "A region of a transcript." [SO:ke] + SO_EXT:0000833 + + + mature_transcript_region + SO_EXT:0000834 + SO_EXT:mature_transcript_region + mature transcript region + "A region of a mature transcript." [SO:ke] + + + primary transcript region + "A part of a primary transcript." [SO:ke] + SO_EXT:0000835 + SO_EXT:primary_transcript_region + primary_transcript_region + + + SO_EXT:0000836 + mRNA_region + SO_EXT:mRNA_region + mRNA region + "A region of an mRNA." [SO:cb] + + + SO_EXT:0000837 + "A region of UTR." [SO:ke] + UTR_region + UTR region + SO_EXT:UTR_region + + + polypeptide_region + SO_EXT:0000839 + positional + SO_EXT:polypeptide_region + region or site annotation + "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke] + positional polypeptide feature + + + SO_EXT:spliceosomal_intron_region + "A region within an intron." [SO:ke] + spliceosomal_intron_region + SO_EXT:0000841 + spliceosomal intron region + + + gene_component_region + gene component region + SO_EXT:gene_component_region + SO_EXT:0000842 + + + "A region of a CDS." [SO:cb] + CDS_region + CDS region + SO_EXT:0000851 + SO_EXT:CDS_region + + + SO_EXT:exon_region + exon_region + exon region + "A region of an exon." [RSC:cb] + SO_EXT:0000852 + + + homologous_region + homologous region + "A region that is homologous to another region." [SO:ke] + homolog + SO_EXT:homologous_region + homologue + SO_EXT:0000853 + + + paralogous region + SO_EXT:paralogous_region + paralog + paralogue + paralogous_region + SO_EXT:0000854 + "A homologous_region that is paralogous to another region." [SO:ke] + + + orthologous_region + ortholog + orthologue + SO_EXT:orthologous_region + orthologous region + SO_EXT:0000855 + "A homologous_region that is orthologous to another region." [SO:ke] + + + polyadenylated_mRNA + SO_EXT:polyadenylated_mRNA + "An mRNA that is polyadenylated." [SO:xp] + SO_EXT:0000871 + polyadenylated mRNA + + + "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp] + SO_EXT:0000902 + transgene + SO_EXT:transgene + + + cloned cDNA insert + SO_EXT:cloned_cDNA_insert + SO_EXT:0000913 + cloned_cDNA_insert + "A clone insert made from cDNA." [SO:xp] + + + SO_EXT:0000932 + pre-edited mRNA + SO_EXT:pre_edited_mRNA + pre_edited_mRNA + + + res site + SO_EXT:0000947 + SO_EXT:resolution_site + "A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as] + resolution_site + resolution site + + + inversion site + SO_EXT:0000948 + inversion_site + SO_EXT:inversion_site + "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma] + + + SO_EXT:0000954 + DNA chromosome + DNA_chromosome + "Structural unit composed of a self-replicating, DNA molecule." [SO:ma] + SO_EXT:DNA_chromosome + + + consensus_region + SO_EXT:0000994 + consensus region + SO_EXT:consensus_region + + + SO_EXT:predicted_gene + predicted_gene + SO_EXT:0000996 + predicted gene + + + gene fragment + gene_fragment + SO_EXT:gene_fragment + SO_EXT:0000997 + + + BAC_end + BAC end + BES + SO_EXT:0000999 + BAC end sequence + "A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke] + SO_EXT:BAC_end + + + SO_EXT:intron_domain + intron domain + intron_domain + SO_EXT:0001014 + + + aberration_junction + SO_EXT:0001021 + aberration breakpoint + chromosome_breakpoint + SO_EXT:chromosome_breakpoint + chromosome breakpoint + + + SO_EXT:0001023 + SO_EXT:allele + allele + "An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop] + allelomorph + + + SO_EXT:0001024 + SO_EXT:haplotype + "A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop] + haplotype + + + SO_EXT:0001026 + genome + "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop] + SO_EXT:genome + + + SO_EXT:0001037 + MGE + mobile genetic element + "A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355] + mobile_genetic_element + SO_EXT:mobile_genetic_element + + + SO_EXT:integrated_mobile_genetic_element + "An MGE that is integrated into the host chromosome." [SO:ke] + SO_EXT:0001039 + integrated_mobile_genetic_element + integrated mobile genetic element + + + transcription-control region + transcriptional_cis_regulatory_region + transcriptional cis regulatory region + "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative] + SO_EXT:transcriptional_cis_regulatory_region + SO_EXT:0001055 + + + sequence_alteration + SO_EXT:0001059 + SO_EXT:sequence_alteration + "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke] + sequence variation + sequence alteration + + + "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] + sequence variant + sequence_variant + VAAST:sequence_variant + SO_EXT:0001060 + SO_EXT:sequence_variant + ANNOVAR:unknown + Jannovar:sequence_variant + + + propep + propeptide + "Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR] + SO_EXT:0001062 + SO_EXT:propeptide + + + polypeptide motif + "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual] + polypeptide_motif + SO_EXT:0001067 + SO_EXT:polypeptide_motif + + + polypeptide_structural_region + structural_region + SO_EXT:0001070 + polypeptide structural region + "Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb] + SO_EXT:polypeptide_structural_region + + + SO_EXT:intramembrane_polypeptide_region + SO_EXT:0001075 + intramembrane + "Polypeptide region present in the lipid bilayer." [EBIBS:GAR] + intramembrane polypeptide region + intramembrane_polypeptide_region + + + SO_EXT:transmembrane_polypeptide_region + "Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual] + transmembrane + transmembrane polypeptide region + transmem + transmembrane_polypeptide_region + SO_EXT:0001077 + + + 2nary structure + SO_EXT:polypeptide_secondary_structure + secondary structure region + secondary_structure + SO_EXT:0001078 + secondary structure + polypeptide_secondary_structure + polypeptide secondary structure + "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR] + + + polypeptide_structural_motif + structural_motif + SO_EXT:0001079 + SO_EXT:polypeptide_structural_motif + polypeptide structural motif + "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR] + + + SO_EXT:coiled_coil + coiled + SO_EXT:0001080 + coiled_coil + "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual] + coiled coil + + + post_translationally_modified_region + post_translational_modification + mod_res + SO_EXT:post_translationally_modified_region + modified residue + SO_EXT:0001089 + "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual] + + + act_site + "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual] + SO_EXT:catalytic_residue + catalytic residue + active site residue + SO_EXT:0001104 + catalytic_residue + + + SO_EXT:peptide_helix + "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR] + peptide_helix + SO_EXT:0001114 + helix + + + right handed helix + SO_EXT:right_handed_peptide_helix + "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR] + SO_EXT:0001116 + right_handed_peptide_helix + helix + + + alpha_helix + a-helix + SO_EXT:0001117 + SO_EXT:alpha_helix + "The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR] + helix + + + SO_EXT:RNA_polymerase_promoter + SO_EXT:0001203 + RNA_polymerase_promoter + RNA polymerase promoter + "A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb] + + + "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb] + SO_EXT:0001204 + Phage RNA Polymerase Promoter + SO_EXT:Phage_RNA_Polymerase_Promoter + Phage_RNA_Polymerase_Promoter + + + T7_RNA_Polymerase_Promoter + T7 RNA Polymerase Promoter + SO_EXT:T7_RNA_Polymerase_Promoter + "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb] + SO_EXT:0001207 + + + noncoding region of exon + SO_EXT:0001214 + SO_EXT:noncoding_region_of_exon + "The maximal intersection of exon and UTR." [SO:ke] + noncoding_region_of_exon + + + SO_EXT:coding_region_of_exon + coding region of exon + coding_region_of_exon + "The region of an exon that encodes for protein sequence." [SO:ke] + SO_EXT:0001215 + + + SO_EXT:replicon + SO_EXT:0001235 + replicon + "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207] + + + "A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb] + amino_acid + amino acid + SO_EXT:amino_acid + SO_EXT:0001237 + + + "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke] + SO_EXT:assembly + SO_EXT:0001248 + assembly + + + fragment assembly + physical map + SO_EXT:fragment_assembly + SO_EXT:0001249 + fragment_assembly + "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke] + + + restriction map + BACmap + SO_EXT:0001250 + SO_EXT:fingerprint_map + fingerprint_map + FPCmap + "A fingerprint_map is a physical map composed of restriction fragments." [SO:ke] + fingerprint map + FPC + + + sequence_collection + SO_EXT:0001260 + SO_EXT:sequence_collection + "A collection of discontinuous sequences." [SO:ke] + sequence collection + + + "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke] + SO_EXT:0001261 + overlapping feature set + overlapping_feature_set + SO_EXT:overlapping_feature_set + + + SO_EXT:CDS_fragment + CDS_fragment + SO_EXT:0001384 + incomplete CDS + CDS fragment + + + biomaterial_region + "A region which is intended for use in an experiment." [SO:cb] + biomaterial region + SO_EXT:0001409 + SO_EXT:biomaterial_region + + + "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb] + SO_EXT:experimental_feature + experimental output artefact + experimental_output_artefact + analysis feature + experimental_feature + SO_EXT:0001410 + + + "A region defined by its disposition to be involved in a biological process." [SO:cb] + SO_EXT:biological_region + biological_region + SO_EXT:0001411 + biological region + + + topologically defined region + SO_EXT:topologically_defined_region + topologically_defined_region + "A region that is defined according to its relations with other regions within the same sequence." [SO:cb] + SO_EXT:0001412 + + + insertion breakpoint + "The point within a chromosome where a insertion begins or ends." [SO:cb] + SO_EXT:0001414 + SO_EXT:insertion_breakpoint + insertion_breakpoint + + + SO_EXT:deletion_breakpoint + SO_EXT:0001415 + "The point within a chromosome where a deletion begins or ends." [SO:cb] + deletion_breakpoint + deletion breakpoint + + + five_prime_flanking_region + "A flanking region located five prime of a specific region." [SO:chado] + SO_EXT:0001416 + SO_EXT:five_prime_flanking_region + five prime flanking region + 5' flanking region + + + three prime flanking region + SO_EXT:three_prime_flanking_region + "A flanking region located three prime of a specific region." [SO:chado] + three_prime_flanking_region + SO_EXT:0001417 + 3' flanking region + + + splice_junction + splice boundary + SO_EXT:splice_junction + "The boundary between an intron and an exon." [SO:ke] + splice junction + SO_EXT:0001421 + + + expressed sequence assembly + SO_EXT:expressed_sequence_assembly + expressed_sequence_assembly + "A sequence assembly derived from expressed sequences." [SO:ke] + SO_EXT:0001428 + + + DNA binding site + SO_EXT:DNA_binding_site + "A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke] + SO_EXT:0001429 + DNA_binding_site + + + single nucleotide variant + SO_EXT:SNV + SO_EXT:0001483 + "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm] + SNV + + + variant_collection + "A collection of one or more sequences of an individual." [SO:ke] + SO_EXT:0001507 + variant collection + SO_EXT:variant_collection + + + peptide_localization_signal + "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke] + SO_EXT:0001527 + peptide localization signal + localization signal + SO_EXT:peptide_localization_signal + + + nuclear_localization_signal + SO_EXT:nuclear_localization_signal + SO_EXT:0001528 + "A polypeptide region that targets a polypeptide to the nucleus." [SO:ke] + NLS + + + "A polypeptide region that targets a polypeptide to the endosome." [SO:ke] + SO_EXT:0001529 + endosomal_localization_signal + SO_EXT:endosomal_localization_signal + endosomal localization signal + + + lysosomal_localization_signal + lysosomal localization signal + SO_EXT:lysosomal_localization_signal + "A polypeptide region that targets a polypeptide to the lysosome." [SO:ke] + SO_EXT:0001530 + + + "A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke] + NES + nuclear_export_signal + SO_EXT:nuclear_export_signal + nuclear export signal + SO_EXT:0001531 + + + "A region recognized by a recombinase." [SO:ke] + recombination signal sequence + SO_EXT:recombination_signal_sequence + recombination_signal_sequence + SO_EXT:0001532 + + + structural variant + Jannovar:structural_variant + SO_EXT:0001537 + SO_EXT:structural_variant + VAT:svOverlap + structural_variant + "A sequence variant that changes one or more sequence features." [SO:ke] + + + SO_EXT:0001564 + VAAST:gene_variant + SO_EXT:gene_variant + gene structure variant + "A sequence variant where the structure of the gene is changed." [SO:ke] + gene_variant + snpEff:GENE + Jannovar:gene_variant + + + SO_EXT:0001576 + transcript variant + Jannovar:transcript_variant + SO_EXT:transcript_variant + transcript_variant + VAAST:transcript_variant + snpEff:TRANSCRIPT + "A sequence variant that changes the structure of the transcript." [SO:ke] + + + SO_EXT:coding_sequence_variant + "A sequence variant that changes the coding sequence." [SO:ke] + codon_variant + coding sequence variant + codon variant + coding_sequence_variant + snpEff:CDS + VEP:coding_sequence_variant + coding variant + Jannovar:coding_sequence_variant + snpEff:CODON_CHANGE + Seattleseq:coding + VAAST:coding_sequence_variant + SO_EXT:0001580 + + + Seattleseq:stop-gained-near-splice + Seattleseq:stop-gained + SO_EXT:0001587 + nonsense + ANNOVAR:stopgain + VEP:stop_gained + stop_gained + SO_EXT:stop_gained + stop gained + VAT:prematureStop + "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide." [SO:ke] + nonsense codon + VAAST:stop_gained + snpEff:STOP_GAINED + stop codon gained + Jannovar:stop_gained + + + targeting_vector + SO_EXT:targeting_vector + "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467] + targeting vector + SO_EXT:0001644 + + + genetic_marker + SO_EXT:genetic_marker + genetic marker + SO_EXT:0001645 + "A measurable sequence feature that varies within a population." [SO:db] + + + inframe variant + ANNOVAR:nonframeshift substitution + ANNOVAR:nonframeshift block substitution + SO_EXT:inframe_variant + SO_EXT:0001650 + inframe_variant + VAAST:inframe_variant + "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke] + cds-indel + + + nucleotide to protein binding site + SO_EXT:nucleotide_to_protein_binding_site + SO_EXT:0001654 + nucleotide_to_protein_binding_site + "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] + + + SO_EXT:nucleotide_binding_site + nucleotide binding site + SO_EXT:0001655 + nucleotide_binding_site + "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb] + np_bind + + + SO_EXT:promoter_element + promoter_element + promoter element + SO_EXT:0001659 + + + "DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml] + specific transcription factor binding site + SO_EXT:proximal_promoter_element + proximal promoter element + SO_EXT:0001668 + proximal_promoter_element + + + regulatory_promoter_element + "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659] + regulatory promoter element + SO_EXT:regulatory_promoter_element + SO_EXT:0001678 + + + SO_EXT:0001679 + transcription regulatory region + "A regulatory region that is involved in the control of the process of transcription." [SO:ke] + transcription_regulatory_region + SO_EXT:transcription_regulatory_region + + + sequence_motif + SO_EXT:0001683 + SO_EXT:sequence_motif + sequence motif + "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif] + + + SO_EXT:histone_modification + histone modification site + SO_EXT:0001700 + histone_modification + "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone] + histone modification + + + histone_methylation_site + SO_EXT:histone_methylation_site + histone methylation + SO_EXT:0001701 + "A histone modification site where the modification is the methylation of the residue." [SO:ke] + histone methylation site + + + H3K9 tri-methylation site + "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] + H3K9_trimethylation_site + SO_EXT:0001707 + H3K9Me3 + SO_EXT:H3K9_trimethylation_site + + + SO_EXT:0001720 + "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke] + SO_EXT:epigenetically_modified_region + epigenetically modified region + epigenetically_modified_region + + + "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke] + H3K9 di-methylation site + H3K9Me2 + SO_EXT:H3K9_dimethylation_site + SO_EXT:0001728 + H3K9_dimethylation_site + + + H3K9_methylation_site + "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke] + SO_EXT:H3K9_methylation_site + H3K9 methylation site + SO_EXT:0001736 + + + SO_EXT:0001747 + open_chromatin_region + SO_EXT:open_chromatin_region + open chromatin region + "A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb] + + + SO_EXT:mating_type_region + "A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke] + mating type region + mating_type_region + SO_EXT:0001789 + + + exon variant + "A sequence variant that changes exon sequence." [SO:ke] + Jannovar:exon_variant + SO_EXT:0001791 + exon_variant + SO_EXT:exon_variant + ANNOVAR:exonic + snpEff:EXON + VAAST:exon_variant + + + transmembrane helix + transmembrane_helix + SO_EXT:0001812 + SO_EXT:transmembrane_helix + "A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah] + + + protein altering variant + VEP:protein_altering_variant + SO_EXT:protein_altering_variant + "A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr] + SO_EXT:0001818 + protein_altering_variant + + + AFLP_fragment + amplified fragment length polymorphism + SO_EXT:0001830 + AFLP-PCR + amplified fragment length polymorphism PCR + SO_EXT:AFLP_fragment + "A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea] + AFLP fragment + AFLP + + + "A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923] + SO_EXT:0001861 + sterol_regulatory_element + SO_EXT:sterol_regulatory_element + + + SO_EXT:feature_variant + feature_variant + feature alteration + "A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke] + SO_EXT:0001878 + + + SO_EXT:0001882 + SO_EXT:feature_fusion + "A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke] + feature_fusion + feature fusion + + + "A feature fusion where the deletion brings together transcript regions." [SO:ke] + SO_EXT:0001886 + transcript_fusion + SO_EXT:transcript_fusion + transcript fusion + + + SO_EXT:0001906 + feature truncation + SO_EXT:feature_truncation + Jannovar:feature_truncation + VEP:feature_truncation + "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke] + feature_truncation + + + Jannovar:coding_transcript_variant + coding_transcript_variant + "A transcript variant of a protein coding gene." [SO:ke] + SO_EXT:coding_transcript_variant + SO_EXT:0001968 + coding transcript variant + + + G-box + SO_EXT:G_box + G_box + "A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml] + GBF binding sequence + SO_EXT:0001980 + + + SO_EXT:0001992 + nonsynonymous variant + non_synonymous_coding + "A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke] + SO_EXT:nonsynonymous_variant + nonsynonymous_variant + + + SO_EXT:0002031 + SO_EXT:shRNA + "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke] + shRNA + short hairpin RNA + small hairpin RNA + + + SO_EXT:sequence_comparison + SO_EXT:0002072 + sequence_comparison + + + "A transcript feature that has been predicted but is not yet validated." [SO:ke] + predicted_transcript + predicted transcript + SO_EXT:0002138 + SO_EXT:predicted_transcript + + + regulatory region + SO_EXT:regulatory_region + SO_EXT:0005836 + "A region of sequence that is involved in the control of a biological process." [SO:ke] + regulatory_region + + + SO_EXT:primer_binding_site + primer_binding_site + SO_EXT:0005850 + "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] + primer binding site + + + "A gene that can be substituted for a related gene at a different site in the genome." [SGD:se] + gene_cassette + SO_EXT:0005853 + gene cassette + SO_EXT:gene_cassette + + + SO_EXT:gene_group + SO_EXT:0005855 + "A collection of related genes." [SO:ma] + gene group + gene_group + + + "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml] + syntenic region + SO_EXT:0005858 + syntenic_region + SO_EXT:syntenic_region + + + biochemical_region_of_peptide + "A region of a peptide that is involved in a biochemical function." [EBIBS:GAR] + SO_EXT:0100001 + biochemical motif + biochemical_region + biochemical region of peptide + SO_EXT:biochemical_region_of_peptide + + + SO_EXT:0100011 + "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR] + SO_EXT:cleaved_peptide_region + cleaved peptide region + cleaved_peptide_region + + + SO_EXT:0100018 + polypeptide binding motif + binding + "A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR] + polypeptide_binding_motif + SO_EXT:polypeptide_binding_motif + + + SO_EXT:polypeptide_catalytic_motif + SO_EXT:0100019 + "A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR] + polypeptide catalytic motif + polypeptide_catalytic_motif + catalytic_motif + + + polypeptide_conserved_region + "A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR] + polypeptide conserved region + SO_EXT:0100021 + SO_EXT:polypeptide_conserved_region + + + "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke] + substitution + SO_EXT:substitution + SO_EXT:1000002 + + + SO_EXT:transversion + SO_EXT:1000017 + transversion + "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] + + + "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke] + pyrimidine_to_purine_transversion + SO_EXT:1000018 + pyrimidine to purine transversion + SO_EXT:pyrimidine_to_purine_transversion + + + T_to_G_transversion + "A transversion from T to G." [SO:ke] + T to G transversion + SO_EXT:1000022 + SO_EXT:T_to_G_transversion + + + alternatively_spliced_transcript + SO_EXT:1001187 + SO_EXT:alternatively_spliced_transcript + alternatively spliced transcript + "A transcript that is alternatively spliced." [SO:xp] + + + SO_EXT:5_prime_LTR_unit_or_region + For: 5' LTR(s)/5' long terminal repeat(s) + 5' LTR + SO_EXT:five_prime_LTR or (SO_EXT:repeat_unit and proper_part_of some SO_EXT:five_prime_LTR) + 5' long terminal repeat + 5-prime LTR unit or region + SO_EXT:5-prime LTR unit or region + + + SO_EXT:long_terminal_repeat or (SO_EXT:repeat_unit and proper_part_of some SO_EXT:long_terminal_repeat) + long terminal repeat + SO_EXT:LTR unit or region + LTR + For: LTR(s)/long terminal repeat(s) + SO_EXT:LTR_unit_or_region + LTR unit or region + + + SO_EXT:sequence_variant and (SO_EXT:alternatively_spliced_transcript or (CHEBI:peptide and translated_from some SO_EXT:alternatively_spliced_transcript)) + alternative splice isoform + splice form + splice isoform + SO_EXT:alternative_splice_variant + alternatively spliced form + splice variant + SO_EXT:alternative splice variant + alternative splice product + splicing variant + alternatively spliced isoform + alternative splice variant + + + (BFO:occurrent and causally_effects some SO:conserved) or SO:conserved + biological conservation + evolutionary conservation + biological conservation process or quality + SO_EXT:biological_conservation_process_or_quality + SO_EXT:biological conservation process or quality + + + biological sequence + SO_EXT:region or CHEBI:oligonucleotide or CHEBI:polynucleotide or CHEBI:peptide or generically_depends_on some (CHEBI:oligonucleotide or CHEBI:polynucleotide or CHEBI:peptide) + SO_EXT:biological_sequence + SO_EXT:biological sequence + For: sequence/sequences (n.) + + + complementary DNA + SO_EXT:cDNA + bearer_of some SO:cDNA + SO_EXT:complementary DNA + cDNA + + + SO_EXT:CDS or SO_EXT:CDS_region + SO_EXT:coding sequence + CDS + coding sequence + coding region + SO_EXT:coding_sequence + + + direct repeat unit or region + SO_EXT:direct_repeat or (SO_EXT:repeat_unit and proper_part_of some SO_EXT:direct_repeat) + direct sequence repeat + For: direct repeat(s) + direct repeat + SO_EXT:direct_repeat_unit_or_region + SO_EXT:direct repeat unit or region + + + double-stranded cDNA + bearer_of some SO:double_stranded_cDNA + double-stranded complementary DNA + SO_EXT:double-stranded cDNA + SO_EXT:double_stranded_complementary_DNA + + + SO_EXT:engineered_biological_sequence + sequence construct + SO_EXT:engineered biological sequence + SO_EXT:engineered_region or (SO_EXT:biological_sequence and has_proper_part some SO_EXT:engineered_region) + engineered biological sequence + + + enhancer trap or trap construct + SO_EXT:enhancer_trap_or_trap_construct + For: enhancer trap(s) + SO_EXT:enhancer_trap_construct or (SO_EXT:insertion and derives_from some SO_EXT:enhancer_trap_construct) + enhancer trap + SO_EXT:enhancer trap or trap construct + + + epigenetic mark + epigenetic modification entity + SO_EXT:epigenetic modification entity + SO_EXT:molecular_indicator_or_label_or_marker_or_tag and output_of some SO_EXT:epigenetic_modification_process + epigenetic marker + SO_EXT:epigenetic_modification_entity + For: epigenetic mark(s), epigenetic marker(s) + + + epigenetic perturbation + epigenetic modification entity or process + SO_EXT:epigenetic_modification_entity_or_process + epigenetic marking + epigenetic edit + SO_EXT:epigenetic modification entity or process + epigenetic modification + epigenetic alteration + SO_EXT:epigenetic_modification_entity or SO_EXT:epigenetic_modification_process + epigenetic change + For: epigenetic, epigenetic alteration(s), epigenetic change(s), epigenetic edit(s), epigenetic marking(s), epigenetic modification(s), epigenetic perturbation(s) + + + gene fusion + fusion gene + SO_EXT:fusion_gene or SO_EXT:gene_fusion + SO_EXT:fusion_gene_or_gene_fusion + fusion gene/gene fusion + SO_EXT:fusion gene/gene fusion + + + SO_EXT:gene product + gene product + SO_EXT:gene_product + SO_EXT:transcript or CHEBI_PR_EXT:protein + + + SO_EXT:gene trap or trap construct + For: gene trap(s) + SO_EXT:gene_trap_or_trap_construct + gene trap or trap construct + gene trap + SO_EXT:gene_trap_construct or (SO_EXT:insertion and derives_from some SO_EXT:gene_trap_construct) + + + gene trapping process + For: gene trapping + BFO:occurrent and has_causal_agent some SO_EXT:gene_trap_or_trap_construct + gene trapping + SO_EXT:gene_trapping_process + SO_EXT:gene trapping process + + + bearer_of some SO:genomic_DNA + SO_EXT:genomic DNA + genomic DNA + SO_EXT:genomic_DNA + gDNA + + + SO_EXT:genotype or (BFO:independent_continuant and contains_or_has_proper_part some SO_EXT:genotype) + genotype + SO_EXT:genotype_or_entity_with_genotype + SO_EXT:genotype or entity with genotype + genotype or entity with genotype + + + SO_EXT:inverted repeat unit or region + SO_EXT:inverted_repeat_unit_or_region + For: inverted repeat(s) + inverted repeat unit or region + inverted repeat + SO_EXT:inverted_repeat or (SO_EXT:repeat_unit and proper_part_of some SO_EXT:inverted_repeat) + + + microsatellite repeat + SO_EXT:microsatellite_unit_or_region + STR + SO_EXT:microsatellite unit or region + microsatellite unit or region + SO_EXT:microsatellite or (SO_EXT:repeat_unit and proper_part_of some SO_EXT:microsatellite) + short tandem repeat + microsatellite + For: microsatellite(s) + + + (SO:non_synonymous and inheres_in some SO_EXT:missense_variant) or SO_EXT:missense_variant + For: missense + SO_EXT:missense quality or entity + SO_EXT:missense_quality_or_entity + missense + missense quality or entity + + + For: nonsense + nonsense quality or entity + nonsense + SO_EXT:nonsense quality or entity + (SO:non_synonymous and inheres_in some SO_EXT:stop_gained) or SO_EXT:stop_gained + SO_EXT:nonsense_quality_or_entity + + + SO_EXT:normal_or_wild_type_or_present + sequence wild-typeness, normalness or presence + SO_EXT:sequence wild-typeness, normalness or presence + For: + + PATO:normal or SO:wild_type + + + BFO:independent_continuant and ((bearer_of some SO_EXT:sequence_nullness) or (contains_or_has_proper_part some (BFO:independent_continuant and bearer_of some SO_EXT:sequence_nullness)) + null-sequence entity + SO_EXT:null-sequence entity + For: null/nulls (n./nonmodifying) + SO_EXT:null_sequence_entity + + + physical mapping + physical mapping process + BFO:occurrent and has_output some SO_EXT:fragment_assembly + SO_EXT:physical mapping process + SO_EXT:physical_mapping_process + For: physical mapping + + + SO_EXT:point_mutation or (SO_EXT:sequence_alteration and SO_EXT:amino_acid) or (BFO:occurrent and has_output some (SO_EXT:point_mutation or (SO_EXT:sequence_alteration and SO_EXT:amino_acid)) + point mutation entity or process + For: point mutation(s) + SO_EXT:point_mutation_entity_or_process + SO_EXT:point mutation entity or process + point mutation + + + SO_EXT:polymorphism + SO_EXT:polymorphism entity or quality + polymorphism entity or quality + polymorphism + SO:polymorphic_variant or (SO_EXT:sequence_feature and bearer_of some SO:polymorphic_variant) or SO_EXT:polymorphic_sequence_variant or SO_EXT:SNP or SO_EXT:MNP + + + For: radiation hybrid mapping + radiation hybrid mapping process + radiation hybrid mapping + SO_EXT:radiation_hybrid_mapping_process + BFO:occurrent and has_output some SO_EXT:RH_map + SO_EXT:radiation hybrid mapping process + + + For: satellite(s) + satellite + satellite unit or region + SO_EXT:satellite unit or region + SO_EXT:satellite_DNA or (SO_EXT:repeat_unit and proper_part_of some SO_EXT:satellite_DNA) + satellite repeat + SO_EXT:satellite_unit_or_region + + + sequence perturbation + SO_EXT:sequence_alteration or SO_EXT:sequence_alteration_process or (BFO:independent_continuant and output_of some SO_EXT:sequence_alteration_process) + sequence alteration entity or process + SO_EXT:sequence alteration entity or process + SO_EXT:sequence_alteration_entity_or_process + sequence alteration + sequence change + sequence modification + sequence mutation + For: alteration/alterations, change/changes (n.), edit/edits (n.), modification/modifications, mutation/mutational/mutations, perturbation/perturbations + sequence edit + + + (BFO:occurrent and has_output some (SO_EXT:sequence_alteration or SO_EXT:post_translationally_modified_region)) or GO:'chromatin modification' or GO:'macromolecule modification' or GO:'protein processing' or GO:'RNA processing' + sequence alteration process + sequence editing + sequence mutation process + sequence perturbation process + SO_EXT:sequence_alteration_process + sequence processing + SO_EXT:sequence alteration process + sequence change process + For: alter/altered/altering/alters, change(v.)/changed/changes(v.)/changing, edit(v.)/edited/editing/edits(v.), manipulate/manipulated/manipulates/manipulating/manipulation/manipulations, modified/modifies/modify/modifying, mutate/mutated/mutates/mutating, perturbate/perturbated/perturbates/perturbating, process(v.)/processed/processes(v.)/processing + sequence manipulation + sequence modification process + + + sequence-altered entity + SO_EXT:sequence_altered_entity + SO_EXT:sequence-altered entity + SO_EXT:sequence_variant or (BFO:independent_continuant and causally_affected_or_effected_by some SO_EXT:sequence_alteration_process) + For: mutant (as nonmodifying word), mutants + + + SO_EXT:sequence-altered entity or alteration process + SO_EXT:sequence_altered_entity_or_alteration_process + SO_EXT:sequence_altered_entity or SO_EXT:sequence_alteration_process + sequence-altered entity or alteration process + For: mutant (as modifying word) + + + SO_EXT:sequence assembly entity or process + SO_EXT:sequence_assembly_entity_or_process + sequence assembly entity or process + For: assembly/assemblies + SO_EXT:assembly or (BFO:occurrent and has_output some SO_EXT:assembly) + + + BFO:occurrent and causally_effects some SO:circular + sequence circularization + For: circularise/circularize, circularised/circularized, circularises/circularizes, circularising/circularizing + SO_EXT:sequence circularization + SO_EXT:sequence_circularization + + + SO_EXT:sequence_cloned_entity + For: clone/clones (n.) + sequence-cloned entity + SO_EXT:sequence-cloned entity + SO_EXT:clone or SO_EXT:clone_insert or (BFO:occurrent and has_part_or_contains some (SO_EXT:clone or SO_EXT:clone_insert)) + + + For: clone(v.)/cloned/clones(v.)/cloning + sequence cloning process + SO_EXT:sequence_cloning_process + SO_EXT:sequence cloning process + BFO:occurrent and results_in_formation_of some SO_EXT:sequence_cloned_entity + + + sequence coding function + BFO:realizable_entity and inheres_in some has_prototype o transcribed_to some BFO:independent_continuant + For: code/coded/codes/coding, encode/encoded/encodes/encoding + SO_EXT:sequence_coding_function + SO_EXT:sequence coding function + + + sequence copy entity + For: copy/copies (n.) + SO_EXT:sequence copy entity + SO_EXT:chromosomal_duplication or SO_EXT:duplication or (bearer_of o concretizes some SO_EXT:sequence_feature) + SO_EXT:sequence_copy_entity + + + SO_EXT:sequence deletion entity or process + del + sequence deletion + sequence deletion entity or process + For: deletion/deletions + SO_EXT:sequence_deletion_entity_or_process + SO_EXT:deletion or SO_EXT:sequence_deletion_process + + + For: delete/deleted/deletes/deleting, excise/excised/excises/excising/excision/excisions + BFO:occurrent and results_in_formation_of some SO_EXT:deletion (SO_EXT:0000159) + SO_EXT:sequence deletion process + sequence deletion process + sequence excision + SO_EXT:sequence_deletion_process + + + For: downstream + BFO:dependent_continuant and inheres_in some (is_downstream_of_sequence_of some SO_EXT:sequence_feature) + SO_EXT:sequence downstreamness + sequence downstreamness + SO_EXT:sequence_downstreamness + + + sequence duplication entity or process + SO_EXT:sequence_duplication_entity_or_process + SO_EXT:sequence duplication entity or process + sequence duplication + SO_EXT:chromosomal_duplication or SO_EXT:duplication or SO_EXT:sequence_duplication_process + + + sequence duplication process + SO_EXT:sequence duplication process + SO_EXT:sequence_duplication_process + BFO:occurrent and results_in_formation_of some (SO_EXT:chromosomal_duplication or SO_EXT:duplication) + + + (bearer_of some SO:fusion) or SO_EXT:sequence_fusion_process + For: fusion/fusions + SO_EXT:sequence fusion entity or process + sequence fusion + SO_EXT:sequence_fusion_entity_or_process + sequence fusion entity or process + + + For: adjoin/adjoined/adjoining/adjoins, fuse/fused/fuses/fusing, join/joined/joining/joins, link(v.)/linked/linking/links(v.) + sequence fusion process or quality + SO_EXT:sequence_fusion_process + SO_EXT:sequence fusion process or quality + (BFO:occurrent and results_in_formation_of some (bearer_of some SO:fusion)) or (BFO:dependent_continuant and effected_by some (BFO:occurrent and results_in_formation_of some (bearer_of some SO:fusion))) + + + SO_EXT:sequence_insertion_entity_or_process + sequence insertion + sequence insertion entity or process + SO_EXT:sequence insertion entity or process + For: insertion/insertions + SO_EXT:insertion or SO_EXT:sequence_insertion_process + + + BFO:occurrent and has_output some SO_EXT:insertion + sequence insertion process + SO_EXT:sequence insertion process + For: insert(v.)/inserted/inserting/inserts(v.) + SO_EXT:sequence_insertion_process + + + SO_EXT:sequence_inversion_process or SO_EXT:inversion + SO_EXT:sequence_inversion_entity_or_process + SO_EXT:sequence inversion entity or process + For: inversion/inversions + sequence inversion + sequence inversion entity or process + + + For: invert/inverted/inverting/inverts + sequence inversion process + BFO:occurrent and results_in_formation_of some SO_EXT:inversion + SO_EXT:sequence_inversion_process + SO_EXT:sequence inversion process + + + sequence linearization + BFO:occurrent and causally_effects some SO:linear + SO_EXT:sequence linearization + For: linearise/linearize, linearised/linearized, linearises/linearizes, linearising/linearizing + SO_EXT:sequence_linearization + + + For: null (adjective/modifying), nullisomic/nullisomy + SO_EXT:sequence nullness + sequence nullness + SO_EXT:sequence_nullness + BFO:quality and causally_effected_by some SO_EXT:null_mutation + + + SO_EXT:sequence nullness or absence + sequence nullness or absence + SO_EXT:sequence_nullness or PATO:absent + For: - + SO_EXT:sequence_nullness_or_absence + + + For: motif/motifs + SO_EXT:sequence_or_structure_motif + SO_EXT:sequence or structure motif + sequence or structure motif + SO_EXT:sequence_motif or SO_EXT:polypeptide_structural_motif or SO_EXT:polypeptide_secondary_structure or SO_EXT:polypeptide_motif + + + SO_EXT:meiotic_recombination_region or SO_EXT:mitotic_recombination_region or (BFO:independent_continuant and has_part_or_contains some (SO_EXT:meiotic_recombination_region or SO_EXT:mitotic_recombination_region)) + SO_EXT:sequence_recombinant_entity + sequence-recombinant entity + For: recombinant (as nonmodifying noun), recombinants + SO_EXT:sequence-recombinant entity + + + sequence repeat unit or region + SO_EXT:repeat_unit or SO_EXT:repeat_region + For: repeat/repeated/repeating/repeats + sequence repeat + SO_EXT:sequence_repeat_unit_or_region + SO_EXT:sequence repeat unit or region + + + BFO:occurrent and realizes some SO:rescue + For: rescue/rescued/rescues/rescuing + SO_EXT:sequence rescue process + SO_EXT:sequence_rescue_process + sequence rescue process + + + sequence retrotransposition entity or process + sequence retrotransposition + For: retrotransposition/retrotranspositions + SO_EXT:sequence retrotransposition entity or process + SO_EXT:sequence_retrotransposition_entity_or_process + (SO_EXT:sequence_feature and bearer_of some SO:retrotranposed) or SO_EXT:'sequence retrotransposition process' + + + For: replacement/replacements, substitution/substitutions + SO_EXT:sequence substitution entity or process + SO_EXT:sequence_substitution_entity_or_process + SO_EXT:substitution or SO_EXT:sequence_substitution_process + sequence substitution + sequence substitution entity or process + sequence replacement + + + sequence substitution process + For: exchange/exchanged/exchanges/exchanging, replace/replaced/replaces/replacing, substitute/substituted/substitutes/substituting + SO_EXT:sequence_substitution_process + SO_EXT:sequence substitution process + sequence exchange + sequence replacement process + BFO:occurrent and results_in_formation_of some SO_EXT:substitution + + + SO_EXT:sequence truncation entity or process + SO_EXT:feature_truncation or SO_EXT:sequence_truncation_process + sequence truncation entity or process + sequence truncation + SO_EXT:sequence_truncation_entity_or_process + + + SO_EXT:sequence_truncation_process + sequence truncation process + BFO:occurrent and has_output some SO_EXT:feature_truncation + SO_EXT:sequence truncation process + + + BFO:independent_continuant and not causally_affected_or_effected_by some SO_EXT:sequence_alteration_process + For: nonmutant (noun/nonmodifying word), nonmutants + nonmutant entity + SO_EXT:sequence-unaltered entity + SO_EXT:sequence_unaltered_entity + sequence-unaltered entity + + + sequence upstreamness + SO_EXT:sequence_upstreamness + SO_EXT:sequence upstreamness + For: upstream + BFO:dependent_continuant and inheres_in some (is_upstream_of_sequence_of some SO_EXT:sequence_feature) + + + SO_EXT:sequence_variant_entity + SO_EXT:sequence variant entity + SO_EXT:sequence_alteration or SO_EXT:sequence_variant + sequence variant entity + For: variant/variants (nonmodifying) + + + SO_EXT:sequence variant entity or quality + SO_EXT:sequence_variant_entity or PATO:variant + sequence variant entity or quality + SO_EXT:sequence_variant_or_variation + For: variant (modifying) + + + SO_EXT:sequence_alteration or PATO:variant + SO_EXT:sequence_variation_entity_or_quality + sequence variation + For: variation/variations + sequence variation entity or quality + SO_EXT:sequence variation entity or quality + + + SO_EXT:splice acceptor + splice acceptor site + SO_EXT:cryptic_splice_acceptor or SO_EXT:three_prime_cis_splice_site or SO_EXT:trans_splice_acceptor_site + SO_EXT:splice_acceptor + splice acceptor + + + splice donor site + SO_EXT:splice donor + SO_EXT:splice_donor + splice donor + SO_EXT:cryptic_splice_donor or SO_EXT:five_prime_cis_splice_site or SO_EXT:trans_splice_donor_site + + + tandem repeat unit or region + SO_EXT:tandem_repeat or (SO_EXT:repeat_unit and proper_part_of some SO_EXT:tandem_repeat) + tandem repeat + SO_EXT:tandem_repeat_unit_or_region + SO_EXT:tandem repeat unit or region + + + TIR + For: TIR(s)/terminal inverted repeat(s), ITR(s)/inverted terminal repeat(s) + inverted terminal repeat + SO_EXT:terminal inverted repeat unit or region + terminal inverted repeat + SO_EXT:terminal_inverted_repeat_unit_or_region + SO_EXT:terminal_inverted_repeat or (SO_EXT:repeat_unit and proper_part_of some SO_EXT:terminal_inverted_repeat) + ITR + terminal inverted repeat unit or region + + + transgenesis + SO_EXT:transgenesis + For: transgenesis + SO_EXT:transgenesis + BFO:sequence_alteration_process and results_in_formation_of some (SO_EXT:insertion and SO_EXT:transgene) + + + SO_EXT:transgenic entity + For: transgenic/transgenics, Tg + transgenic entity + SO_EXT:transgenic_entity + transgene or (BFO:independent_continuant and has_part_or_contains some SO_EXT:transgene) + + + BFO:independent_continuant and bearer_of some SO:wild_type + SO_EXT:wild-type entity + wild-type entity + SO_EXT:wild_type_entity + + + SO_EXT:wild_type_entity_or_quality + SO:wild_type or (BFO:independent_continuant and bearer_of some SO:wild_type) + SO_EXT:wild-typeness or wild-type entity + WT + wild-type + wild type + wild-typeness or wild-type entity + wildtype + + + UBERON:processual entity + UBERON:0000000 + "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity." [span:ProcessualEntity] + processual entity + + + cervix uteri + canalis cervicis uteri + neck of uterus + UBERON:uterine cervix + UBERON:0000002 + uterine cervix + cervical canal + caudal segment of uterus + "Lower, narrow portion of the uterus where it joins with the top end of the vagina." [http://en.wikipedia.org/wiki/Cervix, http://orcid.org/0000-0002-6601-2165] + uterine cervix + cervix of uterus + cervical canal of uterus + + + UBERON:0000004 + peripheral olfactory organ + proboscis + "the organ that is specialized for smell and is part of the respiratory system" [MP:0002233\,MESH\:A01.456.505.733\,MGI\:cwg] + nasus + UBERON:olfactory apparatus + nasal sac + olfactory apparatus + nose + + + UBERON:0000006 + island of pancreas + pancreatic insula + island of Langerhans + pancreatic islet + "the clusters of hormone-producing cells that are scattered throughout the pancreas" [MP:0005215\,MA\:0000127\,MESH\:A03.734.414] + islets of langerhans + islet of Langerhans + UBERON:islet of Langerhans + + + UBERON:0000007 + "The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]." [http://en.wikipedia.org/wiki/Pituitary_gland, ZFIN:curator] + pituitary gland + hypophysis cerebri + UBERON:pituitary gland + pituitary body + glandula pituitaria + hypophysis + pituitary + + + tunica submucosa + UBERON:0000009 + submucosa + submucosa of region of organ + submucous layer + organ submucosa + submucosa of organ + region of submucosa + tela submucosa + UBERON:submucosa + "A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]." [http://en.wikipedia.org/wiki/Submucosa] + + + nucleus amygdalae basalis, pars lateralis + lateral part of the basolateral nucleus + nucleus amygdaloideus basalis, pars lateralis magnocellularis + UBERON:peripheral nervous system + nucleus basalis lateralis amygdalae + "A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." [GO:0007422] + PNS + UBERON:0000010 + lateral part of the basal amygdalar nucleus + pars peripherica; systema nervosum periphericum + peripheral nervous system + + + sympathetic nervous system + pars sympathica divisionis autonomici systematis nervosi + pars sympathica divisionis autonomici systematis nervosi + UBERON:sympathetic nervous system + "The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]." [GO:0048485] + sympathetic nervous system + UBERON:0000013 + sympathetic part of autonomic division of nervous system + + + UBERON:zone of skin + skin zone + portion of skin + skin + region of skin + zone of skin + skin region + UBERON:0000014 + "Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis." [http://en.wikipedia.org/wiki/Skin, http://orcid.org/0000-0002-6601-2165] + + + UBERON:anatomical boundary + "A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures." [CARO:0000010] + anatomical boundary + UBERON:0000015 + + + "An organ that is capable of transducing sensory stimulus to the nervous system." [https://github.com/obophenotype/uberon/issues/549, https://orcid.org/0000-0002-6601-2165] + organ of sensory organ system + UBERON:sense organ + UBERON:0000020 + sense organ system organ + sensory system organ + organ of sensory system + organ of sense organ system + sensor + sense organ + sensory organ + sensory organ system organ + Sinnesorgan + + + UBERON:cutaneous appendage + "Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales." [https://orcid.org/0000-0002-6601-2165] + epidermal growth + UBERON:0000021 + skin appendage + cutaneous appendage + + + feather + "one of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins. The beta-keratins in feathers, beaks and claws — and the claws, scales and shells of reptiles — are composed of protein strands hydrogen-bonded into beta-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the α-keratins of mammalian hair, horns and hoof. The exact signals that induce the growth of feathers on the skin are not known but it has been found that the transcription factor cDermo-1 induces the growth of feathers on skin and scales on the leg." [http://en.wikipedia.org/wiki/Feather] + UBERON:0000022 + UBERON:feather + + + UBERON:wing + "Appendage that is shaped in order to produce lift for flight through the air." [UBERON:cjm] + wing + UBERON:0000023 + aliform appendage + + + UBERON:forelimb wing + "Forelimb that is used to produce lift for flight through the air." [] + forelimb wing + UBERON:0000024 + + + anatomical tube + "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported." [http://orcid.org/0000-0002-6601-2165] + tube + UBERON:tube + UBERON:0000025 + + + "Major subdivision of an organism that protrudes from the body[DOS, CARO]." [CARO:DOS] + UBERON:appendage + extremity + appendage + appendages + limbs/digits/tail + extremitaet + UBERON:0000026 + + + nodus lymphaticus + UBERON:0000029 + UBERON:lymph node + lymph gland + lymph node + "Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph." [BTO:0000784] + + + cephalic area + head (volume) + "The head is the anterior-most division of the body [GO]." [GO:0060322, http://en.wikipedia.org/wiki/Head] + UBERON:0000033 + UBERON:head + head + + + wall of serous sac + UBERON:serous membrane + serous membrane + UBERON:0000042 + serosa + tunica serosa + "multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer." [http://en.wikipedia.org/wiki/Serous_membrane, http://purl.obolibrary.org/obo/uberon/tracker/86] + + + tendo + "Dense regular connective tissue that connects muscle to bone[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, http://en.wikipedia.org/wiki/Tendon, VSAO:0000073] + UBERON:tendon + tendon + UBERON:0000043 + sinew + + + posterior root ganglion + spinal ganglion + dorsal root ganglion + ganglion sensorium nervi spinalis + DRG + dorsal root ganglia + dorsal root ganglion + UBERON:dorsal root ganglion + ganglion spinalis + ganglion of dorsal root + UBERON:0000044 + "* Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP)" [NIFSTD:birnlex_2596] + ganglion spinale + + + ganglia + neural ganglion + "A biological tissue mass, most commonly a mass of nerve cell bodies." [http://en.wikipedia.org/wiki/Ganglion, http://purl.obolibrary.org/obo/uberon/tracker/300] + UBERON:ganglion + ganglion + UBERON:0000045 + + + sensory patch + macula + maculae + "Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified]." [MESH:A09.246.631.909.625.125] + acoustic maculae + sensory macula + UBERON:0000054 + UBERON:macula + acoustic macula + macula + + + UBERON:vessel + "A tubular structure that contains, conveys body fluid, such as blood or lymph." [https://orcid.org/0000-0002-6601-2165] + vessel + UBERON:0000055 + + + UBERON:ureter + metanephric duct + "Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs." [GO:0090189, http://en.wikipedia.org/wiki/Ureter] + ureter + UBERON:0000056 + + + "A tubular structure that transports secreted or excreted substances." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm#ducts] + UBERON:duct + duct + ducts + UBERON:0000058 + anatomical duct + + + wall of organ + anatomical wall + UBERON:0000060 + UBERON:anatomical wall + "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] + organ wall + + + anatomical structure + connected biological structure + UBERON:0000061 + UBERON:anatomical structure + "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003] + biological structure + + + anatomical unit + UBERON:organ + "Anatomical structure that performs a specific function or group of functions [WP]." [http://en.wikipedia.org/wiki/Organ_(anatomy)] + UBERON:0000062 + body organ + element + organ + + + "A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity." [UBERON:cjm] + UBERON:organ subunit + organ segment + UBERON:0000063 + organ subunit + organ region with fixed fiat boundary + segment of organ + + + UBERON:organ part + regional part of organ + cardinal organ part + "A multicellular structure that is a part of an organ." [] + organ part + UBERON:0000064 + + + respiratory tract + UBERON:respiratory tract + UBERON:0000065 + "Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts" [https://orcid.org/0000-0002-6601-2165] + + + UBERON:embryo stage part + embryo stage part + UBERON:0000067 + embryonic stage part + "A stage that is part of the embryo stage." [https://orcid.org/0000-0002-6601-2165] + + + UBERON:0000072 + respiratory tract + "An section of a respiratory tract." [UBERON:cjm] + UBERON:proximo-distal subdivision of respiratory tract + proximo-distal subdivision of respiratory tract + subdivision of respiratory tract + + + UBERON:0000073 + "Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS." [NIFSTD:birnlex_1157] + part of nervous system + UBERON:regional part of nervous system + regional part of nervous system + + + UBERON:0000074 + UBERON:renal glomerulus + malphigian glomerulus + glomerular tuft + renal glomeruli + glomerulus renis + renal corpuscle + renal glomerulus + "A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO]." [http://en.wikipedia.org/wiki/Glomerulus, MP:0005325] + glomerular capillary tuft + + + skeletal system subdivision + UBERON:subdivision of skeletal system + skeletal system part + "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] + subdivision of skeletal system + UBERON:0000075 + + + mixed endoderm/mesoderm-derived structure + "An anatomical structure that develops from the endoderm and the mesoderm." [https://orcid.org/0000-0002-6601-2165] + UBERON:mixed endoderm/mesoderm-derived structure + UBERON:0000077 + + + mixed ectoderm/mesoderm/endoderm-derived structure + UBERON:0000078 + UBERON:mixed ectoderm/mesoderm/endoderm-derived structure + "An anatomical structure that develops from the ectoderm, mesoderm and endoderm." [https://orcid.org/0000-0002-6601-2165] + + + mesonephroi + Wolffian body + "The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo." [GO:0001823, http://en.wikipedia.org/wiki/Mesonephros] + opisthonephros + amphibian adult kidney + mesonephros + opisto nephros + corpus Wolffi + UBERON:0000080 + opistonephros + UBERON:mesonephros + mesonephric kidney + middle kidney + + + renal tubules + mesonephric tubule + UBERON:0000083 + tubuli mesonephrici + UBERON:mesonephric tubule + "A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]." [http://en.wikipedia.org/wiki/Mesonephric_tubules] + + + UBERON:0000084 + ureteric bud + diverticulum + diverticulum metanephricum + metanephric bud + ureteric diverticulum + UBERON:ureteric bud + metanephric diverticulum + gemma ureterica + "An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]" [http://www.ncbi.nlm.nih.gov/pubmed/19828308, https://sourceforge.net/tracker/?group_id=36855&atid=440764, MP:0010979] + ureteric ampulla + + + "A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum." [MP:0012130] + UBERON:0000085 + morula (2-16 cells) + morula + UBERON:morula + + + UBERON:0000086 + "A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes." [http://en.wikipedia.org/wiki/Zona_pellucida] + pellucid zone + zona striata + oolemma + striated membrane + vitelline membrane + vitelline envelope + UBERON:zona pellucida + zona pellucida + zona radiata + + + embryoblastus; massa cellularis interna; pluriblastus senior + UBERON:0000087 + "A mass of cells that develop into the body of the embryo and some extraembryonic tissues" [ISBN:0-683-40008-8, MGI:pvb] + embryoblast + pluriblast + UBERON:inner cell mass + ICM + inner cell mass + + + UBERON:0000088 + massa cellularis externa + UBERON:trophoblast + trophoblast layer + trophoblast + "the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta" [ISBN:0-683-40008-8, MP:0005031] + trophoblastus + trophoderm + + + endomesoderm + UBERON:0000089 + "." [GO:dph, http://en.wikipedia.org/wiki/Hypoblast, https://sourceforge.net/p/geneontology/ontology-requests/9676/, ZFIN:cvs] + hypoblastus + UBERON:hypoblast (generic) + mesendoderm + future endoderm and mesoderm + hypoblast (generic) + hypoblast + + + UBERON:sulcus + UBERON:0000093 + "A depression or fissure in the surface of an organ." [http://en.wikipedia.org/wiki/Sulcus_(anatomy)] + sulcus + + + "Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]" [FMA:7145] + membrane organ + membrane of organ + UBERON:membrane organ + UBERON:0000094 + + + "portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]" [http://en.wikipedia.org/wiki/Cardiac_neural_crest] + UBERON:cardiac neural crest + cardiac neural crest complex + cardiac neural crest + complexus cristae neuralis cardiacus + UBERON:0000095 + + + pulmonary lobe + lung lobe + lobe of lung + UBERON:lobe of lung + UBERON:0000101 + "A lung lobe is one of the rounded projections that compose the lung[GO]." [GOC:GO] + pulminory lobe + + + life cycle + life + UBERON:0000104 + entire life cycle + "An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism." [https://orcid.org/0000-0002-6601-2165] + UBERON:life cycle + entire lifespan + lifespan + + + life cycle stage + UBERON:life cycle stage + "A spatiotemporal region encompassing some part of the life cycle of an organism." [https://orcid.org/0000-0002-6601-2165] + UBERON:0000105 + + + zygote stage + 1-cell stage + zygote + fertilized egg stage + one-cell stage + zygotum + UBERON:zygote stage + UBERON:0000106 + "A stage at which the organism is a single cell produced by means of sexual reproduction." [http://en.wikipedia.org/wiki/Zygote] + one cell stage + fertilized egg stage + + + cleavage stage + UBERON:cleavage stage + "The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula." [GO:0040016, http://en.wikipedia.org/wiki/Cleavage_(embryo)] + UBERON:0000107 + + + UBERON:blastula stage + blastula stage + "An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [http://en.wikipedia.org/wiki/Blastula] + UBERON:0000108 + + + UBERON:gastrula stage + blastocystis trilaminaris stage + trilaminar stage + trilaminar germ stage + gastrula stage + UBERON:0000109 + trilaminar disk stage + trilaminar blastocyst stage + trilaminar blastoderm stage + "A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm." [GO:0007369] + + + UBERON:0000113 + "The stage of being a sexually mature adult animal." [https://orcid.org/0000-0002-6601-2165] + UBERON:post-juvenile adult stage + post-juvenile adult stage + + + lung epithelial tissue + UBERON:0000115 + "The epithelial layer of the lung." [MP:0006382] + pulmonary epithelium + lung epithelium + epithelium of lung + epithelial tissue of lung + UBERON:lung epithelium + + + lung saccule + "Primitive gas exchange portion of the lung composed of type I and type II cells[GO]." [GO:0060430] + UBERON:lung saccule + UBERON:0000116 + + + UBERON:respiratory tube + respiratory tube + segment of tracheobronchial tree + "A tube in the respiratory system. Examples: bronchus, bronchiole, trachea." [GO:0030323, http://orcid.org/0000-0002-6601-2165] + UBERON:0000117 + + + primary lung bud + lung bud + "Structure derived from foregut that becomes a lung[GO]." [GO:0060431, http://en.wikipedia.org/wiki/Respiratory_bud] + gemma respiratoria + respiratory diverticulum + gemma pulmonalis + UBERON:0000118 + lung bud + UBERON:lung bud + + + sheath of cells + "Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium." [https://orcid.org/0000-0002-6601-2165] + cell sheath + layer of cells + UBERON:cell layer + UBERON:0000119 + cell layer + + + blood brain barrier + UBERON:0000120 + "Cell layer consisting of lining cells that separates the central nervous system and the bloodstream. The BBB may consist of endothelial cells or glial cells. An endothelial barrier may have arisen independently several times during evolution. In bichir and lungfish the barrier is formed by brain endothelial cells, while in sturgeon it is formed by a complex perivascular glial sheath, but with no detectable tight junctions." [http://dx.doi.org/10.1002/glia.20642, http://en.wikipedia.org/wiki/Blood-brain_barrier] + BBB + blood-brain barrier + UBERON:blood brain barrier + + + "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [CARO:0001001, FBbt:00005099, FBC:DOS] + funiculus + UBERON:0000122 + nerve fiber bundle + UBERON:neuron projection bundle + neuron projection bundle + neural fiber bundle + + + UBERON:0000125 + neuraxis nucleus + nucleus of CNS + nervous system nucleus + neuronal nucleus + nucleus of neuraxis + UBERON:neural nucleus + neural nucleus + "A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO)" [NIFSTD:nlx_28443] + + + UBERON:0000126 + "Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves" [NIFSTD:nlx_28532] + cranial neural nucleus + nucleus nervi cranialis + cranial nerve nucleus + UBERON:cranial nerve nucleus + nucleus of cranial nerve + + + membranous organ component + UBERON:membranous layer + UBERON:0000158 + membranous layer + + + pars analis recti + cloacal chamber + canalis analis + mesenteron + anal canal viewed anatomically + cloaca + UBERON:anal canal + anal canal + "The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus." [http://en.wikipedia.org/wiki/Anal_canal] + anal pad + anal canal + anus + anatomical anal canal + UBERON:0000159 + + + bowel + UBERON:intestine + intestine + intestinal tract + "Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine." [GOC:GO, http://en.wikipedia.org/wiki/Intestine] + UBERON:0000160 + + + orifice + "Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]." [FMA:3724] + UBERON:orifice + anatomical orifice + UBERON:0000161 + + + sinus urogenitalis + primitive urogenital sinus + UBERON:0000164 + UGS + fetal UGS + UBERON:primitive urogenital sinus + "the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females" [MP:0010116\,ISBN\:0-683-40008-8] + + + cavum oris + UBERON:mouth + stoma + mouth + rima oris + stomatodaeum + oral region + UBERON:0000165 + trophic apparatus + cavital oralis + regio oralis + mouth cavity + "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks)." [http://en.wikipedia.org/wiki/Mouth, https://github.com/obophenotype/uberon/wiki/The-digestive-tract] + oral vestibule + vestibulum oris + cavitas oris + vestibule of mouth + + + bucca + oral cavity + cavity of mouth + buccal cavity + UBERON:oral cavity + "Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)" [https://github.com/obophenotype/uberon/wiki/The-digestive-tract, https://orcid.org/0000-0002-6601-2165, ISBN10:0073040584] + UBERON:0000167 + + + segment of colon + "A section dividing a colon along a proximal-distal axis." [UBERON:cjm] + UBERON:proximal-distal subdivision of colon + proximal-distal subdivision of colon + UBERON:0000168 + + + organ of apparatus respiratorius + organ of respiratory system + UBERON:0000171 + apparatus respiratorius organ + respiratory organ + UBERON:respiration organ + respiratory system organ + respiration organ + breathing organ + "Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms." [GO:0007585] + gas exchange organ + + + excretion + "A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity" [GO:0007588, UBERON:cjm] + waste substance + UBERON:excreta + excreted substance + portion of excreted substance + UBERON:0000174 + excreta + + + "A fluid that is composed of blood plasma and erythrocytes." [FMA:9670, http://en.wikipedia.org/wiki/Blood, UBERON:cjm] + UBERON:blood + portion of blood + whole blood + vertebrate blood + UBERON:0000178 + blood + + + blood or blood analog + circulating fluid + UBERON:haemolymphatic fluid + haemolymphatic fluid + UBERON:0000179 + "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs." [] + + + lateral lumbar region of abdomen + latus + lateral region + UBERON:0000180 + "A region of the posterior torso (lower back) beneath the ribs and above the ilium." [http://en.wikipedia.org/wiki/Abdomen#9-region_scheme, http://en.wikipedia.org/wiki/Latus_(anatomy)] + regio lateralis + UBERON:lateral lumbar region of abdomen + flank + lateral region of abdomen + + + dorsal telencephalon + UBERON:pallium + dorsal part of telencephalon + dorsal telencephalic area + pallium + UBERON:0000203 + "Dorsal part (roof region) of the telencephalon[GO]." [GO:0021543, http://en.wikipedia.org/wiki/Pallium_(neuroanatomy), ISBN10:0471888893] + area dorsalis telencephali + + + area ventralis telencephali + subpallium + ventral telencephalon + "Dorsal part (base region) of the telencephalon." [GO:0021544, GO_REF:0000021, http://www.ncbi.nlm.nih.gov/pubmed/12626695, ISBN10:0471888893] + ventral part of telencephalon + UBERON:ventral part of telencephalon + UBERON:0000204 + + + UBERON:tetrapod frontal bone + tetrapod frontal bone + "the bone forming the forehead and roof of the eye orbit" [http://en.wikipedia.org/wiki/Frontal_bone, MP:0000107\,ISBN\:0-683-40008-8\,PMID\:7914451] + os frontale + UBERON:0000209 + + + os parietale + UBERON:tetrapod parietal bone + tetrapod parietal bone + UBERON:0000210 + "In humans: bone forming side and roof of cranium. Each bone is irregularly quadrilateral in form, and has two surfaces, four borders, and four angles." [http://en.wikipedia.org/wiki/Parietal_bone, ZFA:0000514] + + + ligament organ + UBERON:ligament + ligament + UBERON:0000211 + "Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000073] + + + "A closed space between the embryo and the amnion which contains the amniotic fluid and is formed by the fusion of the parts of the anterior and posterior amniotic folds." [MP:0011199] + cavitas amniotica + amniotic cavity + UBERON:0000301 + UBERON:amniotic cavity + + + UBERON:amnion + UBERON:0000305 + "the thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected" [MP:0005029\,MGI\:csmith] + amnion + + + UBERON:0000309 + wall fo trunk + "The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity." [MP:0003385] + UBERON:body wall + body wall + + + "The upper ventral region of an animal's torso." [http://en.wikipedia.org/wiki/Breast] + UBERON:breast + mamma + mammary part of chest + breast + mammary region + UBERON:0000310 + + + extensor + UBERON:extensor muscle + extensor muscle + "A muscle that, upon contraction, tends to straighten a joint or limb. The antagonist of a flexor muscle[BTO]. Any of the muscles that increase the angle between members of a limb, as by straightening the elbow or knee or bending the wrist or spine backward. The movement is usually directed backward, with the notable exception of the knee joint. In humans, certain muscles of the hand and foot are named for this function. In the hand these include the extensor carpi radialis brevis, extensor carpi radialis longus, and extensor carpi ulnaris, which run from the humerus (bone of the upper arm) along the back of the forearm to the metacarpal bones at the back of the hand[Britannica]" [http://www.britannica.com/EBchecked/topic/198909/extensor-muscle] + UBERON:0000311 + + + colonic mucous membrane + colonic mucosa + mucosa of colon + colon mucosa + UBERON:0000317 + large bowel mucosa + colon mucous membrane + "Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells." [http://orcid.org/0000-0002-6601-2165] + mucosa of large bowel + UBERON:colonic mucosa + colonic mucosa + + + late embryo + embryo late growth stage + UBERON:late embryo + "An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching." [BGEE:ANiknejad] + UBERON:0000323 + embryo late stage + + + UBERON:gut wall + wall of gut + digestive tract wall + wall of digestive tract + "The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity)." [UBERON:cjm] + gut wall + UBERON:0000328 + wall of alimentary tract + + + mucosa of organ of ileum + ileum mucosa + ileal mucous membrane + mucous membrane of ileum + UBERON:0000331 + mucosa of ileum + ileum mucous membrane + UBERON:ileal mucosa + ileal mucosa + ileum organ mucosa + "A mucosa that is part of a ileum [Automatically generated definition]." [OBOL:automatic] + ileum mucosa of organ + organ mucosa of ileum + + + gland of bowel mucosa + mucosa of organ of intestine gland + gland of mucosa of bowel + gland of mucosa of organ of intestine + bowel organ mucosa gland + glandulae intestinales + mucous membrane of intestine gland + gland of intestine mucous membrane + gland of organ mucosa of bowel + gland of bowel mucosa of organ + intestine mucous membrane gland + gland of bowel organ mucosa + gland of mucous membrane of intestine + glandula intestinalis + mucosa of bowel gland + gland of mucosa of intestine + gland of intestinal mucosa + UBERON:intestinal gland + intestinal gland + intestinal mucosa gland + intestine mucosa gland + organ mucosa of bowel gland + bowel mucosa of organ gland + gland of intestine mucosa + mucosa of organ of bowel gland + gland of intestine mucosa of organ + gland of organ mucosa of intestine + "A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]." [https://orcid.org/0000-0002-6601-2165] + UBERON:0000333 + mucosa of intestine gland + gland of mucosa of organ of bowel + intestine organ mucosa gland + mucous membrane of bowel gland + gland of bowel mucous membrane + bowel mucous membrane gland + gland of intestine organ mucosa + bowel mucosa gland + gland of mucous membrane of bowel + intestine mucosa of organ gland + organ mucosa of intestine gland + + + mucosa + mucosal region + tunica mucosa + region of mucosa + mucosa of organ + UBERON:mucosa + UBERON:0000344 + mucous membrane + "A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]" [http://en.wikipedia.org/wiki/Mucous_membrane] + organ mucosa + mucosa of organ part + + + UBERON:0000345 + "A dielectric (electrically insulating) material consisting of protein and fat that forms a layer, the myelin sheath, usually around only the axon of a neuron. Myelin is about 40 % water; the dry mass of myelin is about 70 - 85 % lipids and about 15 - 30 % proteins. Some of the proteins that make up myelin are myelin basic protein (MBP), myelin oligodendrocyte glycoprotein (MOG), and proteolipid protein (PLP). The primary lipid of myelin is a glycolipid called galactocerebroside (GalC). The intertwining hydrocarbon chains of sphingomyelin serve to strengthen the myelin sheath." [http://en.wikipedia.org/wiki/Myelin] + UBERON:myelin + myelin + + + "A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]." [BIRNLEX:Limbic_system, http://en.wikipedia.org/wiki/Limbic_system] + UBERON:limbic system + UBERON:0000349 + limbic system + visceral brain + + + parenchyma + UBERON:0000353 + UBERON:parenchyma + "functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues." [http://en.wikipedia.org/wiki/Parenchyma] + + + "The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]." [GO:0001824, http://en.wikipedia.org/wiki/Blastocyst] + blastocystis + blastocyst + UBERON:blastocyst + UBERON:0000358 + blastula + + + pyramides renales + kidney medulla + UBERON:renal medulla + renal marrow + renal pyramids + medulla of kidney + UBERON:0000362 + renal pyramids set + renal medulla + renal medullae set + medulla renalis + renal medullae + "the inner portion of the kidney consisting of the renal pyramids" [MP:0003014\,ISBN\:0-683-40008-8\,MGI\:smb] + medullary pyramids + + + UBERON:urothelium + "An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra." [http://en.wikipedia.org/wiki/Urothelium] + UBERON:0000365 + urothelium + uroepithelium + + + flexor + UBERON:0000366 + UBERON:flexor muscle + flexor muscle + "A muscle that when contracted acts to bend a joint or limb in the body." [BTO:0001257] + + + UBERON:0000387 + UBERON:meniscus + articular disc + "crescent-shaped fibrocartilaginous structure present in the knee, acromioclavicular, sternoclavicular, and temporomandibular joints[2] that, in contrast to articular disks, only partly divides a joint cavity.[3] A small meniscus also occurs in the radio-carpal joint." [http://en.wikipedia.org/wiki/Meniscus_(anatomy)] + meniscus + + + UBERON:lens nucleus + lens nucleus + "The core of the crystalline lens, surrounded by the cortex." [BTO:0001633] + UBERON:0000390 + nucleus of lens + + + leptomeninx + "pia mater or arachnoid mater." [http://en.wikipedia.org/wiki/Leptomeninges, http://purl.obolibrary.org/obo/uberon/tracker/300] + pia-arachnoid + UBERON:leptomeninx + arachnoidea mater et pia mater + leptomeninges + UBERON:0000391 + + + spiral ganglion + ganglion spirale cochleae + UBERON:0000395 + "The group of nerve cell bodies that conveys auditory sensation from the organ of Corti to the hindbrain and resides on the cochlear part of the vestibulocochlear nerve (eighth cranial nerve)[MP]. distributed to the hair cells of the spiral organ. The cochlear fibers arise in bipolar cells in the spiral ganglion in the modiolus." [http://www.dartmouth.edu/~humananatomy/part_8/chapter_44.html, MP:0002855] + cochlear part of vestibulocochlear ganglion + ganglion spirale + ganglion of Corti + Corti's ganglion + vestibulocochlear VIII ganglion cochlear component + ganglion cochlearis + vestibulocochlear ganglion cochlear component + UBERON:cochlear ganglion + spiral ganglion of cochlea + cochlear ganglion + + + dermal papillae + dermal papilla + papillae dermis + DPC + skin papilla + UBERON:dermal papilla + papilla corii + hair papilla + follicular papilla + papilla of corium + papilla dermatis + "A small, nipple-like interdigitation of the dermis into the epidermis." [http://en.wikipedia.org/wiki/Dermal_papillae] + dermal papilla cell + hair follicle dermal papilla + papilla dermis + UBERON:0000412 + + + prostatic gland epithelium + epithelium of prostatic gland + epithelial tissue of prostate + "The prostate epithelium." [MP:0001168] + epithelium of prostate + prostate gland epithelium + UBERON:0000428 + prostatic epithelium + prostate epithelial tissue + epithelial tissue of prostate gland + epithelium of prostate gland + prostate epithelium + UBERON:prostate epithelium + prostate gland epithelial tissue + + + UBERON:trabecula + "A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP]." [GO:0060343, http://en.wikipedia.org/wiki/Trabecula] + UBERON:0000440 + trabecula + + + lymphoid follicle + "." [http://purl.obolibrary.org/obo/uberon/tracker/6, http://purl.obolibrary.org/obo/uberon/tracker/7] + lymphoid nodule + UBERON:lymphoid follicle + nodulus lymphoideus + UBERON:0000444 + nodulus lymphaticus + folliculus lymphaticus + nodular lymphoid tissue + lymphatic nodule + lymphatic follicle + + + exocrine gland secretion + bodily secretion + exocrine gland fluid + UBERON:0000456 + exocrine gland fluid or secretion + UBERON:bodily secretion + exocrine gland fluid/secretion + "A portion of organism substance that is produced by exocrine glands." [UBERON:cjm] + external secretion + secreted substance + + + organism substance + body fluid or substance + body substance + organism substance + portion of body substance + UBERON:organism substance + "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body." [CARO:MAH] + UBERON:0000463 + + + UBERON:anatomical space + "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures." [CARO:MAH] + lumen space + UBERON:0000464 + anatomical space + + + "Anatomical entity that has mass." [CARO:MAH] + UBERON:material anatomical entity + UBERON:0000465 + material anatomical entity + + + UBERON:0000466 + "Anatomical entity that has no mass." [CARO:MAH] + immaterial physical anatomical entity + UBERON:immaterial anatomical entity + immaterial anatomical entity + + + "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." [CARO:0000011] + connected anatomical system + UBERON:0000467 + anatomical system + organ system + body system + UBERON:anatomical system + + + organism + UBERON:multicellular organism + Koerper + whole body + multi-cellular organism + "Anatomical structure that is an individual member of a species and consists of more than one cell." [CARO:0000012, CARO:MAH, http://en.wikipedia.org/wiki/Multi-cellular_organism] + UBERON:0000468 + multicellular organism + whole organism + body + + + UBERON:0000470 + cell component + cell part + "Anatomical structure that is a direct part of the cell." [CARO:MAH] + UBERON:cell part + + + compound organ component + UBERON:compound organ component + UBERON:0000471 + "Multi-tissue structure that is part of a compound organ." [CARO:0000019, CARO:MAH] + + + "A gonad of a male animal. A gonad produces and releases sperm." [UBERON:cjm] + testicle + male gonad + testes + testiculus + gonad of male reproductive system + UBERON:0000473 + orchis + UBERON:testis + gonad of male genitalia + testis + + + organism subdivision + "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." [CARO:0000032, CARO:DOS, CARO:MAH] + body part + cardinal body part + body region + UBERON:organism subdivision + UBERON:0000475 + anatomic region + + + UBERON:acellular anatomical structure + "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue." [CARO:MAH] + acellular anatomical structure + UBERON:0000476 + + + UBERON:anatomical cluster + UBERON:0000477 + anatomical cluster + "Anatomical group that has its parts adjacent to one another." [CARO:MAH] + + + UBERON:extraembryonic structure + extra-embryonic structure + extraembryonic tissue + UBERON:0000478 + extraembryonic structure + "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." [CARO:DOS, CARO:MAH, https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279] + + + tissue + "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." [CARO:0000043] + portion of tissue + UBERON:0000479 + UBERON:tissue + tissue portion + + + "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types." [CARO:0000055, CARO:MAH] + UBERON:0000481 + UBERON:multi-tissue structure + multi-tissue structure + + + portion of epithelium + "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]." [CARO:MAH, http://en.wikipedia.org/wiki/Epithelium] + epithelial tissue + UBERON:epithelium + epithelium + UBERON:0000483 + + + UBERON:simple cuboidal epithelium + epithelium simplex cuboideum + simple cuboidal epithelium + UBERON:0000484 + "Unilaminar epithelium that consists of a single layer of cuboidal cells." [CARO:MAH, http://en.wikipedia.org/wiki/Simple_cuboidal_epithelium] + + + UBERON:0000485 + simple columnar epithelium + simple columnar epithelium + "Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]" [CARO:MAH, FMA:FMA, http://en.wikipedia.org/wiki/Simple_columnar_epithelium] + UBERON:simple columnar epithelium + epithelium simplex columnare + + + laminated epithelium + UBERON:0000486 + multilaminar epithelium + UBERON:multilaminar epithelium + stratified epithelium + "Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]" [CARO:MAH, FMA:FMA, http://en.wikipedia.org/wiki/Stratified_epithelium] + + + UBERON:0000487 + UBERON:simple squamous epithelium + "Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]" [CARO:MAH, FMA:45565, http://en.wikipedia.org/wiki/Simple_squamous_epithelium] + simple squamous epithelium + epithelium simplex squamosum + + + heterogenous epithelium + UBERON:0000488 + atypical epithelium + "Epithelium that consists of epithelial cells not arranged in one ore more layers." [CARO:MAH] + UBERON:atypical epithelium + + + "Compound organ that contains one or more macroscopic anatomical spaces." [CARO:MAH] + UBERON:0000489 + cavitated organ + cavitated compound organ + UBERON:cavitated compound organ + + + UBERON:0000490 + simple epithelium + "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]" [CARO:MAH, FMA:45561] + UBERON:unilaminar epithelium + unilaminar epithelium + + + mucus + "Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water." [http://en.wikipedia.org/wiki/Mucus] + UBERON:0000912 + UBERON:mucus + + + anterior subdivision of trunk + thorax + "Subdivision of trunk that lies between the head and the abdomen." [UBERON:cjm] + upper body + UBERON:0000915 + thoracic segment of trunk + UBERON:thoracic segment of trunk + + + UBERON:abdomen + "The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column." [UBERON:cjm] + belly + celiac region + adult abdomen + abdomen + UBERON:0000916 + abdominopelvis + abdominopelvic region + + + UBERON:embryo + "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [BTO:0000379, FB:FBrf0039741, FB:FBrf0041814, GO:0009790, http://en.wikipedia.org/wiki/Embryo] + embryonic organism + embryo + developing organism + developmental tissue + UBERON:0000922 + + + embryonic germ layers + embryonic germ layer + germ layer + UBERON:germ layer + UBERON:0000923 + germinal layer + "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm." [http://en.wikipedia.org/wiki/Germ_layer] + + + UBERON:ectoderm + embryonic ectoderm + ectoderm + UBERON:0000924 + "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue." [http://en.wikipedia.org/wiki/Ectoderm] + + + "Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut." [http://en.wikipedia.org/wiki/Endoderm] + UBERON:0000925 + entoderm + endoderm + UBERON:endoderm + + + embryonic mesoderm + mesodermal mantle + UBERON:0000926 + entire mesoderm + UBERON:mesoderm + mesoderm + "The middle germ layer of the embryo, between the endoderm and ectoderm." [http://en.wikipedia.org/wiki/Mesoderm] + + + ventral nerve cord + UBERON:ventral nerve cord + "The pair of closely united ventral longitudinal nerves with their segmental ganglia that is characteristic of many elongate invertebrates (as earthworms)[BTO]. A large process bundle that runs along the vental mid-line extending from the ventral region of the nerve ring[WB]. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms[GO]." [BTO:0002328, GO:0007419, http://en.wikipedia.org/wiki/Ventral_nerve_cord, WB:Paper00000938] + UBERON:0000934 + ventral cord + + + anterior cerebral commissure + AC + commissura rostralis + commissura rostral + UBERON:0000935 + "A bundle of myelinated nerve fibers passing transversely through the lamina terminalis and connecting symmetrical parts of the two cerebral hemispheres; it consists of a smaller anterior part (pars anterior commissurae anterioris) and a larger posterior part (pars posterior commissurae anterioris)." [BTO:0002169] + commissura anterior + anterior commissural nucleus + precommisure + paleocortical commissure + anterior commissure + rostral commissure + Commissura anterior cerebri + UBERON:anterior commissure + + + UBERON:imaginal disc + imaginal disk + UBERON:0000939 + imaginal disc + "one of the parts of a holometabolous insect larva that will become a portion of the outside of the adult insect during the pupal transformation." [http://en.wikipedia.org/wiki/Imaginal_disc] + + + Ventricular + UBERON:0000945 + anterior intestine + stomach + gaster + "An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium." [http://en.wikipedia.org/wiki/Stomach, https://orcid.org/0000-0002-6601-2165, ISBN10:0073040584] + UBERON:stomach + ventriculus + mesenteron + + + UBERON:cardial valve + valve of heart + cardial valve + UBERON:0000946 + stomodaeal valve + "A membranous fold of the heart that prevents reflux of fluid" [MP:0000285\,MESH\:A07.541.510\,PMID\:7926784] + heart valve + heart valve + heart valves + cardiac valve + + + UBERON:0000947 + trunk of aortic tree + arteria maxima + aorta + "The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation" [http://en.wikipedia.org/wiki/Aorta, MP:0000272\,ISBN\:0-683-40008-8\,MESH\:A07.231.114.056, UBERON:cjm] + trunk of systemic arterial tree + UBERON:aorta + + + vertebrate heart + chambered heart + UBERON:heart + "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ." [http://en.wikipedia.org/wiki/Heart, UBERON:cjm] + UBERON:0000948 + cardium + heart + Herz@de + + + "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]." [http://en.wikipedia.org/wiki/Brain, http://purl.obolibrary.org/obo/uberon/tracker/300] + UBERON:0000955 + encephalon + suprasegmental structures + brain + suprasegmental levels of nervous system + UBERON:brain + synganglion + the brain + + + pallium of the brain + cortex of cerebral hemisphere + "The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex." [NIFSTD:birnlex_1494] + UBERON:0000956 + cortical plate (CTXpl) + cortical plate (areas) + cortex cerebri + cerebral cortex + brain cortex + UBERON:cerebral cortex + cortex cerebralis + + + UBERON:lamina + UBERON:0000957 + lamina + "Any thin layer or plate." [http://en.wikipedia.org/wiki/Lamina_of_the_vertebral_arch] + laminar tissue + + + UBERON:medulla of organ + UBERON:0000958 + medulla + medulla of organ + "Middle part of an organ, surrounded by the cortex." [UBERON:cjm] + + + "A decussation of the diencephalon where the fibers of the optic nerve cross" [http://en.wikipedia.org/wiki/Optic_chiasm, MGI:llw2, MP:0009770, UBERON:cjm] + chiasma nervorum opticorum + optic chiasma + UBERON:0000959 + UBERON:optic chiasma + decussation of optic nerve fibers + chiasma + optic chiasm + chiasma opticum + optic chiasm (Rufus of Ephesus) + + + cornea of camera-type eye + UBERON:0000964 + UBERON:cornea + cornea + "the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure" [MP:0001312\,ISBN\:0-683-40008-8\,MESH\:A09.371.060.217] + tunica cornea + + + UBERON:retina + UBERON:0000966 + retina + Netzhaut + retina of camera-type eye + tunica interna of eyeball + "The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." [http://en.wikipedia.org/wiki/Retina, ZFIN:curator] + inner layer of eyeball + + + UBERON:eye + visual apparatus + UBERON:0000970 + eye + light-detecting organ + "An organ that detects light." [https://orcid.org/0000-0002-6601-2165] + + + collum + UBERON:0000974 + "An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column." [UBERON:cjm] + neck + UBERON:neck + neck (volume) + + + UBERON:sternum + vertebrate sternum + breastbone + UBERON:0000975 + "A midventral endochondral skeletal element which represents the origin site of the pectoral muscles[PHENOSCAPE:ad]." [PHENOSCAPE:ad] + sternum + + + humerus bone + UBERON:humerus + proximal metapterygial mesomere of pectoral fin + UBERON:0000976 + mesomere 1 of pectoral appendage + "Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah]" [AAO:0000679, PHENOSCAPE:mah] + humeri + humerus + proximal metapterygial mesomere of pectoral appendage + + + UBERON:0000978 + "The portion of the hindlimb that contains both the stylopod and zeugopod." [http://en.wikipedia.org/wiki/Leg#Limb] + tetrapod leg + leg + lower extremity + UBERON:leg + + + shankbone + tibia + "The major preaxial endochondral bone in the posterior zeugopod[Phenoscape]." [PHENOSCAPE:mah] + UBERON:0000979 + UBERON:tibia + shinbone + + + thigh bone + os femoris + proximal metapterygial mesomere of pelvic appendage + os longissimum + UBERON:femur + proximal metapterygial mesomere of pelvic fin + mesomere 1 of pevlic appendage + femur + os femorale + "Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]." [http://en.wikipedia.org/wiki/Femur, VSAO:0000186] + UBERON:0000981 + femoral bone + + + articular joint + UBERON:skeletal joint + skeletal joint + "Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, http://en.wikipedia.org/wiki/Joint, VSAO:0000101] + UBERON:0000982 + + + pons cerebri + pons Varolii + UBERON:pons + pons + UBERON:0000988 + pons of Varolius + "The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum." [VHOG:0001176] + + + phallus + penes + UBERON:0000989 + "A intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination" [http://en.wikipedia.org/wiki/Penis, MP:0005187\,ISBN\:0-683-40008-8, UBERON:cjm] + penis + UBERON:penis + + + "Reproductive organ that produces and releases eggs (ovary) or sperm (testis)." [http://en.wikipedia.org/wiki/Gonad, ISBN:0140512888, ZFA:0000413, ZFIN:curator] + UBERON:gonad + gonada + UBERON:0000991 + gonad + + + gonad of reproductive system of female organism + genitalia of female organism gonada + female reproductive system gonada + UBERON:female gonad + ovary + gonada of reproductive system of female organism + gonad of female organism reproductive system + genitalia of female organism gonad + female reproductive system gonad + gonad of female reproductive system + gonad of genitalia of female organism + ovarium + gonad of female organism genitalia + ovum-producing ovary + female gonad + gonada of female organism reproductive system + gonada of female organism genitalia + female organism reproductive system gonad + female organism reproductive system gonada + gonada of female reproductive system + gonada of genitalia of female organism + female organism genitalia gonad + reproductive system of female organism gonada + ovaries + UBERON:0000992 + reproductive system of female organism gonad + female organism genitalia gonada + "the gonad of a female organism which contains germ cells" [http://en.wikipedia.org/wiki/Ovary, MP:0001126\,ISBN\:0-683-40008-8] + + + UBERON:oviduct + tubular parts of female reproductive system + tuba uterina + oviduct + female reproductive tracts + ovarian tube + tuba uterinae + UBERON:0000993 + ovarian duct + "A tube or collection of tubes in an animal from the ovaries to the outside of the body." [UBERON:cjm] + uterine tube + + + "the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth" [MP:0001120\,MGI\:csmith] + UBERON:0000995 + UBERON:uterus + uterus + + + vesicular gland + UBERON:seminal vesicle + UBERON:0000998 + vesicular seminalis + vesicular glands + seminal vesicle + glandula seminalis + vas efferens + glandula vesiculosa + vesiculae seminales + vesiculæ seminales + vesiculæ seminales + gon_male_sves + "Either of a pair of glandular pouches that lie one on either side of the male reproductive tract and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct." [BTO:0001234, http://en.wikipedia.org/wiki/Seminal_vesicle] + vesicula seminalis + + + UBERON:cuticle + "tough but flexible, non-mineral outer coverings of an organism, or parts of an organism, that provide protection. Cuticles are non-homologous, differing in their origin, structure and chemical composition[WP]." [http://en.wikipedia.org/wiki/Cuticle, http://sourceforge.net/tracker/?func=detail&aid=3348965&group_id=36855&atid=440764] + cuticular exoskeleton + cuticula + cuticle + UBERON:0001002 + + + UBERON:0001003 + UBERON:skin epidermis + skin epidermis + "The outer layer of the skin[WP]. cellular, multilayered epithelium derived from the ectoderm[ZFA]." [http://en.wikipedia.org/wiki/Epidermis_(skin), ISBN10:0073040584] + vertebrate epidermis + adult epidermis + + + "Functional system which consists of structures involved in respiration." [http://en.wikipedia.org/wiki/Respiratory_system, UBERON:cjm] + Atmungssystem + respiratory system + UBERON:0001004 + apparatus respiratorius + UBERON:respiratory system + respiratory system + systema respiratorium + apparatus respiratorius + + + UBERON:respiratory airway + UBERON:0001005 + respiratory airway + "An airway through which respiratory air passes in organisms." [http://en.wikipedia.org/wiki/Trachea] + + + UBERON:digestive system + "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes." [FB:gg, http://en.wikipedia.org/wiki/Digestive_system, NLM:alimentary+system] + gut + UBERON:0001007 + digestive system + alimentary system + alimentary tract + gastrointestinal system + + + adipose tissue + "Portion of connective tissue composed of adipocytes enmeshed in areolar tissue" [http://en.wikipedia.org/wiki/Adipose_tissue, MP:0000003\,MESH\:A10.165.114\,MGI\:cwg, UBERON:cjm] + adipose + bodyfat + fatty tissue + UBERON:0001013 + UBERON:adipose tissue + fatty depot + fat + fat tissue + + + set of muscles + musculature system + musculi + set of skeletal muscles + musculature + muscles set + UBERON:0001015 + muscle group + muscle system + UBERON:musculature + "A subdivision of the muscular system corresponding to a subdisivision of an organism." [http://en.wikipedia.org/wiki/Muscular_system, https://orcid.org/0000-0002-6601-2165] + muscles + musculature + + + "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [http://en.wikipedia.org/wiki/Nervous_system, http://uri.neuinfo.org/nif/nifstd/birnlex_844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, ZFIN:curator] + UBERON:0001016 + nervous system + UBERON:nervous system + neurological system + systema nervosum + + + systema nervosum centrale + UBERON:0001017 + neuraxis + CNS + UBERON:central nervous system + central nervous system + "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord." [GO:0021551, http://www.frontiersinzoology.com/content/7/1/29, https://sourceforge.net/p/geneontology/ontology-requests/11422/] + + + "A group of axons linking two or more neuropils and having a common origin, termination[FBbt]." [http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html] + nerve tract + UBERON:axon tract + tract of neuraxis + axonal tract + axon tract + UBERON:0001018 + tract + neuraxis tract + + + UBERON:nerve fasciculus + nerve fiber tract + nerve fasciculus + "A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed)." [FBbt:00005101, http://uri.neuinfo.org/nif/nifstd/birnlex_872] + nerve fasciculus + neural fasciculus + UBERON:0001019 + fasciculus + nerve bundle + + + UBERON:nervous system commissure + nervous system commissure + neuraxis commissure + commissure of neuraxis + "Axon tract that crosses the midline of the central nervous system[NIF, modified]. In the context of Drosophila refers to a broad band of axons connecting equivalent neuropils each side of the brain[FBbt]." [http://purl.obolibrary.org/obo/uberon/tracker/300, http://purl.obolibrary.org/obo/uberon/tracker/325, NIFSTD:nlx_anat_20090513] + UBERON:0001020 + + + UBERON:0001021 + neural subtree + UBERON:nerve + nerves + "An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures." [FBbt:00005105, UBERON:cjm] + peripheral nerve + nerve + + + set of sense organs + sensory organ system + sensory subsystem + sense organ subsystem + sense organs + UBERON:sensory system + sense organs set + UBERON:0001032 + sensory systems + sensory system + organa sensuum + organa sensuum + "Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information." [http://en.wikipedia.org/wiki/Sensory_system] + + + UBERON:0001033 + gustatory system + taste system + UBERON:gustatory system + "The sensory system for the sense of taste." [NIFSTD:nlx_anat_090803] + gustatory organ system + + + quill + fur + coat hair + coat/ hair + strand of hair + UBERON:strand of hair + UBERON:0001037 + "A filament, mostly protein, that grows from follicles found in the dermis[WP]." [http://en.wikipedia.org/wiki/Hair] + microchaeta + hair + setulae + whisker + vibrissa + + + vesicula umbilicalis + UBERON:yolk sac + saccus vitellinus + yolk sac + "A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]." [http://en.wikipedia.org/wiki/Yolk_sac] + UBERON:0001040 + + + proenteron + "Anterior subdivision of a digestive tract." [http://orcid.org/0000-0002-6601-2165] + foregut + UBERON:0001041 + UBERON:foregut + praeenteron + + + gullet + oesophagus + UBERON:esophagus + UBERON:0001043 + esophagus + "Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993)." [http://en.wikipedia.org/wiki/Esophagus, http://www.rivm.nl/interspeciesinfo/inter/oesophagus/] + + + "Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]." [GO:0007494, http://en.wikipedia.org/wiki/Midgut] + UBERON:0001045 + UBERON:midgut + midgut + mesenteron + + + "The caudalmost subdivision of a digestive tract." [UBERON:cjm] + UBERON:hindgut + UBERON:0001046 + metenteron + hindgut + + + UBERON:0001047 + "Large synaptic bouton found in areas like olfactory bulb, cerebellar cortex and thalamus, that contacts many post-synaptic targets[NIF]." [http://ccdb.ucsd.edu/SAO/images/glomerulus_sw_512x512.jpg, http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html] + neural glomerulus + UBERON:neural glomerulus + + + future organ + primordia + placode + UBERON:primordium + bud + UBERON:0001048 + rudiment + "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]." [BTO:0001886, FB:DJS, FB:FBrf0089570, http://flybase.org/reports/FBrf0178740.html] + primordium + + + UBERON:0001049 + neural primordium + neural tube + tubus neuralis + UBERON:neural tube + presumptive central nervous system + "In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]." [http://en.wikipedia.org/wiki/Neural_tube] + + + intestinum rectum + terminal portion of large intestine + rectal sac + UBERON:rectum + rectum + terminal portion of intestine + UBERON:0001052 + "the terminal portion of the intestinal tube, terminating with the anus" [MP:0000492\,ISBN\:0-683-40008-8, UBERON:cjm] + + + "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [CARO:MAH, FMA:62955] + anatomical entity + UBERON:anatomical entity + UBERON:0001062 + + + discus intervertebralis + UBERON:intervertebral disk + UBERON:0001066 + intervertebral disk + "A pad of fibrocartilage between the articular surfaces of two successive vertebral centra which has nucleus pulposus at its core." [http://en.wikipedia.org/wiki/Intervertebral_disk, ISBN10:0073040584] + intervertebral disc + spinal disk + spinal disc + intervertebral fibrocartilage + + + urine + UBERON:urine + "Excretion that is the output of a kidney" [http://en.wikipedia.org/wiki/Urine] + UBERON:0001088 + + + calcareous tooth + "Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food." [http://en.wikipedia.org/wiki/Tooth_(animal), UBERON:cjm] + dental element + dentine containing tooth + UBERON:calcareous tooth + tooth + UBERON:0001091 + vertebrate tooth + + + incisor + incisor tooth + UBERON:0001098 + UBERON:incisor tooth + "Incisors are the first kind of tooth in heterodont mammals. They are located in the premaxilla above and mandible below. [WP,unvetted]." [http://en.wikipedia.org/wiki/Incisor_tooth] + + + "A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control" [MP:0002279] + diaphragm + thoracic diaphragm + midriff + diaphragm muscle + UBERON:diaphragm + UBERON:0001103 + phren + diaphragm of thorax + + + lobus hepatis + lobe of liver + hepatic lobe + UBERON:lobe of liver + UBERON:0001113 + liver lobe + "Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe." [http://en.wikipedia.org/wiki/Liver#Lobes] + + + UBERON:left lobe of liver + left hepatic lobe + lobus hepaticus sinister + liver left lobe + UBERON:0001115 + left lobe of liver + left liver lobe + lobus hepatis sinister + "The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted]." [http://en.wikipedia.org/wiki/Left_lobe_of_liver] + + + lobus (glandula thyroidea) + thyroid gland lobe + UBERON:lobe of thyroid gland + lobe of thyroid gland + UBERON:0001118 + lobuli glandulae thyroideae + "A lobe of tissue that is part of a thyroid gland." [UBERON:cjm] + thyroid lobe + + + right lobe of thyroid gland + lobus dexter (glandula thyroidea) + right thyroid lobe + "A lobe of thyroid gland that is in the right side of a thyroid gland." [OBOL:automatic] + UBERON:0001119 + UBERON:right lobe of thyroid gland + thyroid gland right lobe + + + left lobe of thyroid gland + UBERON:left lobe of thyroid gland + lobus sinister (glandula thyroidea) + thyroid gland left lobe + "A lobe of thyroid gland that is in the left side of a thyroid gland." [OBOL:automatic] + UBERON:0001120 + left thyroid lobe + + + vertebral column + UBERON:0001130 + spinal column + UBERON:vertebral column + "Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]." [https://orcid.org/0000-0002-6601-2165, https://sourceforge.net/tracker/?func=detail&aid=3530322&group_id=76834&atid=2257941, VSAO:0000185] + dorsal spine + vertebral region + columna vertebralis + + + parathyroid secreting cell + parathyroid gland + parathyroid + UBERON:parathyroid gland + "The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism." [http://en.wikipedia.org/wiki/Parathyroid_gland, MP:0000678\,ISBN\:0-683-40008-8] + epithelial body + UBERON:0001132 + + + heart myocardium textus muscularis + muscle tissue of heart muscle + muscle tissue of heart myocardium + UBERON:cardiac muscle tissue + muscle tissue of muscle of heart + textus muscularis of heart myocardium + cardiac musculature + cardiac muscle muscle tissue + heart muscle textus muscularis + muscle tissue of cardiac muscle + textus muscularis of heart muscle + cardiac muscle textus muscularis + textus muscularis of cardiac muscle + "Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]." [ZFA:0005280] + muscle of heart muscle tissue + myocardium muscle tissue + textus muscularis of muscle of heart + UBERON:0001133 + muscle of heart textus muscularis + muscle tissue of myocardium + myocardium textus muscularis + textus muscularis of myocardium + cardiac muscle + cardiac muscle tissue + heart muscle muscle tissue + heart myocardium muscle tissue + + + skeletal muscle system + skeletal muscle tissue + "Muscle tissue that consists primarily of skeletal muscle fibers." [https://github.com/obophenotype/uberon/issues/324] + UBERON:skeletal muscle tissue + UBERON:0001134 + somatic muscle + + + textus muscularis levis; textus muscularis nonstriatus + non-striated muscle + UBERON:0001135 + textus muscularis nonstriatus + involuntary muscle + smooth muscle tissue + smooth muscle + UBERON:smooth muscle tissue + "Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]." [GO:0006939, http://en.wikipedia.org/wiki/Smooth_muscle_tissue] + + + back of body proper + dorsum + "A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.." [BSPO:0000063, http://en.wikipedia.org/wiki/Dorsum_(anatomy), UBERONREF:0000006] + UBERON:0001137 + dorsal part of organism + UBERON:dorsum + back + + + intestinum caecum + UBERON:0001153 + blindgut + blind intestine + caecum + UBERON:caecum + caecum + cecum + intestinum crassum caecum + intestinum crassum cecum + "A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction." [http://en.wikipedia.org/wiki/Cecum] + + + UBERON:0001155 + UBERON:colon + colon + large bowel + hindgut + "Last portion of the large intestine before it becomes the rectum." [http://en.wikipedia.org/wiki/Colon_(anatomy), UBERON:cjm, ZFIN:curator] + + + UBERON:0001179 + "Anatomical cavity bounded by visceral and parietal peritoneum" [http://en.wikipedia.org/wiki/Peritoneal_cavity, UBERON:cjm] + peritoneal cavity + UBERON:peritoneal cavity + saccus serosus peritonei + cavitas peritonealis + + + mucosa of organ of ventriculus + UBERON:0001199 + stomach mucosa + ventriculus organ mucosa + mucous membrane of ventriculus + organ mucosa of stomach + stomach mucosa of organ + ventriculus mucous membrane + stomach organ mucosa + mucosa of organ of stomach + tunica mucosa gastris + tunica mucosa (gaster) + "The mucosal layer that lines the stomach." [http://orcid.org/0000-0002-6601-2165] + mucous membrane of stomach + tunica mucosa gastricae + Magenschleimhaut + UBERON:mucosa of stomach + mucosa of stomach + stomach mucous membrane + mucosa of ventriculus + ventriculus mucosa + gastric mucosa + ventriculus mucosa of organ + organ mucosa of ventriculus + gastric mucous membrane + + + organ mucosa of small intestine + small intestine mucosa of organ + tunica mucosa (intestinum tenue) + small bowel organ mucosa + small bowel mucous membrane + mucous membrane of small bowel + mucosa of small bowel + tunica mucosa intestini tenuis + small intestine mucosa + small intestine mucous membrane + UBERON:0001204 + mucous membrane of small intestine + "A mucosa that is part of a small intestine [Automatically generated definition]." [OBOL:automatic] + UBERON:mucosa of small intestine + small bowel mucosa + mucosa of organ of small bowel + small bowel mucosa of organ + organ mucosa of small bowel + mucosa of small intestine + small intestinal mucosa + mucosa of organ of small intestine + small intestine organ mucosa + + + "A mucosa that is part of a large intestine [Automatically generated definition]." [OBOL:automatic] + large intestine mucosa + UBERON:mucosa of large intestine + mucous membrane of large intestine + mucosa of organ of large intestine + large intestinal mucosa + UBERON:0001207 + large intestine organ mucosa + large intestine mucosa of organ + organ mucosa of large intestine + mucosa of large intestine + large intestine mucous membrane + tunica mucosa intestini crassi + + + aggregated lymphoid nodule + Peyer's patch + aggregated lymphoid follicle of intestine + noduli lymphoidei aggregati + Peyers gland + "the protruding lymphoid tissue located on the mucosa of the intestine that is composed of densely packed B cell follicles" [MP:0000696\,MESH\:A10.549.600\,PMID\:15841100\,UBERON\:cjm] + UBERON:0001211 + Peyers patch + UBERON:Peyer's patch + + + kidney pelvis + UBERON:renal pelvis + renal pelvis + pelvis of ureter + p. renallis + pyelum + "A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]." [MP:0004194] + UBERON:0001224 + + + kidney cortex + "Outer cortical portion of the kidney, between the renal capsule and the renal medulla." [http://en.wikipedia.org/wiki/Renal_cortex] + UBERON:cortex of kidney + cortex of kidney + renal cortex + UBERON:0001225 + cortex renalis + + + capsula glomerularis + glomerular capsule + "A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus" [http://en.wikipedia.org/wiki/Bowman%27s_capsule, MP:0002828\,MGI\:pvb] + renal glomerular capsule + Muellerian capsule + Mueller capsule + Bowman's capsule + UBERON:glomerular capsule + pronephric glomerular capsule + malphigian capsule + Bowmans capsule + UBERON:0001230 + capsula glomeruli + bowman's capsule + + + UBERON:nephron tubule + tubulus renalis + UBERON:0001231 + kidney tubule + "An epithelial tube that is part of the nephron, the functional part of the kidney." [GO:0072078, http://en.wikipedia.org/wiki/Renal_tubule] + nephron tubule + uriniferous tubule + + + renal collecting tubule + ureteric tree + "The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient" [GO:0072044, http://en.wikipedia.org/wiki/Collecting_tubule] + UBERON:collecting duct of renal tubule + kidney collecting tubule + collecting tubule + kidney collecting duct + collecting duct of renal tubule + tubulus renalis colligens + arcuate renal tubule + tubulus renalis arcuatus + collecting duct + UBERON:0001232 + junctional tube + collecting duct system + + + right adrenal gland + "An adrenal gland that is in the right side of the abdomen" [OBOL:automatic] + UBERON:0001233 + UBERON:right adrenal gland + glandula suprarenalis dexter + right suprarenal gland + + + UBERON:left adrenal gland + "An adrenal gland that is in the left side of the abdomen" [OBOL:automatic] + left adrenal gland + glandula suprarenalis sinister + left suprarenal gland + UBERON:0001234 + + + intestine organ mucosa + mucous membrane of bowel + mucosa of bowel + "The innermost membrane of the four coats of the intestinal wall, the other three being the submucosa, muscular layers, and serosa. (Berk et al., Gastroenterology, 4th ed, v.3, p1479)" [MESH:A03.492.411.369] + intestine mucous membrane + intestine mucosa of organ + organ mucosa of intestine + UBERON:0001242 + bowel mucous membrane + bowel mucosa + bowel mucosa of organ + organ mucosa of bowel + UBERON:intestinal mucosa + tunica mucosa intestini + mucosa of organ of intestine + intestine mucosa + bowel organ mucosa + mucous membrane of intestine + mucosa of intestine + intestinal mucosa + mucosa of organ of bowel + + + UBERON:anus + "Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts." [http://en.wikipedia.org/wiki/Anus, ZFIN:curator] + proctodeum + opening of terminal part of digestive tract + anus + UBERON:0001245 + anal orifice + anal opening + + + "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]." [GO:0031016] + UBERON:0001264 + pancreas + UBERON:pancreas + + + UBERON:epithelium of stomach + ventriculus epithelial tissue + UBERON:0001276 + gastric epithelium + stomach epithelium + stomach epithelial tissue + "The epithelial layer of the stomach ." [MP:0000471] + epithelial tissue of stomach + epithelium of stomach + epithelial tissue of ventriculus + epithelium of ventriculus + ventriculus epithelium + + + epithelial tissue of intestine + epithelium of intestine + "The innermost membrane of the four coats of the intestinal wall, the other three being the submucosa, muscular layers, and serosa. (Berk et al., Gastroenterology, 4th ed, v.3, p1479)" [http://en.wikipedia.org/wiki/Intestinal_epithelium, MESH:A03.492.411.369] + bowel epithelium + UBERON:0001277 + intestinal epithelium + UBERON:intestinal epithelium + intestine epithelial tissue + epithelial tissue of bowel + epithelium of bowel + intestine epithelium + bowel epithelial tissue + + + sinusoid of liver + UBERON:0001281 + hepatic sinusoid + hepatic sinusoids + UBERON:hepatic sinusoid + liver hepatic sinusoids + liver sinusoidal blood vessel + "Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers." [http://en.wikipedia.org/wiki/Hepatic_sinusoid, ZFIN:curator] + vas sinusoideum + sinusoidal blood vessel of liver + liver sinusoid + vas capillare sinusoideum + + + bile canaliculi + biliary canaliculus + UBERON:0001283 + "An intercellular channel that takes up bile from hepatocytes, transporting it to the bile ducts." [MP:0008991] + bile capillary + bile canaliculus + UBERON:bile canaliculus + + + UBERON:nephron + UBERON:0001285 + nephron + "The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]" [http://en.wikipedia.org/wiki/Nephron, http://www.ncbi.nlm.nih.gov/pubmed/9268568] + nephroneum + tubulus renalis + + + UBERON:0001287 + kidney proximal convoluted tubule + "The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule." [GO:0072019] + PCT + tubulus contortus proximalis + proximal convoluted renal tubule + tubulus convolutus proximalis + first convoluted tubule + 1st convoluted tubule + UBERON:proximal convoluted tubule + tubulus contortus proximalis + proximal convoluted tubule + renal proximal convoluted tubule + + + epididymis + "the elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens" [MP:0002631\,MGI\:pvb] + epididymus + UBERON:0001301 + UBERON:epididymis + Nebenhoden@ge + + + UBERON:ovarian follicle + follicle of ovary + ovary follicle + folliculi ovarici vesiculosi + egg follicle + ovarian follicle + UBERON:0001305 + "A spherical aggregation of cells in the ovary that contains a single oocyte[WP,modified]." [http://en.wikipedia.org/wiki/Ovarian_follicle, http://www.repropedia.org/ovarian-follicle] + folliculi ovarici primarii + follicle of ovary viewed macroscopically + + + UBERON:0001322 + ischiatic nerve + ischiadic nerve + "A large nerve that supplies nearly the whole of the skin of the leg, the muscles of the back of the thigh, and those of the leg and foot. It begins in the lower back and runs through the buttock and down the lower limb." [http://en.wikipedia.org/wiki/Sciatic_nerve] + UBERON:sciatic nerve + sciatic nerve + nervus sciaticus + nervus ischiadicus + + + UBERON:0001323 + n. tibialis + "The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]." [http://en.wikipedia.org/wiki/Tibial_nerve] + medial popliteal nerve + tibial nerve + UBERON:tibial nerve + + + lobe of prostate + UBERON:0001328 + "A portion of a prostate that forms a lobe." [https://github.com/obophenotype/uberon/issues/665] + prostatic lobe + UBERON:lobe of prostate + lobe of prostate gland + prostate gland lobe + + + anterior lobe of prostate gland + prostate gland anterior lobe + commissura prostatae + isthmus of prostate gland + UBERON:0001329 + prostatic isthmus + prostate gland anterior lobe + UBERON:prostate gland anterior lobe + anterior prostate + anterior prostate gland + commissure of prostate + anterior lobe of prostate + isthmus of prostate + isthmus prostatae + + + penis zone of skin + UBERON:0001331 + UBERON:skin of penis + skin of penis + zone of skin of penis + "A zone of skin that is part of a penis [Automatically generated definition]." [OBOL:automatic] + penis skin + penile skin + + + tubuli seminiferi + tubuli seminiferi + "the tubules in the testes where spermatogenesis occurs" [MP:0002216\,ISBN\:0-683-40008-8\,MGI\:csmith] + UBERON:seminiferous tubule of testis + seminiferous cord + seminiferous tubule + seminiferous tubule of testis + UBERON:0001343 + testis - seminiferous tubule + + + UBERON:white adipose tissue + "Connective tissue consisting of fat-storing cells and arranged in lobular groups or along minor blood vessels[MP,modified]" [ISBN:0-683-40008-8, MP:0005670] + textus adiposus albus + adipocytus unigutturalis + unilocular adipose tissue + textus adiposus albus + white adipose tissue + UBERON:0001347 + white fat + + + UBERON:0001348 + UBERON:brown adipose tissue + brown adipose tissue + brown fat + multilocular adipose tissue + textus adiposus fuscus + textus adiposus fuscus + "A thermogenic form of adipose tissue that is composed of brown adipocytes[MP,modified]" [MGI:smb, MP:0011698] + adipocytus multigutturalis + + + UBERON:0001349 + UBERON:vestibule + vestibule + "Anatomical cavity that connects an organ cavity, organ cavity subdivision or cavity of body part subdivision to the exterior, completely or partially surrounded by organs or organ parts that are lined by epithelium. Examples: preputial cavity, vestibule of vagina.[FMA]" [FMA:20192, FMA:FMA, http://en.wikipedia.org/wiki/Vestibule_(disambiguation)#Anatomy] + + + external auditory canal + external acoustic meatus + external auditory meatus + "A tube running from the outer ear to the middle ear. The human ear canal extends from the pinna to the eardrum and is about 26 mm in length and 7 mm in diameter." [http://en.wikipedia.org/wiki/External_acoustic_meatus] + external acoustic tube + UBERON:0001352 + ear canal + auditory meatus + auditory canal + UBERON:external acoustic meatus + external auditory tube + + + quadriceps muscle of thigh + quadriceps muscle of the thigh + quadriceps muscle + "One of the muscles belong to the group consisting of the rectus femoris and the three heads of the vastus (lateralis, medialis, intermedius)." [ISBN10:0073040584] + UBERON:0001377 + quadricep muscle + musculus quadriceps femoris + quadriceps + quadriceps femoris muscle + quadriceps femoris + UBERON:quadriceps femoris + + + UBERON:muscle of leg + leg muscle organ + muscle of hindlimb zeugopod or stylopod + "A muscle that is part of the region of the hindlimb between the pelvis and ankle." [http://en.wikipedia.org/wiki/Leg_muscle, https://orcid.org/0000-0002-6601-2165] + leg skeletal muscle tissue + muscle of upper or lower hindlimb segment + muscle organ of leg + leg muscle + UBERON:0001383 + muscle of thigh or crus + leg skeletal muscle + muscle of leg + muscle of upper/lower leg + skeletal muscle of leg + + + UBERON:tibialis anterior + musculus tibialis anterior + ibialis anticus + tibialis cranialis + tibialis anterior muscle + tibilais cranialis + tibialis anterior + "In human anatomy, the tibialis anterior is a muscle that originates in the upper two-thirds of the lateral surface of the tibia and inserts into the medial cuneiform and first metatarsal bones of the foot. Its acts to invert the foot. It is situated on the lateral side of the tibia; it is thick and fleshy above, tendinous below. This muscle overlaps the anterior tibial vessels and deep peroneal nerve in the upper part of the leg. [WP,unvetted]. The M. tibialis cranialis is a muscle that flexes the tarsometatarsus. It originates on the craniodistal aspect of the femur and proximal tibiotarsus and inserts on the cranial surface of the tarsometarsus[EvoWiki]." [http://en.wikipedia.org/wiki/Tibialis_anterior_muscle, http://evolutionwiki.org/wiki/M._tibialis_cranialis] + UBERON:0001385 + anterior tibialis + + + extensor digitorum longus muscle + "A penniform muscle of the lateral front part of the hindlimb responsible for extension of the digits and dorsiflexion of the ankle." [MP:0004246] + UBERON:extensor digitorum longus + extensor digitorum longus + toe extensor + musculus extensor digitorum longus + UBERON:0001386 + toe extensor muscle + + + UBERON:gastrocnemius + m.gastrocnemius + musculus gastrocnemius + gastrocnemius muscle + "The most superficial muscle of the triceps surae group, in the posterior portion of the lower hindleg." [ISBN10:0073040584, MP:0013188, UBERON:cjm] + UBERON:0001388 + gastrocnemius + m. gastrocnemius + + + "A deep muscle of the triceps surae group, in the superficial posterior compartment of the leg." [http://en.wikipedia.org/wiki/Soleus_muscle, UBERON:cjm] + UBERON:soleus muscle + soleus + UBERON:0001389 + soleus muscle + + + UBERON:skin of limb + "A zone of skin that is part of a limb [Automatically generated definition]." [OBOL:automatic] + limb zone of skin + zone of skin of limb + UBERON:0001419 + limb skin + skin of limb + + + radius bone + UBERON:0001423 + UBERON:radius bone + radius + "The major preaxial endochondral bone in the anterior zeugopod[Phenoscape]." [PHENOSCAPE:mah] + + + UBERON:ulna + UBERON:0001424 + "The major postaxial endochondral bone in the anterior zeugopod[Phenoscape]." [PHENOSCAPE:mah] + ulna + + + carpus bone + UBERON:carpal bone + UBERON:0001435 + carpal bone + carpal skeleton bone + "A bone that is part of the carpal skeleton. Examples: scaphoid, lunate, capitate[cjm]." [https://orcid.org/0000-0002-6601-2165] + bone of carpus + carpal + + + epiphysis + epiphyses + bone epiphysis + end of long bone + long bone epiphysis + UBERON:epiphysis + UBERON:0001437 + "The head of a long bone that articulates with a neighboring skeletal element and is separated from the shaft by the epiphyseal plate until bone growth stops. At that time, the plate disappears and the head and shaft are united[MESH,modified]." [MESH:A02.835.232.251, UBERON:cjm] + + + diaphyseal end of long bone + "Zone of long bone that is between the epiphysis and diaphysis. Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA]" [FMA:24014, http://en.wikipedia.org/wiki/Metaphysis] + long bone metaphysis + UBERON:0001438 + UBERON:metaphysis + metaphysis + metaphyses + + + substantia corticalis + compact bone + cortical bone + cortical region of bone + bony cortex + substantia compacta (pars ossea) + cortical bone tissue + compact bone tissue + compact bone tissue + UBERON:0001439 + "the outer layers of solid, hard bone that covers spongy bone; consists of parallel osteons containing mineral deposits and interstitial lamellae" [MP:0003797\,ISBN\:0-683-40008-8\,MGI\:hdene] + UBERON:compact bone tissue + + + pectoral limb skeleton + skeleton of free upper limb + "The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle" [https://orcid.org/0000-0002-6601-2165] + fore limb skeleton + forelimb skeleton + upper limb skeleton + UBERON:0001440 + set of bones of upper limb + skeleton of forelimb + UBERON:forelimb skeleton + bones of upper limb + forelimb skeleton + skeleton of pectoral limb + skeleton of upper limb + ossa membri superioris + free upper limb skeleton + + + hind limb skeleton + skeleton of free lower limb + lower limb skeleton + ossa membri inferioris + "Subdivision of skeleton consisting of all skeletal elements in an hindlimb region." [https://orcid.org/0000-0002-6601-2165] + UBERON:0001441 + hindlimb skeleton + hind-limb skeleton + UBERON:hindlimb skeleton + set of bones of lower limb + hindlimb skeleton + skeleton of lower limb + free lower limb skeleton + bones of lower limb + + + UBERON:0001443 + "Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA]." [FMA:9576, http://en.wikipedia.org/wiki/Chest] + pectus + UBERON:chest + front of thorax + ventral part of thoracic region + anterolateral part of thorax + chest + thoracic body wall + thorax + + + UBERON:0001444 + head region + subdivision of head + head subdivision + region of head + UBERON:subdivision of head + + + UBERON:0001446 + fibula + UBERON:fibula + "The major postaxial endochondral bone in the posterior zeugopod[Phenoscape]." [PHENOSCAPE:mah] + + + tarsus osseus + bone of tarsus + ossa tarsalia + tarsal bone + UBERON:0001447 + "A bone that is part of the tarsal skeleton. Examples: calcaneus, talus, centralia." [https://orcid.org/0000-0002-6601-2165] + UBERON:tarsal bone + hind mesopodium + tarsal + bone of ankle + ankle bone + ossa tarsi + bony tarsus + bone of tarsal skeleton + + + metatarsal bone + ossa metatarsi + "The metatarsus or metatarsal bones are a group of five long bones in the pes located between the tarsal bones of the hind- and mid-pes and the phalanges of the toes. Lacking individual names, the metatarsal bones are numbered from the medial side (side of big toe): the first, second, third, fourth, and fifth metatarsal. The metatarsals are analogous to the metacarpal bones of the manus. [WP,unvetted]." [http://en.wikipedia.org/wiki/Metatarsal_bone] + metatarsal + ossa metatarsalia + UBERON:metatarsal bone + UBERON:0001448 + + + fibulare + calcaneum + os calcis + UBERON:0001450 + calcaneus + UBERON:calcaneus + calcaneal bone + calcanei + os tarsi fibulare + "The postaxial bone of the proximal tarsals series[Phenoscape]." [PHENOSCAPE:mah] + heel bone + + + middle cuneiform bone of foot + "Endochondral tarsal bone articulating with centralia and metatarsal 2." [http://en.wikipedia.org/wiki/Intermediate_cuneiform_bone, VSAO:0005053] + second cuneiform bone of foot + foot distal carpal bone 2 + os cuneiforme secundum + intermediate cuneiform + UBERON:0001453 + second cuneiform bone + tarsal 2 + cuneiforme 2 + os cuneiforme intermedium + distal tarsal bone 2 + UBERON:distal tarsal bone 2 + intermediate cuneiform bone + os tarsale II + distal tarsal 2 + middle cuneiform + mesocuneiforme + 2nd cuneiform + os cuneiforme intermedium + + + face + UBERON:0001456 + facia/facies + UBERON:face + "A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and olfactory apparatus (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc)." [http://orcid.org/0000-0002-6601-2165] + visage + + + UBERON:arm + brachium + arm + upper extremity + "The part of the forelimb extending from the shoulder to the autopod[cjm]." [http://en.wikipedia.org/wiki/Arm] + UBERON:0001460 + + + elbow + elbow region + UBERON:0001461 + cubital region + UBERON:elbow + articulatio cubiti + elbow limb segment + "The elbow is the region surrounding the elbow-joint—the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific]." [http://en.wikipedia.org/wiki/Elbow] + + + digit 1 of manus + fore digit I + pollex + hand digit 1 + finger 1 + "1st (preaxial) digit of the manus[Wikipedia]." [http://en.wikipedia.org/wiki/Thumb, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553264] + fore limb digit 1 + first digit of hand + UBERON:0001463 + digit 1 of fore-paw + manual digit I + first finger + manual digit 1 + UBERON:manual digit 1 + manual digit 1 + + + UBERON:0001465 + knee region + UBERON:knee + knee + "A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod." [https://orcid.org/0000-0002-6601-2165] + + + pedal digit + pedal digit (phalangeal portion) plus soft tissue + foot digit + "A digit that is part of a pes (foot)." [https://orcid.org/0000-0002-6601-2165] + hindlimb digit + digiti pedis + UBERON:0001466 + UBERON:pedal digit + digit of terminal segment of lower limb + digiti pedis + pes digit + toe + digitipedis + hind_digit + hind digit + digit of foot + digitus pedis + + + articulatio humeri + UBERON:shoulder + shoulder + UBERON:0001467 + "A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle)." [UBERON:cjm] + shoulder region + + + UBERON:skin of prepuce of penis + foreskin of penis + UBERON:0001471 + skin of prepuce of penis + preputial skin + "the loose fold of skin that covers the penis" [MP:0003553\,NCBI\:matt] + penis foreskin + + + vas lymphaticum + lymph vessel + UBERON:0001473 + "A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO]." [BTO:0000752, http://en.wikipedia.org/wiki/Lymphatic_vessel] + UBERON:lymphatic vessel + lymphatic vessel + + + bone element + UBERON:0001474 + bone + bone organ + bone element + UBERON:bone element + "Skeletal element that is composed of bone tissue." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000057] + + + "An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]." [http://en.wikipedia.org/wiki/Articular_capsule] + fibrous capsule of joint + articular capsule + capsula articularis + UBERON:0001484 + joint fibrous capsule + capsulae articulares + joint capsule + UBERON:articular capsule + + + UBERON:knee joint + "The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]." [http://en.wikipedia.org/wiki/Knee] + joint of knee + knee joint + UBERON:0001485 + articulatio genus + + + joints of foot + hind limb autopod joint + joint of pes + pes joint + joint of terminal segment of free lower limb + UBERON:pes joint + foot joint + articulationes pedis + "A skeletal joint that is part of a pes [Automatically generated definition]." [OBOL:automatic] + pedal joint + UBERON:0001487 + + + "A joint that connects the hindlimb autopod and zeugopod skeletons." [http://en.wikipedia.org/wiki/Ankle, https://orcid.org/0000-0002-6601-2165, MESH:A02.835.583.378.062] + mortise joint + talocrural joint + ankle joint + talocrural articulation + UBERON:0001488 + UBERON:ankle joint + + + joint of hand + UBERON:manus joint + joint of manus + articulationes manus + hand joint + joint of terminal segment of free upper limb + "A skeletal joint that is part of a manus (hand) [Automatically generated definition]." [OBOL:automatic] + manus joint + UBERON:0001489 + manual joint + + + joint of elbow + articulatio cubiti + joint of cubital region + elbow joint + UBERON:elbow joint + "A joint that connects the forelimb zeugopod and stylopod skeletons[Obol]." [http://en.wikipedia.org/wiki/Elbow, https://orcid.org/0000-0002-6601-2165] + cubital region joint + UBERON:0001490 + + + UBERON:wrist joint + "A joint connecting the forelimb zeugopod skeleton with the carpal skeleton." [http://en.wikipedia.org/wiki/Wrist, https://orcid.org/0000-0002-6601-2165, https://sourceforge.net/tracker/?group_id=76834&atid=1205376] + wrist joint + joint of wrist + joint of carpal region + UBERON:0001491 + carpal region joint + + + ascending thoracic aorta + UBERON:ascending aorta + aorta ascendens + UBERON:0001496 + ascending aorta + pars ascendens aortae + "The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart’s axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia]" [GO:0035905, http://en.wikipedia.org/wiki/Ascending_aorta] + pars ascendens aortae + + + UBERON:muscle of arm + muscle of upper arm or lower arm + muscle of arm + upper arm / lower arm muscle + UBERON:0001499 + arm muscle + "A muscle organ that is part of an arm [Automatically generated definition]." [OBOL:automatic] + arm skeletal muscle + arm muscle system + arm skeletal muscle tissue + + + UBERON:0001508 + "the convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery" [MP:0004113\,ISBN\:0-683-40008-8] + UBERON:arch of aorta + arch of aorta + arcus aortae + aortic arch + thoracic aorta + + + skin of leg + zone of skin of leg + leg zone of skin + UBERON:skin of leg + UBERON:0001511 + "A zone of skin that is part of a leg [Automatically generated definition]." [OBOL:automatic] + leg skin + + + skin of pes + zone of skin of distal free limb segment of lower extremity + inferior member autopod zone of skin + lower extremity distal free limb segment zone of skin + hindlimb distal free limb segment zone of skin + zone of skin of terminal segment of free lower limb + zone of skin of inferior member autopod + zone of skin of autopod of hind limb + zone of skin of autopod of inferior member + zone of skin of hind limb autopod + autopod of hind limb zone of skin + zone of skin of foot + zone of skin of inferior member distal free limb segment + distal free limb segment of inferior member zone of skin + autopod of hindlimb zone of skin + foot skin + zone of skin of autopod of hindlimb + "A zone of skin that is part of a pes [Automatically generated definition]." [OBOL:automatic] + hind limb distal free limb segment zone of skin + inferior member distal free limb segment zone of skin + foot zone of skin + hind limb autopod zone of skin + UBERON:0001513 + terminal segment of free lower limb zone of skin + lower extremity autopod zone of skin + zone of skin of hindlimb distal free limb segment + autopod of lower extremity zone of skin + zone of skin of hindlimb autopod + hindlimb autopod zone of skin + skin of foot + zone of skin of lower extremity autopod + zone of skin of autopod of lower extremity + zone of skin of distal free limb segment of hindlimb + UBERON:skin of pes + autopod of inferior member zone of skin + distal free limb segment of hindlimb zone of skin + distal free limb segment of hind limb zone of skin + zone of skin of hind limb distal free limb segment + zone of skin of lower extremity distal free limb segment + distal free limb segment of lower extremity zone of skin + zone of skin of distal free limb segment of hind limb + zone of skin of distal free limb segment of inferior member + + + aorta descendens + UBERON:0001514 + pars descendens aortae + "The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]." [GO:0035906, http://en.wikipedia.org/wiki/Descending_aorta] + descending aorta + UBERON:descending aorta + pars descendens aortae + + + UBERON:thoracic aorta + thoracic part of aorta + UBERON:0001515 + aorta thoracalis + thoracic aorta + "the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest" [MP:0010468\,http\://www.medterms.com] + pars thoracica aortae + + + pars abdominalis aortae + abdominal part of aorta + pars abdominalis aortae + descending abdominal aorta + "Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]." [BTO:0002976, http://en.wikipedia.org/wiki/Abdominal_aorta] + abdominal aorta + UBERON:0001516 + abdominal part of aorta + aorta abdominalis + UBERON:abdominal aorta + + + musculus flexor carpi ulnaris + flexor carpi ulnaris muscle + UBERON:flexor carpi ulnaris muscle + UBERON:0001522 + "The flexor carpi ulnaris muscle (FCU) is a muscle of the human forearm that acts to flex and adduct the manus. [WP,unvetted]." [http://en.wikipedia.org/wiki/Flexor_carpi_ulnaris_muscle] + flexor carpi ulnaris + + + UBERON:flexor digitorum profundus + flexor digitorum profundus + musculus flexor digitorum profundus + UBERON:0001523 + "A muscle in the forearm that flexes the manual digits[WP,modified]." [http://en.wikipedia.org/wiki/Flexor_digitorum_profundus_muscle] + flexor digitorum profundus muscle + + + "the short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery" [MP:0010663\,MGI\:csmith] + brachiocephalic artery + UBERON:brachiocephalic artery + truncus brachiocephalicus + innominate artery + brachiocephalic trunk + UBERON:0001529 + truncus brachiocephalicus + + + common carotid artery plus branches + carotid artery system + common carotid artery + a. carotis communis + "A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]." [http://en.wikipedia.org/wiki/Common_carotid_artery] + UBERON:common carotid artery plus branches + trunk of common carotid tree + UBERON:0001530 + + + arteria subclavia + arteria subclavia + UBERON:subclavian artery + subclavian arterial tree + arterial tree of upper limb + subclavian artery + pectoral artery + UBERON:0001533 + PA + "One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta" [https://orcid.org/0000-0002-6601-2165, ISBN10:0073040584] + + + "The subclavian artery that supplies the right pectoral appendage" [UBERON:cjm] + UBERON:0001534 + right subclavian artery + UBERON:right subclavian artery + + + left common carotid artery + left common carotid artery + "In human anatomy, the common carotid artery is an artery that supplies the head and neck with oxygenated blood; it divides in the neck to form the external and internal carotid arteries. [WP,unvetted]." [http://en.wikipedia.org/wiki/Left_common_carotid_artery] + trunk of left common carotid tree + UBERON:0001536 + UBERON:left common carotid artery plus branches + left common carotid artery plus branches + + + "A tube extending from the mouth to the anus." [http://en.wikipedia.org/wiki/Talk\:Human_gastrointestinal_tract, http://sourceforge.net/tracker/?func=detail&atid=440764&aid=2991587&group_id=36855] + UBERON:0001555 + digestive tube + digestive tract + enteric tract + UBERON:digestive tract + gut tube + digestive canal + + + upper respiratory tract + UBERON:upper respiratory tract + UBERON:0001557 + "The segment of the respiratory tract that starts proximally with the olfactory apparatus and ends distally with the cricoid cartilage, before continuing to the trachea." [UBERON:cjm] + + + UBERON:0001560 + organ neck + UBERON:neck of organ + neck of organ + + + jowl + "A fleshy subdivision of one side of the face bounded by an eye, ear and the nose." [http://en.wikipedia.org/wiki/Cheek, UBERON:cjm] + UBERON:0001567 + buccae + cheek + UBERON:cheek + + + olfactory fila + cranial nerve I + CN-I + olfactory i nerve + nerve I + olfactory nerve + "Nerve that carries information from the olfactory epithelium to the olfactory bulb[Butler and Hodos]." [http://en.wikipedia.org/wiki/Olfactory_nerve, ISBN:0471209627] + first cranial nerve + UBERON:olfactory nerve + fila olfactoria + UBERON:0001579 + olfactory I + nerve of smell + olfactoria fila + nervus olfactorius + nervus olfactorius [i] + Olfactory nerve [I] + + + left subclavian artery + "The subclavian artery that supplies the left pectoral appendage" [UBERON:cjm] + UBERON:0001584 + UBERON:left subclavian artery + + + venous network + "A congregation of multiple veins." [http://en.wikipedia.org/wiki/Venous_plexus] + venous plexus + UBERON:0001593 + UBERON:venous plexus + plexus venosus + rete venosum + + + coronary vessel + UBERON:coronary artery + coronary artery + "An artery that supplies the myocardium." [http://en.wikipedia.org/wiki/Coronary_circulation#Coronary_anatomy, UBERON:cjm] + coronary arterial tree + UBERON:0001621 + + + muscle organ + "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]." [GO:0007517] + UBERON:muscle organ + UBERON:0001630 + + + UBERON:artery + arterial tree organ part + arterial system + arteries + UBERON:0001637 + "An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]." [AEO:JB] + artery + arterial vessel + arterial subtree + + + "Any of the tubular branching vessels that carry blood from the capillaries toward the heart." [http://en.wikipedia.org/wiki/Vein] + UBERON:0001638 + vein + vascular element + UBERON:vein + vena + venae + venous tree organ part + + + CN-V + UBERON:0001645 + nervus trigeminus + fifth cranial nerve + trigeminal nerve + cranial nerve V + trigeminal nerve tree + UBERON:trigeminal nerve + trigeminal nerve [V] + trigeminal v nerve + nerve V + trigeminal V + "Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw)." [http://en.wikipedia.org/wiki/Trigeminal_nerve, ISBN:0471209627] + trigeminus + nervus trigeminus [v] + nervus trigeminus + + + UBERON:right pulmonary artery + arteria pulmonalis dextra + "The pulmonary arteries carry blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood. In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung. [WP,unvetted]." [http://en.wikipedia.org/wiki/Right_pulmonary_artery] + right main pulmonary artery + right pulmonary arterial tree + right pulmonary artery + UBERON:0001651 + + + "The pulmonary arteries carry blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood. In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung. [WP,unvetted]." [http://en.wikipedia.org/wiki/Left_pulmonary_artery] + arteria pulmonalis sinistra + left main pulmonary artery + left pulmonary arterial tree + UBERON:0001652 + left pulmonary artery + UBERON:left pulmonary artery + + + semilunar ganglion + 5th ganglion + UBERON:0001675 + Gasser's ganglion + trigeminal V ganglion + Gasserian ganglia + ganglion trigeminale + trigeminal ganglia + trigeminus ganglion + fifth ganglion + ganglion semilunare + "A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear." [ZFIN:curator] + trigeminal ganglion + gV + Gasserian ganglion + ganglion of trigeminal nerve + UBERON:trigeminal ganglion + + + temporal bone + UBERON:temporal bone + os temporale + "the large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous" [MP:0005272\,ISBN\:0-683-40008-8] + UBERON:0001678 + + + nasal bone + nasal@fr + adnasal@fr + UBERON:nasal bone + nasals + os nasale + "One of two small oblong bones, varying in size and form in different individuals; they are placed side by side at the middle and upper part of the face, and form, by their junction, 'the bridge' of the nose[WP]. Paired dermal bones, likened to a bone tube, positioned lateral to the supraethmoid. Nasal bones are transversed by the anterior most part of the supraorbital canals and bear one neuromast foramen in zebrafish[ZFA]." [http://en.wikipedia.org/wiki/Nasal_bone, ZFIN:curator] + UBERON:0001681 + + + mammaliam mandible + mandibula + UBERON:0001684 + mandible + mandibular series + inferior maxillary bone + mandibulla + UBERON:mandible + "A dentary bone that is the only bone in one of the lateral halves of the lower jaw skeleton." [http://en.wikipedia.org/wiki/Human_mandible, http://en.wikipedia.org/wiki/Mandible] + + + UBERON:0001690 + auditory apparatus + ear + UBERON:ear + auris + "Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals." [GO:0042471, http://en.wikipedia.org/wiki/Ear] + + + outer ear + auris externa + external ear + UBERON:external ear + "Part of the ear external to the tympanum (eardrum). It typically consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO]." [GO:0042473, http://en.wikipedia.org/wiki/External_ear] + auricular region of head + UBERON:0001691 + + + "Subdivision of skeleton that is an anterolateral part of the cranium and structurally supports the eye. Includes bones formed and located in sclerotic layer of eyeball." [http://en.wikipedia.org/wiki/Orbit_(anatomy), TAO:0001410, UBERON:cjm] + UBERON:orbit of skull + orbit + UBERON:0001697 + eye socket + bony orbit + orbital region + orbit of skull + orbit of skull + + + UBERON:geniculate ganglion + genicular ganglion + "the group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve)" [MP:0001082\,ISBN\:0-683-40008-8] + internal genu + UBERON:0001700 + ganglion geniculi nervi facialis + ganglion genicularum + geniculate ganglion + gVII + facial VII ganglion + ganglion geniculi + geniculate ganglion + facial ganglion + + + UBERON:nail + "A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP]." [http://en.wikipedia.org/wiki/Nail_(anatomy)] + nail + UBERON:0001705 + nail/claw + talon + + + "The nasal septum separates the left and right airways in the nose, dividing the two nostrils. It is depressed by the Depressor septi nasi muscle. [WP,unvetted]." [http://en.wikipedia.org/wiki/Nasal_septum] + septum of the nose + septum mobile nasi + UBERON:0001706 + septum nasi + nasal septum + UBERON:nasal septum + septal cartilage + + + cavum nasi + UBERON:nasal cavity + olfactory chamber cavity + cavitas nasi + UBERON:0001707 + nasal conduit space + cavity of nose + cavity of olfactory apparatus + olfactory chamber + cavitas nasalis + nasal pit + olfactory cavity + olfactory pit + nasal cavity + "An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present." [http://orcid.org/0000-0002-6601-2165] + nasal fossa + nasal canal + + + "A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane" [UBERON:cjm] + blephara + palpebra + palpebrae + blepharon + eye lid + UBERON:0001711 + eyelid + UBERON:eyelid + + + ganglion of cranial neural tree organ + cranial ganglion/nerve + cranial nerve ganglion + cranial neural ganglion + cranial neural tree organ ganglion + ganglion of cranial nerve + cranial ganglion + head ganglion + cranial ganglion part of peripheral nervous system + presumptive cranial ganglia + cranial ganglion + "the groups of nerve cell bodies associated with the twelve cranial nerves" [MP:0001081\,ISBN\:0-683-40008-8\,MGI\:csmith\,PMID\:9362461] + cranial ganglia + UBERON:cranial ganglion + UBERON:0001714 + + + UBERON:secondary palate + palatum definitivum + palatum + palatum secundarium + "The part of the palate formed from the fusion of the two palatine shelves, extensions of the maxillary prominences." [http://en.wikipedia.org/wiki/Secondary_palate, http://www.indiana.edu/~anat550/hnanim/face/face.html] + roof of mouth + secondary palate + UBERON:0001716 + oral roof + definitive palate + + + cochlear nucleus + "Any of the nuclei of the cochlear nuclear complex." [UBERON:cjm] + UBERON:0001720 + cochlear VIII nucleus + UBERON:cochlear nucleus + nucleus of cochlear nerve + cochlear nucleus of eighth cranial nerve + statoacoustic (VIII) nucleus + cochlear nucleus of acoustic nerve + vestibulocochlear nucleus + + + "A muscular organ in the floor of the mouth." [FEED:rd] + tongue + glossus + UBERON:tongue + UBERON:0001723 + + + rhinopharynx + nasopharynx + nasal part of pharynx + "the section of the pharynx that lies above the soft palate" [MP:0002251\,MGI\:cwg] + UBERON:nasopharynx + UBERON:0001728 + epipharynx + Nasenrachenraum + pars nasalis pharyngis + + + mesopharynx + UBERON:0001729 + "the portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis" [MP:0002252\,MGI\:cwg] + oral part of pharynx + oropharynx + UBERON:oropharynx + pars oralis pharyngis + + + larynx + "A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration." [http://en.wikipedia.org/wiki/Larynx, UBERON:cjm] + UBERON:0001737 + UBERON:larynx + Kehlkopf@ge + + + UBERON:0001744 + "Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP]." [http://en.wikipedia.org/wiki/Lymphoid_tissue] + lymphatic tissue + lymphocytic tissue + lymphoid tissue + UBERON:lymphoid tissue + + + "Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000069] + dentin + dentine + UBERON:dentine + dentine of tooth + UBERON:0001751 + + + "The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window)[GO]." [GO:0042474, http://en.wikipedia.org/wiki/Middle_ear] + UBERON:0001756 + auris media + UBERON:middle ear + middle ear + + + UBERON:0001757 + auricula (auris externa) + auricle of external ear + auricle of ear + pinna of ear + pinnae + UBERON:pinna + auricle + pinna + auricula + "Visible part of the ear that resides outside of the head. The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch). The filtering effect of the human pinna preferentially selects sounds in the frequency range of human speech. In various species, the pinna can also signal mood and radiate heat." [http://en.wikipedia.org/wiki/Pinna_(anatomy)] + + + paradentium + "The tissues that invest or help to invest and support the teeth, including the periodontal ligament, gingivae, cementum, and alveolar and supporting bone[BTO]." [BTO:0001021, http://en.wikipedia.org/wiki/Periodontium] + tooth supporting structure + UBERON:0001758 + periodontal membrane + periodontal ligament + periodontium + UBERON:periodontium + + + "the small curved bones that extends horizontally along the lateral wall of the nasal passage" [MP:0002244\,ISBN\:0-683-40008-8] + turbinate + nasal turbinate + turbinate bone + conchae nasales + concha + turbinal + UBERON:0001762 + nasal concha + UBERON:nasal concha + + + maxillary sinus + antrum of Highmore + sinus maxilliaris + "One of the paired paranasal sinuses, located in the body of the maxilla, communicating with the middle meatus of the nasal cavity." [http://en.wikipedia.org/wiki/Maxillary_sinus, MESH:A04.531.621.578] + UBERON:maxillary sinus + maxillary antrum + highmore antrum + UBERON:0001764 + + + eye anterior chamber + anterior chamber + camera oculi anterior + camera anterior + camera anterior bulbi + "the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens" [MP:0005205\,MESH\:A09.371.060.067] + UBERON:0001766 + camera anterior bulbi oculi + anterior chamber of eyeball + UBERON:anterior chamber of eyeball + anterior chamber of eye + + + UBERON:0001768 + pars iridica retinae + "the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]." [http://en.wikipedia.org/wiki/Uvea, MP:0005197] + tunica vasculosa of eyeball + uveal tract + tunica vasculatis oculi + vascular layer of eyeball + uvea + UBERON:uvea + tunica vasculosa bulbi + uvea + + + UBERON:0001769 + iris + UBERON:iris + "the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye" [MP:0001322\,ISBN\:0-683-40008-8] + irises + irides + anterior uvea + + + UBERON:pupil + UBERON:0001771 + "the central circular aperture of the iris through which light rays enter the eye" [MP:0001317\,ISBN\:0-683-40008-8] + pupil + + + endothelium corneale + e. anterius corneae + endothelium camerae anterioris bulbi + epithelial tissue of cornea + cornea epithelium + "the smooth stratified squamous epithelium that covers the outer surface of the cornea" [MP:0006000\,MESH\:A09.371.060.217.325\,MGI\:smb] + anterior endothelium of cornea + corneal epithelium + UBERON:corneal epithelium + epithelium anterius corneae + cornea epithelial tissue + anterior corneal epithelium + epithelium corneæ anterior layer + external epithelium of cornea + endothelium anterius corneae + UBERON:0001772 + epithelium posterius corneae + epithelium of cornea + epithelium anterius (cornea) + + + sclera + scleral capsule + UBERON:sclera + "Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]." [http://en.wikipedia.org/wiki/Sclera, ZFIN:ZDB-PUB-050701-15] + UBERON:0001773 + + + torso muscle organ + trunk muscle organ + trunk muscle + muscle of trunk + skeletal muscle of trunk + UBERON:skeletal muscle of trunk + trunk musculature + muscle organ of trunk + muscle organ of torso + body musculature + "A skeletal muscle organ that is part of the trunk region." [UBERON:cjm] + UBERON:0001774 + + + UBERON:layer of retina + retina layer + layer of retina + retinal neuronal layer + "Any of the layers that make up the retina[MP]." [MP:0003727] + UBERON:0001781 + retina neuronal layer + retinal layer + + + pigmented layer of retina + retinal pigment epithelium + pigmented retinal epithelium + retinal pigmented epithelium + pigmented epithelium + p. pigmentosa retinae + stratum pigmentosa retinae + "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup[ZFA]. the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells, and is firmly attached to the underlying choroid and overlying retinal visual cells[WP]." [http://en.wikipedia.org/wiki/Retinal_pigment_epithelium, ZFIN:curator] + epithelium, retinal pigment + UBERON:0001782 + PRE + RPE + outer pigmented layer of retina + retinal pigment layer + pigmented retina + pigmented retina epithelium + stratum pigmentosum (retina) + UBERON:pigmented layer of retina + pigment epithelium of retina + + + nervus cranialis + UBERON:cranial nerve + cranial nerves + cranial nerve + cranial neural tree organ + UBERON:0001785 + "Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord." [http://en.wikipedia.org/wiki/Cranial_nerve] + + + centre of macula + fovea centralis + UBERON:fovea centralis + UBERON:0001786 + "A depression in the inner retinal surface within the macula lutea, the photoreceptor layer of which is entirely cones and which is specialized for maximum visual acuity" [http://en.wikipedia.org/wiki/Fovea, UBERON:cjm] + fovea centralis in macula + centre of fovea + + + retinal photoreceptor layer + UBERON:photoreceptor layer of retina + photoreceptor layer of retina + layer of rods and cones + UBERON:0001787 + stratum segmentorum externorum et internorum (retina) + retina photoreceptor layer + "The layer within the retina where the photoreceptor cell receptor segments reside." [http://en.wikipedia.org/wiki/Layer_of_rods_and_cones, ZFA:0000143] + + + retina, outer nuclear layer + retinal outer nuclear layer + UBERON:outer nuclear layer of retina + external nuclear layer + stratum nucleare externum (retina) + "The layer within the retina where the photoreceptor cell bodies reside." [ZFA:0001464] + UBERON:0001789 + layer of outer granules + outer nuclear layer of retina + neural retina outer nuclear layer + retina outer nuclear layer + + + retina outer plexiform layer + UBERON:0001790 + retinal outer plexiform layer + retina, outer plexiform layer + UBERON:outer plexiform layer of retina + outer plexiform layer + stratum plexiforme externum + outer plexiform layer of retina + "The layer within the retina where the bipolar cells synapse with the photoreceptor cells[ZFA]. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells[GO]." [ZFA:0001330] + + + neural retina inner nuclear layer + intermediate cell layer + layer of inner granules + stratum nucleare internum + retina, inner nuclear layer + retina inner nuclear layer + inner nuclear layer + retinal inner nuclear layer + inner nuclear layer of retina + UBERON:0001791 + UBERON:inner nuclear layer of retina + "Cytoarchitectural layer of retina containing closely packed cell bodies, the majority of which are bipolar cells (adapted from Wikipedia)." [NIFSTD:nlx_93816] + + + retinal ganglion cell layer + UBERON:ganglionic layer of retina + stratum ganglionicum (retina) + GCL layer + retina ganglion cell layer + RGC layer + ganglionic layer of retina + retina ganglion layer + retina, ganglion cell layer + stratum ganglionicum retinae + ganglionic cell layer of retina + "Cytoarchitectural layer of retina that contains somata of retinal ganglion cells, bounded by the stratum opticum and the inner plexiform layer" [NIFSTD:nlx_36500] + UBERON:0001792 + retinal ganglion layer + + + stratum plexiforme internum retinae + "Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia)" [NIFSTD:nlx_20558] + retinal inner plexiform layer + stratum plexifome internum + internal plexiform layer of retina + stratum plexiforme internum + retina, inner plexiform layer + retina inner plexiform layer + retinal internal plexiform layer + UBERON:inner plexiform layer of retina + inner plexiform layer of retina + UBERON:0001795 + inner plexiform layer + + + humor aquosus + "A thick watery refractive medium that fills the space between the lens and the cornea[WP]." [http://en.wikipedia.org/wiki/Aqueous_humor] + UBERON:0001796 + aqueous humor + aqueous humor of eyeball + UBERON:aqueous humor of eyeball + aqueous humour + + + UBERON:vitreous humor + whole portion of vitreous humor + humor vitreus + vitreous humor + humor vitreous + UBERON:0001797 + ocular fluid + humoral fluid + vitreous + vitreous humour + vitreous fluid + "transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina" [MP:0002699] + + + "The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells." [MP:0000960] + UBERON:sensory ganglion + ganglion sensorium + UBERON:0001800 + sensory ganglion + + + epithelium of lens + lens epithelial tissue + eye lens epithelial tissue + "A layer of epithelial cells that is part of the eye." [UBERON:cjm] + epithelial tissue of eye lens + UBERON:epithelium of lens + epithelial tissue of lens + epithelium lentis + epithelium of eye lens + UBERON:0001803 + lens epithelium + eye lens epithelium + + + capsula lentis + UBERON:capsule of lens + "the elastic, clear, membrane-like structure, that is outer most layer of the lens" [MP:0003236\,MGI\:smb\,PMID\:15483628] + UBERON:0001804 + capsule of lens + lens capsule + + + visceral nervous system ganglion + ganglion of autonomic nervous system + autonomic ganglion + UBERON:0001805 + ganglion autonomicum + "ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion." [http://en.wikipedia.org/wiki/Autonomic_ganglion] + UBERON:autonomic ganglion + autonomic nervous system ganglion + ganglion of visceral nervous system + + + sympathetic part of autonomic division of nervous system ganglion + ganglion sympatheticum + ganglion of sympathetic part of autonomic division of nervous system + UBERON:sympathetic ganglion + ganglion sympathicum + ganglion of sympathetic nervous system + "A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia" [MP:0001008, UBERON:cjm] + sympathetic ganglion + UBERON:0001806 + sympathetic nervous system ganglion + + + "Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord." [http://en.wikipedia.org/wiki/Paravertebral_ganglion, ZFIN:curator] + UBERON:paravertebral ganglion + sympathetic chain ganglia + ganglion trunci sympathetici + paravertebral ganglion + paravertebral ganglia + UBERON:0001807 + paravertebral ganglion + ganglia trunci sympathici + ganglion of sympathetic trunk + ganglion trunci sympathici + ganglia of sympathetic trunk + sympathetic chain ganglion + + + ganglion parasympathicum + UBERON:parasympathetic ganglion + parasympathetic ganglion + UBERON:0001808 + "Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands." [NIFSTD:nlx_anat_100303] + + + "." [http://en.wikipedia.org/wiki/Enteric_ganglia] + enteric ganglion + UBERON:0001809 + UBERON:enteric ganglion + intramural ganglion + + + wall of conjunctival sac + "the mucous membrane that lines the inner surface of the eyelids and the front of the eyeball" [MP:0001310\,MESH\:A09.371.060.200\,MGI\:csmith] + conjunctivas + UBERON:conjunctiva + conjunctivae + UBERON:0001811 + conjunctiva + + + UBERON:palpebral fissure + UBERON:0001819 + rima palpebrarum + palpebral fissure + "Orifice separating upper and lower eyelids. In the human adult this measures about 10mm vertically and 30 mm horizontally. It can be reduced in size in fetal alcohol syndrome. In Trisomy 9 the palpebral fissures can be upslanting. [WP,modified]." [http://en.wikipedia.org/wiki/Palpebral_fissure] + + + glandula sebaceae + "A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]." [http://en.wikipedia.org/wiki/Sebaceous_gland, MP:0000647] + sebaceous gland + UBERON:0001821 + glandula sebacea + UBERON:sebaceous gland + sebaceous follicle + + + "One of the cartilage structures in the nose that provide form and support[WP]." [http://en.wikipedia.org/wiki/Nasal_cartilage] + UBERON:0001823 + UBERON:nasal cartilage + nasal cartilage + cartilage of nose + + + UBERON:paranasal sinus + UBERON:0001825 + paranasal sinus + "the paired air-filled cavities surrounded by the bones of the face that are lined by mucous membranes and are continuous with the nasal cavity" [MP:0002240\,ISBN\:0-683-40008-8] + nasal sinus + + + UBERON:lip + labia oris + "One of the two fleshy folds which surround the opening of the mouth." [http://en.wikipedia.org/wiki/Lip, http://www.medterms.com/script/main/art.asp?articlekey=9458] + UBERON:0001833 + lip + lips + + + sailva normalis + saliva atomaris + "A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions." [GO:0046541, http://en.wikipedia.org/wiki/Saliva] + UBERON:0001836 + salivary gland secretion + saliva + saliva molecularis + UBERON:saliva + + + "One of three half-circular, interconnected tubes located inside each ear[WP]." [http://en.wikipedia.org/wiki/Semicircular_canal] + UBERON:semicircular canal + ductus semicirculares + UBERON:0001840 + semicircular canal + semicircular ducts + scc + semicircular canals + canalis semicircularis + + + anterior semicircular canal + canalis semircularis posterior + UBERON:0001841 + UBERON:anterior semicircular canal + rostral vertical semicircular canal + anterior semicircular canals + anterior semicircular duct + superior semicircular canal + + + caudal vertical semicircular canal + posterior semicircular canals + UBERON:0001842 + UBERON:posterior semicircular canal + pars superior of labyrinth + posterior semicircular canal + canalis semicircularis posterior + posterior semicircular duct + + + lateral semicircular duct + lateral semicircular canal + horizontal semicircular canal + lateral semicircular canals + UBERON:lateral semicircular canal + UBERON:0001843 + + + cochlear organ + "the spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified]." [http://en.wikipedia.org/wiki/Cochlea, MP:0000031\,ISBN\:0-683-40008-8] + cochlea + cochlear duct + lagena + UBERON:cochlea + UBERON:0001844 + cochlear part of bony labyrinth + cochleae + + + "Transudate contained in the osseous labyrinth outside the membranous labyrinth.[FMA]" [FMA:FMA, http://en.wikipedia.org/wiki/Perilymph] + UBERON:perilymph + perilymph + perilympha + liquor cotunnii + UBERON:0001845 + + + labyrinth + otocyst + inner ear + auris interna + internal ear + "Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation." [http://en.wikipedia.org/wiki/Internal_ear, http://www.ncbi.nlm.nih.gov/pubmed/16217737, ZFIN:curator] + UBERON:0001846 + UBERON:internal ear + + + "Outermost layer of an organ[WP]." [http://en.wikipedia.org/wiki/Cortex_(anatomy)] + UBERON:0001851 + cortex + UBERON:cortex + cortex + cortex of organ + + + Scarpa's fluid + UBERON:0001852 + endolymphatic fluid + "Transudate contained within the membranous labyrinth.[FMA]" [FMA:61112, http://en.wikipedia.org/wiki/Endolymph] + UBERON:endolymph + endolympha + endolymph + + + UBERON:0001853 + UBERON:utricle of membranous labyrinth + "the larger of the two otolith organs in the vestibule" [http://en.wikipedia.org/wiki/Utricle_(ear), MP:0006090\,ISBN\:0-8036-0655-99\,MGI\:smb\,PMID\:15363417] + utriculus (labyrinthus vestibularis) + membranous labyrinth utricle + utricle of membranous labyrinth + utriculus + utricle + + + membranous labyrinth saccule + sacculus (labyrinthus vestibularis) + saccule + sacculus + UBERON:saccule of membranous labyrinth + sacculus + "the smaller of the two otolith organs in the vestibule" [http://en.wikipedia.org/wiki/Saccule, MP:0006089\,ISBN\:0-8036-0655-99\,MGI\:smb\,PMID\:15363417] + UBERON:0001854 + saccule of membranous labyrinth + + + scala media + cochlear aqueduct + scala of Loewenberg + ductus cochlearis + "An endolymph filled cavity inside the cochlea, located in between the scala tympani and the scala vestibuli, separated by the basilar membrane and Reissner's membrane (the vestibular membrane) respectively. Houses the organ of Corti[WP]." [http://en.wikipedia.org/wiki/Cochlear_duct] + membranous cochlea + UBERON:0001855 + Reissner's canal + cochlea duct + Reissners canal + scala medias + UBERON:cochlear duct of membranous labyrinth + cochlear duct of membranous labyrinth + cochlear duct + + + UBERON:endolymphatic duct + "the small membranous canal, connecting with both saccule and utricle of the membranous labyrinth, passing through the aqueduct of vestibule, and terminating in the endolymphatic sac" [MP:0006011\,MGI\:anna\,MGI\:smb] + UBERON:0001860 + ductus endolymphaticus + endolymphatic duct + ductus endolymphaticus + + + vestibular apparatus + UBERON:0001862 + inner ear vestibular component + "The part of the membranous labyrinth that includes the utricle and saccule lodged within the vestibule and the semicircular ducts lodged eccentrically in the corresponding canals." [BTO:0001856] + vestibular labyrinth + UBERON:vestibular labyrinth + labyrinthus vestibularis + + + cartilage of outer ear + external ear cartilage + outer ear cartilage + UBERON:0001867 + auricular region of head cartilage + cartilage of auricular region + cartilage of external ear + UBERON:cartilage of external ear + auricular region cartilage + cartilage of auricular region of head + "A cartilage that is part of a external ear [Automatically generated definition]." [OBOL:automatic] + + + frontal lobe cortex + "Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified]." [NIFSTD:nlx_anat_20090601] + UBERON:frontal cortex + UBERON:0001870 + cortex of frontal lobe + grey matter of frontal lobe + frontal cortex + gray matter of frontal lobe + frontal neocortex + + + lobus temporalis + "Lower lateral part of the cerebral hemisphere. (MSH)" [NIFSTD:birnlex_1160] + UBERON:0001871 + temporal lobe + UBERON:temporal lobe + + + regio parietalis + lobus parietalis + UBERON:0001872 + "Upper central part of the cerebral hemisphere. (MSH)" [NIFSTD:birnlex_1148] + parietal lobe + UBERON:parietal lobe + + + UBERON:0001873 + UBERON:caudate nucleus + Ammon horn fields + "Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species." [NIFSTD:birnlex_1373] + caudatus + caudate nucleus + nucleus caudatus + caudatum + + + nucleus putamen + putamen + "Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion." [NIFSTD:birnlex_809] + UBERON:0001874 + UBERON:putamen + + + amygdaloid nucleus + amygdaloid nuclear groups + archistriatum + amygdala + corpus amygdalae + corpus amygdaloideum + UBERON:amygdala + nucleus amygdalae + UBERON:0001876 + amygdaloid area + amygdaloid body + amygdaloid nuclear complex + amygdaloid complex + amygdaloid nuclear group + "Subcortical brain region lying anterior to the hippocampal formation in the temporal lobe and anterior to the temporal horn of the lateral ventricle in some species. It is usually subdivided into several groups. Functionally, it is not considered a unitary structure (MM)." [NIFSTD:birnlex_1241] + + + UBERON:island of Calleja + UBERON:0001881 + islands of Calleja + Calleja island + island of Calleja + islands of Calleja (olfactory tubercle) + insulae olfactoriae + insula callejae + "One of the seven small groups of granule cells in the polymorph layer of the olfactory tubercle and one large group, the insula magna, which lies along the border between septum, nucleus accumbens and nucleus of the diagonal band." [http://www.ncbi.nlm.nih.gov/pubmed/80412, MP:0010010] + + + nucleus accumbens + "A region of the brain consisting of a collection of neurons located in the forebrain ventral to the caudate and putamen. (caudoputamen in rodent) and continuous with these structures. There is no distinct boundary between the nucleus accumbens and the caudate/putamen, but in rodents, it can be identified by its lack of traversing fiber bundles in comparison to the dorsal striatum. Its principle neuron is the medium spiny neuron. Together with the neostriatum (caudate nucleus and putamen), the nucleus accumbens forms the striatum." [NIFSTD:birnlex_727] + colliculus nuclei caudati + nucleus accumbens septi + UBERON:0001882 + UBERON:nucleus accumbens + colliculus of caudate nucleus + accumbens nucleus + + + tuberculum olfactorium + "Region in the ventral telencephalon, prominent in rodents, but present in all mammals, consisting of a laminated cortical part and the cap/hilus region. It is traditionally viewed as part of the olfactory cortex but recognized by some as having a striatal character. According to many authors, the structure of the OT transitions from cortical like to striatal like along the lateral medial axis. (Maryann Martone)" [NIFSTD:nlx_anat_1005037] + UBERON:0001883 + olfactory tubercle + UBERON:olfactory tubercle + + + diaphragmatic nerve + UBERON:phrenic nerve + nervus phrenicus + phrenic nerve + "A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium." [VHOG:0000728] + phrenic + UBERON:0001884 + + + hippocampal dentate gyrus + area dentata + dentate gyrus of hippocampal formation + dentate gyrus + "Part of the hippocampal formation forming a 'V' or 'U' shaped structure with the opening bounded by hippocampal area CA3. It consists of 3 layers from superficial to deep: molecular, granule cell and polymorphic or hilar layer." [NIFSTD:birnlex_1178] + UBERON:dentate gyrus of hippocampal formation + dentate area (dentate gyrus) + dentate area + gyrus dentatus + UBERON:0001885 + + + UBERON:forebrain + "The most anterior region the brain including both the telencephalon and diencephalon." [http://en.wikipedia.org/wiki/Forebrain, ZFIN:ZDB-PUB-961014-576] + forebrain + prosencephalon + UBERON:0001890 + + + mesencephalon + "Organ component of neuraxis that has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct[FMA]. The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally[ZFA]. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]." [FMA:61993, GO:0030901, http://en.wikipedia.org/wiki/Midbrain, ZFIN:curator] + UBERON:0001891 + UBERON:midbrain + midbrain + + + rhombomere + future rhombencephalon + hindbrain neuromeres + UBERON:rhombomere + hindbrain neuromere + UBERON:0001892 + "A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]." [http://en.wikipedia.org/wiki/Rhombomere, ZFIN:curator] + rhombomere + rhombomeres + + + cerebrum + "Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres." [AAO:0010479, XAO:0000012] + telencephalon + endbrain + UBERON:telencephalon + UBERON:0001893 + + + betweenbrain + between brain + interbrain + mature diencephalon + diencephalon + thalamencephalon + UBERON:diencephalon + diencephalon + "Organ component of neuraxis that has as its parts the epithalamus, thalamus, hypothalamus, subthalamus[FMA]. The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis)." [FMA:62001, http://en.wikipedia.org/wiki/Diencephalon, ZFIN:curator] + UBERON:0001894 + + + metepencephalon + medulla oblonzata + UBERON:medulla oblongata + bulbus + medulla oblongata + "Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]." [FMA:62004, GO:0021550, http://en.wikipedia.org/wiki/Bone_marrow_of_ovary_oblongata] + UBERON:0001896 + + + thalamus opticus + thalami + wider thalamus + UBERON:0001897 + dorsal plus ventral thalamus + "Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87)." [NIFSTD:birnlex_954] + UBERON:dorsal plus ventral thalamus + thalamencephalon + + + "A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]." [http://en.wikipedia.org/wiki/Hypothalamus, ZFIN:curator] + hypothalamus + UBERON:0001898 + preoptico-hypothalamic region + UBERON:hypothalamus + hypothalamus + preoptico-hypothalamic area + + + UBERON:0001902 + small intestinal epithelium + epithelium of small bowel + epithelial tissue of small bowel + small bowel epithelial tissue + epithelium of small intestine + UBERON:epithelium of small intestine + "An epithelium that is part of a small intestine [Automatically generated definition]." [OBOL:automatic] + epithelial tissue of small intestine + small intestine epithelial tissue + small intestine epithelium + mid intestine epithelium + small bowel epithelium + + + pineal body + UBERON:0001905 + corpus pineale + pineal + epiphysis cerebri + epiphysis + UBERON:pineal body + conarium + stirnorgan + "A midline, cone like structure located in the dorso-caudal roof of the 3rd ventricle, attached by peduncles to the habenular and posterior commissures. The stalk contains nerve fibers, blood vessels, connective tissue and parenchymal cells (Paxinos, The Rat Central Nervous System, 2nd ed, pg 399)." [NIFSTD:birnlex_1184] + glandula pinealis + pineal gland + pineal gland (Galen) + pineal organ + frontal organ + + + lobe of mammary gland + "A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males." [BTO:0000817, http://en.wikipedia.org/wiki/Mammary_gland, UBERON:cjm] + mammae + glandula mammaria + mamma + UBERON:0001911 + UBERON:mammary gland + mammary gland + glandula mammaria + lactiferous gland + Brustdruese + dug + + + UBERON:0001913 + "Secretion produced by the mammary gland during lactation." [UBERON:cjm] + mammary gland milk + UBERON:milk + milk + + + UBERON:0001915 + endothelium of blood capillary + endothelium of capillary + endothelium of capillary vessel + capillary endothelium + "An endothelium that is part of a capillary [Automatically generated definition]." [OBOL:automatic] + capillary vessel endothelium + UBERON:endothelium of capillary + blood capillary endothelium + + + inferior colliculus + corpus bigeminum posterioris + caudal colliculus + corpus bigeminalis caudalis + "Part of the midbrain tectum, consisting of paired predominantly gray matter elevations on the dorsal aspect of the midbrain, located caudal to the superior colliculus, dorsal to the periaqueductal gray of the cerebral aqueduct and rostral to the cerebellum. According to Neuronames, the inferior colliculus comprises the central, pericentral and external nucleus and two predominantly white matter structures, the brachium of the inferior colliculus and the commissure of the inferior colliculus (MM)." [NIFSTD:birnlex_806] + posterior colliculus + UBERON:inferior colliculus + UBERON:0001946 + colliculus caudalis + posterior corpus quadrigeminum + inferior colliculi + colliculus inferior + corpus quadrigeminum inferius + + + "A multi-tissue structure that is part of a spinal cord." [OBOL:automatic] + spinal cord part + UBERON:regional part of spinal cord + regional part of spinal cord + UBERON:0001948 + + + isocortex (sensu lato) + cerebral neocortex + "The term neocortex refers to those areas of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN)" [http://uri.neuinfo.org/nif/nifstd/birnlex_2547, OldNeuroNames:754] + UBERON:0001950 + neocortex (isocortex) + nucleus hypoglossalis + nonolfactory cortex + homogenetic cortex + homotypical cortex + iso-cortex + neopallium + neopallial cortex + UBERON:neocortex + neocortex + + + hippocampus major + hippocampus proprius + Ammon's horn + Ammons horn + hippocampus + ammon gyrus + "A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum." [NIFSTD:birnlex_721] + ammon horn + hippocampus proper + cornu ammonis + Ammon horn fields + Ammon's horn + UBERON:0001954 + UBERON:Ammon's horn + + + mucosa associated lymphoid tissue + mucosal-associated lymphatic tissue + "diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO]." [http://en.wikipedia.org/wiki/Mucosa-associated_lymphoid_tissue] + UBERON:0001961 + epithelio-lymphoid tissue + mucosa-associated lymphoid tissue + UBERON:mucosa-associated lymphoid tissue + mucosa-associated lymphoid tissue + mucosa associated lymphatic tissue + mucosal-associated lymphoid tissue + MALT + + + "Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO]." [http://en.wikipedia.org/wiki/Gut-associated_lymphoid_tissue] + UBERON:0001962 + gut-associated lymphoid tissue + UBERON:gut-associated lymphoid tissue + gut associated lymphoid tissue + GALT + + + "The liquid component of blood, in which erythrocytes are suspended." [UBERON:cjm] + blood plasma + UBERON:blood plasma + UBERON:0001969 + blood plasm + portion of blood plasma + + + "vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium." [http://dx.doi.org/10.1002/cphy.c120027, http://en.wikipedia.org/wiki/Bile] + UBERON:0001970 + UBERON:bile + bile + gall + fel + + + serosa of abdominal part of esophagus + serous membrane of gullet + serous membrane of esophagus + esophagus serous membrane + gullet serous membrane + serosa of gullet + serous coat of oesophagus + tunica serosa oesophageae + serous membrane of oesophagus + esophagus serosa + gullet serosa + "A serous membrane that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] + serosa of oesophagus + oesophagus serous membrane + serosa of esophagus + UBERON:0001975 + UBERON:serosa of esophagus + oesophagus serosa + + + serum + blood serum + UBERON:serum + "Liquid derived from blood plasma that has clotting factors removed." [http://en.wikipedia.org/wiki/Serum_(blood), UBERON:cjm] + UBERON:0001977 + + + UBERON:venule + venule + UBERON:0001979 + venula + "One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins" [MP:0004125\,MESH\:A07.231.432.952] + + + UBERON:0001980 + UBERON:arteriole + arteriole + arteriola + "The smallest division of the artery located between the muscular arteries and the capillaries[GO]." [GO:0014830] + + + UBERON:0001981 + vas sanguineum + region of vascular tree organ + blood vessel + UBERON:blood vessel + "A vessel through which blood circulates in the body." [BTO:0001102, http://en.wikipedia.org/wiki/Blood_vessel] + vascular tree organ region + + + UBERON:0001982 + capillary vessel + UBERON:capillary + "Any of the smallest blood vessels connecting arterioles with venules." [http://en.wikipedia.org/wiki/Capillary, ISBN10:0073040584] + blood capillary + capillary + + + intestinal crypt + "the tubular intestinal glands found in the mucosal membranes" [MP:0000490\,ISBN\:0-683-40008-8] + Lieberkuhn's gland + crypt of Lieberkuhn + crypt of Lieberkühn + Lieberkuhn's glands + intestinal crypts + crypts of Lieberkühn + follicles of lieberkuhn + UBERON:0001983 + lieberkuhn crypt + Lieberkuhn crypt + UBERON:crypt of Lieberkuhn + crypt of lieberkuhn + Lieberkuhn gland + + + endothelium + UBERON:endothelium + "A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]" [FMA:63916, MESH:A10.272.491] + UBERON:0001986 + + + placenta + eutherian placenta + "organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell." [http://en.wikipedia.org/wiki/Placenta, http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/06placenta.htm] + UBERON:placenta + allantoic placenta + UBERON:0001987 + + + porción de mierda@en + droppings + piece of shit + portion of faeces + fecal material + ordure + fecal matter + UBERON:feces + UBERON:0001988 + feces + partie de la merde@fr + merde@fr + portion of excrement + excrement + stool + teil der fäkalien@de + spoor + portionem cacas + faeces + matières fécales@fr + portion of fecal material + portion of feces + portion of fecal matter + "Portion of semisolid bodily waste discharged through the anus[MW,modified]" [http://en.wikipedia.org/wiki/Feces, http://www.merriam-webster.com/dictionary/feces] + + + chondroid cartilage + UBERON:hyaline cartilage tissue + UBERON:0001994 + hyaline cartilage + "Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000094] + hyaline cartilage tissue + + + UBERON:0001995 + UBERON:fibrocartilage + stratified cartilage tissue + fibrocartilage + fibrocartilage tissue + "Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000103] + + + olfactory epithelium + main olfactory epithelium + nasal epithelium + nasal sensory epithelium + olfactory membrane + pseudostratified main olfactory epithelium + "A sensory epithelium inside the nasal cavity that is responsible for detecting odors[WP]." [http://en.wikipedia.org/wiki/Olfactory_epithelium] + UBERON:olfactory epithelium + MOE + sensory olfactory epithelium + olfactory sensory epithelium + nasal cavity olfactory epithelium + UBERON:0001997 + + + pulmonary artery + UBERON:pulmonary artery + pulmonary arterial tree + arteria pulmonalis + UBERON:0002012 + truncus pulmonalis + pulmonary arterial tree organ part + "An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.." [http://en.wikipedia.org/wiki/Pulmonary_artery, UBERON:cjm] + + + fibrous capsule of kidney + UBERON:kidney capsule + kidney capsule + "the tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage" [MP:0011383\,MGI\:anna] + capsule of kidney + renal capsule + UBERON:0002015 + + + pulmonary venous tree organ part + UBERON:pulmonary vein + pulmonary vein + venae pulmonales + "Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]." [GO:0060577] + UBERON:0002016 + + + gray mater + grisea + UBERON:0002020 + "A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons." [http://en.wikipedia.org/wiki/Gray_matter, UBERON:cjm] + grey substance + substantia grisea + gray matter of neuraxis + gray matter + UBERON:gray matter + grey matter of neuraxis + neuronal grey matter + gray matter + grey matter + + + stratum Malphighi + basal cell layer of skin + basal cell layer of epidermis + epidermis stratum basale + UBERON:0002025 + UBERON:stratum basale of epidermis + basal layer of epidermis + stratum germinativum + stratum germinosum of epidermis + stratum basale of epidermis + epidermis sensorial layer + stratum basalis of epidermis + rete Malphighii + Malpighian layer + epidermis basal layer + epidermis stratum germinativum + epidermal basal stratum + "the deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells" [MP:0001231\,ISBN\:0-683-40008-8] + + + "the layer of polyhedral cells in the epidermis found between the stratum granulosum and stratum basale; shrinkage and adhesion of these cells gives a spiny or prickly appearance" [MP:0001236\,ISBN\:0-683-40008-8] + stratum malphighii + epidermis stratum spinosum + prickle cell layer + UBERON:stratum spinosum of epidermis + UBERON:0002026 + stratum spinosum of epidermis + squamous cell layer of epidermis + stratum spinosum + epidermis prickle cell layer + prickle cell layer of epidermis + + + "the outer layer of the epidermis, consisting of several layers of flat keratinized non-nucleated cells" [MP:0001240\,ISBN\:0-683-40008-8] + stratum corneum epidermidis + keratinized squame layer of epidermis + UBERON:0002027 + epidermis stratum corneum + horny layer of epidermis + cornified layer + stratum corneum of epidermis + UBERON:stratum corneum of epidermis + + + rhombencephalon + hindbrain + UBERON:0002028 + "The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]." [http://en.wikipedia.org/wiki/Rhombencephalon, ZFA:0000029, ZFIN:curator] + UBERON:hindbrain + + + epithelial tissue of gall bladder + "The simple columnar epithelial lining of the gall bladder." [MP:0009492] + UBERON:epithelium of gall bladder + gallbladder epithelial tissue + epithelial tissue of gallbladder + epithelium of gallbladder + gall bladder epithelial tissue + UBERON:0002029 + epithelium of gall bladder + gall bladder epithelium + biliary epithelium + gallbladder epithelium + + + bronchi epithelium + bronchial trunk epithelium + bronchus epithelium + bronchus epithelial tissue + epithelium of bronchus + bronchial trunk epithelial tissue + "An epithelium that is part of a bronchus [Automatically generated definition]." [OBOL:automatic] + bronchi epithelial tissue + epithelial tissue of bronchial trunk + epithelial tissue of bronchi + epithelium of bronchial trunk + epithelium of bronchi + epithelial tissue of bronchus + UBERON:epithelium of bronchus + UBERON:0002031 + bronchial epithelium + + + "Muscle tissue that contains fibers that are divided by transverse bands into striations." [CL:0000737, GOC:dph, GOC:mtg_muscle] + striated muscle + UBERON:striated muscle tissue + striated muscle tissue + UBERON:0002036 + + + "Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]." [BTO:0000232, https://sourceforge.net/tracker/index.php?func=detail&aid=3291162&group_id=76834&atid=1205376, ISBN:3764351209, MESH:A08.186.211.132.810.428.200, ZFA:0000100] + epencephalon-1 + corpus cerebelli + cerebellum + parencephalon + UBERON:0002037 + UBERON:cerebellum + + + nucleus of basis pedunculi + "Predominantly gray matter midbrain structure lying dorsal to the crus cerebri and ventral to the midbrain tegmentum. It is divided into a dorsal, cellularly compact region known as the pars compacta and a more ventrally located, containing more loosely packed cells, the pars reticulata. The most lateral region of the reticulata is identified as the pars lateralis (MM)." [NIFSTD:birnlex_789] + Soemmering's substance + UBERON:0002038 + substancia nigra + UBERON:substantia nigra + nucleus pigmentosus subthalamo-peduncularis + substantia nigra + substantia nigra (Soemmerringi) + + + terminal bronchus + UBERON:terminal bronchus + UBERON:0002041 + + + thyroid gland + "A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]." [BTO:0001379, http://en.wikipedia.org/wiki/Thyroid] + UBERON:thyroid gland + glandula thyroidea + UBERON:0002046 + thyroid + + + pulmo + "Respiration organ that develops as an oupocketing of the esophagus." [UBERON:cjm] + lung + UBERON:lung + UBERON:0002048 + + + vasculature + UBERON:vasculature + UBERON:0002049 + vascular network + "An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face." [ZFA:0005249] + + + UBERON:0002050 + UBERON:embryonic structure + "Anatomical structure that is part of an embryo." [BTO:0000174, ZFIN:curator] + embryonic anatomical structure + embryonale Struktur + developing embryonic structure + developing structure + embryonic structure + + + truncus arteriosus + UBERON:0002061 + UBERON:truncus arteriosus + "The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles." [http://en.wikipedia.org/wiki/Truncus_arteriosus_(embryology)] + + + atrioventricular cushion + endocardial cushion + cardiac cushion + UBERON:0002062 + AV cushion + endocardial cushion tissue + endocardial cushions + UBERON:endocardial cushion + "The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]." [GO:0003197, http://en.wikipedia.org/wiki/Atrioventricular_cushions, ZFIN:curator] + + + UBERON:0002063 + sinus venosus + venarum sinus + "The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart." [http://en.wikipedia.org/wiki/Sinus_venosus, http://www.ncbi.nlm.nih.gov/pubmed/20735616] + sinus venarum + UBERON:sinus venosus + venosus + sinus venosus cordis + venarum + + + UBERON:0002067 + cutis + corium + "The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]." [http://en.wikipedia.org/wiki/Dermis, ZFIN:curator] + vertebrate dermis + UBERON:dermis + dermis + + + stratum granulosum of epidermis + UBERON:0002069 + epidermis granular layer + "the layer of flattened cells containing basophilic granules of keratohyalin and lying just above the stratum spinosum (spiny layer) of the epidermis" [MP:0001239\,ISBN\:0-683-40008-8] + stratum granulosum + UBERON:stratum granulosum of epidermis + epidermis stratum granulosum + granular layer of epidermis + + + UBERON:hair follicle + UBERON:0002073 + folliculus pili + "A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO]." [http://en.wikipedia.org/wiki/Hair_follicle] + hair follicle + + + UBERON:hair shaft + scapus pili + UBERON:0002074 + "The non-growing portion of a hair which protrudes from the skin, i.e., from the follicle[BTO]. the cuticle, and/or cortex and/or medulla of a hair[MP]." [BTO:0004672, MP:0003809] + shaft of hair + hair shaft + + + splanchnic tissue + "An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen." [BTO:0001491, http://en.wikipedia.org/wiki/Viscus] + Organsystem@ge + visceral tissue + visceral organ system + viscus + UBERON:viscus + viscera + UBERON:0002075 + visceral organ + + + UBERON:0002078 + heart right atrium + atrium dextrum + right cardiac atrium + "A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve." [http://en.wikipedia.org/wiki/Right_atrium, http://orcid.org/0000-0002-6601-2165] + right atrium of heart + UBERON:right cardiac atrium + right atrium + right cardiac atrium + cardiac right atrium + + + UBERON:0002079 + cardiac left atrium + UBERON:left cardiac atrium + left cardiac atrium + heart left atrium + left atrium of heart + left atrium + left cardiac atrium + atrium sinistrum + "A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve." [http://en.wikipedia.org/wiki/Left_atrium, http://orcid.org/0000-0002-6601-2165] + + + right ventricle of heart + UBERON:heart right ventricle + ventriculus dexter + cardiac right ventricle + UBERON:0002080 + "A cardiac ventricle that is in the right side of the heart." [UBERON:cjm] + heart right ventricle + right ventricle + right cardiac ventricle + + + atrium + Cardiac atria + cardiac atria + atrial tissue + atria + "Cardiac chamber in which blood enters the heart." [http://en.wikipedia.org/wiki/Heart_atrium, UBERON:cjm] + UBERON:0002081 + heart atrium + atrium of heart + cardiac atrium + UBERON:cardiac atrium + + + heart ventricle + cardiac ventricle + UBERON:0002082 + lower chamber of heart + UBERON:cardiac ventricle + ventricle of heart + "Cardiac chamber through which blood leaves the heart." [http://en.wikipedia.org/wiki/Ventricle_(heart), UBERON:cjm] + + + left ventricle of heart + left ventricle + heart left ventricle + left cardiac ventricle + UBERON:heart left ventricle + cardiac left ventricle + UBERON:0002084 + ventriculus sinister cordis + "A cardiac ventricle that is in the left side of the heart." [UBERON:cjm] + + + interatrial septal wall + atrial septum + "A cardiac septum that divides the left and right atria of the heart." [UBERON:cjm] + interatrial septum + UBERON:interatrial septum + UBERON:0002085 + atrium septum + + + atrioventricular canal + atrial canal + AV canal + ependymal canal + "The part of the heart connecting the atrium to the cardiac ventricle[ZFA]. In the developing heart, the constriction between the atrium and ventricle constitutes the atrial canal, and indicates the site of the future atrioventricular valves[WP]." [http://en.wikipedia.org/wiki/Atrioventricular_canal, http://purl.obolibrary.org/obo/uberon/tracker/38, ZFA:0001315] + atrio-ventricular canal + UBERON:atrioventricular canal + UBERON:0002087 + canalis atrioventricularis + + + appendicular skeleton + UBERON:appendicular skeleton + entire appendicular skeleton + "Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]." [http://en.wikipedia.org/wiki/Appendicular_skeleton, https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] + appendicular skeleton + UBERON:0002091 + skeleton appendiculare + + + septum membranaceum + intraventricular septum + ventricular septum + interventricular septum of heart + "Cardiac septum which separates the right ventricle from the left ventricle.[FMA]" [FMA:7133] + interventriculare cordis + interventricular septum + heart interventricular septum + septum inferius + s. interventriculare cordis + UBERON:0002094 + ventricle septum + UBERON:interventricular septum + heart ventricular septum + + + mesentery + "Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon." [FMA:7144, http://en.wikipedia.org/wiki/Mesentery, http://en.wikipedia.org/wiki/Mesentery#Mesentery_.28general.29] + mesentery (generic) + generic mesentery + UBERON:mesentery + UBERON:0002095 + + + spiral septa + cardiac septum + heart septa + UBERON:0002099 + septum of heart + "The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles." [MESH:A07.541.459] + cardiac septa + UBERON:cardiac septum + heart septum + + + "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present." [http://en.wikipedia.org/wiki/Torso, TAO:0001115, UBERONREF:0000006] + trunk region + thoracolumbar region + UBERON:0002100 + UBERON:trunk + torso + trunk + Rumpf + + + UBERON:0002101 + UBERON:limb + extremities + extremity + "A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts." [UBERONREF:0000003] + tetrapod limb + limb sensu vertebrata + limb + pentadactyl limb + free limb + + + foreleg + free upper limb + pectoral limb + UBERON:0002102 + free part of upper limb + superior member + "A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts." [UBERONREF:0000003] + membrum superius + UBERON:forelimb + forelimb + forelimb + upper limb + upper extremity + anteriormost limb + fore limb + + + UBERON:0002103 + free lower limb + lower extremity + membrum inferius + UBERON:hindlimb + hind-limb + hindlimb + free part of lower limb + pelvic appendage + hindlimb + lower limb + "A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts." [http://en.wikipedia.org/wiki/Hindlimb, http://en.wikipedia.org/wiki/Lower_limb, UBERONREF:0000003] + membrum inferius + inferior member + hind limb + + + "the organ that functions to filter blood and to store red corpuscles and platelets" [MP:0000689\,ISBN\:0-683-40008-8] + spleen + UBERON:0002106 + lien + UBERON:spleen + + + jecur + iecur + liver + UBERON:liver + "An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]." [BTO:0000759, http://en.wikipedia.org/wiki/Liver] + UBERON:0002107 + + + "Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]." [http://en.wikipedia.org/wiki/Small_intestine, ISBN10:0073040584] + UBERON:small intestine + small bowel + mid intestine + intestinum tenue + anterior intestine + small intestine + small intestine + UBERON:0002108 + + + vesica biliaris + gall bladder + vesica fellea + UBERON:0002110 + UBERON:gall bladder + gall bladder + "An organ that aids digestion and stores bile produced by the liver[WP]." [http://en.wikipedia.org/wiki/Gallbladder] + gallbladder + + + UBERON:kidney + kidney + UBERON:0002113 + "A paired organ of the urinary tract which has the production of urine as its primary function." [http://anatomy.uams.edu/anatomyhtml/kidney.html, http://en.wikipedia.org/wiki/Kidney] + + + proximal intestine + duodenum + UBERON:0002114 + "The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one)." [http://en.wikipedia.org/wiki/Duodenum, ISBN:0815318960] + upper intestine + UBERON:duodenum + + + mid-intestine + intestinum jejunum + UBERON:0002115 + "the portion of the small intestine that extends from the duodenum to the ileum" [MP:0004002\,MGI\:monikat] + UBERON:jejunum + jejunum + middle intestine + + + "the portion of the small intestine that extends from the jejunum to the colon" [MP:0002581\,ISBN\:0-683-40008-8\,MGI\:csmith] + UBERON:0002116 + posterior intestine + UBERON:ileum + ileum + intestinum ileum + distal intestine + lower intestine + + + thymic cortex + UBERON:0002123 + thymus cortex + "the outer part of a thymus lobule that surrounds the medulla and is composed of closely packed lymphocytes" [MP:0002371\,ISBN\:0-683-40008-8] + UBERON:cortex of thymus + cortex of thymus + + + thymus gland medulla + medulla of thymus + "Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size." [http://en.wikipedia.org/wiki/Thymus#Medulla] + UBERON:0002124 + thymus medulla + UBERON:medulla of thymus + medulla of thymus gland + + + UBERON:cerebellar cortex + UBERON:0002129 + cortex cerebellaris + cortex cerebelli + cerebellar cortex + "The superficial gray matter of the cerebellum. It consists of three main layers, the molecular layer, the Purkinje cell layer and the granule cell layer." [NIFSTD:birnlex_1566] + cortex of cerebellar hemisphere + + + atrio-ventricular valve + UBERON:0002133 + "A cardial valve in the atrioventricular region that separates the atrium from the ventricle and prevent backflow from the ventricles into the atria during systole." [https://en.wikipedia.org/wiki/Heart_valve#Atrioventricular_valves, UBERON:cjm] + UBERON:atrioventricular valve + atrioventricular valve + AV valve + + + right atrioventricular valve + tricuspid valve + valvula tricuspidalis + UBERON:tricuspid valve + UBERON:0002134 + "An atrioventricular valve that is part of the outflow part of the right atrium." [UBERON:cjm] + valva atrioventricularis dextra + + + mitral valve + bicuspid valve + valva atrioventricularis sinistra + valva mitralis + UBERON:mitral valve + UBERON:0002135 + "An atrioventricular valve that is part of the outflow part of the left atrium." [UBERON:cjm] + left atrioventricular valve + + + aortic valve + valva aortae + UBERON:aortic valve + UBERON:0002137 + "Cardiac valve which has as its parts the anterior, right posterior and left posterior cusps, attached to the fibrous ring of aortic valve.[FMA]" [FMA:FMA, http://en.wikipedia.org/wiki/Aortic_valve] + + + pulmonic valve + pulmonary valve + "the semilunar valve of the heart that lies between the right ventricle and the pulmonary artery." [http://en.wikipedia.org/wiki/Pulmonary_valve] + UBERON:0002146 + UBERON:pulmonary valve + valva trunci pulmonalis + + + "Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]" [FMA:FMA, http://en.wikipedia.org/wiki/Right_lung] + UBERON:right lung + right lung + UBERON:0002167 + + + UBERON:left lung + "Lung which consists of the left upper lobe and left lower lobe.[FMA]" [FMA:FMA, http://en.wikipedia.org/wiki/Left_lung] + left lung + UBERON:0002168 + + + pulmonary alveolar sac + air sac + "The small terminal dilation of the alveolar ducts around which the alveoli form pocket-like clusters" [http://en.wikipedia.org/wiki/Alveolar_sac, MP:0010902] + UBERON:0002169 + sacculus alveolaris + alveolar sac + UBERON:alveolar sac + + + right primary bronchus + bronchus principalis dexter + UBERON:right main bronchus + right principal bronchus + "The main bronchus on the right side." [http://en.wikipedia.org/wiki/Right_main_bronchus, https://orcid.org/0000-0002-6601-2165] + right main bronchus + right major bronchus + UBERON:0002177 + right bronchus + + + left main bronchus + left primary bronchus + "The main bronchus on the left side." [http://en.wikipedia.org/wiki/Left_main_bronchus] + left bronchus + UBERON:left main bronchus + left major bronchus + UBERON:0002178 + left principal bronchus + bronchus principalis sinister + + + funiculus lateralis medullae spinalis + lateral funiculus of spinal cord + lateral funiculus of spinal cord + lateral funiculus + UBERON:lateral funiculus of spinal cord + lateral white column of spinal cord + "The most lateral of the bundles of the anterior nerve roots is generally taken as a dividing line that separates the antero-lateral region into two parts, viz. , an anterior funiculus, between the anterior median fissure and the most lateral of the anterior nerve roots; and a lateral funiculus, between the exit of these roots and the postero-lateral sulcus. [WP,unvetted]." [http://en.wikipedia.org/wiki/Lateral_funiculus] + UBERON:0002179 + + + UBERON:0002182 + bronchus principalis + UBERON:main bronchus + major bronchus + "One of two branches of the trachea." [http://en.wikipedia.org/wiki/Main_bronchus] + main bronchus + principal bronchus + extrapulmonary bronchus + proximal bronchus + primary bronchus + mainstem bronchus + + + "the upper conducting airways of the lung; these airways arise from the terminus of the trachea" [MP:0002264\,ISBN\:0-397-51047-0\,MESH\:A04.411.125\,MGI\:cwg] + UBERON:0002185 + bronchial trunk + bronchus + UBERON:bronchus + bronchi + bronchial tissue + + + bronchiolus + UBERON:0002186 + UBERON:bronchiole + bronchiole + "the conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching" [MP:0002267\,ISBN\:0-397-51047-0\,MGI\:cwg] + lobular bronchiole + bronchioli + + + terminal bronchiole + UBERON:terminal bronchiole + bronchioli terminalis + terminal bronchiole tube + bronchiolus terminalis + "the last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls" [MP:0002268\,ISBN\:0-397-51047-0\,MGI\:cwg] + UBERON:0002187 + + + fatty layer of subcutaneous tissue + UBERON:subcutaneous adipose tissue + panniculus adiposus telae subcutaneae + UBERON:0002190 + "A portion of adipose tissue that is part of the hypodermis, beneath the dermis." [http://orcid.org/0000-0002-6601-2165] + subcutaneous adipose tissue + panniculus adiposus (tela subcutanea) + subcutaneous fat + hypodermis fat layer + subcutaneous fat layer + + + vasculature of head + adult head vasculature + vasculature of adult head + vascular network of adult head + head vascular network + vascular network of head + "Vasculature that is part of a head [Automatically generated definition]." [OBOL:automatic] + adult head vascular network + UBERON:0002200 + cranial vasculature + head vasculature + UBERON:vasculature of head + + + vascular network of eye + UBERON:0002203 + "Vasculature that is part of the eye region." [https://sourceforge.net/tracker/?func=detail&aid=3489658&group_id=76834&atid=994726, OBOL:automatic] + optic vasculature + ocular blood vessel + eye vascular network + ocular vasculature + UBERON:vasculature of eye + vasculature of eye + eye vasculature + + + UBERON:0002204 + "Anatomical system that consists of the muscular and skeletal systems." [VSAO:0000031, VSAO:curator] + musculoskeletal system + UBERON:musculoskeletal system + musculo-skeletal system + + + UBERON:fibrous joint + "Nonsynovial joint in which the articulating bones or cartilages are connected by ligaments. Examples: sagittal suture, inferior tibiofibular syndesmosis, gomphosis.[FMA]" [FMA:FMA, http://en.wikipedia.org/wiki/Fibrous_joint] + junctura fibrosa + articulatio fibrosa + fibrous joint + UBERON:0002209 + + + "A continuation of the neuron projection bundle component of a nerve inside, crossing or immediately outside the central nervous system." [UBERON:cjm] + UBERON:0002211 + radix nervi + initial segment of nerve + nerve root + UBERON:nerve root + + + saccular macula + UBERON:0002212 + saccular macula of membranous labyrinth + saccular maculs + membranous labyrinth saccule macula + macula of saccule of membranous labyrinth + macula sacculi + saccule of membranous labyrinth macula + "the oval neuroepithelial sensory receptor in the anterior wall of the saccule; hair cells of the neuroepithelium support the statoconial membrane and have terminal arborizations of vestibular nerve fibers around their bodies" [MP:0004330\,MGI\:anna] + UBERON:macula of saccule of membranous labyrinth + macula of membranous labyrinth saccule + macula sacculi + macula of saccule + macula of sacculus (labyrinthus vestibularis) + saccule macula + macula saccule + sacculus (labyrinthus vestibularis) macula + + + "the neuroepithelial sensory receptor in the inferolateral wall of the utricle; hair cells of the neuroepithelium support the statoconial membrane and have terminal arborizations of vestibular nerve fibers around their bodies; normally sensitive to linear acceleration in the longitudinal axis of the body and to gravitational influences" [MP:0004333\,MGI\:anna] + macula of utriculus (labyrinthus vestibularis) + macula of membranous labyrinth utricle + macula of utricle + UBERON:0002214 + macula utricle + UBERON:macula of utricle of membranous labyrinth + macula utriculi + macula of utricle of membranous labyrinth + utricular macula + utricle macula + utricle of membranous labyrinth macula + macula utriculi + membranous labyrinth utricle macula + utriculus (labyrinthus vestibularis) macula + + + articulatio synoviale + "Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]" [FMA:7501, http://en.wikipedia.org/wiki/Synovial_joint] + synovial joint + UBERON:synovial joint + diarthrosis joint + diarthrosis + diarthrodial joints + UBERON:0002217 + diarthroses + + + UBERON:tympanic ring + tympanic membrane annulus + ectotympanic ring + tympanic annulus + "A C-shaped membranous bone that provides physical support to the tympanic membrane. The tympanic ring develops sequentially from an initial primordium in the first branchial arch growing in a circumferential fashion around the first pharyngeal cleft into the second branchial arch (Mallo and Gridley, 1996). In most mammals, the tympanic ring exists only during embryonic life, when it coordinates proper development and positioning of the eardrum (see below), and then becomes integrated into the temporal bone[PMID]." [http://www.ncbi.nlm.nih.gov/pubmed/11237469, MP:0000030] + tympanic anulus + os tympanicum + tympanic ring + UBERON:0002218 + + + UBERON:0002222 + cartilage connective tissue + UBERON:perichondrium + perichondral region of cartilage element + perichondral region of cartilage + perichondrium + "Fibrous connective tissue that surrounds cartilage." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000036] + + + UBERON:endolymphatic sac + UBERON:0002223 + "From the posterior wall of the saccule a canal, the ductus endolymphaticus, is given off; this duct is joined by the ductus utriculosaccularis, and then passes along the aquaeductus vestibuli and ends in a blind pouch, the endolymphatic sac, on the posterior surface of the petrous portion of the temporal bone, where it is in contact with the dura mater. Studies suggest that the endolymphatic duct and endolymphatic sac perform both absorptive and secretory, as well as phagocytic and immunodefensive,functions . [WP,unvetted]." [http://en.wikipedia.org/wiki/Endolymphatic_sac] + saccus endolymphaticus + saccus endolymphaticus + endolymphatic sac + + + space of thoracic compartment + chest cavity + UBERON:thoracic cavity + pectoral cavity + cavity of chest + UBERON:0002224 + cavitas thoracis + thoracic cavity + cavity of thorax + "Body cavity subdivision which is enclosed by the thoracic wall and the diaphragm[FMA]." [FMA:7565, http://en.wikipedia.org/wiki/Thoracic_cavity] + + + UBERON:0002226 + lamina basilaris ductus cochlearis + basilar membrane + UBERON:basilar membrane of cochlea + "A stiff structural element that separates two liquid-filled tubes that run along the coil of the cochlea, the scala media and the scala tympani[WP]." [http://en.wikipedia.org/wiki/Basilar_membrane] + basilar membrane of cochlea + + + "The organ of Corti (or spiral organ) is the organ in the inner ear of mammals that contains auditory sensory cells, or 'hair cells.' [WP,unvetted]." [http://en.wikipedia.org/wiki/Organ_of_Corti] + papilla basilaris + Corti's organ + UBERON:spiral organ of cochlea + UBERON:0002227 + organum spirale + spiral organ of Corti + spiral organ of cochlea + spiral organ + organ of Corti + basilar papilla + cochlear spiral organ + + + pleural rib + UBERON:rib + "An intersegmental rod-shaped bone that forms in the peritoneal membrane and attach to the vertebral parapophyses. They protect and support internal organs. In most vertebrates, ribs surround the chest. they enable lungs to expand by expanding the chest, they also protect the lungs, heart, and other internal organs of the thorax. In some animals, especially snakes, ribs may provide support and protection for the entire body." [http://en.wikipedia.org/wiki/Rib, ZFIN:curator] + ribs + rib + dorsal rib + UBERON:0002228 + + + UBERON:0002233 + "The overlaying membrane of the cochlear duct, an extracellular matrix of the inner ear that contacts the stereocilia bundles of specialized sensory hair cells; sound induces movement of these hair cells relative to the tectorial membrane, deflects the stereocilia, and leads to fluctuations in hair cell membrane potential, transducing sound into electrical signals[MP,modified]" [J:77634, MGI:anna, MP:0003149] + tectorial membrane of cochlea + tectorial membrane + tectorial membrane of spiral organ of cochlea + UBERON:tectorial membrane of cochlea + + + spinal cord + spinal medulla + fissura cerebro-cerebellaris + SpC + UBERON:spinal cord + cerebrocerebellar fissure + cerebro-cerebellar fissure + spinal cord structure + fissura cerebrocerebellaris + UBERON:0002240 + medulla spinalis + "Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)" [NIFSTD:birnlex_1709] + + + "either one of the pair of tubular extensions from the uterine body where the uterus and the uterine tubes meet; uterine horns are anterior Mullerian duct-derived structures" [MP:0009085\,MGI\:anna] + UBERON:0002247 + cornu uteri + UBERON:uterine horn + uterine horn + + + organum vomeronasale + Jacobson's organ + UBERON:0002255 + UBERON:vomeronasal organ + VNO + organ of Jacobsen + organon vomeronasale + vomeronasal organ + "An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base." [VHOG:0000665] + + + UBERON:0002256 + UBERON:dorsal horn of spinal cord + dorsal horn of spinal cord + cornu dorsale + dorsal gray column of spinal cord + dorsal horn spinal cord + spinal cord dorsal horn + spinal cord dorsal horns + "The pronounced, dorsolaterally oriented ridge of grey matter in each lateral half of the spinal cord[MP]. the dorsal (more towards the back) grey matter of the spinal cord. It receives several types of sensory information from the body, including light touch, proprioception, and vibration. This information is sent from receptors of the skin, bones, and joints through sensory neurons whose cell bodies lie in the dorsal root ganglion[WP]. The dorsal region of the mature spinal cord contains neurons that process and relay sensory input[GO]." [GO:0021516, http://en.wikipedia.org/wiki/Posterior_horn_of_spinal_cord, https://sourceforge.net/tracker/?group_id=36855&atid=440764, MP:0006282] + posterior gray horn of spinal cord + posterior horn of spinal cord + posterior grey column of spinal cord + cornu posterius medullae spinalis + dorsal gray horn + dorsal grey column of spinal cord + dorsal gray matter of spinal cord + spinal cord posterior horn + posterior gray column of spinal cord + dorsal horn of the spinal cord + + + ventral gray matter of spinal cord + cornu anterius medullae spinalis + UBERON:0002257 + anterior gray column of spinal cord + ventral region of spinal cord + spinal cord anterior horn + ventral grey column of spinal cord + spinal cord ventral horn + ventral horn of the spinal cord + anterior column + anterior column of the spinal cord + "The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO]." [GO:0021517, http://en.wikipedia.org/wiki/Anterior_horn_of_spinal_cord, https://sourceforge.net/tracker/?group_id=36855&atid=440764, MP:0005112] + anterior gray horn of spinal cord + ventral gray column of spinal cord + UBERON:ventral horn of spinal cord + anterior horn + ventral grey horn + ventral horn spinal cord + ventral horns spinal cord + anterior grey column of spinal cord + ventral spinal cord + ventral horn of spinal cord + anterior horn (spinal cord) + + + radix anterior nervi spinalis + root ventralis nervi spinalis + ventral spinal nerve root + "The ventral roots contain efferent motor axons. Similar to the dorsal roots, the ventral roots continue out from the spinal column, and meet and mix with their corresponding dorsal nerve root at a point after the ganglion." [NIFSTD:nlx_anat_20090209] + ventral roots + motor root of spinal nerve + ventral spinal root + anterior root of spinal nerve + motor spinal root + anterior root + radix motoria (nervus spinalis) + spinal nerve ventral root + ventral root of spinal cord + radix anterior (nervus spinalis) + UBERON:ventral root of spinal cord + UBERON:0002260 + anterior spinal root + root motoria nervi spinalis + ventral root of spinal nerve + anterior nerve root + + + root dorsali nervi spinalis + sensory spinal root + dorsal root of spinal cord + posterior root of spinal nerve + sensory root of spinal nerve + dorsal spinal nerve root + root sensoria nervi spinalis + radix sensoria (nervus spinalis) + radix dorsalis + radix posterior (nervus spinalis) + "The dorsal roots contain afferent sensory axons. The dorsal roots of each side continue outwards, along the way forming a dorsal root ganglion (also called a spinal ganglion)." [NIFSTD:nlx_anat_20090208] + radix posterior + dorsal roots + radix posterior nervi spinalis + UBERON:dorsal root of spinal cord + UBERON:0002261 + dorsal spinal root + dorsal root of spinal nerve + dorsal root + + + olfactory lobe + bulbus olfactorius (Morgagni) + olfactory bulb + UBERON:olfactory bulb + olfactory lobe (Barr & Kiernan) + UBERON:0002264 + bulbus olfactorius + bulbus olfactorius + "A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO]." [BTO:0000961, http://en.wikipedia.org/wiki/Olfactory_bulb] + + + olfactory peduncle + tractus olfactorium + UBERON:0002265 + "White matter tract that contains projections from the olfactory bulb to other parts of the brain" [http://en.wikipedia.org/wiki/Olfactory_tract, ISBN10:0471888893, NIFSTD:birnlex_1663, UBERON:cjm] + pedunclulus olfactorius + UBERON:olfactory tract + tractus olfactorius + olfactory tract + olfactory stalk + + + main olfactory organ + olfactory neuroepithelium + olfactory organ + organum olfactorium + UBERON:main olfactory organ + organ olfactus + UBERON:0002268 + + + spiral sulcus + "A concavity in the floor of the cochlear duct, formed by either the overhanging vestibular lip (inner spiral sulcus) or the spiral prominence and the spiral organ (outer spiral sulcus)." [] + sulcus spiralis + UBERON:spiral sulcus + UBERON:0002277 + + + "At the hinder part of the medial wall of the vestibule is the orifice of the vestibular aqueduct, which extends to the posterior surface of the petrous portion of the temporal bone. It transmits a small vein, and contains a tubular prolongation of the membranous labyrinth, the ductus endolymphaticus, which ends in a cul-de-sac between the layers of the dura mater within the cranial cavity. [WP,unvetted]." [http://en.wikipedia.org/wiki/Vestibular_aqueduct] + vestibular aqueduct + UBERON:0002279 + UBERON:vestibular aqueduct + aqueductus vestibuli + + + "Acellular structure composed of calcium carbonate located in the otolith organ." [http://en.wikipedia.org/wiki/Otolith, ZFIN:curator] + otoconia + statoconium + otoconial crystal + UBERON:otolith + otolith + immature otolith + otoliths + statolith + immature otoliths + statoconia + otoconium + UBERON:0002280 + + + "A membrane inside the cochlea of the inner ear. It separates scala media from scala vestibuli. Together with the basilar membrane it creates a compartment in the cochlea filled with endolymph, which is important for the function of the organ of Corti. It primarily functions as a diffusion barrier, allowing nutrients to travel from the perilymph to the endolymph of the membranous labyrinth. Histologically, the membrane is composed of two layers of flattened epithelium, separated by a basal lamina. Its structure suggests that its function is transport of fluid and electrolytes." [http://en.wikipedia.org/wiki/Reissner's_membrane] + Reissner's membrane + vestibular membrane + vestibular membrane of cochlear duct + UBERON:vestibular membrane of cochlear duct + vestibular membrane of Reissner + membrana vestibularis ductus cochlearis + vestibular membrane + Reissner membrane + paries vestibularis ductus cochlearis + UBERON:0002281 + superior wall of cochlear duct + vestibular wall of cochlear duct + + + vascular stria of cochlear duct + psalterial cord + stria vascularis of cochlear duct + UBERON:stria vascularis of cochlear duct + stria vascularis ductus cochlearis + stria vascularis of cochlea + UBERON:0002282 + "The upper portion of the spiral ligament contains numerous capillary loops and small blood vessels, and is termed the stria vascularis. It produces endolymph for the scala media, one of the three fluid-filled compartments of the cochlea. [WP,unvetted]." [http://en.wikipedia.org/wiki/Stria_vascularis] + vascular stripe of cochlear duct + stria vascularis + + + lateral ventricle + UBERON:0002285 + lateral ventricles + telencephalon lateral ventricle + telencephalic ventricle + UBERON:telencephalic ventricle + telencephalic ventricle + forebrain ventricle + lateral ventricle of brain + Telencephalic ventricles + tectal ventricle + "A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere" [http://en.wikipedia.org/wiki/Lateral_ventricle, https://orcid.org/0000-0002-6601-2165] + telencephalic vesicle + + + mesencephalic vesicle + midbrain cerebral aqueduct + aqueduct of Sylvius + cerebral aqueduct proper + aqueductus mesencephali + UBERON:0002289 + mesencephalic ventricle + Aqueduct ofSylvius + aqueduct + cerebral aqueduct + medial tectal ventricle + cerebral aquaduct + tectal ventricle + cerebral aqueduct of Sylvius + Sylvian aqueduct + aqueduct (Sylvius) + aqueduct of midbrain + mesencephalic duct + "Part of ventricular system of brain consisting of a narrow channel in the midbrain connecting the third and fourth ventricles. (Maryann Martone)" [NIFSTD:birnlex_1261] + UBERON:midbrain cerebral aqueduct + midbrain ventricle + aqueductus mesencephali + midbrain cerebral aqueduct + + + UBERON:0002291 + central canal + UBERON:central canal of spinal cord + central canal of spinal cord + central canal, spinal cord/medulla + central canal of spinal cord + ventricle of spinal cord + spinal cord central canal + "Spinal cord structure that is part of the ventricular system and is filled with cerebral-spinal fluid and runs the length of the spinal cord." [http://www.ncbi.nlm.nih.gov/pubmed/23409159, ZFIN:curator] + canalis centralis + + + biliary system + UBERON:0002294 + biliary tract + biliary apparatus + UBERON:biliary system + "Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree)." [http://en.wikipedia.org/wiki/Biliary_system] + + + scala media + UBERON:0002295 + UBERON:scala media + "the division of the spiral canal of the cochlea that contains the organ of Corti (the neuroepithelial receptor organ for hearing)" [MP:0003169\,MGI\:anna\,PMID\:1680563] + cochlear duct + + + brainstem + truncus encephali + "Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]." [http://en.wikipedia.org/wiki/Brainstem, ISBN10:0471888893, MP:0005277, ZFA:0001707] + accessory medullary lamina of pallidum + lamina medullaris accessoria + truncus encephalicus + brain stem + lamina pallidi incompleta + lamella pallidi incompleta + UBERON:0002298 + UBERON:brainstem + lamina medullaris incompleta pallidi + + + alveolus pulmonis + alveolus pulmonis + respiratory alveolus + alveolus of lung + respiratory alveoli + UBERON:alveolus of lung + "Spherical outcropping of the respiratory bronchioles and primary site of gas exchange with the blood. Alveoli are particular to mammalian lungs. Different structures are involved in gas exchange in other vertebrates[WP]." [http://en.wikipedia.org/wiki/Pulmonary_alveolus] + pulmonary alveolus + alveoli + lung alveolus + UBERON:0002299 + + + neocortex layer + "One of the layers of the neocortex." [UBERON:cjm] + UBERON:0002301 + cerebral cortex layer + UBERON:layer of neocortex + layer of neocortex + layer of neocortex + + + UBERON:layer of dentate gyrus + UBERON:0002304 + layer of dentate gyrus + dentate gyrus layer + dentate gyrus cell layer + "One of the three layers of the dentate gyrus of the hippocampal formation." [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2492885/, UBERON:cjm] + + + "The layers of the laminar structure of the hippocampus." [http://en.wikipedia.org/wiki/Hippocampus_anatomy#Hippocampal_Cells_and_Layers, MP:0000813] + layer of hippocampus + cytoarchitectural fields of hippocampal formation + UBERON:0002305 + UBERON:layer of hippocampus + hippocampus layer + + + brain nucleus + "A neural nucleus that is part of the brain." [http://orcid.org/0000-0002-6601-2165] + UBERON:0002308 + nucleus of brain + UBERON:nucleus of brain + + + pyramidal cell layer of the hippocampus + hippocampus pyramidal cell layer + gyrus occipitalis inferior + pyramidal layer of hippocampus + UBERON:hippocampus pyramidal layer + hippocampus pyramidal layer + stratum pyramidale hippocampi + hippocampal pyramidal cell layer + "A cytoarchitectural term denoting the layer of the hippocampus in which pyramidal cells are predominant. Its location is superficial to the Stratum oriens; it is deep to the Stratum radiatum in area CA1 and area CA2 and deep to the Stratum lucidum in area CA3 (Stephan-75) (NeuroNames)." [NIFSTD:birnlex_1444] + hippocampus stratum pyramidale + UBERON:0002313 + gyrus occipitalis tertius + hippocampal pyramidal layer + stratum pyramidale + + + tectum of midbrain + "Dorsal part of the midbrain, consisting of the superior and inferior colliculi and the pretectal nuclei (MM)." [NIFSTD:birnlex_1032] + neuraxis tectum + UBERON:0002314 + t. mesencephali + tectum mesencephali + midbrain tectum + mesencephalic tectum + tectum + UBERON:midbrain tectum + tectum mesencephalicum + + + "The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue." [MP:0008503] + spinal cord gray matter + spinal cord grey matter + grey matter of spinal cord + gray substance of spinal cord + UBERON:0002315 + gray matter of spinal cord + grey substance of spinal cord + spinal cord grey substance + gray matter of spinal cord + UBERON:gray matter of spinal cord + + + white matter + CNS white matter + white matter of neuraxis + substantia alba + UBERON:0002316 + white substance + UBERON:white matter + "Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system." [http://en.wikipedia.org/wiki/White_matter, https://orcid.org/0000-0002-6601-2165] + neuronal white matter + CNS tracts and commissures + white mater + + + "Regional part of cerebellum consisting of the myelinated axons lying deep to the granule cell layer, excluding the deep cerebellar nuclei and the cerebellar peduncles." [NIFSTD:birnlex_1562] + UBERON:white matter of cerebellum + white matter of cerebellum + UBERON:0002317 + substantia centralis medullaris cerebelli + medullary substance of cerebellum + substantia medullaris cerebelli + cerebellum white matter + cerebellar white matter + + + UBERON:mesangium + mesangium + UBERON:0002319 + "inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries." [http://en.wikipedia.org/wiki/Mesangium, http://sourceforge.net/tracker/?group_id=76834&atid=974957] + + + coelomic cavity + coelomic cavity lumen + coelemic cavity lumen + celom + coelom + space of body compartment + hemocoel + UBERON:0002323 + "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] + UBERON:coelemic cavity lumen + coelome + body cavity + + + notochorda + embryonic notocord + "A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube." [http://en.wikipedia.org/wiki/Notochord, http://purl.obolibrary.org/obo/uberon/tracker/25, http://tolweb.org/Chordata/2499, ISBN:0815318960] + UBERON:notochord + UBERON:0002328 + notochord + notocord + + + somite + epimere mesoderm + epimere + somitus + UBERON:0002329 + somites + somitic mesoderm + UBERON:somite + "Somites are spheres of epithelial cells that form sequentially along the anterior–posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm." [http://dx.doi.org/10.1111/j.1439-0426.2012.01987.x, http://en.wikipedia.org/wiki/Somite] + epithelial somite + + + "Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]." [http://en.wikipedia.org/wiki/Exocrine_gland] + UBERON:exocrine system + exocrine glandular system + UBERON:0002330 + exocrine system + + + UBERON:0002333 + UBERON:pulmonary trunk + pulmonary artery (trunk) + main pulmonary artery + pulmonary trunk + trunk of pulmonary arterial tree + "An arterial trunk which is continuous with the heart and branches into the pulmonary arteries." [UBERON:cjm] + + + corpus callosum + UBERON:corpus callosum + UBERON:0002336 + "White matter structure containing massive numbers of commissural fibers connecting cortical areas in the two cerebral hemispheres.it is subdivided into a genu, a rostrum, a body, and a splenium. (MM)" [NIFSTD:birnlex_1087] + + + UBERON:0002342 + neural crest material + "A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]." [MP:0009846] + NC + UBERON:neural crest + neural crest + crista neuralis + + + UBERON:neurectoderm + neural ectoderm + presumptive central nervous system + neuaral ectoderm + UBERON:0002346 + neuroectoderm + epithelium tubi neuralis; neuroectoderma + neurectoderm + "Embryonic ectoderm that gives rise to nervous tissue." [http://en.wikipedia.org/wiki/Neuroectoderm] + ventral neurogenic region + + + heart muscle + muscle of heart + cardiac muscle + UBERON:myocardium + myocardium + "the middle layer of the heart, comprised mainly of striated cardiac muscle fibers" [MP:0005329\,ISBN\:0-683-40008-8] + UBERON:0002349 + heart myocardium + + + node of Keith-Flack + Koch's node + sinuatrial node + SA nodal muscle tissue + SA node + sinuatrial nodal muscle tissue + nodus sinuatrialis + sinoatrial node + UBERON:sinoatrial node + "The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]." [GO:0003163, http://en.wikipedia.org/wiki/Sinoatrial_node] + nodus sinuatrialis + sinoatrial node + sinu-atrial node + sinus node of Keith and Flack + sinus node + cardiac pacemaker + UBERON:0002351 + + + lesser pelvis + UBERON:0002355 + pelvis + pelvis region + true pelvis + pelvic region + UBERON:pelvis + "lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs." [http://en.wikipedia.org/wiki/Pelvis, UBERON:cjm] + + + UBERON:meninx + meninx + meningeal layer + layer of meninges + "Membrane organ that surrounds the brain and the spinal cord." [FMA:9589, http://en.wikipedia.org/wiki/Meninx, http://www.shsu.edu/~bio_mlt/Chap15.html] + UBERON:0002360 + + + pial membrane + pia + pia mater of neuraxis + UBERON:pia mater + "The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals." [NIFSTD:nlx_anat_090209] + pia mater + UBERON:0002361 + + + UBERON:dura mater + UBERON:0002363 + pachymeninges + dura mater + dura mater of neuraxis + "Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections." [NIFSTD:nlx_anat_090206] + dura + + + ear drum + membranous wall of tympanic cavity + tympanum + UBERON:0002364 + Rivinus' membrane + UBERON:tympanic membrane + myrinx + paries membranaceus cavi tympani + eardrum + tympanic membrane + lateral wall of tympanic cavity + "A thin membrane that separates the external ear from the middle ear, consisting of two epithelia (one part of the the external accoustic meatus epithelium, the other part of the tympanic cavity epithelium) with a fibrous layer between them. Its function is to transmit sound from the air to the ossicles inside the middle ear. The malleus bone bridges the gap between the eardrum and the other ossicles. Rupture or perforation of the eardrum can lead to conductive hearing loss. [WP,unvetted]." [http://en.wikipedia.org/wiki/Tympanic_membrane, http://www.ncbi.nlm.nih.gov/pubmed/11237469] + + + UBERON:0002365 + exocrine gland + ducted gland + glandula exocrina + UBERON:exocrine gland + "A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas" [http://en.wikipedia.org/wiki/Exocrine_gland] + + + UBERON:0002367 + prostate + "The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid." [GO:0030850, http://en.wikipedia.org/wiki/Prostate] + prostata + prostate gland + UBERON:prostate gland + male prostate + + + UBERON:0002368 + "Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]." [http://en.wikipedia.org/wiki/Endocrine_gland] + endocrine gland + glandula endocrina + UBERON:endocrine gland + ductless gland + ductless gland + glandulae endocrinae + + + UBERON:0002369 + suprarenal capsule + "Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]." [BTO:0000047, http://en.wikipedia.org/wiki/Adrenal_gland] + suprarenal gland + glandula suprarenalis + interrenal gland + glandula adrenalis + adrenal medulla cell + epinephros + glandula suprarenalis + adrenal + atrabiliary capsule + adrenal gland + adrenal capsule + epinephric gland + UBERON:adrenal gland + + + UBERON:thymus + thymus organ + thymus gland + "Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop." [http://en.wikipedia.org/wiki/Thymus, NLM:thymus] + thymus + UBERON:0002370 + + + medulla of bone + medulla ossea + "the soft tissue that fills the cavities of bones" [MP:0002397\,MGI\:cwg] + bone marrow + UBERON:bone marrow + medulla ossium + UBERON:0002371 + + + "A bone that is part of the metacarpal skeleton." [http://en.wikipedia.org/wiki/Metacarpal_bone, https://orcid.org/0000-0002-6601-2165] + metacarpal + UBERON:0002374 + metacarpal bone + UBERON:metacarpal bone + + + UBERON:0002378 + muscle organ of abdomen + UBERON:muscle of abdomen + abdominal muscle + muscle of abdomen + abdomen muscle + "Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis." [http://en.wikipedia.org/wiki/Abdominal_muscle] + abdominal wall muscle + abdomen muscle organ + abdominal wall musculature + + + Bindegewebe + textus connectivus + UBERON:0002384 + connective tissue + UBERON:connective tissue + "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000017] + portion of connective tissue + + + "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]." [GO:0060537, http://en.wikipedia.org/wiki/Muscle_tissue, https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764] + textus muscularis + UBERON:0002385 + portion of muscle tissue + UBERON:muscle tissue + muscle tissue + muscular tissue + + + brachial region zeugopod + antebrachium + zeugopod of brachial region + lower segment of arm + UBERON:0002386 + proximal segment of free upper limb zeugopod + middle limb segment of arm + antebrachium + middle limb segment of forelimb + UBERON:forelimb zeugopod + antibrachium + arm middle limb segment + regio antebrachialis + zeugopod of forelimb + fore epipodium + middle limb segment of proximal segment of free upper limb + antebrachial region + arm zeugopod + lower arm + middle limb segment of brachial region + forelimb zeugopodium + zeugopod of arm + forearm + proximal segment of free upper limb middle limb segment + forelimb epipodium + brachial region middle limb segment + "The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants." [PHENOSCAPE:curators] + forelimb zygopod + forelimb zeugopod + intermediate segment of free upper limb + zeugopod of proximal segment of free upper limb + + + pes + foot + hindlimb autopod + hind limb autopodium + hindlimb distal free limb segment + UBERON:0002387 + "distal portion of the hind limb, including tarsal region, metatarsal region and digits." [http://en.wikipedia.org/wiki/Foot, http://en.wikipedia.org/wiki/Pes_(anatomy)] + UBERON:pes + terminal segment of free lower limb + pes + hindlimb autopodium + + + digit of manus + UBERON:0002389 + forelimb digit + hand digit + fore digit + finger + manual digit (phalangeal portion) plus soft tissue + digit of hand + UBERON:manual digit + manual digit + "A digit that is part of a manus (hand)." [http://orcid.org/0000-0002-6601-2165] + digitus manus + + + tuba auditoria + internal auditory tube + eustachian tube + pharyngotympanic tube + UBERON:0002393 + tuba auditiva; tuba auditoria; tuba auditivea + UBERON:pharyngotympanic tube + pharyngo-tympanic tube + tuba pharyngotympanica + "Organ with organ cavity which connects the cavity of the middle ear to the cavity of the pharynx. Examples: There are only two pharyngotympanic tubes, the right and the left pharyngotympanic tubes.[FMA]" [FMA:FMA, http://en.wikipedia.org/wiki/Eustachian_tube] + tuba auditiva + auditory tube + + + gall duct + bile tube + UBERON:0002394 + UBERON:bile duct + hepatic duct + bile duct + "Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine." [http://en.wikipedia.org/wiki/Bile_duct, UBERON:cjm] + biliary duct + + + talus + "A proximal tarsal bone resulting from fusion of intermedium and fibulare." [http://en.wikipedia.org/wiki/Talus_bone, UBERON:cjm] + major ankle bone + UBERON:talus + astragalus bone + os trigonum + UBERON:0002395 + astragalus + astragaloid bone + os tarsi tibiale + + + maxillae + UBERON:0002397 + UBERON:maxilla + "The bone which normally forms the lateral upper jaw in osteichthyans, including tetrapods." [http://en.wikipedia.org/wiki/Maxilla, http://palaeos.com/vertebrates/glossary/glossaryM.html] + maxilla + maxillary bone + + + forelimb autopodium + hand + manus + terminal segment of free upper limb + hand region + UBERON:manus + UBERON:0002398 + forelimb autopod + "distal segment of the fore limb, including carpal region, metacarpal region and digits." [http://en.wikipedia.org/wiki/Hand, http://en.wikipedia.org/wiki/Manus_(anatomy)] + + + UBERON:immune system + UBERON:0002405 + "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies." [http://en.wikipedia.org/wiki/Immune_system] + immune system + + + UBERON:0002406 + UBERON:pericardial sac + "a double-walled sac containing the heart and the roots of the great vessels. " [http://en.wikipedia.org/wiki/Pericardium] + pericardial sac + pericardium + + + autonomic nervous system + "The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]." [GO:0048483] + peripheral autonomic nervous system + pars autonomica systematis nervosi peripherici + autonomic part of peripheral nervous system + divisio autonomica systematis nervosi peripherici + UBERON:autonomic nervous system + ANS + UBERON:0002410 + visceral nervous system + autonomic division of peripheral nervous system + divisio autonomica systematis nervosi peripherici + + + "The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, UBERON:cjm, VSAO:0000184] + vertebrae + vertebra bone + UBERON:0002412 + UBERON:vertebra + vertebra + + + cervical vertebrae + vertebrae cervicales + cervical vertebra + UBERON:0002413 + "A vertebra that is located in the cervical region of the vertebral column." [http://orcid.org/0000-0002-6601-2165] + UBERON:cervical vertebra + + + UBERON:lumbar vertebra + UBERON:0002414 + "Large vertebra of the movable part of the vertebral column, characterized by the absence of the foramen transversarium within the transverse process, and by the absence of facets on the sides of the body." [http://en.wikipedia.org/wiki/Lumbar_vertebrae] + lumbar vertebra + + + caudal subdivision + UBERON:0002415 + "An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail" [AEO:0000109, http://en.wikipedia.org/wiki/Tail] + tail + UBERON:tail + + + UBERON:cartilage tissue + "Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, http://sourceforge.net/tracker/?func=detail&atid=2257941&aid=3396584&group_id=76834, PSPUB:0000170, VSAO:0000040] + cartilage tissue + cartilaginous tissue + cartilage + UBERON:0002418 + chondrogenic tissue + cartilage tissue + cartilages + + + "A gland that is part of a skin of body [Automatically generated definition]." [OBOL:automatic] + UBERON:0002419 + glandulae cutis + set of skin glands + skin gland + skin glands + UBERON:skin gland + skin glands set + + + basal ganglia + "An individual member of a collection of basal ganglia. Basal ganglia are subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF,modified]." [NIFSTD:birnlex_826] + nuclei basales + basal nucleus + UBERON:0002420 + basal ganglion of telencephalon + basal ganglion + UBERON:basal ganglion + + + seahorse + "Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment]." [https://orcid.org/0000-0002-6601-2165] + formatio hippocampi + archipallium + primal cortex + UBERON:hippocampal formation + hippocampus (Crosby) + UBERON:0002421 + major hippocampus + hippocampal formation + + + hindbrain ventricle + ventricle IV + IVth ventricle + 4th ventricle + UBERON:fourth ventricle + ventricle of rhombencephalon + "Part of the ventricular system of the brain, forming a single large irregularly shaped cavity located on the midline of the rhombencephalon, between the medulla, pons and the isthmus ventrally and the cerebellum dorsally. It is continuous with the cerebral aqueduct anteriorally and the central canal of the spinal cord posteriorly. It communicates with the subarachnoid space through its lateral and median apertures." [NIFSTD:birnlex_1256] + fourth ventricle proper + rhombencephalic ventricle + ventricle of hindbrain + fourth ventricle + UBERON:0002422 + ventriculus quartus + + + liver and biliary system + UBERON:hepatobiliary system + hepatobiliary system + hepaticobiliary system + liver/biliary system + UBERON:0002423 + "The part of the digestive system that contains the liver and the biliary system" [UBERON:cjm] + + + oral epithelium + epithelium of oral mucosa + "An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues" [https://orcid.org/0000-0002-6601-2165] + UBERON:oral epithelium + epithelium of mucosa of mouth + UBERON:0002424 + + + bone of extremity + limb bone + UBERON:0002428 + bone of limb + UBERON:limb bone + "A bone that is part of a limb [Automatically generated definition]." [OBOL:automatic] + free limb bone + + + striatum + corpus striatum + striated nucleus + caudate putamen + corpus striatum (Zilles) + UBERON:0002435 + striate nucleus + neuraxis striatum + striatum of neuraxis + striatum + UBERON:striatum + dorsal striatum + "A region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO]." [GOC:jl, http://en.wikipedia.org/wiki/Striatum] + neostriatum + + + decidous membrane + decidua basalis + UBERON:0002450 + UBERON:decidua + extraembryonic placenta + extraembryonic part of placenta + maternal placenta + maternal decidual layer + maternal part of placenta + decidua + uterine decidua + "Uterine lining (endometrium) during a pregnancy, which forms the maternal part of the placenta. It is formed under the influence of progesterone and forms highly-characteristic cells." [http://en.wikipedia.org/wiki/Decidua] + placenta maternal decidual layer + endometrium + + + nerve trunk + trunk of peripheral nerve + UBERON:nerve trunk + peripheral nerve trunk + UBERON:0002464 + trunk of nerve + + + UBERON:autopod region + UBERON:0002470 + distal segment of free limb + paw/hand/foot/hoof + autopodial segment + manus/pes + paw + pod + autopodium + autopodial element + distal free limb segment + autopodium region + distal segment of limb + autopodial limb segment + autopod region + "Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot" [https://orcid.org/0000-0002-6601-2165] + + + UBERON:0002471 + zygopod + zygopodium + zeugopod + zeugopodial limb segment + zeugopodium + middle free limb segment + middle limb segment + zeugopod limb segment + UBERON:zeugopod + epipodium + "The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus)." [PHENOSCAPE:curators] + middle segment of free limb + + + UBERON:0002472 + proximal segment of free limb + proximal free limb segment + stylopodium + propodium + stylopodial limb segment + "The proximal free limb segment. Includes as parts the stylopod skeleton." [UBERON:cjm] + UBERON:stylopod + stylopod + + + commissure of cerebrum + UBERON:intercerebral commissure + interhemispheric commissure + intercerebral commissure + "A commissure that connects the two cerebral hemispheres. Examples: anterior commissure, corpus callosum." [http://orcid.org/0000-0002-6601-2165] + inter-hemispheric commissure + UBERON:0002473 + + + UBERON:0002481 + calcium tissue + UBERON:bone tissue + osteogenic tissue + bone tissue + "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000047] + osseous tissue + bone + + + trabecular bone tissue + cancellated bone + spongy bone tissue + "bone tissue that has a lattice-like or spongy structure; it is highly vascular and contains intercommunicating spaces filled with bone marrow" [MP:0000130\,ISBN\:0-683-40008-8\,MGI\:csmith] + spongy bone + substantia spongiosa ossium + trabecular substance + cancellous bone tissue + substantia spongiosa + trabecular bone + UBERON:trabecular bone tissue + cancellous bone + substantia trabecularis ossium + UBERON:0002483 + + + UBERON:0002484 + UBERON:bone marrow cavity + "the medullary cavities of the bones where bone marrow is stored" [MP:0000065\,ISBN\:0-683-40008-8\,PMID\:10709991] + bone marrow cavity + medullary cavity + cavity of cancellous bone + marrow cavity + + + UBERON:coronal suture + UBERON:0002489 + coronal suture + coronal suture of skull + frontoparietal suture + fronto-parietal suture + sutura coronalis + "the dense, fibrous connective tissue joint between the tetrapod parietal bones and the frontal bone" [MP:0003840\,ISBN\:0-8036-0655-99\,MGI\:smb] + + + UBERON:0002495 + "Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd]." [http://en.wikipedia.org/wiki/Long_bone, VSAO:wd] + UBERON:long bone + long bone + os longum + + + oval window of petrous part of temporal bone + oval window + UBERON:0002501 + UBERON:oval window + fenestra ovalis + "the oval opening on the medial wall of the tympanic cavity leading into the vestibule, close to the foot of the stapes" [MP:0004479\,ISBN\:0-683-40008-8] + vestibular window + fenestra vestibuli + + + round window of inner ear + fenestra cochleae + UBERON:0002502 + cochlear window + round window + fenestra rotunda + UBERON:round window of inner ear + "the opening on the medial wall of the middle ear leading into the cochlea, closed in life by the secondary tympanic membrane; serves to regulate fluid pressure in the inner ear" [MP:0004480\,ISBN\:0-683-40008-8] + round window of petrous part of temporal bone + + + iris epithelium + epithelium pigmentosum (iris) + epithelium pigmentosum iridis + iris epithelial tissue + pigmented epithelium of iris + UBERON:iris epithelium + epithelium of iris + UBERON:0002506 + "An epithelium that is part of a iris [Automatically generated definition]." [OBOL:automatic] + iris pigmented epithelium + epithelial tissue of iris + iris epithelium + + + UBERON:0002513 + cartilaginous bone + UBERON:endochondral bone + ossified chondrogenic bone + endochondral bone + "Replacement bone that forms within cartilage." [GO:0001958, GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000145] + + + UBERON:intramembranous bone + intramembranous bone + "Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]." [GO:0001957, http://en.wikipedia.org/wiki/Intramembranous_ossification] + membrane bone + UBERON:0002514 + + + physis + epiphyseal cartilage + long bone epiphyseal plate + growth plate + epiphyseal disk + UBERON:0002516 + epiphyseal growth disk + epiphyseal growth plate + epiphyseal plate + epiphyseal growth plate cartilage + "A hyaline cartilage plate in the metaphysis at each end of a long bone. The plate is found in children and adolescents; in adults, who have stopped growing, the plate is replaced by an epiphyseal line." [http://en.wikipedia.org/wiki/Epiphyseal_plate] + epiphysial plate + UBERON:epiphyseal plate + cartilago epiphysialis + lamina epiphysialis + + + saccule and utricle + "the crystalline particles composed of calcium carbonate and a protein which adhere to the gelatinous membrane of the maculae of the utricle and saccule (otolithic membrane)" [MP:0002894\,ISBN\:0-683-40008-8\,MGI\:llw2] + utricle and saccule + UBERON:otolith organ + UBERON:0002518 + otolith organs + otolith organ + + + segment of limb + limb segment + extremity part + region of limb + "A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles." [https://orcid.org/0000-0002-6601-2165] + limb region + subdivision of limb + UBERON:0002529 + free limb segment + UBERON:limb segment + + + Druese + UBERON:gland + "an organ that functions as a secretory or excretory organ" [MP:0002163\,MGI\:csmith] + UBERON:0002530 + glandular organ + glandula + gland + + + ectoblast + UBERON:0002532 + epiblast + epiblastus + "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]" [http://en.wikipedia.org/wiki/Epiblast, ZFIN:curator] + epiblast (generic) + UBERON:epiblast (generic) + blastocyst + primitive ectoderm + + + "The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node." [BTO:0001445] + post-anal tail bud + tailbud + tail bud + UBERON:post-anal tail bud + tail bud mesenchyme + UBERON:0002533 + end bud + + + visceral arch + UBERON:0002539 + pharyngeal arches + arcus pharyngei + "One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches." [http://orcid.org/0000-0002-6601-2165, http://www.ncbi.nlm.nih.gov/pubmed/16313389, ZFA:yb] + pharyngeal arch + UBERON:pharyngeal arch + + + germ ring + "The thickend rim of the blastoderm evident during late blastula and gastrula stages[FishBase]. Embryonic structure which is a uniform thickened annulus at the blastoderm margin, consisting of two layers in addition to the EVL, the epiblast and the hypoblast. The germ ring is formed by the involution of the blastoderm back upon itself[ZFA]" [http://www.fishbase.org/glossary/Glossary.php?q=germ%20ring] + UBERON:0002541 + UBERON:germ ring + + + scale + "A small rigid plate that grows out of an animal's skin to provide protection. In lepidopteran (butterfly and moth) species, scales are plates on the surface of the insect wing, and provide coloration. Scales are quite common and have evolved multiple times with varying structure and function." [http://en.wikipedia.org/wiki/Scale_(zoology)] + UBERON:scale + UBERON:0002542 + scales + scale tissue + + + digit (phalangeal portion) plus soft tissue + limb digit + "A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans)." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/420] + UBERON:digit + acropodial unit + UBERON:0002544 + digit + + + cranial placode + UBERON:cranial placode + "Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic." [http://www.ncbi.nlm.nih.gov/books/NBK53175/, https://github.com/seger/aao/issues/4, https://orcid.org/0000-0002-6601-2165, https://sourceforge.net/tracker/?func=detail&aid=3561940&group_id=76834&atid=1127722] + UBERON:0002546 + cranial placodes + + + UBERON:larva + UBERON:0002548 + larval organism + larva + "A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle." [http://en.wikipedia.org/wiki/Larva] + + + anatomical cavity + UBERON:0002553 + "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina." [FMA:67552] + UBERON:anatomical cavity + + + prepiriform region + pyriform area + eupalaeocortex + prepiriform cortex + UBERON:prepyriform area + prepyriform area + lateral olfactory gyrus + piriform olfactory cortex + UBERON:0002590 + regio praepiriformis + prepyriform cortex + gyrus olfactorius lateralis + area prepiriformis + palaeocortex II + piriform cortex (price) + (pre-)piriform cortex + + + neuropilus + "A cluster of ➞neurites that is part of a ➞nervous system and forms a network of dendrites and axons where ➞synapses are present and in which neuronal somata do not occur." [http://www.ncbi.nlm.nih.gov/pubmed/21062451] + neuropil + UBERON:neuropil + UBERON:0002606 + + + cochlear nuclear complex + cochlear nuclei + "The cochlear nuclei consist of: (a) the dorsal cochlear nucleus, corresponding to the tuberculum acusticum on the dorso-lateral surface of the inferior peduncle; and (b) the ventral or accessory cochlear nucleus, placed between the two divisions of the nerve, on the ventral aspect of the inferior peduncle. [WP,unvetted]." [http://en.wikipedia.org/wiki/Cochlear_nuclei] + UBERON:0002610 + UBERON:cochlear nuclear complex + nuclei cochleares + + + "Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia." [NIFSTD:birnlex_1167] + regional part of brain + brain biological structure + brain anatomical structure + segment of brain + brain part + UBERON:regional part of brain + anatomical structure of brain + neuroanatomical region + biological structure of brain + neuraxis segment + UBERON:0002616 + + + lateral septal nucleus + nucleus lateralis septi + nucleus septi lateralis + lateral parolfactory nucleus + lateral septum + lateral septal nucleus (cajal) + "Regional part of the septal nuclei, lying dorsal and slightly lateral to the medial septal nucleus. The lateral septum receives the bulk of projections of areas projecting to the septal nuclei (Adapted from Brodal, 1981)." [NIFSTD:birnlex_1321] + lateral septum nucleus + UBERON:lateral septal nucleus + nucleus septalis lateralis + UBERON:0002667 + + + fasciculus pyramidalis + tractus corticospinalis + fasciculus cerebro-spinalis + "The corticospinal fibers that arise from the pyramidal cells within the cerebral cortex layer V of the precentral motor area, the premotor area and the postcentral gyrus, then descend into and through the medulla to form the lateral corticospinal tract and the anterior corticospinal tract." [ISBN:0-683-40008-8, MP:0002878] + corticospinal fibers + pyramid (Willis) + UBERON:corticospinal tract + tractus pyramidalis + corticospinal tract + fibrae corticospinales + UBERON:0002707 + tractus cortico-spinalis + + + UBERON:0002743 + basal forebrain area + basal forebrain + pars basalis telencephali + UBERON:basal forebrain + "A region of the brain consisting of ventral and rostral subcortical regions of the telencephalon, including among others, the basal ganglia, septal nuclei, amygdala, ventral pallidum, substantia innominata, and basal nucleus of Meynert." [Neurolex:birnlex_1560] + + + regional part of cerebellar cortex + "A regional part of brain that is part of a cerebellar cortex [Automatically generated definition]." [OBOL:automatic] + UBERON:regional part of cerebellar cortex + segment of cerebellar cortex + UBERON:0002749 + cerebellar cortical segment + + + apex of cochlear canal + cupula of cochlea + UBERON:apex of cochlea + cochlea apex + "The cupula is a structure in the vestibular system, sensing proprioception. The cupula is located within the ampullae of each of the three semicircular canals. As fluid rushes by the cupula, hair cells within it sense rotational acceleration, and transmit the corresponding signal to the brain through the vestibulocochlear nerve (CN VIII) In their natural orientation within the head, the cupulae are located on the medial aspect of the semicircular canals. In this orientation, the kinocilia rest on the posterior aspect of the cupula. [WP,unvetted]." [http://en.wikipedia.org/wiki/Apex_of_cochlea] + cupula of the cochlear canal + apex of the cochlear canal + UBERON:0002819 + apex of cochlea + + + vestibulocochlear ganglion vestibular component + vestibular ganglion + nucleus nervi oculomotorii, pars medialis + UBERON:0002824 + vestibulocochlear VIII ganglion vestibular component + Scarpa's ganglion + UBERON:vestibular ganglion + "The ganglion of the vestibular nerve. It contains the cell bodies of the bipolar primary afferent neurons whose peripheral processes form synaptic contact with hair cells of the vestibular sensory end organs[WP,unvetted]. Distributed to the maculae of the utricle and saccule and to the ampullary crests of the semicircular ducts. The vestibular fibers arise in bipolar cells in the vestibular ganglion in the internal acoustic meatus." [http://en.wikipedia.org/wiki/Scarpa%27s_ganglion, http://www.dartmouth.edu/~humananatomy/part_8/chapter_44.html] + vestibular part of vestibulocochlear ganglion + + + c1281209 + nucleus acustici accessorici + nucleus cochlearis anterior + UBERON:ventral cochlear nucleus + ventral cochlear nucleus + "The ventral cochlear nucleus (or anterior, or accessory), placed between the two divisions of the cochlear nerve, is on the ventral aspect of the inferior peduncle. Composed of several regions of distinct cell types, this nucleus serves primarily as a relay station for ascending auditory information. Bushy cells in the anterior ventral cochlear nucleus (AVCN), which receive end bulbs of held from auditory nerve fibers, project to the superior olivary complex through the trapezoid body and intermediate acoustic stria. Other cell types project to the lateral lemniscus and the inferior colliculus directly. [WP,unvetted]." [http://en.wikipedia.org/wiki/Ventral_cochlear_nucleus] + nucleus cochlearis ventralis + UBERON:0002828 + ventral cochlear nuclei + ventral cochlear nucleus + ventral coclear nucleus + ventral division of cochlear nucleus + accessory cochlear nucleus + anterior cochlear nucleus + + + "The group of nerve cell bodies located on the dorsal spinal roots within the vertebral column at the level of the lumbar vertebrae." [MP:0006404] + lumbar dorsal root ganglion + UBERON:0002836 + UBERON:lumbar dorsal root ganglion + lumbar spinal ganglion + lumbar dorsal root ganglion + + + third lumbar dorsal root ganglion + UBERON:0002858 + third lumbar spinal ganglion + UBERON:third lumbar dorsal root ganglion + third lumbar dorsal root ganglion + + + UBERON:olfactory cortex + UBERON:0002894 + olfactory areas + archaeocortex + olfactory lobe + olfactory cortex + "Aggregate brain region defined as those areas of cerebral cortex receiving direct synaptic input from the olfactory bulb (Price, 1973). It usually includes the piriform cortex and sometimes other areas." [NIFSTD:birnlex_2707] + archeocortex + + + "A sensory epithelium that is part of a gustatory system." [OBOL:automatic] + UBERON:gustatory epithelium + gustatory epithelium + UBERON:0002926 + + + UBERON:dentate gyrus pyramidal layer + dentate gyrus pyramidal layer + UBERON:0002929 + + + segment of cerebellum + UBERON:0002946 + UBERON:regional part of cerebellum + "A regional part of brain that is part of a cerebellum [Automatically generated definition]." [OBOL:automatic] + regional part of cerebellum + + + granular layer of cerebellar cortex + granular layer of cerebellum + cerebellum granule layer + UBERON:0002956 + cerebellar granular layer + "The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer." [GO:0021681] + granule cell layer of cerebellar cortex + cerebellar granule cell layer + UBERON:granular layer of cerebellar cortex + cerebellum granule cell layer + stratum granulosum cerebelli + cerebellar granule layer + + + cerebellum molecular layer + UBERON:molecular layer of cerebellar cortex + cerebellum molecular cell layer + "The molecular layer is the outermost layer of the cerebellar cortex. It contains the parallel fibers of the granule cells, interneurons such as stellate and basket cells, and the dendrites of the underlying Purkinje cells" [GO:0021679] + fasciculi thalami + thalamic fiber tracts + molecular layer of cerebellar cortex + cerebellar molecular layer + UBERON:0002974 + + + "A small muscle on the posterior aspect of the elbow joint." [http://en.wikipedia.org/wiki/Anconeus_muscle] + musculus anconaeus + musculus anconeus + UBERON:anconeus muscle + anconeus muscle + m. anconeus + UBERON:0002989 + anconeus + aconeus + + + UBERON:septum + UBERON:0003037 + septa + septum + "A wall, dividing a cavity or structure into smaller ones[WP]." [http://en.wikipedia.org/wiki/Septum] + + + otocyst + "The saccular invagination of ectoderm from which the vertebrate inner ear develops[BTO]. Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells[ZFA]. epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP]" [BTO:0002661, http://en.wikipedia.org/wiki/Otic_vesicle, MP:0009806, ZFIN:curator] + auditory vesicle + ear vesicle + OV + UBERON:ear vesicle + acoustic vesicle + otic vesicle + UBERON:0003051 + + + VZ + ventricular zone + ventricular zone of brain + "Proliferative region that is part of the ventricular system." [ZFA:0001083] + UBERON:ventricular zone + UBERON:0003053 + brain ventricular zone + + + "A single row of glia at the dorsal midline of the developing neural tube along the entire anterior-posterior axis. This region provides inductive signals for the specification of neuronal cell types and of the specification of neural crest cells. The cells comprising the roof plate are the precursors to radial glial cells." [GO:0021509, http://www.ncbi.nlm.nih.gov/pubmed/15378040] + UBERON:roof plate + alar plate + roof plate + UBERON:0003054 + roofplate + + + UBERON:periderm + periderm + epidermis epithelial layer + skin periderm + epitrichium + UBERON:0003055 + "A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis." [ISBN:9780878932504] + periderm + epidermis outer layer + EVL + + + posterior ICM + ventral blood island + "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]." [http://en.wikipedia.org/wiki/Blood_island_of_umbilical_vesicle] + blood island + UBERON:blood island + caudal hematopoietic tissue + blood islands + posterior blood island + VBI + UBERON:0003061 + + + UBERON:primitive knot + DMZ + embryo organizer + Henson's node + "organizer for gastrulation in vertebrates. The primitive knot starts as a regional knot of cells that forms on the blastodisc immediately anterior to where the outer layer of cells will begin to migrate inwards - an area known as the primitive streak. Posterior to the node is the primitive pit, where the cells of the epiblast (the upper layer of embryonic cells) initially begin to invaginate. This invagination expands posteriorly into the primitive groove as the cells layers continue to move into the space between the embryonic cells and the yolk. This differentiates the embryo into the germ layers - endoderm, mesoderm, and ectoderm. The primitive knot migrates posteriorly as gastrulation proceeds, eventually being absorbed into the tail bud.[WP]. the regional thickening of cells at the rostral tip of the vertebrate primitive streak through which gastrulating cells migrate anteriorally to form tissues in the future head and neck; this region organizes the formation of the three embryonic layers and establishes the longitudinal axis and the polarity of the embryo[MP]." [http://en.wikipedia.org/wiki/Primitive_knot, http://en.wikipedia.org/wiki/Regional_specification#Dorsal.2Fventral_axis_.26_organizer, MP:0004066] + primitive node + dorsal marginal zone + Spemann's organizer + Hensen node + embryonic shield + organizer + embryonic organizer + shield + Hensen's node + Spemann Mangold organizer + nodus primitivus + UBERON:0003062 + primitive knot + + + "The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements." [http://www.ncbi.nlm.nih.gov/pubmed/12784288, ZFIN:yb] + UBERON:0003066 + arcus pharyngeus secundus + 2nd arch + visceral arch 2 + second branchial arch + second visceral arch + pharyngeal arches 2 + branchial arch 2 + 2nd pharyngeal arch + hyoid bars + 2nd visceral arch + hyoid arch + UBERON:pharyngeal arch 2 + pharyngeal arch 2 + pharyngeal arch 2 + second pharyngeal arch + + + UBERON:dorsolateral placode + dorsolateral placodes + "Lateral neurogenic placodes positioned dorsal of the epibranchial placodes." [ZFIN:curator] + UBERON:0003067 + dorsolateral placode + + + "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord." [GO:0048318, http://en.wikipedia.org/wiki/Chordamesoderm] + axial mesoderm + chordamesoderm + UBERON:0003068 + UBERON:axial mesoderm + + + ear/otic placode + otic placode + auditory placode + UBERON:0003069 + octaval placode + UBERON:otic placode + octaval VIII placode + "A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK]" [http://en.wikipedia.org/wiki/Otic_placode, NCBIBook:NBK53175] + placoda otica + ear placode + + + eyecup + ophtalmic cup + eye cup + "Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]." [:Optic_cup_(embryology), MP:0004269, ZFA:0001202] + UBERON:optic cup + optic cup + ocular cup + UBERON:0003072 + + + Wolffian duct + Leydig's duct + UBERON:0003074 + mesonephric duct + UBERON:mesonephric duct + archinephric duct + ductus mesonephricus; ductus Wolffi + renal duct + "Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]." [http://en.wikipedia.org/wiki/Mesonephric_duct, ZFIN:curator] + + + UBERON:0003075 + neural plate + lamina neuralis + UBERON:neural plate + "A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]" [http://en.wikipedia.org/wiki/Neural_plate, ISBN:0815318960, OMD:neural+plate, ZFIN:curator] + presumptive central nervous system + + + "The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]" [GO:0048339] + UBERON:paraxial mesoderm + UBERON:0003077 + somitic mesoderm + paraxial mesoderm + paraxial mesenchyme + mesoderma paraxiale + + + floor plate + floorplate + bodenplatte + "The specialized glial structure (non-neuronal cells) situated at the ventral midline of the embryonic neural tube; this structure spans the anteroposterior axis from the midbrain to the tail regions, separating the left and right basal plates of the developing neural tube, and serves as an organizer to ventralize tissues in the embryo as well as to guide neuronal positioning and differentiation along the dorsoventral axis of the neural tube." [GO:0021508, http://en.wikipedia.org/wiki/Floor_plate, http://www.ncbi.nlm.nih.gov/pubmed/15738958, MGI:anna] + ventral plate + UBERON:floor plate + UBERON:0003079 + FP + + + lateral mesoderm + "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [http://en.wikipedia.org/wiki/Lateral_plate_mesoderm, MP:0010117] + mesoderma laminae lateralis + lateral plate + lateral plate mesoderm + UBERON:lateral plate mesoderm + lateral plate mesenchyme + UBERON:0003081 + + + UBERON:0003082 + muscle plate + myotome + UBERON:myotome + myomere + myotome region + myotomes + myotomus + myomeres + "A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells." [AEO:0001018] + + + "Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]." [http://en.wikipedia.org/wiki/Sclerotome, XB:curator] + sclerotome + sclerotomes + sclerotomus + UBERON:sclerotome + UBERON:0003089 + + + surface region + surface structure + anatomical surface feature + UBERON:surface structure + "Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism." [http://orcid.org/0000-0002-6601-2165, http://purl.obolibrary.org/obo/uberon/tracker/24] + surface feature + UBERON:0003102 + + + "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types." [CARO:0000024] + organ + compound organ + UBERON:0003103 + UBERON:compound organ + + + "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]." [BTO:0001393, http://en.wikipedia.org/wiki/Mesenchyme, ZFIN:curator] + UBERON:mesenchyme + mesenchyme + UBERON:0003104 + mesenchyma + mesenchymal tissue + mesenchyme tissue + portion of mesenchymal tissue + portion of mesenchyme tissue + + + aortic arch 3 + "The vessels formed within the third pair of branchial arches in embryogenesis" [MP:0006356] + UBERON:0003120 + carotid arch + pharyngeal arch artery 3 + 3rd branchial arch artery + third branchial arch artery + UBERON:pharyngeal arch artery 3 + third aortic arch + AA3 + 3rd arch artery + 3rd aortic arch artery + 3rd pharyngeal arch artery + + + aortic arch 4 + UBERON:0003121 + 4th pharyngeal arch artery + 4th branchial arch artery + systemic arch + fourth aortic arch + "The vessels formed within the fourth pair of branchial arches in embryogenesis" [MP:0006354] + pharyngeal arch artery 4 + UBERON:pharyngeal arch artery 4 + AA4 + 4th arch artery + fourth branchial arch artery + 4th aortic arch artery + + + pulmonary arch + 6th aortic arch artery + aortic arch 6 + sixth aortic arch + 6th pharyngeal arch artery + 6th branchial arch artery + UBERON:0003123 + UBERON:pharyngeal arch artery 6 + AA6 + pharyngeal arch artery 6 + sixth branchial arch artery + "The vessels formed within the sixth pair of branchial arches in embryogenesis" [MP:0006355] + 6th arch artery + + + chorion frondosum + UBERON:0003124 + chorion + uterine chorion + UBERON:chorion + fetal chorion + chorionic sac + embryonic chorion + "the outermost extraembryonic membrane" [MP:0002836\,MESH\:A10.615.284.473] + chorion (vertebrates) + + + tracheal tubule + windpipe + UBERON:trachea + UBERON:0003126 + vertebrate trachea + "The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]." [GO:0060438, http://en.wikipedia.org/wiki/Vertebrate_trachea] + cartilaginous trachea + trachea + + + "Upper portion of the skull that excludes the mandible (when present in the organism)." [http://en.wikipedia.org/wiki/Cranium_(anatomy), UBERON:cjm] + bones of cranium + skull minus mandible + UBERON:0003128 + calvarium + upper part of skull + UBERON:cranium + skeletal system of head + set of bones of cranium + cranium + epicranial plate + ossa cranii + + + UBERON:skull + UBERON:0003129 + skull + cranial skeleton + "Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]." [http://en.wikipedia.org/wiki/Skull, http://sourceforge.net/tracker/?func=detail&aid=2962656&group_id=76834&atid=1205376, http://www.ncbi.nlm.nih.gov/pubmed/11523816] + skeletal system of head + + + UBERON:0003133 + genitalia + UBERON:reproductive organ + reproductive system organ + sex organ + reproductive organ + genital organ + "An organ involved in reproduction" [UBERON:xp] + + + reproductive organ of female organism + female reproductive system organ + reproductive system organ of female organism + female organism sex organ + "A female organ involved in reproduction" [UBERON:xp] + UBERON:0003134 + sex organ of female organism + UBERON:female reproductive organ + female reproductive gland/organ + female sex organ + female reproductive organ + female organism reproductive system organ + female organism reproductive structure + female organism reproductive organ + reproductive structure of female organism + + + reproductive organ of male organism + male reproductive system organ + male organism sex organ + reproductive system organ of male organism + "A male organ involved in reproduction" [UBERON:xp] + male reproductive gland/organ + male sex organ + sex organ of male organism + UBERON:0003135 + UBERON:male reproductive organ + male reproductive organ + reproductive structure of male organism + male organism reproductive organ + male organism reproductive system organ + male organism reproductive structure + + + UBERON:alveolus + alveolus + "organ part that has the form of a hollow cavity[WP]." [http://en.wikipedia.org/wiki/Alveolus] + UBERON:0003215 + + + metanephros associated mesenchyme + metanephric blastema + metanephric mesoderm + UBERON:0003220 + metanephrogenic mesenchyme + UBERON:metanephric mesenchyme + metanephric mesenchyme + "one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO]" [GO:0072075, http://en.wikipedia.org/wiki/Metanephric_blastema] + + + UBERON:phalanx + digit long bone + phalanges + phalanx + phalange + phalanx bone + "Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits." [http://en.wikipedia.org/wiki/Phalanx_bones, VSAO:0000199] + long bone of digit + UBERON:0003221 + + + mammary epithelium + mammary gland epithelium + lactiferous gland epithelium + UBERON:epithelium of mammary gland + epithelium of mammary gland + "the epithelial layer of the luminal surfaces of the mammary gland" [MP:0009504\,MGI\:csmith] + mammary gland epithelial tissue + UBERON:0003244 + epithelium of lactiferous gland + + + epithelium of otic placode + "An epithelium that is part of a otic placode [Automatically generated definition]." [OBOL:automatic] + UBERON:0003249 + epithelial tissue of otic placode + UBERON:epithelium of otic placode + otic placode epithelium + otic epithelium + otic placode epithelial tissue + + + "An extraembryonic structure that develops_from a endoderm and is part of a yolk sac." [OBOL:automatic] + UBERON:yolk sac endoderm + UBERON:0003257 + yolk sac endoderm + + + foregut endoderm + UBERON:0003258 + endoderm of foregut + UBERON:endoderm of foregut + "An endoderm that is part of a foregut [Automatically generated definition]." [OBOL:automatic] + + + UBERON:0003267 + "A calcareous tooth that is part of the upper jaw region. In mammals, the upper jaw teeth are attached to the maxilla." [UBERON:cjm] + UBERON:tooth of upper jaw + tooth of upper jaw + upper jaw tooth + + + lower jaw vertebrate tooth + lower jaw calcareous tooth + UBERON:0003268 + UBERON:tooth of lower jaw + tooth of lower jaw + calcareous tooth of lower jaw + lower jaw dentine containing tooth + lower jaw tooth + "A calcareous tooth that is part of the lower jaw region. In mammals, the lower jaw teeth are attached to the mandible (dentary)." [UBERON:cjm] + + + mesentery of esophagus + esophagus mesentery + gullet mesentery + mesentery of oesophagus + meso-esophagus + "A mesentery that is part of a esophagus [Automatically generated definition]." [OBOL:automatic] + UBERON:mesentery of oesophagus + mesentery of gullet + UBERON:0003283 + oesophagus mesentery + + + UBERON:gland of diencephalon + interbrain gland + "Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis." [http://orcid.org/0000-0002-6601-2165] + gland of diencephalon + diencephalon gland + UBERON:0003296 + + + integumental gland + "A gland that is part of a integumental system [Automatically generated definition]." [OBOL:automatic] + integumental system gland + UBERON:0003297 + UBERON:gland of integumental system + gland of integumental system + integumentary gland + + + "A floor plate that is part of a neural tube [Automatically generated definition]." [OBOL:automatic] + floor plate neural tube + neural tube floor plate + floor plate of neural tube + UBERON:floor plate of neural tube + floorplate of neural tube + floorplate neural tube + neural tube floorplate + UBERON:0003306 + + + mature diencephalon floorplate + between brain floor plate + UBERON:floor plate of diencephalon + floor plate of mature diencephalon + interbrain floor plate + diencephalon floorplate + floorplate of mature diencephalon + diencephalon floor plate + floor plate of between brain + floorplate of interbrain + floor plate diencephalon + UBERON:0003309 + interbrain floorplate + floor plate diencephalic region + between brain floorplate + mature diencephalon floor plate + floorplate of between brain + floor plate of diencephalon + floorplate of diencephalon + floor plate of interbrain + "A floor plate that is part of a diencephalon [Automatically generated definition]." [OBOL:automatic] + floorplate diencephalon + + + UBERON:mesenchyme of mammary gland + mammary mesenchyme + "Mesenchyme that is part of a developing mammary gland." [OBOL:automatic] + mesenchyme of lobe of mammary gland + lactiferous gland mesenchyme + mesenchyme of mammary gland + lobe of breast mesenchyme + mesenchyme of lobe of breast + mesenchyme of lactiferous gland + lobe of mammary gland mesenchyme + mammary gland mesenchyme + UBERON:0003326 + + + ganglion of peripheral nervous system + UBERON:ganglion of peripheral nervous system + "A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO)." [NIFSTD:birnlex_2548] + peripheral nervous system ganglion + UBERON:0003338 + + + lamina epithelialis mucosa + UBERON:epithelium of mucosa + UBERON:0003350 + lamina epithelialis mucosae + epithelium of mucosa + "A layer of epithelial cells on the surface of the mucosa." [BTO:0003752] + + + pharynx epithelial tissue + "An epithelium that is part of a pharynx [Automatically generated definition]." [OBOL:automatic] + epithelial tissue of pharynx + epithelium of pharynx + UBERON:0003351 + pharyngeal epithelium + pharynx epithelium + UBERON:pharyngeal epithelium + + + UBERON:0003374 + chorionic epithelium + chorion ectoderm + "A extraembryonic structure that develops_from a ectoderm and is part of a chorion." [OBOL:automatic] + chorionic ectoderm + UBERON:chorionic ectoderm + chorion epithelium + + + "A cartilage element that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] + cartilage of respiratory system + respiratory system cartilage + apparatus respiratorius cartilage + cartilage of apparatus respiratorius + UBERON:0003406 + UBERON:cartilage of respiratory system + + + lower gastrointestinal tract gland + gland of lower gastrointestinal tract + gland of digestive tract + gland of gut + UBERON:gland of gut + digestive tract gland + gut gland + "A gland that is part of a digestive tract [Automatically generated definition]." [OBOL:automatic] + UBERON:0003408 + + + abdominal fat pad + UBERON:abdominal fat pad + abdominal fat depot + "The encapsulated adipose tissue in the abdomen." [MP:0000010] + UBERON:0003427 + fat pad of abdomen + abdomen fat pad + + + "The encapsulated adipose tissue associated with the ovaries or testes." [MP:0005335] + UBERON:gonadal fat pad + gonadal fat pad + fat pad of gonads + fat pad of gonad + gonadal fat depot + gonadal fat pad + gonad-associated fat pad + UBERON:0003428 + gonad fat pad + + + UBERON:0003431 + leg nerve + UBERON:leg nerve + "A nerve that is part of a leg [Automatically generated definition]." [OBOL:automatic] + nerve of leg + + + "A nerve that is part of a limb [Automatically generated definition]." [OBOL:automatic] + limb nerve + UBERON:limb nerve + nerve of limb + UBERON:0003440 + + + nerve of hindlimb + UBERON:0003442 + "A nerve that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] + lower extremity nerve + inferior member nerve + hind limb nerve + nerve of lower extremity + nerve of inferior member + nerve of hind limb + hindlimb nerve + UBERON:hindlimb nerve + + + chest cavity nerve + nerve of cavity of thorax + UBERON:0003443 + nerve of chest cavity + "A nerve that is located in a thoracic cavity [Automatically generated definition]." [OBOL:automatic] + nerve of pectoral cavity + nerve of cavity of chest + nerve of thoracic cavity + pectoral cavity nerve + cavity of chest nerve + UBERON:thoracic cavity nerve + cavity of thorax nerve + thoracic cavity nerve + + + UBERON:upper jaw incisor + upper incisor + incisor of upper jaw + maxillary incisor tooth + incisor tooth of palatoquadrate arch + upper jaw incisor tooth + palatoquadrate arch incisor + "An incisor tooth that is part of a upper jaw [Automatically generated definition]." [OBOL:automatic] + premaxillary tooth + incisor of palatoquadrate arch + upper jaw incisor + palatoquadrate arch incisor tooth + UBERON:0003450 + incisor tooth of upper jaw + + + UBERON:lower jaw incisor + incisor of lower jaw + lower incisor + lower jaw incisor tooth + incisor tooth of ventral mandibular arch + mandibular incisor + lower jaw incisor + "An incisor tooth that is part of a lower jaw [Automatically generated definition]." [OBOL:automatic] + incisor of ventral mandibular arch + ventral mandibular arch incisor + UBERON:0003451 + incisor tooth of lower jaw + ventral mandibular arch incisor tooth + + + UBERON:head bone + adult head bone organ + "A bone that is part of a head [Automatically generated definition]." [OBOL:automatic] + adult head bone + bone organ of head + craniofacial bone + bone of head + head bone + head bone organ + UBERON:0003457 + bone organ of adult head + bone of adult head + + + UBERON:neck bone + neck bone organ + neck bone + bone organ of neck (volume) + bone of neck (volume) + neck (volume) bone + bone of neck + neck (volume) bone organ + bone organ of neck + "A bone that is part of a neck [Automatically generated definition]." [OBOL:automatic] + UBERON:0003458 + + + arm bone + bone organ of proximal segment of free upper limb + bone of arm + "A bone that is part of the region of the forelimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia" [https://orcid.org/0000-0002-6601-2165] + brachial region bone + UBERON:0003460 + bone of upper extremity + bone of brachial region + proximal segment of free upper limb bone organ + bone of proximal segment of free upper limb + UBERON:arm bone + brachial region bone organ + bone organ of arm + arm bone organ + bone organ of brachial region + proximal segment of free upper limb bone + + + "A bone that is connected via a shoulder joint (i.e. glenohumeral or acromioclavicular joints). The shoulder bones are the clavicle, scapula and humerus - but note that these are only considered to be shoulder bones when a true shoulder is present, as in most tetrapods." [UBERON:cjm] + shoulder-articulating bone + bone of shoulder + UBERON:0003461 + shoulder bone + UBERON:shoulder bone + + + facial bone + "A bone that is part of a facial skeleton [Automatically generated definition]." [OBOL:automatic] + UBERON:facial bone + bone of viscerocranium + UBERON:0003462 + viscerocranium bone + facial bone + bone of facial skeleton + facial skeleton bone + + + trunk bone + bone of trunk + UBERON:0003463 + trunk bone organ + torso bone + UBERON:trunk bone + torso bone organ + bone organ of torso + bone organ of trunk + "A bone that is part of a trunk [Automatically generated definition]." [OBOL:automatic] + bone of torso + + + hind limb bone organ + inferior member bone organ + bone organ of lower extremity + lower extremity bone organ + bone organ of inferior member + bone organ of hind limb + UBERON:hindlimb bone + hindlimb bone + bone organ of hindlimb + bone of lower extremity + hind limb bone + inferior member bone + bone of inferior member + "A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle)" [https://orcid.org/0000-0002-6601-2165] + lower extremity bone + bone of hind limb + hindlimb bone organ + UBERON:0003464 + bone of hindlimb + + + bone organ of proximal segment of free upper limb middle limb segment + bone organ of antebrachial region + bone organ of middle limb segment of brachial region + intermediate segment of free upper limb bone organ + bone of zeugopod of proximal segment of free upper limb + bone organ of zeugopod of arm + UBERON:forelimb zeugopod bone + bone of middle limb segment of arm + middle limb segment of proximal segment of free upper limb bone + zeugopod of proximal segment of free upper limb bone + bone of proximal segment of free upper limb zeugopod + bone organ of zeugopod of proximal segment of free upper limb + arm zeugopod bone organ + brachial region middle limb segment bone + proximal segment of free upper limb zeugopod bone + bone of arm middle limb segment + bone organ of zeugopod of brachial region + lower segment of arm bone + middle limb segment of arm bone + zeugopod of arm bone + bone of arm zeugopod + zeugopod of proximal segment of free upper limb bone organ + bone organ of proximal segment of free upper limb zeugopod + bone organ of arm middle limb segment + bone of lower arm + proximal segment of free upper limb zeugopod bone organ + bone of middle limb segment of brachial region + antebrachial region bone + bone of antebrachial region + lower segment of arm bone organ + intermediate segment of free upper limb bone + UBERON:0003466 + arm middle limb segment bone + proximal segment of free upper limb middle limb segment bone organ + middle limb segment of arm bone organ + bone of proximal segment of free upper limb middle limb segment + bone of zeugopod of arm + antebrachial region bone organ + bone organ of lower arm + bone of brachial region middle limb segment + bone organ of brachial region middle limb segment + middle limb segment of brachial region bone + lower arm bone + "A bone that is part of a lower arm [Automatically generated definition]." [OBOL:automatic] + bone of intermediate segment of free upper limb + bone of zeugopod of brachial region + arm zeugopod bone + zeugopod of brachial region bone + bone of brachial region zeugopod + arm middle limb segment bone organ + bone of lower segment of arm + middle limb segment of brachial region bone organ + bone organ of intermediate segment of free upper limb + bone organ of lower segment of arm + middle limb segment of proximal segment of free upper limb bone organ + zeugopod of brachial region bone organ + bone organ of brachial region zeugopod + proximal segment of free upper limb middle limb segment bone + brachial region zeugopod bone + bone of middle limb segment of proximal segment of free upper limb + bone organ of middle limb segment of arm + forelimb zeugopod bone + brachial region middle limb segment bone organ + zeugopod of arm bone organ + bone organ of arm zeugopod + brachial region zeugopod bone organ + bone organ of middle limb segment of proximal segment of free upper limb + + + UBERON:respiratory system artery + "An artery that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] + respiratory system artery + UBERON:0003469 + + + "A vein that is part of a tail [Automatically generated definition]." [http://en.wikipedia.org/wiki/Tail_vein, OBOL:automatic] + post-vent region vein + vein of post-vent region + tail vein + UBERON:0003481 + vein of tail + caudal vein + UBERON:tail vein + + + head blood vessel + blood vessel of head + adult head blood vessel + blood vessel of adult head + UBERON:head blood vessel + UBERON:0003496 + "A blood vessel that is part of a head [Automatically generated definition]." [OBOL:automatic] + + + blood vessel of abdomen + UBERON:abdomen blood vessel + abdomen blood vessel + "A blood vessel that is part of an abdomen [Automatically generated definition]." [OBOL:automatic] + UBERON:0003497 + + + UBERON:heart blood vessel + blood vessel of heart + heart blood vessel + cardiac blood vessel + "A blood vessel that is part of a heart [Automatically generated definition]." [OBOL:automatic] + UBERON:0003498 + + + blood vessel of neck (volume) + blood vessel of neck + neck (volume) blood vessel + neck blood vessel + UBERON:0003502 + "A blood vessel that is part of a neck [Automatically generated definition]." [OBOL:automatic] + UBERON:neck blood vessel + + + UBERON:leg blood vessel + "A blood vessel that is part of a leg [Automatically generated definition]." [OBOL:automatic] + blood vessel of leg + UBERON:0003503 + leg blood vessel + + + respiratory system blood vessel + apparatus respiratorius blood vessel + blood vessel of apparatus respiratorius + UBERON:respiratory system blood vessel + UBERON:0003504 + "A blood vessel that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] + blood vessel of respiratory system + + + arterial blood vessel + "A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta." [https://orcid.org/0000-0002-6601-2165] + UBERON:0003509 + UBERON:arterial blood vessel + + + pulmonary vascular element + "A blood vessel that is part of a lung [Automatically generated definition]." [OBOL:automatic] + blood vessel of lung + UBERON:0003512 + UBERON:lung blood vessel + lung blood vessel + + + blood vessel of torso + blood vessel of trunk + UBERON:0003513 + torso blood vessel + trunk blood vessel + UBERON:trunk blood vessel + "A blood vessel that is part of a trunk [Automatically generated definition]." [OBOL:automatic] + + + blood vessel of limb + UBERON:0003514 + "A blood vessel that is part of a limb [Automatically generated definition]." [OBOL:automatic] + limb blood vessel + UBERON:limb blood vessel + + + UBERON:hindlimb blood vessel + hind limb blood vessel + blood vessel of lower extremity + inferior member blood vessel + lower extremity blood vessel + blood vessel of hind limb + UBERON:0003516 + hindlimb blood vessel + blood vessel of inferior member + blood vessel of hindlimb + "A blood vessel that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] + + + "A blood vessel that is part of a thoracic cavity [Automatically generated definition]." [OBOL:automatic] + blood vessel of cavity of thorax + cavity of thorax blood vessel + chest cavity blood vessel + blood vessel of pectoral cavity + blood vessel of cavity of chest + blood vessel of thoracic cavity + thoracic cavity blood vessel + UBERON:thoracic cavity blood vessel + UBERON:0003519 + cavity of chest blood vessel + pectoral cavity blood vessel + blood vessel of chest cavity + + + UBERON:0003524 + blood vessel of tail + "A blood vessel that is part of a tail [Automatically generated definition]." [OBOL:automatic] + blood vessel of post-vent region + tail blood vessel + post-vent region blood vessel + UBERON:tail blood vessel + + + capillary of respiratory system + respiratory system capillary + respiratory system capillary vessel + capillary of apparatus respiratorius + "A capillary that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] + UBERON:respiratory system capillary + UBERON:0003526 + blood capillary of respiratory system + respiratory system blood capillary + capillary vessel of apparatus respiratorius + capillary vessel of respiratory system + blood capillary of apparatus respiratorius + apparatus respiratorius blood capillary + apparatus respiratorius capillary + apparatus respiratorius capillary vessel + + + UBERON:brain gray matter + grey substance of brain + "A gray matter that is part of a brain [Automatically generated definition]." [OBOL:automatic] + gray matter of brain + UBERON:0003528 + grey matter of brain + brain gray matter + brain grey matter + brain grey substance + + + lower extremity skin + UBERON:0003532 + hind limb skin + skin of hindlimb + skin of lower extremity + lower limb skin + skin of lower limb + skin of inferior member + UBERON:hindlimb skin + skin of hind limb + "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] + inferior member skin + hindlimb skin + + + portion of connective tissue of head + textus connectivus of adult head + adult head connective tissue + adult head textus connectivus + UBERON:head connective tissue + portion of connective tissue of adult head + UBERON:0003566 + head connective tissue + connective tissue of head + head textus connectivus + adult head portion of connective tissue + "A portion of connective tissue that is part of a head [Automatically generated definition]." [OBOL:automatic] + textus connectivus of head + connective tissue of adult head + head portion of connective tissue + + + UBERON:0003567 + textus connectivus of abdomen + "A portion of connective tissue that is part of an abdomen [Automatically generated definition]." [OBOL:automatic] + abdomen portion of connective tissue + portion of connective tissue of abdomen + UBERON:abdomen connective tissue + connective tissue of abdomen + abdomen connective tissue + abdomen textus connectivus + + + UBERON:0003569 + "A portion of connective tissue that is part of a leg [Automatically generated definition]." [OBOL:automatic] + leg portion of connective tissue + connective tissue of leg + portion of connective tissue of leg + leg connective tissue + leg textus connectivus + UBERON:leg connective tissue + textus connectivus of leg + + + portion of connective tissue of respiratory system + UBERON:respiratory system connective tissue + textus connectivus of apparatus respiratorius + apparatus respiratorius connective tissue + "A portion of connective tissue that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] + textus connectivus of respiratory system + apparatus respiratorius portion of connective tissue + portion of connective tissue of apparatus respiratorius + UBERON:0003570 + apparatus respiratorius textus connectivus + connective tissue of respiratory system + respiratory system connective tissue + respiratory system portion of connective tissue + respiratory system textus connectivus + connective tissue of apparatus respiratorius + + + connective tissue of lobe of breast + "The fibrous supportive tissue of the mammary gland." [MP:0009507] + connective tissue of lactiferous gland + mammary gland connective tissue + UBERON:0003584 + UBERON:mammary gland connective tissue + connective tissue of lobe of mammary gland + lactiferous gland portion of connective tissue + lactiferous gland connective tissue + connective tissue of mammary gland + + + "A portion of connective tissue that is part of a trunk [Automatically generated definition]." [OBOL:automatic] + UBERON:trunk connective tissue + textus connectivus of torso + torso connective tissue + textus connectivus of trunk + trunk connective tissue + trunk textus connectivus + torso textus connectivus + connective tissue of torso + trunk portion of connective tissue + torso portion of connective tissue + connective tissue of trunk + UBERON:0003586 + portion of connective tissue of torso + portion of connective tissue of trunk + + + limb textus connectivus + "A portion of connective tissue that is part of a limb [Automatically generated definition]." [OBOL:automatic] + textus connectivus of limb + UBERON:0003587 + UBERON:limb connective tissue + limb connective tissue + portion of connective tissue of limb + connective tissue of limb + limb portion of connective tissue + + + hind limb connective tissue + "A portion of connective tissue that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] + connective tissue of inferior member + connective tissue of hind limb + connective tissue of hindlimb + connective tissue of lower extremity + UBERON:0003589 + hindlimb connective tissue + UBERON:hindlimb connective tissue + + + UBERON:limb long bone + UBERON:0003606 + "A long bone that is part of a limb [Automatically generated definition]." [OBOL:automatic] + long bone of limb + limb long bone + + + long bone of superior member + forelimb long bone + UBERON:forelimb long bone + superior member long bone + UBERON:0003607 + "A long bone that is part of a forelimb [Automatically generated definition]." [OBOL:automatic] + long bone of anteriormost limb + long bone of upper extremity + long bone of fore limb + fore limb long bone + upper extremity long bone + anteriormost limb long bone + long bone of forelimb + + + lower extremity long bone + UBERON:0003608 + long bone of inferior member + long bone of hind limb + long bone of hindlimb + UBERON:hindlimb long bone + hindlimb long bone + long bone of lower extremity + inferior member long bone + hind limb long bone + "A long bone that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] + + + hand digit 2 + 2nd digit of hand + manual digit II + manual digit 2 + fore digit II + fore limb digit 2 + second finger + UBERON:0003622 + digit 2 of fore-paw + finger 2 + second digit of hand + UBERON:manual digit 2 + "2nd digit of the manus." [http://en.wikipedia.org/wiki/Index_finger] + 2nd finger + + + toe 1 + hallux + UBERON:pedal digit 1 + digit 1 of hind-paw + great toe + digit 1 of pes + preaxial digit of hindlimb + hind limb digit 1 + pedal digit 1 + pedal digit 1 + first toe + digitus primus (I) pedis + hind digit I + foot digit 1 + hallex + hallux; digitus primus [I] + digitus primus pedis + hind digit 1 + pes digit I + "1st digit of the hind autopod." [http://en.wikipedia.org/wiki/Hallux] + large toe + pedal digit I + UBERON:0003631 + + + toe 2 + hind digit II + digitus secundus (II) pedis + hind limb digit 2 + digit 2 of hind-paw + second digit of foot + UBERON:pedal digit 2 + pedal digit II + hind digit 2 + pedal digit 2 + second toe + foot digit 2 + digitus secundus pedis + UBERON:0003632 + "2nd digit of the hind autopod." [https://orcid.org/0000-0002-6601-2165] + pes digit II + digitus secundus [ii] + 2nd toe + + + UBERON:0003643 + "An arterial blood vessel that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] + UBERON:respiratory system arterial blood vessel + respiratory system arterial blood vessel + + + toe 2 metatarsus + foot digit 2 metatarsal bone + metatarsal bone of digit 2 + UBERON:metatarsal bone of digit 2 + metatarsal bone of foot digit 2 + second metatarsal bone + metatarsal bone digit 2 + metatarsal II + metatarsal bone of digit II + toe 2 metatarsal + "A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 2." [OBOL:automatic] + hindlimb digit 2 metatarsus + UBERON:0003651 + metatarsal 2 + + + dens molaris + molar tooth + "Molars are the rearmost and most complicated kind of tooth in most mammals." [http://en.wikipedia.org/wiki/Molar_(tooth)] + UBERON:0003655 + molaris + molar + UBERON:molar tooth + + + mesopodium bone + mesopodial bone + UBERON:mesopodium bone + UBERON:0003656 + carpal/tarsal bone + basipodium bone + mesopod bone + "A bone that is part of a mesopodial skeleton." [https://orcid.org/0000-0002-6601-2165] + + + UBERON:limb joint + UBERON:0003657 + skeletal limb joint + joint of limb + limb joint + "Any joint that is part of a (free) limb." [https://orcid.org/0000-0002-6601-2165] + joint of limb skeletal system + + + limb muscle organ + "Any muscle organ that is part of a limb [Automatically generated definition]." [OBOL:automatic] + limb skeletal muscle + limb muscle + UBERON:limb muscle + UBERON:0003661 + muscle organ of limb + + + upper limb skeletal muscle + UBERON:forelimb muscle + musculature of arm + fore limb muscle organ + forelimb muscle + muscle of upper limb + "Any muscle organ that is part of a forelimb." [OBOL:automatic] + muscle of free upper limb + UBERON:0003662 + free upper limb muscle + forelimb muscle organ + musculature of the arm + arm muscle system + + + inferior member muscle organ + hind limb muscle organ + UBERON:hindlimb muscle + muscle of posterior limb + muscle organ of hind limb + lower limb skeletal muscle + hindlimb muscle + UBERON:0003663 + muscle organ of lower extremity + muscle of free lower limb + free lower limb muscle + lower extremity muscle organ + "Any muscle organ that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] + muscle organ of inferior member + muscle organ of hindlimb + hindlimb muscle organ + + + upper secondary molar tooth + UBERON:upper jaw molar + molar tooth of upper jaw + upper molar tooth + UBERON:0003666 + upper jaw molar tooth + upper molar + upper jaw molar + "A molar tooth that is part of a upper jaw [Automatically generated definition]." [OBOL:automatic] + maxillary secondary molar tooth + upper permanent molar tooth + + + UBERON:0003684 + cavity of compartment of abdomen + space of abdominal compartment + cavity of abdominal compartment + "body cavity of the human body (and animal bodies) that holds the bulk of the viscera. It is located below (or inferior to) the thoracic cavity, and above the pelvic cavity. It is a part of the abdominopelvic cavity. Organs of the abdominal cavity include the stomach, liver, gallbladder, spleen, pancreas, small intestine, kidneys, and large intestine. The abdominal cavity is lined with a protective membrane termed the peritoneum. The kidneys are located in the abdominal cavity behind the peritoneum, in the retroperitoneum. The viscera are also covered, in the front, with a layer of peritoneum called the greater omentum (or omental apron)." [http://en.wikipedia.org/wiki/Abdominal_cavity] + cavitas abdominis + abdominal cavity + UBERON:abdominal cavity + + + UBERON:0003685 + suture joint of skull + cranium suture + UBERON:cranial suture + cranial suture + suture of cranium + "Fibrous joint in which the articulating bones or cartilages of the skull are connected by sutural ligaments (scant amount of collagenous dense connective tissue). Examples: sagittal suture, frontal suture." [FMA:71385, http://en.wikipedia.org/wiki/Suture_(joint), ISBN:3110148986] + + + UBERON:retroperitoneal space + spatium retroperitoneale + retroperitoneal space + retroperitoneum + "Anatomical space in the abdominal cavity behind (retro) the peritoneum. It has no specific delineating anatomical structures. Organs are retroperitoneal if they only have peritoneum on their anterior side." [http://en.wikipedia.org/wiki/Retroperitoneal_space] + UBERON:0003693 + + + articulationes metacarpophalangeae + UBERON:metacarpophalangeal joint + UBERON:0003695 + MP joint + metacarpo-phalangeal joint + "The metacarpophalangeal joints (MCP) are of the condyloid kind, formed by the reception of the rounded heads of the metacarpal bones into shallow cavities on the proximal ends of the first phalanges, with the exception of that of the thumb, which presents more of the characters of a ginglymoid joint. Arthritis of the MCP is a distinguishing feature of Rheumatoid Arthritis, as opposed to the distal interphalangeal joint in osteoarthritis. [WP,unvetted]." [http://en.wikipedia.org/wiki/Metacarpophalangeal_joint] + metacarpal phalangeal joint + metacarpophalangeal joint + + + metatarsal-phalangeal joint + metatarsalphalangeal joint + metatarsophalangeal + UBERON:0003696 + UBERON:metatarsophalangeal joint + metatarsal joint + metatarsophalangeal joint + metatarsophalangeal articulation + articulationes metatarsophalangeae + "The metatarsophalangeal articulations are the joints between the metatarsal bones of the foot and the proximal bones of the toes . They are condyloid joints meaning an elliptical or rounded surface (of the metatarsal bones) come close to the shallow cavities (of the proximal phalanges). The ligaments are the plantar and two collateral." [http://en.wikipedia.org/wiki/Metatarsophalangeal_articulations] + + + tendo calcaneus + calcaneal tendon + Achille's tendon + "The Achilles tendon is a tendon of the posterior leg. It serves to attach the plantaris, gastrocnemius (calf) and soleus muscles to the calcaneus (heel) bone." [http://en.wikipedia.org/wiki/Achilles_tendon] + UBERON:0003701 + UBERON:calcaneal tendon + calcaneal tendon + Achilles' tendon + tendo Achillis + Achilles tendon + + + nerve tissue + UBERON:0003714 + neural tissue + nervous tissue + UBERON:neural tissue + "Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature." [FMA:9642] + portion of neural tissue + + + UBERON:0003718 + neuromuscular spindle + muscle stretch receptor + neuromuscular spindle + muscle spindle + UBERON:muscle spindle + "The sensory organs in muscle that are involved in the stretch reflex." [MP:0004069] + + + metapodi bone + metacarpal or metatarsal bone + UBERON:0003821 + metapodial bone + metacarpal/metatarsal + UBERON:metapodium bone + metacarpal/metatarsal bone + metapodium bone + metapodium bone + "A bone of the metapodial skeleton" [https://orcid.org/0000-0002-6601-2165] + + + "A bone that is part of a hindlimb stylopod [Automatically generated definition]." [https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376, OBOL:automatic] + UBERON:upper leg bone + upper leg bone + UBERON:0003826 + femur + + + bone of abdominal segment of trunk + "A bone that is part of an abdominal segment of trunk [Automatically generated definition]." [OBOL:automatic] + abdominal segment of trunk bone organ + abdominal segment of trunk bone + UBERON:0003828 + UBERON:abdominal segment bone + abdominal segment bone + bone organ of abdominal segment of trunk + + + apparatus respiratorius muscle organ + UBERON:0003831 + UBERON:respiratory system muscle + respiratory system muscle + muscle organ of apparatus respiratorius + muscle organ of respiratory system + "Any muscle organ that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] + respiratory system muscle organ + + + UBERON:0003833 + abdominal segment of trunk muscle organ + UBERON:abdominal segment muscle + abdominal segment muscle + "A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]." [OBOL:automatic] + muscle organ of abdominal segment of trunk + + + "A blood vessel that is part of a thorax [Automatically generated definition]." [OBOL:automatic] + thorax blood vessel + blood vessel of thorax + thoracic segment blood vessel + upper body blood vessel + UBERON:0003834 + UBERON:thoracic segment blood vessel + + + blood vessel of abdominal segment of trunk + UBERON:abdominal segment blood vessel + abdominal segment blood vessel + "A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]." [OBOL:automatic] + UBERON:0003835 + abdominal segment of trunk blood vessel + + + portion of connective tissue of thorax + connective tissue of thorax + UBERON:thoracic segment connective tissue + upper body connective tissue + textus connectivus of thorax + thorax portion of connective tissue + thoracic segment connective tissue + UBERON:0003837 + thorax textus connectivus + thorax connective tissue + "A portion of connective tissue that is part of a thorax [Automatically generated definition]." [OBOL:automatic] + + + abdominal segment of trunk portion of connective tissue + textus connectivus of abdominal segment of trunk + UBERON:0003838 + abdominal segment connective tissue + "A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]." [OBOL:automatic] + abdominal segment of trunk connective tissue + UBERON:abdominal segment connective tissue + abdominal segment of trunk textus connectivus + portion of connective tissue of abdominal segment of trunk + connective tissue of abdominal segment of trunk + + + limb joint of anteriormost limb + joint of free upper limb + limb joint of fore limb + superior member joint of limb + UBERON:forelimb joint + joint of limb of upper extremity + fore limb limb joint + upper extremity limb joint + joint of limb of forelimb + upper extremity joint of limb + forelimb joint + superior member limb joint + forelimb joint of limb + limb joint of forelimb + limb joint of upper extremity + "A limb joint that is part of a forelimb [Automatically generated definition]." [OBOL:automatic] + forelimb limb joint + UBERON:0003839 + joint of limb of anteriormost limb + joint of limb of fore limb + anteriormost limb limb joint + limb joint of superior member + anteriormost limb joint of limb + fore limb joint of limb + joint of limb of superior member + + + joint of free lower limb + limb joint of lower extremity + hindlimb limb joint + hindlimb joint of limb + limb joint of hindlimb + joint of limb of inferior member + joint of limb of hind limb + lower extremity joint of limb + limb joint of hind limb + "A limb joint that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] + hindlimb joint + UBERON:hindlimb joint + limb joint of inferior member + joint of limb of hindlimb + hind limb limb joint + inferior member joint of limb + joint of lower limb + hind limb joint of limb + inferior member limb joint + UBERON:0003840 + lower extremity limb joint + joint of limb of lower extremity + + + distal free limb segment limb joint + limb joint of autopod + distal free limb segment joint of limb + limb joint of distal free limb segment + "A limb joint that is part of an autopod [Automatically generated definition]." [OBOL:automatic] + autopod joint of limb + joint of limb of distal free limb segment + paw joint + UBERON:0003841 + UBERON:autopod joint + autopod joint + joint of limb of autopod + autopod limb joint + + + UBERON:0003842 + central lumen + lumen of neural tube + neural lumen + "An anatomical space that surrounded_by a neural tube." [OBOL:automatic] + UBERON:neural tube lumen + neural tube neural lumen + neural tube lumen + cavity of neural tube + neurocoel + + + epithelial tissue of thymus + "An epithelium that is part of a thymus, forming a supporting framework[MP,modified]." [MP:0009544] + thymus gland epithelium + thymus epithelial tissue + epithelium of thymus + epithelial tissue of thymus gland + thymus epithelium + UBERON:0003846 + epithelium of thymus gland + thymic epithelial tissue + thymus gland epithelial tissue + thymic epithelium + UBERON:thymus epithelium + + + UBERON:0003859 + mesenchyme of upper extremity + mesenchyme of anteriormost limb + mesenchyme of fore limb + forelimb mesenchyme + superior member mesenchyme + mesenchyme of forelimb + UBERON:forelimb mesenchyme + mesenchyme of superior member + fore limb mesenchyme + "Mesenchyme that is part of a developing forelimb [Automatically generated definition]." [OBOL:automatic] + anteriormost limb mesenchyme + upper extremity mesenchyme + + + UBERON:hippocampal field + subdivision of hippocampus + hippocampal field + "a part or parts of the hippocampus that have a particular function" [MP:0008262\,MGI\:csmith] + hippocampus subdivision + hippocampal region + UBERON:0003876 + hippocampus region + + + regio i hippocampi proprii + CA1 + CA1 field of the hippocampus + regio superior + region CA1 + region i of ammon's horn + "Part of hippocampus proper bounded by CA2 and the subiculum, characterized by pyramidal neurons that receive projections from pyramidal neurons of CA3 via the Schaffer collaterals." [NIFSTD:birnlex_1197] + cornu ammonis 1 + region i of hippocampus proper + field CA1 of hippocampus + CA1 field of Ammon's horn + regio i cornus ammonis + CA1 field + prosubiculum = distal ca1 + CA1 field of hippocampus + UBERON:0003881 + field CA1 + UBERON:CA1 field of hippocampus + CA1 field of the Ammon horn + CA1 field of hippocampus + hippocampus CA1 + CA1 field of cornu ammonis + regio superior of the hippocampus + field CA1, Ammon's horn (Lorente de Ns) + region 1 of Ammon's horn + + + regio ii cornus ammonis + "Part of hippocampus proper bounded by areas CA3 and CA1, characterized by a narrow layer of large pyramidal cells, similar in size to CA3 pyramidal cells, but which lack the mossy fiber input from the dentate gyrus (adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 460)" [NIFSTD:birnlex_1362] + field CA2 of hippocampus + CA2 field + CA2 field of Ammon's horn + region II of ammon's horn + UBERON:0003882 + field CA2 + CA2 field of hippocampus + CA2 + CA2 field of the Ammon horn + cornu Ammonis 2 + region CA2 + region II of hippocampus proper + CA2 field of the hippocampus + UBERON:CA2 field of hippocampus + CA2 field of hippocampus + hippocampus CA2 + CA2 field of cornu ammonis + region 2 of Ammon's horn + field CA2, Ammon's horn (Lorente de Ns) + regio ii hippocampi proprii + + + region 3 of Ammon's horn + CA3 + CA3 field of the hippocampus + region CA3 + CA3 field of the Ammon horn + cornu Ammonis 3 + region III of ammon's horn + CA3 + regio III cornus ammonis + "Part of hippocampus proper bounded by the hilus of the dentate gyrus and area CA2, characterized by large pyramidal cells and a dense projection from dentate gyrus granule cell mossy fibers." [http://neurolex.org/wiki/Category\:CA3] + field CA3, Ammon's horn (Lorente de Ns) + region III of hippocampus proper + UBERON:0003883 + CA3 field of hippocampus + CA3 field of Ammon's horn + CA3 field + regio III cornus ammonis + UBERON:CA3 field of hippocampus + field CA3 + CA3 field of hippocampus + regio inferior + regio III hippocampi proprii + field CA3 of hippocampus + CA3 field of cornu ammonis + regio hippocampi proprii III + hippocampus CA3 + + + "An anatomical cavity that has the potential to develop into a coelemic cavity lumen." [OBOL:automatic] + UBERON:body cavity precursor + UBERON:0003886 + body cavity precursor + + + extraembryonic celom + "the fluid-filled spaces formed within the mass of extraembryonic mesoderm that later fuse to become a large extraembryonic cavity" [MP:0011200\,ISBN-10\:1405118660\,ISBN\:0-12-402035-6] + extraembryonic coelom + chorion cavity + UBERON:extraembryonic coelom + exocoelomic cavity + chorionic cavity + UBERON:0003888 + extraembryonic coelomic cavity + extra-embryonic coelomic cavity + exocoelomic cavity + + + "paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]." [GO:0061205, http://en.wikipedia.org/wiki/Paramesonephric_duct, http://www.usm.maine.edu/bio/courses/bio205/bio205_26_sex.html] + Müllerian duct + Muellerian duct + ductus paramesonephricus + paramesonephric duct + UBERON:0003890 + UBERON:Mullerian duct + Mullerian duct + + + UBERON:stroma + stromal connective tissue + UBERON:0003891 + stroma + "Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma." [] + + + "A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP]." [http://en.wikipedia.org/wiki/Capsule_(anatomy)] + UBERON:0003893 + UBERON:capsule + capsule + + + retinal neural layer + neural retinal epithelium + "The part of the retina that contains neurons and photoreceptor cells[GO]." [GO:0003407] + UBERON:0003902 + neural layer of retina + neuroretina + UBERON:retinal neural layer + stratum nervosum (retina) + neural retina + + + sinusoidal capillary + sinusoidal blood vessel endothelium + "small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]." [http://en.wikipedia.org/wiki/Sinusoid_(blood_vessel)] + UBERON:0003909 + endothelium of irregular blood filled space + sinusoidal blood vessel + UBERON:sinusoid + sinusoid + sinusoidal endothelium + + + UBERON:tooth-like structure + UBERON:0003913 + tooth-like structure + tooth-like organ + "hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food." [http://orcid.org/0000-0002-6601-2165] + + + epithelial or endothelial tube + UBERON:epithelial tube + UBERON:0003914 + epithelial tube + "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." [GO:0060562, http://www.ncbi.nlm.nih.gov/pubmed/12526790] + + + endothelial tube + "Any endothelium that has the quality of being cylindrical [Automatically generated definition]." [OBOL:automatic] + UBERON:endothelial tube + UBERON:0003915 + + + fat body + UBERON:fat pad + fat pad + "A mass of closely packed fat cells (adipose tissue) surrounded by fibrous tissue septa[TMD]." [BTO:0000444, GO:0060613, http://medical-dictionary.thefreedictionary.com/fat+pad] + UBERON:0003916 + + + UBERON:kidney mesenchyme + mesenchyme of kidney + kidney mesenchyme + "Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]." [GO:0072074] + UBERON:0003918 + + + "A blood vessel that carries blood from the capillaries toward the heart" [http://www.thefreedictionary.com/venous+blood+vessel] + UBERON:venous blood vessel + venous tree organ segment + segment of venous tree organ + UBERON:0003920 + venous blood vessel + + + photoreceptor outer segment layer + retina photoreceptor layer outer segment + UBERON:photoreceptor outer segment layer + UBERON:0003926 + + + "A duct that is part of a digestive system [Automatically generated definition]." [OBOL:automatic] + gastrointestinal system duct + digestive system duct + duct of gastrointestinal system + UBERON:digestive system duct + duct of digestive system + UBERON:0003928 + + + gastrodermis + alimentary tract epithelium + "An epithelium that lines the lumen of the digestive tract." [UBERON:cjm] + gut epithelium + UBERON:digestive tract epithelium + digestive tract epithelium + gut epithelial tissue + epithelial tissue of gut + digestive tract epithelial tissue + epithelial tissue of digestive tract + epithelium of gut + UBERON:0003929 + epithelium of digestive tract + + + cartilage of cranium + cranial cartilage + UBERON:cranial cartilage + cranium cartilage + "A cartilage element that is part of the cranial skeleton." [https://orcid.org/0000-0002-6601-2165, ZFA:0001458] + UBERON:0003933 + + + reproductive system gland + gland of genitalia + genitalia gland + reproductive gland + "Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction." [MP:0000653] + sex gland + UBERON:sex gland + gland of reproductive system + UBERON:0003937 + + + "The neural tissue involved in the transmission of motor signals" [MP:0001051] + UBERON:somatic motor system + somatic motor system + UBERON:0003945 + + + labyrinthine layer + labyrinthine layer of placenta + "The placental layers where embryonic blood vessels are surrounded by trophoblast cells and maternal blood" [MP:0001716] + UBERON:placenta labyrinth + placenta labyrinth + placental labyrinth + UBERON:0003946 + + + "The brain ventricles or their associated choroid plexuses" [MP:0002200] + brain ventricle/choroid plexus + UBERON:0003947 + UBERON:brain ventricle/choroid plexus + + + aqueous drainage system + "The structures associated with drainage of the aqueous humor from the eye, that include the trabecular meshwork, Schlemm's canal, the uveoscleral network, and the aqueous veins" [MP:0005198] + UBERON:0003956 + UBERON:aqueous drainage system + + + UBERON:0003978 + anatomical valve + UBERON:valve + valve + + + "A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP]." [http://en.wikipedia.org/wiki/Conus_arteriosus, MP:0009464] + UBERON:0003983 + UBERON:conus arteriosus + conus arteriosus + + + UBERON:Hassall's corpuscle + thymic corpuscle + capsule of Hassal's corpuscle + Hassall's corpuscle + "The small spherical bodies of epithelial cells found in the medulla of the thymus, that are arranged in a concentric pattern around clusters of degenerating lymphocytes, eosinophils and macrophages" [MP:0009539] + UBERON:0003987 + + + spinal cord motor column + "The subclasses of motor neurons which are organized into longitudinally oriented columns that occupy distinct and, in some cases, discontinuous domains along the rostrocaudal axis of the spinal cord; motor neurons within a single column send their axons to a common peripheral target" [MP:0009685] + UBERON:0003990 + UBERON:spinal cord motor column + + + olfactory bulb layer + "." [MP:0009946] + cytoarchitectural part of olfactory bulb + UBERON:0004001 + UBERON:olfactory bulb layer + + + lobular parts of the cerebellar cortex + UBERON:0004004 + "one of the the ten gyri of the cerebellar cortex" [MP:0009964] + UBERON:cerebellum lobule + cerebellum lobule + + + UBERON:0004013 + egg cylinder + UBERON:egg cylinder + "The transient cup-like structure of the epiblast that consists of a single layer of embryonic cells" [MP:0003085] + + + mesenchyma dermatomiale + UBERON:dermatome + cutis plate + dermatome + dermatomal mesenchyme + "A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells." [AEO:0001017, AEO:JB] + epimere mesoderm + UBERON:0004016 + + + periocular mesenchyme + periocular mesenchyme + UBERON:0004017 + "The mesenchymal cells that give rise to the corneal endothelium, corneal stroma, sclera, iris stroma, ciliary muscle, ciliary stroma, and trabecular meshwork of the eye[MP]." [http://www.ncbi.nlm.nih.gov/pubmed/3709965, MP:0004054] + UBERON:periocular mesenchyme + + + spongiotrophoblast layer of placenta + UBERON:spongiotrophoblast layer + UBERON:0004021 + "The structure of the outer structural layer of the rodent placenta[MP]." [http://www.ncbi.nlm.nih.gov/pubmed/19829370, MP:0004255] + spongiotrophoblast layer + + + UBERON:0004023 + "The transient proliferative population of neurons that expands exponentially during late prenatal development; it is a continuous germinal zone distinct from the ventricular zone that surrounds the brain ventricles[MP]." [MP:0004274] + embryonic subventricular zone + embryonic/fetal subventricular zone + fetal subventricular zone + ganglionic eminence + subependymal layer + UBERON:ganglionic eminence + + + medial ganglionic eminence + UBERON:medial ganglionic eminence + "A distinct elevation of a transient proliferating cell mass of the fetal subventricular zone; this mass contributes most of its cells to the neocortex; however, hippocampal neurons, thalamus, septum and olfactory bulb neurons are also partly derived from the MGE." [MP:0004276] + UBERON:0004024 + + + UBERON:lateral ganglionic eminence + "A distinct elevation of a transient proliferating cell mass of the fetal subventricular zone; this mass contributes most of its cells to the striatum; however, neocortex, thalamus, septum and olfactory bulb neurons are also partly derived from the LGE" [MP:0004277] + lateral ganglionic eminence + UBERON:0004025 + + + chorionic plate + UBERON:chorionic plate + "hat portion of the chorionic wall in the region of its uterine attachment, which gives rise to chorionic villi; it consists of the mesoderm that lines the chorionic vesicle and, on the maternal side, of the trophoblast that lines the intervillous spaces; in the last half of gestation, the mesodermal connective tissue is largely replaced by fibrinoid material, and the amnionic membrane is adherent to the fetal side of the plate." [http://www.medilexicon.com/medicaldictionary.php?t=69523, MP:0004560] + UBERON:0004027 + + + scleral sinus + "The vascular structure encircling the anterior chamber of the eye, through which the aqueous humor is returned to the blood circulation" [http://en.wikipedia.org/wiki/Schlemm's_canal, MP:0005204] + UBERON:canal of Schlemm + sinus venosus of sclera + Schlemm's canal + sinus venosus sclerae + UBERON:0004029 + canal of Schlemm + scleral venous sinus + + + UBERON:0004043 + "The spherical enlargement at the base of each semicircular canal where they connect with the utricle, containing the crista ampullaris which detects movement of the fluid within the canals" [http://en.wikipedia.org/wiki/Osseous_ampullae, MP:0008488] + semicircular duct ampulla + ampullae osseae + membraneous ampulla of the semicircular duct + semicircular canal ampulla + UBERON:semicircular canal ampulla + + + UBERON:0004044 + UBERON:anterior visceral endoderm + AVE + anterior visceral endoderm + "The extraembryonic tissue that is responsible for the proper orientation of the anterior-posterior axis of the embryo and for appropriate patterning of adjacent embryonic tissue" [MP:0008533] + + + anterior definitive endoderm + UBERON:anterior definitive endoderm + "The mesendoderm which first migrates from the node and which gives rise to the gut" [MP:0008926] + UBERON:0004046 + + + future brain marginal layer + neural tube intermediate zone + neural tube mantle layer + "The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer." [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009690] + UBERON:0004061 + UBERON:neural tube mantle layer + + + "The region of a cerebellar lobule that resides in the central section of the cerebellum between the two hemispheres; " [MP:0009957] + UBERON:0004070 + UBERON:cerebellum vermis lobule + cerebellum vermis lobule + + + vermic lobule VII + folium-tuber vermis (VII) + cerebellum vermis lobule VII + "The folium vermis is a short, narrow, concealed band at the posterior extremity of the vermis, consisting apparently of a single folium, but in reality marked on its upper and under surfaces by secondary fissures. Laterally, it expands in either hemisphere into a considerable lobule, the superior semilunar lobule (lobulus semilunaris superior; postero-superior lobules), which occupies the posterior third of the upper surface of the hemisphere, and is bounded below by the horizontal sulcus. The superior semilunar lobules and the folium vermis form the lobus semilunaris." [http://en.wikipedia.org/wiki/Folium_(vermis), MP:0009995] + folium of vermis of cerebellum + UBERON:0004081 + UBERON:cerebellum vermis lobule VII + folium of cerebellum + lobule VII of cerebellum vermis + neuraxis folium + + + UBERON:brain ventricle + cerebral ventricle + region of ventricular system of brain + "one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid" [http://purl.obolibrary.org/obo/uberon/tracker/300] + brain ventricles + brain ventricle + UBERON:0004086 + + + lower face + "The middle of the face including the nose and its associated bony structures[MW]." [HP:0000309, http://www.merriam-webster.com/medical/midface] + midface/lower face + snout + UBERON:0004089 + midface + UBERON:midface + + + kidney collecting duct system + renal collecting system + tubulus renalis colligens + UBERON:renal collecting system + UBERON:0004100 + collecting duct system + "The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. It participates in electrolyte and fluid balance through reabsorption and excretion, processes regulated by the hormones aldosterone and antidiuretic hormone." [HP:0004742, http://en.wikipedia.org/wiki/Collecting_duct_system] + + + opening + ostia + anatomical conduit + "Any tube, opening or passage that connects two distinct anatomical spaces." [UBERON:cjm] + UBERON:0004111 + UBERON:anatomical conduit + ostium + + + tympanum + cavitas tympani + UBERON:0004114 + tympanic cavity + cavity of middle ear + middle ear cavity + cavitas tympanica + anatomical cavity of middle ear + middle-ear cavity + UBERON:tympanic cavity + "small cavity surrounding the bones of the middle ear." [http://en.wikipedia.org/wiki/Tympanic_cavity] + + + UBERON:pharyngeal pouch + pharyngeal pouches + "An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches." [http://orcid.org/0000-0002-6601-2165, http://www.ncbi.nlm.nih.gov/pubmed/23020903, ZFA:0001106] + branchial pouch + visceral pouches + pharyngeal pouch + visceral pouch + UBERON:0004117 + + + "An anatomical structure that develops (entirely or partially) from the endoderm." [https://orcid.org/0000-0002-6601-2165] + UBERON:endoderm-derived structure + endoderm-derived structure + UBERON:0004119 + + + "An anatomical structure that develops (entirely or partially) from the mesoderm." [https://orcid.org/0000-0002-6601-2165] + mesoderm-derived structure + UBERON:0004120 + UBERON:mesoderm-derived structure + + + ectoderm-derived structure + UBERON:ectoderm-derived structure + UBERON:0004121 + "An anatomical structure that develops (entirely or partially) from the ectoderm." [https://orcid.org/0000-0002-6601-2165] + + + "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction." [VHOG:0000286] + UG tract + genitourinary tract + urogenital tract + genitourinary system + urogenital system + Urogenitalsystem + GU tract + UBERON:0004122 + UBERON:genitourinary system + + + layer of myocardium + UBERON:0004123 + myocardium layer + "Any of the layers of the myocardium. Example: compact layer, trabecular layer." [UBERON:cjm] + myocardial layer + UBERON:myocardial layer + + + myocardial compact layer + compact subepicardial layer + heart compact layer + subepicardium layer + myocardial compact layer + "outer dense layer of the myocardium uniting the epicardium and myocardium[MP]." [MP:0004056] + compact subepicardial myocardium + UBERON:myocardial compact layer + subepicardial layer + UBERON:0004125 + myocardium compact layer + subepicardium + + + UBERON:optic vesicle + ocular vesicle + optic vesicle + "The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]." [GO:0003404, http://en.wikipedia.org/wiki/Optic_vesicles] + evagination + UBERON:0004128 + eye vesicle + + + growth plate cartilage + growth plate + UBERON:growth plate cartilage + "cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow." [GO:0003417] + UBERON:0004129 + + + "A cortical cell layer of the cerebellum. Examples: the granular (inner+outer) layer, molecular layer, Purkinje cell layer, and the ventricular layer of the embryo." [ncithesaurus:Cortical_Cell_Layer_of_the_Cerebellum, UBERON:cjm] + layer of cerebellar cortex + cerebellar layer + UBERON:cerebellar layer + cell layer of cerebellar cortex + layer of cerebellum + UBERON:0004130 + gray matter layer of cerebellum + + + proximal kidney tubule + renal proximal tubule + kidney proximal tubule + UBERON:0004134 + proximal tubule + UBERON:proximal tubule + "In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]." [GO:0072014] + + + kidney distal tubule + UBERON:distal tubule + "The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments" [GO:0072017] + UBERON:0004135 + distal tubule + renal distal tubule + + + UBERON:0004142 + "The outflow tract septum is a partition in the outflow tract" [GO:0003148] + UBERON:outflow tract septum + outflow tract septum + + + heart outflow tract + cardiac outflow tract + arterial (outflow) pole + UBERON:0004145 + outflow tract + "The outflow tract is the portion of the heart through which blood flows into the arteries" [GO:0003151] + UBERON:outflow tract + + + UBERON:cardiac vein + vein of heart + cardiac vein + "Vein of heart that drains the myocardium" [UBERON:cjm] + cardiac vein + coronary vein + coronary vein + heart vein + UBERON:0004148 + + + "A cardiac chamber surrounds an enclosed cavity within the heart" [GO:0003205] + chamber of heart + UBERON:0004151 + cardiac chamber + UBERON:cardiac chamber + heart chamber + + + interatrial septum primum + UBERON:atrial septum primum + atrial septum primum + "In the developing heart, the cavity of the primitive atrium becomes subdivided into right and left chambers by a septum, the septum primum, which grows downward into the cavity. The increasingly smaller gap below it (before it fuses with the endocardial cushion) is known as the ostium primum. The septum primum eventually fuses with the endocardial cushion, closing the ostium primum off completely. Meanwhile, perforations appear in the superior part of the septum primum, forming the ostium secundum. This will eventually form part of the fossa ovalis." [GO:0003284] + UBERON:0004154 + atrial septum primum + Septum primum + + + interatrial septum secundum + Septum secundum + UBERON:0004155 + atrial septum secundum + "." [GO:0003285, http://en.wikipedia.org/wiki/Septum_secondum] + UBERON:atrial septum secundum + + + UBERON:0004161 + "A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]." [http://en.wikipedia.org/wiki/Septum_transversum, VHOG:0000019] + septum transversum + UBERON:septum transversum + transverse septum + + + hematopoeitic organ + organ of haemopoietic system + hemopoietic organ + haematological system organ + hematopoietic system organ + haemopoietic system organ + organa haemopoietica organ + UBERON:0004177 + organ of hematopoietic system + UBERON:hemopoietic organ + "Organ that is part of the hematopoietic system." [GOC:Obol] + organ of organa haemopoietica + organ of haematological system + + + lobe of mammary gland adipose tissue + "The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts" [GO:0060611] + lactiferous gland fatty tissue + lobe of breast fatty tissue + fatty tissue of lobe of breast + fat tissue of mammary gland + fat tissue of lobe of breast + lobe of breast fat tissue + fat tissue of lobe of mammary gland + mammary gland fat tissue + lactiferous gland adipose tissue + fatty tissue of lactiferous gland + mammary gland fat + mammary gland fatty tissue + lobe of breast adipose tissue + lobe of mammary gland fat tissue + fatty tissue of mammary gland + adipose tissue of lactiferous gland + adipose tissue of mammary gland + lobe of mammary gland fatty tissue + fatty tissue of lobe of mammary gland + mammary gland adipose tissue + fat tissue of lactiferous gland + lactiferous gland fat tissue + UBERON:0004180 + UBERON:mammary gland fat + + + CSB + UBERON:comma-shaped body + UBERON:0004198 + "The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron" [GO:0072049] + comma-shaped body + + + S-shaped body + "The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron" [GO:0072050] + SSB + stage II nephron + UBERON:S-shaped body + UBERON:0004199 + + + inner medullary collecting duct + "The inner medullary collecting duct is the portion of the collecting duct that lies in the renal inner medulla" [GO:0072061] + kidney inner medulla collecting duct + UBERON:0004205 + UBERON:inner medullary collecting duct + papillary collecting duct + inner renal medulla collecting duct + + + UBERON:nephrogenic mesenchyme + mesenchyme of nephron + nephrogenic mesenchyme + UBERON:0004208 + nephron mesenchyme + "Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron" [GO:0072076] + + + UBERON:renal vesicle + renal vesicle + "The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells. " [GO:0072077] + stage I nephron + UBERON:0004209 + + + epithelial tissue of nephron + UBERON:0004211 + epithelium of nephron + UBERON:nephron epithelium + nephron epithelial tissue + "The nephron epithelium is a tissue that covers the surface of a nephron" [GO:0072088] + nephron epithelium + + + apparatus respiratorius non-striated muscle + respiratory system smooth muscle tissue + involuntary muscle of apparatus respiratorius + UBERON:0004225 + apparatus respiratorius smooth muscle + non-striated muscle of apparatus respiratorius + "A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] + UBERON:respiratory system smooth muscle + airway smooth muscle cell + involuntary muscle of respiratory system + apparatus respiratorius smooth muscle tissue + respiratory system involuntary muscle + respiratory system smooth muscle + smooth muscle of respiratory system + smooth muscle tissue of apparatus respiratorius + smooth muscle tissue of respiratory system + respiratory smooth muscle + respiratory system non-striated muscle + smooth muscle of apparatus respiratorius + airway smooth muscle + apparatus respiratorius involuntary muscle + non-striated muscle of respiratory system + + + lower respiratory tract smooth muscle + involuntary muscle of lower respiratory tract + UBERON:0004233 + non-striated muscle of lower respiratory tract + smooth muscle tissue of lower respiratory tract + "A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]." [OBOL:automatic] + smooth muscle of lower respiratory tract + UBERON:lower respiratory tract smooth muscle + lower respiratory tract smooth muscle tissue + lower respiratory tract non-striated muscle + lower respiratory tract involuntary muscle + + + non-striated muscle of blood vessel + blood vessel involuntary muscle + "smooth muscle found within, and composing the majority of the wall of blood vessels." [http://en.wikipedia.org/wiki/Vascular_smooth_muscle] + UBERON:blood vessel smooth muscle + vascular smooth muscle tissue + UBERON:0004237 + involuntary muscle of blood vessel + blood vessel smooth muscle + smooth muscle tissue of blood vessel + smooth muscle of blood vessel + blood vessel smooth muscle tissue + vascular smooth muscle + blood vessel non-striated muscle + + + bronchial trunk smooth muscle + bronchial trunk non-striated muscle + bronchus involuntary muscle + non-striated muscle of bronchi + smooth muscle tissue of bronchial trunk + smooth muscle of bronchi + bronchi smooth muscle tissue + bronchial trunk smooth muscle tissue + bronchus smooth muscle + UBERON:bronchus smooth muscle + involuntary muscle of bronchi + bronchi smooth muscle + bronchus non-striated muscle + bronchial smooth muscle + bronchi non-striated muscle + smooth muscle tissue of bronchus + smooth muscle of bronchus + bronchi involuntary muscle + UBERON:0004242 + bronchial trunk involuntary muscle + non-striated muscle of bronchus + non-striated muscle of bronchial trunk + smooth muscle of bronchial trunk + smooth muscle tissue of bronchi + "A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition]." [OBOL:automatic] + bronchus smooth muscle tissue + involuntary muscle of bronchus + involuntary muscle of bronchial trunk + + + back bone + bone of back + "A bone that is part of the dorsal region of an animal." [http://orcid.org/0000-0002-6601-2165] + dorsal region bone + UBERON:0004247 + bone of dorsum + UBERON:bone of dorsum + + + upper arm bone + "A bone that is part of a forelimb stylopod [Automatically generated definition]." [https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376, OBOL:automatic] + UBERON:upper arm bone + UBERON:0004250 + + + hindlimb zeugopod bone + zeugopod of inferior member bone + bone of inferior member zeugopod + bone organ of middle limb segment of hindlimb + bone organ of middle limb segment of inferior member + middle limb segment of inferior member bone + zeugopod of hindlimb bone + bone of hind limb middle limb segment + zeugopod of lower extremity bone organ + bone organ of lower extremity zeugopod + bone organ of zeugopod of lower extremity + hind limb middle limb segment bone + bone of middle limb segment of hindlimb + zeugopod of hind limb bone organ + middle limb segment of hind limb bone organ + middle limb segment of hindlimb bone organ + intermediate segment of free lower limb bone + bone organ of lower leg + zeugopod of leg bone + bone organ of intermediate segment of free lower limb + bone of zeugopod of hindlimb + bone of middle limb segment of hind limb + bone of middle limb segment of inferior member + bone of zeugopod of lower extremity + hindlimb zeugopod bone organ + hind limb zeugopod bone + inferior member middle limb segment bone organ + bone organ of lower extremity middle limb segment + zeugopod of hind limb bone + bone of hindlimb middle limb segment + bone of intermediate segment of free lower limb + bone organ of zeugopod of hind limb + bone organ of zeugopod of inferior member + bone of lower extremity middle limb segment + lower extremity zeugopod bone organ + lower leg bone + bone organ of inferior member zeugopod + zeugopod of inferior member bone organ + bone of zeugopod of inferior member + bone organ of hind limb middle limb segment + bone organ of inferior member middle limb segment + UBERON:0004251 + lower extremity zeugopod bone + intermediate segment of free lower limb bone organ + zeugopod of leg bone organ + bone organ of zeugopod of hindlimb + bone of inferior member middle limb segment + bone organ of middle limb segment of hind limb + bone of hindlimb zeugopod + hind limb zeugopod bone organ + inferior member zeugopod bone organ + lower extremity middle limb segment bone + bone organ of hindlimb middle limb segment + middle limb segment of lower extremity bone organ + bone organ of hind limb zeugopod + bone organ of zeugopod of leg + inferior member zeugopod bone + bone of lower extremity zeugopod + zeugopod of lower extremity bone + middle limb segment of lower extremity bone + bone of zeugopod of leg + bone of hind limb zeugopod + middle limb segment of hindlimb bone + middle limb segment of hind limb bone + bone of lower leg + "A bone that is part of a lower leg [Automatically generated definition]." [OBOL:automatic] + UBERON:hindlimb zeugopod bone + bone organ of middle limb segment of lower extremity + hindlimb middle limb segment bone organ + hindlimb zeugopod bone + inferior member middle limb segment bone + middle limb segment of inferior member bone organ + bone of zeugopod of hind limb + lower extremity middle limb segment bone organ + zeugopod of hindlimb bone organ + hindlimb middle limb segment bone + bone organ of hindlimb zeugopod + bone of middle limb segment of lower extremity + hind limb middle limb segment bone organ + + + UBERON:forelimb stylopod muscle + muscle of arm + UBERON:0004255 + forelimb stylopod muscle + skeletal muscle of upper arm + "Any muscle organ that is part of a forelimb stylopod (upper arm)[Automatically generated definition]." [OBOL:automatic] + upper arm muscle + muscle of upper arm + + + calf muscle + muscle of leg + UBERON:hindlimb zeugopod muscle + hindlimb zeugopod muscle + lower leg muscle + UBERON:0004256 + "Any muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition]." [OBOL:automatic] + + + UBERON:lower leg blood vessel + hindlimb zeugopod blood vessel + "A blood vessel that is part of a lower leg [Automatically generated definition]." [OBOL:automatic] + lower leg blood vessel + UBERON:0004261 + + + skin of zeugopod of lower extremity + middle limb segment of hind limb skin + middle limb segment of hindlimb skin + skin of middle limb segment of hindlimb + skin of hind limb zeugopod + zeugopod of hind limb skin + skin of hindlimb middle limb segment + middle limb segment of lower extremity skin + zeugopod of lower extremity skin + skin of lower extremity zeugopod + skin of hindlimb zeugopod + hind limb zeugopod skin + skin of hind limb middle limb segment + skin of inferior member middle limb segment + inferior member zeugopod skin + skin of middle limb segment of hind limb + skin of middle limb segment of inferior member + zeugopod of leg skin + skin of zeugopod of hindlimb + intermediate segment of free lower limb skin + hind limb middle limb segment skin + lower extremity middle limb segment skin + "A zone of skin that is part of a lower leg [Automatically generated definition]." [OBOL:automatic] + zeugopod of hindlimb skin + skin of zeugopod of hind limb + skin of zeugopod of inferior member + middle limb segment of inferior member skin + skin of inferior member zeugopod + zeugopod of inferior member skin + skin of lower extremity middle limb segment + lower extremity zeugopod skin + skin of middle limb segment of lower extremity + hindlimb middle limb segment skin + skin of lower leg + UBERON:0004264 + skin of intermediate segment of free lower limb + skin of zeugopod of leg + UBERON:lower leg skin + lower leg skin + inferior member middle limb segment skin + hindlimb zeugopod skin + + + UBERON:upper leg connective tissue + upper leg connective tissue + UBERON:0004266 + "A portion of connective tissue that is part of a hindlimb stylopod [Automatically generated definition]." [OBOL:automatic] + + + lower leg connective tissue + UBERON:lower leg connective tissue + UBERON:0004270 + "A portion of connective tissue that is part of a lower leg [Automatically generated definition]." [OBOL:automatic] + + + set of all bones + "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body." [VSAO:0000026] + UBERON:0004288 + skeleton + UBERON:skeleton + set of bones of body + + + "The bilaminar epithelium formed from the myotome and dermatome." [AEO:0000214] + UBERON:dermomyotome + dermamyotome + dermomyotomes + dermomyotome + UBERON:0004290 + + + terminal phalanx + phalanx distalis + phalanx distalis + ungual phalanx + distal phalanx + UBERON:0004300 + UBERON:distal phalanx + "Distal-most phalanx within a digit." [UBERON:cjm] + + + phalanx 1 + UBERON:proximal phalanx + proximal phalanx + "Proximal-most phalanx within a digit." [UBERON:cjm] + phalanx I + UBERON:0004302 + proximal-most phalanx + + + cranial vault + calva + vault of skull + "Upper part of skull, consisting of parietals, frontals, post-parietals, and in some species the squamosal and a portion of the alisphenoid" [http://en.wikipedia.org/wiki/Calvaria_(skull), http://www.ncbi.nlm.nih.gov/pubmed/11523816, MP:0000076] + UBERON:0004339 + skullcap + calvarium + skull vault + UBERON:vault of skull + calvaria + + + allantois + "A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG]." [http://en.wikipedia.org/wiki/Allantois, VHOG:0000738] + UBERON:allantois + UBERON:0004340 + allantoic bud + + + "The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]" [http://en.wikipedia.org/wiki/Primitive_streak, MP:0002231] + UBERON:primitive streak + primitive streak - blastopore - germ ring + primitive streak + UBERON:0004341 + + + UBERON:0004345 + UBERON:trophectoderm + trophectoderm + "outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition" [MP:0005028] + + + UBERON:0004347 + UBERON:limb bud + gemmae membrorum + limb buds + limbbud + limb bud + "An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]." [http://en.wikipedia.org/wiki/Limb_bud, https://orcid.org/0000-0002-6601-2165, ISBN:9780878932504, MP:0005650] + + + apical ectodermal ridge + UBERON:0004356 + "multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. " [http://en.wikipedia.org/wiki/Apical_ectodermal_ridge, MP:0001676] + crista ectodermalis apicalis + apical epidermal ridge + AER + UBERON:apical ectodermal ridge + + + paired limb/fin bud + "An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]." [https://orcid.org/0000-0002-6601-2165, ISBN:9780878932504, MP:0005650] + UBERON:0004357 + paired appendage bud + limb - fin bud + paired limb/fin bud + UBERON:paired limb/fin bud + + + pharyngeal arch 1 + arcus pharyngeus primus + 1st pharyngeal arch + first pharyngeal arch + 1st visceral arch + branchial arch 1 + first branchial arch + 1st arch + UBERON:pharyngeal arch 1 + visceral arch 1 + "The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries" [] + first visceral arch + mandibular arch + UBERON:0004362 + + + pharyngeal arch arteries + arteriae arcuum pharyngeorum + pharyngeal arch artery + aortic arch + branchial aortic arches + PAA + pharyngeal arch artery + aortic arches + pharyngeal arch artery + a. arcuum pharyngeorum + UBERON:pharyngeal arch artery + UBERON:0004363 + embryonic aortic arch artery + branchial arch artery + aortic arch artery + "One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]" [MP:0002672] + + + "thickened trophoblast of the blastocyst in rodents that becomes the fetal portion of the placenta" [http://www.ncbi.nlm.nih.gov/pubmed/19829370, MP:0001717] + epamniotic cone + placenta - ectoplacental cone + UBERON:0004364 + ectoplacental cone + UBERON:ectoplacental cone + + + UBERON:0004366 + UBERON:extraembryonic ectoderm + extraembryonic ectoderm + "layer of the endoderm of the extraembryonic tissue." [MP:0002583] + + + UBERON:0004369 + Reichert's membrane + UBERON:Reichert's membrane + "An nonvascular extraembryonic basement membrane that forms on the inner surface of the trophectoderm during placenta morphogenesis and is secreted by the distal parietal endoderm; required for the maternofetal exchange of nutrients and is important for the postgastrulation development[MP]. a thick multilayered basement membrane between the parietal endoderm cells and the trophoblast cells" [http://dx.doi.org/10.1007/BF00184752, MP:0003954] + + + bone of appendage + bone of free segment of appendicular skeleton + appendage bone + "A bone that is part of an appendage [Automatically generated definition]." [OBOL:automatic] + UBERON:0004375 + bone of free limb or fin + UBERON:bone of free limb or fin + + + UBERON:distal metaphysis + UBERON:0004377 + "A metaphysis that is in the distal side of a diaphysis." [OBOL:automatic] + distal diaphyseal end of long bone + distal metaphysis + + + UBERON:distal epiphysis + "An epiphysis that is on the distal side of the bone." [UBERON:cjm] + distal epiphysis + UBERON:0004379 + distal end of long bone + + + "An epiphysis that is on the proximal side of the bone." [UBERON:cjm] + proximal end of long bone + UBERON:0004380 + UBERON:proximal epiphysis + proximal epiphysis + + + skeleton of limb + "The collection of all skeletal elements in an individual limb." [https://orcid.org/0000-0002-6601-2165] + set of bones of limb + limb skeleton + UBERON:skeleton of limb + UBERON:0004381 + free limb skeleton + + + UBERON:epiphysis of tibia + tibial epiphysis + "An epiphysis that is part of a tibia [Automatically generated definition]." [OBOL:automatic] + epiphysis of tibia + UBERON:0004383 + + + "An epiphysis that is part of a femur [Automatically generated definition]." [OBOL:automatic] + UBERON:epiphysis of femur + epiphysis of femur + UBERON:0004384 + femoral epiphysis + + + radial epiphysis + epiphysis of radius + UBERON:0004385 + UBERON:epiphysis of radius + "An epiphysis that is part of a radius [Automatically generated definition]." [OBOL:automatic] + + + "An epiphysis that is part of an ulna [Automatically generated definition]." [OBOL:automatic] + epiphysis of ulna + UBERON:epiphysis of ulna + UBERON:0004386 + ulnar epiphysis + + + distal head of femur + distal epiphysis of femur + UBERON:0004406 + UBERON:distal epiphysis of femur + distal femoral epiphysis + "A distal epiphysis that is part of a femur [Automatically generated definition]." [OBOL:automatic] + + + UBERON:distal epiphysis of radius + "A distal epiphysis that is part of a radius [Automatically generated definition]." [OBOL:automatic] + UBERON:0004407 + lower end of radius + distal end of radius + distal epiphysis of radius + + + distal epiphysis of ulna + UBERON:0004408 + distal end of ulna + lower end of ulna + UBERON:distal epiphysis of ulna + "A distal epiphysis that is part of a ulna [Automatically generated definition]." [OBOL:automatic] + + + UBERON:proximal epiphysis of femur + capital femoral epiphysis + UBERON:0004412 + "A proximal epiphysis that is part of a femur [Automatically generated definition]." [OBOL:automatic] + proximal femoral epiphysis + proximal epiphysis of femur + + + "A proximal epiphysis that is part of a radius [Automatically generated definition]." [OBOL:automatic] + upper end of radius + UBERON:proximal epiphysis of radius + proximal epiphysis of radius + proximal radial epiphysis + proximal end of radius + UBERON:0004413 + + + UBERON:0004451 + trunk or cervical vertebra + UBERON:trunk or cervical vertebra + presacral vertebra + "A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra." [UBERONREF:0000006] + + + articulatio radiocarpea + wrist + fore mesopodium + fore basipodium + manus mesopodium + regio carpalis + "A mesopodium that is part of a manus. Includes as parts the carpal skeleton and associated tissues[cjm]. The anatomical region surrounding the carpus including the distal parts of the bones of the forearm and the proximal parts of the metacarpus or five metacarpal bones and the series of joints between these bones, thus referred to as wrist joints. This region also includes the carpal tunnel, the anatomical snuff box, the flexor retinaculum, and the extensor retinaculum[WP,unvetted]" [http://en.wikipedia.org/wiki/Wrist, https://orcid.org/0000-0002-6601-2165] + carpal segment + carpus + carpal limb segment + UBERON:0004452 + hand mesopodium + wrist region + carpal region + UBERON:carpal region + + + UBERON:0004454 + tarsal region + hock + ankle + hind basipodium + hind mesopodium + ankle region + articulatio talocruralis + "mesopodial segment of the pes, including the tarsal skeleton and associated tissues." [http://en.wikipedia.org/wiki/Ankle, https://orcid.org/0000-0002-6601-2165] + tarsal limb segment + UBERON:tarsal region + + + cavity lining + UBERON:0004457 + UBERON:cavity lining + + + body cavity or lining + UBERON:0004458 + UBERON:body cavity or lining + + + UBERON:cardiac muscle tissue of myocardium + "A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]." [OBOL:automatic] + UBERON:0004493 + cardiac muscle tissue of myocardium + + + UBERON:anatomical projection + anatomical protrusion + "A projection or outgrowth of tissue from a larger body or organ." [http://en.wikipedia.org/wiki/Process_(anatomy)] + UBERON:0004529 + protrusion + anatomical projection + projection + + + UBERON:bony projection + "Anatomical projection that is composed of bone tissue." [VSAO:wd] + projection of bone + UBERON:0004530 + bony projection + bone process + + + "Anatomical system that has as its parts the heart and blood vessels." [BTO:0000088] + UBERON:cardiovascular system + cardiovascular system + CV system + Herz und Gefaesssystem + UBERON:0004535 + + + "A vascular network consisting of blood vessels." [https://orcid.org/0000-0002-6601-2165] + blood vessel system + blood vascular network + UBERON:blood vasculature + set of blood vessels + UBERON:0004537 + blood system + blood vasculature + blood vessels + + + UBERON:left kidney + UBERON:0004538 + left kidney + "A kidney that is part of a left side of organism [Automatically generated definition]." [OBOL:automatic] + + + right kidney + UBERON:0004539 + "A kidney that is part of a right side of organism [Automatically generated definition]." [OBOL:automatic] + UBERON:right kidney + + + UBERON:0004573 + "An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart." [http://en.wikipedia.org/wiki/Artery#Systemic_arteries, UBERON:cjm] + systemic artery + systemic arterial subtree + UBERON:systemic artery + + + UBERON:lumbar vertebra 1 + first lumbar vertebra + L1 vertebra + lumbar vertebra 1 + UBERON:0004617 + + + UBERON:lumbar vertebra 3 + UBERON:0004619 + L3 vertebra + third lumbar vertebra + lumbar vertebra 3 + + + UBERON:lumbar vertebra 4 + UBERON:0004620 + L4 vertebra + lumbar vertebra 4 + fourth lumbar vertebra + + + fifth lumbar vertebra + UBERON:lumbar vertebra 5 + L5 vertebra + UBERON:0004621 + lumbar vertebra 5 + + + UBERON:0004637 + periotic capsule + auditory capsule + "The capsule surrounding the inner ear mechanism." [http://www.biology-online.org/dictionary/Otic_capsule] + otic capsule element + UBERON:otic capsule + otic capsule + otic region + otic capsule + otic capsule endochondral element + periotic + + + UBERON:0004638 + "An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart" [https://orcid.org/0000-0002-6601-2165] + UBERON:blood vessel endothelium + blood vessel endothelium + + + wall of aorta + UBERON:aorta wall + aorta wall + UBERON:0004663 + Aortic wall + "An anatomical wall that is part of an aorta, enclosing the luminal space." [UBERON:cjm] + + + "The sensory system for the sense of balance." [NIFSTD:nlx_anat_090819] + vestibular system + UBERON:0004681 + vestibular organ system + UBERON:vestibular system + vestibular system + + + Harderian gland epithelium + UBERON:0004694 + harderian gland epithelium + "An epithelium that is part of a Harderian gland [Automatically generated definition]." [OBOL:automatic] + UBERON:Harderian gland epithelium + epithelium of harderian gland + + + pelvic/pectoral appendage + pectoral or pelvic appendage + limb/fin + UBERON:paired limb/fin + "An appendage that is part of a appendage girdle complex." [http://sourceforge.net/p/geneontology/ontology-requests/8818/, OBOL:automatic] + limb or fin + paired limb/fin + girdle-associated appendage + UBERON:0004708 + + + hindlimb/pelvic fin + UBERON:pelvic appendage + pelvic appendage + posterior paired appendage + posterior limb/fin + pelvic appendage + "Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues." [VSAO:0000150] + pelvic limb/fin + UBERON:0004709 + + + forelimb or pectoral fin + pectoral limb/fin + UBERON:pectoral appendage + "Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues." [VSAO:0000150-modified] + anterior paired appendage + anterior limb/fin + forelimb - pectoral fin + pectoral appendage + UBERON:0004710 + forelimb/pectoral fin + + + UBERON:jugular vein + jugular vein + UBERON:0004711 + vena jugularis + "The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava." [http://en.wikipedia.org/wiki/Jugular_vein] + jugular + + + UBERON:conceptus + "The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]." [BTO:0003834, http://en.wikipedia.org/wiki/Conceptus] + UBERON:0004716 + embryo plus adnexa + conceptus + + + vermis cerebelli [I-X] + vermal regions + cerebellum vermis + vermis of cerebellum [I-X] + UBERON:0004720 + cerebellar vermis + "A subregion of the cerebellar cortex, consisting of the most medial zone of the cerebellar cortex, stradding the midline. May be continuous with the lateral cerebellar hemispheres in some areas of the cerebellum, e.g., dorsally, or separated by deeper fissures in others (e.g., ventrally)" [NIFSTD:birnlex_1106] + vermis of cerebellum + vermal parts of the cerebellum + vermis cerebelli + UBERON:cerebellar vermis + vermis + + + "The crista ampullaris is the sensory organ of rotation located in the semicircular canal of the inner ear. The function of the crista ampullaris is to sense angular acceleration and deceleration." [http://en.wikipedia.org/wiki/Crista_ampullaris] + UBERON:0004721 + UBERON:crista ampullaris + cristae ampullares + ampullary crest + crista ampullaris + ampullary crest of semicircular duct + + + pyriform cortex + olfactory pallium + UBERON:piriform cortex + piriform area + piriform cortex + pyriform lobe + eupalaeocortex + "the subdivision of the laminated olfactory cortex with only three main layers that receive monosynaptic input from the olfactory bulb via the lateral olfactory tract; it is located bilaterally in the ventrolateral forebrain and is commonly divided into anterior and posterior regions" [MP:0010009\,PMID\:17714095] + area prepiriformis + palaeocortex II + cortex piriformis + regio praepiriformis + paleopallium + primary olfactory areas + UBERON:0004725 + primary olfactory cortex + piriform lobe + + + vestibulocochlear VIII nerve cochlear component + vestibulocochlear nerve cochlear component + auditory nerve + cochlear root of eighth cranial nerve + UBERON:0004727 + "A nerve in the head that carries signals from the cochlea of the inner ear to the brain. It is part of the vestibulocochlear nerve, the 8th cranial nerve which is found in higher vertebrates; the other portion of the 8th cranial nerve is the vestibular nerve which carries spatial orientation information from the semicircular canals. The cochlear nerve is a sensory nerve, one which conducts to the brain information about the environment, in this case acoustic energy impinging on the tympanic membrane. The cochlear nerve arises from within the cochlea and extends to the brainstem, where its fibers make contact with the cochlear nucleus, the next stage of neural processing in the auditory system[WP]." [ISBN:Wikipedia\:Cochlear_nerve] + cochlear root of acoustic nerve + nervus vestibulocochlearis + UBERON:cochlear nerve + cochlear nerve + + + neuromere + UBERON:0004731 + neural tube segment + UBERON:neuromere + neural tube metameric segment + "A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres)." [http://dx.doi.org/10.1016/j.tins.2013.06.004] + neuromeres + neuromere + neural metamere + neural segment + + + neuromere + UBERON:0004732 + segmental subdivision of nervous system + UBERON:segmental subdivision of nervous system + "Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres." [FBbt:00005140, http://orcid.org/0000-0002-6601-2165] + + + "The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified]." [VHOG:0001022] + dentale + UBERON:0004742 + os dentale + dentary bone + UBERON:dentary + dentaries + dentary + sur-angulaire + + + UBERON:0004755 + "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000015] + UBERON:skeletal tissue + skeletal tissue + + + dermal skeletal element + UBERON:0004756 + UBERON:dermal skeletal element + "dermis-derived entity that is made of skeletal tissue." [] + dermal element + + + UBERON:0004765 + "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles." [https://orcid.org/0000-0002-6601-2165] + UBERON:skeletal element + skeletal element + + + cranial bone + UBERON:0004766 + "A bone that is part of a cranium." [UBERON:automatic] + cranium bone + UBERON:cranial bone + + + UBERON:0004768 + "Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular" [https://orcid.org/0000-0002-6601-2165] + bone of lower jaw + lower jaw bone + UBERON:bone of lower jaw + + + UBERON:0004769 + UBERON:diaphysis + body of long bone + "Subdivision of long bone which forms the part of the bone between the two epiphyses, excluding the metaphyses[FMA,modified]." [FMA:24013, http://en.wikipedia.org/wiki/Diaphysis] + diaphysis + long bone diaphysis + shaft of long bone + + + mucosa of gut + digestive tract mucosa + gut mucuous membrane + "A mucosa that is part of a gastrointestinal system." [OBOL:automatic] + gut mucosa + UBERON:0004786 + UBERON:gastrointestinal system mucosa + gastrointestinal system mucosa + + + UBERON:blood vessel layer + blood vessel layer + UBERON:0004797 + "Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia." [UBERON:cjm] + + + airway epithelium + UBERON:0004802 + respiratory tract epithelium + "the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi" [MP:0010942\,ISBN\:0-683-40008-8\,MGI\:anna] + epithelial tissue of respiratory tract + respiratory tract epithelial tissue + respiratory epithelium + epithelium of respiratory tract + UBERON:respiratory tract epithelium + + + UBERON:0004807 + apparatus respiratorius epithelium + "An epithelium that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] + epithelium of apparatus respiratorius + UBERON:respiratory system epithelium + epithelial tissue of apparatus respiratorius + epithelial tissue of respiratory system + respiratory system epithelium + epithelium of respiratory system + apparatus respiratorius epithelial tissue + respiratory system epithelial tissue + + + UBERON:0004808 + epithelium of gastrointestinal system + gastrointestinal system epithelium + digestive system epithelial tissue + UBERON:gastrointestinal system epithelium + gastrointestinal system epithelial tissue + epithelium of digestive system + digestive system epithelium + "An epithelium that is part of a digestive system [Automatically generated definition]." [OBOL:automatic] + epithelial tissue of gastrointestinal system + epithelial tissue of digestive system + + + epithelium of salivary gland + UBERON:0004809 + epithelial tissue of salivary gland + UBERON:salivary gland epithelium + "An epithelium that is part of a salivary gland [Automatically generated definition]." [OBOL:automatic] + salivary gland epithelial tissue + salivary gland epithelium + + + tubulus renalis epithelial tissue + "the cellular avascular layer of the renal tubule luminar surfaces" [MP:0009640\,MGI\:csmith] + epithelium of renal tubule + kidney tubule epithelium + epithelium of tubulus renalis + nephron tubule epithelial tissue + epithelial tissue of tubulus renalis + renal tubule epithelial tissue + UBERON:0004810 + epithelial tissue of nephron tubule + nephron tubule epithelium + epithelium of nephron tubule + epithelial tissue of renal tubule + UBERON:nephron tubule epithelium + tubulus renalis epithelium + nephron tubule epithelium + + + UBERON:upper respiratory tract epithelium + upper respiratory tract epithelial tissue + UBERON:0004814 + "An epithelium that is part of a upper respiratory tract [Automatically generated definition]." [OBOL:automatic] + epithelial tissue of upper respiratory tract + upper respiratory tract epithelium + epithelium of upper respiratory tract + + + lower respiratory tract epithelial tissue + UBERON:lower respiratory tract epithelium + "An epithelium that is part of a lower respiratory tract [Automatically generated definition]." [OBOL:automatic] + UBERON:0004815 + lower respiratory tract epithelium + epithelial tissue of lower respiratory tract + epithelium of lower respiratory tract + + + epithelium of kidney + UBERON:0004819 + epithelial tissue of kidney + kidney epithelium + kidney epithelial tissue + renal epithelium + "the cellular avascular layer of the kidney luminar surfaces" [MP:0004967\,MGI\:csmith] + UBERON:kidney epithelium + + + pulmonary alveolus epithelium + alveolus epithelial tissue + "The epithelial layer of the alveoli[MP]. The layer of cells covering the lining of the tiny air sacs at the end of the bronchioles[BTO]." [BTO:0003511, MP:0010898] + alveolar epithelium + UBERON:pulmonary alveolus epithelium + epithelial tissue of alveolus + UBERON:0004821 + pulmonary alveolus epithelium + epithelium of alveolus + pulmonary alveolar epithelium + epithelium of pulmonary alveolus + alveolus epithelium + + + UBERON:cardiovascular system endothelium + "An endothelium that is part of the cardiovascular system." [https://orcid.org/0000-0002-6601-2165] + UBERON:0004852 + cardiovascular system endothelium + vascular endothelia + + + retinal blood vessels + UBERON:vasculature of retina + retinal vasculature + UBERON:0004864 + vasa sanguinea retinae + set of blood vessels of retina + set of retinal blood vessels + retina vasculature + "A vasculature that is part of a retina [Automatically generated definition]." [OBOL:automatic] + retina vasculature of camera-type eye + retinal blood vessels set + vasculature of retina + + + UBERON:0004877 + "Visceral endoderm, a population of extraembyonic endoderm, is an extraembryonic tissue that functions in a regulatory capacity but does not contribute directly to the formation of any adult organs[PMID:15905405]. primitive endoderm-derived tissue which remains in contact with and surrounds the extra-embryonic ectoderm and the epiblast and provides signals for the differentiation and patterning of the epiblast; a small number of visceral endoderm cells also contribute to the endoderm of the embryonic gut[MP]." [http://www.ncbi.nlm.nih.gov/pubmed/15905405, MP:0011186] + UBERON:visceral endoderm + visceral endoderm + + + UBERON:0004883 + mesenchyme of lung + "The mass of tissue made up of mesenchymal cells in the lung." [GO:0060484] + lung-associated mesenchyme + pulmonary mesenchyme + UBERON:lung mesenchyme + lung mesenchyme + + + UBERON:interalveolar septum + UBERON:0004893 + alveolar septum + interalveolar septum + "A the thin septum that separates adjacent pulmonary alveoli, containing connective tissue constituents of the respiratory tissue and the capillary network of the blood supply of the lung." [http://en.wikipedia.org/wiki/Alveolar_septum, LG:0012625] + septum interalveolare + + + UBERON:0004905 + "Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts." [] + articulation + UBERON:articulation + + + gut ectoderm + UBERON:0004906 + UBERON:ectodermal part of digestive tract + ectodermal gut + ectodermal part of digestive tract + "A portion of the gut that is derived from ectoderm." [GO:0007439] + + + "The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum." [http://en.wikipedia.org/wiki/Alimentary_canal#Upper_gastrointestinal_tract] + upper GI tract + upper digestive tract + UBERON:upper digestive tract + UBERON:0004908 + upper gastrointestinal tract + + + "An epithelium surrounding a gonad." [OBOL:automatic] + gonadal epithelium + epithelium of gonad + gonadal sheath + UBERON:epithelium of gonad + gonad epithelium + UBERON:0004909 + + + UBERON:0004910 + UBERON:epithelium of male gonad + testis epithelium + "An epithelium surrounding a testis." [OBOL:automatic] + epithelium of male gonad + + + segment of intestinal tract + alimentary system subdivision + "A proximal-distal subdivision of the digestive tract." [http://orcid.org/0000-0002-6601-2165] + subdivision of digestive tract + subdivision of alimentary system + UBERON:0004921 + UBERON:subdivision of digestive tract + intestinal tract + + + subependymal plate + SVZ + postnatal subventricular zone + UBERON:postnatal subventricular zone + subventricular zone + postnatal subependymal zone + UBERON:0004922 + SEZ + adult subventricular zone + "A mitotically active layer of cells surrounding the brain ventricles in the adult that consists of migrating neuroblasts, astrocytes and transitory amplifying progenitor cells[MP]." [MP:0004275] + postnatal subventricular zone + postnatal subependymal layer + subependymal zone + subventricular zone of brain + subependymal layer + postnatal subependymal plate + brain subventricular zone + + + UBERON:0004923 + "A part of a wall of an organ that forms a layer." [UBERON:cjm] + UBERON:organ component layer + organ component layer + + + nerve cord + "A cluster of ➞neurons that is the most prominent longitudinally extending condensed part of a ➞nervous system." [http://www.ncbi.nlm.nih.gov/pubmed/21062451] + UBERON:0005053 + UBERON:nerve cord + + + "An organ part that is part of a long bone [Automatically generated definition]." [OBOL:automatic] + UBERON:0005055 + zone of long bone + long bone zone + UBERON:zone of long bone + + + UBERON:immune organ + UBERON:0005057 + "An organ that is part of a immune system [Automatically generated definition]." [OBOL:automatic] + immune system organ + immune organ + + + hemopoietic or lymphoid gland + "A gland that is part of a hemolymphoid system [Automatically generated definition]." [OBOL:automatic] + haemolymphoid system gland + UBERON:hemolymphoid system gland + UBERON:0005058 + hemolymphoid system gland + + + neural fold + UBERON:0005062 + "One of the two elevated edges of the neural groove[GO,MP]." [GO:0001842, http://en.wikipedia.org/wiki/Neural_fold, MP:0011256] + medullary fold + UBERON:neural fold + + + "A hole in a tube[GO]." [GO:0060609] + tube lumen + UBERON:tube lumen + UBERON:0005082 + + + UBERON:0005085 + ectodermal placode + "An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]" [GO:0060788] + UBERON:ectodermal placode + + + UBERON:hair follicle placode + "An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO]." [GO:0060789] + UBERON:0005086 + hair gem + hair peg + hair follicle placode + + + muscle element + muscle structure + musculus + "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]." [GO:0061061] + muscle + UBERON:muscle structure + UBERON:0005090 + + + mesonephric epithelium + UBERON:mesonephric epithelium + "An epithelium that is part of a mesonephros [Automatically generated definition]." [OBOL:automatic] + UBERON:0005103 + + + UBERON:0005107 + cap mesenchyme + condensed mesenchyme + metanephric cap + "The metanephric cap is formed by the condensation of metanephric mesenchymal cells surrounding the ureteric bud tip[GO]. Mesenchyme closely apposed to the tips of the buds is called cap mesenchyme; it will later go on to form nephrons etc[GUDMAP]." [GO:0072185, http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] + UBERON:metanephric cap + + + epithelial bud + UBERON:epithelial bud + "A bud is a protrusion that forms from an epithelial sheet by localized folding." [GO:0060572] + UBERON:0005153 + + + UBERON:0005154 + UBERON:epithelial cord + "A cord of epithelial cells without a lumen and usually several cells thick." [AEO:0000216] + epithelial cord + + + "Any anatomical structure that is part of the reproductive system." [http://orcid.org/0000-0002-6601-2165] + reproductive structure + reproductive system element + UBERON:reproductive structure + UBERON:0005156 + reproductive system structure + + + UBERON:0005157 + epithelial fold + UBERON:epithelial fold + "An epithelial sheet bent on a linear axis." [GO:0060571] + + + multi-cell-part structure + UBERON:multi cell part structure + multi cell part structure + multi-cell-component structure + cell part cluster + "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." [CARO:0001000] + UBERON:0005162 + + + interstitium + UBERON:interstitial tissue + interstitial tissue + UBERON:0005169 + "connective tissue between the cellular elements of a structure." [http://medical-dictionary.thefreedictionary.com/tissue] + + + abdomen element + abdomen organ + "An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland." [http://orcid.org/0000-0002-6601-2165] + UBERON:0005172 + UBERON:abdomen element + + + UBERON:abdominal segment element + "An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region." [http://orcid.org/0000-0002-6601-2165] + abdominal segment element + abdominal segment organ + UBERON:0005173 + + + dorsal region element + dorsal region organ + back organ + "An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back." [http://orcid.org/0000-0002-6601-2165] + UBERON:dorsal region element + UBERON:0005174 + + + trunk organ + trunk region element + UBERON:trunk region element + UBERON:0005177 + "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions." [http://orcid.org/0000-0002-6601-2165] + + + UBERON:0005178 + "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli." [http://orcid.org/0000-0002-6601-2165] + UBERON:thoracic cavity element + thoracic cavity element + thoracic cavity organ + + + "An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis." [http://orcid.org/0000-0002-6601-2165] + UBERON:pelvic region element + pelvis region organ + pelvis organ + pelvic region element + UBERON:0005179 + pelvic element + + + UBERON:thoracic segment organ + UBERON:0005181 + upper body organ + thoracic segment organ + "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions." [http://orcid.org/0000-0002-6601-2165] + + + kidney medulla collecting duct + renal medulla collecting duct + medullary collecting duct + UBERON:renal medulla collecting duct + UBERON:0005185 + "The portion of the collecting duct that resides in the renal medulla" [UBERON:cjm] + + + "A vein that is part of a thorax [Automatically generated definition]." [OBOL:automatic] + UBERON:thoracic vein + UBERON:0005194 + thoracic vein + + + right atrium valve + right atrium valves + superior vena cava valve + UBERON:0005208 + "A valve that is part of a right atrium [Automatically generated definition]." [OBOL:automatic] + UBERON:right atrium valve + valve of right atrium + + + UBERON:0005253 + cephalic mesenchyme + "Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells." [ISBN:0683400088, MP:0011260] + desmocranium + cranial mesenchyme + UBERON:head mesenchyme + head mesenchyme + + + UBERON:0005256 + trunk mesenchyme + trunk and cervical mesenchyme + "Mesenchyme that is part of a developing trunk." [OBOL:automatic] + UBERON:trunk mesenchyme + + + UBERON:embryonic tissue + UBERON:0005291 + embryonic tissue + developing tissue + portion of embryonic tissue + "A portion of tissue that is part of an embryo." [OBOL:automatic] + + + extraembryonic tissue + UBERON:0005292 + UBERON:extraembryonic tissue + "Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo." [https://orcid.org/0000-0002-6601-2165] + extra-embryonic tissue + + + UBERON:genital ridge + indifferent gonadal ridge + crista gonadalis + gonadal ridge + genital ridge + "the elevation of thickened mesothelium and underlying mesenchyme found on the ventromedial border of the embryonic mesonephros in which the primordial germ cells become embedded, establishing it as the primordium of the testis or ovary" [MP:0011411\,MGI\:anna] + UBERON:0005294 + + + primitive sex cord + "Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female." [http://en.wikipedia.org/wiki/Sex_cords, http://www.answers.com/topic/sex-cord] + sex cord + gonad cord + genital cord + gonadal cord + UBERON:sex cord + UBERON:0005295 + + + testis sex cord + testis primitive sex cord + testis cord + UBERON:testis sex cord + primary sex cord + UBERON:0005297 + testis primary sex cords + "The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP]." [http://en.wikipedia.org/wiki/Testis_cords] + + + regeneration blastema + blastemata + "A blastema is a mass of cells capable of growth and regeneration into organs or body parts. Historically blastema have been thought to be composed of undifferentiated pluripotent cells, but recent research indicates that in some organisms blastema may retain memory of tissue origin.[1] Blastemata are typically found in the early stages of an organism's development such as in embryos, and in the regeneration of tissues, organs and bone[WP]. A regenerating tissue composed of a proliferative mass of undifferentiated progenitor cells from which new differentiated structures arise[ZFA]." [http://en.wikipedia.org/wiki/Blastema, ZFA:0001270, ZFIN:ZDB-PUB-061108-12] + blastema + UBERON:blastema + UBERON:0005306 + + + "A unique club-shaped epithelial structure that develops at the tip of the mammary duct at the onset of puberty under the action of circulating hormones." [MGI:anna] + UBERON:mammary duct terminal end bud + mammary duct terminal end bud + UBERON:0005313 + + + "The chorioallantoic membrane is a vascular membrane found in eggs of some amniotes, such as birds and reptiles. It is formed by the fusion of the mesodermal layers of two developmental structures: the allantois and the chorion. Three different layers compose the chorioallantoic membrane; these are called the chorionic epithelium, the mesenchyme and the allantoic epithelium. Blood capillaries and sinuses are found between epithelial cells of the chorionic layer, allowing close contact (within 0.2 N<m) with air found in pores of the shell membrane of the egg. As a result, the chorioallantoic membrane allows exchange of gases, such as oxygen, to developing embryos. During embryonic development of birds, the chorioallantoic membrane also plays an essential role in bone formation by transporting calcium into the embryo from the eggshell. Chorioalloantoic membranes from developing chicken eggs are routinely used in biological and biomedical research to investigate development, angiogenesis, tumors, and to propagate and investigate viruses or helminths." [http://en.wikipedia.org/wiki/Chorioallantoic_membrane] + UBERON:0005335 + chorioallantois + chorioallantoic membrane + UBERON:chorioallantoic membrane + + + outflow tract of ventricle + UBERON:outflow tract of ventricle + UBERON:0005337 + heart ventricle outflow tract + ventricular outflow tract + "A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]." [http://en.wikipedia.org/wiki/Ventricular_outflow_tract] + outflow part of ventricle + + + UBERON:dorsal telencephalic commissure + "A fiber tracts that connect the dorsal region of the two cerebral hemispheres and span the longitudinal fissure, including the corpus callosum and hippocampal commissure[MP]." [MP:0008219] + UBERON:0005340 + dorsal telencephalic commissure + dorsal commissure + + + UBERON:ventral commissure + "The fiber tracts that connect the ventral region of the two cerebral hemispheres and span the longitudinal fissure, including the anterior and the habenular commissures[MP]." [MP:0008220] + UBERON:0005341 + ventral commissure + + + Rathke's cleft + hypophyseal diverticulum + Rathke's cyst + UBERON:Rathke's pouch + Rathke's pocket + Rathke's pouch + UBERON:0005356 + hypophyseal pouch + craniopharyngeal pouch + Rathke pouch + pituitary diverticulum + craniobuccal pouch + nasohypophyseal pouch + pouch of Rathke + "A pouch of ectoderm that grows out from the upper surface of the embryonic stomodeum and gives rise to the anterior and intermediate lobes of the pituitary gland[MP]. In embryogenesis, Rathke's pouch is a depression in the roof of the developing mouth in front of the buccopharyngeal membrane. It gives rise to the anterior pituitary (adenohypophysis), a part of the endocrine system[WP]." [http://en.wikipedia.org/wiki/Rathke's_pouch, MP:0003817] + + + UBERON:ventricle of nervous system + region of wall of ventricular system of neuraxis + ventricular layer + "A layer in the central nervous system that lines system of communicating cavities in the brain and spinal cord." [http://purl.obolibrary.org/obo/uberon/tracker/300] + ventricle of nervous system + UBERON:0005358 + + + "the region of white matter of the spinal cord that is located between the dorsal and ventral spinal roots" [MP:0009678\,ISBN\:0-683-40008-8] + UBERON:spinal cord lateral column + UBERON:0005374 + lateral column + spinal cord lateral column + + + UBERON:0005381 + granular layer of the dentate gyrus + UBERON:dentate gyrus granule cell layer + dentate gyrus granule cell layer + DG granule cell layer + Dentate gyrus, granule cell layer + granular layer of dentate gyrus + "Granule cell layer is also called the DG principal cell layer. This one of the three layers of dentate gyrus that lies deep to the molecular layer and is made of densely packed layer that is four to eight granule cells thick." [NIFSTD:birnlex_4129] + + + dorsal basal ganglia + striated body + "Dorsal components of the striatum comprising the caudate nucleus and the putamen, in species that have distinct nuclei; the caudoputamen in species which don't." [NIFSTD:nlx_anat_1010001] + dorsal basal ganglion + UBERON:0005382 + corpus striatum + striatum dorsal region + striatum dorsale + UBERON:dorsal striatum + caudoputamen + dorsal striatum + + + caudate putamen + caudate-putamen + neostriatum + "Regional part of telencephalon in some species, e.g., rodent, equivalent to the dorsal striatum (caudate nucleus and putamen). Unlike the dorsal striatum of primates, for example, the caudoputamen is not split into separate nuclei by the fibers of the internal capsule. Rather, the internal capsule splits into fiber bundles which course through the structure." [NIFSTD:nlx_anat_100312] + caudateputamen + caudoputamen + caudate-putamen + UBERON:caudate-putamen + caudate putamen (striatum) + caudate putamen + dorsal striatum + UBERON:0005383 + caudateputamen + striatum + + + nasal mucosa + nasal cavity epithelium + UBERON:0005384 + "An epithelium that lines the nasal cavity." [UBERON:cjm] + UBERON:nasal cavity epithelium + nasal epithelium + + + UBERON:0005388 + UBERON:photoreceptor array + light-sensitive tissue + "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] + photoreceptor array + + + neocortex layer I + molecular layer + layer I of neocortex + "The most superficial layer of the neocortex characterized by a paucity of cell bodies." [NIFSTD:nlx_anat_090807] + neocortex plexiform layer + cortical layer I + UBERON:cortical layer I + molecular layer of neocortex + layer 1 of neocortex + plexiform layer of neocortex + lamina molecularis isocorticis [lamina I] + plexiform layer + molecular layer of cerebral cortex + UBERON:0005390 + neocortex layer 1 + neocortex molecular layer + molecular layer of isocortex [layer i] + cerebral cortex, layer 1 + + + layer of medium-sized and large pyramidal cells + lamina pyramidalis externa isocorticis [lamina iii] + neocortex layer III + cortical layer III + layer III of neocortex + UBERON:0005392 + layer 3 of neocortex + lamina pyramidalis externa + UBERON:cortical layer III + external pyramidal cell layer + external pyramidal layer of isocortex [layer iii] + external pyramidal cell layer of neocortex + external pyramidal layer of cerebral cortex + isocortex, deep supragranular pyramidal layer + neocortex external pyramidal cell layer + pyramidal layer + "Layer of neocortex lying deep to the external granule cell layer defined cytoarchitecturally by numerous small pyramidal neurons." [NIFSTD:nlx_anat_090809] + external pyramidal layer of neocortex + cerebral cortex, layer 3 + neocortex layer 3 + + + "One of: the common carotid artery, or its branches, the external and internal carotid arteries." [http://en.wikipedia.org/wiki/Carotid_artery, https://sourceforge.net/tracker/?func=detail&aid=3486870&group_id=76834&atid=994764] + carotid artery + carotid + subdivision of common carotid artery + carotid artery segment + UBERON:0005396 + UBERON:carotid artery segment + common carotid arterial subdivision + + + UBERON:0005399 + "A sex gland that is part of a male reproductive system." [OBOL:automatic] + male reproductive gland + accessory sex gland + UBERON:male reproductive gland + + + UBERON:cerebral hemisphere gray matter + cerebral grey matter + UBERON:0005401 + "A gray matter that is part of a cerebral hemisphere." [OBOL:automatic] + cerebral gray matter + cerebral hemisphere gray matter + cerebral hemisphere grey matter + + + ventral striatum + "A composite structure of the telencephalon that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes the nucleus accumbens, the most ventral portions of the caudate nucleus and the putamen, the rostrolateral portion of the anterior perforated substance, the islands of Calleja and a rostral subcommissural portion of substantia innominata. The boundary between the ventral striatum and dorsal striatum is indistinct in sections stained for Nissl substance (Heimer-1995; adapted from Brain Info)." [NIFSTD:nlx_57107] + striatum ventrale + UBERON:0005403 + UBERON:ventral striatum + striatum ventral region + + + CVO + UBERON:circumventricular organ + circumventricular organ + circumventricular organ of neuraxis + circumventricular organ + "Any of any of the secretory or sensory organs located in the brain region around or in relation to the ventricular system that are characterized by extensive vasculature and a lack of a normal blood brain barrier (BBB) and allow for the linkage between the central nervous system and peripheral blood flow." [MP:0013562] + UBERON:0005408 + + + alimentary tract + gastrointestinal system + UBERON:gastrointestinal system + gastrointestinal tract + gastro-intestinal system + alimentary system + gastrointestinal (GI) tract + GI tract + gastrointestinal system + UBERON:0005409 + + + UBERON:0005411 + UBERON:bony otic capsule + "the cartilage or bony capsule surrounding the inner ear mechanism" [MP:0000039\,ISBN\:0-683-40008-8] + bony otic capsule + otic capsule bone + + + UBERON:0005414 + ZPA + zona activitatis polarisantis + zone of polarizing activity + "An area of mesenchymal cells that contains signals which instruct the developing limb or fin bud to form along the anterior/posterior axis." [http://en.wikipedia.org/wiki/Zone_of_polarizing_activity, UBERON:cjm] + UBERON:zone of polarizing activity + + + "A limb bud that develops into a forelimb." [UBERON:cjm] + forelimb bud + UBERON:0005417 + anterior limb bud + limb bud - forelimb + UBERON:forelimb bud + upper limb bud + arm bud + + + limb bud - hindlimb + hind limb bud + hindlimb bud + UBERON:hindlimb bud + leg bud + "A limb bud that develops into a hindlimb." [UBERON:cjm] + posterior limb bud + UBERON:0005418 + + + UBERON:pectoral appendage bud + "A limb bud that develops into a forelimb or pectoral fin." [OBOL:automatic] + pectoral appendage bud + pectoral fin buds + pectoral fin bud + UBERON:0005419 + forelimb - pectoral fin bud + + + hindlimb/pelvic fin bud + pelvic appendage bud + UBERON:pelvic appendage bud + pelvic fin bud + UBERON:0005420 + "A limb bud that develops into a hindlimb or pelvic fin." [OBOL:automatic] + + + UBERON:developing anatomical structure + developmental tissue + UBERON:0005423 + developing structure + developmental structure + developing anatomical structure + + + "Portion of tissue that is the outer layer of the optic cup and will become the retinal pigmented epithelium." [ZFIN:curator] + future pigmented layer + future PRE + future pigmented retinal epithelium + optic cup outer layer + outer layer optic cup + UBERON:presumptive retinal pigmented epithelium + presumptive pigmented epithelium + UBERON:0005424 + presumptive retinal pigmented epithelium + future retinal pigmented epithelium + presumptive pigmented epithelia + future RPE + + + inner layer optic cup + optic cup inner layer + presumptive neural retina + future NR + presumptive retina + future neural epithelium + future neural layer + "Portion of tissue that is the inner layer of the optic cup and will become the neural retina." [ZFIN:curator] + UBERON:0005425 + future neural retina + future retinal neural layer + UBERON:presumptive neural retina + presumptive retinas + + + saccus aorticus + "The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates" [MP:0012510] + aortic sac + UBERON:0005432 + UBERON:aortic sac + + + cervical region + UBERON:0005434 + region of neck + neck subdivision + UBERON:cervical region + cervical region + subdivision of neck + + + definitive endoderm + Embryonic endoderm + UBERON:definitive endoderm + UBERON:0005439 + + + ductus arteriosum + "A fetal blood vessel connecting the pulmonary artery with the descending aorta[MESH]. In the developing fetus, the ductus arteriosus is a shunt connecting the pulmonary artery to the aortic arch. It allows most of the blood from the right ventricle to bypass the fetus' fluid-filled lungs, protecting the lungs from being overworked and allowing the left ventricle to strengthen. There are two other fetal shunts, the ductus venosus and the foramen ovale[MP]. the fetal vessel that connects the left pulmonary artery with the descending aorta; the ductus arteriosus normally regresses into a fibrous cord, the ligamentum arteriousum after birth[MP]" [http://en.wikipedia.org/wiki/Ductus_arteriosus, MESH:A07.541.278.395, MP:0010564] + ductus arteriosus + ductus layton + ductus botalli + ductus Botallo + UBERON:ductus arteriosus + ductus arteriosis + UBERON:0005440 + fetal ductus arteriosus + Botallo's duct + arterial canal + arterial duct + + + segment of manus + regio manus + "A segment of autopod that is part of a manus." [OBOL:automatic] + hand subdivision + segment of hand + UBERON:segment of manus + UBERON:0005451 + subdivision of hand + + + UBERON:lower back + lombus + dorsum of abdomen + UBERON:0005462 + back of abdomen + regio lumbalis + loin + abdominal back + lumbar region of back + lumbar part of back + lumbos + "Subdivision of abdominal segment of trunk which in humans is demarcated from the front of the abdomen by the posterior surface of the anterior layer of the thoracolumbar fascia and the anterior surface of the lumbar vertebral column; together with the front of the abdomen, it constitutes the abdomen[Modified from FMA]." [FMA:61681] + lower back + posterior part of abdomen + lower back + + + UBERON:0005483 + lobe of thymus + thymus lobe + UBERON:thymus lobe + + + thymus primordium + UBERON:thymus primordium + UBERON:0005562 + thymic primordium + thymic rudiment + "A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]." [ZFA:0001077] + + + "A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum." [XAO:0001002] + lateral diverticula + lung endoderm + UBERON:0005597 + lung primordium + lung diverticulum + UBERON:lung primordium + + + lens subcapsular epithelium + UBERON:lens anterior epithelium + "A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex." [UBERON:cjm] + subcapsular lens epithelium + anterior surface of lens + anterior epithelium of lens vesicle + lens anterior epithelium + UBERON:0005614 + + + secondary palatal shelf + UBERON:secondary palatal shelf + palatal shelf + palatine shelf + secondary palatal shelf + "The outgrowths of the embryonic maxillary prominences that come together during prenatal development to form the secondary palate" [http://medical-dictionary.thefreedictionary.com/palatal+shelves, http://www.indiana.edu/~anat550/hnanim/face/face.html] + UBERON:0005619 + lateral palatine process + palatal shelves + + + semilunar valves + UBERON:semi-lunar valve + semilunar valve + "the valves that gate the flow of blood from the ventricles into the aorta and pulmonary trunk" [MP:0002746\,MGI\:pvb] + UBERON:0005623 + semi-lunar valve + + + vascular plexus + plexus vasculosus + "A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part." [http://www.medilexicon.com/medicaldictionary.php?t=70052] + UBERON:0005629 + UBERON:vascular plexus + + + UBERON:extraembryonic membrane + UBERON:0005631 + extraembryonic membrane + "Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo." [ISBN10:0073040584] + + + UBERON:extraembryonic mesoderm + UBERON:0005728 + "." [http://www.ana.ed.ac.uk/database/humat/notes/extraemb/mesoder.htm] + extraembryonic mesoderm + extra-embryonic mesoderm + extraembryonic mesenchyme + + + UBERON:adventitia + "An outermost connective tissue covering of an organ, vessel, or other structure[WP]." [http://en.wikipedia.org/wiki/Adventitia] + UBERON:0005742 + adventitia + + + bone foramen + foramens@fr + foramina@fr + UBERON:0005744 + "Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves." [TAO:curator] + UBERON:bone foramen + + + UBERON:glomerular tuft + "The capillary loops of the kidney that normally function as a filtration unit[MP]." [http://en.wikipedia.org/wiki/Glomerulus, http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron, MP:0005325] + UBERON:0005749 + glomerular tuft + glomerular capillary tuft + glomerulus + + + UBERON:acellular membrane + "A acellular anatomical structure that is the bounding layer of a anatomical structure." [OBOL:automatic] + acellular membrane + UBERON:0005764 + + + basement membrane of epithelium + UBERON:0005769 + "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina." [http://en.wikipedia.org/wiki/Basement_membrane, http://orcid.org/0000-0002-6601-2165] + UBERON:basement membrane of epithelium + membrana basalis + basement membrane of connective tissue + basement membrane + + + glomerular basement membrane + UBERON:0005777 + UBERON:glomerular basement membrane + glomerular filtration membrane + glomerular capillary basement membrane + "the layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter" [MP:0011348\,MGI\:anna] + + + segment of aorta + UBERON:0005800 + aortic section + aortic segment + UBERON:section of aorta + section of aorta + "Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle." [ncithesaurus:Aortic_Segment] + portion of aorta + + + aorta dorsalis + dorsal aortic root + aortae dorsales + dorsal aorta + "The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch[BTO]. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once[GO]. Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]." [BTO:0004673, GO:0035907, http://en.wikipedia.org/wiki/Dorsal_aorta, https://sourceforge.net/tracker/?func=detail&aid=3316981&group_id=36855&atid=440764] + DA + dorsal aortæ + UBERON:dorsal aorta + dorsal aorta root + UBERON:0005805 + + + mesenchyme condensation + developing mesenchymal condensation + UBERON:0005856 + "A delimited region of dense mesenchyme within looser mesenchyme." [AEO:0000148] + UBERON:developing mesenchymal condensation + + + UBERON:mandibular prominence + mandibular prominence + mandibular process + "the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip" [MP:0010939\,ISBN\:0-683-40008-8] + mandibular swelling + UBERON:0005867 + prominentia mandibularis + + + maxillary process + maxillary process of embryo + prominentia maxilaris + UBERON:0005868 + embryonic maxillary process + maxillary prominence + "the paired dorsal prominences formed by bifurcation of the first pharyngeal arches in the embryo that unite with the ipsilateral medial nasal process to form the upper jaw" [MP:0010940\,ISBN\:0-683-40008-8] + UBERON:maxillary prominence + + + nasal pit + UBERON:olfactory pit + UBERON:0005870 + olfactory pit + "An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO]." [GO:0060166, http://en.wikipedia.org/wiki/Nasal_pit] + + + digit or predigit + UBERON:0005881 + "A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis." [UBERON:cjm] + autopodial extension + limb outgrowth + UBERON:autopodial extension + + + UBERON:0005893 + UBERON:leg bone + leg bone + "A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx" [https://orcid.org/0000-0002-6601-2165] + + + UBERON:insect leg + imaginal disc-derived leg + "The walking appendages of each segment of the ventral adult external thorax[FBbt]. A leg derived from an imaginal disc[GO]." [FBbt:00004640, GO:0007480] + insect leg + UBERON:0005895 + + + bone of pectoral limb autopod + "A bone that is part of the manus skeleton. Note that this includes the carpal bones." [https://orcid.org/0000-0002-6601-2165] + forelimb autopodium bone + bone of pectoral limb autopodium + hand bone + forelimb autopod bone + bone of hand skeleton + UBERON:manus bone + bone of hand + UBERON:0005897 + manus bone + bone of manus + + + bone of foot + "A bone that is part of the pes skeleton" [https://orcid.org/0000-0002-6601-2165] + foot bone + UBERON:0005899 + bone of pes + bone of foor proper or tarsal skeleton + bone of pedal skeleton + pes bone + UBERON:pes bone + + + occipital region of head + occipital region + basicranial region + back of head + occipital part of head + UBERON:0005902 + UBERON:occipital region + "Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles." [TAO:0001414, UBERONREF:0000007] + + + duct of male reproductive system + UBERON:duct of male reproductive system + UBERON:0005904 + "Any of the ducts that are part of a male reproductive system." [http://orcid.org/0000-0002-6601-2165] + + + UBERON:serous sac + serous sac + "Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]" [FMA:9689] + UBERON:0005906 + + + "Multilaminar epithelium, which of consists of more than one layer of epithelial cells, in contact with a basement membrane, that can undergo distention and contraction without losing its integrity and consistency. Examples: urothelium.[FMA]" [FMA:63914, FMA:FMA, http://en.wikipedia.org/wiki/Transitional_epithelium] + UBERON:0005910 + UBERON:transitional epithelium + epithelium transitionale + transitional epithelium + + + UBERON:endo-epithelium + "Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]" [FMA:69065] + UBERON:0005911 + endo-epithelium + endoderm-derived epithelium + endoepithelium + + + UBERON:0005913 + bone organ zone + zone of bone organ + UBERON:zone of bone organ + + + hair bulb + "The lower segment of the hair that circles the dermal papilla and the hair matrix." [ncithesaurus:Hair_Bulb] + UBERON:0005932 + hair follicle bulb + bulb of hair follicle + UBERON:bulb of hair follicle + + + UBERON:0005933 + UBERON:hair root sheath + hair root sheath + + + UBERON:0005941 + hair inner root sheath + hair follicle inner root sheath + inner sheath of hair follicle + inner root sheath + internal root sheath of hair follicle + UBERON:hair inner root sheath + "A multilayered tube composed of terminally differentiated hair follicle keratinocytes that is surrounded by the outer root sheath; the layers of the inner root sheath include the companion layer, Henle's layer, Huxley's layer and the inner root sheath cuticle[MP]." [https://sourceforge.net/tracker/?func=detail&aid=3213510&group_id=76834&atid=1205376, MP:0010685] + inner root sheath of hair follicle + + + outer root sheath of hair follicle + external root sheath of hair follicle + hair outer root sheath + "It surrounds the hair follicle like a sleeve all the way to the bulb. The outer root sheath is essentially a stratified epithelium that is contiguous with the epidermis." [https://sourceforge.net/tracker/?func=detail&aid=3213510&group_id=76834&atid=1205376, Keratin.com:http\://www.keratin.com/] + UBERON:hair outer root sheath + UBERON:0005942 + outer root sheath + outer hair sheath + ORS + hair follicle outer root sheath + + + UBERON:0005953 + pulmonary conus + right ventricle pulmonary outflow tract + conus arteriosus + UBERON:outflow part of right ventricle + right ventricular outflow tract + arterial cone + RVOT + pulmonary cone + conus arteriosus (infundibulum) + pulmonary conus + outflow tract of right ventricle + infundibulum of right ventricle + outflow part of right ventricle + "Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk" [MP:0010428] + + + UBERON:0005956 + UBERON:outflow part of left ventricle + vestibulum aortae + Sibson vestibule + "Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta." [MP:0010429] + outflow part of left ventricle + outflow tract of left ventricle + aortic vestibule + LVOT + left ventricular outflow + heart left ventricle outflow tract + left ventricular outflow tract + + + endocardial ridge + conotruncal cushion + "One of the pair of spiral mesenchymal swellings in the primordial ventricular outflow tract, that eventually fuse to form the conotruncal septum, dividing the subvalvular outflow tract and contributing to the membranous interventricular septum[MP]" [http://www.ncbi.nlm.nih.gov/pubmed/8823298, MP:0010585] + outflow tract endocardial cushion + outflow tract cushion + conotruncal ridge + aortico-pulmonary spiral ridges + UBERON:conotruncal ridge + bulbar ridge + spiral ridge + UBERON:0005967 + + + ligamentum pectinatum + Hueck's ligament + trabecular mesh + scleral trabecule + ligamentum pectinatum iridis + scleral trabeculae + scribiform ligament + scleral trabecular + cribiform ligament + eye trabecular meshwork + iridis + pectinate ligament + "A fenestrated endothelial-like tissue situated at the intersection of the cornea and the iris[GO]. The trabecular meshwork is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). The tissue is spongy and lined by trabeculocytes; it allows fluid to drain into a set of tubes called Schlemm's canal flowing into the blood system[WP]. A porelike structure surrounding the entire circumference of the anterior chamber through which aqueous humor circulates to the canal of Schlemm.[GAID] the pore-like structure surrounding the entire circumference of the anterior chamber through which aqueous humor circulates[MP]." [GO:0002930, http://en.wikipedia.org/wiki/Trabecular_meshwork, MP:0005203] + pectinate ligament of iris + eye trabecular meshwork + reticulum trabeculare + trabecular meshwork + UBERON:0005969 + ligamentum pectinatum anguli iridocornealis + reticulum trabeculare sclerae + UBERON:eye trabecular meshwork + ligamentum peactin-tum iridis + trabecular meshwork of the eye + + + UBERON:0005970 + UBERON:brain commissure + brain commissure + "any of the nerve fiber tracts that span the longitudinal fissure between the cerebral and/or cerebellar hemispheres of the brain" [MP:0002199\,ISBN\:0-683-40008-8\,MGI\:csmith] + + + UBERON:tunnel of Corti + tunnel of Corti + UBERON:0005972 + "A triangular, fluid-filled space normally found between the inner and outer rows of supporting pillar cells in the organ of Corti." [MP:0003151] + + + "The laminar structure of the heart" [MP:0010545] + heart layer + UBERON:0005983 + UBERON:heart layer + + + coronary vessel + "Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation" [MP:0010551] + UBERON:0005985 + UBERON:coronary vessel + + + skin appendage + UBERON:0006003 + adnexae cutis + "Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers." [http://code.google.com/p/caro2/issues/detail?id=5, http://orcid.org/0000-0002-6601-2165] + skin adnexa + skin adnexal structure + integumentary adnexa + UBERON:integumentary adnexa + + + UBERON:0006012 + interdigital region + interdigit + UBERON:interdigital region + interdigit region + + + interdigit region of pes + foot interdigit region + UBERON:0006014 + foot interdigital region + "An interdigital region that is part of a pes." [OBOL:automatic] + pedal interdigit region + interdigital region between pedal digits + UBERON:interdigital region between pedal digits + + + "A membranous region of skin between the digits." [http://en.wikipedia.org/wiki/Interdigital_webbing] + webbed interdigital region + UBERON:webbed interdigital region + syndactylous interdigital region + interdigital webbing + UBERON:0006015 + + + "An interdigital region that adjacent_to a digit 1 and adjacent_to a digit 2." [OBOL:automatic] + UBERON:interdigital region between digits 1 and 2 + interdigital region between digits 1 and 2 + interdigital region between digits I and II + UBERON:0006016 + + + UBERON:0006022 + UBERON:interdigital region between digits 3 and 4 + interdigital region between digits 3 and 4 + interdigital region between digits III and IV + "An interdigital region that adjacent_to a digit 3 and adjacent_to a digit 4." [OBOL:automatic] + + + limb digit 1 + UBERON:digit 1 + "A digit that is part of a digit 1 plus metapodial segment." [OBOL:automatic] + UBERON:0006048 + autopod digit 1 + digit 1 + digit I + + + UBERON:0006049 + digit II + UBERON:digit 2 + limb digit 2 + second digit + digit 2 + autopod digit 2 + "A digit that is part of a digit 2 plus metapodial segment." [OBOL:automatic] + + + limb digit 3 + UBERON:digit 3 + third digit + digit III + autopod digit 3 + "A digit that is part of a digit 3 plus metapodial segment." [OBOL:automatic] + digit 3 + UBERON:0006050 + + + digit V + UBERON:digit 5 + "A digit that is part of a digit 5 plus metapodial segment." [OBOL:automatic] + UBERON:0006052 + limb digit 5 + fifth digit + digit 5 + autopod digit 5 + digiti minimi + + + UBERON:multi-limb segment region + "A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions)." [https://orcid.org/0000-0002-6601-2165] + multi-limb segment region + UBERON:0006058 + + + "The distal portion of Bulbus cordis that forms an outflow channel and gives rise to the proximal conus cordis." [UBERON:gg] + bulbus cordis rostral half + rostral half of bulbus cordis + UBERON:0006060 + conotruncus + cardiac conotruncus + UBERON:conotruncus + + + cochlear canal + spiral vessel + UBERON:cochlear canal + wall of cochlea + UBERON:0006106 + cochlear canal + spiral canal of cochlea + + + "A funiculus of neuraxis that is part of a spinal cord." [OBOL:automatic] + white column of spinal cord + UBERON:funiculus of spinal cord + funiculus of spinal cord + UBERON:0006127 + spinal cord funiculus + + + UBERON:0006133 + UBERON:funiculus of neuraxis + funiculus of neuraxis + "The cerebrospinal nerves consist of numerous nerve fibers collected together and enclosed in membranous sheaths. A small bundle of fibers, enclosed in a tubular sheath, is called a funiculus; if the nerve is of small size, it may consist only of a single funiculus; but if large, the funiculi are collected together into larger bundles or fasciculi, which are bound together in a common membranous investment. Examples include: Anterior funiculus of the spinal cord Lateral funiculus of the spinal cord Posterior funiculus of the spinal cord Funiculus solitarius of the medulla Funiculus separans" [http://en.wikipedia.org/wiki/Funiculus_%28neurology%29] + + + neurofibra + neurofibra + neurofibrum + nerve fibers + UBERON:nerve fiber + UBERON:0006134 + nerve fiber + nerve fibre + "A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system." [http://en.wikipedia.org/wiki/Nervous_system_fiber] + + + UBERON:myelinated nerve fiber + UBERON:0006135 + "Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH)" [ncithesaurus:Myelinated_Nerve_Fiber] + myelinated nerve fiber + + + UBERON:0006206 + UBERON:iridocorneal angle + "Acute angle occurring between the iris and the cornea at the periphery of the anterior chamber of the eye[MP]." [MP:0004221] + iridocorneal angle + anterior chamber angle + + + aortic septum + UBERON:aortico-pulmonary spiral septum + aortico-pulmonary septum + septum aorticopulmonale + UBERON:0006207 + aorticopulmonary septum + aortico-pulmonary spiral septum + "The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions." [http://en.wikipedia.org/wiki/Aorticopulmonary_septum, MP:0010650] + spiral septum + + + UBERON:mural trophectoderm + mural trophectoderm + UBERON:0006265 + mural trophoblast + "Trophectoderm that surrounds blastocyst cavity." [http://www.ncbi.nlm.nih.gov/pubmed/16341078] + + + polar trophectoderm + polar trophoblast + UBERON:polar trophectoderm + "Trophectoderm that surrounds the inner cell mass (ICM)." [http://www.ncbi.nlm.nih.gov/pubmed/16341078] + UBERON:0006280 + + + eye chamber + eyeball chamber + chamber of eye + "A segment of the eyeball that is filled with refractive media" [UBERON:cjm] + UBERON:chamber of eyeball + UBERON:0006311 + chamber of eyeball + + + UBERON:0006312 + "Body substance in a liquid or semi-solid state in the eyeball which serves to refract light." [UBERON:cjm] + ocular refractive media + UBERON:ocular refractive media + + + bodily fluid + "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not." [http://en.wikipedia.org/wiki/Body_fluid, MESH:A12.207] + UBERON:0006314 + body fluid + UBERON:bodily fluid + + + "A nucleus of brain that is part of a brainstem." [OBOL:automatic] + brainstem nucleus + brain stem nucleus + UBERON:brainstem nucleus + UBERON:0006331 + + + snout + UBERON:snout + "." [http://en.wikipedia.org/wiki/Snout] + UBERON:0006333 + muzzle + + + ureteric bud ampulla + ureteric ampulla + ampulla of ureter + ureteric bud tip + ureteric tip + "The terminal end of the ureteric tree; the ureteric tip cells are proliferating immature cells located at the branching points that induce the adjacent cap mesenchyme to undergo nephrogenesis." [http://www.gudmap.org/Organ_Summaries/Metanephros/Ureteric_tip.html, MP:0011760] + UBERON:ureteric bud tip + UBERON:0006364 + + + contour hair + UBERON:strand of vibrissa hair + "A specialized hair usually employed for tactile sensation. Vibrissae hair grow around the nostrils, above the lips, and on other parts of the face of most mammals, and all primates except humans. vibrissae are different from other hairs because they are implanted in a special hair follicle incorporating a capsule of blood called a blood sinus and heavily innervated by sensory nerves[WP]." [http://en.wikipedia.org/wiki/Whiskers, https://sourceforge.net/tracker/?func=detail&aid=3213510&group_id=76834&atid=1205376] + vibrissa hair + sinus hair + strand of vibrissa hair + UBERON:0006378 + tactile hair + vibrissa + touch hair + vibrissae + + + lobe of right lung + lobe of the right lung + UBERON:0006518 + "A lobe of lung that is part of a right lung." [OBOL:automatic] + right lung lobe + UBERON:right lung lobe + + + kidney convoluted tubule + renal convoluted tubule + "Any region of a nephron tubule that is convoluted. Examples: distal convoluted tubule, proximal convoluted tuble." [UBERON:cjm] + UBERON:0006534 + UBERON:renal convoluted tubule + convoluted tubule + + + mammary gland fluid + mammary gland secretion + UBERON:0006539 + lactiferous gland secretion + UBERON:mammary gland fluid/secretion + lactiferous gland fluid + mammary gland secreted fluid + "A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards." [UBERON:cjm] + mammary gland fluid/secretion + secretion of mammary gland + + + UBERON:0006553 + "A tube in the kidney that collect and transport urine." [ZFIN:ZDB-PUB-071029-9] + UBERON:renal duct + renal duct + + + excretory tube + "A tube that is part of a excretory system." [OBOL:automatic] + UBERON:excretory tube + UBERON:0006555 + + + pharyngeal tube + UBERON:0006562 + "The pharynx is the part of the digestive system immediately posterior to the mouth[GO]." [GO:0060465] + UBERON:pharynx + pharynx + anterior part of foregut + + + vestibular organ + balance organ + UBERON:vestibular organ + "An organ that is part of a vestibular system." [OBOL:automatic] + UBERON:0006585 + + + UBERON:otolymph + "Transduate located within the osseus labyrinth. Otolymph can be further classified with respect to whether it is within the membranous labyrinth (endolymph) or outside the mebranous labyrinth (perilymph)." [http://orcid.org/0000-0002-6601-2165] + labyrinthine fluid + otolymph + UBERON:0006586 + + + UBERON:presumptive structure + UBERON:0006598 + presumptive structure + "Portion of embryonic tissue determined by fate mapping to become a structure." [GOC:CVS, GOC:YMB, ZFA:0001116] + future structure + presumptive structures + + + tunica albuginea corporis spongiosi + UBERON:0006610 + tunica albuginea corporum cavernosorum + "Denser fibrous covering over one of: penis, testicles or ovaries." [http://en.wikipedia.org/wiki/Tunica_albuginea] + UBERON:tunica albuginea + tunica albuginea + + + UBERON:shell + UBERON:0006612 + shell + "A rigid covering that envelops an object." [http://en.wikipedia.org/wiki/Seashell, http://ncicb.nci.nih.gov/xml/owl/EVS/Shell] + + + UBERON:0006615 + UBERON:venous sinus + "A large vein or channel for the circulation of venous blood" [http://medical-dictionary.thefreedictionary.com/venous+sinus] + venous sinus + blood sinus + + + tunica albuginea testis + testis tunica albuginea + tunica albuginea (testicles) + UBERON:tunica albuginea of testis + tunica albuginea of testis + UBERON:0006643 + "the dense fibrous connective tissue layer that covers the testis." [MP:0013738] + tunica albuginea (testis) + + + interphalangeal joint + UBERON:0006658 + inter-phalangeal joint + "A joint that connects one phalanx to another along a proximodistal axis." [http://orcid.org/0000-0002-6601-2165] + inter-phalanx joint + UBERON:interphalangeal joint + + + tunica muscularis + muscular layer + muscular coat + muscular coat + tunica externa + tunica muscularis + muscularis propria + UBERON:muscular coat + transverse muscular fibers + UBERON:0006660 + muscularis layer + "A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis." [http://en.wikipedia.org/wiki/Muscular_layer] + muscularis + muscularis externa + + + UBERON:central tendon of diaphragm + UBERON:0006670 + "the three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers" [MP:0012061\,MGI\:csmith] + centrum tendineum diaphragmatis + central tendon + centrum tendineum + central tendon of diaphragm + + + mesopodium region + mesopodial limb segment + carpus/tarsus + mesopodial segment + UBERON:mesopodium region + UBERON:0006716 + mesopod + "The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus)" [http://en.wikipedia.org/wiki/Carpus_and_tarsus_of_land_vertebrates, https://orcid.org/0000-0002-6601-2165, MA:th] + + + UBERON:cochlear modiolus + "the central cone shaped core of spongy bone about which turns the spiral canal" [MP:0003309\,ISBN\:0-683-40008-8\,MGI\:anna] + columella cochleae + UBERON:0006723 + modiolus of cochlea + cochlea modiolus + cochlear modiolus + + + spiral ligament of cochlear duct + spiral ligament of cochlea + spiral cochlear ligament + UBERON:0006725 + UBERON:spiral ligament + spiral ligament + "A spiral thickening of the fibrous lining of the cochlear wall. Spiral ligament secures the membranous cochlear duct to the bony spiral canal of the cochlea. Its spiral ligament fibrocytes function in conjunction with the stria vascularis to mediate cochlear ion homeostasis." [http://en.wikipedia.org/wiki/Spiral_ligament, https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=3557974&group_id=76834, MESH:MESH] + ligamentum spirale ductus cochlearis + + + left superior vena cava + left anterior vena cava + UBERON:0006765 + UBERON:left anterior vena cava + + + right superior vena cava + UBERON:0006766 + UBERON:right anterior vena cava + right anterior vena cava + + + "The layer of the epiphyseal plate of a long bone where chondrocytes mature and enlarge[MP]." [https://sourceforge.net/tracker/?func=detail&aid=3442184&group_id=76834&atid=1205376, MP:0000165] + long bone hypertrophic chondrocyte zone + zone of hypertrophic chondrocytes + epiphyseal plate hypertrophic zone + maturation zone + UBERON:0006772 + hypertrophic chondrocyte zone + UBERON:long bone epiphyseal plate hypertrophic zone + long bone epiphyseal plate hypertrophic zone + + + long bone epiphyseal plate ossification zone + UBERON:long bone epiphyseal plate ossification zone + "layer of the epiphyseal plate where new bone matrix is deposited[MP]." [MP:0006399] + UBERON:0006773 + epiphyseal plate ossification zone + + + UBERON:zone of epiphyseal plate + UBERON:0006775 + zone of epiphyseal plate + + + "A group of neurons that provides a nervous signal to a tissue." [AEO:JB] + efferent nerve + UBERON:efferent nerve + UBERON:0006798 + + + caput ulnae + UBERON:proximal epiphysis of ulna + proximal end of ulna + caput ulnae + head of ulna + proximal epiphysis of ulna + UBERON:0006822 + upper end of ulna + "The head of ulna presents an articular surface, part of which, of an oval or semilunar form, is directed downward, and articulates with the upper surface of the triangular articular disk which separates it from the wrist-joint; the remaining portion, directed lateralward, is narrow, convex, and received into the ulnar notch of the radius." [http://en.wikipedia.org/wiki/Head_of_ulna] + + + hypercoracocïde@fr + "Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage." [VSAO:0000157] + scapula bone + scapula + scapulas + scapula@fr + hypercoracocïdeum@fr + UBERON:scapula + scapulae + UBERON:0006849 + + + UBERON:0006853 + "A region of nephron tubule that is part of a cortex of kidney." [OBOL:automatic] + cortical tubule + UBERON:renal cortex tubule + renal cortex tubule + kidney cortex tubule + + + adrenal gland - interrenal gland + "This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]" [GO:0030325] + UBERON:adrenal/interrenal gland + adrenal - interrenal gland + UBERON:0006858 + adrenal gland/interrenal tissue + suprarenal gland - interrenal gland + adrenal/interrenal gland + + + swimbladder + gas bladder + air bladder + UBERON:swim bladder + fish maw + "A thin membranous, sometimes alveolated sac in the dorsal portion of the abdominal cavity. Contains a varying mixture of gases, not identical to the composition of air. May be one, two or three chambered. May be connected to the gut by a tube, the ductus pneumaticus (then called physostomous) or unconnected (then called physoclistous)." [http://www.briancoad.com/Dictionary/S.htm] + swim bladder + UBERON:0006860 + + + body of femur + UBERON:0006862 + corpus femoris + femoral diaphysis + "A diaphysis that is part of a femur[Automatically generated definition]." [http://en.wikipedia.org/wiki/Body_of_femur, OBOL:automatic] + shaft of femur + femoral shaft + UBERON:diaphysis of femur + diaphysis of femur + + + UBERON:seminal fluid secreting gland + UBERON:0006868 + seminal fluid secreting gland + "A gland that secretes a seminal fluid." [OBOL:automatic] + + + handplate + "An autopod plate that has the potential to develop into a manus." [OBOL:automatic] + UBERON:0006875 + distal part of forelimb bud + hand plate + UBERON:handplate + + + organ vasculature + "A vasculature that is part of a organ." [OBOL:automatic] + UBERON:0006876 + set of blood vessels of organ + vasculature of organ + UBERON:vasculature of organ + + + "The darker-colored muscle tissue of some mammals, composed of slow twitch muscle fibers." [BTO:0002317] + slow skeletal muscle tissue + slow muscle tissue + UBERON:0006907 + red muscle + UBERON:slow muscle tissue + slow-twitch skeletal muscle + slow muscle + + + UBERON:0006908 + UBERON:fast muscle tissue + "The paler-colored muscle tissue of some mammals, composed of fast twitch muscle fibers." [BTO:0002318] + fast muscle tissue + fast muscle + fast skeletal muscle tissue + white muscle + + + gut cavity + lumen of gut + UBERON:lumen of digestive tract + lumen of digestive tract + UBERON:0006909 + gut lumen + lumen of digestive tract + digestive tract lumen + lumen of alimentary tract + "An anatomical space that surrounded_by a digestive tract." [OBOL:automatic] + + + UBERON:0006914 + UBERON:squamous epithelium + "An epithelium characterised by its most superficial layer consisting of squamous epithelial cells." [http://en.wikipedia.org/wiki/Squamous_epithelium] + squamous epithelium + + + UBERON:digestive gland + "A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion." [The_American_Heritage_Dictionary_of_the_English_Language:Fourth_Edition._2000.] + UBERON:0006925 + digestive gland + digestive system gland + + + "An epithelium that is part of a vestibular labyrinth." [OBOL:automatic] + vestibular epithelium + vestibular sensory epithelium + UBERON:vestibular epithelium + inner ear vestibular component epithelium + UBERON:0006932 + epithelium of vestibular labyrinth + + + "Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue." [BTO:0000314] + sensory epithelium + neuroepithelium + UBERON:0006934 + UBERON:sensory epithelium + + + inner ear epithelium + UBERON:0006937 + UBERON:inner ear epithelium + "the epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals" [MP:0003308\,MGI\:csmith] + + + "Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface." [CARO:MAH] + UBERON:0006983 + anatomical point + UBERON:anatomical point + + + UBERON:0006984 + UBERON:anatomical surface + anatomical surface + "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n" [CARO:0001002] + + + adult organism + adults + UBERON:0007023 + UBERON:adult organism + "A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage." [OBOL:automatic] + + + embryonic digestive tube + future gut + primordial digestive tube + future digestive tract + primitive gut + future digestive tube + UBERON:0007026 + primordial gut + presumptive gut + UBERON:presumptive gut + + + UBERON:primary circulatory organ + UBERON:0007100 + primary circulatory organ + adult heart + "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]." [GO:0007507] + + + "A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth." [BTO:0000838] + UBERON:meconium + UBERON:0007109 + meconium + + + UBERON:deciduous tooth + UBERON:0007115 + "One of the first set of teeth in the growth development of humans and many other mammals[WP]." [http://en.wikipedia.org/wiki/Deciduous_teeth] + dentes decidui + deciduous tooth + primary tooth + temporary tooth + + + umbilical region + UBERON:umbilicus + "The pit in the center of the abdominal wall marking the point where the umbilical cord entered in the fetus." [http://en.wikipedia.org/wiki/Navel, MESH:A01.047.849] + umbilical part of abdomen + UBERON:0007118 + navel + umbilicus + + + UBERON:pharyngeal pouch 1 + 1st arch pouch endoderm + 1st arch branchial pouch + UBERON:0007122 + visceral pouch 1 + first visceral pouch + hyomandibular pouch + "A pharyngeal pouch that is between pharyngeal arches 1 and 2." [http://www.ncbi.nlm.nih.gov/pubmed/16313389, ISBN10:0124020607, VHOG:0000970] + pharyngeal pouches 1 + 1st arch branchial pouch endoderm + 1st branchial pouch + 1st pharyngeal pouch endoderm + pharyngeal pouch 1 + first pharyngeal pouch + first arch pharyngeal pouch + + + "A pharyngeal pouch that between pharyngeal arches 3 and 4." [http://en.wikipedia.org/wiki/Pharyngeal_pouch_(embryology)#Third_pouch, http://www.ncbi.nlm.nih.gov/pubmed/16313389, ISBN10:0124020607] + 3rd arch branchial pouch + pharyngeal pouches 3 + UBERON:0007124 + visceral pouch 3 + third pharyngeal pouch + third visceral pouch + 3rd branchial pouch + 3rd arch branchial pouch endoderm + third arch pharyngeal pouch + 3rd pharyngeal pouch endoderm + pharyngeal pouch 3 + UBERON:pharyngeal pouch 3 + + + anterior kidney + head kidney + "Teleost head kidney consists of fused bilateral lobes located in the anterior part of the kidney. It is analogous to the mammalian bone marrow and the primary site of definitive hematopoiesis[ZFA,modified]." [http://dx.doi.org/10.1242/dev.00427, ZFIN:ZDB-PUB-040923-1] + kidney marrow + UBERON:0007132 + UBERON:head kidney + + + trunk ganglia + "Ganglion which is located in the trunk." [ZFIN:curator] + UBERON:trunk ganglion + trunk ganglion + UBERON:0007134 + body ganglion + + + stroma of bone marrow + UBERON:0007195 + bone marrow stroma + "The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis." [http://en.wikipedia.org/wiki/Bone_marrow#Stroma] + UBERON:stroma of bone marrow + + + tracheobronchial tree + UBERON:0007196 + "The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells." [http://en.wikipedia.org/wiki/Tracheobronchial_tree] + tracheobronchial system + UBERON:tracheobronchial tree + + + "Mesenchyme that develops_from a cranial neural crest." [OBOL:automatic] + UBERON:0007213 + head neural crest derived mesenchyme + head mesenchyme from neural crest + UBERON:mesenchyme derived from head neural crest + head mesenchyme from cranial neural crest + mesenchyme derived from head neural crest + + + "An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching." [BGEE:ANiknejad] + embryo late growth stage + UBERON:0007220 + UBERON:late embryonic stage + late embryonic stage + embryo late (growth) stage + embryo late stage + + + "Of or pertaining to the period of time immediately following birth, or to the newborn." [http://en.wikipedia.org/wiki/Infant, http://en.wiktionary.org/wiki/neonatal] + UBERON:0007221 + UBERON:neonate stage + neonate stage + neonatal stage + newborn stage + + + 2-cell stage + UBERON:0007232 + 2 cell stage + two-cell stage + UBERON:2 cell stage + + + UBERON:4 cell stage + 4-cell stage + UBERON:0007233 + four-cell stage + 4 cell stage + + + UBERON:0007236 + eight-cell stage + 8-cell stage + UBERON:8 cell stage + 8 cell stage + + + nuclear complex of neuraxis + "Gray matter of the central nervous system which is a collection of clustered nuclei." [UBERON:cjm] + UBERON:nuclear complex of neuraxis + neural nuclei + nuclear complex + cluster of neural nuclei + UBERON:0007245 + + + pectoral appendage skeleton + cheiropterygium + "Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle." [VSAO:0005000, VSAO:NI] + UBERON:0007272 + UBERON:pectoral appendage skeleton + + + "The collection of all skeletal elements in a pelvic appendage region." [https://orcid.org/0000-0002-6601-2165] + UBERON:pelvic appendage skeleton + pelvic appendage skeleton + UBERON:0007273 + + + UBERON:appendage blood vessel + "A blood vessel that is part of a limb/fin." [OBOL:automatic] + UBERON:0007301 + appendage blood vessel + + + saphenous vein + UBERON:saphenous vein + UBERON:0007318 + "Either of two main superficial veins of the leg, one larger than the other, that begin at the foot." [BTO:0001808] + + + UBERON:roof of mouth + palatum + palate + "A multi-tissue structure consisting of bone and soft tissue that forms a part of the roof of the oral cavity. In mammals this is the combination of the primary palate (premaxilla) and the secondary palate. In early tetrapods it consists of the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones." [https://orcid.org/0000-0002-6601-2165] + UBERON:0007375 + roof of mouth + primary or secondary palate + roof of buccal cavity + roof of oral cavity + + + hypodermis + "The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]." [GO:0008544] + UBERON:outer epithelium + outer epithelium + hypoderm + epidermis + outer epidermal layer + outer epithelial layer + UBERON:0007376 + + + egg + "The hard-shelled reproductive body produced by a bird and especially by the common domestic chicken; also: its contents used as food." [BTO:0000369, http://en.wikipedia.org/wiki/Egg_(biology)] + UBERON:0007379 + UBERON:egg + + + neuraxis decussation + "Nerve fibers crossing the midline of the neuraxis relative to their point of origin, on a course to from one level of the nervous system to another. (CUMBO, Heimer, L. The Human Brain, 2nd ed., 1995, pg 6)" [NIFSTD:nlx_144064] + neuraxis chiasma + decussation of neuraxis + UBERON:0007418 + neuraxis chiasm + neural decussation + UBERON:neural decussation + + + UBERON:decussation of diencephalon + "A neural decussation that is part of a diencephalon." [OBOL:automatic] + UBERON:0007425 + decussation of diencephalon + diencephalon decussation + + + UBERON:0007475 + matrix-based tissue + UBERON:matrix-based tissue + "A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified." [AEO:JB] + + + UBERON:0007497 + UBERON:developing epithelial placode + developing epithelial placode + epithelial placode + "A domain of columnar epithelium in an embryo that represents the early stage of the development of the epithelial component of a new anatomical structure." [AEO:0000218, JB:DEF] + + + "An epithelial tube that is open at one end only." [AEO:JB, UBERONREF:0000001] + UBERON:epithelial sac + epithelial sac + UBERON:0007499 + + + UBERON:0007502 + "A complex of interlinking epithelial tubules." [AEO:JB] + UBERON:epithelial plexus + epithelial plexus + + + UBERON:0007503 + UBERON:epithelial vesicle + epithelial vesicle + "A closed epithelium with a lumen." [AEO:JB] + + + UBERON:0007524 + dense mesenchyme tissue + "Mesenchyme with little extracellular matrix." [AEO:JB] + UBERON:dense mesenchyme tissue + + + UBERON:0007529 + UBERON:loose mesenchyme tissue + loose mesenchyme tissue + "Mesenchyme whose cells are embedded in obvious amounts of extracellular matrix." [AEO:JB] + + + "Mesenchymal cells that are migrating." [AEO:JB] + UBERON:migrating mesenchyme population + migrating mesenchyme population + UBERON:0007530 + + + regenerating anatomical structure + "An anatomical structure that is undergoing regeneration." [http://orcid.org/0000-0002-6601-2165] + UBERON:0007567 + regenerating tissue + UBERON:regenerating anatomical structure + regenerative tissue + + + UBERON:0007592 + "Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]" [FMA:64798] + ciliated columnar epithelium + UBERON:ciliated columnar epithelium + + + "Epithelium bearing vibratile cilia on the free surface." [http://medical-dictionary.thefreedictionary.com/ciliated+epithelium] + ciliated epithelium + UBERON:ciliated epithelium + UBERON:0007601 + + + "Stratified cuboidal epithelia is a rare type of epithelial tissue composed of cuboidally shaped cells arranged in multiple layers. They protect areas such as ducts of sweat glands, mammary glands, and salivary glands." [http://en.wikipedia.org/wiki/Stratified_cuboidal_epithelium] + UBERON:stratified cuboidal epithelium + stratified cuboidal epithelium + UBERON:0007603 + epithelium stratificatum cuboideum + + + musculus extensor digitorum + extensor digitorum + extensor digitorum communis muscle + extensor communis + UBERON:extensor digitorum communis + UBERON:0007612 + extensor digitorum communis + "A muscle on the back of the forearm that extends the fingers and wrist." [BTO:0001343, http://en.wikipedia.org/wiki/Extensor_digitorum_muscle] + + + layer of synovial tissue + synovium + UBERON:0007616 + UBERON:layer of synovial tissue + synovial tissue + "A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]." [BTO:0001338, http://www.britannica.com/EBchecked/topic/578563/synovial-tissue] + + + pigment epithelium of eye + UBERON:0007625 + eye pigment epithelium + "epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules." [MP:0005200] + UBERON:pigment epithelium of eye + + + UBERON:0007635 + nucleus of medulla oblongata + "A neural nucleus that is part of a medulla oblongata." [OBOL:automatic] + UBERON:nucleus of medulla oblongata + + + anatomical junction + "An anatomical structure that connects two structures" [http://code.google.com/p/caro2/issues/detail?id=15] + UBERON:anatomical junction + anatomical junction + UBERON:0007651 + + + UBERON:region of nephron tubule + region of renal tubule + renal tubule region + region of nephron tubule + UBERON:0007685 + + + organ field + "Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue." [FBbt:00005426, http://flybase.org/reports/FBrf0178740.html, JB:DEF] + UBERON:0007688 + future organ + developmental field + UBERON:anlage + anlage + + + "An axon tract that is part of a brain." [OBOL:automatic] + UBERON:tract of brain + brain tract + tract of brain + landmark tracts + UBERON:0007702 + + + UBERON:0007771 + gland of epidermis + epidermal gland + UBERON:epidermis gland + epidermis gland + "A gland that is part of a epidermis." [OBOL:automatic] + + + transduate + UBERON:0007779 + UBERON:transduate + "Body substance in liquid state, which is derived from plasma by passage through the (intact) wall of capillaries without further processing by secretory cells or glands." [FMA:12276] + + + exudate + UBERON:0007780 + "Exudates are fluids, cells, or other cellular substances that are slowly discharged from blood vessels usually from inflamed tissues." [MESH:A12.383] + transudates and exudate + UBERON:exudate + + + serous fluid + "Transudate contained in a serous sac." [FMA:20932] + UBERON:serous fluid + UBERON:0007794 + + + UBERON:vascular system + UBERON:0007798 + vascular system + "Anatomical system that consists of all blood and lymph vessels." [UBERON:cjm] + Gefaesssystem@ge + + + abdominal adipose tissue + UBERON:0007808 + UBERON:adipose tissue of abdominal region + adipose tissue of abdominal region + "Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots." [CALOHA:paula, http://orcid.org/0000-0002-6601-2165, http://purl.obolibrary.org/obo/uberon/tracker/259, MGI:csmith] + abdominal fat + intra-abdominal fat + + + girdle bone + UBERON:0007828 + UBERON:girdle bone/zone + girdle bone/zone + "A bone that is part of a appendage girdle region." [OBOL:automatic] + + + UBERON:0007829 + bone of pectoral girdle + UBERON:pectoral girdle bone + "A bone that is part of a pectoral girdle region." [OBOL:automatic] + pectoral girdle bone + + + membrane bone + UBERON:0007842 + "Bone element that arises as a result of intramembranous ossification." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000023] + UBERON:membrane bone + + + cartilage organ + cartilage + chondrogenic element + cartilage element + cartilaginous element + UBERON:cartilage element + UBERON:0007844 + "Skeletal element that is composed of cartilage tissue and may be permanent or transient." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000000] + + + regular connective tissue + "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue." [FMA:20103] + UBERON:regular connective tissue + UBERON:0007845 + + + dense fibrous connective tissue + "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts)." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000050] + UBERON:dense regular connective tissue + dense regular collagenous tissue + dense regular connective tissue + dense regular collagenous connective tissue + regular dense connective tissue + typus regularis (textus connectivus collagenosus compactus) + UBERON:0007846 + + + cranial bone + UBERON:0007914 + "A bone that is part of a craniocervical region." [OBOL:automatic] + bone of craniocervical region + head or neck bone + UBERON:bone of craniocervical region + + + irregular bone + "The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid." [http://en.wikipedia.org/wiki/Irregular_bone] + os irregulare + UBERON:0008001 + UBERON:irregular bone + os irregulare + + + hypertrophic cartilage zone + UBERON:0008187 + UBERON:hypertrophic cartilage zone + + + pneumatic bone + os pneumaticum + pneumatized bone + UBERON:0008193 + UBERON:pneumatized bone + hollow bone + "A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]." [http://www.medilexicon.com/medicaldictionary.php?t=11303] + + + forehead + fore head + "The part of the face above the eyes[MESH]. In human anatomy, the forehead is the fore part of the head. It is, formally, an area of the head bounded by three features, two of the skull and one of the scalp. The top of the forehead is marked by the hairline, the edge of the area where hair on the scalp grows. The bottom of the forehead is marked by the supraorbital ridge, the bone feature of the skull above the eyes. The two sides of the forehead are marked by the temporal ridge, a bone feature that links the supraorbital ridge to the coronal suture line and beyond[WP]." [http://en.wikipedia.org/wiki/Forehead, MESH:A01.456.505.580] + UBERON:forehead + UBERON:0008200 + sinciput + + + UBERON:0008202 + UBERON:bone of hip region + bone of hip region + + + tibialis muscle + UBERON:tibialis + tibialis + "Either of two muscles of the calf of the leg." [Fast_Health_Medical_Dictionary:http\://www.fasthealth.com/dictionary/] + UBERON:0008230 + + + tooth bud + tooth germ + "A knoblike tooth primordium developing into an enamel organ surrounded by a dental sac and encasing the odontogenic papilla." [BTO:0001838] + UBERON:tooth bud + UBERON:0008281 + + + iliac region + inguen + "The external junctural region between the lower part of the abdomen and the thigh." [MESH:A01.047.365] + UBERON:0008337 + groin area + iliac fossa viewed surgically + iliac region + inguen + groin region + groin + inguinal region + inguinal region + inguinal part of abdomen + UBERON:inguinal part of abdomen + + + proximale tubule epithelium + UBERON:proximale tubular epithelium + "The cells lining the proximal tubule are cuboidal epithelial cells with deep basal membrane invaginations that provide a large basal surface area. The long microvilli (the brush border) lining the tubule lumen, maximize luminal surface area and make these cells ideally suited for both reabsorptive and secretory functions." [Renal_Physiology:Section_7\,_Chapter_3] + proximale tubular epithelium + UBERON:0008404 + + + UBERON:0008439 + webbed interdigital region between pedal digits + UBERON:webbed interdigital region between pedal digits + toe web + "A webbed interdigital region that is part of a pes." [OBOL:automatic] + + + proximal endoderm + inner cell mass derived hypoblast + visceral endoderm + "A thin monolayer of small cuboidal cells that make up the lower layer of the bilaminar embryonic disc, beneath the epiblast." [MP:0011183] + primitive endoderm + primary endoderm + UBERON:0008776 + UBERON:inner cell mass derived hypoblast + hypoblast + + + "A limb segment that is part of a hindlimb." [OBOL:automatic] + subdivision of free lower limb + lower limb segment + UBERON:lower limb segment + UBERON:0008784 + segment of free lower limb + free lower limb segment + free lower limb subdivision + + + UBERON:upper limb segment + UBERON:0008785 + free upper limb segment + segment of free upper limb + "A limb segment that is part of a forelimb." [OBOL:automatic] + upper limb segment + subdivision of free upper limb + free upper limb subdivision + + + parietal endoderm + "primitive endoderm-derived tissue that lines the luminal surface of the mural trophectoderm[MP]" [http://www.ncbi.nlm.nih.gov/pubmed/19201946, MP:0011187] + distal endoderm + UBERON:parietal endoderm + UBERON:0008800 + + + copulatory organ + "An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP]." [http://en.wikipedia.org/wiki/Intromittent_organ] + UBERON:intromittent organ + intromittent organ + UBERON:0008811 + + + embryonic head + UBERON:0008816 + UBERON:embryonic head + "A head that is part of a embryo." [OBOL:automatic] + + + UBERON:superior mediastinum + mediastinum superius + "The superior mediastinum is that portion of the interpleural space which lies between the manubrium sterni in front, and the upper thoracic vertebrae behind." [http://en.wikipedia.org/wiki/Superior_mediastinum] + UBERON:0008818 + superior mediastinum + superior mediastinal part of chest + + + UBERON:0008831 + internal spiral sulcus + "A concavity in the floor of the cochlear duct formed by the overhanging vestibular lip." [http://www.drugs.com/dict/inner-spiral-sulcus.html] + inner spiral sulcus + UBERON:inner spiral sulcus + sulcus spiralis internus + + + external spiral sulcus + UBERON:0008832 + UBERON:outer spiral sulcus + outer spiral sulcus + sulcus spiralis externus + "A concavity in the outer wall of the cochlear duct between the spiral prominence and the spiral organ." [http://www.drugs.com/dict/outer-spiral-sulcus.html] + + + UBERON:0008845 + "A ligament that does not connect two skeletal elements." [http://orcid.org/0000-0002-6601-2165] + UBERON:nonskeletal ligament + nonskeletal ligament + fibrous ligament + non-skeletal ligament + + + skeletal ligament + "Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, http://orcid.org/0000-0002-6601-2165] + UBERON:0008846 + articular ligament + articular larua + UBERON:skeletal ligament + true ligament + + + "closed space within the ectoplacental cone, formed by the fusion of the parts of the amniotic fold that separate it from the amniotic cavity[MP]. a developmental cavity that exists in some mammals and is derived by division of the proamniotic space; it is further removed from the embryo than the amniotic cavity in some mammals" [http://www.medilexicon.com/medicaldictionary.php?s=epamniotic+cavity, MP:0011207] + epamniotic cavity + epamniotic cavity + UBERON:0008851 + UBERON:ectoplacental cavity + ectoplacental cavity + + + osteoid tissue + pre-bone + prebone tissue + "Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000046] + UBERON:0008883 + osteoid + prebone + UBERON:osteoid + + + fin + UBERON:fin + "An external projection of an aquatic animal as a fish used in propelling or guiding the body[BTO]." [BTO:0004649, http://en.wikipedia.org/wiki/Fin] + UBERON:0008897 + + + UBERON:0008907 + UBERON:dermal bone + dermal bone + "Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000130] + + + "An extraembryonic epithelium that is formed by the delaminated cells of the primitive endoderm (hypoblast) that goes on to form the yolk sac. In mammals, as in avians, these cells do not produce any part of the newborn organism (i.e. they are extraembryonic)" [http://www.ana.ed.ac.uk/database/humat/notes/extraemb/mesoder.htm, https://orcid.org/0000-0002-6601-2165, ISBN:9780878932504] + UBERON:extraembryonic endoderm + extraembryonic endoderm + UBERON:0008945 + + + auditory bullae + tympanic bulla + UBERON:0008959 + "A hollow bony structure on the ventral, posterior portion of the skull of placental mammals that encloses parts of the middle and inner ear. In most species, it is formed by the tympanic part of the temporal bone." [http://en.wikipedia.org/wiki/Auditory_bulla] + auditory bulla + bulla tympanica + UBERON:auditory bulla + + + UBERON:0008962 + forelimb bone + free forelimb bone + UBERON:forelimb bone + "A bone that is part of a forelimb region. Examples: humerus, any of the phalanges. Counter-example: scapula (a bone of the pectoral girdle). Note that we consider the forelimb to end at the shoulder." [https://orcid.org/0000-0002-6601-2165] + + + UBERON:0008979 + cadaver + dead body + UBERON:carcass + carcass + "A dead body." [BTO:0001965] + + + renal parenchyma + parenchyma of kidney + kidney parenchyma + UBERON:0008987 + UBERON:renal parenchyma + "The functional tissue of the kidney, consisting of the nephrons." [BTO:0003604] + + + UBERON:stomach region + UBERON:0009034 + stomach region + "An organ part that is part of a stomach." [OBOL:automatic] + + + solitary nucleus + solitary nuclear complex + nucleus tractus solitarii medullae oblongatae + nucleus solitarius + Geschmackskern@ge + nucleus of the tractus solitarius + solitary tract nucleus + nucleus of the solitary tract + "A neural nucleus that is part of the solitary tract nuclear complex. The solitary tract and nucleus are structures in the brainstem that carry and receive visceral sensation and taste from the facial (VII), glossopharyngeal (IX) and vagus (X) cranial nerves. [WP,unvetted]." [http://en.wikipedia.org/wiki/Solitary_nucleus, OBOL:automatic] + solitary nucleus + nucleus tracti solitarii + UBERON:nucleus of solitary tract + nucleus tractus solitarii + nuclei tractus solitarii + nucleus of solitary tract + UBERON:0009050 + nucleus of tractus solitarius + + + UBERON:epibranchial ganglion + "Cranial ganglion which develops from an epibranchial placode." [http://www.ncbi.nlm.nih.gov/pubmed/20133851, ZFIN:curator] + epibranchial ganglion + UBERON:0009127 + epibranchial ganglia + + + UBERON:pleuroperitoneal membrane + pleuroperitoneal membranes + pleuroperitoneal fold + pleuroperitoneal membrane + "A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities." [http://en.wikipedia.org/wiki/Pleuroperitoneal, http://medical-dictionary.thefreedictionary.com/pleuroperitoneal+membrane] + UBERON:0009133 + + + "A vein that is part of a craniocervical region." [OBOL:automatic] + UBERON:0009141 + vein of head and neck + UBERON:craniocervical region vein + craniocervical region vein + head and neck veins + craniocervical vein + + + pharyngeal region + UBERON:0009145 + pharyngeal region of foregut + UBERON:pharyngeal region of foregut + + + UBERON:0009149 + "opening in the septum primum between the two atria of the embryonic heart[TMD]." [http://en.wikipedia.org/wiki/Primary_interatrial_foramen, http://medical-dictionary.thefreedictionary.com/foramen+primum] + ostium primum + interatrial foramen primum + primary interatrial foramen + foramen primum + UBERON:foramen primum + + + "Any suture between cranial and/or facial bones." [GO:0097094] + UBERON:craniofacial suture + articulation of skull bones + joint of the skull bones + UBERON:0009198 + craniofacial suture + + + UBERON:0009201 + nephric duct + "A nephric duct is a tube that drains a primitive kidney[GO]." [GO:0072176] + UBERON:nephric duct + + + handplate mesenchyme + "Mesenchyme that is part of a handplate." [OBOL:automatic] + hand plate mesenchyme + UBERON:0009523 + mesenchyme of handplate + UBERON:mesenchyme of handplate + + + UBERON:distal segment of digit + "A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium)." [http://dx.doi.org/10.1038/nature10346] + distal digit segment + digit tip + tip of digit + UBERON:0009551 + distal segment of digit + + + UBERON:distal segment of manual digit + fingertip + finger digit tip + finger distal segment + tip of finger + distal segment of manual digit + finger tip + UBERON:0009552 + forelimb digit tip + "A segment of the manual digit containing the distal phalanx" [http://orcid.org/0000-0002-6601-2165] + + + unguis + UBERON:0009564 + hoof, claw or nail + UBERON:distal limb integumentary appendage + "A nail, hoof or claw." [http://www.ncbi.nlm.nih.gov/pubmed/11710767] + distal limb integumentary appendage + hoof or claw + + + region of trunk + subdivision of trunk + UBERON:0009569 + trunk subdivision + UBERON:subdivision of trunk + + + UBERON:0009571 + "In protostomes (such as insects, snails and worms) as well as deuterostomes (vertebrates), the midline is an embryonic region that functions in patterning of the adjacent nervous tissue. The ventral midline in insects is a cell population extending along the ventral surface of the embryo and is the region from which cells detach to form the ventrally located nerve cords. In vertebrates, the midline is originally located dorsally. During development, it folds inwards and becomes the ventral part of the dorsally located neural tube and is then called the ventral midline, or floor plate." [GOC:bf, GOC:go_curators, http://www.ncbi.nlm.nih.gov/pubmed/12075342] + ventral midline + UBERON:ventral midline + + + interdigital mesenchyme + UBERON:0009585 + mesenchyme of interdigital region + "Mesenchyme that is part of a developing interdigital region." [OBOL:automatic] + interdigit mesenchyme + interdigital region mesenchyme + UBERON:interdigital region mesenchyme + + + mesenchyme of interdigital region between digits 1 and 2 + mesenchyme of interdigital region between digits I and II + UBERON:0009596 + UBERON:mesenchyme of interdigital region between digits 1 and 2 + "An interdigital region mesenchyme that is part of a interdigital region between digits 1 and 2." [OBOL:automatic] + + + UBERON:0009623 + spinal neural root + spinal root + root of spinal nerve + spinal nerve root + UBERON:spinal nerve root + "The paired bundles of nerve fibers entering and leaving the spinal cord at each segment. The dorsal and ventral nerve roots join to form the mixed segmental spinal nerves. The dorsal roots are generally afferent, formed by the central projections of the spinal (dorsal root) ganglia sensory cells, and the ventral roots efferent, comprising the axons of spinal motor and autonomic preganglionic neurons. There are, however, some exceptions to this afferent/efferent rule." [MESH:A08.800.800.720.725] + + + UBERON:midbrain nucleus + "Nucleus located in the midbrain." [ZFIN:curator] + UBERON:0009661 + midbrain nucleus + + + UBERON:hindbrain nucleus + "Nucleus located within the hindbrain." [ZFIN:curator] + hindbrain nucleus + UBERON:0009662 + + + UBERON:telencephalic nucleus + "A nucleus of brain that is part of a telencephalon." [OBOL:automatic] + UBERON:0009663 + telencephalic nucleus + + + UBERON:head fold of embryonic disc + "The crescent-shaped, ventrally located fold of the embryonic disc at the future cephalic end of the developing embryo" [MP:0011257] + UBERON:0009746 + head fold + head fold of embryonic disc + + + cephalic neural fold + UBERON:0009748 + UBERON:cephalic neural fold + "The elevated margins of the neural groove that are located in the future cephalic region of the embryo" [MP:0011259] + + + "The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells." [MP:0011261] + UBERON:0009749 + limb mesoderm + UBERON:limb mesenchyme + limb mesenchyme + + + UBERON:0009751 + "The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures" [MP:0011264] + heart mesenchyme + cardiac mesenchyme + UBERON:cardiac mesenchyme + + + proximal interphalangeal joint + UBERON:0009767 + "An inter-phalangeal joint that connects a proximal phalanx to either a medial or distal phalanx." [http://orcid.org/0000-0002-6601-2165] + UBERON:proximal interphalangeal joint + + + UBERON:renal tubule + "A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis." [GO:0061333, GOC:dph, GOC:mtg_kidney_jan10, http://dx.doi.org/10.1371/journal.pone.0099864] + renal tubule (generic) + tubule of excretory system + UBERON:0009773 + renal tubule + + + intestinal pouch + digestive tract diverticulum + UBERON:digestive tract diverticulum + diverticulum of gut + "Branch or outpocketing of the digestive tract." [https://orcid.org/0000-0002-6601-2165] + UBERON:0009854 + + + UBERON:sac + diverticulum + sac + pouch + UBERON:0009856 + + + UBERON:secondary heart field + second heart field + UBERON:0009889 + anterior/second heart field + "A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract)." [GO:0003139, GOC:mtg_heart, GOC:rl] + secondary heart field + anterior heart field + SHF + + + UBERON:0009911 + UBERON:lobule + lobule + + + UBERON:0009912 + UBERON:anatomical lobe + "A portion of an organ, such as the liver, lung, breast, or brain." [ncithesaurus:Lobe] + anatomical lobe + + + "A narrow layer of cells located between the granule cell layer and hilus of the dentate gyrus, where adult neurogenesis occurs. " [http://en.wikipedia.org/wiki/Subgranular_zone] + subgranular zone + UBERON:0009952 + UBERON:dentate gyrus subgranular zone + dentate gyrus subgranular zone + subgranular zone of dentate gyrus + + + placodae neurogenicae + "Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia." [http://www.ncbi.nlm.nih.gov/pubmed/11523831, UBERON:cjm] + UBERON:0009955 + neurogenic placode + UBERON:neurogenic placode + neurogenic placodes + + + UBERON:bladder lumen + "A anatomical space that is enclosed by a urinary bladder." [OBOL:automatic] + cavity of urinary bladder + urinary bladder lumen + bladder lumen + lumen of urinary bladder + bladder cavity + UBERON:0009958 + + + UBERON:0010000 + "An anatomical structure that has more than one cell as a part." [CARO:0010000] + multicellular structure + UBERON:multicellular anatomical structure + multicellular anatomical structure + + + set of nuclei of neuraxis + UBERON:aggregate regional part of brain + UBERON:0010009 + "A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]." [NIFSTD:nlx_anat_20090509] + aggregate regional part of brain + + + basal ganglia + basal ganglia set + subcortical nuclei + cerebral nuclei + UBERON:0010011 + collection of basal ganglia + basal nuclei + UBERON:collection of basal ganglia + "Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum." [NIFSTD:birnlex_826] + basal nuclei (basal ganglia) + set of basal ganglia + + + "An organ of the digestive tract that is capable of retaining and storing food" [https://orcid.org/0000-0002-6601-2165] + UBERON:0010039 + UBERON:food storage organ + food storage organ + + + gland of oral opening + UBERON:oral gland + "Gland of the epithelium lining the oral cavity. The most common are the salivary glands." [ISBN10:0073040584] + oral region gland + mouth gland + UBERON:0010047 + oral cavity gland + gland of oral region + oral gland + + + open anatomical space + "An anatomical space with at least one opening to another space or the exterior." [AEO:0000221] + UBERON:open anatomical space + UBERON:0010064 + + + "An epithelium consisting of cuboidal epithelial cells." [http://en.wikipedia.org/wiki/Cuboidal_epithelium] + cuboidal epithelium + UBERON:cuboidal epithelium + UBERON:0010077 + + + UBERON:autopod plate + UBERON:0010130 + autopod plate + "The distal elements of the developing limb of vertebrates that will give rise to the pedal appendages (e.g. manus, pes, paw)" [http://sourceforge.net/tracker/?func=detail&aid=3519614&group_id=76834&atid=1109502, MP:0004576] + limb plate + + + specialized muscle tissue of heart + conducting tissue of heart + specialized conducting tissue of heart + "Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers." [http://orcid.org/0000-0002-6601-2165] + UBERON:0010131 + UBERON:conducting tissue of heart + + + UBERON:0010133 + UBERON:neuroendocrine gland + neuroendocrine gland + "any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli" [MP:0000631\,ISBN\:0-683-40008-8] + + + UBERON:secretory circumventricular organ + UBERON:0010134 + secretory circumventricular organ + "A circumventricular organ that is capable of secreting substances into the cerebrospinal fluid." [UBERON:cjm] + + + UBERON:0010136 + epithelial sheet + "An epithelial sheet is a flat surface consisting of closely packed epithelial cells." [GO:0002011] + UBERON:epithelial sheet + + + UBERON:0010137 + polarized epithelium + UBERON:polarized epithelium + "A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis." [GO:0001738] + + + "Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male." [BTO:0004798] + male accessory gland + male accessory sex gland + UBERON:male accessory sex gland + UBERON:0010147 + + + "A gelatinous secretion used in the mating of some species. It is deposited by a male into a female genital tract and later hardens into a plug or glues the tract together." [http://en.wikipedia.org/wiki/Mating_plug] + sphragis + UBERON:0010148 + mating plug + copulatory plug + sperm plug + UBERON:mating plug + sement + copulation plug + vaginal plug + + + blood vessel lumen + UBERON:0010161 + "An anatomical cavity that surrounded_by a blood vessel." [OBOL:automatic] + UBERON:lumen of blood vessel + lumen of blood vessel + + + UBERON:post-anal tail tip + end of tail + tail tip + UBERON:0010162 + post-anal tail tip + "The distal end of the tail" [UBERON:cjm] + + + UBERON:collection of hairs + collection of hairs + set of hairs + pili + UBERON:0010164 + hairs + hairs set + "An anatomical cluster that composed_primarily_of a strand of hair." [OBOL:automatic] + + + coat pelt + hair coat + pelt + UBERON:coat of hair + set of coat hairs + coat of hair + "." [http://en.wikipedia.org/wiki/Coat_(animal)] + UBERON:0010166 + pelage + + + "A roughly circular bulge in a surface." [EHDAA2:0003250] + protuberance + UBERON:0010188 + UBERON:protuberance + + + UBERON:0010190 + UBERON:pair of dorsal aortae + pair of dorsal aortae + paired dorsal aortae + "the paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation" [MP:0004787\,ISBN\:0-914294-08-3] + + + carotid duct + ductus caroticus + UBERON:carotid duct + "A segment of the embryonic dorsal aorta between points of juncture with the third and fourth arch arteries; it regresses early in development to allow the carotid axis to take its definitive appearance." [http://www.medilexicon.com/medicaldictionary.php?s=ductus+caroticus, MP:MP] + UBERON:0010198 + + + fibrin clot + blood clot + thrombus + UBERON:blood clot + coagulated blood + UBERON:0010210 + hemostatic plug + "A semisolid gelatinous mass of coagulated blood that consists of red blood cells, white blood cells, and platelets entrapped in a fibrin network." [BTO:0000102, http://en.wikipedia.org/wiki/Thrombus] + + + bulbus oculi + eyeball of camera-type eye + "The camera-type eye apart from its appendages/adnexa." [http://en.wikipedia.org/wiki/Globe_(human_eye)] + UBERON:0010230 + eye globe + globe + eyeball + eye + UBERON:eyeball of camera-type eye + + + UBERON:umbilical blood vessel + umbilical cord blood vessel + umbilical vessel + umbilical cord blood vessels + allantoic vessel + umbilical vasculature + umbilical blood vessel + UBERON:0010260 + "One of the three blood vessels, usually one large umbilical vein and two small umbilical arteries, buried within Wharton’s jelly, that transport blood to and from the placenta, where exchange between the mother and fetus takes place; the umbilical vein carries oxygenated, nutrient-rich blood from the placenta to the fetus, and the umbilical arteries carry deoxygenated, nutrient-depleted blood from the fetus to the placenta." [MP:0003230] + + + extraembryonic epithelium + UBERON:0010303 + extra-embryonic epithelium + "An epithelium that is part of a extraembryonic structure." [OBOL:automatic] + UBERON:extraembryonic epithelium + + + future eye + "Developing anatomical structure that develops into the eyeball and associated structures." [ZFA:0001678] + UBERON:0010312 + immature eye + UBERON:immature eye + + + neural crest-derived structure + UBERON:0010313 + "An anatomical structure that develops from the neural crest." [https://orcid.org/0000-0002-6601-2165] + UBERON:neural crest-derived structure + + + UBERON:0010314 + UBERON:structure with developmental contribution from neural crest + structure with developmental contribution from neural crest + "An anatomical structure that has some part that develops from the neural crest." [https://orcid.org/0000-0002-6601-2165] + + + UBERON:0010316 + germ layer / neural crest + UBERON:germ layer / neural crest + + + UBERON:limb bud mesenchyme + "Mesenchyme that is part of a limb bud." [OBOL:automatic] + limb bud mesenchyme + UBERON:0010328 + + + paired limb/fin bud mesenchyme + UBERON:paired limb/fin bud mesenchyme + UBERON:0010329 + "Mesenchyme that is part of a limb/fin bud." [OBOL:automatic] + + + ossification centre + center of ossification + centrum ossificationis + "The first step in ossification of the cartilage is that the cartilage cells, at the point where ossification is commencing and which is termed a ossification center, enlarge and arrange themselves in rows. The matrix in which they are imbedded increases in quantity, so that the cells become further separated from each other. A deposit of calcareous material now takes place in this matrix, between the rows of cells, so that they become separated from each other by longitudinal columns of calcified matrix, presenting a granular and opaque appearance. Here and there the matrix between two cells of the same row also becomes calcified, and transverse bars of calcified substance stretch across from one calcareous column to another. Thus there are longitudinal groups of the cartilage cells enclosed in oblong cavities, the walls of which are formed of calcified matrix which cuts off all nutrition from the cells; the cells, in consequence, atrophy, leaving spaces called the primary areolC&." [http://en.wikipedia.org/wiki/Ossification_center] + UBERON:0010355 + centrum ossificationis + UBERON:ossification center + ossification center + + + secondary ossification centre + centrum ossificationis secundarium + UBERON:0010357 + secondary ossification center + UBERON:secondary ossification center + "A secondary ossification center is the area of ossification that appears after the primary ossification center has already appeared - most of which appear during the postnatal and adolescent years. Most bones have more than one secondary ossification center. In long bones, the secondary centres appear in the epiphyses." [http://en.wikipedia.org/wiki/Ossification_center#Secondary] + + + endochondral element + UBERON:0010363 + UBERON:endochondral element + endochondral replacement element + "A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000139] + + + UBERON:odontoid tissue + "Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000063] + UBERON:0010365 + odontoid tissue + tooth tissue + dental tissue + tooth hard tissue + odontogenic tissue + + + UBERON:0010371 + "Epithelium composed of cells that develops from the ectoderm[FMA,modified]." [FMA:69064] + ectoderm-derived epithelium + ecto-epithelium + UBERON:ecto-epithelium + + + UBERON:mesenchyme from somatopleure + UBERON:0010377 + mesenchyme from somatopleure + "Mesenchyme that develops_from a somatopleure." [OBOL:automatic] + + + UBERON:epidermis suprabasal layer + suprabasal layer of epidermis + epidermis suprabasal layer + "Any layer of the epidermis that is superior to the stratum basale" [UBERON:cjm\,MP\:0001233\,PMID\:10469309] + suprabasal cell layer of skin + UBERON:0010402 + + + UBERON:0010405 + UBERON:spinal cord lateral motor column + spinal cord lateral motor column + "Column of motor neurons which innervate muscles in the limb; motor neurons in the lateral motor column are further organized into pools, each of which innervates a specific muscle in the limb" [MP:MP] + + + UBERON:0010410 + inguinal fat pad + "encapsulated adipose tissue found in the groin" [MGI:csmith] + fat depot of inguinal region + inguinal fat depot + UBERON:inguinal fat pad + + + UBERON:0010411 + "encapsulated adipose tissue found on the dorsal side of the peritoneum" [MGI:csmith, MP:0005337] + retroperitoneal fat depot + retroperitoneal fat pad + UBERON:retroperitoneal fat pad + + + UBERON:0010419 + vibrissa follicle + vibrissa follicle + UBERON:vibrissa follicle + follicle of sinus hair + "one of the tubular invaginations of the epidermis enclosing the hair roots and from which grow the vibrissae located on the muzzle and face of many species" [MP:0010234\,MGI\:llw2] + follicle of vibrissa + + + ciliary processes + "The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens." [http://en.wikipedia.org/wiki/Ciliary_processes] + set of ciliary processes + UBERON:0010427 + processus ciliares + processus ciliares + ciliary processes set + ciliary process + UBERON:ciliary processes + ciliary processes + + + UBERON:0010428 + os planum + UBERON:flat bone + flat bone + "A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow." [http://en.wikipedia.org/wiki/Flat_bone] + + + "A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels." [http://en.wikipedia.org/wiki/Pseudostratified_columnar_epithelium, http://medical-dictionary.thefreedictionary.com/pseudostratified+epithelium] + UBERON:0010498 + UBERON:pseudostratified columnar epithelium + pseudostratified columnar epithelium + + + pseudostratified ciliated columnar epithelium + UBERON:0010499 + UBERON:pseudostratified ciliated columnar epithelium + epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) + "Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile." [NCIT:NCIT] + + + "A strand of hair that is part of a coat of hair." [OBOL:automatic] + pelage hair + UBERON:0010509 + UBERON:strand of pelage hair + strand of pelage hair + + + "A truncal hair that has a single constriction and bend about midway along the hair shaft, and contains two or more air cells in the medulla" [MP:0000405] + UBERON:0010510 + auchene hair + strand of auchene hair + UBERON:strand of auchene hair + + + UBERON:strand of awl hair + awl hair + "A truncal hairs that is straight, but shorter than a guard hair, and contain two or more air cells in the medulla" [http://en.wikipedia.org/wiki/Awn_hair, MP:0000400] + strand of awl hair + UBERON:0010511 + + + guard hair + "A long, straight truncal hair that contains two air cells in the medulla[MP]. A strand of hair from the top layer consisting of longer, often coarser, straight shafts of hair that stick out through the underfur. This is usually the visible layer for most mammals and contains most of the pigmentation." [http://en.wikipedia.org/wiki/Guard_hair, MP:0006365] + strand of guard hair + UBERON:strand of guard hair + guardhair + UBERON:0010512 + + + strand of zigzag hair + UBERON:strand of zigzag hair + zigzag hair + UBERON:0010513 + "A truncal hair that has two or more sharp bends with diameter constrictions at the bends, and contain one air cell in the medulla." [MP:0006366] + + + microcirculatory vessel + "A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses." [MESH:A07.231.432, UBERON:cjm, ZFA:0005251] + UBERON:0010523 + UBERON:microcirculatory vessel + microcirculatory vessels + + + limb/fin segment + UBERON:0010538 + UBERON:paired limb/fin segment + paired limb/fin segment + "An appendage segment that is part of a limb/fin." [OBOL:automatic] + + + UBERON:limb skeleton subdivision + "Skeletal subdivision that is a segment of the limb skeleton." [VSAO:0005018, VSAO:NI] + UBERON:0010712 + limb skeleton subdivision + + + cuneiform + UBERON:0010721 + distal tarsal + os cuneiform + os cuneiforme + distal tarsal bone + "There are three cuneiform bones in the human foot: the medial cuneiform the intermediate cuneiform also known as the middle the lateral cuneiform. They are located between the navicular bone and the first, second and third metatarsal bones and are medial to the cuboid bone[WP, unvetted, human specific]." [http://en.wikipedia.org/wiki/Cuneiform_%28anatomy%29] + cuneiform bone + distal tarsal bone + UBERON:distal tarsal bone + + + bone of appendage girdle complex + "A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle)." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] + bone of extended limb/fin region + UBERON:0010740 + UBERON:bone of appendage girdle complex + limb bone + + + UBERON:bone of pectoral complex + "A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] + bone of pectoral complex + UBERON:0010741 + forelimb bone + bone of forelimb or pectoral fin or pectoral girdle + + + bone of pelvic complex + hindlimb bone + UBERON:0010742 + UBERON:bone of pelvic complex + "A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] + + + central zone of follice + reaction center of follicle + germinal center + nodule + UBERON:0010754 + lymhpoid nodule + UBERON:germinal center + "A collection of activated B cells at the center of a secondary follicle, formed after B cells become activated and migrate to the center." [CL:tm, http://en.wikipedia.org/wiki/Germinal_center, https://orcid.org/0000-0002-6601-2165] + light zone of follicle + + + "A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg." [https://orcid.org/0000-0002-6601-2165] + appendage segment + UBERON:subdivision of organism along appendicular axis + subdivision of organism along appendicular axis + appendicular segment + UBERON:0010758 + + + UBERON:0010858 + interlimb + UBERON:inter limb-segment region + inter limb-segment region + + + UBERON:tragus + tragal part of pinna + tragus + "A small pointed eminence of the external ear, situated in front of the concha, and projecting backward over the meatus." [http://en.wikipedia.org/wiki/Tragus_(ear)] + UBERON:0010887 + + + "Muscles of the pelvic girdle, hindlimb or pelvic fin." [https://orcid.org/0000-0002-6601-2165] + pelvic girdle and hind limb muscles + UBERON:pelvic complex muscle + muscle of lower limb + muscle of pelvic girdle and leg + lower limb muscle + UBERON:0010890 + pelvic complex muscle + + + pectoral girdle and fore limb muscles + pectoral complex muscle + "A muscle of a pectoral girdle, pectoral fin or anterior limb." [https://orcid.org/0000-0002-6601-2165] + muscle of pectoral girdle and limb + UBERON:pectoral complex muscle + UBERON:0010891 + + + UBERON:ossicle + UBERON:0010911 + ossicle + "Skeletal element that is often isolated, small, and variable in composition." [PSPUB:0000169, VSAO:0000132] + + + skeletal subdivision + "Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] + UBERON:0010912 + subdivision of skeleton (in vivo) + UBERON:subdivision of skeleton + subdivision of skeleton + + + UBERON:vertebral element + vertebral element + UBERON:0010913 + "Skeletal element that forms around the notochord and is part of the vertebral column." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000184] + + + cartilago articularis + hyaline cartilage + UBERON:articular cartilage of joint + articular cartilage of joint + "A thin layer of cartilage, usually hyaline, on the articular surface of bones in synovial joints." [BTO:0001572] + UBERON:0010996 + articular cartilage + joint-associated cartilage + + + "Cartilage of the lower jaw that give rise to a portion of the anguloarticular compound bone." [ZFA:0001644] + UBERON:0011002 + articular cartilage element + UBERON:articular cartilage element + + + splanchnocranium cartilage + "A cartilage element that is part of a splanchnocranium." [OBOL:automatic] + UBERON:0011004 + pharyngeal arch cartilage + pharyngeal arch cartilages + UBERON:pharyngeal arch cartilage + + + UBERON:extrinsic extensor muscle of manus + extrinsic extensor muscle of hand + UBERON:0011024 + extrinsic extensor muscle of manus + "The extrinsic extensor muscles of the hand are located in the back of the forearm and have long tendons connecting them to bones in the hand, where they exert their action." [http://en.wikipedia.org/wiki/Extrinsic_extensor_muscles_of_the_hand] + + + perilymphatic channel + perilymphatic duct + cochlear aqueduct + "A channel containing perilymph passing through the temporal bone, connecting the scala tympani of the cochlea to the subarachnoid space." [http://en.wikipedia.org/wiki/Perilymphatic_duct, MESH:A09.246.631.246.280] + UBERON:perilymphatic channel + perilymphatic space + ductus perilymphaticus + UBERON:0011060 + + + endolymphatic space + UBERON:endolymphatic space + UBERON:0011078 + + + "Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis." [FMA:7491] + solid joint + UBERON:0011134 + nonsynovial joint + UBERON:nonsynovial joint + + + "A cartilage element that lies between two successive vertebral centra." [ISBN10:0073040584] + intervertebral cartilage + UBERON:intervertebral cartilage + UBERON:0011135 + + + axial skeletal system + UBERON:axial skeletal system + UBERON:0011137 + "Subdivision of the skeletal system which consists of the axial skeleton plus associated joints." [https://orcid.org/0000-0002-6601-2165] + + + synovial joint of free limb segment + "Any synovial joint that is part of a (free) limb." [https://orcid.org/0000-0002-6601-2165] + UBERON:0011139 + UBERON:synovial limb joint + synovial limb joint + + + neurocranium bone + UBERON:0011164 + "A bone that is part of a neurocranium [Automatically generated definition]." [OBOL:automatic] + UBERON:neurocranium bone + chondrocranium bone + + + UBERON:0011215 + UBERON:central nervous system cell part cluster + neuraxis layer + cell part cluster of neuraxis + central nervous system cell part cluster + "A multi cell part structure that is part of a central nervous system." [OBOL:automatic] + + + UBERON:organ system subdivision + UBERON:0011216 + "A subdivision of an anatomical system." [] + organ system subdivision + + + UBERON:0011250 + "A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones." [https://orcid.org/0000-0002-6601-2165] + UBERON:autopod bone + autopod bone + + + UBERON:0011270 + dorsum of trunk + back of trunk + trunk back + dorsal trunk + UBERON:dorsal trunk + "The part of the trunk that is in the dorsum[cjm]." [http://en.wikipedia.org/wiki/Human_back, UBERONREF:0000006] + dorsal part of trunk + + + predominantly gray regional part of telencephalon + gray matter of telencephalon + UBERON:0011300 + UBERON:gray matter of telencephalon + "A portion of gray matter that is part of a telencephalon." [OBOL:automatic] + + + skeletal parts of limb/fin + limb/fin skeleton + "The collection of all skeletal elements in an individual limb or fin." [https://orcid.org/0000-0002-6601-2165] + UBERON:0011582 + paired limb/fin skeleton + skeleton of limb/fin + UBERON:paired limb/fin skeleton + + + cell condensation + UBERON:0011585 + UBERON:cell condensation + "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995)." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000006] + + + maxillary teeth + UBERON:maxillary tooth + UBERON:0011593 + maxillary tooth + "A tooth that is attached to a maxilla[TAO,modified]." [TAO:0001627] + + + UBERON:bone of upper jaw + upper jaw bone + UBERON:0011597 + bone of upper jaw + "Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species)." [https://orcid.org/0000-0002-6601-2165] + + + subdivision of organism along main body axis + "A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column." [https://orcid.org/0000-0002-6601-2165] + main body segment + UBERON:0011676 + axial subdivision of organism + body segment + UBERON:subdivision of organism along main body axis + + + UBERON:0011679 + proximal tarsal bone + "A tarsal bone that connected_to a hindlimb zeugopod skeleton." [OBOL:automatic] + UBERON:proximal tarsal bone + + + pineal stalk + habenula + UBERON:0011768 + epiphyseal stalk + UBERON:pineal gland stalk + pineal gland stalk + + + vagus nerve nucleus + tenth cranial nerve nucleus + nucleus of vagus nerve + nucleus of Xth nerve + vagal nucleus + vagal X nucleus + nucleus of vagal nerve + "A cranial nerve nucleus that is associated with a vagus nerve." [OBOL:automatic] + UBERON:vagus nerve nucleus + nucleus of vagal X nerve + vagus nucleus + UBERON:0011775 + nodosal nucleus + + + UBERON:nucleus of spinal cord + spinal cord nucleus + UBERON:0011777 + "A neural nucleus that is part of the spinal cord." [UBERON:cjm] + nucleus of spinal cord + + + head nerve + cephalic nerve + UBERON:0011779 + "A nerve that is part of a head." [OBOL:automatic] + nerve of head region + UBERON:nerve of head region + + + "Ectodermal placode that does not develop into a component of the nervous system." [http://www.ncbi.nlm.nih.gov/pubmed/11523831, UBERON:cjm] + UBERON:non-neurogenic ectodermal placode + non-neurogenic ectodermal placode + UBERON:0011814 + + + UBERON:0011817 + UBERON:follicle placode + follicle placode + + + irregular connective tissue + "Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium." [FMA:20107] + UBERON:0011821 + UBERON:irregular connective tissue + + + dense irregular connective tissue + "Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium." [FMA:20109, http://en.wikipedia.org/wiki/Dense_irregular_connective_tissue] + UBERON:0011822 + irregular dense connective tissue + typus irregularis (textus connectivus collagenosus compactus) + UBERON:dense irregular connective tissue + + + UBERON:dense connective tissue + UBERON:0011823 + "Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets" [http://en.wikipedia.org/wiki/Dense_connective_tissue] + dense connective tissue + + + musculus plantaris + plantaris + UBERON:plantaris + plantaris + "Plantaris is a vestigial structure and one of the superficial muscles of the posterior crural compartment of the leg. It is innervated by the tibial nerve (S1, S2) . It is composed of a thin muscle belly and a long thin tendon. It is approximately 2-4 inches long, and is absent in 7 - 10% of the human population. It is one of the plantar flexors in the superior compartment of the leg along with the gastrocnemius, and soleus. The plantaris is considered an unimportant muscle, it mainly acts with gastrocnemius[WP]." [http://en.wikipedia.org/wiki/Plantaris_muscle] + UBERON:0011905 + + + UBERON:0011919 + "masses of developing blood cells attached to endothelium in the yolk sac" [MP:0011204] + yolk sac blood islands + yolk sac blood island + UBERON:yolk sac blood island + visceral yolk sac blood island + + + coelomic cavity + coelem + "The structure that contains the coelemic cavity." [http://en.wikipedia.org/wiki/Body_cavity, http://en.wikipedia.org/wiki/Coelom] + UBERON:coelom + UBERON:0011997 + coelom + + + epithelium-associated lymphoid tissue + UBERON:0012069 + UBERON:epithelium-associated lymphoid tissue + + + UBERON:0012101 + perinatal stage + "The period spanning the range immediately before and after birth" [] + UBERON:perinatal stage + + + centrale + os centrale + central mesopodium bone + UBERON:0012131 + UBERON:centrale + "Endochondral bone located between the proximal and distal rows of carpals or tarsals and thus representing the central carpals or tarsals[PHENOSCAPE]." [PHENOSCAPE:AMAO] + centralia + + + UBERON:0012139 + segment of autopod + UBERON:segment of autopod + + + nucleusa ccumbens core + UBERON:0012170 + UBERON:core of nucleus accumbens + core of nucleus accumbens + nucleus accumbens core + core of nucleus accumbens + core region of nucleus accumbens + accumbens nucleus, core + accumbens nucleus core + + + intercostal space + UBERON:intercostal space + UBERON:0012198 + "A space in the rib cage between two successive ribs." [UBERON:cjm] + + + UBERON:ureteric bud trunk + "ureteric bud cells that elongate to form a rigid structure (stalk) consisting of polarized epithelial cells without branching; the stalks differentiate into the collecting system of the mature kidney, while the tip cells interact with the adjacent cells of the metanephric mesenchyme, inducing their conversion into nephrons." [MP:0011761] + ureteric trunk + ureteric stalk + ureteric bud stalk + ureteric bud trunk + UBERON:0012238 + + + lumen of thyroid follicle + thyroid follicular space + UBERON:0012246 + thyroid follicular lumen + UBERON:thyroid follicular lumen + thyroid follicle lumen + "A follicular lumen is the closed cavity within a follicle of the thyroid gland. It is surrounded by follicular cells and filled with colloid, a concentrated solution of thyroglobulin" [http://en.wikipedia.org/wiki/Follicular_lumen] + + + UBERON:0012274 + "An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]" [http://en.wikipedia.org/wiki/Columnar_epithelium] + UBERON:columnar epithelium + columnar epithelium + + + "Epithelium that derives from the mesoderm. [Automatically generated definition]." [OBOL:automatic] + meso-epithelium + mesoderm-derived epithelium + mesoepithelium + UBERON:0012275 + UBERON:meso-epithelium + + + "encapsulated adipose tissue associated with the mammary gland" [MGI:csmith] + UBERON:0012282 + UBERON:mammary fat pad + mammary fat pad + + + "encapsulated adipose tissue associated with the femur" [MP:0008905] + UBERON:femoral fat pad + femoral fat pad + femoral fat depot + UBERON:0012283 + + + "One of five swellings formed during the development of the face" [http://www.indiana.edu/~anat550/hnanim/face/face.html] + embryonic facial process + primordium of face + UBERON:0012314 + facial primordium + embryonic facial prominence + UBERON:embryonic facial prominence + + + UBERON:holocrine gland + UBERON:0012344 + "any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen." [MP:0013543] + holocrine gland + + + "thin, pigmented, keratinised, hairless epidermis covering subcutaneous, collagenous, and adipose tissue." [http://en.wikipedia.org/wiki/Paw#Common_characteristics, https://orcid.org/0000-0002-6601-2165] + paw pad + autopod pad + UBERON:0012348 + UBERON:autopod pad + + + "A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton." [https://orcid.org/0000-0002-6601-2165] + UBERON:0012357 + digit bone + UBERON:digitopodium bone + digitopodium bone + + + "A bone that is part of a the manual digitopodium skeleton - i.e. the fingers or the metacarpal skeleton." [https://orcid.org/0000-0002-6601-2165] + UBERON:0012358 + UBERON:manual digitopodium bone + manual digitopodium bone + bone of forelimb digitopodium + + + pedal digitopodium bone + UBERON:pedal digitopodium bone + "A bone that is part of a the pedal digitopodium skeleton - i.e. the toes or the metatarsal skeleton." [https://orcid.org/0000-0002-6601-2165] + UBERON:0012359 + bone of hindlimb digitopodium + + + bone of jaw + UBERON:bone of jaw + jaw bone + UBERON:0012360 + "A bone element that is part of a jaw region." [OBOL:automatic] + + + microvilli + "A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified]" [GO:0005902, http://en.wikipedia.org/wiki/Microvillus] + UBERON:layer of microvilli + microvillus + UBERON:0012423 + layer of microvilli + + + UBERON:brush border layer + brush border + brush border membrane + brush border layer + UBERON:0012424 + "The microvilli-covered surface of simple cuboidal epithelium and simple columnar epithelium cells found in certain locations of the body. Found in small intestine and kidney" [http://en.wikipedia.org/wiki/Brush_border] + + + brush border microvillus layer of intestine + "A brush border layer that is part of a intestine." [OBOL:automatic] + intestinal brush border + UBERON:0012427 + UBERON:intestinal brush border layer + intestinal brush border layer + + + hemopoietic tissue + UBERON:0012429 + textus haemopoieticus + UBERON:hemopoietic tissue + "Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue" [http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue] + haemopoietic tissue + hematopoietic tissue + + + closed anatomical space + enclosed anatomical space + UBERON:0012467 + UBERON:enclosed anatomical space + "An anatomical space with no opening to another space or to the exterior." [AEO:0000222] + + + UBERON:0012652 + colorectum + "The subdivision of the digestive tract that consists of the colon and the rectum." [UBERON:cjm] + UBERON:colorectum + + + "Any vein within the general circulation that transports blood back to the right atrium of the heart." [ncithesaurus:Systemic_Vein] + systemic venous tree organ part + UBERON:0013140 + systemic vein + UBERON:systemic vein + + + UBERON:capillary bed + capillary bed + "A localized group of blood capillaries." [AEO:0001002] + microcirculatory bed + UBERON:0013141 + + + early mesencephalic vesicle + UBERON:0013147 + UBERON:early mesencephalic vesicle + mesencephalic vesicle + + + brain vesicle + primitive brain vesicle + future brain vesicle + UBERON:future brain vesicle + early brain vesicle + UBERON:0013150 + + + UBERON:molariform tooth + molariform tooth + "A molar or premolar" [ISBN10:0073040584] + molariform + UBERON:0013164 + cheek tooth + postcanine tooth + + + front of body proper + ventrum + ventral part of organism + ventral region of organism + UBERON:ventrum + UBERON:0013235 + "A major organism subdivisionthat is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane." [BSPO:0000068, UBERONREF:0000006] + + + "The bregma is the anatomical point on the skull at which the coronal suture is intersected perpendicularly by the sagittal suture." [http://en.wikipedia.org/wiki/Bregma] + UBERON:0013406 + bregma + UBERON:bregma + + + UBERON:subdivision of oviduct + subdivision of oviduct + subdivision of uterine tube + zone of uterine tube + UBERON:0013515 + "A section through the tube or network of tubes that connects the ovaries to the outside of the body." [UBERON:cjm] + subdivision of oviduct + uterine tube zone + + + subdivision of tube + UBERON:0013522 + UBERON:subdivision of tube + + + "A metapodium bone that is part of a digit 2 plus metapodial segment." [OBOL:automatic] + metapodium II + metapodium 2 + UBERON:0013582 + metapodium bone 2 + UBERON:metapodium bone 2 + + + foot pad of pes + UBERON:pedal autopod pad + "A autopod pad that is part of a pes." [OBOL:automatic] + pedal autopod pad + UBERON:0013623 + pedal foot pad + + + UBERON:epithelium of intestinal villus + villous epithelium + UBERON:0013636 + "A epithelium that is part of a intestinal villus." [OBOL:automatic] + villus epithelium + epithelium of intestinal villus + intestinal villus epithelium + + + UBERON:0013682 + peripheral retina + peripheral region of retina + UBERON:peripheral region of retina + + + UBERON:0013685 + foramen of skull + cranial conduit + cranial foramen + "Anatomical space that is an opening in a bone of the skull." [http://orcid.org/0000-0002-6601-2165, TAO:curator] + foramina of the skull + UBERON:foramen of skull + foramen of skull + + + clunis + buttock + "A zone of soft tissue located on the posterior of the lateral side of the pelvic region corresponding to the gluteal muscles." [http://en.wikipedia.org/wiki/Buttocks, UBERON:cjm] + regio glutealis + gluteal part of pelvic girdle + UBERON:buttock + gluteal region + buttocks + UBERON:0013691 + + + "Anatomical projection that is part of the integumentl system." [http://orcid.org/0000-0002-6601-2165] + integumentary projection + UBERON:integumentary projection + UBERON:0013703 + + + integumentary system layer + UBERON:integumentary system layer + "A organ component layer that is part of a integumental system." [OBOL:automatic] + UBERON:0013754 + + + digestive system element + digestive organ + UBERON:digestive system element + UBERON:0013765 + "Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements." [UBERON:cjm] + digestive system organ + + + "Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart." [http://en.wikipedia.org/wiki/Great_vessels] + UBERON:great vessel of heart + UBERON:0013768 + great vessel of heart + great vessel of thorax + + + embryonic body + UBERON:embryoid body + embryoid body + UBERON:0014374 + "Embryoid bodies (EBs) are three-dimensional aggregates of pluripotent stem cells." [EFO:0004988] + + + neural crest mesenchyme + UBERON:0014387 + "Mesenchyme that develops_from the neural crest[Automatically generated definition]." [OBOL:automatic] + neural crest derived mesenchyme + mesenchyme derived from neural crest + mesenchyme from neural crest + UBERON:mesenchyme derived from neural crest + + + kidney collecting duct epithelium + collecting duct of renal tubule epithelium + epithelium of collecting duct of renal tubule + epithelium of renal collecting tubule + "The simple cuboidal epithelium lining the lumen of kidney collecting ducts." [MGI:anna, MP:0011843] + UBERON:0014388 + UBERON:kidney collecting duct epithelium + + + proximal mesopodial bone + UBERON:0014395 + "A proximal mesopodial endochondral element that is composed primarily of a bone tissue." [OBOL:automatic] + UBERON:proximal mesopodial bone + + + UBERON:sinusoidal space + sinusoidal space + lumen of sinusoid + UBERON:0014399 + sinusoid lumen + "A anatomical space that is enclosed by a sinusoid." [OBOL:automatic] + + + UBERON:white matter lamina of neuraxis + white matter lamina of neuraxis + UBERON:0014530 + + + isthmus of Gyrus fornicatus + "The white laminae of cerebellum is subdivision of the cerebellar cortex comprised of myelinated axons lying deep to the granule cell layer of the cerebellar cortex." [http://neurolex.org/wiki/Category\:White_laminae_of_cerebellum] + isthmus cinguli + white matter lamina of cerebellum + UBERON:white matter lamina of cerebellum + white laminae of cerebellum + lamina alba of cerebellar cortex + isthmus of the cingulate gyrus + isthmus-2 + laminae albae of cerebellar cortex + UBERON:0014540 + isthmus gyri cinguli + white lamina of cerebellum + laminae albae of cerebellar cortex + isthmus gyri cingulatus + + + CA1 part of stratum pyramidale hippocampi + CA1 stratum pyramidale hippocampi + UBERON:0014548 + stratum pyramidale of the CA1 field + stratum pyramidale of CA1 + CA1 stratum pyramidale + field CA1, pyramidal layer + UBERON:pyramidal layer of CA1 + "CA1 part of stratum pyramidale hippocampi" [NIFSTD:birnlex_4110] + pyramidal layer of CA1 + CA1 pyramidal cell layer + CA1 stratum pyramidale hippocampi + + + "A subdivision of a layer of the hippocampus (e.g. stratum moleculare) covering all or port of a hippocampal field (e.g. CA1)." [http://orcid.org/0000-0002-6601-2165] + UBERON:0014567 + UBERON:layer of hippocampal field + layer of hippocampal field + + + base of the cochlear canal + UBERON:base of cochlear canal + base of cochlear canal + UBERON:0014626 + + + UBERON:spinoocerebellum + UBERON:0014643 + "A phylogenetic subdivision of the cerenellum, the intermediate part, which regulates body and limb movements. It receives proprioception input from the dorsal columns of the spinal cord (including the spinocerebellar tract) and the trigeminal nerve, as well as from visual and auditory systems. It sends fibres to deep cerebellar nuclei which in turn project to both the cerebral cortex and the brain stem, thus providing modulation of descending motor systems." [http://en.wikipedia.org/wiki/Anatomy_of_the_cerebellum#Phylogenetic_and_functional_divisions] + spinoocerebellum + paleocerebellum + + + "Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin)." [OBOL:automatic] + UBERON:pectoral appendage muscle + UBERON:0014794 + pectoral appendage muscle + + + pelvic appendage muscle + "Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin)." [OBOL:automatic] + UBERON:0014795 + UBERON:pelvic appendage muscle + + + UBERON:0014892 + "A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles)." [GOC:dos] + skeletal muscle organ + UBERON:skeletal muscle organ + + + intersomitic vessel + intersegmental vessel + intersomitic vessels + segmental vessel + UBERON:intersomitic vessel + UBERON:0014907 + intersegmental vessels + "One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites." [MGI:anna] + intersomitic blood vessel + + + Virchow-Robin space + UBERON:perivascular space + perivascular space + "The space between a blood vessel and the pia mater." [ncithesaurus:Perivascular_Space] + perivascular spaces + UBERON:0014930 + perivascular region + + + radius element + radius endochondral element + "A radius bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + UBERON:radius endochondral element + UBERON:0015001 + + + UBERON:ulna endochondral element + UBERON:0015003 + "A ulna bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + ulna element + ulna endochondral element + + + tibia endochondral element + UBERON:0015004 + tibia element + UBERON:tibia endochondral element + "A tibia bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + + + UBERON:vertebra endochondral element + UBERON:0015005 + "A vertebra bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + vertebra endochondral element + vertebra element + + + UBERON:0015007 + "A vertebral endochondral element in the cervical region of the vertebral column." [UBERON:cjm] + cervical vertebra endochondral element + UBERON:cervical vertebra endochondral element + cervical vertebra element + + + UBERON:0015009 + "A lumbar vertebra bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + lumbar vertebra element + lumbar vertebra endochondral element + UBERON:lumbar vertebra endochondral element + + + fibula endochondral element + UBERON:0015013 + UBERON:fibula endochondral element + "A fibula bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + fibula element + + + UBERON:0015014 + calcaneum element + "A calcaneum bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + UBERON:calcaneum endochondral element + calcaneum endochondral element + + + UBERON:0015019 + rib element + "A rib bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + rib endochondral element + UBERON:rib endochondral element + + + forelimb endochondral element + "A forelimb bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + UBERON:forelimb endochondral element + UBERON:0015021 + + + "A hindlimb bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + UBERON:hindlimb endochondral element + UBERON:0015022 + hindlimb endochondral element + + + phalanx element + UBERON:0015023 + phalanx endochondral element + UBERON:phalanx endochondral element + "A phalanx bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + + + "A pedal digit metatarsal bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + pedal digit metatarsal endochondral element + UBERON:0015036 + pedal digit metatarsal element + UBERON:pedal digit metatarsal endochondral element + + + pedal digit 2 metatarsal element + "A pedal digit 2 metatarsal bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + pedal digit 2 metatarsal endochondral element + UBERON:pedal digit 2 metatarsal endochondral element + pedal digit II metatarsal endochondral element + UBERON:0015038 + + + UBERON:manual digit metacarpus endochondral element + manual digit metacarpus endochondral element + "A manual digit metacarpus bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + UBERON:0015042 + manual digit metacarpus element + + + carpus endochondral element + UBERON:0015049 + carpus element + "A carpus bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + UBERON:carpus endochondral element + + + UBERON:tarsus endochondral element + "A tarsus bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + UBERON:0015050 + tarsus element + tarsus endochondral element + + + femur element + UBERON:0015052 + "A femur bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + femur endochondral element + UBERON:femur endochondral element + + + "A humerus bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + UBERON:0015053 + humerus element + humerus endochondral element + UBERON:humerus endochondral element + + + scapula element + UBERON:0015057 + scapula endochondral element + UBERON:scapula endochondral element + "A scapula bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + + + limb bone endochondral element + "A limb bone or its cartilage or pre-cartilage precursor." [UBERON:endochondral] + UBERON:limb endochondral element + limb endochondral element + UBERON:0015061 + + + UBERON:0015063 + "A endochondral element that is part of a autopod region." [OBOL:automatic] + autopod endochondral element + UBERON:autopod endochondral element + + + central mesopodium element + UBERON:0015067 + "Endochondral element located between the proximal and distal rows of carpals or tarsals and thus representing the central carpals or tarsals[PHENOSCAPE]." [PHENOSCAPE:AMAO] + UBERON:centrale endochondral element + centralia + centrale endochondral element + + + proximal tarsal endochondral element + "A proximal mesopodial endochondral element that is part of a hindlimb." [OBOL:automatic] + UBERON:proximal tarsal endochondral element + UBERON:0015081 + + + distal tarsal endochondral element + UBERON:0015099 + "A distal mesopodial endochondral element that is part of a hindlimb." [OBOL:automatic] + UBERON:distal tarsal endochondral element + + + distal tarsal bone 2 endochondral element + UBERON:0015105 + UBERON:distal tarsal bone 2 endochondral element + + + mesenteric fat pad + "Encapsulated adipose tissue associated with the mesentery" [MP:0008903] + mesenteric fat depot + UBERON:mesenteric fat pad + UBERON:0015143 + + + "A region of somite adjacent to presomitic mesoderm." [http://orcid.org/0000-0002-6601-2165] + inter-somited border + UBERON:0015178 + intersomitic boundary + somite boundary + segmental border + intersomitic fissure + somite border + intersomitic junction + UBERON:somite border + + + UBERON:lateral structure + UBERON:0015212 + lateral structure + "Any structure that is placed on one side of the left-right axis of a bilaterian." [http://orcid.org/0000-0002-6601-2165] + + + cardiac pump + cardiac structure + circulatory organ + UBERON:circulatory organ + heart or heart like organ + UBERON:0015228 + "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile." [http://orcid.org/0000-0002-6601-2165] + + + heterogeneous tissue + UBERON:heterogeneous tissue + portion of heterogeneous tissue + UBERON:0015757 + + + respiratory conduit + "Any anatomical conduit which is part of the upper respiratory tract" [UBERON:cjm] + UBERON:0015787 + upper respiratory conduit + UBERON:upper respiratory conduit + + + "A zone of skin that is part of a autopod region." [OBOL:automatic] + UBERON:0015790 + UBERON:autopod skin + autopod skin + paw skin + + + UBERON:0015796 + hepatic blood vessel + liver blood vessel + UBERON:liver blood vessel + "A blood vessel that is part of a liver." [OBOL:automatic] + + + "A epithelium that is part of a ear." [OBOL:automatic] + UBERON:0015807 + UBERON:ear epithelium + ear epithelium + + + "A epithelium that is part of a camera-type eye." [OBOL:automatic] + UBERON:eye epithelium + UBERON:0015808 + eye epithelium + + + UBERON:0015833 + foregut epithelium + "A epithelium that is part of a foregut." [OBOL:automatic] + UBERON:foregut epithelium + + + "A capillary that is part of a lung." [OBOL:automatic] + UBERON:pulmonary capillary + pulmonary capillary + UBERON:0016405 + capillary of lung + + + UBERON:0016447 + "A strand of hair that is part of a trunk." [OBOL:automatic] + trunk hair + hair of trunk + UBERON:hair of trunk + + + UBERON:0016459 + posterior pole of lens + polus posterior lentis + UBERON:posterior pole of lens + "the central point on the posterior surface of the lens." [http://www.medilexicon.com/medicaldictionary.php?t=70707] + polus posterior (lens) + + + UBERON:0016467 + antitragal part of pinna + "The antitragus is a feature of human ear anatomy. It is a small tubercle that points anteriorly. It is separated from the tragus by the intertragic notch." [http://en.wikipedia.org/wiki/Antitragus] + antitragus + UBERON:antitragus + + + UBERON:frontal lobe + lobi frontales + frontal lobe + lobus frontalis + "Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border." [FMA:61824] + UBERON:0016525 + + + lobe of cerebral hemisphere + cerebral lobe + "Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]." [FMA:61823] + regional organ part of cerebral cortex + lobi cerebri + UBERON:0016526 + cerebral hemisphere lobe + lobes of the brain + lobe of cerebral cortex + lobe parts of cerebral cortex + UBERON:lobe of cerebral hemisphere + segment of cerebral cortex + cerebral cortical segment + + + cortex of cerebral lobe + neocortical part of cerebral hemisphere + UBERON:0016529 + cortex of lobe of cerebral hemisphere + cortex of cerebral hemisphere lobe + UBERON:cortex of cerebral lobe + "Grey matter neocortex region of a lobe of the cerebral hemisphere." [UBERON:cjm] + + + UBERON:0016530 + parietal neocortex + cortex of parietal lobe + UBERON:parietal cortex + parietal lobe cortex + "Gray matter of the parietal region of the neocortex, located in the parietal lobe of gyrencephalic animals. It is continuous anteriorly with the frontal cortex, posteriorly with the occipital cortex and medially with the insular cortex and with the temporal cortex on the posterior/inferior border." [NIFSTD:nlx_79282] + parietal cortex + + + "Gray matter of the temporal region of the neocortex, located in the temporal lobe in gyrencephalic animals" [NIFSTD:nlx_94939] + UBERON:0016538 + temporal neocortex + temporal cortex + cortex of temporal lobe + temporal lobe cortex + UBERON:temporal cortex + + + central nervous system gray matter layer + grey matter layer of neuraxis + UBERON:0016548 + "A layer of of the central nervous system that is part of gray matter." [http://orcid.org/0000-0002-6601-2165] + CNS gray matter layer + UBERON:central nervous system gray matter layer + CNS grey matter layer + gray matter layer of neuraxis + + + UBERON:spinal cord column + UBERON:0016550 + spinal cord column + + + pit + "An roughly circular indentation in a surface." [AEO:0000204, AEO:JB] + UBERON:pit + UBERON:0016566 + + + UBERON:0016879 + presumptive central nervous system + future CNS + "Primordium that develops into the central nervous system" [http://orcid.org/0000-0002-6601-2165] + future central nervous system + UBERON:future central nervous system + + + "The joint that is formed by the union of the humerus, the scapula (or shoulder blade), and the clavicle (or collarbone). Commonly thought of as a single joint, the shoulder is actually made up of two separate joints - the glenohumeral and acromioclavicular joints" [http://www.innerbody.com/image/skel17.html] + UBERON:shoulder joint + joint of shoulder region + shoulder joint + UBERON:0016884 + + + UBERON:transitional anatomical structure + UBERON:0016888 + "An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development." [AEO:0000132, AEO:JB] + transitional anatomical structure + + + descending limb of arch of aorta + UBERON:descending trunk of arch of aorta + descending trunk of arch of aorta + descending trunk of aortic arch + descending aortic arch + UBERON:0016920 + + + ventral body wall + UBERON:0017648 + UBERON:ventral body wall + "The ventral part of the body wall" [UBERON:cjm] + + + UBERON:developing mesenchymal structure + developing mesenchymal structure + "A mesenchyme-derived anatomical entity undergoing a transtion to become another structure." [AEO:0001016, AEO:JB] + UBERON:0017650 + + + "A viscus that is part of a abdomen." [OBOL:automatic] + set of abdominal viscera + abdominal viscera + abdominal viscera set + abdominal viscera + UBERON:abdominal viscera + UBERON:0017672 + + + "A mesopodial endochondral element that is in the most proximal part of the mesopodial skeleton, connected to the zeugopodial skeleton." [UBERON:cjm] + UBERON:0017750 + UBERON:proximal mesopodial endochondral element + proximal mesopodial endochondral element + + + "An endochondral element in the distal portion of the mesopodial skeleton, between the central mesopodial skeleton and the metapodial skeleton" [UBERON:cjm] + UBERON:0018099 + UBERON:distal mesopodial endochondral element + distal mesopodial endochondral element + + + UBERON:distal mesopodial bone + "A distal mesopodial endochondral element that is composed primarily of a bone tissue." [OBOL:automatic] + UBERON:0018102 + distal mesopodial bone + + + layer of muscle tissue + UBERON:layer of muscle tissue + UBERON:0018260 + "Any organ component layer that consists of muscle tissue." [UBERON:cjm] + + + UBERON:0018264 + "The dorsal region of the lateral ganglionic eminence. The cells in this area give rise to embryonic interneuron precursors that will migrate tangentially to the olfactory bulb." [GO:0021851] + UBERON:dorsal lateral ganglionic eminence + dorsal lateral ganglionic eminence + + + UBERON:nucleus of the bulbocavernosus + "The term nucleus of the bulbocavernosus refers to a cluster of motoneurons located in the anterior gray column of lumbar segments 5 and 6 of the spinal cord in the rat. Functionally it belongs to the somatic motoneuron pools of the subcortical motor system ( Swanson-2004 )" [NeuroNames:2700] + nucleus of the bulbospongiosus + spinal nucleus of the bulbocavernosus + nucleus of the bulbocavernosus + nucleus of the bulbocavernosus + UBERON:0018545 + + + bladder organ + "A membranous sac in animals that serves as the receptacle of a liquid or contains gas." [BTO:0000123] + UBERON:bladder organ + UBERON:0018707 + + + "Any region of epithelium that is part of a skin region." [UBERON:cjm] + UBERON:skin epithelium + skin epithelium + UBERON:0019204 + + + "A central point or region on the anterior or posterior surface of the lens" [] + lens pole + pole of lens + UBERON:0019210 + zone of lens + UBERON:pole of lens + lens zone + + + outer digit + outermost digit + UBERON:0019221 + lateral digit + digit 1 or 5 + UBERON:digit 1 or 5 + + + UBERON:0019222 + UBERON:digit 2, 3 or 4 + digit 2, 3 or 4 + medial digit + mesoaxial digit + + + outermost manual digit + outer manual digit + UBERON:0019231 + UBERON:manual digit 1 or 5 + lateral manual digit + manual digit 1 or 5 + lateral finger + + + manual digit 2, 3 or 4 + mesoaxial manual digit + medial manual digit + mesoxaxial finger + UBERON:manual digit 2, 3 or 4 + UBERON:0019232 + + + outer pedal digit + lateral toe + lateral pedal digit + UBERON:pedal digit 1 or 5 + pedal digit 1 or 5 + UBERON:0019241 + outermost pedal digit + + + UBERON:pedal digit 2, 3 or 4 + mesoxaxial ftoe + pedal digit 2, 3 or 4 + UBERON:0019242 + medial pedal digit + mesoaxial pedal digit + + + UBERON:early embryo + UBERON:0019248 + early embryo + + + UBERON:4-8 cell stage embryo + UBERON:0019250 + 4-8 cell embryo + 4-8 cell stage embryo + four-to-eight cell embryo + + + 8-cell stage embryo + eight-cell embryo + 8-cell embryo + UBERON:0019252 + UBERON:8-cell stage embryo + + + gray matter of hindbrain + UBERON:0019263 + UBERON:gray matter of hindbrain + gray matter of the hindbrain + + + gray matter of forebrain + UBERON:gray matter of forebrain + UBERON:0019264 + + + UBERON:0019294 + telencephalic commissures + commissure of telencephalon + UBERON:commissure of telencephalon + + + UBERON:sensory organ epithelium + sensory organ epithelium + UBERON:0019304 + + + nose epithelium + UBERON:nose epithelium + UBERON:0019306 + + + integumental exocrine gland + UBERON:exocrine gland of integumental system + exocrine gland of integumental system + "An exocrine gland that is part of a integumental system." [GOC:dos, UBERON:cjm] + integumental system exocrine gland + UBERON:0019319 + + + UBERON:0022303 + nervous system cell part layer + UBERON:nervous system cell part layer + "Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]." [NIFSTD:nlx_149357] + + + neural system + UBERON:0023879 + UBERON:neural system + "A set of neural structures that subserve a specific function, e.g., visual system" [NIFSTD:nlx_anat_090802] + neural system + + + UBERON:circuit part of central nervous system + UBERON:0024914 + circuit part of central nervous system + circuit part of central nervous system + "A collection of neuronal components interacting in a functional circuit. A neural circuit is bounded by the nervous sytem regions in which its participating neuronal components are contained (BB)." [NIFSTD:birnlex_2513] + + + sensorimotor + UBERON:0025534 + sensorimotor + UBERON:sensorimotor + + + spiral prominence of cochlea + spiral prominence of cochlear duct + spiral prominence of cochlear duct + UBERON:spiral prominence of cochlear duct + prominentia spiralis ductus cochlearis + UBERON:0028194 + "a projecting portion of the spiral ligament of the cochlea, bounding the lower edge of the stria vascularis and containing within it a blood vessel, the vas prominens." [http://medical-dictionary.thefreedictionary.com/spiral+prominence+of+cochlear+duct] + + + UBERON:0034705 + "An embryonic or larval epithelium that is committed to form part of the nervous system." [AEO:0001008, AEO:JB] + neuroepithelium + UBERON:developing neuroepithelium + developing neuroepithelium + embryonic neuroepithelium + + + differentiating neuroepithelium + UBERON:differentiating neuroepithelium + "A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells." [AEO:0001010] + UBERON:0034707 + + + cranial nerve or tract + cranial neuron projection bundle + UBERON:0034713 + neuron projection bundle from brain + "Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain" [ISBN10:0471888893, UBERON:cjm] + UBERON:cranial neuron projection bundle + cranial nerve fiber tract + cranial nerve fiber bundle + + + "A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology." [UBERON:cjm] + morphological feature + UBERON:morphological feature + UBERON:0034768 + + + lymphomyeloid tissue + UBERON:lymphomyeloid tissue + UBERON:0034769 + + + UBERON:multi organ part structure + "An multicellular anatomical structure that has subparts of multiple organs as a part." [CARO:0020001] + multi organ part structure + anatomical cluster + UBERON:0034921 + + + UBERON:cell cluster + UBERON:0034922 + "A cluster of cells, largely surrounded by a morphological boundary." [CARO:0020002] + cell cluster + + + UBERON:0034923 + "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] + disconnected anatomical group + UBERON:disconnected anatomical group + + + "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [UBERON:cjm] + anatomical collection + UBERON:0034925 + UBERON:anatomical collection + + + UBERON:external soft tissue zone + external soft tissue zone + UBERON:0034929 + "A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures." [UBERON:cjm] + + + organ zone + UBERON:0034944 + UBERON:zone of organ + organ sector + zone of organ + organ zonal region + + + ductal epithelium + UBERON:0034969 + UBERON:epithelial layer of duct + epithelial layer of duct + duct epithelium + + + thymus subunit + UBERON:0035075 + lobe or lobule of thymus + UBERON:thymus subunit + + + "The top of the head." [UBERON:EJS] + vertex + top of head + UBERON:1000019 + UBERON:top of head + vertex of head + + + ventral mesoderm + UBERON:2000083 + UBERON:ventral mesoderm + + + UBERON:yolk + yolk + "Nutrient store for embryonic development in the form of semicrystalline phospholipoprotein and contained within yolk granules. Kimmel et al, 1995." [ZFIN:curator] + UBERON:2000084 + + + UBERON:2000164 + UBERON:ventral mesenchyme + ventral mesenchyme + + + UBERON:2000280 + UBERON:medial division + medial division + + + UBERON:2000468 + anterior crista primordia + anterior crista primordium + UBERON:anterior crista primordium + + + UBERON:lateral division + lateral division + UBERON:2000532 + + + UBERON:2000732 + somite 3 + UBERON:somite 3 + "Undifferentiated mesodermal component of early trunk or tail segment or metamere, derived from paraxial mesoderm; forms the myotome, sclerotome and perhaps dermatome. Kimmel et al, 1995." [ZFIN:curator] + + + UBERON:2001463 + UBERON:melanophore stripe + stripe + melanophore stripe + stripes + + + "Tooth that is attached to the premaxilla." [TAO:wd] + premaxillary tooth + UBERON:2001626 + UBERON:premaxillary tooth + + + UBERON:pad + pads + "Surface structure that is a portion of the integument thickened relative to surrounding area." [TAO:wd] + pad + UBERON:2001977 + + + "Surface structure that is a small, fleshy protuberance." [TAO:wd] + papillae + papilla + UBERON:2001995 + UBERON:papilla + dermal papilla + + + UBERON:melanophore spot + UBERON:2002283 + melanophore spot + spot + spots + + + "Surface structure that is a visible mark on the body resulting from pigmentation." [TAO:wd] + UBERON:body marking + markings + UBERON:2002284 + body marking + + + "Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse" [http://en.wikipedia.org/wiki/Capillary#Types, http://en.wikipedia.org/wiki/Fenestra_(histology)] + fenestrated capillary vessel + fenestrated capillary + UBERON:2005260 + UBERON:fenestrated capillary + + + UBERON:2005411 + UBERON:common crus + common crus + + + external integument structure + "Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument." [AAO:EJS] + UBERON:3000961 + UBERON:external integument structure + + + UBERON:3011048 + genital system + UBERON:genital system + + + mineralized skeletal tissue + "Skeletal tissue that is mineralized." [XAO:0004039, XAO:EJS] + UBERON:4000013 + UBERON:mineralized skeletal tissue + + + UBERON:mineralized cartilage tissue + "Cartilage tissue that is mineralized." [PSPUB:0000170] + mineralized cartilage tissue + UBERON:4000088 + + + second phalanx + "Second most proximal phalanx in manual or pedal digits." [] + UBERON:4100005 + UBERON:second phalanx + + + "A centrale found in the pes." [] + pedal centrale + UBERON:pedal centrale + UBERON:4200011 + + + UBERON:tuber + "Eminence or swelling on anatomical surface." [] + tuber + UBERON:4200132 + + + suture + "Line of junction between two parts immovably connected. Modified from Henderson's Dictionary of Biological Terms." [] + UBERON:suture + UBERON:4200215 + + + surface of bone + bone surface + UBERON:4200230 + UBERON:surface of bone + "An anatomical surface that is part of a bone" [] + + + "A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis." [http://orcid.org/0000-0002-6601-2165] + digit ray + digit digitopodial subdivision + UBERON:5002544 + UBERON:digit plus metapodial segment + digit plus metapodial segment + + + alveolus or bronchus + For: bronchoalveolar + UBERON_EXT:alveolus or bronchus + bronchoalveolar + UBERON_EXT:alveolus_or_bronchus + UBERON:alveolus or UBERON:bronchus + + + UBERON_EXT:baby + baby + UBERON_EXT:baby_or_infant + For: baby/babies, infant/infants, infantile + infant + UBERON:'multicellular organism' and existence_starts_with some UBERON:'infant stage' and existence_ends_with some UBERON:'infant stage' + + + UBERON_EXT:body + UBERON_EXT:body (proper or whole multicellular organism) + body (proper or whole multicellular organism) + UBERON:'body proper' or UBERON:'multicellular organism' + body + For: body/bodies + +For: body/bodies (body proper or whole multicellular organism) + + + bone + For: bone, bony, osseous +Not for: bones (use UBERON:'bone element') + bone element or tissue + UBERON:'bone element' or UBERON:'bone tissue' + UBERON_EXT:bone element or tissue + UBERON_EXT:bone_element_or_tissue + + + UBERON_EXT:bronchiole_or_bronchus + UBERON:bronchiole or UBERON:bronchus + For: bronchial(ly) + bronchiole or bronchus + bronchial + UBERON_EXT:bronchiole or bronchus + + + UBERON_EXT:cartilage_element_or_tissue + For: cartilage/cartilaginous/cartilaginously, chondral/chondrally + UBERON:'cartilage element' or UBERON:'cartilage tissue' + cartilage + cartilaginous + UBERON_EXT:cartilage element or tissue + cartilage element or tissue + + + clump of cells + population of cells + cell cluster + cell group + For: cell(ular) clump(s)/cluster(s)/group(s)/mass(es)/population(s) + UBERON_EXT:cell clump/cluster/group/mass/population + cell clump/cluster/group/mass/population + UBERON:'cell cluster' or UBERON:'cell group' + group of cells + cell population + UBERON_EXT:cell_clump_or_cluster_or_group_or_mass_or_population + cluster of cells + cell clump + cell mass + mass of cells + + + UBERON_EXT:childhood + UBERON:'juvenile stage' and results_in_maturation_of some NCBITAXON:'Homo sapiens' + UBERON_EXT:childhood + For: childhood + childhood + + + UBERON_EXT:cranium or head + For: cranial/cranially + cranial + UBERON:cranium or UBERON:head + cranium or head + UBERON_EXT:cranium_or_head + + + UBERON:'embryo stage' or UBERON:'embryo stage part' + embryonic period + embryonic stage + embryonic stage or stage part + For: embryonic stage(s) + UBERON_EXT:embryonic stage or stage part + UBERON_EXT:embryonic_stage_or_stage_part + + + UBERON_EXT:face_or_skull + UBERON:face or UBERON:skull + craniofacial + For: craniofacial/craniofacially + face or skull + UBERON_EXT:face or skull + + + follicle + UBERON:'bursal follicle' or UBERON:'dental follicle' or UBERON:'feather follicle' or UBERON:'hair follicle' or UBERON:'lymphoid follicle' or UBERON:'ovarian follicle' or UBERON:'prostate glandular acinus' or UBERON:'thyroid follicle' + follicular + For: follicle/follicles/follicular + UBERON_EXT:follicle + UBERON_EXT:follicle + + + forepaw + UBERON_EXT:forepaw + For: forepaw/forepaws + UBERON:manus and UBERON_EXT:paw + UBERON_EXT:forepaw + + + UBERON:heart or UBERON:lung + cardiopulmonary + UBERON_EXT:heart_or_lung + For: cardiopulmonary + UBERON_EXT:heart or lung + heart or lung + + + UBERON_EXT:hindpaw + UBERON:pes and UBERON_EXT:paw + hindpaw + UBERON_EXT:hindpaw + For: hindpaw/hindpaws + + + UBERON:'Ammon\'s horn' or UBERON:'hippocampal formation' + UBERON_EXT:hippocampus_proper_or_hippocampal_formation + hippocampus + hippocampus proper or hippocampal formation + UBERON_EXT:hippocampus proper or hippocampal formation + hippocampal + For: hippocampal/hippocampi/hippocampus + + + UBERON_EXT:lens + For: lens/lenses/lenticular + UBERON:'compound eye corneal lens' or UBERON:'lens of camera-type eye' + UBERON_EXT:lens + lens + + + UBERON:'muscle structure' or UBERON:'muscle tissue' + For: muscle, muscular +Not for: muscles (use UBERON:'muscle structure') + muscle + muscular + UBERON_EXT:muscle_structure_or_tissue + muscle structure or tissue + UBERON_EXT:muscle structure or tissue + + + UBERON_EXT:neural_tissue_or_nerve_or_nervous_system + UBERON_EXT:neural tissue, nerve, or nervous system + For: neural(ly) + neural + neural tissue, nerve, or nervous system + UBERON:'neural tissue' or UBERON:nerve or UBERON:'nervous system' + + + UBERON_EXT:optic nerve + optic nerve + UBERON_EXT:optic_nerve + For: optic nerve(s) + UBERON:'cranial nerve II' or UBERON:'neuron projection bundle connecting eye with brain' + + + UBERON_EXT:paw + (UBERON:manus or UBERON:pes) and part_of some NCBITAXON:Mammalia and bearer_of some PATO:soft + UBERON_EXT:paw + paw + For: paw(s) + + + UBERON_EXT:placode + For: placode(s), placodal + UBERON:'developing epithelial placode' or UBERON:'ectodermal placode' or UBERON:'epidermal placode' or UBERON:'eye primordium' + UBERON_EXT:placode + placode + + + skeletal muscle + skeletal muscle organ or tissue + UBERON:'skeletal muscle organ' or UBERON:'skeletal muscle tissue' + UBERON_EXT:skeletal_muscle_organ_or_tissue + For: skeletal muscle +Not for: skeletal muscles (use UBERON:'skeletal muscle organ') + UBERON_EXT:skeletal muscle organ or tissue + + + skin or dermis + dermal + For: dermal(ly) + UBERON_EXT:skin or dermis + UBERON_EXT:skin_or_dermis + UBERON_EXT:zone_of_skin_or_skin_of_body or UBERON:dermis + + + UBERON_EXT:synovial_membrane + UBERON:'synovial membrane of synovial joint' or UBERON:'synovial membrane of synovial tendon sheath' + UBERON_EXT:synovial membrane + synovial membrane + For: synovial membrane(s) + + + UBERON_EXT:vascular system, vasculature, or vessel + UBERON_EXT:vascular_system_or_vasculature_or_vessel + vascular system, vasculature, or vessel + vascular + UBERON:'vascular system' or UBERON:vasculature or UBERON:vessel + For: vascular(ly) + + + UBERON_EXT:vestibule or vestibular system + vestibule or vestibular system + For: vestibular + vestibular + UBERON_EXT:vestibule_or_vestibular_system + UBERON:vestibule or UBERON:'vestibular system' + + + For: skin, cutaneous(ly) + UBERON_EXT:skin + skin + UBERON:'zone of skin' or UBERON:'skin of body' + UBERON_EXT:zone_of_skin_or_skin_of_body + + + UBERON extension classes + + + knowtator color assignment + + + + + + + diff --git a/src/test/resources/iaa_test_project/Profiles/Default.xml b/src/test/resources/iaa_test_project/Profiles/Default.xml new file mode 100644 index 00000000..fdbbfd68 --- /dev/null +++ b/src/test/resources/iaa_test_project/Profiles/Default.xml @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/src/test/resources/iaa_test_project/iaa/Class and span matcher.dat b/src/test/resources/iaa_test_project/iaa/Class and span matcher.dat index eea09e5a..9ccb9068 100644 --- a/src/test/resources/iaa_test_project/iaa/Class and span matcher.dat +++ b/src/test/resources/iaa_test_project/iaa/Class and span matcher.dat @@ -7,59 +7,59 @@ option under the Edit menu that will allow you to paste the copied data as text. type matches non-matches All classes 348 108 -5'-cytidylyl group 0 1 -5'-guanylyl group 0 2 -5'-uridylyl group 0 3 -acid 2 0 -adenine group 0 1 -alanine 0 1 -alanine residue 0 1 -alcohols 4 0 -amino acids 0 6 -amino-acid residues 0 7 -anaesthetic 2 10 -canonical nucleoside residues 0 1 -carbon 0 4 -carboxy group 0 10 -cytidyl groups 0 1 -cytosin-1-yl group 0 1 -deoxyribonucleic acids 54 3 -double-stranded DNA 10 4 -drug 0 2 -glutamate residue 0 1 -glutamate(1-) 0 1 -glutamate(2-) 0 1 -glycine 2 0 -guanine group 0 3 -guanosyl groups 0 2 -histidine 2 0 -hydrogencarbonate 2 0 -inhibitor 0 2 -magnesium dichloride 4 0 -messenger RNA 30 0 -metal cations 0 1 -metals 0 1 -molecular entities 0 4 -nucleotidyl groups 0 3 -oligopeptides 8 0 -peptides 10 0 -phosphate(3-) 0 1 -phosphates 0 1 -pigment 0 3 -potassium chloride 4 0 -proline 0 7 -proline residue 0 7 -protease inhibitor 4 0 -proteins 118 3 -ribonucleic acids 46 0 -single-stranded DNA 12 0 -sodium chloride 2 0 -sodium dodecyl sulfate 4 0 -sodium phosphates 2 0 -sucrose 8 0 -terpenes 6 0 -tert-pentyl group 2 0 -tris 6 0 -uracil-1-yl group 0 3 -uridyl groups 0 3 -water 4 3 +CHEBI:1432 0 1 +CHEBI:1542 2 0 +CHEBI:1644 0 1 +CHEBI:1699 54 3 +CHEBI:1836 0 1 +CHEBI:2352 0 1 +CHEBI:2352 0 1 +CHEBI:2388 0 2 +CHEBI:2445 0 2 +CHEBI:2446 0 2 +CHEBI:2613 0 3 +CHEBI:2627 0 7 +CHEBI:2724 0 3 +CHEBI:2724 0 3 +CHEBI:2757 2 0 +CHEBI:2998 0 1 +CHEBI:3036 2 0 +CHEBI:3075 0 3 +CHEBI:3075 0 1 +CHEBI:3075 0 1 +CHEBI:3075 0 3 +CHEBI:3244 0 1 +CHEBI:3248 0 1 +CHEBI:3287 0 7 +CHEBI:3369 46 0 +CHEBI:3369 30 0 +CHEBI:3379 0 1 +CHEBI:3522 0 2 +CHEBI:3752 2 0 +CHEBI:3767 4 0 +CHEBI:3886 2 10 +CHEBI:4688 0 10 +CHEBI:470 10 4 +CHEBI:916 12 0 +CHEBI_15377 4 3 +CHEBI_16670 10 0 +CHEBI_17544 2 0 +CHEBI_17992 8 0 +CHEBI_23367 0 4 +CHEBI_25213 0 1 +CHEBI_25613 0 3 +CHEBI_25676 8 0 +CHEBI_26020 0 1 +CHEBI_26710 2 0 +CHEBI_27594 0 4 +CHEBI_30879 4 0 +CHEBI_32588 4 0 +CHEBI_33521 0 1 +CHEBI_33708 0 7 +CHEBI_33709 0 6 +CHEBI_35186 6 0 +CHEBI_36080 118 3 +CHEBI_37586 2 0 +CHEBI_6636 4 0 +CHEBI_8984 4 0 +CHEBI_9754 6 0 diff --git a/src/test/resources/iaa_test_project/iaa/Class and span matcher.html b/src/test/resources/iaa_test_project/iaa/Class and span matcher.html index 0e19d1e7..18429b6d 100644 --- a/src/test/resources/iaa_test_project/iaa/Class and span matcher.html +++ b/src/test/resources/iaa_test_project/iaa/Class and span matcher.html @@ -4,408 +4,89 @@

    Class and span matcher

    Annotations match if they have the same class assignment and the same spans.
    -

    For more detailed documentation on IAA please see the IAA - documentation. +

    For more detailed documentation on Iaa please see the Iaa documentation.

    -

    2-way IAA Results

    -IAA calculated on 4 documents. +

    2-way Iaa Results

    +Iaa calculated on 4 documents.

    tabular data

    all annotations = matches + non-matches -
    IAA = matches / all annotations +
    Iaa = matches / all annotations

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
    TypeIAAmatchesnon-matches
    All classes76.15%348109
    5'-cytidylyl group0.00%01
    5'-guanylyl group0.00%02
    5'-uridylyl group0.00%03
    acid100.00%20
    adenine group0.00%01
    alanine0.00%01
    alanine residue0.00%01
    alcohols100.00%40
    amino acids0.00%06
    amino-acid residues0.00%07
    anaesthetic16.67%210
    canonical nucleoside residues0.00%02
    carbon0.00%04
    carboxy group0.00%010
    cytidyl groups0.00%01
    cytosin-1-yl group0.00%01
    deoxyribonucleic acids94.74%543
    double-stranded DNA71.43%104
    drug0.00%02
    glutamate residue0.00%01
    glutamate(1-)0.00%01
    glutamate(2-)0.00%01
    glycine100.00%20
    guanine group0.00%03
    guanosyl groups0.00%02
    histidine100.00%20
    hydrogencarbonate100.00%20
    inhibitor0.00%02
    magnesium dichloride100.00%40
    messenger RNA100.00%300
    metal cations0.00%01
    metals0.00%01
    molecular entities0.00%04
    nucleotidyl groups0.00%03
    oligopeptides100.00%80
    peptides100.00%100
    phosphate(3-)0.00%01
    phosphates0.00%01
    pigment0.00%03
    potassium chloride100.00%40
    proline0.00%07
    proline residue0.00%07
    protease inhibitor100.00%40
    proteins97.52%1183
    ribonucleic acids100.00%460
    single-stranded DNA100.00%120
    sodium chloride100.00%20
    sodium dodecyl sulfate100.00%40
    sodium phosphates100.00%20
    sucrose100.00%80
    terpenes100.00%60
    tert-pentyl group100.00%20
    tris100.00%60
    uracil-1-yl group0.00%03
    uridyl groups0.00%03
    water57.14%43
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    TypeIaamatchesnon-matches
    All classes76.32%348108
    CHEBI:14320.00%01
    CHEBI:1542100.00%20
    CHEBI:16440.00%01
    CHEBI:169994.74%543
    CHEBI:18360.00%01
    CHEBI:23520.00%01
    CHEBI:23520.00%01
    CHEBI:23880.00%02
    CHEBI:24450.00%02
    CHEBI:24460.00%02
    CHEBI:26130.00%03
    CHEBI:26270.00%07
    CHEBI:27240.00%03
    CHEBI:27240.00%03
    CHEBI:2757100.00%20
    CHEBI:29980.00%01
    CHEBI:3036100.00%20
    CHEBI:30750.00%03
    CHEBI:30750.00%01
    CHEBI:30750.00%01
    CHEBI:30750.00%03
    CHEBI:32440.00%01
    CHEBI:32480.00%01
    CHEBI:32870.00%07
    CHEBI:3369100.00%460
    CHEBI:3369100.00%300
    CHEBI:33790.00%01
    CHEBI:35220.00%02
    CHEBI:3752100.00%20
    CHEBI:3767100.00%40
    CHEBI:388616.67%210
    CHEBI:46880.00%010
    CHEBI:47071.43%104
    CHEBI:916100.00%120
    CHEBI_1537757.14%43
    CHEBI_16670100.00%100
    CHEBI_17544100.00%20
    CHEBI_17992100.00%80
    CHEBI_233670.00%04
    CHEBI_252130.00%01
    CHEBI_256130.00%03
    CHEBI_25676100.00%80
    CHEBI_260200.00%01
    CHEBI_26710100.00%20
    CHEBI_275940.00%04
    CHEBI_30879100.00%40
    CHEBI_32588100.00%40
    CHEBI_335210.00%01
    CHEBI_337080.00%07
    CHEBI_337090.00%06
    CHEBI_35186100.00%60
    CHEBI_3608097.52%1183
    CHEBI_37586100.00%20
    CHEBI_6636100.00%40
    CHEBI_8984100.00%40
    CHEBI_9754100.00%60

    match data

    -
    +
  • matches for Mike Bada
    • +
  • matches for Kristin Garcia
    • +

    non-match data

    -
    +
  • non-matches for Mike Bada
    • +
  • non-matches for Kristin Garcia
    • +

    Pair-wise agreement

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
    Gold standard setcompared settrue positivesfalse positivesfalse negativesprecisionrecallF-score
    Kristin GarciaMike Bada174872266.67%88.78%76.15%
    Mike BadaKristin Garcia174228788.78%66.67%76.15%
    + +
    Gold standard setcompared settrue positivesfalse positivesfalse negativesprecisionrecallF-score
    Mike BadaKristin Garcia174228688.78%66.92%76.32%
    Kristin GarciaMike Bada174862266.92%88.78%76.32%
    Precision and recall are given equal weight for the F-score. diff --git a/src/test/resources/iaa_test_project/iaa/Class and span matcher.matches.Kristin Garcia.html b/src/test/resources/iaa_test_project/iaa/Class and span matcher.matches.Kristin Garcia.html index 528f32af..44f127fb 100644 --- a/src/test/resources/iaa_test_project/iaa/Class and span matcher.matches.Kristin Garcia.html +++ b/src/test/resources/iaa_test_project/iaa/Class and span matcher.matches.Kristin Garcia.html @@ -3,3943 +3,775 @@ Class and span matcher

    Matches for Kristin Garcia

    -Each annotation that was considered a match is shown in the text that it was found in. The matching annotations from the -other annotation sets are also shown. -
    -

    5'-cytidylyl group

    -

    5'-guanylyl group

    -

    5'-uridylyl group

    -

    acid

    -
    -

    Text source name = 11532192.txt -

    e at the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered w -

      -
    • - acid -
        -
      • Kristin Garcia
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    • - acid -
        -
      • Mike Bada
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    -

    adenine group

    -

    alanine

    -

    alanine residue

    -

    alcohols

    -
    -

    Text source name = 11319941.txt -

    al images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% glutarald -

      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 -

      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    -

    amino acids

    -

    amino-acid residues

    -

    anaesthetic

    -
    -

    Text source name = 11532192.txt -

    parate group of the same age. - - Anesthesia protocol avoids IOP alteration and allows detection of diurnal differences - - All IOPs were assessed using an anesthetic regime of 99 mg/kg ketamine and 9 mg/kg xylazine (defined as 1X). - Initial experiments suggested that an almost identical dose (100 mg/kg ketamine and -

      -
    • - anesthetic -
        -
      • Kristin Garcia
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    -

    canonical nucleoside residues

    -

    carbon

    -

    carboxy group

    -

    cytidyl groups

    -

    cytosin-1-yl group

    -

    deoxyribonucleic acids

    -
    -

    Text source name = 11597317.txt -

    1 and BRCA2 are involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during - the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of repair of - spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either B -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    clear foci during the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of - repair of spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either BRCA1 or BRCA2 are - sensitive to damaging agents that form double-strand breaks (DSBs), as are other -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    es of DNA damage. Chromosomal DNA is shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. - (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to suppress RAD51–BRCA2 - interactions until DNA damage is present. When damage occurs, Rad51 is recr -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    subnuclear RAD51 foci with normal efficiency, suggesting that these proteins are required for the formation of - recombinase complexes at the sites of DNA damage [20,21]. Finally, genetic measurements of recombination - frequency have shown that Brca1-/- embryonic stem (ES) cells are deficient in recombin -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    onal DSB repair [22,23]. The similarity between phenotypes associated with BRCA1 and BRCA2 deficiency, together with - data showing a similar effect of DNA damage on distribution of BRCA1 and BRCA2 in repair-proficient cells, - led to the hypothesis that BRCA2, like BRCA1, is required for efficient recombi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric filaments on DNA. A BRC4 peptide was - also reported to inhibit the RAD51–DNA interaction. These experiments raise the possibility that the - full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    l population due to a mutated W (White spotted) gene. GC1 and MT4 are mouse germ cell and Sertoli cell lines, - respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger (if - any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two a -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ing of one of the eight BRC repeats from human BRCA2. Expression of a single BRC repeat (BRC4) had previously been - reported to act as an inhibitor of DNA repair by Chen et al [27]. These investigators showed that expression - of constructs containing the BRC4 repeat in MCF-7 cells enhances the radiosensi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    BRCA2 as grey bars. (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to - suppress RAD51–BRCA2 interactions until DNA damage is present. When damage occurs, Rad51 is recruited to - damaged sites where is polymerizes into nucleoprotein filaments. In this model, BRCA2 is -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ognition site. Transient transfection of an I-SceI expression vector results in the production of a DSB in the first - mutated copy of GFP. One or both DNA ends formed by the break invade(s) the homologous sequence in the second - mutant GFP copy, resulting in repair of the DSB via a homology-mediated gene -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    –DNA interaction. These experiments raise the possibility that the full-length BRCA2 protein could act as a negative - regulator of inappropriate RAD51–DNA interaction. - - The final experiment reported by Davies et al [26] is particularly important with respect to understanding the - mechanism(s) through whi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8420|8423
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8420|8423
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to the regions - of ssDNA that form during normal DNA replication. BRCA2 may thus promote RAD51 assembly into recombinational - repair complexes via a negative regulatory mechanism (i.e. by blocking RAD51– -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    gene conversion occurs via the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - inter -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    event a substantial fraction of Rad51 from being sequestered in a nonfunctional form. In a BRCA2-defective cell, - mutant Rad51 becomes associated with DNA at random sites and is therefore not readily recruited to sites of - damage. (b) Positive regulation. BRCA2 is proposed to be required for Rad51 to ass -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    r by Davies et al, data provide evidence for a plausible mechanism of the dominant negative effect associated with - expression of a single BRC repeat. DNA binding assays and electron microscopy methods were used to show that - a BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    gaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment from - mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics (Hunt -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    and homologous recombination - - Abstract - - Two recent papers provide new evidence relevant to the role of the breast cancer susceptibility gene BRCA2 in - DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in homology-dependent - (recombinational) repair of DNA double-strand br -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    li cell lines, respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger - (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C - antibody was raised against a -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ve cells - - Pierce et al have designed a set of recombination substrates for measuring the level of homologous recombination in - vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the easily detected - green fluorescent protein), one of which contains a restriction site -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    gure 2 are not mutually exclusive. BRCA2 could prevent inappropriate RAD51 assembly in the absence of damage and - promote functional RAD51 assembly at DNA lesions during the damage response. Further experiments are clearly - required to clarify the functional interactions between BRCA2 and RAD51 during re -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ole in assembly of RAD51 at damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to - 'mediate' assembly of RAD51 at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, - including XRCC2, XRCC3, RAD51B, RAD51C and RAD51D, may function as a complex that actively p -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    s and electron microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to - assemble into oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA - interaction. These experiments raise the possibility that the full-length BRCA2 protein co -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    97), was cloned in-frame into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences - at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    tgtctgaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment - from mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    clear sites with BRCA1 [9], a number of additional results have provided evidence that both BRCA1 and BRCA2 are - involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during the S - phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably si -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ty gene BRCA2 in DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in - homology-dependent (recombinational) repair of DNA double-strand breaks. The second paper, by Davies et al, - begins to address the mechanism through which BRCA2 makes its contribution to recombinationa -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ia the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - interactions. BRCA2–Rad51 int -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
      -
    -

    double-stranded DNA

    -
    -

    Text source name = 11597317.txt -

    air complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding preference - for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory - factors, such as BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestra -

      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    rand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as - BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional - form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might b -

      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involv -

      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    mage occurs. For example, previous studies indicated that RAD51 shows little binding preference for single-strand DNA - (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as BRCA2, - are required to suppress RAD51–dsDNA interactions to prevent sequestration of -

      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    cluding the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. -

      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    -

    drug

    -

    glutamate residue

    -

    glutamate(1-)

    -

    glutamate(2-)

    -

    glycine

    -
    -

    Text source name = 11604102.txt -

    d by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate - exon selection in neurons is antagonized by a second RNA-binding protein, brPTB (brain- -

      -
    • - glycine -
        -
      • Kristin Garcia
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    • - glycine -
        -
      • Mike Bada
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    -

    guanine group

    -

    guanosyl groups

    -

    histidine

    -
    -

    Text source name = 11604102.txt -

    equences at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins - were mixed with Freund's adjuvant and injected into rabbits to generate the anti-DAZ -

      -
    • - His -
        -
      • Kristin Garcia
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    • - His -
        -
      • Mike Bada
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    -

    hydrogencarbonate

    -
    -

    Text source name = 11532192.txt -

    derstanding of the molecular mechanisms controlling diurnal rhythms of IOP and that may be relevant to glaucoma. - - Car2 deficiency does not alter IOP - - Bicarbonate formation is important for aqueous humor secretion from the ciliary processes and carbonic - anhydrase (CA) facilitates this secretion. There are multi -

      -
    • - Bicarbonate -
        -
      • Kristin Garcia
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    • - Bicarbonate -
        -
      • Mike Bada
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    -

    inhibitor

    -

    magnesium dichloride

    -
    -

    Text source name = 11604102.txt -

    ay, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Protease Inhibit -

      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose gradients in - 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for 2 hours at - 4°C. Fractions of 0.5 ml were collected from the bottom of the tubes and analyze -

      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    -

    messenger RNA

    -
    -

    Text source name = 11604102.txt -

    tting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family - in the regulation of mRNA translation is supported by lines of cir -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    lso interacts through its proline-rich domain with two microfilament-associated proteins profilin and Mena, which may - facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming - growth factor-β family that is required for generating dorsal mesoderm at the -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ressed later, in the cytoplasm of pachytene spermatocytes [5]. Genetic and biochemical studies suggest a role for the - DAZ family in the regulation of mRNA translation. Drosophila Boule mutants was defective in the translation - of the meiosis-specific CDC25 homologue, Twine [11], and DAZL was found to be -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    . Its predominant expression in testes suggests a role in spermatogenesis. Its subcellular localization indicates - that it is not directly involved in mRNA translation. - - Background - - Spermatogenesis is a complex developmental process in which male germ cells progress through mitotic proliferation, - meiotic -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, pre-mRNA - processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA translation is supporte -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the - alternative splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The - ability of Nova-1 to activate exon selection in neurons is antagonized by a seco -

      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    proteins may act together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be - involved in the transport of the mRNAs of the target genes of DAZL. Alternatively, DAZL and DAZAP1 may act - antagonistically to regulate the timing and the level of expression. Such an anta -

      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and characterized [16]. Prrp binds to a 340 nt - sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also int -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    mouse testes, DAZAP1 was found both in the nuclei and in the cytoplasm. Its absence from polyribosomes indicates - that it is not directly involved in mRNA translation. - - Materials and methods - - Isolation of mouse Dazap1 cDNA clones - - Dazap1 cDNA clones were isolated from a mouse testis cDNA library (#93730 -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ee-hybrid system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich - segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechanisms of its action, we - used a yeast two-hybrid s -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    and brain, and even less in other tissues. This pattern of expression is similar to that of the human DAZAP1 (14). - RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at embryonic day 15, similar to - Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted througho -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    r to that of the human DAZAP1 (14). RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at - embryonic day 15, similar to Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted - throughout testes development, in both the prenatal and postnatal periods. Dazl1 and Da -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    haracterization of the mouse Dazap1 gene and its protein product. The subcellular localization of DAZAP1 suggests - that it is not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 cDNA - - Mouse Dazap1 cDNA clones were isolated by library screening, and the 5' end of the -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its - proline-rich domain with two microfilament-associated proteins profilin and M -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA transcription, pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the - DAZ family in the regulation of mRNA translation is supported by lines of circumstantial evidence, including - the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from p -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    -

    metal cations

    -

    metals

    -

    molecular entities

    -

    nucleotidyl groups

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    oligopeptides

    -
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    Text source name = 11604102.txt -

    was conjugated to KLH as carrier and injected into a goat. The anti-DAZAP1-P antibody thus produced was purified on - an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM Tris, pH - 8.0) -

      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 18831|18843
        • -
      -
    • - oligopeptide -
        -
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      • class = oligopeptides
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      • spans = 18831|18843
        • -
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    Text source name = 11604102.txt -

    on resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid residues of the mouse - DAZAP1 was synthesized in vitro using the services of Bethyl Laboratories (Montgomery, TX). Th -

      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 18509|18521
        • -
      -
    • - oligopeptide -
        -
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      • class = oligopeptides
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      • spans = 18509|18521
        • -
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    Text source name = 11604102.txt -

    ntibody was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid residue at the - C-terminus. Both antibodies recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay ( -

      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 9799|9811
        • -
      -
    • - oligopeptide -
        -
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        • -
      • class = oligopeptides
        • -
      • spans = 9799|9811
        • -
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    Text source name = 11604102.txt -

    ntron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 - (starting from aa #197), was cloned in-fr -

      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 17939|17951
        • -
      -
    • - oligopeptide -
        -
      • Mike Bada
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      • class = oligopeptides
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      • spans = 17939|17951
        • -
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    peptides

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    Text source name = 11597317.txt -

    - - The second paper providing evidence, by Davies et al [26], is a biochemical study of the interaction between the - homologous recombinase RAD51 and a peptide consisting of one of the eight BRC repeats from human BRCA2. - Expression of a single BRC repeat (BRC4) had previously been reported to act as an inhib -

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    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
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      • spans = 7420|7427
        • -
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    • - peptide -
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      • class = peptides
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      • spans = 7420|7427
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    Text source name = 11597317.txt -

    on microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These - experiments raise the possibility that the full-length BRCA2 protein could act as a neg -

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    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 8224|8231
        • -
      -
    • - peptide -
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      • class = peptides
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      • spans = 8224|8231
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    Text source name = 11597317.txt -

    t negative effect associated with expression of a single BRC repeat. DNA binding assays and electron microscopy - methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interact -

      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 8126|8133
        • -
      -
    • - peptide -
        -
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        • -
      • class = peptides
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      • spans = 8126|8133
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    Text source name = 11597317.txt -

    ge has occurred and factors required for 'productive' assembly of RAD51 at damaged sites are in place). As mentioned - previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction could reflect a role of - full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another pot -

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    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 10885|10892
        • -
      -
    • - peptide -
        -
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        • -
      • class = peptides
        • -
      • spans = 10885|10892
        • -
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    Text source name = 11604102.txt -

    ontaining the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the services of Bethyl - Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier and injected into a goat. The - anti-DAZAP1-P antibody thus produced was purified on an affinity column containing the -

      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 18673|18680
        • -
      -
    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 18673|18680
        • -
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    phosphate(3-)

    -

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    -

    pigment

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    Text source name = 11604102.txt -

    n at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose - gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for - 2 hours at 4°C. Fractions of 0.5 ml were collected from the bottom of the tu -

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    • - KCl -
        -
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        • -
      • class = potassium chloride
        • -
      • spans = 20325|20328
        • -
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    • - KCl -
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      • class = potassium chloride
        • -
      • spans = 20325|20328
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    , Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Prot -

      -
    • - KCl -
        -
      • Kristin Garcia
        • -
      • class = potassium chloride
        • -
      • spans = 19828|19831
        • -
      -
    • - KCl -
        -
      • Mike Bada
        • -
      • class = potassium chloride
        • -
      • spans = 19828|19831
        • -
      -
    -

    proline

    -

    proline residue

    -

    protease inhibitor

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    Text source name = 11604102.txt -

    ontaining 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, - Madison, WI), and a mixture of 10 protease inhibitors provided in the Protease Inhibitors Set (Roche - Molecular Biochemicals, Indianapolis, IN). Homogenates were centrifuged at 1,000 × g for 10 minutes to -

      -
    • - protease inhibitors -
        -
      • Kristin Garcia
        • -
      • class = protease inhibitor
        • -
      • spans = 19941|19960
        • -
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    • - protease inhibitors -
        -
      • Mike Bada
        • -
      • class = protease inhibitor
        • -
      • spans = 19941|19960
        • -
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    Text source name = 11604102.txt -

    KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 - protease inhibitors provided in the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, IN). - Homogenates were centrifuged at 1,000 × g for 10 minutes to pellet cell debris and nuclei. Afte -

      -
    • - Protease Inhibitors -
        -
      • Kristin Garcia
        • -
      • class = protease inhibitor
        • -
      • spans = 19977|19996
        • -
      -
    • - Protease Inhibitors -
        -
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        • -
      • class = protease inhibitor
        • -
      • spans = 19977|19996
        • -
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    proteins

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    Text source name = 11597317.txt -

    sites are in place). As mentioned previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction - could reflect a role of full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another potential role for BRCA2 in promoting RAD51-dependent recombinational repair is a posi -

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    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 10968|10975
        • -
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    • - protein -
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      • class = proteins
        • -
      • spans = 10968|10975
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    Text source name = 11604102.txt -

    clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its proline-rich domain - with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 mRNA - to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth fact -

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    • - proteins -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 14459|14467
        • -
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      • class = proteins
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      • spans = 14459|14467
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    y virtue of their expression of GFP. - - Moynahan et al [24] have used such a GFP recombination substrate to demonstrate that cells with defective BRCA2 protein - are deficient in their ability to repair the I-SceI-induced DSB through homologous recombination. Expression of - I-SceI resulted in 1 out of 1400 cell -

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    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 4454|4461
        • -
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    • - protein -
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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 4454|4461
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    Text source name = 11604102.txt -

    R1P and FXR2P, that were identified through their interaction with another polysomal-associated RNA-binding protein, - the fragile X mental retardation protein [21]. Both FXR1P and FXR2P are associated with the polyribosomes - [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be -

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    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 12395|12402
        • -
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      • class = proteins
        • -
      • spans = 12395|12402
        • -
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    Text source name = 11604102.txt -

    tein product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins share 98% identity and their sequences are highly similar to the Xenopus orthologue - Prrp, especially in the RBDs. Dazap1 is expressed throughout test -

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    • - proteins -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 1338|1346
        • -
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        • -
      • class = proteins
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      • spans = 1338|1346
        • -
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    Text source name = 11604102.txt -

    Both primer pairs annealed across intron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 ( -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 17904|17911
        • -
      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 17904|17911
        • -
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    Text source name = 11604102.txt -

    se genomic DNA. The PCR primers span over introns and produce much larger (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti - DAZAP1-C antibody was raised against a recombinant protein containing the C-terminal pr -

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    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 9569|9576
        • -
      -
    • - protein -
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      • class = proteins
        • -
      • spans = 9569|9576
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    Text source name = 11597317.txt -

    mpletely independent of its defect in BRCA2. First, in the same study [24], recombination in a mouse ES cell line - that expresses only truncated BRCA2 protein was measured. This line was found to have lower recombination - efficiency than isogenic cells expressing full-length BRCA2 (the defect observed was ab -

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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 5648|5655
        • -
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      • class = proteins
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      • spans = 5648|5655
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    Text source name = 11604102.txt -

    absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. This finding - is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardat -

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    • - proteins -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 12233|12241
        • -
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      • class = proteins
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      • spans = 12233|12241
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    Text source name = 11604102.txt -

    em to isolate two human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed - predominantly in testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal - portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to R -

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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 4280|4287
        • -
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    Text source name = 11597317.txt -

    breaks (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with - the RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have b -

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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 2328|2335
        • -
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    Text source name = 11604102.txt -

    P and FXR2P are associated with the polyribosomes [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be defined. These proteins may act - together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be involved in the - transport of the mRNAs of -

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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 12568|12576
        • -
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      • spans = 12568|12576
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    ant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements - [5,6]. The sequence of this large protein (3418 amino acids) offers very little clue to its function, - although there are eight repeated segments (termed BRC repeats) in the middle of the prot -

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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 1330|1337
        • -
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    Text source name = 11604102.txt -

    nds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse testes, DAZAP1 w -

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    • - protein -
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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 15193|15200
        • -
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      • spans = 15193|15200
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    Text source name = 11604102.txt -

    end of the cDNA was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region - (UTR), an open reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession - No: AF225910). The coding region shares 89% similarity with that of the human orth -

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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 4916|4923
        • -
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      • Mike Bada
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      • class = proteins
        • -
      • spans = 4916|4923
        • -
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    Text source name = 11604102.txt -

    NA-binding domains (RBDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved - evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with X -

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    • - proteins -
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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 5506|5514
        • -
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      • Mike Bada
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      • class = proteins
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      • spans = 5506|5514
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    Text source name = 11597317.txt -

    nts on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These experiments raise the - possibility that the full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA - interaction. - - The final experiment reported by Davies et al [26] is particularly importa -

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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 8355|8362
        • -
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      • Mike Bada
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      • class = proteins
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      • spans = 8355|8362
        • -
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    Text source name = 11597317.txt -

    he small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, consistent - with the fact that the truncation protein lacks a nuclear localization signal [28]. Davies et al showed - CAPAN-1 cells to be defective in nuclear localization of RAD51, raising the possibility -

      -
    • - protein -
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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 8923|8930
        • -
      -
    • - protein -
        -
      • Mike Bada
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      • class = proteins
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      • spans = 8923|8930
        • -
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    Text source name = 11319941.txt -

    , agenesis of the corpus callosum, and abnormalities other forebrain structure including widespread neocortical - ectopias [46, 47]. The MARCKS-related protein gene is expressed in the striatum during early brain - development in the rat [48]. - - The location of the QTL modulating striatal neuron number to the d -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 21850|21857
        • -
      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 21850|21857
        • -
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    Text source name = 11604102.txt -

    em, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA binding domains and a proline - rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to RNA - homopolymers. We now report our characterization of the mouse Dazap1 gene and its pr -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 4367|4374
        • -
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    • - protein -
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      • Mike Bada
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      • class = proteins
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      • spans = 4367|4374
        • -
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    Text source name = 11604102.txt -

    ng dorsal mesoderm at the blastula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of - DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST search of - the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with -

      -
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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 14808|14816
        • -
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      • Mike Bada
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      • class = proteins
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      • spans = 14808|14816
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    Text source name = 11604102.txt -

    illigrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on His-Bind metal chelation - resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid -

      -
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        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 18397|18405
        • -
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      • class = proteins
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      • spans = 18397|18405
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    Text source name = 11597317.txt -

    tein (3418 amino acids) offers very little clue to its function, although there are eight repeated segments (termed - BRC repeats) in the middle of the protein that are highly conserved among mammalian orthologs [7,8]. - - Breast cancer susceptibility genes and DNA repair - - Following the landmark discovery by Sc -

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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 1483|1490
        • -
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      • Mike Bada
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      • class = proteins
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      • spans = 1483|1490
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    Text source name = 11604102.txt -

    by centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by the - Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of tissue - extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-D -

      -
    • - Protein -
        -
      • Kristin Garcia
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    Z gene family and to understanding the mechanisms of its action, we used a yeast two-hybrid system to isolate two - human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly - in testes. It encodes a protein with two RNA binding domains and a proline rich C-term -

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    ifferent from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction with another - polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both FXR1P and FXR2P - are associated with the polyribosomes [22]. - - The significance of the interaction -

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    e for direct RAD51 interaction. Cells lacking BRCA1/2 fail to form damage-induced subnuclear RAD51 foci with normal - efficiency, suggesting that these proteins are required for the formation of recombinase complexes at the - sites of DNA damage [20,21]. Finally, genetic measurements of recombination frequency -

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    ) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by - the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μ -

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    ed in CAPAN-1 cells, the same human tumor line examined by Moynahan et al [24]. It had been shown previously that the - small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, - consistent with the fact that the truncation protein lacks a nuclear localization signa -

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    acts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser degree in spleen, - liver, lung and brain (Figure 4). The protein was also present in the ovary. The expression of DAZAP1 during - germ cell development paralleled that of DAZL (Figure 5). It is present at a low level -

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    RI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences at the junctions were verified by DNA - sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on - His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with Fre -

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    t. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed by Western - blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translatio -

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    s a change of reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences betwee -

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    increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted with the anti-DAZAP1-P antibody. - - Figure 5 Western blot -

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    the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody - was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid r -

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    he two RBDs are especially highly conserved. They share 98% and 97% similarity and 97% and 92% identity, - respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA binding specificity. - The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% similarity and -

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    gene to be discovered, and was isolated through positional cloning using data from families with inherited breast - cancer [4]. Cells with mutant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate - gross chromosomal rearrangements [5,6]. The sequence of this large protein (3418 ami -

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    riginal URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast tw -

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    s recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting of mouse - tissue extracts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser - degree in spleen, liver, lung and brain (Figure 4). The protein was also present in t -

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    ential role for BRCA2 in promoting RAD51-dependent recombinational repair is a positive role in assembly of RAD51 at - damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to 'mediate' assembly of RAD51 - at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, includin -

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    ty of Nova-1 to activate exon selection in neurons is antagonized by a second RNA-binding protein, brPTB - (brain-enriched polypyrimidine tract-binding protein), which interacts with Nova-1 and inhibits its function - [24]. DAZAP1 could function in a similar manner by binding to DAZL and inhibiting its functio -

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    of DAZAP1 increased afterward, as the testes contained increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted -

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    striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the gene encoding the myristoylated - alanine-rich C kinase substrate (MARCKS protein). This molecule is important in cerebral development. - MARCKS-deficient mice have a high incidence of exencephaly, agenesis of the corpus callosum, an -

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    nal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in neurons is - antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding protein), - which interacts with Nova-1 and inhibits its function [24]. DAZAP1 could function in a -

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    erved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for - proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. T -

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    . Second, in an independent study, Powell was able to compare derivatives of CAPAN-1 that differed only in their - ability to express full-length BRCA2 protein (S. Powell, personal communication, 2001). In these experiments, - the derivative expressing full-length BRCA2 yielded 10-fold more recombinants than c -

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    ce, including the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from polyribosomes indicates - that it is not directly involved in protein synthesis. This finding is different from two RNA-binding - proteins, FXR1P and FXR2P, that were identified through their interaction with another poly -

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    AP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic interaction - between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding - protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNAs encoding neuron -

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    f expression. Such an antagonistic interaction between two interacting RNA-binding proteins is exemplified by the - neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of N -

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    titutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus - Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. They share - 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prr -

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    sophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and spermatogonia, an -

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    via homologous recombination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of - BRCA2 on one homolog and codes for a protein truncated at amino acid 1981 on the other homolog. The authors - indicate that the level of I-SceI-induced recombination in CAPAN-1 is over 100-fold le -

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    (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with the - RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have been indi -

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    logous recombination in vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the - easily detected green fluorescent protein), one of which contains a restriction site for I-SceI, a yeast - intron encoded endonuclease with an 18 base pair recognition site. Transient transfect -

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    mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast two-hybrid system through its - interaction with a putative male infertility factor, DAZ (Deleted in Azoospermi -

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    ation of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a R -

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    to the Xenopus orthologue Prrp, especially in the RBDs. Dazap1 is expressed throughout testis development. Western - blot detects a single 45 kD DAZAP1 protein that is most abundant in the testis. Although a majority of DAZAP1 - is present in the cytoplasmic fraction, they are not associated with polyribosomes -

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    share 85%, 90%, and 97% similarity with segments in the human 3' UTR, respectively. These segments probably contain - regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse -

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    infertility factor, DAZ (Deleted in Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ - and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a - proline-rich C-terminal portion, and is expressed most abundantly in the testis. To under -

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    ribonucleic acids

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    n Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like - protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is - expressed most abundantly in the testis. To understand the biological function o -

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    Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s and the - Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and the mouse - sequences, and between the mouse and Xenopus sequences are marked by #'s and * -

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    ch domain with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 - mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth factor-β family that is - required for generating dorsal mesoderm at the blastula stage of Xenopus embryoge -

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    the level of expression. Such an antagonistic interaction between two interacting RNA-binding proteins is - exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative - splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. -

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    human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in - testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 - protein interacted with both DAZ and DAZL in vitro. It also bound to RNA homopolyme -

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    VLE that binds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse -

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    Text source name = 11604102.txt -

    The 5' end of the cDNA was isolated by 5' RACE [15], using prdap11 (ttgcgggccatatccttg, #749–732) as the primer for - cDNA synthesis from mouse testis RNA, and prdap37 (ttgttgccacgtgggcg, #734–718) and an adaptor primer as the - primers for PCR amplification. The PCR products were cloned into a TA cloning -

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    Text source name = 11604102.txt -

    BLAST search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, and possibly DAZAP1, may help to - identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolution -

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    mbers of Drosophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both - sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and -

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    Text source name = 11604102.txt -

    article's original URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identifi -

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      • spans = 430|433
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    Text source name = 11604102.txt -

    coding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in - neurons is antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding - protein), which interacts with Nova-1 and inhibits its function [24]. DAZAP1 coul -

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    • - RNA -
        -
      • Kristin Garcia
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      • class = ribonucleic acids
        • -
      • spans = 13225|13228
        • -
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    • - RNA -
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    Text source name = 11604102.txt -

    with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity - with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. - They share 98% and 97% similarity and 97% and 92% identity, respectively, betwee -

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    Text source name = 11604102.txt -

    erved. They share 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These - proteins may therefore have a similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 - and Prrp are less conserved (81% similarity and 71% identity). There is an insert -

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        • -
      • spans = 5910|5913
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    Text source name = 11604102.txt -

    DAZL and DAZAP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic - interaction between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear - RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNA -

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        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12918|12921
        • -
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    • - RNA -
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        • -
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    Text source name = 11604102.txt -

    communication). The genomic structure of Dazap1, delineated here, should facilitate the generating of Dazap1 null - mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of -

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        -
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      • class = ribonucleic acids
        • -
      • spans = 13965|13968
        • -
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    • - RNA -
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    Text source name = 11604102.txt -

    ressed most abundantly in the testis. - - Figure 3 Developmental expression of Dazap1 and Dazl in mouse testes. RT-PCR was performed on total testicular RNAs - isolated from day 15 (El 5) and day 17 (El 7) embryos, new born mice (Day 0), and mice at various days after birth. - Wv/Wv testes contain diminished g -

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    • - RNAs -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 9119|9123
        • -
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    • - RNAs -
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    Text source name = 11604102.txt -

    rose gradient. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed - by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localiz -

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        • -
      • spans = 11715|11718
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    Text source name = 11604102.txt -

    ch fractions was analyzed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA -

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        • -
      • spans = 11805|11808
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    Text source name = 11604102.txt -

    finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both - FXR1P and FXR2P are associated with the polyribosomes [22]. - - The significance of -

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      • Kristin Garcia
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      • spans = 12341|12344
        • -
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    Text source name = 11604102.txt -

    stula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of DAZAP1 and Prrp suggests that - these proteins may bind to similar RNA sequences. However, a BLAST search of the GenBank for the 340 nt VLE - sequence failed to identify any mammalian sequences with significant homology. F -

      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 14837|14840
        • -
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    Text source name = 11604102.txt -

    n with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and - DAZL in vitro. It also bound to RNA homopolymers. We now report our characterization of the mouse Dazap1 gene - and its protein product. The subcellular localization of DAZAP1 suggests th -

      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 4436|4439
        • -
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    • - RNA -
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    Text source name = 11604102.txt -

    97% similarity with segments in the human 3' UTR, respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human pr -

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        -
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        • -
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        • -
      • spans = 5355|5358
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    • - RNA -
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    Text source name = 11604102.txt -

    es [12]. The absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. - This finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their - interaction with another polysomal-associated RNA-binding protein, the fragile -

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        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12221|12224
        • -
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      • Mike Bada
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      • spans = 12221|12224
        • -
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    single-stranded DNA

    -
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    Text source name = 11597317.txt -

    BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-lik -

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    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 12990|12995
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      -
    • - ssDNA -
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    Text source name = 11597317.txt -

    nction difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; ssDNA = - single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like - protein.. Cell. 19 -

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    • - single-strand DNA -
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        • -
      • spans = 12998|13015
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    • - single-strand DNA -
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    Text source name = 11597317.txt -

    recruited into a functional repair complex when damage occurs. For example, previous studies indicated that RAD51 - shows little binding preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This - result could mean that regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA in -

      -
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        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10146|10163
        • -
      -
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    Text source name = 11597317.txt -

    d to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional form. Alternatively, or - in addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to - the regions of ssDNA that form during normal DNA replication. BRCA2 may thus prom -

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        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10435|10440
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    • - ssDNA -
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    Text source name = 11597317.txt -

    nctional repair complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding - preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that - regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA interacti -

      -
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        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10165|10170
        • -
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    • - ssDNA -
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    Text source name = 11597317.txt -

    al form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might be important for preventing - RAD51 from binding to the regions of ssDNA that form during normal DNA replication. BRCA2 may thus promote - RAD51 assembly into recombinational repair complexes via a negative regulatory mechan -

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        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10524|10529
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        -
      • Mike Bada
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    sodium chloride

    -
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    Text source name = 11604102.txt -

    urified on an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of deb -

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      • class = sodium chloride
        • -
      • spans = 18936|18940
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    • - NaCl -
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    sodium dodecyl sulfate

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    Text source name = 11604102.txt -

    etermined by the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of - tissue extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-DAZAP1-C - antibody (at a 1/2,000 dilution) or the anti-DAZAP1-P antibody (at a 1/5,000 dilution). -

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    • - SDS -
        -
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        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 19342|19345
        • -
      -
    • - SDS -
        -
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    Text source name = 11604102.txt -

    taining the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 -

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    • - SDS -
        -
      • Kristin Garcia
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 18969|18972
        • -
      -
    • - SDS -
        -
      • Mike Bada
        • -
      • class = sodium dodecyl sulfate
        • -
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        • -
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    sodium phosphates

    -
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    Text source name = 11319941.txt -

    ply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, 0.5-1.0 ml ip) and perfused - through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) followed by 1.25% - glutaraldehyde/1.0% paraformaldehyde in 0.1 M PB (pH 7.40) over a period of 2 to 4 min. An additional -

      -
    • - sodium phosphate -
        -
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        • -
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        • -
      • spans = 26402|26418
        • -
      -
    • - sodium phosphate -
        -
      • Mike Bada
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        • -
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    sucrose

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    Text source name = 11604102.txt -

    se gradient analyses of the post- mitochondria fraction showed that, unlike DAZL, DAZAP1 did not co-sediment with - polyribosomes (Figure 6). - - Figure 6 Sucrose gradient analyses shows that DAZAP1 is not associated with polyribosomes. The - post-mitochondrial supernatant of mouse testis extracts was analyzed on -

      -
    • - Sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11395|11402
        • -
      -
    • - Sucrose -
        -
      • Mike Bada
        • -
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    Text source name = 11604102.txt -

    analyses shows that DAZAP1 is not associated with polyribosomes. The post-mitochondrial supernatant of mouse testis - extracts was analyzed on a 15–45% sucrose gradient. Sedimentation was from left to right. The presence of - DAZAP1 and DAZL in each fractions was analyzed by Western blotting. - - Discussion - - RNA- -

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    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11562|11569
        • -
      -
    • - sucrose -
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    Text source name = 11604102.txt -

    [12]. Similar analyses showed that a majority of DAZAP1 in adult mouse testes was also present in the cytoplasmic - fraction (data not shown). However, sucrose gradient analyses of the post- mitochondria fraction showed that, - unlike DAZL, DAZAP1 did not co-sediment with polyribosomes (Figure 6). - - Figure 6 Su -

      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11240|11247
        • -
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    • - sucrose -
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    Text source name = 11604102.txt -

    uclei. After an additional centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the - supernatant were applied to 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged - in a Beckman SW41 rotor at 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were -

      -
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        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 20285|20292
        • -
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    • - sucrose -
        -
      • Mike Bada
        • -
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        • -
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    terpenes

    -
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    Text source name = 11532192.txt -

    esia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and wood - shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in wood - shavings alters drug resistance and decreases the effect of anesthetic agents in both ra -

      -
    • - Terpene -
        -
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        • -
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        • -
      • spans = 25559|25566
        • -
      -
    • - Terpene -
        -
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    Text source name = 11532192.txt -

    of anesthesia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and - wood shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in - wood shavings alters drug resistance and decreases the effect of anesthetic agents i -

      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
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        • -
      • spans = 25549|25557
        • -
      -
    • - terpenes -
        -
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        • -
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    Text source name = 11532192.txt -

    may be important. We use wood shavings for bedding and wood shavings expose the mice to terpenes. Terpene - administration or environmental exposure to terpenes in wood shavings alters drug resistance and decreases - the effect of anesthetic agents in both rats and mice [40-45]. - - Risk factors for increased IOP - -

      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
      -
    • - terpenes -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
      -
    -

    tert-pentyl group

    -
    -

    Text source name = 11319941.txt -

    lution digital images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% g -

      -
    • - tert-pentyl -
        -
      • Kristin Garcia
        • -
      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    • - tert-pentyl -
        -
      • Mike Bada
        • -
      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    -

    tris

    -
    -

    Text source name = 11604102.txt -

    oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of - debris by centrifugation at 10,000 × g for 10 m -

      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to - 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at - 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were collected from the bott -

      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ham Pharmacia Biotech, Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors -

      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    -

    uracil-1-yl group

    -

    uridyl groups

    -

    water

    -
    -

    Text source name = 11532192.txt -

    containing white pine bedding and covered with polyester filters. For most experiments, the mice were fed NIH31 (6 % - fat) chow ad libitum, and their water was acidified to pH 2.8 to 3.2. B6 mice develop diet induced diabetes - when maintained on a high fat diet [76]. To ensure that we were analyzing the e -

      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    f sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, - 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) - followed by 1.25% glutaraldehyde/1.0 -

      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    +Each concept that was considered a match is shown in the text that it was found in. The matching annotations from the other concept sets are also shown. +
    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    • +
      • Mike Bada
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    • +
      • Mike Bada
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    • +
      • Mike Bada
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    • +
      • Mike Bada
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    +

    CHEBI_15377

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    +

    CHEBI_16670

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    +

    CHEBI_17544

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    +

    CHEBI_17992

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    +

    CHEBI_23367

    +

    CHEBI_25213

    +

    CHEBI_25613

    +

    CHEBI_25676

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    +

    CHEBI_26020

    +

    CHEBI_26710

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    +

    CHEBI_27594

    +

    CHEBI_30879

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    +

    CHEBI_32588

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    +

    CHEBI_33521

    +

    CHEBI_33708

    +

    CHEBI_33709

    +

    CHEBI_35186

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    +

    CHEBI_36080

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    +

    CHEBI_37586

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    +

    CHEBI_6636

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    +

    CHEBI_8984

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    +

    CHEBI_9754

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    diff --git a/src/test/resources/iaa_test_project/iaa/Class and span matcher.matches.Mike Bada.html b/src/test/resources/iaa_test_project/iaa/Class and span matcher.matches.Mike Bada.html index d015f523..ae0799a1 100644 --- a/src/test/resources/iaa_test_project/iaa/Class and span matcher.matches.Mike Bada.html +++ b/src/test/resources/iaa_test_project/iaa/Class and span matcher.matches.Mike Bada.html @@ -3,3943 +3,775 @@ Class and span matcher

    Matches for Mike Bada

    -Each annotation that was considered a match is shown in the text that it was found in. The matching annotations from the -other annotation sets are also shown. -
    -

    5'-cytidylyl group

    -

    5'-guanylyl group

    -

    5'-uridylyl group

    -

    acid

    -
    -

    Text source name = 11532192.txt -

    e at the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered w -

      -
    • - acid -
        -
      • Mike Bada
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    • - acid -
        -
      • Kristin Garcia
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    -

    adenine group

    -

    alanine

    -

    alanine residue

    -

    alcohols

    -
    -

    Text source name = 11319941.txt -

    al images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% glutarald -

      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 -

      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    -

    amino acids

    -

    amino-acid residues

    -

    anaesthetic

    -
    -

    Text source name = 11532192.txt -

    parate group of the same age. - - Anesthesia protocol avoids IOP alteration and allows detection of diurnal differences - - All IOPs were assessed using an anesthetic regime of 99 mg/kg ketamine and 9 mg/kg xylazine (defined as 1X). - Initial experiments suggested that an almost identical dose (100 mg/kg ketamine and -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    • - anesthetic -
        -
      • Kristin Garcia
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    -

    canonical nucleoside residues

    -

    carbon

    -

    carboxy group

    -

    cytidyl groups

    -

    cytosin-1-yl group

    -

    deoxyribonucleic acids

    -
    -

    Text source name = 11597317.txt -

    1 and BRCA2 are involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during - the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of repair of - spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either B -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    97), was cloned in-frame into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences - at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    and homologous recombination - - Abstract - - Two recent papers provide new evidence relevant to the role of the breast cancer susceptibility gene BRCA2 in - DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in homology-dependent - (recombinational) repair of DNA double-strand br -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    subnuclear RAD51 foci with normal efficiency, suggesting that these proteins are required for the formation of - recombinase complexes at the sites of DNA damage [20,21]. Finally, genetic measurements of recombination - frequency have shown that Brca1-/- embryonic stem (ES) cells are deficient in recombin -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ia the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - interactions. BRCA2–Rad51 int -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ole in assembly of RAD51 at damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to - 'mediate' assembly of RAD51 at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, - including XRCC2, XRCC3, RAD51B, RAD51C and RAD51D, may function as a complex that actively p -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ty gene BRCA2 in DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in - homology-dependent (recombinational) repair of DNA double-strand breaks. The second paper, by Davies et al, - begins to address the mechanism through which BRCA2 makes its contribution to recombinationa -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    BRCA2 as grey bars. (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to - suppress RAD51–BRCA2 interactions until DNA damage is present. When damage occurs, Rad51 is recruited to - damaged sites where is polymerizes into nucleoprotein filaments. In this model, BRCA2 is -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    r by Davies et al, data provide evidence for a plausible mechanism of the dominant negative effect associated with - expression of a single BRC repeat. DNA binding assays and electron microscopy methods were used to show that - a BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    event a substantial fraction of Rad51 from being sequestered in a nonfunctional form. In a BRCA2-defective cell, - mutant Rad51 becomes associated with DNA at random sites and is therefore not readily recruited to sites of - damage. (b) Positive regulation. BRCA2 is proposed to be required for Rad51 to ass -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ognition site. Transient transfection of an I-SceI expression vector results in the production of a DSB in the first - mutated copy of GFP. One or both DNA ends formed by the break invade(s) the homologous sequence in the second - mutant GFP copy, resulting in repair of the DSB via a homology-mediated gene -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    es of DNA damage. Chromosomal DNA is shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. - (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to suppress RAD51–BRCA2 - interactions until DNA damage is present. When damage occurs, Rad51 is recr -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    clear sites with BRCA1 [9], a number of additional results have provided evidence that both BRCA1 and BRCA2 are - involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during the S - phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably si -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    gene conversion occurs via the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - inter -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    gaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment from - mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics (Hunt -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    clear foci during the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of - repair of spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either BRCA1 or BRCA2 are - sensitive to damaging agents that form double-strand breaks (DSBs), as are other -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ve cells - - Pierce et al have designed a set of recombination substrates for measuring the level of homologous recombination in - vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the easily detected - green fluorescent protein), one of which contains a restriction site -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    tgtctgaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment - from mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ing of one of the eight BRC repeats from human BRCA2. Expression of a single BRC repeat (BRC4) had previously been - reported to act as an inhibitor of DNA repair by Chen et al [27]. These investigators showed that expression - of constructs containing the BRC4 repeat in MCF-7 cells enhances the radiosensi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    s and electron microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to - assemble into oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA - interaction. These experiments raise the possibility that the full-length BRCA2 protein co -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    l population due to a mutated W (White spotted) gene. GC1 and MT4 are mouse germ cell and Sertoli cell lines, - respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger (if - any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two a -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to the regions - of ssDNA that form during normal DNA replication. BRCA2 may thus promote RAD51 assembly into recombinational - repair complexes via a negative regulatory mechanism (i.e. by blocking RAD51– -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    onal DSB repair [22,23]. The similarity between phenotypes associated with BRCA1 and BRCA2 deficiency, together with - data showing a similar effect of DNA damage on distribution of BRCA1 and BRCA2 in repair-proficient cells, - led to the hypothesis that BRCA2, like BRCA1, is required for efficient recombi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric filaments on DNA. A BRC4 peptide was - also reported to inhibit the RAD51–DNA interaction. These experiments raise the possibility that the - full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    –DNA interaction. These experiments raise the possibility that the full-length BRCA2 protein could act as a negative - regulator of inappropriate RAD51–DNA interaction. - - The final experiment reported by Davies et al [26] is particularly important with respect to understanding the - mechanism(s) through whi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8420|8423
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8420|8423
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    gure 2 are not mutually exclusive. BRCA2 could prevent inappropriate RAD51 assembly in the absence of damage and - promote functional RAD51 assembly at DNA lesions during the damage response. Further experiments are clearly - required to clarify the functional interactions between BRCA2 and RAD51 during re -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    li cell lines, respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger - (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C - antibody was raised against a -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    -

    double-stranded DNA

    -
    -

    Text source name = 11597317.txt -

    cluding the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. -

      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    mage occurs. For example, previous studies indicated that RAD51 shows little binding preference for single-strand DNA - (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as BRCA2, - are required to suppress RAD51–dsDNA interactions to prevent sequestration of -

      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involv -

      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    air complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding preference - for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory - factors, such as BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestra -

      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    rand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as - BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional - form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might b -

      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    -

    drug

    -

    glutamate residue

    -

    glutamate(1-)

    -

    glutamate(2-)

    -

    glycine

    -
    -

    Text source name = 11604102.txt -

    d by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate - exon selection in neurons is antagonized by a second RNA-binding protein, brPTB (brain- -

      -
    • - glycine -
        -
      • Mike Bada
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    • - glycine -
        -
      • Kristin Garcia
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    -

    guanine group

    -

    guanosyl groups

    -

    histidine

    -
    -

    Text source name = 11604102.txt -

    equences at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins - were mixed with Freund's adjuvant and injected into rabbits to generate the anti-DAZ -

      -
    • - His -
        -
      • Mike Bada
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    • - His -
        -
      • Kristin Garcia
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    -

    hydrogencarbonate

    -
    -

    Text source name = 11532192.txt -

    derstanding of the molecular mechanisms controlling diurnal rhythms of IOP and that may be relevant to glaucoma. - - Car2 deficiency does not alter IOP - - Bicarbonate formation is important for aqueous humor secretion from the ciliary processes and carbonic - anhydrase (CA) facilitates this secretion. There are multi -

      -
    • - Bicarbonate -
        -
      • Mike Bada
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    • - Bicarbonate -
        -
      • Kristin Garcia
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    -

    inhibitor

    -

    magnesium dichloride

    -
    -

    Text source name = 11604102.txt -

    ay, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Protease Inhibit -

      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose gradients in - 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for 2 hours at - 4°C. Fractions of 0.5 ml were collected from the bottom of the tubes and analyze -

      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    -

    messenger RNA

    -
    -

    Text source name = 11604102.txt -

    Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and characterized [16]. Prrp binds to a 340 nt - sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also int -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    tting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family - in the regulation of mRNA translation is supported by lines of cir -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ee-hybrid system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich - segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechanisms of its action, we - used a yeast two-hybrid s -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    and brain, and even less in other tissues. This pattern of expression is similar to that of the human DAZAP1 (14). - RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at embryonic day 15, similar to - Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted througho -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    proteins may act together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be - involved in the transport of the mRNAs of the target genes of DAZL. Alternatively, DAZL and DAZAP1 may act - antagonistically to regulate the timing and the level of expression. Such an anta -

      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    . Its predominant expression in testes suggests a role in spermatogenesis. Its subcellular localization indicates - that it is not directly involved in mRNA translation. - - Background - - Spermatogenesis is a complex developmental process in which male germ cells progress through mitotic proliferation, - meiotic -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    mouse testes, DAZAP1 was found both in the nuclei and in the cytoplasm. Its absence from polyribosomes indicates - that it is not directly involved in mRNA translation. - - Materials and methods - - Isolation of mouse Dazap1 cDNA clones - - Dazap1 cDNA clones were isolated from a mouse testis cDNA library (#93730 -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA transcription, pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the - DAZ family in the regulation of mRNA translation is supported by lines of circumstantial evidence, including - the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from p -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, pre-mRNA - processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA translation is supporte -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    lso interacts through its proline-rich domain with two microfilament-associated proteins profilin and Mena, which may - facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming - growth factor-β family that is required for generating dorsal mesoderm at the -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its - proline-rich domain with two microfilament-associated proteins profilin and M -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    haracterization of the mouse Dazap1 gene and its protein product. The subcellular localization of DAZAP1 suggests - that it is not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 cDNA - - Mouse Dazap1 cDNA clones were isolated by library screening, and the 5' end of the -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ressed later, in the cytoplasm of pachytene spermatocytes [5]. Genetic and biochemical studies suggest a role for the - DAZ family in the regulation of mRNA translation. Drosophila Boule mutants was defective in the translation - of the meiosis-specific CDC25 homologue, Twine [11], and DAZL was found to be -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the - alternative splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The - ability of Nova-1 to activate exon selection in neurons is antagonized by a seco -

      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    r to that of the human DAZAP1 (14). RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at - embryonic day 15, similar to Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted - throughout testes development, in both the prenatal and postnatal periods. Dazl1 and Da -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    -

    metal cations

    -

    metals

    -

    molecular entities

    -

    nucleotidyl groups

    -

    oligopeptides

    -
    -

    Text source name = 11604102.txt -

    on resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid residues of the mouse - DAZAP1 was synthesized in vitro using the services of Bethyl Laboratories (Montgomery, TX). Th -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 18509|18521
        • -
      -
    • - oligopeptide -
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      • class = oligopeptides
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      • spans = 18509|18521
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    ntron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 - (starting from aa #197), was cloned in-fr -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 17939|17951
        • -
      -
    • - oligopeptide -
        -
      • Kristin Garcia
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      • class = oligopeptides
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      • spans = 17939|17951
        • -
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    Text source name = 11604102.txt -

    ntibody was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid residue at the - C-terminus. Both antibodies recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay ( -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 9799|9811
        • -
      -
    • - oligopeptide -
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      • Kristin Garcia
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      • class = oligopeptides
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      • spans = 9799|9811
        • -
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    was conjugated to KLH as carrier and injected into a goat. The anti-DAZAP1-P antibody thus produced was purified on - an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM Tris, pH - 8.0) -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 18831|18843
        • -
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    • - oligopeptide -
        -
      • Kristin Garcia
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      • class = oligopeptides
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      • spans = 18831|18843
        • -
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    peptides

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    Text source name = 11597317.txt -

    t negative effect associated with expression of a single BRC repeat. DNA binding assays and electron microscopy - methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interact -

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    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 8126|8133
        • -
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    • - peptide -
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      • spans = 8126|8133
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    Text source name = 11604102.txt -

    ontaining the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the services of Bethyl - Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier and injected into a goat. The - anti-DAZAP1-P antibody thus produced was purified on an affinity column containing the -

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    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 18673|18680
        • -
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    • - peptide -
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      • class = peptides
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      • spans = 18673|18680
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    - - The second paper providing evidence, by Davies et al [26], is a biochemical study of the interaction between the - homologous recombinase RAD51 and a peptide consisting of one of the eight BRC repeats from human BRCA2. - Expression of a single BRC repeat (BRC4) had previously been reported to act as an inhib -

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        • -
      • class = peptides
        • -
      • spans = 7420|7427
        • -
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    • - peptide -
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      • spans = 7420|7427
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    ge has occurred and factors required for 'productive' assembly of RAD51 at damaged sites are in place). As mentioned - previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction could reflect a role of - full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another pot -

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        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 10885|10892
        • -
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      • class = peptides
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      • spans = 10885|10892
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    Text source name = 11597317.txt -

    on microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These - experiments raise the possibility that the full-length BRCA2 protein could act as a neg -

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    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 8224|8231
        • -
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      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 8224|8231
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    phosphate(3-)

    -

    phosphates

    -

    pigment

    -

    potassium chloride

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    , Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Prot -

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    • - KCl -
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        • -
      • class = potassium chloride
        • -
      • spans = 19828|19831
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      • class = potassium chloride
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      • spans = 19828|19831
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    n at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose - gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for - 2 hours at 4°C. Fractions of 0.5 ml were collected from the bottom of the tu -

      -
    • - KCl -
        -
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        • -
      • class = potassium chloride
        • -
      • spans = 20325|20328
        • -
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    • - KCl -
        -
      • Kristin Garcia
        • -
      • class = potassium chloride
        • -
      • spans = 20325|20328
        • -
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    proline

    -

    proline residue

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    protease inhibitor

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    ontaining 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, - Madison, WI), and a mixture of 10 protease inhibitors provided in the Protease Inhibitors Set (Roche - Molecular Biochemicals, Indianapolis, IN). Homogenates were centrifuged at 1,000 × g for 10 minutes to -

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    • - protease inhibitors -
        -
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        • -
      • class = protease inhibitor
        • -
      • spans = 19941|19960
        • -
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    • - protease inhibitors -
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        • -
      • class = protease inhibitor
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      • spans = 19941|19960
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    KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 - protease inhibitors provided in the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, IN). - Homogenates were centrifuged at 1,000 × g for 10 minutes to pellet cell debris and nuclei. Afte -

      -
    • - Protease Inhibitors -
        -
      • Mike Bada
        • -
      • class = protease inhibitor
        • -
      • spans = 19977|19996
        • -
      -
    • - Protease Inhibitors -
        -
      • Kristin Garcia
        • -
      • class = protease inhibitor
        • -
      • spans = 19977|19996
        • -
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    proteins

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    sites are in place). As mentioned previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction - could reflect a role of full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another potential role for BRCA2 in promoting RAD51-dependent recombinational repair is a posi -

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        • -
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        • -
      • spans = 10968|10975
        • -
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      • spans = 10968|10975
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    absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. This finding - is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardat -

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      • spans = 12233|12241
        • -
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    tein (3418 amino acids) offers very little clue to its function, although there are eight repeated segments (termed - BRC repeats) in the middle of the protein that are highly conserved among mammalian orthologs [7,8]. - - Breast cancer susceptibility genes and DNA repair - - Following the landmark discovery by Sc -

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      • spans = 1483|1490
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    titutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus - Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. They share - 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prr -

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      • class = proteins
        • -
      • spans = 5706|5713
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    P and FXR2P are associated with the polyribosomes [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be defined. These proteins may act - together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be involved in the - transport of the mRNAs of -

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      • spans = 12568|12576
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    the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody - was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid r -

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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 9690|9697
        • -
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    y virtue of their expression of GFP. - - Moynahan et al [24] have used such a GFP recombination substrate to demonstrate that cells with defective BRCA2 protein - are deficient in their ability to repair the I-SceI-induced DSB through homologous recombination. Expression of - I-SceI resulted in 1 out of 1400 cell -

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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 4454|4461
        • -
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    mpletely independent of its defect in BRCA2. First, in the same study [24], recombination in a mouse ES cell line - that expresses only truncated BRCA2 protein was measured. This line was found to have lower recombination - efficiency than isogenic cells expressing full-length BRCA2 (the defect observed was ab -

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        • -
      • spans = 5648|5655
        • -
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    Text source name = 11319941.txt -

    striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the gene encoding the myristoylated - alanine-rich C kinase substrate (MARCKS protein). This molecule is important in cerebral development. - MARCKS-deficient mice have a high incidence of exencephaly, agenesis of the corpus callosum, an -

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    • - protein -
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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 21580|21587
        • -
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    mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast two-hybrid system through its - interaction with a putative male infertility factor, DAZ (Deleted in Azoospermi -

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      • Mike Bada
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      • class = proteins
        • -
      • spans = 549|556
        • -
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      • class = proteins
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    via homologous recombination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of - BRCA2 on one homolog and codes for a protein truncated at amino acid 1981 on the other homolog. The authors - indicate that the level of I-SceI-induced recombination in CAPAN-1 is over 100-fold le -

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      • Mike Bada
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        • -
      • spans = 4776|4783
        • -
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    t. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed by Western - blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translatio -

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      • class = proteins
        • -
      • spans = 11727|11735
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    by centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by the - Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of tissue - extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-D -

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      • Mike Bada
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        • -
      • spans = 19243|19250
        • -
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    , agenesis of the corpus callosum, and abnormalities other forebrain structure including widespread neocortical - ectopias [46, 47]. The MARCKS-related protein gene is expressed in the striatum during early brain - development in the rat [48]. - - The location of the QTL modulating striatal neuron number to the d -

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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 21850|21857
        • -
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      • spans = 21850|21857
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    e for direct RAD51 interaction. Cells lacking BRCA1/2 fail to form damage-induced subnuclear RAD51 foci with normal - efficiency, suggesting that these proteins are required for the formation of recombinase complexes at the - sites of DNA damage [20,21]. Finally, genetic measurements of recombination frequency -

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    sophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and spermatogonia, an -

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      • Mike Bada
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      • class = proteins
        • -
      • spans = 3183|3191
        • -
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    R1P and FXR2P, that were identified through their interaction with another polysomal-associated RNA-binding protein, - the fragile X mental retardation protein [21]. Both FXR1P and FXR2P are associated with the polyribosomes - [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be -

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      • Mike Bada
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      • class = proteins
        • -
      • spans = 12395|12402
        • -
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      • spans = 12395|12402
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    ed in CAPAN-1 cells, the same human tumor line examined by Moynahan et al [24]. It had been shown previously that the - small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, - consistent with the fact that the truncation protein lacks a nuclear localization signa -

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      • Mike Bada
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        • -
      • spans = 8808|8815
        • -
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      • spans = 8808|8815
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    em, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA binding domains and a proline - rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to RNA - homopolymers. We now report our characterization of the mouse Dazap1 gene and its pr -

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      • spans = 4367|4374
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    Text source name = 11604102.txt -

    riginal URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast tw -

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    he two RBDs are especially highly conserved. They share 98% and 97% similarity and 97% and 92% identity, - respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA binding specificity. - The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% similarity and -

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        • -
      • spans = 5872|5880
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    se genomic DNA. The PCR primers span over introns and produce much larger (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti - DAZAP1-C antibody was raised against a recombinant protein containing the C-terminal pr -

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      • Mike Bada
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      • class = proteins
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    Text source name = 11604102.txt -

    infertility factor, DAZ (Deleted in Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ - and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a - proline-rich C-terminal portion, and is expressed most abundantly in the testis. To under -

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      • spans = 809|816
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    Text source name = 11597317.txt -

    . Second, in an independent study, Powell was able to compare derivatives of CAPAN-1 that differed only in their - ability to express full-length BRCA2 protein (S. Powell, personal communication, 2001). In these experiments, - the derivative expressing full-length BRCA2 yielded 10-fold more recombinants than c -

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      • spans = 5979|5986
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    Text source name = 11604102.txt -

    NA-binding domains (RBDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved - evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with X -

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      • Mike Bada
        • -
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        • -
      • spans = 5506|5514
        • -
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    tein product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins share 98% identity and their sequences are highly similar to the Xenopus orthologue - Prrp, especially in the RBDs. Dazap1 is expressed throughout test -

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    nal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in neurons is - antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding protein), - which interacts with Nova-1 and inhibits its function [24]. DAZAP1 could function in a -

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    ng dorsal mesoderm at the blastula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of - DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST search of - the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with -

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    to the Xenopus orthologue Prrp, especially in the RBDs. Dazap1 is expressed throughout testis development. Western - blot detects a single 45 kD DAZAP1 protein that is most abundant in the testis. Although a majority of DAZAP1 - is present in the cytoplasmic fraction, they are not associated with polyribosomes -

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    f expression. Such an antagonistic interaction between two interacting RNA-binding proteins is exemplified by the - neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of N -

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    s a change of reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences betwee -

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    s recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting of mouse - tissue extracts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser - degree in spleen, liver, lung and brain (Figure 4). The protein was also present in t -

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    ation of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a R -

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    of DAZAP1 increased afterward, as the testes contained increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted -

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    nds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse testes, DAZAP1 w -

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    share 85%, 90%, and 97% similarity with segments in the human 3' UTR, respectively. These segments probably contain - regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse -

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    RI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences at the junctions were verified by DNA - sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on - His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with Fre -

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    he small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, consistent - with the fact that the truncation protein lacks a nuclear localization signal [28]. Davies et al showed - CAPAN-1 cells to be defective in nuclear localization of RAD51, raising the possibility -

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    acts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser degree in spleen, - liver, lung and brain (Figure 4). The protein was also present in the ovary. The expression of DAZAP1 during - germ cell development paralleled that of DAZL (Figure 5). It is present at a low level -

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    ce, including the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from polyribosomes indicates - that it is not directly involved in protein synthesis. This finding is different from two RNA-binding - proteins, FXR1P and FXR2P, that were identified through their interaction with another poly -

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    clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its proline-rich domain - with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 mRNA - to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth fact -

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    (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with the - RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have been indi -

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    illigrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on His-Bind metal chelation - resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid -

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    ifferent from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction with another - polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both FXR1P and FXR2P - are associated with the polyribosomes [22]. - - The significance of the interaction -

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    ty of Nova-1 to activate exon selection in neurons is antagonized by a second RNA-binding protein, brPTB - (brain-enriched polypyrimidine tract-binding protein), which interacts with Nova-1 and inhibits its function - [24]. DAZAP1 could function in a similar manner by binding to DAZL and inhibiting its functio -

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    em to isolate two human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed - predominantly in testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal - portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to R -

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    Both primer pairs annealed across intron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 ( -

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    erved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for - proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. T -

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    end of the cDNA was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region - (UTR), an open reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession - No: AF225910). The coding region shares 89% similarity with that of the human orth -

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    increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted with the anti-DAZAP1-P antibody. - - Figure 5 Western blot -

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    Z gene family and to understanding the mechanisms of its action, we used a yeast two-hybrid system to isolate two - human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly - in testes. It encodes a protein with two RNA binding domains and a proline rich C-term -

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    gene to be discovered, and was isolated through positional cloning using data from families with inherited breast - cancer [4]. Cells with mutant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate - gross chromosomal rearrangements [5,6]. The sequence of this large protein (3418 ami -

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    AP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic interaction - between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding - protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNAs encoding neuron -

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    logous recombination in vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the - easily detected green fluorescent protein), one of which contains a restriction site for I-SceI, a yeast - intron encoded endonuclease with an 18 base pair recognition site. Transient transfect -

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    ential role for BRCA2 in promoting RAD51-dependent recombinational repair is a positive role in assembly of RAD51 at - damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to 'mediate' assembly of RAD51 - at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, includin -

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    ) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by - the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μ -

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    breaks (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with - the RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have b -

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    ant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements - [5,6]. The sequence of this large protein (3418 amino acids) offers very little clue to its function, - although there are eight repeated segments (termed BRC repeats) in the middle of the prot -

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    nts on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These experiments raise the - possibility that the full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA - interaction. - - The final experiment reported by Davies et al [26] is particularly importa -

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    ribonucleic acids

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    BLAST search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, and possibly DAZAP1, may help to - identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolution -

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    article's original URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identifi -

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    ch domain with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 - mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth factor-β family that is - required for generating dorsal mesoderm at the blastula stage of Xenopus embryoge -

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    erved. They share 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These - proteins may therefore have a similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 - and Prrp are less conserved (81% similarity and 71% identity). There is an insert -

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    DAZL and DAZAP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic - interaction between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear - RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNA -

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        • -
      • class = ribonucleic acids
        • -
      • spans = 12918|12921
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12918|12921
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ressed most abundantly in the testis. - - Figure 3 Developmental expression of Dazap1 and Dazl in mouse testes. RT-PCR was performed on total testicular RNAs - isolated from day 15 (El 5) and day 17 (El 7) embryos, new born mice (Day 0), and mice at various days after birth. - Wv/Wv testes contain diminished g -

      -
    • - RNAs -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 9119|9123
        • -
      -
    • - RNAs -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 9119|9123
        • -
      -
    -
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    Text source name = 11604102.txt -

    communication). The genomic structure of Dazap1, delineated here, should facilitate the generating of Dazap1 null - mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 13965|13968
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 13965|13968
        • -
      -
    -
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    Text source name = 11604102.txt -

    coding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in - neurons is antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding - protein), which interacts with Nova-1 and inhibits its function [24]. DAZAP1 coul -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 13225|13228
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 13225|13228
        • -
      -
    -
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    Text source name = 11604102.txt -

    human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in - testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 - protein interacted with both DAZ and DAZL in vitro. It also bound to RNA homopolyme -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 4297|4300
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
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      • spans = 4297|4300
        • -
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    Text source name = 11604102.txt -

    Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s and the - Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and the mouse - sequences, and between the mouse and Xenopus sequences are marked by #'s and * -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 6368|6371
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
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      • spans = 6368|6371
        • -
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    Text source name = 11604102.txt -

    n with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and - DAZL in vitro. It also bound to RNA homopolymers. We now report our characterization of the mouse Dazap1 gene - and its protein product. The subcellular localization of DAZAP1 suggests th -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 4436|4439
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 4436|4439
        • -
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    Text source name = 11604102.txt -

    VLE that binds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 15181|15184
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 15181|15184
        • -
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    -
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    Text source name = 11604102.txt -

    es [12]. The absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. - This finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their - interaction with another polysomal-associated RNA-binding protein, the fragile -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 12221|12224
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12221|12224
        • -
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    -
    -

    Text source name = 11604102.txt -

    rose gradient. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed - by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localiz -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 11715|11718
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 11715|11718
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    mbers of Drosophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both - sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 3171|3174
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 3171|3174
        • -
      -
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    Text source name = 11604102.txt -

    the level of expression. Such an antagonistic interaction between two interacting RNA-binding proteins is - exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative - splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 12985|12988
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12985|12988
        • -
      -
    -
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    Text source name = 11604102.txt -

    stula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of DAZAP1 and Prrp suggests that - these proteins may bind to similar RNA sequences. However, a BLAST search of the GenBank for the 340 nt VLE - sequence failed to identify any mammalian sequences with significant homology. F -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 14837|14840
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 14837|14840
        • -
      -
    -
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    Text source name = 11604102.txt -

    n Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like - protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is - expressed most abundantly in the testis. To understand the biological function o -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 844|847
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 844|847
        • -
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    -
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    Text source name = 11604102.txt -

    The 5' end of the cDNA was isolated by 5' RACE [15], using prdap11 (ttgcgggccatatccttg, #749–732) as the primer for - cDNA synthesis from mouse testis RNA, and prdap37 (ttgttgccacgtgggcg, #734–718) and an adaptor primer as the - primers for PCR amplification. The PCR products were cloned into a TA cloning -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 15847|15850
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 15847|15850
        • -
      -
    -
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    Text source name = 11604102.txt -

    finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both - FXR1P and FXR2P are associated with the polyribosomes [22]. - - The significance of -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 12341|12344
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12341|12344
        • -
      -
    -
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    Text source name = 11604102.txt -

    97% similarity with segments in the human 3' UTR, respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human pr -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 5355|5358
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 5355|5358
        • -
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    Text source name = 11604102.txt -

    ch fractions was analyzed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 11805|11808
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 11805|11808
        • -
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    Text source name = 11604102.txt -

    with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity - with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. - They share 98% and 97% similarity and 97% and 92% identity, respectively, betwee -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 5694|5697
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 5694|5697
        • -
      -
    -

    single-stranded DNA

    -
    -

    Text source name = 11597317.txt -

    BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-lik -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 12990|12995
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 12990|12995
        • -
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    Text source name = 11597317.txt -

    d to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional form. Alternatively, or - in addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to - the regions of ssDNA that form during normal DNA replication. BRCA2 may thus prom -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10435|10440
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10435|10440
        • -
      -
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    Text source name = 11597317.txt -

    nction difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; ssDNA = - single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like - protein.. Cell. 19 -

      -
    • - single-strand DNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 12998|13015
        • -
      -
    • - single-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 12998|13015
        • -
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    Text source name = 11597317.txt -

    recruited into a functional repair complex when damage occurs. For example, previous studies indicated that RAD51 - shows little binding preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This - result could mean that regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA in -

      -
    • - single-strand DNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10146|10163
        • -
      -
    • - single-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10146|10163
        • -
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    Text source name = 11597317.txt -

    nctional repair complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding - preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that - regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA interacti -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10165|10170
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10165|10170
        • -
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    Text source name = 11597317.txt -

    al form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might be important for preventing - RAD51 from binding to the regions of ssDNA that form during normal DNA replication. BRCA2 may thus promote - RAD51 assembly into recombinational repair complexes via a negative regulatory mechan -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10524|10529
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10524|10529
        • -
      -
    -

    sodium chloride

    -
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    Text source name = 11604102.txt -

    urified on an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of deb -

      -
    • - NaCl -
        -
      • Mike Bada
        • -
      • class = sodium chloride
        • -
      • spans = 18936|18940
        • -
      -
    • - NaCl -
        -
      • Kristin Garcia
        • -
      • class = sodium chloride
        • -
      • spans = 18936|18940
        • -
      -
    -

    sodium dodecyl sulfate

    -
    -

    Text source name = 11604102.txt -

    taining the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 -

      -
    • - SDS -
        -
      • Mike Bada
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 18969|18972
        • -
      -
    • - SDS -
        -
      • Kristin Garcia
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 18969|18972
        • -
      -
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    Text source name = 11604102.txt -

    etermined by the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of - tissue extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-DAZAP1-C - antibody (at a 1/2,000 dilution) or the anti-DAZAP1-P antibody (at a 1/5,000 dilution). -

      -
    • - SDS -
        -
      • Mike Bada
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 19342|19345
        • -
      -
    • - SDS -
        -
      • Kristin Garcia
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 19342|19345
        • -
      -
    -

    sodium phosphates

    -
    -

    Text source name = 11319941.txt -

    ply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, 0.5-1.0 ml ip) and perfused - through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) followed by 1.25% - glutaraldehyde/1.0% paraformaldehyde in 0.1 M PB (pH 7.40) over a period of 2 to 4 min. An additional -

      -
    • - sodium phosphate -
        -
      • Mike Bada
        • -
      • class = sodium phosphates
        • -
      • spans = 26402|26418
        • -
      -
    • - sodium phosphate -
        -
      • Kristin Garcia
        • -
      • class = sodium phosphates
        • -
      • spans = 26402|26418
        • -
      -
    -

    sucrose

    -
    -

    Text source name = 11604102.txt -

    analyses shows that DAZAP1 is not associated with polyribosomes. The post-mitochondrial supernatant of mouse testis - extracts was analyzed on a 15–45% sucrose gradient. Sedimentation was from left to right. The presence of - DAZAP1 and DAZL in each fractions was analyzed by Western blotting. - - Discussion - - RNA- -

      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11562|11569
        • -
      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11562|11569
        • -
      -
    -
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    Text source name = 11604102.txt -

    uclei. After an additional centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the - supernatant were applied to 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged - in a Beckman SW41 rotor at 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were -

      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 20285|20292
        • -
      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 20285|20292
        • -
      -
    -
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    Text source name = 11604102.txt -

    se gradient analyses of the post- mitochondria fraction showed that, unlike DAZL, DAZAP1 did not co-sediment with - polyribosomes (Figure 6). - - Figure 6 Sucrose gradient analyses shows that DAZAP1 is not associated with polyribosomes. The - post-mitochondrial supernatant of mouse testis extracts was analyzed on -

      -
    • - Sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11395|11402
        • -
      -
    • - Sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11395|11402
        • -
      -
    -
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    Text source name = 11604102.txt -

    [12]. Similar analyses showed that a majority of DAZAP1 in adult mouse testes was also present in the cytoplasmic - fraction (data not shown). However, sucrose gradient analyses of the post- mitochondria fraction showed that, - unlike DAZL, DAZAP1 did not co-sediment with polyribosomes (Figure 6). - - Figure 6 Su -

      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11240|11247
        • -
      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11240|11247
        • -
      -
    -

    terpenes

    -
    -

    Text source name = 11532192.txt -

    esia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and wood - shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in wood - shavings alters drug resistance and decreases the effect of anesthetic agents in both ra -

      -
    • - Terpene -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25559|25566
        • -
      -
    • - Terpene -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25559|25566
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    may be important. We use wood shavings for bedding and wood shavings expose the mice to terpenes. Terpene - administration or environmental exposure to terpenes in wood shavings alters drug resistance and decreases - the effect of anesthetic agents in both rats and mice [40-45]. - - Risk factors for increased IOP - -

      -
    • - terpenes -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    of anesthesia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and - wood shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in - wood shavings alters drug resistance and decreases the effect of anesthetic agents i -

      -
    • - terpenes -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25549|25557
        • -
      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25549|25557
        • -
      -
    -

    tert-pentyl group

    -
    -

    Text source name = 11319941.txt -

    lution digital images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% g -

      -
    • - tert-pentyl -
        -
      • Mike Bada
        • -
      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    • - tert-pentyl -
        -
      • Kristin Garcia
        • -
      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    -

    tris

    -
    -

    Text source name = 11604102.txt -

    oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of - debris by centrifugation at 10,000 × g for 10 m -

      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to - 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at - 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were collected from the bott -

      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ham Pharmacia Biotech, Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors -

      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    -

    uracil-1-yl group

    -

    uridyl groups

    -

    water

    -
    -

    Text source name = 11532192.txt -

    containing white pine bedding and covered with polyester filters. For most experiments, the mice were fed NIH31 (6 % - fat) chow ad libitum, and their water was acidified to pH 2.8 to 3.2. B6 mice develop diet induced diabetes - when maintained on a high fat diet [76]. To ensure that we were analyzing the e -

      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    f sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, - 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) - followed by 1.25% glutaraldehyde/1.0 -

      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    +Each concept that was considered a match is shown in the text that it was found in. The matching annotations from the other concept sets are also shown. +
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    • +
      • Kristin Garcia
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    • +
      • Kristin Garcia
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    • +
      • Kristin Garcia
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    • +
      • Kristin Garcia
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    • +
      • Kristin Garcia
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    +

    CHEBI_15377

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    +

    CHEBI_16670

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    +

    CHEBI_17544

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    +

    CHEBI_17992

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    +

    CHEBI_23367

    +

    CHEBI_25213

    +

    CHEBI_25613

    +

    CHEBI_25676

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    +

    CHEBI_26020

    +

    CHEBI_26710

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    +

    CHEBI_27594

    +

    CHEBI_30879

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    +

    CHEBI_32588

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    +

    CHEBI_33521

    +

    CHEBI_33708

    +

    CHEBI_33709

    +

    CHEBI_35186

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    +

    CHEBI_36080

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    +

    CHEBI_37586

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    +

    CHEBI_6636

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    +

    CHEBI_8984

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    +

    CHEBI_9754

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    diff --git a/src/test/resources/iaa_test_project/iaa/Class and span matcher.nonmatches.Kristin Garcia.html b/src/test/resources/iaa_test_project/iaa/Class and span matcher.nonmatches.Kristin Garcia.html index 1c85c94e..7cff6d6b 100644 --- a/src/test/resources/iaa_test_project/iaa/Class and span matcher.nonmatches.Kristin Garcia.html +++ b/src/test/resources/iaa_test_project/iaa/Class and span matcher.nonmatches.Kristin Garcia.html @@ -3,545 +3,151 @@ Class and span matcher

    Non-matches for Kristin Garcia

    -Each annotation that was considered a non-match is shown in the text that it was found in. Overlapping annotations from -the other annotation sets are also shown. -
    -

    5'-cytidylyl group

    -

    5'-guanylyl group

    -

    5'-uridylyl group

    -

    acid

    -

    adenine group

    -

    alanine

    -
    -

    Text source name = 11319941.txt -

    y down-regulate synaptic activity in the striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the - gene encoding the myristoylated alanine-rich C kinase substrate (MARCKS protein). This molecule is important - in cerebral development. MARCKS-deficient mice have a high incidence of exenceph -

      -
    • - alanine -
        -
      • Kristin Garcia
        • -
      • class = alanine
        • -
      • spans = 21540|21547
        • -
      -
    • - alanine -
        -
      • Mike Bada
        • -
      • class = alanine residue
        • -
      • spans = 21540|21547
        • -
      -
    -

    alanine residue

    -

    alcohols

    -

    amino acids

    -
    -

    Text source name = 11604102.txt -

    was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region (UTR), an open - reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession No: AF225910). - The coding region shares 89% similarity with that of the human orthologue. The 3' UTR -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 4931|4941
        • -
      -
    • - amino acid residues -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 4931|4950
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 6273|6283
        • -
      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 6273|6283
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nant protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both antibodies recognized in vitro - synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 9835|9845
        • -
      -
    • - amino acid residue -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 9835|9853
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    BDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved evolutionarily. The mouse - and the human proteins differ in 9 amino acids only, with 7 substitutions and two deletions/insertions. The - mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for proline -

      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 5527|5538
        • -
      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 5527|5538
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    bination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of BRCA2 on one homolog and - codes for a protein truncated at amino acid 1981 on the other homolog. The authors indicate that the level of - I-SceI-induced recombination in CAPAN-1 is over 100-fold less than that seen using -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 4797|4807
        • -
      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 4797|4807
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements [5,6]. The - sequence of this large protein (3418 amino acids) offers very little clue to its function, although there are - eight repeated segments (termed BRC repeats) in the middle of the protein that are highl -

      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 1344|1355
        • -
      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 1344|1355
        • -
      -
    -

    amino-acid residues

    -

    anaesthetic

    -

    canonical nucleoside residues

    -

    carbon

    -

    carboxy group

    -

    cytidyl groups

    -

    cytosin-1-yl group

    -

    deoxyribonucleic acids

    -

    double-stranded DNA

    -
    -

    Text source name = 11319941.txt -

    al forebrain [27, 50]. - - Brain volume and neuron number - - It has previously been shown that differences in brain weight are proportional to total brain DNA content and - consequently to total CNS cell number [51, 52]. For this reason, brain weight has been suggested to be a good - surrogate measure for total -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 22890|22893
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 22890|22893
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    ure was .81 (P < .05), which is similar to the reliability seen in previous estimates of neuron number [39, 40]. - - Genotyping and QTL Mapping - - Genomic DNA was extracted from spleens of F2 animals using a high-salt procedure [63]. A set of 82 - microsatellite loci distributed across all autosomes and the X -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 30232|30235
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 30232|30235
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ty gene BRCA2 in DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in - homology-dependent (recombinational) repair of DNA double-strand breaks. The second paper, by Davies et al, - begins to address the mechanism through which BRCA2 makes its contribution to recombinationa -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 455|458
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    d as they contain most ocular structures. - - Analysis of Myoc - - Exons and the proximal promoter of the mouse Myoc gene were amplified from mouse genomic DNA using the - following combinations of primers: - - Exon 1: 5'-cttgcaggagaactttccagaa-3' and 5'-atctcgaaggagattgttatagg-3' - - 5'-gaccagctggagacccaaaccag-3' a -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 38583|38586
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 38583|38586
        • -
      -
    -

    drug

    -

    glutamate residue

    -
    -

    Text source name = 11319941.txt -

    l portion of Chr 10 in proximity with a number of genes known to affect brain development. One of these is Grk2, a - member of the family of ionotropic glutamate receptor genes that is thought to play a role in modulating - Huntington disease [44]. In the mouse, members of this receptor type act to indirectly do -

      -
    • - glutamate -
        -
      • Kristin Garcia
        • -
      • class = glutamate residue
        • -
      • spans = 21235|21244
        • -
      -
    • - glutamate -
        -
      • Mike Bada
        • -
      • class = glutamate(1-)
        • -
      • spans = 21235|21244
        • -
      -
    • - glutamate -
        -
      • Mike Bada
        • -
      • class = glutamate(2-)
        • -
      • spans = 21235|21244
        • -
      -
    -

    glutamate(1-)

    -

    glutamate(2-)

    -

    glycine

    -

    guanine group

    -

    guanosyl groups

    -

    histidine

    -

    hydrogencarbonate

    -

    inhibitor

    -

    magnesium dichloride

    -

    messenger RNA

    -

    metal cations

    -

    metals

    -
    -

    Text source name = 11604102.txt -

    at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were - prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with - Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antib -

      -
    • - metal -
        -
      • Kristin Garcia
        • -
      • class = metals
        • -
      • spans = 18346|18351
        • -
      -
    • - metal -
        -
      • Mike Bada
        • -
      • class = metal cations
        • -
      • spans = 18346|18351
        • -
      -
    -

    molecular entities

    -

    nucleotidyl groups

    -

    oligopeptides

    -

    peptides

    -

    phosphate(3-)

    -

    phosphates

    -
    -

    Text source name = 11532192.txt -

    ormalin fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 M phosphate buffer. All strains other than CBA/CaHN and C57BLKS/J - strains were evaluated. The eyes of CBA/CaJ and BALB/cJ mice were also fixed and processed for -

      -
    • - phosphate -
        -
      • Kristin Garcia
        • -
      • class = phosphates
        • -
      • spans = 38088|38097
        • -
      -
    • - phosphate -
        -
      • Mike Bada
        • -
      • class = phosphate(3-)
        • -
      • spans = 38088|38097
        • -
      -
    -

    pigment

    -

    potassium chloride

    -

    proline

    -
    -

    Text source name = 11604102.txt -

    tion element (VLE) is sufficient for the migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. - Prrp also interacts through its proline-rich domain with two microfilament-associated proteins profilin and - Mena, which may facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The V -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 14405|14412
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 14405|14412
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    o acids only, with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% - identity with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly - conserved. They share 98% and 97% similarity and 97% and 92% identity, respectivel -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5681|5688
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5681|5688
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two - RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the - testis. To understand the biological function of DAZAP1 and the significance of its -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 877|884
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 877|884
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    e segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, - with 7 substitutions and two deleti -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5423|5430
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5423|5430
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    in, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody was raised against a recombinant - protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both ant -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 9724|9731
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 9724|9731
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA - binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% - similarity and 71% identity). There is an insertion of a 58 bp segment in Prrp cDNA that cau -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5950|5957
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5950|5957
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in testes. It encodes a protein - with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both - DAZ and DAZL in vitro. It also bound to RNA homopolymers. We now report our characte -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 4323|4330
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 4323|4330
        • -
      -
    -

    proline residue

    -

    protease inhibitor

    -

    proteins

    -
    -

    Text source name = 11604102.txt -

    nteraction with DAZ and DAZL, we isolated and characterized the mouse Dazap1 gene, and studied its expression and the - subcellular localization of its protein product. - - Results +Each concept that was considered a non-match is shown in the text that it was found in. Overlapping annotations from the other concept sets are also shown. +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16449
      • spanCollection = sgenic [21540, 21547]
    • +
      • Mike Bada
      • class = CHEBI:32441
      • spanCollection = sgenic [21540, 21547]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = inserti [5681, 5688]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = inserti [5681, 5688]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = Dazap1 [4323, 4330]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = Dazap1 [4323, 4330]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = the tra [14405, 14412]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = the tra [14405, 14412]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = y and 9 [5423, 5430]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = y and 9 [5423, 5430]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = and the [5950, 5957]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = and the [5950, 5957]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nthesiz [9724, 9731]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nthesiz [9724, 9731]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nomic s [877, 884]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nomic s [877, 884]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:32484
      • spanCollection = on on gen [21235, 21244]
    • +
      • Mike Bada
      • class = CHEBI:29987
      • spanCollection = on on gen [21235, 21244]
    • +
      • Mike Bada
      • class = CHEBI:14321
      • spanCollection = on on gen [21235, 21244]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = rie [30232, 30235]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = rie [30232, 30235]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = es [38583, 38586]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = es [38583, 38586]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ral [22890, 22893]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ral [22890, 22893]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = A2 [455, 458]
    +

    +

    CHEBI_15377

    +

    CHEBI_16670

    +

    CHEBI_17544

    +

    CHEBI_17992

    +

    CHEBI_23367

    +

    CHEBI_25213

    +

    CHEBI_25613

    +

    CHEBI_25676

    +

    CHEBI_26020

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26020
      • spanCollection = he anteri [38088, 38097]
    • +
      • Mike Bada
      • class = CHEBI:18367
      • spanCollection = he anteri [38088, 38097]
    +

    CHEBI_26710

    +

    CHEBI_27594

    +

    CHEBI_30879

    +

    CHEBI_32588

    +

    CHEBI_33521

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33521
      • spanCollection = ng th [18346, 18351]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25213
      • spanCollection = ng th [18346, 18351]
    +

    CHEBI_33708

    +

    CHEBI_33709

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = served amon [1344, 1355]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = served amon [1344, 1355]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = (BRCA2+) h [4797, 4807]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = (BRCA2+) h [4797, 4807]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = imilar RNA [5527, 5538]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = imilar RNA [5527, 5538]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = p1 genomic [6273, 6283]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = p1 genomic [6273, 6283]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = tected a 4 [9835, 9845]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = tected a 45 kD pro [9835, 9853]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = tory eleme [4931, 4941]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = tory elements. - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 prot -
          -
        • - protein -
            -
          • Kristin Garcia
            • -
          • class = proteins
            • -
          • spans = 1185|1192
            • -
          -
        • - protein product -
            -
          • Mike Bada
            • -
          • class = proteins
            • -
          • spans = 1185|1200
            • -
          -
        -

        ribonucleic acids

        -

        single-stranded DNA

        -

        sodium chloride

        -

        sodium dodecyl sulfate

        -

        sodium phosphates

        -

        sucrose

        -

        terpenes

        -

        tert-pentyl group

        -

        tris

        -

        uracil-1-yl group

        -

        uridyl groups

        -

        water

        +The [4931, 4950]
    +

    CHEBI_35186

    +

    CHEBI_36080

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = n that [1185, 1192]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = n that is most [1185, 1200]
    +

    CHEBI_37586

    +

    CHEBI_6636

    +

    CHEBI_8984

    +

    CHEBI_9754

    diff --git a/src/test/resources/iaa_test_project/iaa/Class and span matcher.nonmatches.Mike Bada.html b/src/test/resources/iaa_test_project/iaa/Class and span matcher.nonmatches.Mike Bada.html index 2c19f4c5..11d229b0 100644 --- a/src/test/resources/iaa_test_project/iaa/Class and span matcher.nonmatches.Mike Bada.html +++ b/src/test/resources/iaa_test_project/iaa/Class and span matcher.nonmatches.Mike Bada.html @@ -3,1901 +3,343 @@ Class and span matcher

    Non-matches for Mike Bada

    -Each annotation that was considered a non-match is shown in the text that it was found in. Overlapping annotations from -the other annotation sets are also shown. -
    -

    5'-cytidylyl group

    -
    -

    Text source name = 11604102.txt -

    [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = 5'-cytidylyl group
        • -
      • spans = 3904|3905
        • -
      -
    -

    5'-guanylyl group

    -
    -

    Text source name = 11604102.txt -

    should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = 5'-guanylyl group
        • -
      • spans = 14030|14031
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    estes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family an -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = 5'-guanylyl group
        • -
      • spans = 3899|3900
        • -
      -
    -

    5'-uridylyl group

    -
    -

    Text source name = 11604102.txt -

    eated here, should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = 5'-uridylyl group
        • -
      • spans = 14019|14020
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid - system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich segment - in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the funct -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = 5'-uridylyl group
        • -
      • spans = 3870|3871
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) stretches interspersed - by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechan -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = 5'-uridylyl group
        • -
      • spans = 3928|3929
        • -
      -
    -

    acid

    -

    adenine group

    -
    -

    Text source name = 11532192.txt -

    he insertion allele. The other allele was identical to the published sequence [22]. The insertion allele also had a - previously reported substitution (A to G, Thr164Ala) in exon 1 and several other single base changes in the - promoter region [22]. The presence or absence of this allele does not associa -

      -
    • - A -
        -
      • Mike Bada
        • -
      • class = adenine group
        • -
      • spans = 16988|16989
        • -
      -
    -

    alanine

    -

    alanine residue

    -
    -

    Text source name = 11319941.txt -

    y down-regulate synaptic activity in the striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the - gene encoding the myristoylated alanine-rich C kinase substrate (MARCKS protein). This molecule is important - in cerebral development. MARCKS-deficient mice have a high incidence of exenceph -

      -
    • - alanine -
        -
      • Mike Bada
        • -
      • class = alanine residue
        • -
      • spans = 21540|21547
        • -
      -
    • - alanine -
        -
      • Kristin Garcia
        • -
      • class = alanine
        • -
      • spans = 21540|21547
        • -
      -
    -

    alcohols

    -

    amino acids

    -

    amino-acid residues

    -
    -

    Text source name = 11604102.txt -

    e proteins were mixed with Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antibody. An - oligopeptide containing the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the - services of Bethyl Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier -

      -
    • - ammo acid residues -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 18545|18563
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and -

      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 6273|6283
        • -
      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 6273|6283
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements [5,6]. The - sequence of this large protein (3418 amino acids) offers very little clue to its function, although there are - eight repeated segments (termed BRC repeats) in the middle of the protein that are highl -

      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 1344|1355
        • -
      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 1344|1355
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nant protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both antibodies recognized in vitro - synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting of mouse -

      -
    • - amino acid residue -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 9835|9853
        • -
      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 9835|9845
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    bination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of BRCA2 on one homolog and - codes for a protein truncated at amino acid 1981 on the other homolog. The authors indicate that the level of - I-SceI-induced recombination in CAPAN-1 is over 100-fold less than that seen using -

      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 4797|4807
        • -
      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 4797|4807
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region (UTR), an open - reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession No: AF225910). - The coding region shares 89% similarity with that of the human orthologue. The 3' UTR sequence -

      -
    • - amino acid residues -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 4931|4950
        • -
      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 4931|4941
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    BDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved evolutionarily. The mouse - and the human proteins differ in 9 amino acids only, with 7 substitutions and two deletions/insertions. The - mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for proline -

      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 5527|5538
        • -
      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 5527|5538
        • -
      -
    -

    anaesthetic

    -
    -

    Text source name = 11532192.txt -

    tely thirty 3 to 4 month old mice were analyzed at each dose and time B-D. Scatter-plots demonstrating no change in - IOP over the 12 minutes following anesthetic administration in three relatively unrelated mouse strains. All - strains consisted of males and females that ranged from 3 to 6 months of age. The sex -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 14779|14789
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    me). The greater the dose the greater the decrease in IOP. At the 5 minute measurement, however, IOP was the same - using all doses suggesting that the anesthetic effect on IOP had not yet occurred. To identify any early - window when it may be possible to assess IOP without an obvious anesthetic effect, 195 mice -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 13227|13237
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    tic dose within 12 minutes of administration. A Mean IOP ± SD is shown for C57BL/6J mice at 5 and 25 minutes after - administration of various doses of anesthetic. The 1X dose consisted of 99 mg/kg ketamine and 9 mg/kg - xylazine. All doses decreased IOP by 25 minutes. At all doses the IOP at 5 minutes was the sa -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 14394|14404
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    he mice to terpenes. Terpene administration or environmental exposure to terpenes in wood shavings alters drug - resistance and decreases the effect of anesthetic agents in both rats and mice [40-45]. - - Risk factors for increased IOP - - Some epidemiological studies implicate factors such as diabetes, vascular hypertensio -

      -
    • - anesthetic agents -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 25688|25705
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    do not immediately identify them as likely glaucoma candidates. - - No effect of anesthetic protocol on IOP during a 12 minute measurement window - - Many anesthetic agents including xylazine lower IOP. Ketamine usually appears to increase IOP [31-33], but - there are reports of ketamine having no effect on IOP or even red -

      -
    • - anesthetic agents -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 22441|22458
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    ronments may contribute to these differences. The relationship between the IOPs we measure and those in conscious - mice depends upon the effect of our anesthetic protocol (intraperitoneal injection of 99 mg/kg ketamine and 9 - mg/kg xylazine). An anesthetic effect could potentially alter IOP and mask genetically -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 22840|22850
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    s (Figure 6). In these experiments, IOP measurements were made between 5 and 12 minutes after administration of - anesthesia. - - Figure 5 No effect of 1X anesthetic dose within 12 minutes of administration. A Mean IOP ± SD is shown for - C57BL/6J mice at 5 and 25 minutes after administration of various doses of ane -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 14237|14247
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    those in conscious mice depends upon the effect of our anesthetic protocol (intraperitoneal injection of 99 mg/kg - ketamine and 9 mg/kg xylazine). An anesthetic effect could potentially alter IOP and mask genetically - determined differences in IOP. Therefore, it is very important to understand this effect. Her -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 22934|22944
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    minutes after administration. Thus, to avoid effects of anesthesia on IOP, all measurements should be made within a - window of up to 12 minutes after anesthetic administration. - - Similarities and differences to rat studies - - Our results agree with the time course of cardiovascular depression caused by intraperi -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 23386|23396
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    own functions do not suggest that they affect aqueous humor dynamics or do not immediately identify them as likely - glaucoma candidates. - - No effect of anesthetic protocol on IOP during a 12 minute measurement window - - Many anesthetic agents including xylazine lower IOP. Ketamine usually appears to increase IOP -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 22370|22380
        • -
      -
    -

    canonical nucleoside residues

    -
    -

    Text source name = 11604102.txt -

    12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) - stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA - [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understan -

      -
    • - residues -
        -
      • Mike Bada
        • -
      • class = canonical nucleoside residues
        • -
      • spans = 3906|3914
        • -
      -
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    BMC Genomics. 2001; 2: 6. - PubMed ID: 11604102 - - Copyright © 2001 Dai et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and - redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along - with the article's original URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility factors - DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast two-hybrid system through its interaction - with a putative male infertility factor, DAZ (Deleted in Azoospermia). In vitro, DAZAP1 interacts with both the Y - chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding domains - (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the testis. To understand the - biological function of DAZAP1 and the significance of its interaction with DAZ and DAZL, we isolated and - characterized the mouse Dazap1 gene, and studied its expression and the subcellular localization of its protein - product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins share 98% identity and their sequences are highly similar to the Xenopus orthologue Prrp, - especially in the RBDs. Dazap1 is expressed throughout testis development. Western blot detects a single 45 kD - DAZAP1 protein that is most abundant in the testis. Although a majority of DAZAP1 is present in the cytoplasmic - fraction, they are not associated with polyribosomes. - - Conclusions - - DAZAP1 is evolutionarily highly conserved. Its predominant expression in testes suggests a role in spermatogenesis. - Its subcellular localization indicates that it is not directly involved in mRNA translation. - - Background - - Spermatogenesis is a complex developmental process in which male germ cells progress through mitotic proliferation, - meiotic division and dramatic morphological changes to form mature sperm. This process is vital for the propagation - of a species, and involves a large portion of the genome of an organism to ensure the quality and quantity of the - final products. It is estimated that mutations in up to 11% of all genes in Drosophila might lead to male sterility - [1]. This is likely to be true for humans also, considering the extremely high incidence (4–5%) of infertility in - men [2]. Among the genes associated with male infertility is the DAZ (Deleted in Azoospermia) gene family. The - family includes the Y-linked DAZ genes that are present only in great apes and old world monkeys [3], and the - autosomal DAZL1 (DAZ-like 1) and BOULE genes [4,5] in all mammals. Deletion of the DAZ genes is found in about 10% - of infertile males with idiopathic azoospermia [2], and disruption of Dazl1 causes infertility in both male and - female mice [6]. Mutations in the DAZ family members of Drosophila[7], C. elegans[8], and Xenopus[9] also affect the - fertility in either males, females, or both sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL are - expressed in the nucleus and cytoplasm of primordial germ cells and spermatogonia, and in the cytoplasm of meiotic - spermatocytes [6,10]. BOULE is expressed later, in the cytoplasm of pachytene spermatocytes [5]. Genetic and - biochemical studies suggest a role for the DAZ family in the regulation of mRNA translation. Drosophila Boule - mutants was defective in the translation of the meiosis-specific CDC25 homologue, Twine [11], and DAZL was found to - be associated with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast - three-hybrid system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich - segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechanisms of its action, we - used a yeast two-hybrid system to isolate two human genes encoding DAZ associated proteins (DAZAPs) [14]. One of - them, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA binding domains and a proline - rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to RNA - homopolymers. We now report our characterization of the mouse Dazap1 gene and its protein product. The subcellular - localization of DAZAP1 suggests that it is not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 cDNA - - Mouse Dazap1 cDNA clones were isolated by library screening, and the 5' end of the cDNA was isolated by 5' RACE - [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region (UTR), an open reading frame for a - protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession No: AF225910). The coding region shares - 89% similarity with that of the human orthologue. The 3' UTR sequence is remarkably conserved. It contains three - segments of 35 bp, 133 bp and 90 bp that share 85%, 90%, and 97% similarity with segments in the human 3' UTR, - respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline (Figure - 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 - substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with - Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. They share - 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore - have a similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved - (81% similarity and 71% identity). There is an insertion of a 58 bp segment in Prrp cDNA that causes a change of - reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s - and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and the - mouse sequences, and between the mouse and Xenopus sequences are marked by #'s and *'s, respectively. - - Genomic structure of Dazap1 and chromosomal mapping - - Several overlapping lambda clones containing mouse Dazap1 genomic sequences were isolated. The locations of exons - were determined by PCR amplification across exon-intron boundaries following by sequencing. All but the first exon - were isolated and mapped. The genomic structure of the human DAZAP1 gene was also determined by blasting the human - genome sequence at National Center for Biotechnology Information with the human DAZAP1 cDNA sequence. The mouse and - the human genes have very similar structures, consisting of 12 exons spanning about 28 kb. All intron insertion - sites are conserved (Table 1). The two RBDs are encoded by exons 1–4 and 5–8, respectively. - - Table 1 Exon-intron Organization of the Mouse and Human DAZAP1 genes - - A pair of PCR primers was designed from Dazap1 intronic sequences that amplified mouse but not hamster genomic - sequences. Using a panel of mouse-hamster radiation hybrids, the mouse Dazap1 gene was mapped to chromosome 10 - placed 27.84 cR from D10Mit260 (lod > 3.0) (data not shown). This region is syntenic to human 19p13.3 where the - human DAZAP1 gene is located [14,17]. It contains no known mutant alleles that are associated with infertility. - - Expression of Dazap1 - - Northern analyses of adult mouse tissues showed the presence of two Dazap1 transcripts of 1.75 kb and 2.4 kb, - respectively (Figure 2). Only the shorter transcript has been isolated in cDNA clones. Dazap1 was expressed most - abundantly in the testis, much less in liver, heart and brain, and even less in other tissues. This pattern of - expression is similar to that of the human DAZAP1 (14). RT-PCR analyses showed that Dazap1 mRNA was already present - in fetal testes at embryonic day 15, similar to Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 - persisted throughout testes development, in both the prenatal and postnatal periods. Dazl1 and Dazap1 transcripts - were also present in the testes of Wv/Wv mutant mice which contained diminished number of germ cells [18]. However, - only Dazap1 was expressed in a mouse germ cell line GCl-spg [19] and a Sertoli cell line MT4. The results suggest - that Dazap1 is expressed in both somatic and germ cells in the testis. - - Figure 2 Expression of Dazap1 in adult mouse tissues. A mouse multiple-tissue Northern blot was hybridized with a - Dazap1 cDNA probe, stripped, and rehybridized with a β-actin probe. Dazap1 is expressed most abundantly in the - testis. - - Figure 3 Developmental expression of Dazap1 and Dazl in mouse testes. RT-PCR was performed on total testicular RNAs - isolated from day 15 (El 5) and day 17 (El 7) embryos, new born mice (Day 0), and mice at various days after birth. - Wv/Wv testes contain diminished germ cell population due to a mutated W (White spotted) gene. GC1 and MT4 are mouse - germ cell and Sertoli cell lines, respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and - produce much larger (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C - antibody was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid residue at the C-terminus. - Both antibodies recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western - blotting of mouse tissue extracts detected a 45 kD protein that was present most abundantly in the testis, and to a - lesser degree in spleen, liver, lung and brain (Figure 4). The protein was also present in the ovary. The expression - of DAZAP1 during germ cell development paralleled that of DAZL (Figure 5). It is present at a low level in the - testes of 6 days old mice which contained only primitive type A spermatogonia. The expression of DAZAP1 increased - afterward, as the testes contained increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various tissue - extracts were applied to a 10% SDS-polyacrylamide gel and western blotted with the anti-DAZAP1-P antibody. - - Figure 5 Western blot analyses of the expression of DAZAP1 and DAZL in mouse testes during postnatal development. - - Subcellular localization of DAZAP1 - - Our previous fractionation of mouse testis extracts showed that most DAZL were present in the post mitochondrial - fraction, and some of them were associated with polyribosomes [12]. Similar analyses showed that a majority of - DAZAP1 in adult mouse testes was also present in the cytoplasmic fraction (data not shown). However, sucrose - gradient analyses of the post- mitochondria fraction showed that, unlike DAZL, DAZAP1 did not co-sediment with - polyribosomes (Figure 6). - - Figure 6 Sucrose gradient analyses shows that DAZAP1 is not associated with polyribosomes. The post-mitochondrial - supernatant of mouse testis extracts was analyzed on a 15–45% sucrose gradient. Sedimentation was from left to - right. The presence of DAZAP1 and DAZL in each fractions was analyzed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA translation is supported by lines of circumstantial evidence, including the association of DAZL - with polyribosomes [12]. The absence of DAZAP1 from polyribosomes indicates that it is not directly involved in - protein synthesis. This finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified - through their interaction with another polysomal-associated RNA-binding protein, the fragile X mental retardation - protein [21]. Both FXR1P and FXR2P are associated with the polyribosomes [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be defined. These proteins may act - together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be involved in the - transport of the mRNAs of the target genes of DAZL. Alternatively, DAZL and DAZAP1 may act antagonistically to - regulate the timing and the level of expression. Such an antagonistic interaction between two interacting - RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the - alternative splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability - of Nova-1 to activate exon selection in neurons is antagonized by a second RNA-binding protein, brPTB - (brain-enriched polypyrimidine tract-binding protein), which interacts with Nova-1 and inhibits its function [24]. - DAZAP1 could function in a similar manner by binding to DAZL and inhibiting its function. Comparing the phenotypes - of Dazl1 and Dazap1 single and double knock-out mice may provide some clues to the significance of their - interaction. Dazl1 knock-out mice have already been generated and studied [6]. The spermatogenic defect in the male - becomes apparent only after day 7 post partum when the germ cells are committing to meiosis (H. Cooke, personal - communication). The genomic structure of Dazap1, delineated here, should facilitate the generating of Dazap1 null - mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural substrates - have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and characterized [16]. - Prrp binds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient - for the migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its - proline-rich domain with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring - of Vg1 mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth factor-β family that is - required for generating dorsal mesoderm at the blastula stage of Xenopus embryogenesis [25]. Sequence conservation - between the RBDs of DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST - search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, and possibly DAZAP1, may help to identify - the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. Its - predominant expression in testes suggests a role in spermatogenesis. In mouse testes, DAZAP1 was found both in the - nuclei and in the cytoplasm. Its absence from polyribosomes indicates that it is not directly involved in mRNA - translation. - - Materials and methods - - Isolation of mouse Dazap1 cDNA clones - - Dazap1 cDNA clones were isolated from a mouse testis cDNA library (#937308, Stratagene, La Jolla, CA) using a human - DAZAP1 cDNA as a probe. The 5' end of the cDNA was isolated by 5' RACE [15], using prdap11 (ttgcgggccatatccttg, - #749–732) as the primer for cDNA synthesis from mouse testis RNA, and prdap37 (ttgttgccacgtgggcg, #734–718) and an - adaptor primer as the primers for PCR amplification. The PCR products were cloned into a TA cloning vector - pCR2.1-TOPO (Invitrogen, Carlsbad CA). Dazap1 clones were identified by colony hybridization and sequenced. The 5' - RACE clone with the longest 5' UTR region and the cDNA clone P21 were ligated together through a unique PmlI site at - # 722 to generate a cDNA clone (Dazap1-C) with a near full-length insert. - - Chromosomal mapping of Dazap1 - - Dazap1 genomic clones were isolated from a mouse 129SV genomic library (#946305, Stragagene), and sequences flanking - each exons were determined. PCR primers (prdap25: cacctccaggatgtgttagc and prdazp26:gtcaccaagggtgtctgaag) were - designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment from mouse but - not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse chromosome fragments in a - hamster background were purchased from Research Genetics (Huntsville, AL). The presence of mouse Dazap1 in the - radiation hybrids was determined by PCR and the results were sent to the MIT server for computerized physical - mapping of the gene. - - Expression of Dazap1 transcripts - - Northern hybridization was carried out according to standard procedures [26] using a mouse Multiple Tissue Northern - Blot #7762–1 from Clontech (Palo Alto, CA). The blot was hybridized sequentially with DAZAP1 and β-actin cDNA - probes, with stripping of the bound probes in between. - - Reverse transcription-polymerase chain reaction (RT-PCR) was carried out as preciously described using an annealing - temperature of 54°C [27]. The primers were prdap35: agctcagggagtacttcaaga and prdap24 :ggagcttgattcttgctgtcc for - Dazap1 which generated a product of 211 bp, and prdaz71: atcgaactggtgtgtcgaagg and prdaz72: ggaggctgcatgtaagtctca - for Dazl1 which generated a product of 245 bp. Both primer pairs annealed across intron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide synthesized in - vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 (starting from aa - #197), was cloned in-frame into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). - Sequences at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed - with Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antibody. An oligopeptide containing - the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the services of Bethyl - Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier and injected into a goat. The - anti-DAZAP1-P antibody thus produced was purified on an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM Tris, pH - 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by the - Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of tissue extracts were - separated on 10% SDS-polyacrylamide gels and blotted with either the anti-DAZAP1-C antibody (at a 1/2,000 dilution) - or the anti-DAZAP1-P antibody (at a 1/5,000 dilution). After incubation with horseradish peroxidase-conjugated - secondary antibodies, the binding of antibodies was detected using the ECL Western Blotting System (Amersham - Pharmacia Biotech, Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, - 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors provided in - the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, IN). Homogenates were centrifuged at 1,000 - × g for 10 minutes to pellet cell debris and nuclei. After an additional centrifugation at 10,000 × g for 10 minutes - to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose gradients in 20 mM Tris, 100 - mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml - were collected from the bottom of the tubes and analyzed by western blotting. - - Acknowledgments - - We thank Gary Kuo for his involvement in the construction of Dazap1 expression vectors, and Ron Swerdloff's group - for helpful discussion. The work was supported by grants from the National Institutes of Health (HD28009 and - HD36347). Y. Vera was supported by an NIH grant (GM56902) on Initiative for Minority Student Development. - - References - - 1. Hackstein JHP, Hochstenbach R, Pearson PL. Towards an understanding of the genetics of human male infertility.. - TIG. 2000;16:565-572. doi: 10.1016/S0168-9525(00)02140-5 - - 2. De Kretser DM. Male infertility.. Lancet. 1997;349:787-790. doi: 10.1016/S0140-6736(96)08341-9 - - 3. Reijo R, Lee T-Y, Salo P, Allagappan R, Brown LG, Rosenberg M, Rozen S, Jaffe T, Straus D, Hovatta O, de la - Chapelle A, Silber S, Page DC. Diverse spermatogenic defects in humans caused by Y chromosome deletions encompassing - a novel RNA-binding protein gene.. Nat Genet. 1995;10:383-393. doi: 10.1038/ng0895-383 - - 4. Cooke HJ, Lee M, Kerr S, Ruggiu M. A murine homologue of the human DAZ gene is autosomal and expressed only in - male and female gonads.. Hum Mol Genet. 1996;5:513-516. doi: 10.1093/hmg/5.4.513 - - 5. Xu EY, Moore FL, Pera RAR. A gene family required for human germ cell development evolved from an ancient meiotic - gene conserved in metazoans.. PNAS. 2001;98:7414-7419. doi: 10.1073/pnas.131090498 - - 6. Ruggiu M, Speed R, Taggart M, McKay SJ, Kilanowski F, Saunders P, Dorin J, Cooke HJ. The mouse DAZLA gene encodes - a cytoplasmic protein essential for gametogenesis.. Nature. 1997;389:73-77. doi: 10.1038/37987 - - 7. Eberhar CG, Maines JZ, Wasserman SA. Meiotic cell cycle requirement for a fly homologue of human Deleted in - Azoospermia.. Nature. 1996;381:783-785. doi: 10.1038/381783a0 - - 8. Karashima T, Sugimoto A, Yamamoto M. Caenorhabditis elegans homologue of the human azoospermia factor DAZ is - required for oogenesis but not for spermatogenesis.. Development. 2000;127:1069-1079. - - 9. Houston DW, Zhang J, Maines JZ, Wasserman SA, King ML. A Xenopus DAZ-like gene encodes an RNA component of germ - plasm and is a functional homologue of Drosophila boule.. Development. 1998;125:171-180. - - 10. Reijo RA, Dorfman DM, Slee R, Renshaw AA, Laughlin KR, Cooke H, Page DC. DAZ family proteins exist through male - germ cell development and transit from nucleus to cytoplasm at meiosis in humans and mice.. Biol Reprod. - 2000;63:1490-1496. - - 11. Maines JZ, Wasserman SA. Post-transcriptional regulation of the meiotic Cdc25 protein Twine by the Daz1 - orthologue Boule.. Nat Cell Biol. 1999;1:171-174. doi: 10.1038/11091 - - 12. Tsui S, Dai T, Warren ST, Salido EC, Yen PH. Association of the infertility factor DAZL1 with actively - translating polyribosomes.. Biol Reprod. 2000;62:1655-1660. - - 13. Venables JP, Ruggiu M, Cooke HJ. The RNA-binding specificity of the mouse Daz1 protein.. Nucl Acids Res. - 2001;29:2479-2483. doi: 10.1093/nar/29.12.2479 - - 14. Tsui S, Dai T, Roettger S, Schempp W, Salido EC, Yen PY. Identification of two novel proteins that interact with - germ-cell specific RNA-binding proteins DAZ and DAZL1.. Genomics. 2000;65:266-273. doi: 10.1006/geno.2000.6169 - - 15. Frohman MA, Dush MK, Martin GR. Rapid production of full-length cDNAs from rare transcripts: amplification using - a single gene-specific oligonucleotide primer.. PNAS. 1988;85:8998-9002. - - 16. Zhao W, Jiang C, Kroll TT, Huber PW. proline-rich protein binds to the localization element of Xenopus Vg1 mRNA - and to ligands involved in actin polymerization.. EMBO J. 2001;20:2315-2325. doi: 10.1093/emboj/20.9.2315 - - 17. DeBry RW, Seldin MF. Human/mouse homology relationships.. Genomics. 1996;33:337-351. doi: 10.1006/geno.1996.0209 - - 18. Fleischman RA. From white spots to stem cells: The role of the Kit receptor in mammalian development.. Trends - Genet. 1993;9:285-290. doi: 10.1016/0168-9525(93)90015-A - - 19. Hofmann MC, Narisawa S, Hess RA, Millan JL. Immortalization of germ cells and somatic testicular cells using the - SV40 large T antigen.. Exp Cell Res. 1992;201:417-435. doi: 90291-F - - 20. Siomi H, Dreyfuss G. RNA-binding proteins as regulators of geneexpression.. Cur Opin Genet Develop. - 1997;7:345-353. doi: 10.1016/S0959-437X(97)80148-7 - - 21. Zhang Y, O'Connor JP, Siomi MC, Srinivasan S, Dutra A, Nussbaum RL, Dreyfuss G. The fragile X mental retardation - syndrome protein interacts with novel homologs FXR1 and FXR2.. EMBO J. 1995;14:5358-5366. - - 22. Siomi MC, Zhang Y, Siomi H, Dreyfuss G. Specific sequences in the fragile X syndrome protein FMR1 and the FXR2 - proteins mediate their binding to 60S ribosomal subunits and the interactions among them.. Mol Cell Biol. - 1996;16:3825-3832. - - 23. Jensen KB, Dredge BK, Stefani G, Zhong R, Buckanovich RJ, Okano HJ, Yang YY, Darnell RB. Nova-1 regulates - neuron-specific alternative splicing and is essential for neuronal viability.. Neuron. 2000;25:359-371. doi: - 10.1016/S0896-6273(00)80900-9 - - 24. Polydorides AD, Okano HJ, Yang YY, Stefani G, Darnell RB. A brain-enriched polypyrimidine tract-binding protein - antagonizes the ability of Nova to regulate neuron-specific alternative splicing.. PNAS. 2000;97:6350-6355. doi: - 10.1073/pnas.110128397 - - 25. Thomson GH, Melton DA. Processed Vg1 protein is an axial mesoderm inducer in Xenopus.. Cell. 1993;74:433-441. - doi: 10.1016/0092-8674(93)80045-G - - 26. Sambrook J, Fritsch EF, Maniatis T. null. Molecular Cloning: A Laboratory Manual 2nd ed, Cold Spring Harbor - Laboratory Press, Cold Spring Harbor,. 1989;null:null-null. - - 27. Salido EC, Yen PH, Mohandas TK, Shapiro LJ. Expression of the X-inactivation-associated gene XIST during - spermatogenesis.. Nat Genet. 1992;2:196-199. doi: 10.1038/ng1192-196 - - -

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    ins. Most tested strains exhibit a diurnal rhythm with IOP being the highest during the dark period of the day. - Homozygosity for a null allele of the carbonic anhydrase II gene (Car2n) does not alter IOP while - homozygosity for a mutation in the leptin receptor gene (Leprdb) that causes obesity and diabetes -

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    evant to glaucoma. - - Car2 deficiency does not alter IOP - - Bicarbonate formation is important for aqueous humor secretion from the ciliary processes and carbonic - anhydrase (CA) facilitates this secretion. There are multiple forms of CA and the CAII isoform is reported to be the - predominant form in the ciliary -

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    rified and sequenced as described [22]. - - Abbreviations - - Intraocular pressure (IOP), C57BL/6J (B6), chromosome (Chr), polymerase chain reaction (PCR), carbonic - anhydrase (CA) - - Acknowledgments - - We thank Norma Buckley, Felicia Farley and Jennifer Smith for their assistance with data entry, references, and figu -

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    ± SD; db/db 422 ± 110 mg/dl ; db/+ 147 ± 19 mg/dl; Anthony Nicholson, The Jackson Laboratory, personal communication) - - Car2 - - To test if deficiency of carbonic anhydrase II leads to decreased IOP, we analyzed mice of a B6 background - that were genetically similar but with normal or mutant alleles of the Car2 -

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    nst both a recombinant protein produced in E. coli and an oligopeptide synthesized in vitro. The insert of a Dazap1 - cDNA clone P21, which encoded the C-terminal portion of DAZAP1 (starting from aa #197), was cloned in-frame - into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, W -

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    e C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an oligopeptide containing the - last 19 amino acid residue at the C-terminus. Both antibodies recognized in vitro synthesized DAZAP1 in an - immunoprecipitation assay (data not shown). Western blotting of mouse tissue e -

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    oteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA - binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL - in vitro. It also bound to RNA homopolymers. We now report our characterizatio -

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    -
    -

    Text source name = 11604102.txt -

    AZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody was raised against a - recombinant protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised - against an oligopeptide containing the last 19 amino acid residue at the C-t -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 9713|9714
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    identity). There is an insertion of a 58 bp segment in Prrp cDNA that causes a change of reading frame and results in - a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s - and the Xe -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 6184|6185
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore have a - similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved - (81% similarity and 71% identity). There is an insertion of a 58 bp segment in P -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 5939|5940
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti - DAZAP1-C antibody was raised against a recombinant protein containing the C-terminal proline-rich portion, - and the anti DAZAP1-P antibody was raised against a -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 9646|9647
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    system (Bio-Rad, Hercules, CA). About 50 μg of tissue extracts were separated on 10% SDS-polyacrylamide gels and - blotted with either the anti-DAZAP1-C antibody (at a 1/2,000 dilution) or the anti-DAZAP1-P antibody (at a - 1/5,000 dilution). After incubation with horseradish peroxidase-conjugated secon -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 19406|19407
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    h both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding - domains (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the testis. To - understand the biological function of DAZAP1 and the significance of its interac -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 890|891
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    he human 3' UTR, respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 5388|5389
        • -
      -
    -

    cytidyl groups

    -
    -

    Text source name = 11604102.txt -

    [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = cytidyl groups
        • -
      • spans = 3904|3905
        • -
      -
    -

    cytosin-1-yl group

    -
    -

    Text source name = 11604102.txt -

    [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = cytosin-1-yl group
        • -
      • spans = 3904|3905
        • -
      -
    -

    deoxyribonucleic acids

    -
    -

    Text source name = 11532192.txt -

    d as they contain most ocular structures. - - Analysis of Myoc - - Exons and the proximal promoter of the mouse Myoc gene were amplified from mouse genomic DNA using the - following combinations of primers: - - Exon 1: 5'-cttgcaggagaactttccagaa-3' and 5'-atctcgaaggagattgttatagg-3' - - 5'-gaccagctggagacccaaaccag-3' a -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 38583|38586
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 38583|38586
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    ure was .81 (P < .05), which is similar to the reliability seen in previous estimates of neuron number [39, 40]. - - Genotyping and QTL Mapping - - Genomic DNA was extracted from spleens of F2 animals using a high-salt procedure [63]. A set of 82 - microsatellite loci distributed across all autosomes and the X -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 30232|30235
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 30232|30235
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    al forebrain [27, 50]. - - Brain volume and neuron number - - It has previously been shown that differences in brain weight are proportional to total brain DNA content and - consequently to total CNS cell number [51, 52]. For this reason, brain weight has been suggested to be a good - surrogate measure for total -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 22890|22893
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 22890|22893
        • -
      -
    -

    double-stranded DNA

    -

    drug

    -
    -

    Text source name = 11532192.txt -

    ng this period in any analyzed strain. Environmental differences may be important. Cage cleanliness, changing - frequency and housing density can alter drug metabolism and the effect of anesthesia in rats [38,39]. The - type of bedding used also may be important. We use wood shavings for bedding and wood sh -

      -
    • - drug -
        -
      • Mike Bada
        • -
      • class = drug
        • -
      • spans = 25369|25373
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    vings for bedding and wood shavings expose the mice to terpenes. Terpene administration or environmental exposure to - terpenes in wood shavings alters drug resistance and decreases the effect of anesthetic agents in both rats - and mice [40-45]. - - Risk factors for increased IOP - - Some epidemiological studies -

      -
    • - drug -
        -
      • Mike Bada
        • -
      • class = drug
        • -
      • spans = 25644|25648
        • -
      -
    -

    glutamate residue

    -

    glutamate(1-)

    -
    -

    Text source name = 11319941.txt -

    l portion of Chr 10 in proximity with a number of genes known to affect brain development. One of these is Grk2, a - member of the family of ionotropic glutamate receptor genes that is thought to play a role in modulating - Huntington disease [44]. In the mouse, members of this receptor type act to indirectly do -

      -
    • - glutamate -
        -
      • Mike Bada
        • -
      • class = glutamate(1-)
        • -
      • spans = 21235|21244
        • -
      -
    • - glutamate -
        -
      • Kristin Garcia
        • -
      • class = glutamate residue
        • -
      • spans = 21235|21244
        • -
      -
    -

    glutamate(2-)

    -
    -

    Text source name = 11319941.txt -

    l portion of Chr 10 in proximity with a number of genes known to affect brain development. One of these is Grk2, a - member of the family of ionotropic glutamate receptor genes that is thought to play a role in modulating - Huntington disease [44]. In the mouse, members of this receptor type act to indirectly do -

      -
    • - glutamate -
        -
      • Mike Bada
        • -
      • class = glutamate(2-)
        • -
      • spans = 21235|21244
        • -
      -
    • - glutamate -
        -
      • Kristin Garcia
        • -
      • class = glutamate residue
        • -
      • spans = 21235|21244
        • -
      -
    -

    glycine

    -

    guanine group

    -
    -

    Text source name = 11604102.txt -

    should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanine group
        • -
      • spans = 14030|14031
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    estes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family an -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanine group
        • -
      • spans = 3899|3900
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    sertion allele. The other allele was identical to the published sequence [22]. The insertion allele also had a - previously reported substitution (A to G, Thr164Ala) in exon 1 and several other single base changes in the - promoter region [22]. The presence or absence of this allele does not associate wi -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanine group
        • -
      • spans = 16993|16994
        • -
      -
    -

    guanosyl groups

    -
    -

    Text source name = 11604102.txt -

    estes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family an -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanosyl groups
        • -
      • spans = 3899|3900
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanosyl groups
        • -
      • spans = 14030|14031
        • -
      -
    -

    histidine

    -

    hydrogencarbonate

    -

    inhibitor

    -
    -

    Text source name = 11597317.txt -

    ptide consisting of one of the eight BRC repeats from human BRCA2. Expression of a single BRC repeat (BRC4) had - previously been reported to act as an inhibitor of DNA repair by Chen et al [27]. These investigators showed - that expression of constructs containing the BRC4 repeat in MCF-7 cells enhances the rad -

      -
    • - inhibitor -
        -
      • Mike Bada
        • -
      • class = inhibitor
        • -
      • spans = 7572|7581
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    cts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, - 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, -

      -
    • - inhibitor -
        -
      • Mike Bada
        • -
      • class = inhibitor
        • -
      • spans = 19887|19896
        • -
      -
    -

    magnesium dichloride

    -

    messenger RNA

    -

    metal cations

    -
    -

    Text source name = 11604102.txt -

    at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were - prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with - Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antib -

      -
    • - metal -
        -
      • Mike Bada
        • -
      • class = metal cations
        • -
      • spans = 18346|18351
        • -
      -
    • - metal -
        -
      • Kristin Garcia
        • -
      • class = metals
        • -
      • spans = 18346|18351
        • -
      -
    -

    metals

    -

    molecular entities

    -
    -

    Text source name = 11532192.txt -

    hese risk factors. - - IOP is increased during the dark period of the day - - Diurnal variation in IOP is common in humans and laboratory animals [53]. The molecular mechanisms underlying - the diurnal rhythm are not defined but increased aqueous humor production or flow occurs during the period of - increased IOP in -

      -
    • - molecular -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 29448|29457
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    d Not genes. Vax1 is localized during development to the anterior ventral forebrain, and is expressed in the striatum - during embryogenesis [28]. This molecule also has an important role in axon guidance: both the anterior - portion of the corpus callosum and the optic chiasm are malformed or absent in Vax1 kn -

      -
    • - molecule -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 22409|22417
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    rior portion of the corpus callosum and the optic chiasm are malformed or absent in Vax1 knockout mice [49]. In - addition, Vax1 interacts with several molecules including sonic hedgehog,Pax2, Pax6, and Rx that are known to - be important during development of the basal forebrain [27, 50]. - - Brain volume and neur -

      -
    • - molecules -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 22626|22635
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    accurate and rapid enough to allow large scale genetic studies of factors determining IOP. Mice have great potential - for helping to characterize the molecular mechanisms affecting IOP. - - Materials and Methods - - Animal husbandry - - All experiments were performed in compliance with the ARVO statement for use of a -

      -
    • - molecular -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 34211|34220
        • -
      -
    -

    nucleotidyl groups

    -
    -

    Text source name = 11532192.txt -

    OP in mouse strains, we analyzed the gene in an assortment of strains with different IOPs. Two alleles were - identified. One of these alleles had a 12 nucleotide insertion in the promoter region (ccagagcagggt, between - positions -340 and -341) compared to the previously published sequence and is called the inse -

      -
    • - nucleotide -
        -
      • Mike Bada
        • -
      • class = nucleotidyl groups
        • -
      • spans = 16685|16695
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ral substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization - element (VLE) is sufficient for the migration and clustering of Vg1 mRNA to the veg -

      -
    • - nt -
        -
      • Mike Bada
        • -
      • class = nucleotidyl groups
        • -
      • spans = 14191|14193
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    etween the RBDs of DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST - search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, an -

      -
    • - nt -
        -
      • Mike Bada
        • -
      • class = nucleotidyl groups
        • -
      • spans = 14903|14905
        • -
      -
    -

    oligopeptides

    -

    peptides

    -

    phosphate(3-)

    -
    -

    Text source name = 11532192.txt -

    ormalin fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 M phosphate buffer. All strains other than CBA/CaHN and C57BLKS/J - strains were evaluated. The eyes of CBA/CaJ and BALB/cJ mice were also fixed and processed for -

      -
    • - phosphate -
        -
      • Mike Bada
        • -
      • class = phosphate(3-)
        • -
      • spans = 38088|38097
        • -
      -
    • - phosphate -
        -
      • Kristin Garcia
        • -
      • class = phosphates
        • -
      • spans = 38088|38097
        • -
      -
    -

    phosphates

    -

    pigment

    -
    -

    Text source name = 11532192.txt -

    nt with this result, mice with albino eyes that are homozygous for tyrosinase or pink eye dilution mutations have - altered diurnal rhythms compared to pigmented mice [75]. Albinism by itself is either not sufficient to alter - the diurnal rhythm of IOP or alters it in different ways depending upon genetic backg -

      -
    • - pigmented -
        -
      • Mike Bada
        • -
      • class = pigment
        • -
      • spans = 33044|33053
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    these abnormalities affect mammalian IOP. Here, we show increased IOP in mice lacking tyrosinase activity compared to - otherwise genetically identical pigmented B6 mice. Additionally, IOP differences between the light and dark - period of the day were detected in the pigmented but not the albino B6 mice. Thus, -

      -
    • - pigmented -
        -
      • Mike Bada
        • -
      • class = pigment
        • -
      • spans = 32669|32678
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    to otherwise genetically identical pigmented B6 mice. Additionally, IOP differences between the light and dark period - of the day were detected in the pigmented but not the albino B6 mice. Thus, albinism can affect the diurnal - pattern of IOP changes. In agreement with this result, mice with albino eyes that a -

      -
    • - pigmented -
        -
      • Mike Bada
        • -
      • class = pigment
        • -
      • spans = 32784|32793
        • -
      -
    -

    potassium chloride

    -

    proline

    -

    proline residue

    -
    -

    Text source name = 11604102.txt -

    tion element (VLE) is sufficient for the migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. - Prrp also interacts through its proline-rich domain with two microfilament-associated proteins profilin and - Mena, which may facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The V -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 14405|14412
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 14405|14412
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two - RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the - testis. To understand the biological function of DAZAP1 and the significance of its -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 877|884
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 877|884
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    e segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, - with 7 substitutions and two deleti -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5423|5430
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5423|5430
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA - binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% - similarity and 71% identity). There is an insertion of a 58 bp segment in Prrp cDNA that cau -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5950|5957
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5950|5957
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    in, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody was raised against a recombinant - protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both ant -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 9724|9731
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 9724|9731
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    o acids only, with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% - identity with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly - conserved. They share 98% and 97% similarity and 97% and 92% identity, respectivel -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5681|5688
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5681|5688
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in testes. It encodes a protein - with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both - DAZ and DAZL in vitro. It also bound to RNA homopolymers. We now report our characte -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 4323|4330
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 4323|4330
        • -
      -
    -

    protease inhibitor

    -

    proteins

    -
    -

    Text source name = 11604102.txt -

    in interacted with both DAZ and DAZL in vitro. It also bound to RNA homopolymers. We now report our characterization - of the mouse Dazap1 gene and its protein product. The subcellular localization of DAZAP1 suggests that it is - not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 -

      -
    • - protein product -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 4522|4537
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nteraction with DAZ and DAZL, we isolated and characterized the mouse Dazap1 gene, and studied its expression and the - subcellular localization of its protein product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins sha -

      -
    • - protein product -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 1185|1200
        • -
      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 1185|1192
        • -
      -
    -

    ribonucleic acids

    -

    single-stranded DNA

    -

    sodium chloride

    -

    sodium dodecyl sulfate

    -

    sodium phosphates

    -

    sucrose

    -

    terpenes

    -

    tert-pentyl group

    -

    tris

    -

    uracil-1-yl group

    -
    -

    Text source name = 11604102.txt -

    eated here, should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uracil-1-yl group
        • -
      • spans = 14019|14020
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid - system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich segment - in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the funct -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uracil-1-yl group
        • -
      • spans = 3870|3871
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) stretches interspersed - by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechan -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uracil-1-yl group
        • -
      • spans = 3928|3929
        • -
      -
    -

    uridyl groups

    -
    -

    Text source name = 11604102.txt -

    eated here, should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uridyl groups
        • -
      • spans = 14019|14020
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) stretches interspersed - by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechan -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uridyl groups
        • -
      • spans = 3928|3929
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid - system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich segment - in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the funct -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uridyl groups
        • -
      • spans = 3870|3871
        • -
      -
    -

    water

    -
    -

    Text source name = 11532192.txt -

    ariation in IOP is common in humans and laboratory animals [53]. The molecular mechanisms underlying the diurnal - rhythm are not defined but increased aqueous humor production or flow occurs during the period of increased - IOP in both rabbits and humans [63-65]. Small changes in the resistance to aqueous hum -

      -
    • - aqueous -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 29529|29536
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      -
    -
    -

    Text source name = 11532192.txt -

    important approaches as they may allow the association of genes with IOP and glaucoma whose currently known functions - do not suggest that they affect aqueous humor dynamics or do not immediately identify them as likely glaucoma - candidates. - - No effect of anesthetic protocol on IOP during a 12 minute measure -

      -
    • - aqueous -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 22266|22273
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    sed aqueous humor production or flow occurs during the period of increased IOP in both rabbits and humans [63-65]. - Small changes in the resistance to aqueous humor drainage may also contribute to diurnal differences in IOP - [66,67]. We first suspected IOP changes with time of day when the IOP of a group of -

      -
    • - aqueous -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 29675|29682
        • -
      -
    +Each concept that was considered a non-match is shown in the text that it was found in. Overlapping annotations from the other concept sets are also shown. +
    +

    +

    +

    • +
      • Mike Bada
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    • +
      • Kristin Garcia
      • class = CHEBI:32484
      • spanCollection = on on gen [21235, 21244]
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    +

    +

    +

    +

    • +
      • Mike Bada
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    • +
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    +

    • +
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    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ral [22890, 22893]
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    +

    • +
      • Mike Bada
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    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = rie [30232, 30235]
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    +

    +

    • +
      • Mike Bada
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    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26020
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    +

    +

    • +
      • Mike Bada
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    +

    +

    • +
      • Mike Bada
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      • spanCollection = p [3904, 3905]
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    +

    +

    • +
      • Mike Bada
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      • spanCollection = alyz [25644, 25648]
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    +

    • +
      • Mike Bada
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      • spanCollection = e ra [25369, 25373]
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    +

    +

    • +
      • Mike Bada
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      • spanCollection = T [14030, 14031]
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    +

    • +
      • Mike Bada
      • class = CHEBI:24459
      • spanCollection = e [3899, 3900]
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    +

    +

    • +
      • Mike Bada
      • class = CHEBI:24460
      • spanCollection = T [14030, 14031]
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    +

    • +
      • Mike Bada
      • class = CHEBI:24460
      • spanCollection = e [3899, 3900]
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    +

    +

    • +
      • Mike Bada
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      • spanCollection = e number [32784, 32793]
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    +

    • +
      • Mike Bada
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      • spanCollection = pathway. [32669, 32678]
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    +

    • +
      • Mike Bada
      • class = CHEBI:26130
      • spanCollection = ise genet [33044, 33053]
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    +

    +

    +

    • +
      • Mike Bada
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      • spanCollection = i [14019, 14020]
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    +

    • +
      • Mike Bada
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      • spanCollection = d [3928, 3929]
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    +

    • +
      • Mike Bada
      • class = CHEBI:27243
      • spanCollection = o [3870, 3871]
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    +

    +

    • +
      • Mike Bada
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      • spanCollection = d [3928, 3929]
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    +

    • +
      • Mike Bada
      • class = CHEBI:27244
      • spanCollection = i [14019, 14020]
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    +

    • +
      • Mike Bada
      • class = CHEBI:27244
      • spanCollection = o [3870, 3871]
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    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:29987
      • spanCollection = on on gen [21235, 21244]
    • +
      • Kristin Garcia
      • class = CHEBI:32484
      • spanCollection = on on gen [21235, 21244]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30755
      • spanCollection = T [14030, 14031]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30755
      • spanCollection = f [16993, 16994]
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    +

    • +
      • Mike Bada
      • class = CHEBI:30755
      • spanCollection = e [3899, 3900]
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    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30756
      • spanCollection = e [16988, 16989]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30758
      • spanCollection = p [3904, 3905]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30759
      • spanCollection = i [14019, 14020]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30759
      • spanCollection = d [3928, 3929]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30759
      • spanCollection = o [3870, 3871]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32441
      • spanCollection = sgenic [21540, 21547]
    • +
      • Kristin Garcia
      • class = CHEBI:16449
      • spanCollection = sgenic [21540, 21547]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = the tra [14405, 14412]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = the tra [14405, 14412]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nthesiz [9724, 9731]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nthesiz [9724, 9731]
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    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = y and 9 [5423, 5430]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = y and 9 [5423, 5430]
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    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = inserti [5681, 5688]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = inserti [5681, 5688]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = Dazap1 [4323, 4330]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = Dazap1 [4323, 4330]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nomic s [877, 884]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nomic s [877, 884]
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    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = and the [5950, 5957]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = and the [5950, 5957]
    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33791
      • spanCollection = otein wi [3906, 3914]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:35222
      • spanCollection = trifuged [19887, 19896]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:35222
      • spanCollection = tivity of [7572, 7581]
    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = be important. Ca [25688, 25705]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = s doses of [14779, 14789]
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    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = he effects [13227, 13237]
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    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = sed IOP du [14394, 14404]
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    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = ask geneti [23386, 23396]
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    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = able infor [22370, 22380]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = A/2J, P = [14237, 14247]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = y anesthet [22840, 22850]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = -33], but [22934, 22944]
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    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = producibility als [22441, 22458]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = n [19406, 19407]
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    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = s [5939, 5940]
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    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = r [18031, 18032]
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    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = c [4336, 4337]
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    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = i [9713, 9714]
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    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = t [9861, 9862]
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    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = r [890, 891]
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    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = f [6184, 6185]
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    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = 9 [9646, 9647]
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    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = d [5388, 5389]
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    +

    +

    CHEBI_15377

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = chromos [22266, 22273]
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    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = is work [29529, 29536]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = he sepa [29675, 29682]
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    CHEBI_16670

    +

    CHEBI_17544

    +

    CHEBI_17992

    +

    CHEBI_23367

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_23367
      • spanCollection = al associ [29448, 29457]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_23367
      • spanCollection = d protei [22409, 22417]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_23367
      • spanCollection = mber of g [22626, 22635]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_23367
      • spanCollection = n differe [34211, 34220]
    +

    CHEBI_25213

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25213
      • spanCollection = ng th [18346, 18351]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33521
      • spanCollection = ng th [18346, 18351]
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    CHEBI_25613

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25613
      • spanCollection = J, C57BL/6 [16685, 16695]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25613
      • spanCollection = rp [14191, 14193]
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    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25613
      • spanCollection = de [14903, 14905]
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    CHEBI_25676

    +

    CHEBI_26020

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    CHEBI_26710

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    CHEBI_27594

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_27594
      • spanCollection = t have a [1189, 1197]
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    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_27594
      • spanCollection = tctgagga [39453, 39461]
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    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_27594
      • spanCollection = aocular [31345, 31353]
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    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_27594
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    CHEBI_30879

    +

    CHEBI_32588

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    CHEBI_33521

    +

    CHEBI_33708

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = to a goat. The ant [18545, 18563]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = p1 genomic [6273, 6283]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = p1 genomic [6273, 6283]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = imilar RNA [5527, 5538]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = imilar RNA [5527, 5538]
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    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = served amon [1344, 1355]
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      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = served amon [1344, 1355]
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    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = tected a 45 kD pro [9835, 9853]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = tected a 4 [9835, 9845]
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    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = (BRCA2+) h [4797, 4807]
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      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
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    +

    • +
      • Mike Bada
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    • +
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    CHEBI_33709

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    CHEBI_35186

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    CHEBI_36080

    +

    +

    • +
      • Mike Bada
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    +

    • +
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    CHEBI_37586

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    CHEBI_8984

    +

    CHEBI_9754

    diff --git a/src/test/resources/iaa_test_project/iaa/Class matcher.dat b/src/test/resources/iaa_test_project/iaa/Class matcher.dat index cd0f3054..61053f17 100644 --- a/src/test/resources/iaa_test_project/iaa/Class matcher.dat +++ b/src/test/resources/iaa_test_project/iaa/Class matcher.dat @@ -7,59 +7,59 @@ option under the Edit menu that will allow you to paste the copied data as text. type matches non-matches All classes 350 106 -5'-cytidylyl group 0 1 -5'-guanylyl group 0 2 -5'-uridylyl group 0 3 -acid 2 0 -adenine group 0 1 -alanine 0 1 -alanine residue 0 1 -alcohols 4 0 -amino acids 0 6 -amino-acid residues 0 7 -anaesthetic 2 10 -canonical nucleoside residues 0 1 -carbon 0 4 -carboxy group 0 10 -cytidyl groups 0 1 -cytosin-1-yl group 0 1 -deoxyribonucleic acids 54 3 -double-stranded DNA 10 4 -drug 0 2 -glutamate residue 0 1 -glutamate(1-) 0 1 -glutamate(2-) 0 1 -glycine 2 0 -guanine group 0 3 -guanosyl groups 0 2 -histidine 2 0 -hydrogencarbonate 2 0 -inhibitor 0 2 -magnesium dichloride 4 0 -messenger RNA 30 0 -metal cations 0 1 -metals 0 1 -molecular entities 0 4 -nucleotidyl groups 0 3 -oligopeptides 8 0 -peptides 10 0 -phosphate(3-) 0 1 -phosphates 0 1 -pigment 0 3 -potassium chloride 4 0 -proline 0 7 -proline residue 0 7 -protease inhibitor 4 0 -proteins 120 1 -ribonucleic acids 46 0 -single-stranded DNA 12 0 -sodium chloride 2 0 -sodium dodecyl sulfate 4 0 -sodium phosphates 2 0 -sucrose 8 0 -terpenes 6 0 -tert-pentyl group 2 0 -tris 6 0 -uracil-1-yl group 0 3 -uridyl groups 0 3 -water 4 3 +CHEBI:1432 0 1 +CHEBI:1542 2 0 +CHEBI:1644 0 1 +CHEBI:1699 54 3 +CHEBI:1836 0 1 +CHEBI:2352 0 1 +CHEBI:2352 0 1 +CHEBI:2388 0 2 +CHEBI:2445 0 2 +CHEBI:2446 0 2 +CHEBI:2613 0 3 +CHEBI:2627 0 7 +CHEBI:2724 0 3 +CHEBI:2724 0 3 +CHEBI:2757 2 0 +CHEBI:2998 0 1 +CHEBI:3036 2 0 +CHEBI:3075 0 3 +CHEBI:3075 0 1 +CHEBI:3075 0 1 +CHEBI:3075 0 3 +CHEBI:3244 0 1 +CHEBI:3248 0 1 +CHEBI:3287 0 7 +CHEBI:3369 46 0 +CHEBI:3369 30 0 +CHEBI:3379 0 1 +CHEBI:3522 0 2 +CHEBI:3752 2 0 +CHEBI:3767 4 0 +CHEBI:3886 2 10 +CHEBI:4688 0 10 +CHEBI:470 10 4 +CHEBI:916 12 0 +CHEBI_15377 4 3 +CHEBI_16670 10 0 +CHEBI_17544 2 0 +CHEBI_17992 8 0 +CHEBI_23367 0 4 +CHEBI_25213 0 1 +CHEBI_25613 0 3 +CHEBI_25676 8 0 +CHEBI_26020 0 1 +CHEBI_26710 2 0 +CHEBI_27594 0 4 +CHEBI_30879 4 0 +CHEBI_32588 4 0 +CHEBI_33521 0 1 +CHEBI_33708 0 7 +CHEBI_33709 0 6 +CHEBI_35186 6 0 +CHEBI_36080 120 1 +CHEBI_37586 2 0 +CHEBI_6636 4 0 +CHEBI_8984 4 0 +CHEBI_9754 6 0 diff --git a/src/test/resources/iaa_test_project/iaa/Class matcher.html b/src/test/resources/iaa_test_project/iaa/Class matcher.html index 85e4fb36..be14c20c 100644 --- a/src/test/resources/iaa_test_project/iaa/Class matcher.html +++ b/src/test/resources/iaa_test_project/iaa/Class matcher.html @@ -4,408 +4,89 @@

    Class matcher

    Annotations match if they have the same class assignment and their spans overlap.
    -

    For more detailed documentation on IAA please see the IAA - documentation. +

    For more detailed documentation on Iaa please see the Iaa documentation.

    -

    2-way IAA Results

    -IAA calculated on 4 documents. +

    2-way Iaa Results

    +Iaa calculated on 4 documents.

    tabular data

    all annotations = matches + non-matches -
    IAA = matches / all annotations +
    Iaa = matches / all annotations

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
    TypeIAAmatchesnon-matches
    All classes76.59%350107
    5'-cytidylyl group0.00%01
    5'-guanylyl group0.00%02
    5'-uridylyl group0.00%03
    acid100.00%20
    adenine group0.00%01
    alanine0.00%01
    alanine residue0.00%01
    alcohols100.00%40
    amino acids0.00%06
    amino-acid residues0.00%07
    anaesthetic16.67%210
    canonical nucleoside residues0.00%02
    carbon0.00%04
    carboxy group0.00%010
    cytidyl groups0.00%01
    cytosin-1-yl group0.00%01
    deoxyribonucleic acids94.74%543
    double-stranded DNA71.43%104
    drug0.00%02
    glutamate residue0.00%01
    glutamate(1-)0.00%01
    glutamate(2-)0.00%01
    glycine100.00%20
    guanine group0.00%03
    guanosyl groups0.00%02
    histidine100.00%20
    hydrogencarbonate100.00%20
    inhibitor0.00%02
    magnesium dichloride100.00%40
    messenger RNA100.00%300
    metal cations0.00%01
    metals0.00%01
    molecular entities0.00%04
    nucleotidyl groups0.00%03
    oligopeptides100.00%80
    peptides100.00%100
    phosphate(3-)0.00%01
    phosphates0.00%01
    pigment0.00%03
    potassium chloride100.00%40
    proline0.00%07
    proline residue0.00%07
    protease inhibitor100.00%40
    proteins99.17%1201
    ribonucleic acids100.00%460
    single-stranded DNA100.00%120
    sodium chloride100.00%20
    sodium dodecyl sulfate100.00%40
    sodium phosphates100.00%20
    sucrose100.00%80
    terpenes100.00%60
    tert-pentyl group100.00%20
    tris100.00%60
    uracil-1-yl group0.00%03
    uridyl groups0.00%03
    water57.14%43
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    TypeIaamatchesnon-matches
    All classes76.75%350106
    CHEBI:14320.00%01
    CHEBI:1542100.00%20
    CHEBI:16440.00%01
    CHEBI:169994.74%543
    CHEBI:18360.00%01
    CHEBI:23520.00%01
    CHEBI:23520.00%01
    CHEBI:23880.00%02
    CHEBI:24450.00%02
    CHEBI:24460.00%02
    CHEBI:26130.00%03
    CHEBI:26270.00%07
    CHEBI:27240.00%03
    CHEBI:27240.00%03
    CHEBI:2757100.00%20
    CHEBI:29980.00%01
    CHEBI:3036100.00%20
    CHEBI:30750.00%03
    CHEBI:30750.00%01
    CHEBI:30750.00%01
    CHEBI:30750.00%03
    CHEBI:32440.00%01
    CHEBI:32480.00%01
    CHEBI:32870.00%07
    CHEBI:3369100.00%460
    CHEBI:3369100.00%300
    CHEBI:33790.00%01
    CHEBI:35220.00%02
    CHEBI:3752100.00%20
    CHEBI:3767100.00%40
    CHEBI:388616.67%210
    CHEBI:46880.00%010
    CHEBI:47071.43%104
    CHEBI:916100.00%120
    CHEBI_1537757.14%43
    CHEBI_16670100.00%100
    CHEBI_17544100.00%20
    CHEBI_17992100.00%80
    CHEBI_233670.00%04
    CHEBI_252130.00%01
    CHEBI_256130.00%03
    CHEBI_25676100.00%80
    CHEBI_260200.00%01
    CHEBI_26710100.00%20
    CHEBI_275940.00%04
    CHEBI_30879100.00%40
    CHEBI_32588100.00%40
    CHEBI_335210.00%01
    CHEBI_337080.00%07
    CHEBI_337090.00%06
    CHEBI_35186100.00%60
    CHEBI_3608099.17%1201
    CHEBI_37586100.00%20
    CHEBI_6636100.00%40
    CHEBI_8984100.00%40
    CHEBI_9754100.00%60

    match data

    -
    +
  • matches for Mike Bada
    • +
  • matches for Kristin Garcia
    • +

    non-match data

    -
    +
  • non-matches for Mike Bada
    • +
  • non-matches for Kristin Garcia
    • +

    Pair-wise agreement

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
    Gold standard setcompared settrue positivesfalse positivesfalse negativesprecisionrecallF-score
    Kristin GarciaMike Bada175862167.05%89.29%76.59%
    Mike BadaKristin Garcia175218689.29%67.05%76.59%
    + +
    Gold standard setcompared settrue positivesfalse positivesfalse negativesprecisionrecallF-score
    Mike BadaKristin Garcia175218589.29%67.31%76.75%
    Kristin GarciaMike Bada175852167.31%89.29%76.75%
    Precision and recall are given equal weight for the F-score. diff --git a/src/test/resources/iaa_test_project/iaa/Class matcher.matches.Kristin Garcia.html b/src/test/resources/iaa_test_project/iaa/Class matcher.matches.Kristin Garcia.html index 54a12f53..13523d4e 100644 --- a/src/test/resources/iaa_test_project/iaa/Class matcher.matches.Kristin Garcia.html +++ b/src/test/resources/iaa_test_project/iaa/Class matcher.matches.Kristin Garcia.html @@ -3,3968 +3,779 @@ Class matcher

    Matches for Kristin Garcia

    -Each annotation that was considered a match is shown in the text that it was found in. The matching annotations from the -other annotation sets are also shown. -
    -

    5'-cytidylyl group

    -

    5'-guanylyl group

    -

    5'-uridylyl group

    -

    acid

    -
    -

    Text source name = 11532192.txt -

    e at the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered w -

      -
    • - acid -
        -
      • Kristin Garcia
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    • - acid -
        -
      • Mike Bada
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    -

    adenine group

    -

    alanine

    -

    alanine residue

    -

    alcohols

    -
    -

    Text source name = 11319941.txt -

    al images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% glutarald -

      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 -

      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    -

    amino acids

    -

    amino-acid residues

    -

    anaesthetic

    -
    -

    Text source name = 11532192.txt -

    parate group of the same age. - - Anesthesia protocol avoids IOP alteration and allows detection of diurnal differences - - All IOPs were assessed using an anesthetic regime of 99 mg/kg ketamine and 9 mg/kg xylazine (defined as 1X). - Initial experiments suggested that an almost identical dose (100 mg/kg ketamine and -

      -
    • - anesthetic -
        -
      • Kristin Garcia
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    -

    canonical nucleoside residues

    -

    carbon

    -

    carboxy group

    -

    cytidyl groups

    -

    cytosin-1-yl group

    -

    deoxyribonucleic acids

    -
    -

    Text source name = 11597317.txt -

    1 and BRCA2 are involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during - the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of repair of - spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either B -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    clear foci during the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of - repair of spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either BRCA1 or BRCA2 are - sensitive to damaging agents that form double-strand breaks (DSBs), as are other -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    es of DNA damage. Chromosomal DNA is shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. - (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to suppress RAD51–BRCA2 - interactions until DNA damage is present. When damage occurs, Rad51 is recr -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    subnuclear RAD51 foci with normal efficiency, suggesting that these proteins are required for the formation of - recombinase complexes at the sites of DNA damage [20,21]. Finally, genetic measurements of recombination - frequency have shown that Brca1-/- embryonic stem (ES) cells are deficient in recombin -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    onal DSB repair [22,23]. The similarity between phenotypes associated with BRCA1 and BRCA2 deficiency, together with - data showing a similar effect of DNA damage on distribution of BRCA1 and BRCA2 in repair-proficient cells, - led to the hypothesis that BRCA2, like BRCA1, is required for efficient recombi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric filaments on DNA. A BRC4 peptide was - also reported to inhibit the RAD51–DNA interaction. These experiments raise the possibility that the - full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    l population due to a mutated W (White spotted) gene. GC1 and MT4 are mouse germ cell and Sertoli cell lines, - respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger (if - any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two a -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ing of one of the eight BRC repeats from human BRCA2. Expression of a single BRC repeat (BRC4) had previously been - reported to act as an inhibitor of DNA repair by Chen et al [27]. These investigators showed that expression - of constructs containing the BRC4 repeat in MCF-7 cells enhances the radiosensi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    BRCA2 as grey bars. (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to - suppress RAD51–BRCA2 interactions until DNA damage is present. When damage occurs, Rad51 is recruited to - damaged sites where is polymerizes into nucleoprotein filaments. In this model, BRCA2 is -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ognition site. Transient transfection of an I-SceI expression vector results in the production of a DSB in the first - mutated copy of GFP. One or both DNA ends formed by the break invade(s) the homologous sequence in the second - mutant GFP copy, resulting in repair of the DSB via a homology-mediated gene -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    –DNA interaction. These experiments raise the possibility that the full-length BRCA2 protein could act as a negative - regulator of inappropriate RAD51–DNA interaction. - - The final experiment reported by Davies et al [26] is particularly important with respect to understanding the - mechanism(s) through whi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8420|8423
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8420|8423
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to the regions - of ssDNA that form during normal DNA replication. BRCA2 may thus promote RAD51 assembly into recombinational - repair complexes via a negative regulatory mechanism (i.e. by blocking RAD51– -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    gene conversion occurs via the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - inter -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    event a substantial fraction of Rad51 from being sequestered in a nonfunctional form. In a BRCA2-defective cell, - mutant Rad51 becomes associated with DNA at random sites and is therefore not readily recruited to sites of - damage. (b) Positive regulation. BRCA2 is proposed to be required for Rad51 to ass -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    r by Davies et al, data provide evidence for a plausible mechanism of the dominant negative effect associated with - expression of a single BRC repeat. DNA binding assays and electron microscopy methods were used to show that - a BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    gaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment from - mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics (Hunt -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    and homologous recombination - - Abstract - - Two recent papers provide new evidence relevant to the role of the breast cancer susceptibility gene BRCA2 in - DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in homology-dependent - (recombinational) repair of DNA double-strand br -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    li cell lines, respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger - (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C - antibody was raised against a -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ve cells - - Pierce et al have designed a set of recombination substrates for measuring the level of homologous recombination in - vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the easily detected - green fluorescent protein), one of which contains a restriction site -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    gure 2 are not mutually exclusive. BRCA2 could prevent inappropriate RAD51 assembly in the absence of damage and - promote functional RAD51 assembly at DNA lesions during the damage response. Further experiments are clearly - required to clarify the functional interactions between BRCA2 and RAD51 during re -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ole in assembly of RAD51 at damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to - 'mediate' assembly of RAD51 at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, - including XRCC2, XRCC3, RAD51B, RAD51C and RAD51D, may function as a complex that actively p -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    s and electron microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to - assemble into oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA - interaction. These experiments raise the possibility that the full-length BRCA2 protein co -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    97), was cloned in-frame into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences - at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    tgtctgaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment - from mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    clear sites with BRCA1 [9], a number of additional results have provided evidence that both BRCA1 and BRCA2 are - involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during the S - phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably si -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ty gene BRCA2 in DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in - homology-dependent (recombinational) repair of DNA double-strand breaks. The second paper, by Davies et al, - begins to address the mechanism through which BRCA2 makes its contribution to recombinationa -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ia the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - interactions. BRCA2–Rad51 int -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
      -
    -

    double-stranded DNA

    -
    -

    Text source name = 11597317.txt -

    air complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding preference - for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory - factors, such as BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestra -

      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    rand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as - BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional - form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might b -

      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involv -

      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    mage occurs. For example, previous studies indicated that RAD51 shows little binding preference for single-strand DNA - (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as BRCA2, - are required to suppress RAD51–dsDNA interactions to prevent sequestration of -

      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    cluding the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. -

      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    -

    drug

    -

    glutamate residue

    -

    glutamate(1-)

    -

    glutamate(2-)

    -

    glycine

    -
    -

    Text source name = 11604102.txt -

    d by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate - exon selection in neurons is antagonized by a second RNA-binding protein, brPTB (brain- -

      -
    • - glycine -
        -
      • Kristin Garcia
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    • - glycine -
        -
      • Mike Bada
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    -

    guanine group

    -

    guanosyl groups

    -

    histidine

    -
    -

    Text source name = 11604102.txt -

    equences at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins - were mixed with Freund's adjuvant and injected into rabbits to generate the anti-DAZ -

      -
    • - His -
        -
      • Kristin Garcia
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    • - His -
        -
      • Mike Bada
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    -

    hydrogencarbonate

    -
    -

    Text source name = 11532192.txt -

    derstanding of the molecular mechanisms controlling diurnal rhythms of IOP and that may be relevant to glaucoma. - - Car2 deficiency does not alter IOP - - Bicarbonate formation is important for aqueous humor secretion from the ciliary processes and carbonic - anhydrase (CA) facilitates this secretion. There are multi -

      -
    • - Bicarbonate -
        -
      • Kristin Garcia
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    • - Bicarbonate -
        -
      • Mike Bada
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    -

    inhibitor

    -

    magnesium dichloride

    -
    -

    Text source name = 11604102.txt -

    ay, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Protease Inhibit -

      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose gradients in - 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for 2 hours at - 4°C. Fractions of 0.5 ml were collected from the bottom of the tubes and analyze -

      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    -

    messenger RNA

    -
    -

    Text source name = 11604102.txt -

    tting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family - in the regulation of mRNA translation is supported by lines of cir -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    lso interacts through its proline-rich domain with two microfilament-associated proteins profilin and Mena, which may - facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming - growth factor-β family that is required for generating dorsal mesoderm at the -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ressed later, in the cytoplasm of pachytene spermatocytes [5]. Genetic and biochemical studies suggest a role for the - DAZ family in the regulation of mRNA translation. Drosophila Boule mutants was defective in the translation - of the meiosis-specific CDC25 homologue, Twine [11], and DAZL was found to be -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    . Its predominant expression in testes suggests a role in spermatogenesis. Its subcellular localization indicates - that it is not directly involved in mRNA translation. - - Background - - Spermatogenesis is a complex developmental process in which male germ cells progress through mitotic proliferation, - meiotic -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, pre-mRNA - processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA translation is supporte -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the - alternative splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The - ability of Nova-1 to activate exon selection in neurons is antagonized by a seco -

      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    proteins may act together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be - involved in the transport of the mRNAs of the target genes of DAZL. Alternatively, DAZL and DAZAP1 may act - antagonistically to regulate the timing and the level of expression. Such an anta -

      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and characterized [16]. Prrp binds to a 340 nt - sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also int -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    mouse testes, DAZAP1 was found both in the nuclei and in the cytoplasm. Its absence from polyribosomes indicates - that it is not directly involved in mRNA translation. - - Materials and methods - - Isolation of mouse Dazap1 cDNA clones - - Dazap1 cDNA clones were isolated from a mouse testis cDNA library (#93730 -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ee-hybrid system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich - segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechanisms of its action, we - used a yeast two-hybrid s -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    and brain, and even less in other tissues. This pattern of expression is similar to that of the human DAZAP1 (14). - RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at embryonic day 15, similar to - Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted througho -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    r to that of the human DAZAP1 (14). RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at - embryonic day 15, similar to Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted - throughout testes development, in both the prenatal and postnatal periods. Dazl1 and Da -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    haracterization of the mouse Dazap1 gene and its protein product. The subcellular localization of DAZAP1 suggests - that it is not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 cDNA - - Mouse Dazap1 cDNA clones were isolated by library screening, and the 5' end of the -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its - proline-rich domain with two microfilament-associated proteins profilin and M -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA transcription, pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the - DAZ family in the regulation of mRNA translation is supported by lines of circumstantial evidence, including - the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from p -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    -

    metal cations

    -

    metals

    -

    molecular entities

    -

    nucleotidyl groups

    -

    oligopeptides

    -
    -

    Text source name = 11604102.txt -

    was conjugated to KLH as carrier and injected into a goat. The anti-DAZAP1-P antibody thus produced was purified on - an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM Tris, pH - 8.0) -

      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 18831|18843
        • -
      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 18831|18843
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    on resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid residues of the mouse - DAZAP1 was synthesized in vitro using the services of Bethyl Laboratories (Montgomery, TX). Th -

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      • class = oligopeptides
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      • spans = 18509|18521
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    ntibody was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid residue at the - C-terminus. Both antibodies recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay ( -

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        -
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      • class = oligopeptides
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      • spans = 9799|9811
        • -
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    ntron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 - (starting from aa #197), was cloned in-fr -

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        -
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      • class = oligopeptides
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      • spans = 17939|17951
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    - - The second paper providing evidence, by Davies et al [26], is a biochemical study of the interaction between the - homologous recombinase RAD51 and a peptide consisting of one of the eight BRC repeats from human BRCA2. - Expression of a single BRC repeat (BRC4) had previously been reported to act as an inhib -

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    on microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These - experiments raise the possibility that the full-length BRCA2 protein could act as a neg -

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      • class = peptides
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    t negative effect associated with expression of a single BRC repeat. DNA binding assays and electron microscopy - methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interact -

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      • class = peptides
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      • spans = 8126|8133
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    ge has occurred and factors required for 'productive' assembly of RAD51 at damaged sites are in place). As mentioned - previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction could reflect a role of - full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another pot -

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      • class = peptides
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      • spans = 10885|10892
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    ontaining the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the services of Bethyl - Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier and injected into a goat. The - anti-DAZAP1-P antibody thus produced was purified on an affinity column containing the -

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      • Kristin Garcia
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      • class = peptides
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      • spans = 18673|18680
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    phosphate(3-)

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    n at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose - gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for - 2 hours at 4°C. Fractions of 0.5 ml were collected from the bottom of the tu -

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    , Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Prot -

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      • class = potassium chloride
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    proline

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    proline residue

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    protease inhibitor

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    ontaining 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, - Madison, WI), and a mixture of 10 protease inhibitors provided in the Protease Inhibitors Set (Roche - Molecular Biochemicals, Indianapolis, IN). Homogenates were centrifuged at 1,000 × g for 10 minutes to -

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      • spans = 19941|19960
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    KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 - protease inhibitors provided in the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, IN). - Homogenates were centrifuged at 1,000 × g for 10 minutes to pellet cell debris and nuclei. Afte -

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      • class = protease inhibitor
        • -
      • spans = 19977|19996
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    proteins

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    Text source name = 11597317.txt -

    sites are in place). As mentioned previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction - could reflect a role of full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another potential role for BRCA2 in promoting RAD51-dependent recombinational repair is a posi -

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      • spans = 10968|10975
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    clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its proline-rich domain - with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 mRNA - to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth fact -

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      • spans = 14459|14467
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    y virtue of their expression of GFP. - - Moynahan et al [24] have used such a GFP recombination substrate to demonstrate that cells with defective BRCA2 protein - are deficient in their ability to repair the I-SceI-induced DSB through homologous recombination. Expression of - I-SceI resulted in 1 out of 1400 cell -

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      • class = proteins
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      • spans = 4454|4461
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    R1P and FXR2P, that were identified through their interaction with another polysomal-associated RNA-binding protein, - the fragile X mental retardation protein [21]. Both FXR1P and FXR2P are associated with the polyribosomes - [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be -

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      • spans = 12395|12402
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    tein product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins share 98% identity and their sequences are highly similar to the Xenopus orthologue - Prrp, especially in the RBDs. Dazap1 is expressed throughout test -

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    Both primer pairs annealed across intron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 ( -

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      • spans = 17904|17911
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    se genomic DNA. The PCR primers span over introns and produce much larger (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti - DAZAP1-C antibody was raised against a recombinant protein containing the C-terminal pr -

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        • -
      • spans = 9569|9576
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    mpletely independent of its defect in BRCA2. First, in the same study [24], recombination in a mouse ES cell line - that expresses only truncated BRCA2 protein was measured. This line was found to have lower recombination - efficiency than isogenic cells expressing full-length BRCA2 (the defect observed was ab -

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    absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. This finding - is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardat -

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    em to isolate two human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed - predominantly in testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal - portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to R -

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    breaks (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with - the RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have b -

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      • spans = 2328|2335
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    P and FXR2P are associated with the polyribosomes [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be defined. These proteins may act - together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be involved in the - transport of the mRNAs of -

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    ant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements - [5,6]. The sequence of this large protein (3418 amino acids) offers very little clue to its function, - although there are eight repeated segments (termed BRC repeats) in the middle of the prot -

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    nds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse testes, DAZAP1 w -

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    end of the cDNA was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region - (UTR), an open reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession - No: AF225910). The coding region shares 89% similarity with that of the human orth -

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      • spans = 4916|4923
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    NA-binding domains (RBDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved - evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with X -

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    nts on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These experiments raise the - possibility that the full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA - interaction. - - The final experiment reported by Davies et al [26] is particularly importa -

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      • spans = 8355|8362
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    he small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, consistent - with the fact that the truncation protein lacks a nuclear localization signal [28]. Davies et al showed - CAPAN-1 cells to be defective in nuclear localization of RAD51, raising the possibility -

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      • spans = 8923|8930
        • -
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    Text source name = 11319941.txt -

    , agenesis of the corpus callosum, and abnormalities other forebrain structure including widespread neocortical - ectopias [46, 47]. The MARCKS-related protein gene is expressed in the striatum during early brain - development in the rat [48]. - - The location of the QTL modulating striatal neuron number to the d -

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      • Kristin Garcia
        • -
      • class = proteins
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      • spans = 21850|21857
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    em, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA binding domains and a proline - rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to RNA - homopolymers. We now report our characterization of the mouse Dazap1 gene and its pr -

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    ng dorsal mesoderm at the blastula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of - DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST search of - the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with -

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      • spans = 14808|14816
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    illigrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on His-Bind metal chelation - resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid -

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      • spans = 18397|18405
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    tein (3418 amino acids) offers very little clue to its function, although there are eight repeated segments (termed - BRC repeats) in the middle of the protein that are highly conserved among mammalian orthologs [7,8]. - - Breast cancer susceptibility genes and DNA repair - - Following the landmark discovery by Sc -

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    by centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by the - Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of tissue - extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-D -

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    Z gene family and to understanding the mechanisms of its action, we used a yeast two-hybrid system to isolate two - human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly - in testes. It encodes a protein with two RNA binding domains and a proline rich C-term -

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      • Kristin Garcia
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      • class = proteins
        • -
      • spans = 4184|4192
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    ifferent from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction with another - polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both FXR1P and FXR2P - are associated with the polyribosomes [22]. - - The significance of the interaction -

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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 12353|12360
        • -
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      • Mike Bada
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    e for direct RAD51 interaction. Cells lacking BRCA1/2 fail to form damage-induced subnuclear RAD51 foci with normal - efficiency, suggesting that these proteins are required for the formation of recombinase complexes at the - sites of DNA damage [20,21]. Finally, genetic measurements of recombination frequency -

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    ) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by - the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μ -

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    ed in CAPAN-1 cells, the same human tumor line examined by Moynahan et al [24]. It had been shown previously that the - small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, - consistent with the fact that the truncation protein lacks a nuclear localization signa -

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    acts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser degree in spleen, - liver, lung and brain (Figure 4). The protein was also present in the ovary. The expression of DAZAP1 during - germ cell development paralleled that of DAZL (Figure 5). It is present at a low level -

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    RI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences at the junctions were verified by DNA - sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on - His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with Fre -

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    t. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed by Western - blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translatio -

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    nteraction with DAZ and DAZL, we isolated and characterized the mouse Dazap1 gene, and studied its expression and the - subcellular localization of its protein product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 prot -

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    s a change of reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences betwee -

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    increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted with the anti-DAZAP1-P antibody. - - Figure 5 Western blot -

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    the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody - was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid r -

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    he two RBDs are especially highly conserved. They share 98% and 97% similarity and 97% and 92% identity, - respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA binding specificity. - The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% similarity and -

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    gene to be discovered, and was isolated through positional cloning using data from families with inherited breast - cancer [4]. Cells with mutant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate - gross chromosomal rearrangements [5,6]. The sequence of this large protein (3418 ami -

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    riginal URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast tw -

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    s recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting of mouse - tissue extracts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser - degree in spleen, liver, lung and brain (Figure 4). The protein was also present in t -

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    ential role for BRCA2 in promoting RAD51-dependent recombinational repair is a positive role in assembly of RAD51 at - damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to 'mediate' assembly of RAD51 - at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, includin -

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    ty of Nova-1 to activate exon selection in neurons is antagonized by a second RNA-binding protein, brPTB - (brain-enriched polypyrimidine tract-binding protein), which interacts with Nova-1 and inhibits its function - [24]. DAZAP1 could function in a similar manner by binding to DAZL and inhibiting its functio -

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    striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the gene encoding the myristoylated - alanine-rich C kinase substrate (MARCKS protein). This molecule is important in cerebral development. - MARCKS-deficient mice have a high incidence of exencephaly, agenesis of the corpus callosum, an -

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    of DAZAP1 increased afterward, as the testes contained increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted -

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    nal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in neurons is - antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding protein), - which interacts with Nova-1 and inhibits its function [24]. DAZAP1 could function in a -

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    erved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for - proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. T -

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    . Second, in an independent study, Powell was able to compare derivatives of CAPAN-1 that differed only in their - ability to express full-length BRCA2 protein (S. Powell, personal communication, 2001). In these experiments, - the derivative expressing full-length BRCA2 yielded 10-fold more recombinants than c -

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    ce, including the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from polyribosomes indicates - that it is not directly involved in protein synthesis. This finding is different from two RNA-binding - proteins, FXR1P and FXR2P, that were identified through their interaction with another poly -

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    AP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic interaction - between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding - protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNAs encoding neuron -

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    f expression. Such an antagonistic interaction between two interacting RNA-binding proteins is exemplified by the - neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of N -

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    titutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus - Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. They share - 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prr -

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    sophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and spermatogonia, an -

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    via homologous recombination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of - BRCA2 on one homolog and codes for a protein truncated at amino acid 1981 on the other homolog. The authors - indicate that the level of I-SceI-induced recombination in CAPAN-1 is over 100-fold le -

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    (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with the - RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have been indi -

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    logous recombination in vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the - easily detected green fluorescent protein), one of which contains a restriction site for I-SceI, a yeast - intron encoded endonuclease with an 18 base pair recognition site. Transient transfect -

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    mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast two-hybrid system through its - interaction with a putative male infertility factor, DAZ (Deleted in Azoospermi -

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    ation of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a R -

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    to the Xenopus orthologue Prrp, especially in the RBDs. Dazap1 is expressed throughout testis development. Western - blot detects a single 45 kD DAZAP1 protein that is most abundant in the testis. Although a majority of DAZAP1 - is present in the cytoplasmic fraction, they are not associated with polyribosomes -

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    share 85%, 90%, and 97% similarity with segments in the human 3' UTR, respectively. These segments probably contain - regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse -

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    infertility factor, DAZ (Deleted in Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ - and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a - proline-rich C-terminal portion, and is expressed most abundantly in the testis. To under -

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    ribonucleic acids

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    n Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like - protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is - expressed most abundantly in the testis. To understand the biological function o -

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    Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s and the - Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and the mouse - sequences, and between the mouse and Xenopus sequences are marked by #'s and * -

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    ch domain with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 - mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth factor-β family that is - required for generating dorsal mesoderm at the blastula stage of Xenopus embryoge -

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    the level of expression. Such an antagonistic interaction between two interacting RNA-binding proteins is - exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative - splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. -

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    human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in - testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 - protein interacted with both DAZ and DAZL in vitro. It also bound to RNA homopolyme -

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    Text source name = 11604102.txt -

    VLE that binds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse -

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        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 15181|15184
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    Text source name = 11604102.txt -

    The 5' end of the cDNA was isolated by 5' RACE [15], using prdap11 (ttgcgggccatatccttg, #749–732) as the primer for - cDNA synthesis from mouse testis RNA, and prdap37 (ttgttgccacgtgggcg, #734–718) and an adaptor primer as the - primers for PCR amplification. The PCR products were cloned into a TA cloning -

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    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 15847|15850
        • -
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    • - RNA -
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    -
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    Text source name = 11604102.txt -

    BLAST search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, and possibly DAZAP1, may help to - identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolution -

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    • - RNA -
        -
      • Kristin Garcia
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        • -
      • spans = 15012|15015
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    • - RNA -
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    Text source name = 11604102.txt -

    mbers of Drosophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both - sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and -

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      • spans = 3171|3174
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    • - RNA -
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    Text source name = 11604102.txt -

    article's original URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identifi -

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      • class = ribonucleic acids
        • -
      • spans = 430|433
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    Text source name = 11604102.txt -

    coding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in - neurons is antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding - protein), which interacts with Nova-1 and inhibits its function [24]. DAZAP1 coul -

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    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 13225|13228
        • -
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    • - RNA -
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    Text source name = 11604102.txt -

    with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity - with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. - They share 98% and 97% similarity and 97% and 92% identity, respectively, betwee -

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    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 5694|5697
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    • - RNA -
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    Text source name = 11604102.txt -

    erved. They share 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These - proteins may therefore have a similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 - and Prrp are less conserved (81% similarity and 71% identity). There is an insert -

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    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 5910|5913
        • -
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    • - RNA -
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      • spans = 5910|5913
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    Text source name = 11604102.txt -

    DAZL and DAZAP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic - interaction between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear - RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNA -

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    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12918|12921
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    • - RNA -
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      • class = ribonucleic acids
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      • spans = 12918|12921
        • -
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    Text source name = 11604102.txt -

    communication). The genomic structure of Dazap1, delineated here, should facilitate the generating of Dazap1 null - mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of -

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    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 13965|13968
        • -
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    • - RNA -
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      • spans = 13965|13968
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    Text source name = 11604102.txt -

    ressed most abundantly in the testis. - - Figure 3 Developmental expression of Dazap1 and Dazl in mouse testes. RT-PCR was performed on total testicular RNAs - isolated from day 15 (El 5) and day 17 (El 7) embryos, new born mice (Day 0), and mice at various days after birth. - Wv/Wv testes contain diminished g -

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    • - RNAs -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 9119|9123
        • -
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    • - RNAs -
        -
      • Mike Bada
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      • class = ribonucleic acids
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      • spans = 9119|9123
        • -
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    Text source name = 11604102.txt -

    rose gradient. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed - by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localiz -

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    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 11715|11718
        • -
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    • - RNA -
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      • Mike Bada
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      • spans = 11715|11718
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    Text source name = 11604102.txt -

    ch fractions was analyzed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA -

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    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 11805|11808
        • -
      -
    • - RNA -
        -
      • Mike Bada
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      • spans = 11805|11808
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    Text source name = 11604102.txt -

    finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both - FXR1P and FXR2P are associated with the polyribosomes [22]. - - The significance of -

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    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12341|12344
        • -
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    • - RNA -
        -
      • Mike Bada
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      • class = ribonucleic acids
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      • spans = 12341|12344
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    Text source name = 11604102.txt -

    stula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of DAZAP1 and Prrp suggests that - these proteins may bind to similar RNA sequences. However, a BLAST search of the GenBank for the 340 nt VLE - sequence failed to identify any mammalian sequences with significant homology. F -

      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 14837|14840
        • -
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    • - RNA -
        -
      • Mike Bada
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      • spans = 14837|14840
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    Text source name = 11604102.txt -

    n with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and - DAZL in vitro. It also bound to RNA homopolymers. We now report our characterization of the mouse Dazap1 gene - and its protein product. The subcellular localization of DAZAP1 suggests th -

      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 4436|4439
        • -
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    • - RNA -
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    Text source name = 11604102.txt -

    97% similarity with segments in the human 3' UTR, respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human pr -

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    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 5355|5358
        • -
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    • - RNA -
        -
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      • spans = 5355|5358
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    Text source name = 11604102.txt -

    es [12]. The absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. - This finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their - interaction with another polysomal-associated RNA-binding protein, the fragile -

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    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12221|12224
        • -
      -
    • - RNA -
        -
      • Mike Bada
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        • -
      • spans = 12221|12224
        • -
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    single-stranded DNA

    -
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    Text source name = 11597317.txt -

    BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-lik -

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    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 12990|12995
        • -
      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
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      • spans = 12990|12995
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    Text source name = 11597317.txt -

    nction difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; ssDNA = - single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like - protein.. Cell. 19 -

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    • - single-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 12998|13015
        • -
      -
    • - single-strand DNA -
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    Text source name = 11597317.txt -

    recruited into a functional repair complex when damage occurs. For example, previous studies indicated that RAD51 - shows little binding preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This - result could mean that regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA in -

      -
    • - single-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10146|10163
        • -
      -
    • - single-strand DNA -
        -
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    Text source name = 11597317.txt -

    d to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional form. Alternatively, or - in addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to - the regions of ssDNA that form during normal DNA replication. BRCA2 may thus prom -

      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10435|10440
        • -
      -
    • - ssDNA -
        -
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    Text source name = 11597317.txt -

    nctional repair complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding - preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that - regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA interacti -

      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10165|10170
        • -
      -
    • - ssDNA -
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    Text source name = 11597317.txt -

    al form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might be important for preventing - RAD51 from binding to the regions of ssDNA that form during normal DNA replication. BRCA2 may thus promote - RAD51 assembly into recombinational repair complexes via a negative regulatory mechan -

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    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10524|10529
        • -
      -
    • - ssDNA -
        -
      • Mike Bada
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        • -
      • spans = 10524|10529
        • -
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    -

    sodium chloride

    -
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    Text source name = 11604102.txt -

    urified on an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of deb -

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        -
      • Kristin Garcia
        • -
      • class = sodium chloride
        • -
      • spans = 18936|18940
        • -
      -
    • - NaCl -
        -
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    sodium dodecyl sulfate

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    Text source name = 11604102.txt -

    etermined by the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of - tissue extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-DAZAP1-C - antibody (at a 1/2,000 dilution) or the anti-DAZAP1-P antibody (at a 1/5,000 dilution). -

      -
    • - SDS -
        -
      • Kristin Garcia
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 19342|19345
        • -
      -
    • - SDS -
        -
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    Text source name = 11604102.txt -

    taining the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 -

      -
    • - SDS -
        -
      • Kristin Garcia
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 18969|18972
        • -
      -
    • - SDS -
        -
      • Mike Bada
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 18969|18972
        • -
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    sodium phosphates

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    Text source name = 11319941.txt -

    ply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, 0.5-1.0 ml ip) and perfused - through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) followed by 1.25% - glutaraldehyde/1.0% paraformaldehyde in 0.1 M PB (pH 7.40) over a period of 2 to 4 min. An additional -

      -
    • - sodium phosphate -
        -
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        • -
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        • -
      • spans = 26402|26418
        • -
      -
    • - sodium phosphate -
        -
      • Mike Bada
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      • spans = 26402|26418
        • -
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    sucrose

    -
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    Text source name = 11604102.txt -

    se gradient analyses of the post- mitochondria fraction showed that, unlike DAZL, DAZAP1 did not co-sediment with - polyribosomes (Figure 6). - - Figure 6 Sucrose gradient analyses shows that DAZAP1 is not associated with polyribosomes. The - post-mitochondrial supernatant of mouse testis extracts was analyzed on -

      -
    • - Sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11395|11402
        • -
      -
    • - Sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
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    Text source name = 11604102.txt -

    analyses shows that DAZAP1 is not associated with polyribosomes. The post-mitochondrial supernatant of mouse testis - extracts was analyzed on a 15–45% sucrose gradient. Sedimentation was from left to right. The presence of - DAZAP1 and DAZL in each fractions was analyzed by Western blotting. - - Discussion - - RNA- -

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    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11562|11569
        • -
      -
    • - sucrose -
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    Text source name = 11604102.txt -

    [12]. Similar analyses showed that a majority of DAZAP1 in adult mouse testes was also present in the cytoplasmic - fraction (data not shown). However, sucrose gradient analyses of the post- mitochondria fraction showed that, - unlike DAZL, DAZAP1 did not co-sediment with polyribosomes (Figure 6). - - Figure 6 Su -

      -
    • - sucrose -
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      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11240|11247
        • -
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    • - sucrose -
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    Text source name = 11604102.txt -

    uclei. After an additional centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the - supernatant were applied to 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged - in a Beckman SW41 rotor at 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were -

      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 20285|20292
        • -
      -
    • - sucrose -
        -
      • Mike Bada
        • -
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        • -
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        • -
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    terpenes

    -
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    Text source name = 11532192.txt -

    esia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and wood - shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in wood - shavings alters drug resistance and decreases the effect of anesthetic agents in both ra -

      -
    • - Terpene -
        -
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        • -
      • class = terpenes
        • -
      • spans = 25559|25566
        • -
      -
    • - Terpene -
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      • Mike Bada
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    Text source name = 11532192.txt -

    of anesthesia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and - wood shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in - wood shavings alters drug resistance and decreases the effect of anesthetic agents i -

      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25549|25557
        • -
      -
    • - terpenes -
        -
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    Text source name = 11532192.txt -

    may be important. We use wood shavings for bedding and wood shavings expose the mice to terpenes. Terpene - administration or environmental exposure to terpenes in wood shavings alters drug resistance and decreases - the effect of anesthetic agents in both rats and mice [40-45]. - - Risk factors for increased IOP - -

      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
      -
    • - terpenes -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
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    -

    tert-pentyl group

    -
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    Text source name = 11319941.txt -

    lution digital images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% g -

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    • - tert-pentyl -
        -
      • Kristin Garcia
        • -
      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    • - tert-pentyl -
        -
      • Mike Bada
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      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    -

    tris

    -
    -

    Text source name = 11604102.txt -

    oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of - debris by centrifugation at 10,000 × g for 10 m -

      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to - 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at - 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were collected from the bott -

      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ham Pharmacia Biotech, Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors -

      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    -

    uracil-1-yl group

    -

    uridyl groups

    -

    water

    -
    -

    Text source name = 11532192.txt -

    containing white pine bedding and covered with polyester filters. For most experiments, the mice were fed NIH31 (6 % - fat) chow ad libitum, and their water was acidified to pH 2.8 to 3.2. B6 mice develop diet induced diabetes - when maintained on a high fat diet [76]. To ensure that we were analyzing the e -

      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    f sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, - 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) - followed by 1.25% glutaraldehyde/1.0 -

      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    +Each concept that was considered a match is shown in the text that it was found in. The matching annotations from the other concept sets are also shown. +
    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    • +
      • Mike Bada
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    • +
      • Mike Bada
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    • +
      • Mike Bada
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    • +
      • Mike Bada
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    +

    CHEBI_15377

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    +

    CHEBI_16670

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    +

    CHEBI_17544

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    +

    CHEBI_17992

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    +

    CHEBI_23367

    +

    CHEBI_25213

    +

    CHEBI_25613

    +

    CHEBI_25676

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    +

    CHEBI_26020

    +

    CHEBI_26710

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    +

    CHEBI_27594

    +

    CHEBI_30879

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    +

    CHEBI_32588

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    +

    CHEBI_33521

    +

    CHEBI_33708

    +

    CHEBI_33709

    +

    CHEBI_35186

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    +

    CHEBI_36080

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = n that [1185, 1192]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = n that is most [1185, 1200]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    +

    CHEBI_37586

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    +

    CHEBI_6636

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    +

    CHEBI_8984

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    +

    CHEBI_9754

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    diff --git a/src/test/resources/iaa_test_project/iaa/Class matcher.matches.Mike Bada.html b/src/test/resources/iaa_test_project/iaa/Class matcher.matches.Mike Bada.html index 30585158..a8deed97 100644 --- a/src/test/resources/iaa_test_project/iaa/Class matcher.matches.Mike Bada.html +++ b/src/test/resources/iaa_test_project/iaa/Class matcher.matches.Mike Bada.html @@ -3,3968 +3,779 @@ Class matcher

    Matches for Mike Bada

    -Each annotation that was considered a match is shown in the text that it was found in. The matching annotations from the -other annotation sets are also shown. -
    -

    5'-cytidylyl group

    -

    5'-guanylyl group

    -

    5'-uridylyl group

    -

    acid

    -
    -

    Text source name = 11532192.txt -

    e at the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered w -

      -
    • - acid -
        -
      • Mike Bada
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    • - acid -
        -
      • Kristin Garcia
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    -

    adenine group

    -

    alanine

    -

    alanine residue

    -

    alcohols

    -
    -

    Text source name = 11319941.txt -

    al images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% glutarald -

      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 -

      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    -

    amino acids

    -

    amino-acid residues

    -

    anaesthetic

    -
    -

    Text source name = 11532192.txt -

    parate group of the same age. - - Anesthesia protocol avoids IOP alteration and allows detection of diurnal differences - - All IOPs were assessed using an anesthetic regime of 99 mg/kg ketamine and 9 mg/kg xylazine (defined as 1X). - Initial experiments suggested that an almost identical dose (100 mg/kg ketamine and -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    • - anesthetic -
        -
      • Kristin Garcia
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    -

    canonical nucleoside residues

    -

    carbon

    -

    carboxy group

    -

    cytidyl groups

    -

    cytosin-1-yl group

    -

    deoxyribonucleic acids

    -
    -

    Text source name = 11597317.txt -

    1 and BRCA2 are involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during - the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of repair of - spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either B -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    97), was cloned in-frame into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences - at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    and homologous recombination - - Abstract - - Two recent papers provide new evidence relevant to the role of the breast cancer susceptibility gene BRCA2 in - DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in homology-dependent - (recombinational) repair of DNA double-strand br -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    subnuclear RAD51 foci with normal efficiency, suggesting that these proteins are required for the formation of - recombinase complexes at the sites of DNA damage [20,21]. Finally, genetic measurements of recombination - frequency have shown that Brca1-/- embryonic stem (ES) cells are deficient in recombin -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ia the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - interactions. BRCA2–Rad51 int -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ole in assembly of RAD51 at damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to - 'mediate' assembly of RAD51 at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, - including XRCC2, XRCC3, RAD51B, RAD51C and RAD51D, may function as a complex that actively p -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ty gene BRCA2 in DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in - homology-dependent (recombinational) repair of DNA double-strand breaks. The second paper, by Davies et al, - begins to address the mechanism through which BRCA2 makes its contribution to recombinationa -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    BRCA2 as grey bars. (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to - suppress RAD51–BRCA2 interactions until DNA damage is present. When damage occurs, Rad51 is recruited to - damaged sites where is polymerizes into nucleoprotein filaments. In this model, BRCA2 is -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    r by Davies et al, data provide evidence for a plausible mechanism of the dominant negative effect associated with - expression of a single BRC repeat. DNA binding assays and electron microscopy methods were used to show that - a BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    event a substantial fraction of Rad51 from being sequestered in a nonfunctional form. In a BRCA2-defective cell, - mutant Rad51 becomes associated with DNA at random sites and is therefore not readily recruited to sites of - damage. (b) Positive regulation. BRCA2 is proposed to be required for Rad51 to ass -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ognition site. Transient transfection of an I-SceI expression vector results in the production of a DSB in the first - mutated copy of GFP. One or both DNA ends formed by the break invade(s) the homologous sequence in the second - mutant GFP copy, resulting in repair of the DSB via a homology-mediated gene -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    es of DNA damage. Chromosomal DNA is shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. - (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to suppress RAD51–BRCA2 - interactions until DNA damage is present. When damage occurs, Rad51 is recr -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    clear sites with BRCA1 [9], a number of additional results have provided evidence that both BRCA1 and BRCA2 are - involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during the S - phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably si -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    gene conversion occurs via the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - inter -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    gaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment from - mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics (Hunt -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    clear foci during the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of - repair of spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either BRCA1 or BRCA2 are - sensitive to damaging agents that form double-strand breaks (DSBs), as are other -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ve cells - - Pierce et al have designed a set of recombination substrates for measuring the level of homologous recombination in - vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the easily detected - green fluorescent protein), one of which contains a restriction site -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    tgtctgaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment - from mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ing of one of the eight BRC repeats from human BRCA2. Expression of a single BRC repeat (BRC4) had previously been - reported to act as an inhibitor of DNA repair by Chen et al [27]. These investigators showed that expression - of constructs containing the BRC4 repeat in MCF-7 cells enhances the radiosensi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    s and electron microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to - assemble into oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA - interaction. These experiments raise the possibility that the full-length BRCA2 protein co -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    l population due to a mutated W (White spotted) gene. GC1 and MT4 are mouse germ cell and Sertoli cell lines, - respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger (if - any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two a -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to the regions - of ssDNA that form during normal DNA replication. BRCA2 may thus promote RAD51 assembly into recombinational - repair complexes via a negative regulatory mechanism (i.e. by blocking RAD51– -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    onal DSB repair [22,23]. The similarity between phenotypes associated with BRCA1 and BRCA2 deficiency, together with - data showing a similar effect of DNA damage on distribution of BRCA1 and BRCA2 in repair-proficient cells, - led to the hypothesis that BRCA2, like BRCA1, is required for efficient recombi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric filaments on DNA. A BRC4 peptide was - also reported to inhibit the RAD51–DNA interaction. These experiments raise the possibility that the - full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    –DNA interaction. These experiments raise the possibility that the full-length BRCA2 protein could act as a negative - regulator of inappropriate RAD51–DNA interaction. - - The final experiment reported by Davies et al [26] is particularly important with respect to understanding the - mechanism(s) through whi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8420|8423
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8420|8423
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    gure 2 are not mutually exclusive. BRCA2 could prevent inappropriate RAD51 assembly in the absence of damage and - promote functional RAD51 assembly at DNA lesions during the damage response. Further experiments are clearly - required to clarify the functional interactions between BRCA2 and RAD51 during re -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    li cell lines, respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger - (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C - antibody was raised against a -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    -

    double-stranded DNA

    -
    -

    Text source name = 11597317.txt -

    cluding the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. -

      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    mage occurs. For example, previous studies indicated that RAD51 shows little binding preference for single-strand DNA - (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as BRCA2, - are required to suppress RAD51–dsDNA interactions to prevent sequestration of -

      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involv -

      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    air complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding preference - for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory - factors, such as BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestra -

      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    rand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as - BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional - form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might b -

      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    -

    drug

    -

    glutamate residue

    -

    glutamate(1-)

    -

    glutamate(2-)

    -

    glycine

    -
    -

    Text source name = 11604102.txt -

    d by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate - exon selection in neurons is antagonized by a second RNA-binding protein, brPTB (brain- -

      -
    • - glycine -
        -
      • Mike Bada
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    • - glycine -
        -
      • Kristin Garcia
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    -

    guanine group

    -

    guanosyl groups

    -

    histidine

    -
    -

    Text source name = 11604102.txt -

    equences at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins - were mixed with Freund's adjuvant and injected into rabbits to generate the anti-DAZ -

      -
    • - His -
        -
      • Mike Bada
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    • - His -
        -
      • Kristin Garcia
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    -

    hydrogencarbonate

    -
    -

    Text source name = 11532192.txt -

    derstanding of the molecular mechanisms controlling diurnal rhythms of IOP and that may be relevant to glaucoma. - - Car2 deficiency does not alter IOP - - Bicarbonate formation is important for aqueous humor secretion from the ciliary processes and carbonic - anhydrase (CA) facilitates this secretion. There are multi -

      -
    • - Bicarbonate -
        -
      • Mike Bada
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    • - Bicarbonate -
        -
      • Kristin Garcia
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    -

    inhibitor

    -

    magnesium dichloride

    -
    -

    Text source name = 11604102.txt -

    ay, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Protease Inhibit -

      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose gradients in - 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for 2 hours at - 4°C. Fractions of 0.5 ml were collected from the bottom of the tubes and analyze -

      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    -

    messenger RNA

    -
    -

    Text source name = 11604102.txt -

    Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and characterized [16]. Prrp binds to a 340 nt - sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also int -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    tting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family - in the regulation of mRNA translation is supported by lines of cir -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ee-hybrid system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich - segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechanisms of its action, we - used a yeast two-hybrid s -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    and brain, and even less in other tissues. This pattern of expression is similar to that of the human DAZAP1 (14). - RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at embryonic day 15, similar to - Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted througho -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    proteins may act together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be - involved in the transport of the mRNAs of the target genes of DAZL. Alternatively, DAZL and DAZAP1 may act - antagonistically to regulate the timing and the level of expression. Such an anta -

      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    . Its predominant expression in testes suggests a role in spermatogenesis. Its subcellular localization indicates - that it is not directly involved in mRNA translation. - - Background - - Spermatogenesis is a complex developmental process in which male germ cells progress through mitotic proliferation, - meiotic -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    mouse testes, DAZAP1 was found both in the nuclei and in the cytoplasm. Its absence from polyribosomes indicates - that it is not directly involved in mRNA translation. - - Materials and methods - - Isolation of mouse Dazap1 cDNA clones - - Dazap1 cDNA clones were isolated from a mouse testis cDNA library (#93730 -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA transcription, pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the - DAZ family in the regulation of mRNA translation is supported by lines of circumstantial evidence, including - the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from p -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, pre-mRNA - processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA translation is supporte -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    lso interacts through its proline-rich domain with two microfilament-associated proteins profilin and Mena, which may - facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming - growth factor-β family that is required for generating dorsal mesoderm at the -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its - proline-rich domain with two microfilament-associated proteins profilin and M -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    haracterization of the mouse Dazap1 gene and its protein product. The subcellular localization of DAZAP1 suggests - that it is not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 cDNA - - Mouse Dazap1 cDNA clones were isolated by library screening, and the 5' end of the -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ressed later, in the cytoplasm of pachytene spermatocytes [5]. Genetic and biochemical studies suggest a role for the - DAZ family in the regulation of mRNA translation. Drosophila Boule mutants was defective in the translation - of the meiosis-specific CDC25 homologue, Twine [11], and DAZL was found to be -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the - alternative splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The - ability of Nova-1 to activate exon selection in neurons is antagonized by a seco -

      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    r to that of the human DAZAP1 (14). RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at - embryonic day 15, similar to Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted - throughout testes development, in both the prenatal and postnatal periods. Dazl1 and Da -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    -

    metal cations

    -

    metals

    -

    molecular entities

    -

    nucleotidyl groups

    -

    oligopeptides

    -
    -

    Text source name = 11604102.txt -

    on resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid residues of the mouse - DAZAP1 was synthesized in vitro using the services of Bethyl Laboratories (Montgomery, TX). Th -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 18509|18521
        • -
      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 18509|18521
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ntron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 - (starting from aa #197), was cloned in-fr -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 17939|17951
        • -
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    • - oligopeptide -
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      • class = oligopeptides
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      • spans = 17939|17951
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    Text source name = 11604102.txt -

    ntibody was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid residue at the - C-terminus. Both antibodies recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay ( -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 9799|9811
        • -
      -
    • - oligopeptide -
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      • Kristin Garcia
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      • class = oligopeptides
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      • spans = 9799|9811
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    Text source name = 11604102.txt -

    was conjugated to KLH as carrier and injected into a goat. The anti-DAZAP1-P antibody thus produced was purified on - an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM Tris, pH - 8.0) -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 18831|18843
        • -
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    • - oligopeptide -
        -
      • Kristin Garcia
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      • class = oligopeptides
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      • spans = 18831|18843
        • -
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    peptides

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    Text source name = 11597317.txt -

    t negative effect associated with expression of a single BRC repeat. DNA binding assays and electron microscopy - methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interact -

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      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 8126|8133
        • -
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    • - peptide -
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    Text source name = 11604102.txt -

    ontaining the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the services of Bethyl - Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier and injected into a goat. The - anti-DAZAP1-P antibody thus produced was purified on an affinity column containing the -

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    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 18673|18680
        • -
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    • - peptide -
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    - - The second paper providing evidence, by Davies et al [26], is a biochemical study of the interaction between the - homologous recombinase RAD51 and a peptide consisting of one of the eight BRC repeats from human BRCA2. - Expression of a single BRC repeat (BRC4) had previously been reported to act as an inhib -

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      • class = peptides
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      • spans = 7420|7427
        • -
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    ge has occurred and factors required for 'productive' assembly of RAD51 at damaged sites are in place). As mentioned - previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction could reflect a role of - full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another pot -

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        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 10885|10892
        • -
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      • class = peptides
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      • spans = 10885|10892
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    Text source name = 11597317.txt -

    on microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These - experiments raise the possibility that the full-length BRCA2 protein could act as a neg -

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        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 8224|8231
        • -
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        • -
      • class = peptides
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      • spans = 8224|8231
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    phosphate(3-)

    -

    phosphates

    -

    pigment

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    potassium chloride

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    , Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Prot -

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      • class = potassium chloride
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      • spans = 19828|19831
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    n at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose - gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for - 2 hours at 4°C. Fractions of 0.5 ml were collected from the bottom of the tu -

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    • - KCl -
        -
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        • -
      • class = potassium chloride
        • -
      • spans = 20325|20328
        • -
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    • - KCl -
        -
      • Kristin Garcia
        • -
      • class = potassium chloride
        • -
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    proline

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    proline residue

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    protease inhibitor

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    ontaining 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, - Madison, WI), and a mixture of 10 protease inhibitors provided in the Protease Inhibitors Set (Roche - Molecular Biochemicals, Indianapolis, IN). Homogenates were centrifuged at 1,000 × g for 10 minutes to -

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      • class = protease inhibitor
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      • spans = 19941|19960
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    KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 - protease inhibitors provided in the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, IN). - Homogenates were centrifuged at 1,000 × g for 10 minutes to pellet cell debris and nuclei. Afte -

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    • - Protease Inhibitors -
        -
      • Mike Bada
        • -
      • class = protease inhibitor
        • -
      • spans = 19977|19996
        • -
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    • - Protease Inhibitors -
        -
      • Kristin Garcia
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      • class = protease inhibitor
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    proteins

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    sites are in place). As mentioned previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction - could reflect a role of full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another potential role for BRCA2 in promoting RAD51-dependent recombinational repair is a posi -

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    absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. This finding - is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardat -

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    tein (3418 amino acids) offers very little clue to its function, although there are eight repeated segments (termed - BRC repeats) in the middle of the protein that are highly conserved among mammalian orthologs [7,8]. - - Breast cancer susceptibility genes and DNA repair - - Following the landmark discovery by Sc -

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    titutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus - Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. They share - 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prr -

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    P and FXR2P are associated with the polyribosomes [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be defined. These proteins may act - together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be involved in the - transport of the mRNAs of -

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    the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody - was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid r -

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      • class = proteins
        • -
      • spans = 9690|9697
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    y virtue of their expression of GFP. - - Moynahan et al [24] have used such a GFP recombination substrate to demonstrate that cells with defective BRCA2 protein - are deficient in their ability to repair the I-SceI-induced DSB through homologous recombination. Expression of - I-SceI resulted in 1 out of 1400 cell -

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        • -
      • spans = 4454|4461
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    mpletely independent of its defect in BRCA2. First, in the same study [24], recombination in a mouse ES cell line - that expresses only truncated BRCA2 protein was measured. This line was found to have lower recombination - efficiency than isogenic cells expressing full-length BRCA2 (the defect observed was ab -

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      • spans = 5648|5655
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    Text source name = 11319941.txt -

    striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the gene encoding the myristoylated - alanine-rich C kinase substrate (MARCKS protein). This molecule is important in cerebral development. - MARCKS-deficient mice have a high incidence of exencephaly, agenesis of the corpus callosum, an -

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    • - protein -
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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 21580|21587
        • -
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    mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast two-hybrid system through its - interaction with a putative male infertility factor, DAZ (Deleted in Azoospermi -

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      • spans = 549|556
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    via homologous recombination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of - BRCA2 on one homolog and codes for a protein truncated at amino acid 1981 on the other homolog. The authors - indicate that the level of I-SceI-induced recombination in CAPAN-1 is over 100-fold le -

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        • -
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    t. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed by Western - blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translatio -

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    by centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by the - Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of tissue - extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-D -

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        • -
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    , agenesis of the corpus callosum, and abnormalities other forebrain structure including widespread neocortical - ectopias [46, 47]. The MARCKS-related protein gene is expressed in the striatum during early brain - development in the rat [48]. - - The location of the QTL modulating striatal neuron number to the d -

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      • Mike Bada
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        • -
      • spans = 21850|21857
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    e for direct RAD51 interaction. Cells lacking BRCA1/2 fail to form damage-induced subnuclear RAD51 foci with normal - efficiency, suggesting that these proteins are required for the formation of recombinase complexes at the - sites of DNA damage [20,21]. Finally, genetic measurements of recombination frequency -

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    sophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and spermatogonia, an -

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    R1P and FXR2P, that were identified through their interaction with another polysomal-associated RNA-binding protein, - the fragile X mental retardation protein [21]. Both FXR1P and FXR2P are associated with the polyribosomes - [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be -

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      • class = proteins
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      • spans = 12395|12402
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      • spans = 12395|12402
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    ed in CAPAN-1 cells, the same human tumor line examined by Moynahan et al [24]. It had been shown previously that the - small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, - consistent with the fact that the truncation protein lacks a nuclear localization signa -

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      • Mike Bada
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      • spans = 8808|8815
        • -
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    em, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA binding domains and a proline - rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to RNA - homopolymers. We now report our characterization of the mouse Dazap1 gene and its pr -

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    riginal URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast tw -

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    he two RBDs are especially highly conserved. They share 98% and 97% similarity and 97% and 92% identity, - respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA binding specificity. - The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% similarity and -

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      • spans = 5872|5880
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    nteraction with DAZ and DAZL, we isolated and characterized the mouse Dazap1 gene, and studied its expression and the - subcellular localization of its protein product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins sha -

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    se genomic DNA. The PCR primers span over introns and produce much larger (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti - DAZAP1-C antibody was raised against a recombinant protein containing the C-terminal pr -

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    Text source name = 11604102.txt -

    infertility factor, DAZ (Deleted in Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ - and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a - proline-rich C-terminal portion, and is expressed most abundantly in the testis. To under -

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    . Second, in an independent study, Powell was able to compare derivatives of CAPAN-1 that differed only in their - ability to express full-length BRCA2 protein (S. Powell, personal communication, 2001). In these experiments, - the derivative expressing full-length BRCA2 yielded 10-fold more recombinants than c -

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    Text source name = 11604102.txt -

    NA-binding domains (RBDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved - evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with X -

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      • Kristin Garcia
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    tein product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins share 98% identity and their sequences are highly similar to the Xenopus orthologue - Prrp, especially in the RBDs. Dazap1 is expressed throughout test -

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    nal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in neurons is - antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding protein), - which interacts with Nova-1 and inhibits its function [24]. DAZAP1 could function in a -

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    ng dorsal mesoderm at the blastula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of - DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST search of - the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with -

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    to the Xenopus orthologue Prrp, especially in the RBDs. Dazap1 is expressed throughout testis development. Western - blot detects a single 45 kD DAZAP1 protein that is most abundant in the testis. Although a majority of DAZAP1 - is present in the cytoplasmic fraction, they are not associated with polyribosomes -

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    f expression. Such an antagonistic interaction between two interacting RNA-binding proteins is exemplified by the - neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of N -

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    s a change of reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences betwee -

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    s recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting of mouse - tissue extracts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser - degree in spleen, liver, lung and brain (Figure 4). The protein was also present in t -

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    ation of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a R -

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    of DAZAP1 increased afterward, as the testes contained increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted -

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    nds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse testes, DAZAP1 w -

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    share 85%, 90%, and 97% similarity with segments in the human 3' UTR, respectively. These segments probably contain - regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse -

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    RI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences at the junctions were verified by DNA - sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on - His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with Fre -

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    he small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, consistent - with the fact that the truncation protein lacks a nuclear localization signal [28]. Davies et al showed - CAPAN-1 cells to be defective in nuclear localization of RAD51, raising the possibility -

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    acts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser degree in spleen, - liver, lung and brain (Figure 4). The protein was also present in the ovary. The expression of DAZAP1 during - germ cell development paralleled that of DAZL (Figure 5). It is present at a low level -

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    ce, including the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from polyribosomes indicates - that it is not directly involved in protein synthesis. This finding is different from two RNA-binding - proteins, FXR1P and FXR2P, that were identified through their interaction with another poly -

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    clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its proline-rich domain - with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 mRNA - to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth fact -

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    (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with the - RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have been indi -

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    illigrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on His-Bind metal chelation - resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid -

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    ifferent from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction with another - polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both FXR1P and FXR2P - are associated with the polyribosomes [22]. - - The significance of the interaction -

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    ty of Nova-1 to activate exon selection in neurons is antagonized by a second RNA-binding protein, brPTB - (brain-enriched polypyrimidine tract-binding protein), which interacts with Nova-1 and inhibits its function - [24]. DAZAP1 could function in a similar manner by binding to DAZL and inhibiting its functio -

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    em to isolate two human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed - predominantly in testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal - portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to R -

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    Both primer pairs annealed across intron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 ( -

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    erved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for - proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. T -

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    end of the cDNA was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region - (UTR), an open reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession - No: AF225910). The coding region shares 89% similarity with that of the human orth -

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    increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted with the anti-DAZAP1-P antibody. - - Figure 5 Western blot -

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    Z gene family and to understanding the mechanisms of its action, we used a yeast two-hybrid system to isolate two - human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly - in testes. It encodes a protein with two RNA binding domains and a proline rich C-term -

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    gene to be discovered, and was isolated through positional cloning using data from families with inherited breast - cancer [4]. Cells with mutant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate - gross chromosomal rearrangements [5,6]. The sequence of this large protein (3418 ami -

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    AP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic interaction - between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding - protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNAs encoding neuron -

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    logous recombination in vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the - easily detected green fluorescent protein), one of which contains a restriction site for I-SceI, a yeast - intron encoded endonuclease with an 18 base pair recognition site. Transient transfect -

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    ential role for BRCA2 in promoting RAD51-dependent recombinational repair is a positive role in assembly of RAD51 at - damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to 'mediate' assembly of RAD51 - at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, includin -

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    ) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by - the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μ -

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    breaks (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with - the RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have b -

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    ant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements - [5,6]. The sequence of this large protein (3418 amino acids) offers very little clue to its function, - although there are eight repeated segments (termed BRC repeats) in the middle of the prot -

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    nts on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These experiments raise the - possibility that the full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA - interaction. - - The final experiment reported by Davies et al [26] is particularly importa -

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    ribonucleic acids

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    BLAST search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, and possibly DAZAP1, may help to - identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolution -

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    article's original URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identifi -

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    ch domain with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 - mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth factor-β family that is - required for generating dorsal mesoderm at the blastula stage of Xenopus embryoge -

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    erved. They share 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These - proteins may therefore have a similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 - and Prrp are less conserved (81% similarity and 71% identity). There is an insert -

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    DAZL and DAZAP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic - interaction between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear - RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNA -

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      • class = ribonucleic acids
        • -
      • spans = 12918|12921
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12918|12921
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ressed most abundantly in the testis. - - Figure 3 Developmental expression of Dazap1 and Dazl in mouse testes. RT-PCR was performed on total testicular RNAs - isolated from day 15 (El 5) and day 17 (El 7) embryos, new born mice (Day 0), and mice at various days after birth. - Wv/Wv testes contain diminished g -

      -
    • - RNAs -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 9119|9123
        • -
      -
    • - RNAs -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 9119|9123
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    communication). The genomic structure of Dazap1, delineated here, should facilitate the generating of Dazap1 null - mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 13965|13968
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 13965|13968
        • -
      -
    -
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    Text source name = 11604102.txt -

    coding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in - neurons is antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding - protein), which interacts with Nova-1 and inhibits its function [24]. DAZAP1 coul -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 13225|13228
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 13225|13228
        • -
      -
    -
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    Text source name = 11604102.txt -

    human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in - testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 - protein interacted with both DAZ and DAZL in vitro. It also bound to RNA homopolyme -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 4297|4300
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
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      • spans = 4297|4300
        • -
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    -
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    Text source name = 11604102.txt -

    Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s and the - Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and the mouse - sequences, and between the mouse and Xenopus sequences are marked by #'s and * -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 6368|6371
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
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      • spans = 6368|6371
        • -
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    Text source name = 11604102.txt -

    n with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and - DAZL in vitro. It also bound to RNA homopolymers. We now report our characterization of the mouse Dazap1 gene - and its protein product. The subcellular localization of DAZAP1 suggests th -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 4436|4439
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
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      • spans = 4436|4439
        • -
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    Text source name = 11604102.txt -

    VLE that binds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 15181|15184
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 15181|15184
        • -
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    -
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    Text source name = 11604102.txt -

    es [12]. The absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. - This finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their - interaction with another polysomal-associated RNA-binding protein, the fragile -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 12221|12224
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12221|12224
        • -
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    -
    -

    Text source name = 11604102.txt -

    rose gradient. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed - by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localiz -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 11715|11718
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 11715|11718
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    mbers of Drosophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both - sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 3171|3174
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 3171|3174
        • -
      -
    -
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    Text source name = 11604102.txt -

    the level of expression. Such an antagonistic interaction between two interacting RNA-binding proteins is - exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative - splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 12985|12988
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12985|12988
        • -
      -
    -
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    Text source name = 11604102.txt -

    stula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of DAZAP1 and Prrp suggests that - these proteins may bind to similar RNA sequences. However, a BLAST search of the GenBank for the 340 nt VLE - sequence failed to identify any mammalian sequences with significant homology. F -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 14837|14840
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 14837|14840
        • -
      -
    -
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    Text source name = 11604102.txt -

    n Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like - protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is - expressed most abundantly in the testis. To understand the biological function o -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 844|847
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 844|847
        • -
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    -
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    Text source name = 11604102.txt -

    The 5' end of the cDNA was isolated by 5' RACE [15], using prdap11 (ttgcgggccatatccttg, #749–732) as the primer for - cDNA synthesis from mouse testis RNA, and prdap37 (ttgttgccacgtgggcg, #734–718) and an adaptor primer as the - primers for PCR amplification. The PCR products were cloned into a TA cloning -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 15847|15850
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 15847|15850
        • -
      -
    -
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    Text source name = 11604102.txt -

    finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both - FXR1P and FXR2P are associated with the polyribosomes [22]. - - The significance of -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 12341|12344
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12341|12344
        • -
      -
    -
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    Text source name = 11604102.txt -

    97% similarity with segments in the human 3' UTR, respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human pr -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 5355|5358
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 5355|5358
        • -
      -
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    Text source name = 11604102.txt -

    ch fractions was analyzed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 11805|11808
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 11805|11808
        • -
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    Text source name = 11604102.txt -

    with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity - with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. - They share 98% and 97% similarity and 97% and 92% identity, respectively, betwee -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 5694|5697
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 5694|5697
        • -
      -
    -

    single-stranded DNA

    -
    -

    Text source name = 11597317.txt -

    BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-lik -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 12990|12995
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 12990|12995
        • -
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    Text source name = 11597317.txt -

    d to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional form. Alternatively, or - in addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to - the regions of ssDNA that form during normal DNA replication. BRCA2 may thus prom -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10435|10440
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10435|10440
        • -
      -
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    Text source name = 11597317.txt -

    nction difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; ssDNA = - single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like - protein.. Cell. 19 -

      -
    • - single-strand DNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 12998|13015
        • -
      -
    • - single-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 12998|13015
        • -
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    Text source name = 11597317.txt -

    recruited into a functional repair complex when damage occurs. For example, previous studies indicated that RAD51 - shows little binding preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This - result could mean that regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA in -

      -
    • - single-strand DNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10146|10163
        • -
      -
    • - single-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10146|10163
        • -
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    Text source name = 11597317.txt -

    nctional repair complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding - preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that - regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA interacti -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10165|10170
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10165|10170
        • -
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    Text source name = 11597317.txt -

    al form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might be important for preventing - RAD51 from binding to the regions of ssDNA that form during normal DNA replication. BRCA2 may thus promote - RAD51 assembly into recombinational repair complexes via a negative regulatory mechan -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10524|10529
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10524|10529
        • -
      -
    -

    sodium chloride

    -
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    Text source name = 11604102.txt -

    urified on an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of deb -

      -
    • - NaCl -
        -
      • Mike Bada
        • -
      • class = sodium chloride
        • -
      • spans = 18936|18940
        • -
      -
    • - NaCl -
        -
      • Kristin Garcia
        • -
      • class = sodium chloride
        • -
      • spans = 18936|18940
        • -
      -
    -

    sodium dodecyl sulfate

    -
    -

    Text source name = 11604102.txt -

    taining the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 -

      -
    • - SDS -
        -
      • Mike Bada
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 18969|18972
        • -
      -
    • - SDS -
        -
      • Kristin Garcia
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 18969|18972
        • -
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    Text source name = 11604102.txt -

    etermined by the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of - tissue extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-DAZAP1-C - antibody (at a 1/2,000 dilution) or the anti-DAZAP1-P antibody (at a 1/5,000 dilution). -

      -
    • - SDS -
        -
      • Mike Bada
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 19342|19345
        • -
      -
    • - SDS -
        -
      • Kristin Garcia
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 19342|19345
        • -
      -
    -

    sodium phosphates

    -
    -

    Text source name = 11319941.txt -

    ply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, 0.5-1.0 ml ip) and perfused - through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) followed by 1.25% - glutaraldehyde/1.0% paraformaldehyde in 0.1 M PB (pH 7.40) over a period of 2 to 4 min. An additional -

      -
    • - sodium phosphate -
        -
      • Mike Bada
        • -
      • class = sodium phosphates
        • -
      • spans = 26402|26418
        • -
      -
    • - sodium phosphate -
        -
      • Kristin Garcia
        • -
      • class = sodium phosphates
        • -
      • spans = 26402|26418
        • -
      -
    -

    sucrose

    -
    -

    Text source name = 11604102.txt -

    analyses shows that DAZAP1 is not associated with polyribosomes. The post-mitochondrial supernatant of mouse testis - extracts was analyzed on a 15–45% sucrose gradient. Sedimentation was from left to right. The presence of - DAZAP1 and DAZL in each fractions was analyzed by Western blotting. - - Discussion - - RNA- -

      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11562|11569
        • -
      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11562|11569
        • -
      -
    -
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    Text source name = 11604102.txt -

    uclei. After an additional centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the - supernatant were applied to 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged - in a Beckman SW41 rotor at 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were -

      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 20285|20292
        • -
      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 20285|20292
        • -
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    -
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    Text source name = 11604102.txt -

    se gradient analyses of the post- mitochondria fraction showed that, unlike DAZL, DAZAP1 did not co-sediment with - polyribosomes (Figure 6). - - Figure 6 Sucrose gradient analyses shows that DAZAP1 is not associated with polyribosomes. The - post-mitochondrial supernatant of mouse testis extracts was analyzed on -

      -
    • - Sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11395|11402
        • -
      -
    • - Sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11395|11402
        • -
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    -
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    Text source name = 11604102.txt -

    [12]. Similar analyses showed that a majority of DAZAP1 in adult mouse testes was also present in the cytoplasmic - fraction (data not shown). However, sucrose gradient analyses of the post- mitochondria fraction showed that, - unlike DAZL, DAZAP1 did not co-sediment with polyribosomes (Figure 6). - - Figure 6 Su -

      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11240|11247
        • -
      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11240|11247
        • -
      -
    -

    terpenes

    -
    -

    Text source name = 11532192.txt -

    esia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and wood - shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in wood - shavings alters drug resistance and decreases the effect of anesthetic agents in both ra -

      -
    • - Terpene -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25559|25566
        • -
      -
    • - Terpene -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25559|25566
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    may be important. We use wood shavings for bedding and wood shavings expose the mice to terpenes. Terpene - administration or environmental exposure to terpenes in wood shavings alters drug resistance and decreases - the effect of anesthetic agents in both rats and mice [40-45]. - - Risk factors for increased IOP - -

      -
    • - terpenes -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    of anesthesia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and - wood shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in - wood shavings alters drug resistance and decreases the effect of anesthetic agents i -

      -
    • - terpenes -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25549|25557
        • -
      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25549|25557
        • -
      -
    -

    tert-pentyl group

    -
    -

    Text source name = 11319941.txt -

    lution digital images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% g -

      -
    • - tert-pentyl -
        -
      • Mike Bada
        • -
      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    • - tert-pentyl -
        -
      • Kristin Garcia
        • -
      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    -

    tris

    -
    -

    Text source name = 11604102.txt -

    oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of - debris by centrifugation at 10,000 × g for 10 m -

      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to - 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at - 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were collected from the bott -

      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ham Pharmacia Biotech, Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors -

      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    -

    uracil-1-yl group

    -

    uridyl groups

    -

    water

    -
    -

    Text source name = 11532192.txt -

    containing white pine bedding and covered with polyester filters. For most experiments, the mice were fed NIH31 (6 % - fat) chow ad libitum, and their water was acidified to pH 2.8 to 3.2. B6 mice develop diet induced diabetes - when maintained on a high fat diet [76]. To ensure that we were analyzing the e -

      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    f sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, - 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) - followed by 1.25% glutaraldehyde/1.0 -

      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    +Each concept that was considered a match is shown in the text that it was found in. The matching annotations from the other concept sets are also shown. +
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    • +
      • Kristin Garcia
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    • +
      • Kristin Garcia
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    • +
      • Kristin Garcia
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    • +
      • Kristin Garcia
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    • +
      • Kristin Garcia
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    +

    CHEBI_15377

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    +

    CHEBI_16670

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    +

    CHEBI_17544

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    +

    CHEBI_17992

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    +

    CHEBI_23367

    +

    CHEBI_25213

    +

    CHEBI_25613

    +

    CHEBI_25676

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    +

    CHEBI_26020

    +

    CHEBI_26710

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    +

    CHEBI_27594

    +

    CHEBI_30879

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    +

    CHEBI_32588

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    +

    CHEBI_33521

    +

    CHEBI_33708

    +

    CHEBI_33709

    +

    CHEBI_35186

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    +

    CHEBI_36080

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = n that is most [1185, 1200]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = n that [1185, 1192]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    +

    CHEBI_37586

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    +

    CHEBI_6636

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    +

    CHEBI_8984

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    +

    CHEBI_9754

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    diff --git a/src/test/resources/iaa_test_project/iaa/Class matcher.nonmatches.Kristin Garcia.html b/src/test/resources/iaa_test_project/iaa/Class matcher.nonmatches.Kristin Garcia.html index facf3f1b..5a191ba8 100644 --- a/src/test/resources/iaa_test_project/iaa/Class matcher.nonmatches.Kristin Garcia.html +++ b/src/test/resources/iaa_test_project/iaa/Class matcher.nonmatches.Kristin Garcia.html @@ -3,520 +3,147 @@ Class matcher

    Non-matches for Kristin Garcia

    -Each annotation that was considered a non-match is shown in the text that it was found in. Overlapping annotations from -the other annotation sets are also shown. -
    -

    5'-cytidylyl group

    -

    5'-guanylyl group

    -

    5'-uridylyl group

    -

    acid

    -

    adenine group

    -

    alanine

    -
    -

    Text source name = 11319941.txt -

    y down-regulate synaptic activity in the striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the - gene encoding the myristoylated alanine-rich C kinase substrate (MARCKS protein). This molecule is important - in cerebral development. MARCKS-deficient mice have a high incidence of exenceph -

      -
    • - alanine -
        -
      • Kristin Garcia
        • -
      • class = alanine
        • -
      • spans = 21540|21547
        • -
      -
    • - alanine -
        -
      • Mike Bada
        • -
      • class = alanine residue
        • -
      • spans = 21540|21547
        • -
      -
    -

    alanine residue

    -

    alcohols

    -

    amino acids

    -
    -

    Text source name = 11604102.txt -

    was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region (UTR), an open - reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession No: AF225910). - The coding region shares 89% similarity with that of the human orthologue. The 3' UTR -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 4931|4941
        • -
      -
    • - amino acid residues -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 4931|4950
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 6273|6283
        • -
      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 6273|6283
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nant protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both antibodies recognized in vitro - synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 9835|9845
        • -
      -
    • - amino acid residue -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 9835|9853
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    BDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved evolutionarily. The mouse - and the human proteins differ in 9 amino acids only, with 7 substitutions and two deletions/insertions. The - mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for proline -

      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 5527|5538
        • -
      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 5527|5538
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    bination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of BRCA2 on one homolog and - codes for a protein truncated at amino acid 1981 on the other homolog. The authors indicate that the level of - I-SceI-induced recombination in CAPAN-1 is over 100-fold less than that seen using -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 4797|4807
        • -
      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 4797|4807
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements [5,6]. The - sequence of this large protein (3418 amino acids) offers very little clue to its function, although there are - eight repeated segments (termed BRC repeats) in the middle of the protein that are highl -

      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 1344|1355
        • -
      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 1344|1355
        • -
      -
    -

    amino-acid residues

    -

    anaesthetic

    -

    canonical nucleoside residues

    -

    carbon

    -

    carboxy group

    -

    cytidyl groups

    -

    cytosin-1-yl group

    -

    deoxyribonucleic acids

    -

    double-stranded DNA

    -
    -

    Text source name = 11319941.txt -

    al forebrain [27, 50]. - - Brain volume and neuron number - - It has previously been shown that differences in brain weight are proportional to total brain DNA content and - consequently to total CNS cell number [51, 52]. For this reason, brain weight has been suggested to be a good - surrogate measure for total -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 22890|22893
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 22890|22893
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    ure was .81 (P < .05), which is similar to the reliability seen in previous estimates of neuron number [39, 40]. - - Genotyping and QTL Mapping +Each concept that was considered a non-match is shown in the text that it was found in. Overlapping annotations from the other concept sets are also shown. +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16449
      • spanCollection = sgenic [21540, 21547]
    • +
      • Mike Bada
      • class = CHEBI:32441
      • spanCollection = sgenic [21540, 21547]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = inserti [5681, 5688]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = inserti [5681, 5688]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = Dazap1 [4323, 4330]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = Dazap1 [4323, 4330]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = the tra [14405, 14412]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = the tra [14405, 14412]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = y and 9 [5423, 5430]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = y and 9 [5423, 5430]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = and the [5950, 5957]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = and the [5950, 5957]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nthesiz [9724, 9731]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nthesiz [9724, 9731]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nomic s [877, 884]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nomic s [877, 884]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:32484
      • spanCollection = on on gen [21235, 21244]
    • +
      • Mike Bada
      • class = CHEBI:29987
      • spanCollection = on on gen [21235, 21244]
    • +
      • Mike Bada
      • class = CHEBI:14321
      • spanCollection = on on gen [21235, 21244]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = rie [30232, 30235]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = rie [30232, 30235]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = es [38583, 38586]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = es [38583, 38586]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ral [22890, 22893]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ral [22890, 22893]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = A2 [455, 458]
    +

    +

    CHEBI_15377

    +

    CHEBI_16670

    +

    CHEBI_17544

    +

    CHEBI_17992

    +

    CHEBI_23367

    +

    CHEBI_25213

    +

    CHEBI_25613

    +

    CHEBI_25676

    +

    CHEBI_26020

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26020
      • spanCollection = he anteri [38088, 38097]
    • +
      • Mike Bada
      • class = CHEBI:18367
      • spanCollection = he anteri [38088, 38097]
    +

    CHEBI_26710

    +

    CHEBI_27594

    +

    CHEBI_30879

    +

    CHEBI_32588

    +

    CHEBI_33521

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33521
      • spanCollection = ng th [18346, 18351]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25213
      • spanCollection = ng th [18346, 18351]
    +

    CHEBI_33708

    +

    CHEBI_33709

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = served amon [1344, 1355]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = served amon [1344, 1355]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = (BRCA2+) h [4797, 4807]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = (BRCA2+) h [4797, 4807]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = imilar RNA [5527, 5538]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = imilar RNA [5527, 5538]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = p1 genomic [6273, 6283]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = p1 genomic [6273, 6283]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = tected a 4 [9835, 9845]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = tected a 45 kD pro [9835, 9853]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = tory eleme [4931, 4941]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = tory elements. - Genomic DNA was extracted from spleens of F2 animals using a high-salt procedure [63]. A set of 82 - microsatellite loci distributed across all autosomes and the X -
          -
        • - DNA -
            -
          • Kristin Garcia
            • -
          • class = double-stranded DNA
            • -
          • spans = 30232|30235
            • -
          -
        • - DNA -
            -
          • Mike Bada
            • -
          • class = deoxyribonucleic acids
            • -
          • spans = 30232|30235
            • -
          -
        -
        -

        Text source name = 11597317.txt -

        ty gene BRCA2 in DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in - homology-dependent (recombinational) repair of DNA double-strand breaks. The second paper, by Davies et al, - begins to address the mechanism through which BRCA2 makes its contribution to recombinationa -

          -
        • - DNA -
            -
          • Kristin Garcia
            • -
          • class = double-stranded DNA
            • -
          • spans = 455|458
            • -
          -
        -
        -

        Text source name = 11532192.txt -

        d as they contain most ocular structures. - - Analysis of Myoc - - Exons and the proximal promoter of the mouse Myoc gene were amplified from mouse genomic DNA using the - following combinations of primers: - - Exon 1: 5'-cttgcaggagaactttccagaa-3' and 5'-atctcgaaggagattgttatagg-3' - - 5'-gaccagctggagacccaaaccag-3' a -

          -
        • - DNA -
            -
          • Kristin Garcia
            • -
          • class = double-stranded DNA
            • -
          • spans = 38583|38586
            • -
          -
        • - DNA -
            -
          • Mike Bada
            • -
          • class = deoxyribonucleic acids
            • -
          • spans = 38583|38586
            • -
          -
        -

        drug

        -

        glutamate residue

        -
        -

        Text source name = 11319941.txt -

        l portion of Chr 10 in proximity with a number of genes known to affect brain development. One of these is Grk2, a - member of the family of ionotropic glutamate receptor genes that is thought to play a role in modulating - Huntington disease [44]. In the mouse, members of this receptor type act to indirectly do -

          -
        • - glutamate -
            -
          • Kristin Garcia
            • -
          • class = glutamate residue
            • -
          • spans = 21235|21244
            • -
          -
        • - glutamate -
            -
          • Mike Bada
            • -
          • class = glutamate(1-)
            • -
          • spans = 21235|21244
            • -
          -
        • - glutamate -
            -
          • Mike Bada
            • -
          • class = glutamate(2-)
            • -
          • spans = 21235|21244
            • -
          -
        -

        glutamate(1-)

        -

        glutamate(2-)

        -

        glycine

        -

        guanine group

        -

        guanosyl groups

        -

        histidine

        -

        hydrogencarbonate

        -

        inhibitor

        -

        magnesium dichloride

        -

        messenger RNA

        -

        metal cations

        -

        metals

        -
        -

        Text source name = 11604102.txt -

        at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were - prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with - Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antib -

          -
        • - metal -
            -
          • Kristin Garcia
            • -
          • class = metals
            • -
          • spans = 18346|18351
            • -
          -
        • - metal -
            -
          • Mike Bada
            • -
          • class = metal cations
            • -
          • spans = 18346|18351
            • -
          -
        -

        molecular entities

        -

        nucleotidyl groups

        -

        oligopeptides

        -

        peptides

        -

        phosphate(3-)

        -

        phosphates

        -
        -

        Text source name = 11532192.txt -

        ormalin fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 M phosphate buffer. All strains other than CBA/CaHN and C57BLKS/J - strains were evaluated. The eyes of CBA/CaJ and BALB/cJ mice were also fixed and processed for -

          -
        • - phosphate -
            -
          • Kristin Garcia
            • -
          • class = phosphates
            • -
          • spans = 38088|38097
            • -
          -
        • - phosphate -
            -
          • Mike Bada
            • -
          • class = phosphate(3-)
            • -
          • spans = 38088|38097
            • -
          -
        -

        pigment

        -

        potassium chloride

        -

        proline

        -
        -

        Text source name = 11604102.txt -

        tion element (VLE) is sufficient for the migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. - Prrp also interacts through its proline-rich domain with two microfilament-associated proteins profilin and - Mena, which may facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The V -

          -
        • - proline -
            -
          • Kristin Garcia
            • -
          • class = proline
            • -
          • spans = 14405|14412
            • -
          -
        • - proline -
            -
          • Mike Bada
            • -
          • class = proline residue
            • -
          • spans = 14405|14412
            • -
          -
        -
        -

        Text source name = 11604102.txt -

        o acids only, with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% - identity with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly - conserved. They share 98% and 97% similarity and 97% and 92% identity, respectivel -

          -
        • - proline -
            -
          • Kristin Garcia
            • -
          • class = proline
            • -
          • spans = 5681|5688
            • -
          -
        • - proline -
            -
          • Mike Bada
            • -
          • class = proline residue
            • -
          • spans = 5681|5688
            • -
          -
        -
        -

        Text source name = 11604102.txt -

        interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two - RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the - testis. To understand the biological function of DAZAP1 and the significance of its -

          -
        • - proline -
            -
          • Kristin Garcia
            • -
          • class = proline
            • -
          • spans = 877|884
            • -
          -
        • - proline -
            -
          • Mike Bada
            • -
          • class = proline residue
            • -
          • spans = 877|884
            • -
          -
        -
        -

        Text source name = 11604102.txt -

        e segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, - with 7 substitutions and two deleti -

          -
        • - proline -
            -
          • Kristin Garcia
            • -
          • class = proline
            • -
          • spans = 5423|5430
            • -
          -
        • - proline -
            -
          • Mike Bada
            • -
          • class = proline residue
            • -
          • spans = 5423|5430
            • -
          -
        -
        -

        Text source name = 11604102.txt -

        in, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody was raised against a recombinant - protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both ant -

          -
        • - proline -
            -
          • Kristin Garcia
            • -
          • class = proline
            • -
          • spans = 9724|9731
            • -
          -
        • - proline -
            -
          • Mike Bada
            • -
          • class = proline residue
            • -
          • spans = 9724|9731
            • -
          -
        -
        -

        Text source name = 11604102.txt -

        and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA - binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% - similarity and 71% identity). There is an insertion of a 58 bp segment in Prrp cDNA that cau -

          -
        • - proline -
            -
          • Kristin Garcia
            • -
          • class = proline
            • -
          • spans = 5950|5957
            • -
          -
        • - proline -
            -
          • Mike Bada
            • -
          • class = proline residue
            • -
          • spans = 5950|5957
            • -
          -
        -
        -

        Text source name = 11604102.txt -

        associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in testes. It encodes a protein - with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both - DAZ and DAZL in vitro. It also bound to RNA homopolymers. We now report our characte -

          -
        • - proline -
            -
          • Kristin Garcia
            • -
          • class = proline
            • -
          • spans = 4323|4330
            • -
          -
        • - proline -
            -
          • Mike Bada
            • -
          • class = proline residue
            • -
          • spans = 4323|4330
            • -
          -
        -

        proline residue

        -

        protease inhibitor

        -

        proteins

        -

        ribonucleic acids

        -

        single-stranded DNA

        -

        sodium chloride

        -

        sodium dodecyl sulfate

        -

        sodium phosphates

        -

        sucrose

        -

        terpenes

        -

        tert-pentyl group

        -

        tris

        -

        uracil-1-yl group

        -

        uridyl groups

        -

        water

        +The [4931, 4950]
    +

    CHEBI_35186

    +

    CHEBI_36080

    +

    CHEBI_37586

    +

    CHEBI_6636

    +

    CHEBI_8984

    +

    CHEBI_9754

    diff --git a/src/test/resources/iaa_test_project/iaa/Class matcher.nonmatches.Mike Bada.html b/src/test/resources/iaa_test_project/iaa/Class matcher.nonmatches.Mike Bada.html index 77265f1c..d6609e57 100644 --- a/src/test/resources/iaa_test_project/iaa/Class matcher.nonmatches.Mike Bada.html +++ b/src/test/resources/iaa_test_project/iaa/Class matcher.nonmatches.Mike Bada.html @@ -3,1876 +3,339 @@ Class matcher

    Non-matches for Mike Bada

    -Each annotation that was considered a non-match is shown in the text that it was found in. Overlapping annotations from -the other annotation sets are also shown. -
    -

    5'-cytidylyl group

    -
    -

    Text source name = 11604102.txt -

    [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = 5'-cytidylyl group
        • -
      • spans = 3904|3905
        • -
      -
    -

    5'-guanylyl group

    -
    -

    Text source name = 11604102.txt -

    should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = 5'-guanylyl group
        • -
      • spans = 14030|14031
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    estes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family an -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = 5'-guanylyl group
        • -
      • spans = 3899|3900
        • -
      -
    -

    5'-uridylyl group

    -
    -

    Text source name = 11604102.txt -

    eated here, should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = 5'-uridylyl group
        • -
      • spans = 14019|14020
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid - system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich segment - in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the funct -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = 5'-uridylyl group
        • -
      • spans = 3870|3871
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) stretches interspersed - by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechan -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = 5'-uridylyl group
        • -
      • spans = 3928|3929
        • -
      -
    -

    acid

    -

    adenine group

    -
    -

    Text source name = 11532192.txt -

    he insertion allele. The other allele was identical to the published sequence [22]. The insertion allele also had a - previously reported substitution (A to G, Thr164Ala) in exon 1 and several other single base changes in the - promoter region [22]. The presence or absence of this allele does not associa -

      -
    • - A -
        -
      • Mike Bada
        • -
      • class = adenine group
        • -
      • spans = 16988|16989
        • -
      -
    -

    alanine

    -

    alanine residue

    -
    -

    Text source name = 11319941.txt -

    y down-regulate synaptic activity in the striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the - gene encoding the myristoylated alanine-rich C kinase substrate (MARCKS protein). This molecule is important - in cerebral development. MARCKS-deficient mice have a high incidence of exenceph -

      -
    • - alanine -
        -
      • Mike Bada
        • -
      • class = alanine residue
        • -
      • spans = 21540|21547
        • -
      -
    • - alanine -
        -
      • Kristin Garcia
        • -
      • class = alanine
        • -
      • spans = 21540|21547
        • -
      -
    -

    alcohols

    -

    amino acids

    -

    amino-acid residues

    -
    -

    Text source name = 11604102.txt -

    e proteins were mixed with Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antibody. An - oligopeptide containing the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the - services of Bethyl Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier -

      -
    • - ammo acid residues -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 18545|18563
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and -

      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 6273|6283
        • -
      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 6273|6283
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements [5,6]. The - sequence of this large protein (3418 amino acids) offers very little clue to its function, although there are - eight repeated segments (termed BRC repeats) in the middle of the protein that are highl -

      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 1344|1355
        • -
      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 1344|1355
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nant protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both antibodies recognized in vitro - synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting of mouse -

      -
    • - amino acid residue -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 9835|9853
        • -
      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 9835|9845
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    bination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of BRCA2 on one homolog and - codes for a protein truncated at amino acid 1981 on the other homolog. The authors indicate that the level of - I-SceI-induced recombination in CAPAN-1 is over 100-fold less than that seen using -

      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 4797|4807
        • -
      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 4797|4807
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region (UTR), an open - reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession No: AF225910). - The coding region shares 89% similarity with that of the human orthologue. The 3' UTR sequence -

      -
    • - amino acid residues -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 4931|4950
        • -
      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 4931|4941
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    BDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved evolutionarily. The mouse - and the human proteins differ in 9 amino acids only, with 7 substitutions and two deletions/insertions. The - mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for proline -

      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 5527|5538
        • -
      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 5527|5538
        • -
      -
    -

    anaesthetic

    -
    -

    Text source name = 11532192.txt -

    tely thirty 3 to 4 month old mice were analyzed at each dose and time B-D. Scatter-plots demonstrating no change in - IOP over the 12 minutes following anesthetic administration in three relatively unrelated mouse strains. All - strains consisted of males and females that ranged from 3 to 6 months of age. The sex -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 14779|14789
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    me). The greater the dose the greater the decrease in IOP. At the 5 minute measurement, however, IOP was the same - using all doses suggesting that the anesthetic effect on IOP had not yet occurred. To identify any early - window when it may be possible to assess IOP without an obvious anesthetic effect, 195 mice -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 13227|13237
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    tic dose within 12 minutes of administration. A Mean IOP ± SD is shown for C57BL/6J mice at 5 and 25 minutes after - administration of various doses of anesthetic. The 1X dose consisted of 99 mg/kg ketamine and 9 mg/kg - xylazine. All doses decreased IOP by 25 minutes. At all doses the IOP at 5 minutes was the sa -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 14394|14404
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    he mice to terpenes. Terpene administration or environmental exposure to terpenes in wood shavings alters drug - resistance and decreases the effect of anesthetic agents in both rats and mice [40-45]. - - Risk factors for increased IOP - - Some epidemiological studies implicate factors such as diabetes, vascular hypertensio -

      -
    • - anesthetic agents -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 25688|25705
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    do not immediately identify them as likely glaucoma candidates. - - No effect of anesthetic protocol on IOP during a 12 minute measurement window - - Many anesthetic agents including xylazine lower IOP. Ketamine usually appears to increase IOP [31-33], but - there are reports of ketamine having no effect on IOP or even red -

      -
    • - anesthetic agents -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 22441|22458
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    ronments may contribute to these differences. The relationship between the IOPs we measure and those in conscious - mice depends upon the effect of our anesthetic protocol (intraperitoneal injection of 99 mg/kg ketamine and 9 - mg/kg xylazine). An anesthetic effect could potentially alter IOP and mask genetically -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 22840|22850
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    s (Figure 6). In these experiments, IOP measurements were made between 5 and 12 minutes after administration of - anesthesia. - - Figure 5 No effect of 1X anesthetic dose within 12 minutes of administration. A Mean IOP ± SD is shown for - C57BL/6J mice at 5 and 25 minutes after administration of various doses of ane -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 14237|14247
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    those in conscious mice depends upon the effect of our anesthetic protocol (intraperitoneal injection of 99 mg/kg - ketamine and 9 mg/kg xylazine). An anesthetic effect could potentially alter IOP and mask genetically - determined differences in IOP. Therefore, it is very important to understand this effect. Her -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 22934|22944
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    minutes after administration. Thus, to avoid effects of anesthesia on IOP, all measurements should be made within a - window of up to 12 minutes after anesthetic administration. - - Similarities and differences to rat studies - - Our results agree with the time course of cardiovascular depression caused by intraperi -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 23386|23396
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    own functions do not suggest that they affect aqueous humor dynamics or do not immediately identify them as likely - glaucoma candidates. - - No effect of anesthetic protocol on IOP during a 12 minute measurement window - - Many anesthetic agents including xylazine lower IOP. Ketamine usually appears to increase IOP -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 22370|22380
        • -
      -
    -

    canonical nucleoside residues

    -
    -

    Text source name = 11604102.txt -

    12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) - stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA - [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understan -

      -
    • - residues -
        -
      • Mike Bada
        • -
      • class = canonical nucleoside residues
        • -
      • spans = 3906|3914
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    BMC Genomics. 2001; 2: 6. - PubMed ID: 11604102 - - Copyright © 2001 Dai et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and - redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along - with the article's original URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility factors - DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast two-hybrid system through its interaction - with a putative male infertility factor, DAZ (Deleted in Azoospermia). In vitro, DAZAP1 interacts with both the Y - chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding domains - (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the testis. To understand the - biological function of DAZAP1 and the significance of its interaction with DAZ and DAZL, we isolated and - characterized the mouse Dazap1 gene, and studied its expression and the subcellular localization of its protein - product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins share 98% identity and their sequences are highly similar to the Xenopus orthologue Prrp, - especially in the RBDs. Dazap1 is expressed throughout testis development. Western blot detects a single 45 kD - DAZAP1 protein that is most abundant in the testis. Although a majority of DAZAP1 is present in the cytoplasmic - fraction, they are not associated with polyribosomes. - - Conclusions - - DAZAP1 is evolutionarily highly conserved. Its predominant expression in testes suggests a role in spermatogenesis. - Its subcellular localization indicates that it is not directly involved in mRNA translation. - - Background - - Spermatogenesis is a complex developmental process in which male germ cells progress through mitotic proliferation, - meiotic division and dramatic morphological changes to form mature sperm. This process is vital for the propagation - of a species, and involves a large portion of the genome of an organism to ensure the quality and quantity of the - final products. It is estimated that mutations in up to 11% of all genes in Drosophila might lead to male sterility - [1]. This is likely to be true for humans also, considering the extremely high incidence (4–5%) of infertility in - men [2]. Among the genes associated with male infertility is the DAZ (Deleted in Azoospermia) gene family. The - family includes the Y-linked DAZ genes that are present only in great apes and old world monkeys [3], and the - autosomal DAZL1 (DAZ-like 1) and BOULE genes [4,5] in all mammals. Deletion of the DAZ genes is found in about 10% - of infertile males with idiopathic azoospermia [2], and disruption of Dazl1 causes infertility in both male and - female mice [6]. Mutations in the DAZ family members of Drosophila[7], C. elegans[8], and Xenopus[9] also affect the - fertility in either males, females, or both sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL are - expressed in the nucleus and cytoplasm of primordial germ cells and spermatogonia, and in the cytoplasm of meiotic - spermatocytes [6,10]. BOULE is expressed later, in the cytoplasm of pachytene spermatocytes [5]. Genetic and - biochemical studies suggest a role for the DAZ family in the regulation of mRNA translation. Drosophila Boule - mutants was defective in the translation of the meiosis-specific CDC25 homologue, Twine [11], and DAZL was found to - be associated with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast - three-hybrid system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich - segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechanisms of its action, we - used a yeast two-hybrid system to isolate two human genes encoding DAZ associated proteins (DAZAPs) [14]. One of - them, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA binding domains and a proline - rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to RNA - homopolymers. We now report our characterization of the mouse Dazap1 gene and its protein product. The subcellular - localization of DAZAP1 suggests that it is not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 cDNA - - Mouse Dazap1 cDNA clones were isolated by library screening, and the 5' end of the cDNA was isolated by 5' RACE - [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region (UTR), an open reading frame for a - protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession No: AF225910). The coding region shares - 89% similarity with that of the human orthologue. The 3' UTR sequence is remarkably conserved. It contains three - segments of 35 bp, 133 bp and 90 bp that share 85%, 90%, and 97% similarity with segments in the human 3' UTR, - respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline (Figure - 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 - substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with - Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. They share - 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore - have a similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved - (81% similarity and 71% identity). There is an insertion of a 58 bp segment in Prrp cDNA that causes a change of - reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s - and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and the - mouse sequences, and between the mouse and Xenopus sequences are marked by #'s and *'s, respectively. - - Genomic structure of Dazap1 and chromosomal mapping - - Several overlapping lambda clones containing mouse Dazap1 genomic sequences were isolated. The locations of exons - were determined by PCR amplification across exon-intron boundaries following by sequencing. All but the first exon - were isolated and mapped. The genomic structure of the human DAZAP1 gene was also determined by blasting the human - genome sequence at National Center for Biotechnology Information with the human DAZAP1 cDNA sequence. The mouse and - the human genes have very similar structures, consisting of 12 exons spanning about 28 kb. All intron insertion - sites are conserved (Table 1). The two RBDs are encoded by exons 1–4 and 5–8, respectively. - - Table 1 Exon-intron Organization of the Mouse and Human DAZAP1 genes - - A pair of PCR primers was designed from Dazap1 intronic sequences that amplified mouse but not hamster genomic - sequences. Using a panel of mouse-hamster radiation hybrids, the mouse Dazap1 gene was mapped to chromosome 10 - placed 27.84 cR from D10Mit260 (lod > 3.0) (data not shown). This region is syntenic to human 19p13.3 where the - human DAZAP1 gene is located [14,17]. It contains no known mutant alleles that are associated with infertility. - - Expression of Dazap1 - - Northern analyses of adult mouse tissues showed the presence of two Dazap1 transcripts of 1.75 kb and 2.4 kb, - respectively (Figure 2). Only the shorter transcript has been isolated in cDNA clones. Dazap1 was expressed most - abundantly in the testis, much less in liver, heart and brain, and even less in other tissues. This pattern of - expression is similar to that of the human DAZAP1 (14). RT-PCR analyses showed that Dazap1 mRNA was already present - in fetal testes at embryonic day 15, similar to Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 - persisted throughout testes development, in both the prenatal and postnatal periods. Dazl1 and Dazap1 transcripts - were also present in the testes of Wv/Wv mutant mice which contained diminished number of germ cells [18]. However, - only Dazap1 was expressed in a mouse germ cell line GCl-spg [19] and a Sertoli cell line MT4. The results suggest - that Dazap1 is expressed in both somatic and germ cells in the testis. - - Figure 2 Expression of Dazap1 in adult mouse tissues. A mouse multiple-tissue Northern blot was hybridized with a - Dazap1 cDNA probe, stripped, and rehybridized with a β-actin probe. Dazap1 is expressed most abundantly in the - testis. - - Figure 3 Developmental expression of Dazap1 and Dazl in mouse testes. RT-PCR was performed on total testicular RNAs - isolated from day 15 (El 5) and day 17 (El 7) embryos, new born mice (Day 0), and mice at various days after birth. - Wv/Wv testes contain diminished germ cell population due to a mutated W (White spotted) gene. GC1 and MT4 are mouse - germ cell and Sertoli cell lines, respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and - produce much larger (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C - antibody was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid residue at the C-terminus. - Both antibodies recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western - blotting of mouse tissue extracts detected a 45 kD protein that was present most abundantly in the testis, and to a - lesser degree in spleen, liver, lung and brain (Figure 4). The protein was also present in the ovary. The expression - of DAZAP1 during germ cell development paralleled that of DAZL (Figure 5). It is present at a low level in the - testes of 6 days old mice which contained only primitive type A spermatogonia. The expression of DAZAP1 increased - afterward, as the testes contained increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various tissue - extracts were applied to a 10% SDS-polyacrylamide gel and western blotted with the anti-DAZAP1-P antibody. - - Figure 5 Western blot analyses of the expression of DAZAP1 and DAZL in mouse testes during postnatal development. - - Subcellular localization of DAZAP1 - - Our previous fractionation of mouse testis extracts showed that most DAZL were present in the post mitochondrial - fraction, and some of them were associated with polyribosomes [12]. Similar analyses showed that a majority of - DAZAP1 in adult mouse testes was also present in the cytoplasmic fraction (data not shown). However, sucrose - gradient analyses of the post- mitochondria fraction showed that, unlike DAZL, DAZAP1 did not co-sediment with - polyribosomes (Figure 6). - - Figure 6 Sucrose gradient analyses shows that DAZAP1 is not associated with polyribosomes. The post-mitochondrial - supernatant of mouse testis extracts was analyzed on a 15–45% sucrose gradient. Sedimentation was from left to - right. The presence of DAZAP1 and DAZL in each fractions was analyzed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA translation is supported by lines of circumstantial evidence, including the association of DAZL - with polyribosomes [12]. The absence of DAZAP1 from polyribosomes indicates that it is not directly involved in - protein synthesis. This finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified - through their interaction with another polysomal-associated RNA-binding protein, the fragile X mental retardation - protein [21]. Both FXR1P and FXR2P are associated with the polyribosomes [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be defined. These proteins may act - together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be involved in the - transport of the mRNAs of the target genes of DAZL. Alternatively, DAZL and DAZAP1 may act antagonistically to - regulate the timing and the level of expression. Such an antagonistic interaction between two interacting - RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the - alternative splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability - of Nova-1 to activate exon selection in neurons is antagonized by a second RNA-binding protein, brPTB - (brain-enriched polypyrimidine tract-binding protein), which interacts with Nova-1 and inhibits its function [24]. - DAZAP1 could function in a similar manner by binding to DAZL and inhibiting its function. Comparing the phenotypes - of Dazl1 and Dazap1 single and double knock-out mice may provide some clues to the significance of their - interaction. Dazl1 knock-out mice have already been generated and studied [6]. The spermatogenic defect in the male - becomes apparent only after day 7 post partum when the germ cells are committing to meiosis (H. Cooke, personal - communication). The genomic structure of Dazap1, delineated here, should facilitate the generating of Dazap1 null - mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural substrates - have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and characterized [16]. - Prrp binds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient - for the migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its - proline-rich domain with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring - of Vg1 mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth factor-β family that is - required for generating dorsal mesoderm at the blastula stage of Xenopus embryogenesis [25]. Sequence conservation - between the RBDs of DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST - search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, and possibly DAZAP1, may help to identify - the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. Its - predominant expression in testes suggests a role in spermatogenesis. In mouse testes, DAZAP1 was found both in the - nuclei and in the cytoplasm. Its absence from polyribosomes indicates that it is not directly involved in mRNA - translation. - - Materials and methods - - Isolation of mouse Dazap1 cDNA clones - - Dazap1 cDNA clones were isolated from a mouse testis cDNA library (#937308, Stratagene, La Jolla, CA) using a human - DAZAP1 cDNA as a probe. The 5' end of the cDNA was isolated by 5' RACE [15], using prdap11 (ttgcgggccatatccttg, - #749–732) as the primer for cDNA synthesis from mouse testis RNA, and prdap37 (ttgttgccacgtgggcg, #734–718) and an - adaptor primer as the primers for PCR amplification. The PCR products were cloned into a TA cloning vector - pCR2.1-TOPO (Invitrogen, Carlsbad CA). Dazap1 clones were identified by colony hybridization and sequenced. The 5' - RACE clone with the longest 5' UTR region and the cDNA clone P21 were ligated together through a unique PmlI site at - # 722 to generate a cDNA clone (Dazap1-C) with a near full-length insert. - - Chromosomal mapping of Dazap1 - - Dazap1 genomic clones were isolated from a mouse 129SV genomic library (#946305, Stragagene), and sequences flanking - each exons were determined. PCR primers (prdap25: cacctccaggatgtgttagc and prdazp26:gtcaccaagggtgtctgaag) were - designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment from mouse but - not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse chromosome fragments in a - hamster background were purchased from Research Genetics (Huntsville, AL). The presence of mouse Dazap1 in the - radiation hybrids was determined by PCR and the results were sent to the MIT server for computerized physical - mapping of the gene. - - Expression of Dazap1 transcripts - - Northern hybridization was carried out according to standard procedures [26] using a mouse Multiple Tissue Northern - Blot #7762–1 from Clontech (Palo Alto, CA). The blot was hybridized sequentially with DAZAP1 and β-actin cDNA - probes, with stripping of the bound probes in between. - - Reverse transcription-polymerase chain reaction (RT-PCR) was carried out as preciously described using an annealing - temperature of 54°C [27]. The primers were prdap35: agctcagggagtacttcaaga and prdap24 :ggagcttgattcttgctgtcc for - Dazap1 which generated a product of 211 bp, and prdaz71: atcgaactggtgtgtcgaagg and prdaz72: ggaggctgcatgtaagtctca - for Dazl1 which generated a product of 245 bp. Both primer pairs annealed across intron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide synthesized in - vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 (starting from aa - #197), was cloned in-frame into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). - Sequences at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed - with Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antibody. An oligopeptide containing - the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the services of Bethyl - Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier and injected into a goat. The - anti-DAZAP1-P antibody thus produced was purified on an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM Tris, pH - 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by the - Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of tissue extracts were - separated on 10% SDS-polyacrylamide gels and blotted with either the anti-DAZAP1-C antibody (at a 1/2,000 dilution) - or the anti-DAZAP1-P antibody (at a 1/5,000 dilution). After incubation with horseradish peroxidase-conjugated - secondary antibodies, the binding of antibodies was detected using the ECL Western Blotting System (Amersham - Pharmacia Biotech, Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, - 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors provided in - the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, IN). Homogenates were centrifuged at 1,000 - × g for 10 minutes to pellet cell debris and nuclei. After an additional centrifugation at 10,000 × g for 10 minutes - to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose gradients in 20 mM Tris, 100 - mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml - were collected from the bottom of the tubes and analyzed by western blotting. - - Acknowledgments - - We thank Gary Kuo for his involvement in the construction of Dazap1 expression vectors, and Ron Swerdloff's group - for helpful discussion. The work was supported by grants from the National Institutes of Health (HD28009 and - HD36347). Y. Vera was supported by an NIH grant (GM56902) on Initiative for Minority Student Development. - - References - - 1. Hackstein JHP, Hochstenbach R, Pearson PL. Towards an understanding of the genetics of human male infertility.. - TIG. 2000;16:565-572. doi: 10.1016/S0168-9525(00)02140-5 - - 2. De Kretser DM. Male infertility.. Lancet. 1997;349:787-790. doi: 10.1016/S0140-6736(96)08341-9 - - 3. Reijo R, Lee T-Y, Salo P, Allagappan R, Brown LG, Rosenberg M, Rozen S, Jaffe T, Straus D, Hovatta O, de la - Chapelle A, Silber S, Page DC. Diverse spermatogenic defects in humans caused by Y chromosome deletions encompassing - a novel RNA-binding protein gene.. Nat Genet. 1995;10:383-393. doi: 10.1038/ng0895-383 - - 4. Cooke HJ, Lee M, Kerr S, Ruggiu M. A murine homologue of the human DAZ gene is autosomal and expressed only in - male and female gonads.. Hum Mol Genet. 1996;5:513-516. doi: 10.1093/hmg/5.4.513 - - 5. Xu EY, Moore FL, Pera RAR. A gene family required for human germ cell development evolved from an ancient meiotic - gene conserved in metazoans.. PNAS. 2001;98:7414-7419. doi: 10.1073/pnas.131090498 - - 6. Ruggiu M, Speed R, Taggart M, McKay SJ, Kilanowski F, Saunders P, Dorin J, Cooke HJ. The mouse DAZLA gene encodes - a cytoplasmic protein essential for gametogenesis.. Nature. 1997;389:73-77. doi: 10.1038/37987 - - 7. Eberhar CG, Maines JZ, Wasserman SA. Meiotic cell cycle requirement for a fly homologue of human Deleted in - Azoospermia.. Nature. 1996;381:783-785. doi: 10.1038/381783a0 - - 8. Karashima T, Sugimoto A, Yamamoto M. Caenorhabditis elegans homologue of the human azoospermia factor DAZ is - required for oogenesis but not for spermatogenesis.. Development. 2000;127:1069-1079. - - 9. Houston DW, Zhang J, Maines JZ, Wasserman SA, King ML. A Xenopus DAZ-like gene encodes an RNA component of germ - plasm and is a functional homologue of Drosophila boule.. Development. 1998;125:171-180. - - 10. Reijo RA, Dorfman DM, Slee R, Renshaw AA, Laughlin KR, Cooke H, Page DC. DAZ family proteins exist through male - germ cell development and transit from nucleus to cytoplasm at meiosis in humans and mice.. Biol Reprod. - 2000;63:1490-1496. - - 11. Maines JZ, Wasserman SA. Post-transcriptional regulation of the meiotic Cdc25 protein Twine by the Daz1 - orthologue Boule.. Nat Cell Biol. 1999;1:171-174. doi: 10.1038/11091 - - 12. Tsui S, Dai T, Warren ST, Salido EC, Yen PH. Association of the infertility factor DAZL1 with actively - translating polyribosomes.. Biol Reprod. 2000;62:1655-1660. - - 13. Venables JP, Ruggiu M, Cooke HJ. The RNA-binding specificity of the mouse Daz1 protein.. Nucl Acids Res. - 2001;29:2479-2483. doi: 10.1093/nar/29.12.2479 - - 14. Tsui S, Dai T, Roettger S, Schempp W, Salido EC, Yen PY. Identification of two novel proteins that interact with - germ-cell specific RNA-binding proteins DAZ and DAZL1.. Genomics. 2000;65:266-273. doi: 10.1006/geno.2000.6169 - - 15. Frohman MA, Dush MK, Martin GR. Rapid production of full-length cDNAs from rare transcripts: amplification using - a single gene-specific oligonucleotide primer.. PNAS. 1988;85:8998-9002. - - 16. Zhao W, Jiang C, Kroll TT, Huber PW. proline-rich protein binds to the localization element of Xenopus Vg1 mRNA - and to ligands involved in actin polymerization.. EMBO J. 2001;20:2315-2325. doi: 10.1093/emboj/20.9.2315 - - 17. DeBry RW, Seldin MF. Human/mouse homology relationships.. Genomics. 1996;33:337-351. doi: 10.1006/geno.1996.0209 - - 18. Fleischman RA. From white spots to stem cells: The role of the Kit receptor in mammalian development.. Trends - Genet. 1993;9:285-290. doi: 10.1016/0168-9525(93)90015-A - - 19. Hofmann MC, Narisawa S, Hess RA, Millan JL. Immortalization of germ cells and somatic testicular cells using the - SV40 large T antigen.. Exp Cell Res. 1992;201:417-435. doi: 90291-F - - 20. Siomi H, Dreyfuss G. RNA-binding proteins as regulators of geneexpression.. Cur Opin Genet Develop. - 1997;7:345-353. doi: 10.1016/S0959-437X(97)80148-7 - - 21. Zhang Y, O'Connor JP, Siomi MC, Srinivasan S, Dutra A, Nussbaum RL, Dreyfuss G. The fragile X mental retardation - syndrome protein interacts with novel homologs FXR1 and FXR2.. EMBO J. 1995;14:5358-5366. - - 22. Siomi MC, Zhang Y, Siomi H, Dreyfuss G. Specific sequences in the fragile X syndrome protein FMR1 and the FXR2 - proteins mediate their binding to 60S ribosomal subunits and the interactions among them.. Mol Cell Biol. - 1996;16:3825-3832. - - 23. Jensen KB, Dredge BK, Stefani G, Zhong R, Buckanovich RJ, Okano HJ, Yang YY, Darnell RB. Nova-1 regulates - neuron-specific alternative splicing and is essential for neuronal viability.. Neuron. 2000;25:359-371. doi: - 10.1016/S0896-6273(00)80900-9 - - 24. Polydorides AD, Okano HJ, Yang YY, Stefani G, Darnell RB. A brain-enriched polypyrimidine tract-binding protein - antagonizes the ability of Nova to regulate neuron-specific alternative splicing.. PNAS. 2000;97:6350-6355. doi: - 10.1073/pnas.110128397 - - 25. Thomson GH, Melton DA. Processed Vg1 protein is an axial mesoderm inducer in Xenopus.. Cell. 1993;74:433-441. - doi: 10.1016/0092-8674(93)80045-G - - 26. Sambrook J, Fritsch EF, Maniatis T. null. Molecular Cloning: A Laboratory Manual 2nd ed, Cold Spring Harbor - Laboratory Press, Cold Spring Harbor,. 1989;null:null-null. - - 27. Salido EC, Yen PH, Mohandas TK, Shapiro LJ. Expression of the X-inactivation-associated gene XIST during - spermatogenesis.. Nat Genet. 1992;2:196-199. doi: 10.1038/ng1192-196 - - -

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    ins. Most tested strains exhibit a diurnal rhythm with IOP being the highest during the dark period of the day. - Homozygosity for a null allele of the carbonic anhydrase II gene (Car2n) does not alter IOP while - homozygosity for a mutation in the leptin receptor gene (Leprdb) that causes obesity and diabetes -

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    evant to glaucoma. - - Car2 deficiency does not alter IOP - - Bicarbonate formation is important for aqueous humor secretion from the ciliary processes and carbonic - anhydrase (CA) facilitates this secretion. There are multiple forms of CA and the CAII isoform is reported to be the - predominant form in the ciliary -

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    rified and sequenced as described [22]. - - Abbreviations - - Intraocular pressure (IOP), C57BL/6J (B6), chromosome (Chr), polymerase chain reaction (PCR), carbonic - anhydrase (CA) - - Acknowledgments - - We thank Norma Buckley, Felicia Farley and Jennifer Smith for their assistance with data entry, references, and figu -

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    ± SD; db/db 422 ± 110 mg/dl ; db/+ 147 ± 19 mg/dl; Anthony Nicholson, The Jackson Laboratory, personal communication) - - Car2 - - To test if deficiency of carbonic anhydrase II leads to decreased IOP, we analyzed mice of a B6 background - that were genetically similar but with normal or mutant alleles of the Car2 -

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    nst both a recombinant protein produced in E. coli and an oligopeptide synthesized in vitro. The insert of a Dazap1 - cDNA clone P21, which encoded the C-terminal portion of DAZAP1 (starting from aa #197), was cloned in-frame - into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, W -

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    e C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an oligopeptide containing the - last 19 amino acid residue at the C-terminus. Both antibodies recognized in vitro synthesized DAZAP1 in an - immunoprecipitation assay (data not shown). Western blotting of mouse tissue e -

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    oteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA - binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL - in vitro. It also bound to RNA homopolymers. We now report our characterizatio -

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    -
    -

    Text source name = 11604102.txt -

    AZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody was raised against a - recombinant protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised - against an oligopeptide containing the last 19 amino acid residue at the C-t -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 9713|9714
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    identity). There is an insertion of a 58 bp segment in Prrp cDNA that causes a change of reading frame and results in - a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s - and the Xe -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 6184|6185
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore have a - similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved - (81% similarity and 71% identity). There is an insertion of a 58 bp segment in P -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 5939|5940
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti - DAZAP1-C antibody was raised against a recombinant protein containing the C-terminal proline-rich portion, - and the anti DAZAP1-P antibody was raised against a -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 9646|9647
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    system (Bio-Rad, Hercules, CA). About 50 μg of tissue extracts were separated on 10% SDS-polyacrylamide gels and - blotted with either the anti-DAZAP1-C antibody (at a 1/2,000 dilution) or the anti-DAZAP1-P antibody (at a - 1/5,000 dilution). After incubation with horseradish peroxidase-conjugated secon -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 19406|19407
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    h both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding - domains (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the testis. To - understand the biological function of DAZAP1 and the significance of its interac -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 890|891
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    he human 3' UTR, respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 5388|5389
        • -
      -
    -

    cytidyl groups

    -
    -

    Text source name = 11604102.txt -

    [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = cytidyl groups
        • -
      • spans = 3904|3905
        • -
      -
    -

    cytosin-1-yl group

    -
    -

    Text source name = 11604102.txt -

    [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = cytosin-1-yl group
        • -
      • spans = 3904|3905
        • -
      -
    -

    deoxyribonucleic acids

    -
    -

    Text source name = 11532192.txt -

    d as they contain most ocular structures. - - Analysis of Myoc - - Exons and the proximal promoter of the mouse Myoc gene were amplified from mouse genomic DNA using the - following combinations of primers: - - Exon 1: 5'-cttgcaggagaactttccagaa-3' and 5'-atctcgaaggagattgttatagg-3' - - 5'-gaccagctggagacccaaaccag-3' a -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 38583|38586
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 38583|38586
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    ure was .81 (P < .05), which is similar to the reliability seen in previous estimates of neuron number [39, 40]. - - Genotyping and QTL Mapping - - Genomic DNA was extracted from spleens of F2 animals using a high-salt procedure [63]. A set of 82 - microsatellite loci distributed across all autosomes and the X -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 30232|30235
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 30232|30235
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    al forebrain [27, 50]. - - Brain volume and neuron number - - It has previously been shown that differences in brain weight are proportional to total brain DNA content and - consequently to total CNS cell number [51, 52]. For this reason, brain weight has been suggested to be a good - surrogate measure for total -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 22890|22893
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 22890|22893
        • -
      -
    -

    double-stranded DNA

    -

    drug

    -
    -

    Text source name = 11532192.txt -

    ng this period in any analyzed strain. Environmental differences may be important. Cage cleanliness, changing - frequency and housing density can alter drug metabolism and the effect of anesthesia in rats [38,39]. The - type of bedding used also may be important. We use wood shavings for bedding and wood sh -

      -
    • - drug -
        -
      • Mike Bada
        • -
      • class = drug
        • -
      • spans = 25369|25373
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    vings for bedding and wood shavings expose the mice to terpenes. Terpene administration or environmental exposure to - terpenes in wood shavings alters drug resistance and decreases the effect of anesthetic agents in both rats - and mice [40-45]. - - Risk factors for increased IOP - - Some epidemiological studies -

      -
    • - drug -
        -
      • Mike Bada
        • -
      • class = drug
        • -
      • spans = 25644|25648
        • -
      -
    -

    glutamate residue

    -

    glutamate(1-)

    -
    -

    Text source name = 11319941.txt -

    l portion of Chr 10 in proximity with a number of genes known to affect brain development. One of these is Grk2, a - member of the family of ionotropic glutamate receptor genes that is thought to play a role in modulating - Huntington disease [44]. In the mouse, members of this receptor type act to indirectly do -

      -
    • - glutamate -
        -
      • Mike Bada
        • -
      • class = glutamate(1-)
        • -
      • spans = 21235|21244
        • -
      -
    • - glutamate -
        -
      • Kristin Garcia
        • -
      • class = glutamate residue
        • -
      • spans = 21235|21244
        • -
      -
    -

    glutamate(2-)

    -
    -

    Text source name = 11319941.txt -

    l portion of Chr 10 in proximity with a number of genes known to affect brain development. One of these is Grk2, a - member of the family of ionotropic glutamate receptor genes that is thought to play a role in modulating - Huntington disease [44]. In the mouse, members of this receptor type act to indirectly do -

      -
    • - glutamate -
        -
      • Mike Bada
        • -
      • class = glutamate(2-)
        • -
      • spans = 21235|21244
        • -
      -
    • - glutamate -
        -
      • Kristin Garcia
        • -
      • class = glutamate residue
        • -
      • spans = 21235|21244
        • -
      -
    -

    glycine

    -

    guanine group

    -
    -

    Text source name = 11604102.txt -

    should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanine group
        • -
      • spans = 14030|14031
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    estes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family an -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanine group
        • -
      • spans = 3899|3900
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    sertion allele. The other allele was identical to the published sequence [22]. The insertion allele also had a - previously reported substitution (A to G, Thr164Ala) in exon 1 and several other single base changes in the - promoter region [22]. The presence or absence of this allele does not associate wi -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanine group
        • -
      • spans = 16993|16994
        • -
      -
    -

    guanosyl groups

    -
    -

    Text source name = 11604102.txt -

    estes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family an -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanosyl groups
        • -
      • spans = 3899|3900
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanosyl groups
        • -
      • spans = 14030|14031
        • -
      -
    -

    histidine

    -

    hydrogencarbonate

    -

    inhibitor

    -
    -

    Text source name = 11597317.txt -

    ptide consisting of one of the eight BRC repeats from human BRCA2. Expression of a single BRC repeat (BRC4) had - previously been reported to act as an inhibitor of DNA repair by Chen et al [27]. These investigators showed - that expression of constructs containing the BRC4 repeat in MCF-7 cells enhances the rad -

      -
    • - inhibitor -
        -
      • Mike Bada
        • -
      • class = inhibitor
        • -
      • spans = 7572|7581
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    cts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, - 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, -

      -
    • - inhibitor -
        -
      • Mike Bada
        • -
      • class = inhibitor
        • -
      • spans = 19887|19896
        • -
      -
    -

    magnesium dichloride

    -

    messenger RNA

    -

    metal cations

    -
    -

    Text source name = 11604102.txt -

    at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were - prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with - Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antib -

      -
    • - metal -
        -
      • Mike Bada
        • -
      • class = metal cations
        • -
      • spans = 18346|18351
        • -
      -
    • - metal -
        -
      • Kristin Garcia
        • -
      • class = metals
        • -
      • spans = 18346|18351
        • -
      -
    -

    metals

    -

    molecular entities

    -
    -

    Text source name = 11532192.txt -

    hese risk factors. - - IOP is increased during the dark period of the day - - Diurnal variation in IOP is common in humans and laboratory animals [53]. The molecular mechanisms underlying - the diurnal rhythm are not defined but increased aqueous humor production or flow occurs during the period of - increased IOP in -

      -
    • - molecular -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 29448|29457
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    d Not genes. Vax1 is localized during development to the anterior ventral forebrain, and is expressed in the striatum - during embryogenesis [28]. This molecule also has an important role in axon guidance: both the anterior - portion of the corpus callosum and the optic chiasm are malformed or absent in Vax1 kn -

      -
    • - molecule -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 22409|22417
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    rior portion of the corpus callosum and the optic chiasm are malformed or absent in Vax1 knockout mice [49]. In - addition, Vax1 interacts with several molecules including sonic hedgehog,Pax2, Pax6, and Rx that are known to - be important during development of the basal forebrain [27, 50]. - - Brain volume and neur -

      -
    • - molecules -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 22626|22635
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    accurate and rapid enough to allow large scale genetic studies of factors determining IOP. Mice have great potential - for helping to characterize the molecular mechanisms affecting IOP. - - Materials and Methods - - Animal husbandry - - All experiments were performed in compliance with the ARVO statement for use of a -

      -
    • - molecular -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 34211|34220
        • -
      -
    -

    nucleotidyl groups

    -
    -

    Text source name = 11532192.txt -

    OP in mouse strains, we analyzed the gene in an assortment of strains with different IOPs. Two alleles were - identified. One of these alleles had a 12 nucleotide insertion in the promoter region (ccagagcagggt, between - positions -340 and -341) compared to the previously published sequence and is called the inse -

      -
    • - nucleotide -
        -
      • Mike Bada
        • -
      • class = nucleotidyl groups
        • -
      • spans = 16685|16695
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ral substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization - element (VLE) is sufficient for the migration and clustering of Vg1 mRNA to the veg -

      -
    • - nt -
        -
      • Mike Bada
        • -
      • class = nucleotidyl groups
        • -
      • spans = 14191|14193
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    etween the RBDs of DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST - search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, an -

      -
    • - nt -
        -
      • Mike Bada
        • -
      • class = nucleotidyl groups
        • -
      • spans = 14903|14905
        • -
      -
    -

    oligopeptides

    -

    peptides

    -

    phosphate(3-)

    -
    -

    Text source name = 11532192.txt -

    ormalin fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 M phosphate buffer. All strains other than CBA/CaHN and C57BLKS/J - strains were evaluated. The eyes of CBA/CaJ and BALB/cJ mice were also fixed and processed for -

      -
    • - phosphate -
        -
      • Mike Bada
        • -
      • class = phosphate(3-)
        • -
      • spans = 38088|38097
        • -
      -
    • - phosphate -
        -
      • Kristin Garcia
        • -
      • class = phosphates
        • -
      • spans = 38088|38097
        • -
      -
    -

    phosphates

    -

    pigment

    -
    -

    Text source name = 11532192.txt -

    nt with this result, mice with albino eyes that are homozygous for tyrosinase or pink eye dilution mutations have - altered diurnal rhythms compared to pigmented mice [75]. Albinism by itself is either not sufficient to alter - the diurnal rhythm of IOP or alters it in different ways depending upon genetic backg -

      -
    • - pigmented -
        -
      • Mike Bada
        • -
      • class = pigment
        • -
      • spans = 33044|33053
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    these abnormalities affect mammalian IOP. Here, we show increased IOP in mice lacking tyrosinase activity compared to - otherwise genetically identical pigmented B6 mice. Additionally, IOP differences between the light and dark - period of the day were detected in the pigmented but not the albino B6 mice. Thus, -

      -
    • - pigmented -
        -
      • Mike Bada
        • -
      • class = pigment
        • -
      • spans = 32669|32678
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    to otherwise genetically identical pigmented B6 mice. Additionally, IOP differences between the light and dark period - of the day were detected in the pigmented but not the albino B6 mice. Thus, albinism can affect the diurnal - pattern of IOP changes. In agreement with this result, mice with albino eyes that a -

      -
    • - pigmented -
        -
      • Mike Bada
        • -
      • class = pigment
        • -
      • spans = 32784|32793
        • -
      -
    -

    potassium chloride

    -

    proline

    -

    proline residue

    -
    -

    Text source name = 11604102.txt -

    tion element (VLE) is sufficient for the migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. - Prrp also interacts through its proline-rich domain with two microfilament-associated proteins profilin and - Mena, which may facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The V -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 14405|14412
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 14405|14412
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two - RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the - testis. To understand the biological function of DAZAP1 and the significance of its -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 877|884
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 877|884
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    e segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, - with 7 substitutions and two deleti -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5423|5430
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5423|5430
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA - binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% - similarity and 71% identity). There is an insertion of a 58 bp segment in Prrp cDNA that cau -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5950|5957
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5950|5957
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    in, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody was raised against a recombinant - protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both ant -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 9724|9731
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 9724|9731
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    o acids only, with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% - identity with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly - conserved. They share 98% and 97% similarity and 97% and 92% identity, respectivel -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5681|5688
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5681|5688
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in testes. It encodes a protein - with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both - DAZ and DAZL in vitro. It also bound to RNA homopolymers. We now report our characte -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 4323|4330
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 4323|4330
        • -
      -
    -

    protease inhibitor

    -

    proteins

    -
    -

    Text source name = 11604102.txt -

    in interacted with both DAZ and DAZL in vitro. It also bound to RNA homopolymers. We now report our characterization - of the mouse Dazap1 gene and its protein product. The subcellular localization of DAZAP1 suggests that it is - not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 -

      -
    • - protein product -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 4522|4537
        • -
      -
    -

    ribonucleic acids

    -

    single-stranded DNA

    -

    sodium chloride

    -

    sodium dodecyl sulfate

    -

    sodium phosphates

    -

    sucrose

    -

    terpenes

    -

    tert-pentyl group

    -

    tris

    -

    uracil-1-yl group

    -
    -

    Text source name = 11604102.txt -

    eated here, should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uracil-1-yl group
        • -
      • spans = 14019|14020
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid - system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich segment - in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the funct -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uracil-1-yl group
        • -
      • spans = 3870|3871
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) stretches interspersed - by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechan -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uracil-1-yl group
        • -
      • spans = 3928|3929
        • -
      -
    -

    uridyl groups

    -
    -

    Text source name = 11604102.txt -

    eated here, should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uridyl groups
        • -
      • spans = 14019|14020
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) stretches interspersed - by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechan -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uridyl groups
        • -
      • spans = 3928|3929
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid - system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich segment - in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the funct -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uridyl groups
        • -
      • spans = 3870|3871
        • -
      -
    -

    water

    -
    -

    Text source name = 11532192.txt -

    ariation in IOP is common in humans and laboratory animals [53]. The molecular mechanisms underlying the diurnal - rhythm are not defined but increased aqueous humor production or flow occurs during the period of increased - IOP in both rabbits and humans [63-65]. Small changes in the resistance to aqueous hum -

      -
    • - aqueous -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 29529|29536
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    important approaches as they may allow the association of genes with IOP and glaucoma whose currently known functions - do not suggest that they affect aqueous humor dynamics or do not immediately identify them as likely glaucoma - candidates. - - No effect of anesthetic protocol on IOP during a 12 minute measure -

      -
    • - aqueous -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 22266|22273
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    sed aqueous humor production or flow occurs during the period of increased IOP in both rabbits and humans [63-65]. - Small changes in the resistance to aqueous humor drainage may also contribute to diurnal differences in IOP - [66,67]. We first suspected IOP changes with time of day when the IOP of a group of -

      -
    • - aqueous -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 29675|29682
        • -
      -
    +Each concept that was considered a non-match is shown in the text that it was found in. Overlapping annotations from the other concept sets are also shown. +
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:14321
      • spanCollection = on on gen [21235, 21244]
    • +
      • Kristin Garcia
      • class = CHEBI:32484
      • spanCollection = on on gen [21235, 21244]
    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = es [38583, 38586]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = es [38583, 38586]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ral [22890, 22893]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ral [22890, 22893]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = rie [30232, 30235]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = rie [30232, 30235]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:18367
      • spanCollection = he anteri [38088, 38097]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26020
      • spanCollection = he anteri [38088, 38097]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:23525
      • spanCollection = p [3904, 3905]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:23526
      • spanCollection = p [3904, 3905]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:23888
      • spanCollection = alyz [25644, 25648]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:23888
      • spanCollection = e ra [25369, 25373]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:24459
      • spanCollection = T [14030, 14031]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:24459
      • spanCollection = e [3899, 3900]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:24460
      • spanCollection = T [14030, 14031]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:24460
      • spanCollection = e [3899, 3900]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:26130
      • spanCollection = e number [32784, 32793]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:26130
      • spanCollection = pathway. [32669, 32678]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:26130
      • spanCollection = ise genet [33044, 33053]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:27243
      • spanCollection = i [14019, 14020]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:27243
      • spanCollection = d [3928, 3929]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:27243
      • spanCollection = o [3870, 3871]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:27244
      • spanCollection = d [3928, 3929]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:27244
      • spanCollection = i [14019, 14020]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:27244
      • spanCollection = o [3870, 3871]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:29987
      • spanCollection = on on gen [21235, 21244]
    • +
      • Kristin Garcia
      • class = CHEBI:32484
      • spanCollection = on on gen [21235, 21244]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30755
      • spanCollection = T [14030, 14031]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30755
      • spanCollection = f [16993, 16994]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30755
      • spanCollection = e [3899, 3900]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30756
      • spanCollection = e [16988, 16989]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30758
      • spanCollection = p [3904, 3905]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30759
      • spanCollection = i [14019, 14020]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30759
      • spanCollection = d [3928, 3929]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30759
      • spanCollection = o [3870, 3871]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32441
      • spanCollection = sgenic [21540, 21547]
    • +
      • Kristin Garcia
      • class = CHEBI:16449
      • spanCollection = sgenic [21540, 21547]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = the tra [14405, 14412]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = the tra [14405, 14412]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nthesiz [9724, 9731]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nthesiz [9724, 9731]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = y and 9 [5423, 5430]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = y and 9 [5423, 5430]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = inserti [5681, 5688]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = inserti [5681, 5688]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = Dazap1 [4323, 4330]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = Dazap1 [4323, 4330]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nomic s [877, 884]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nomic s [877, 884]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = and the [5950, 5957]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = and the [5950, 5957]
    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33791
      • spanCollection = otein wi [3906, 3914]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:35222
      • spanCollection = trifuged [19887, 19896]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:35222
      • spanCollection = tivity of [7572, 7581]
    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = be important. Ca [25688, 25705]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = s doses of [14779, 14789]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = he effects [13227, 13237]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = sed IOP du [14394, 14404]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = ask geneti [23386, 23396]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = able infor [22370, 22380]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = A/2J, P = [14237, 14247]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = y anesthet [22840, 22850]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = -33], but [22934, 22944]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = producibility als [22441, 22458]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = n [19406, 19407]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = s [5939, 5940]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = r [18031, 18032]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = c [4336, 4337]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = i [9713, 9714]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = t [9861, 9862]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = r [890, 891]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = f [6184, 6185]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = 9 [9646, 9647]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:46883
      • spanCollection = d [5388, 5389]
    +

    +

    +

    CHEBI_15377

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = chromos [22266, 22273]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = is work [29529, 29536]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = he sepa [29675, 29682]
    +

    CHEBI_16670

    +

    CHEBI_17544

    +

    CHEBI_17992

    +

    CHEBI_23367

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_23367
      • spanCollection = al associ [29448, 29457]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_23367
      • spanCollection = d protei [22409, 22417]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_23367
      • spanCollection = mber of g [22626, 22635]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_23367
      • spanCollection = n differe [34211, 34220]
    +

    CHEBI_25213

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25213
      • spanCollection = ng th [18346, 18351]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33521
      • spanCollection = ng th [18346, 18351]
    +

    CHEBI_25613

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25613
      • spanCollection = J, C57BL/6 [16685, 16695]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25613
      • spanCollection = rp [14191, 14193]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25613
      • spanCollection = de [14903, 14905]
    +

    CHEBI_25676

    +

    CHEBI_26020

    +

    CHEBI_26710

    +

    CHEBI_27594

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_27594
      • spanCollection = t have a [1189, 1197]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_27594
      • spanCollection = tctgagga [39453, 39461]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_27594
      • spanCollection = aocular [31345, 31353]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_27594
      • spanCollection = e 28 to [19152, 19160]
    +

    CHEBI_30879

    +

    CHEBI_32588

    +

    CHEBI_33521

    +

    CHEBI_33708

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = to a goat. The ant [18545, 18563]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = p1 genomic [6273, 6283]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = p1 genomic [6273, 6283]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = imilar RNA [5527, 5538]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = imilar RNA [5527, 5538]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = served amon [1344, 1355]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = served amon [1344, 1355]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = tected a 45 kD pro [9835, 9853]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = tected a 4 [9835, 9845]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = (BRCA2+) h [4797, 4807]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = (BRCA2+) h [4797, 4807]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = tory elements. + +The [4931, 4950]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = tory eleme [4931, 4941]
    +

    CHEBI_33709

    +

    CHEBI_35186

    +

    CHEBI_36080

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ading frame for [4522, 4537]
    +

    CHEBI_37586

    +

    CHEBI_6636

    +

    CHEBI_8984

    +

    CHEBI_9754

    diff --git a/src/test/resources/iaa_test_project/iaa/Span matcher.html b/src/test/resources/iaa_test_project/iaa/Span matcher.html index b823050a..58ce1e51 100644 --- a/src/test/resources/iaa_test_project/iaa/Span matcher.html +++ b/src/test/resources/iaa_test_project/iaa/Span matcher.html @@ -2,502 +2,235 @@ Span matcher

    Span matcher

    -Annotations match if they have the same spans. For more detailed documentation on IAA please see the IAA documentation. +Annotations match if they have the same spans. For more detailed documentation on Iaa please see the Iaa documentation. -

    2-way IAA Results

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +

    2-way Iaa Results

    +
    TypeIAAmatchesnon-matchesconfused class assignments -
    All classes84.03%38473
    5'-cytidylyl group0.00%01 -
    5'-guanylyl group0.00%02 -
    5'-uridylyl group0.00%03 -
    acid100.00%20 - acid=2 -
    adenine group0.00%01 -
    alanine100.00%10 - alanine residue=1 -
    alanine residue100.00%10 - alanine=1 -
    alcohols100.00%40 - alcohols=4 -
    amino acids66.67%42 - amino-acid residues=4 -
    amino-acid residues57.14%43 - amino acids=4 -
    anaesthetic16.67%210 - anaesthetic=2 -
    canonical nucleoside residues0.00%02 -
    carbon0.00%04 -
    carboxy group0.00%010 -
    cytidyl groups0.00%01 -
    cytosin-1-yl group0.00%01 -
    deoxyribonucleic acids100.00%570 - double-stranded DNA=3 - deoxyribonucleic acids=54 -
    double-stranded DNA92.86%131 - double-stranded DNA=10 - deoxyribonucleic acids=3 -
    drug0.00%02 -
    glutamate residue100.00%10 - glutamate(2-)=1 -
    glutamate(1-)0.00%01 -
    glutamate(2-)100.00%10 - glutamate residue=1 -
    glycine100.00%20 - glycine=2 -
    guanine group0.00%03 -
    guanosyl groups0.00%02 -
    histidine100.00%20 - histidine=2 -
    hydrogencarbonate100.00%20 - hydrogencarbonate=2 -
    inhibitor0.00%02 -
    magnesium dichloride100.00%40 - magnesium dichloride=4 -
    messenger RNA100.00%300 - messenger RNA=30 -
    metal cations100.00%10 - metals=1 -
    metals100.00%10 - metal cations=1 -
    molecular entities0.00%04 -
    nucleotidyl groups0.00%03 -
    oligopeptides100.00%80 - oligopeptides=8 -
    peptides100.00%100 - peptides=10 -
    phosphate(3-)100.00%10 - phosphates=1 -
    phosphates100.00%10 - phosphate(3-)=1 -
    pigment0.00%03 -
    potassium chloride100.00%40 - potassium chloride=4 -
    proline100.00%70 - proline residue=7 -
    proline residue100.00%70 - proline=7 -
    protease inhibitor100.00%40 - protease inhibitor=4 -
    proteins97.52%1183 - proteins=118 -
    ribonucleic acids100.00%460 - ribonucleic acids=46 -
    single-stranded DNA100.00%120 - single-stranded DNA=12 -
    sodium chloride100.00%20 - sodium chloride=2 -
    sodium dodecyl sulfate100.00%40 - sodium dodecyl sulfate=4 -
    sodium phosphates100.00%20 - sodium phosphates=2 -
    sucrose100.00%80 - sucrose=8 -
    terpenes100.00%60 - terpenes=6 -
    tert-pentyl group100.00%20 - tert-pentyl group=2 -
    tris100.00%60 - tris=6 -
    uracil-1-yl group0.00%03 -
    uridyl groups0.00%03 -
    water57.14%43 - water=4 -
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    TypeIaamatchesnon-matchesconfused class assignments
    All classes84.21%38472
    CHEBI:1432100.00%10 + CHEBI:3248=1 +
    CHEBI:1542100.00%20 + CHEBI:1542=2 +
    CHEBI:1644100.00%10 + CHEBI:3244=1 +
    CHEBI:1699100.00%570 + CHEBI:1699=54 + CHEBI:470=3 +
    CHEBI:1836100.00%10 + CHEBI_26020=1 +
    CHEBI:23520.00%01 +
    CHEBI:23520.00%01 +
    CHEBI:23880.00%02 +
    CHEBI:24450.00%02 +
    CHEBI:24460.00%02 +
    CHEBI:26130.00%03 +
    CHEBI:2627100.00%70 + CHEBI:3287=7 +
    CHEBI:27240.00%03 +
    CHEBI:27240.00%03 +
    CHEBI:2757100.00%20 + CHEBI:2757=2 +
    CHEBI:29980.00%01 +
    CHEBI:3036100.00%20 + CHEBI:3036=2 +
    CHEBI:30750.00%03 +
    CHEBI:30750.00%01 +
    CHEBI:30750.00%01 +
    CHEBI:30750.00%03 +
    CHEBI:3244100.00%10 + CHEBI:1644=1 +
    CHEBI:3248100.00%10 + CHEBI:1432=1 +
    CHEBI:3287100.00%70 + CHEBI:2627=7 +
    CHEBI:3369100.00%460 + CHEBI:3369=46 +
    CHEBI:3369100.00%300 + CHEBI:3369=30 +
    CHEBI:33790.00%01 +
    CHEBI:35220.00%02 +
    CHEBI:3752100.00%20 + CHEBI:3752=2 +
    CHEBI:3767100.00%40 + CHEBI:3767=4 +
    CHEBI:388616.67%210 + CHEBI:3886=2 +
    CHEBI:46880.00%010 +
    CHEBI:47092.86%131 + CHEBI:1699=3 + CHEBI:470=10 +
    CHEBI:916100.00%120 + CHEBI:916=12 +
    CHEBI_1537757.14%43 + CHEBI_15377=4 +
    CHEBI_16670100.00%100 + CHEBI_16670=10 +
    CHEBI_17544100.00%20 + CHEBI_17544=2 +
    CHEBI_17992100.00%80 + CHEBI_17992=8 +
    CHEBI_233670.00%04 +
    CHEBI_25213100.00%10 + CHEBI_33521=1 +
    CHEBI_256130.00%03 +
    CHEBI_25676100.00%80 + CHEBI_25676=8 +
    CHEBI_26020100.00%10 + CHEBI:1836=1 +
    CHEBI_26710100.00%20 + CHEBI_26710=2 +
    CHEBI_275940.00%04 +
    CHEBI_30879100.00%40 + CHEBI_30879=4 +
    CHEBI_32588100.00%40 + CHEBI_32588=4 +
    CHEBI_33521100.00%10 + CHEBI_25213=1 +
    CHEBI_3370857.14%43 + CHEBI_33709=4 +
    CHEBI_3370966.67%42 + CHEBI_33708=4 +
    CHEBI_35186100.00%60 + CHEBI_35186=6 +
    CHEBI_3608097.52%1183 + CHEBI_36080=118 +
    CHEBI_37586100.00%20 + CHEBI_37586=2 +
    CHEBI_6636100.00%40 + CHEBI_6636=4 +
    CHEBI_8984100.00%40 + CHEBI_8984=4 +
    CHEBI_9754100.00%60 + CHEBI_9754=6 +
    -
    IAA calculated on 4 documents. +
    Iaa calculated on 4 documents.
    all annotations = matches + non-matches -
    IAA = matches / all annotations +
    Iaa = matches / all annotations

    match data

    -
    +
  • matches for Mike Bada
    • +
  • matches for Kristin Garcia
    • +

    non-match data

    -
    +
  • non-matches for Mike Bada
    • +
  • non-matches for Kristin Garcia
    • +

    Pair-wise agreement

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
    Gold standard setcompared settrue positivesfalse positivesfalse negativesprecisionrecallF-score
    Kristin GarciaMike Bada19269473.56%97.96%84.03%
    Mike BadaKristin Garcia19246997.96%73.56%84.03%
    + +
    Gold standard setcompared settrue positivesfalse positivesfalse negativesprecisionrecallF-score
    Mike BadaKristin Garcia19246897.96%73.85%84.21%
    Kristin GarciaMike Bada19268473.85%97.96%84.21%
    Precision and recall are given equal weight for the F-score. diff --git a/src/test/resources/iaa_test_project/iaa/Span matcher.matches.Kristin Garcia.html b/src/test/resources/iaa_test_project/iaa/Span matcher.matches.Kristin Garcia.html index 7c0a7b7f..0d129d43 100644 --- a/src/test/resources/iaa_test_project/iaa/Span matcher.matches.Kristin Garcia.html +++ b/src/test/resources/iaa_test_project/iaa/Span matcher.matches.Kristin Garcia.html @@ -2,4339 +2,847 @@ Matches for Kristin Garcia

    Matches for Kristin Garcia

    -Each annotation that was considered a match is shown in the text that it was found in. The matching annotations from the -other annotation sets are also shown. For more detailed documentation on IAA please see the IAA documentation. - -

    5'-cytidylyl group

    -

    5'-guanylyl group

    -

    5'-uridylyl group

    -

    acid

    -
    -

    Text source name = 11532192.txt -

    e at the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered w -

      -
    • - acid -
        -
      • Kristin Garcia
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    • - acid -
        -
      • Mike Bada
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    -

    adenine group

    -

    alanine

    -
    -

    Text source name = 11319941.txt -

    y down-regulate synaptic activity in the striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the - gene encoding the myristoylated alanine-rich C kinase substrate (MARCKS protein). This molecule is important - in cerebral development. MARCKS-deficient mice have a high incidence of exenceph -

      -
    • - alanine -
        -
      • Kristin Garcia
        • -
      • class = alanine
        • -
      • spans = 21540|21547
        • -
      -
    • - alanine -
        -
      • Mike Bada
        • -
      • class = alanine residue
        • -
      • spans = 21540|21547
        • -
      -
    -

    alanine residue

    -

    alcohols

    -
    -

    Text source name = 11319941.txt -

    al images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% glutarald -

      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 -

      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    -

    amino acids

    -
    -

    Text source name = 11604102.txt -

    reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 6273|6283
        • -
      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 6273|6283
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    BDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved evolutionarily. The mouse - and the human proteins differ in 9 amino acids only, with 7 substitutions and two deletions/insertions. The - mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for proline -

      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 5527|5538
        • -
      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 5527|5538
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    bination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of BRCA2 on one homolog and - codes for a protein truncated at amino acid 1981 on the other homolog. The authors indicate that the level of - I-SceI-induced recombination in CAPAN-1 is over 100-fold less than that seen using -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 4797|4807
        • -
      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 4797|4807
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements [5,6]. The - sequence of this large protein (3418 amino acids) offers very little clue to its function, although there are - eight repeated segments (termed BRC repeats) in the middle of the protein that are highl -

      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 1344|1355
        • -
      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 1344|1355
        • -
      -
    -

    amino-acid residues

    -

    anaesthetic

    -
    -

    Text source name = 11532192.txt -

    parate group of the same age. - - Anesthesia protocol avoids IOP alteration and allows detection of diurnal differences - - All IOPs were assessed using an anesthetic regime of 99 mg/kg ketamine and 9 mg/kg xylazine (defined as 1X). - Initial experiments suggested that an almost identical dose (100 mg/kg ketamine and -

      -
    • - anesthetic -
        -
      • Kristin Garcia
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    -

    canonical nucleoside residues

    -

    carbon

    -

    carboxy group

    -

    cytidyl groups

    -

    cytosin-1-yl group

    -

    deoxyribonucleic acids

    -
    -

    Text source name = 11597317.txt -

    1 and BRCA2 are involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during - the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of repair of - spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either B -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    clear foci during the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of - repair of spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either BRCA1 or BRCA2 are - sensitive to damaging agents that form double-strand breaks (DSBs), as are other -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    es of DNA damage. Chromosomal DNA is shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. - (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to suppress RAD51–BRCA2 - interactions until DNA damage is present. When damage occurs, Rad51 is recr -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    subnuclear RAD51 foci with normal efficiency, suggesting that these proteins are required for the formation of - recombinase complexes at the sites of DNA damage [20,21]. Finally, genetic measurements of recombination - frequency have shown that Brca1-/- embryonic stem (ES) cells are deficient in recombin -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    onal DSB repair [22,23]. The similarity between phenotypes associated with BRCA1 and BRCA2 deficiency, together with - data showing a similar effect of DNA damage on distribution of BRCA1 and BRCA2 in repair-proficient cells, - led to the hypothesis that BRCA2, like BRCA1, is required for efficient recombi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric filaments on DNA. A BRC4 peptide was - also reported to inhibit the RAD51–DNA interaction. These experiments raise the possibility that the - full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    l population due to a mutated W (White spotted) gene. GC1 and MT4 are mouse germ cell and Sertoli cell lines, - respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger (if - any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two a -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ing of one of the eight BRC repeats from human BRCA2. Expression of a single BRC repeat (BRC4) had previously been - reported to act as an inhibitor of DNA repair by Chen et al [27]. These investigators showed that expression - of constructs containing the BRC4 repeat in MCF-7 cells enhances the radiosensi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    BRCA2 as grey bars. (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to - suppress RAD51–BRCA2 interactions until DNA damage is present. When damage occurs, Rad51 is recruited to - damaged sites where is polymerizes into nucleoprotein filaments. In this model, BRCA2 is -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ognition site. Transient transfection of an I-SceI expression vector results in the production of a DSB in the first - mutated copy of GFP. One or both DNA ends formed by the break invade(s) the homologous sequence in the second - mutant GFP copy, resulting in repair of the DSB via a homology-mediated gene -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    –DNA interaction. These experiments raise the possibility that the full-length BRCA2 protein could act as a negative - regulator of inappropriate RAD51–DNA interaction. - - The final experiment reported by Davies et al [26] is particularly important with respect to understanding the - mechanism(s) through whi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8420|8423
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8420|8423
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to the regions - of ssDNA that form during normal DNA replication. BRCA2 may thus promote RAD51 assembly into recombinational - repair complexes via a negative regulatory mechanism (i.e. by blocking RAD51– -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    gene conversion occurs via the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - inter -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    event a substantial fraction of Rad51 from being sequestered in a nonfunctional form. In a BRCA2-defective cell, - mutant Rad51 becomes associated with DNA at random sites and is therefore not readily recruited to sites of - damage. (b) Positive regulation. BRCA2 is proposed to be required for Rad51 to ass -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    r by Davies et al, data provide evidence for a plausible mechanism of the dominant negative effect associated with - expression of a single BRC repeat. DNA binding assays and electron microscopy methods were used to show that - a BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    gaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment from - mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics (Hunt -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    and homologous recombination - - Abstract - - Two recent papers provide new evidence relevant to the role of the breast cancer susceptibility gene BRCA2 in - DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in homology-dependent - (recombinational) repair of DNA double-strand br -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    li cell lines, respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger - (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C - antibody was raised against a -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ve cells - - Pierce et al have designed a set of recombination substrates for measuring the level of homologous recombination in - vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the easily detected - green fluorescent protein), one of which contains a restriction site -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    gure 2 are not mutually exclusive. BRCA2 could prevent inappropriate RAD51 assembly in the absence of damage and - promote functional RAD51 assembly at DNA lesions during the damage response. Further experiments are clearly - required to clarify the functional interactions between BRCA2 and RAD51 during re -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ole in assembly of RAD51 at damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to - 'mediate' assembly of RAD51 at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, - including XRCC2, XRCC3, RAD51B, RAD51C and RAD51D, may function as a complex that actively p -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    s and electron microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to - assemble into oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA - interaction. These experiments raise the possibility that the full-length BRCA2 protein co -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    97), was cloned in-frame into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences - at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madi -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    tgtctgaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment - from mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    clear sites with BRCA1 [9], a number of additional results have provided evidence that both BRCA1 and BRCA2 are - involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during the S - phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably si -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ty gene BRCA2 in DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in - homology-dependent (recombinational) repair of DNA double-strand breaks. The second paper, by Davies et al, - begins to address the mechanism through which BRCA2 makes its contribution to recombinationa -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ia the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - interactions. BRCA2–Rad51 int -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
      -
    -

    double-stranded DNA

    -
    -

    Text source name = 11319941.txt -

    al forebrain [27, 50]. - - Brain volume and neuron number - - It has previously been shown that differences in brain weight are proportional to total brain DNA content and - consequently to total CNS cell number [51, 52]. For this reason, brain weight has been suggested to be a good - surrogate measure for total -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 22890|22893
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 22890|22893
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    air complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding preference - for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory - factors, such as BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestra -

      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    ure was .81 (P < .05), which is similar to the reliability seen in previous estimates of neuron number [39, 40]. - - Genotyping and QTL Mapping - - Genomic DNA was extracted from spleens of F2 animals using a high-salt procedure [63]. A set of 82 - microsatellite loci distributed across all autosomes and the X -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 30232|30235
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 30232|30235
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    rand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as - BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional - form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might b -

      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involv -

      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    mage occurs. For example, previous studies indicated that RAD51 shows little binding preference for single-strand DNA - (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as BRCA2, - are required to suppress RAD51–dsDNA interactions to prevent sequestration of -

      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    d as they contain most ocular structures. - - Analysis of Myoc - - Exons and the proximal promoter of the mouse Myoc gene were amplified from mouse genomic DNA using the - following combinations of primers: - - Exon 1: 5'-cttgcaggagaactttccagaa-3' and 5'-atctcgaaggagattgttatagg-3' - - 5'-gaccagctggagacccaaaccag-3' a -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 38583|38586
        • -
      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 38583|38586
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    cluding the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. -

      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    -

    drug

    -

    glutamate residue

    -
    -

    Text source name = 11319941.txt -

    l portion of Chr 10 in proximity with a number of genes known to affect brain development. One of these is Grk2, a - member of the family of ionotropic glutamate receptor genes that is thought to play a role in modulating - Huntington disease [44]. In the mouse, members of this receptor type act to indirectly do -

      -
    • - glutamate -
        -
      • Kristin Garcia
        • -
      • class = glutamate residue
        • -
      • spans = 21235|21244
        • -
      -
    • - glutamate -
        -
      • Mike Bada
        • -
      • class = glutamate(2-)
        • -
      • spans = 21235|21244
        • -
      -
    -

    glutamate(1-)

    -

    glutamate(2-)

    -

    glycine

    -
    -

    Text source name = 11604102.txt -

    d by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate - exon selection in neurons is antagonized by a second RNA-binding protein, brPTB (brain- -

      -
    • - glycine -
        -
      • Kristin Garcia
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    • - glycine -
        -
      • Mike Bada
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    -

    guanine group

    -

    guanosyl groups

    -

    histidine

    -
    -

    Text source name = 11604102.txt -

    equences at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins - were mixed with Freund's adjuvant and injected into rabbits to generate the anti-DAZ -

      -
    • - His -
        -
      • Kristin Garcia
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    • - His -
        -
      • Mike Bada
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    -

    hydrogencarbonate

    -
    -

    Text source name = 11532192.txt -

    derstanding of the molecular mechanisms controlling diurnal rhythms of IOP and that may be relevant to glaucoma. - - Car2 deficiency does not alter IOP - - Bicarbonate formation is important for aqueous humor secretion from the ciliary processes and carbonic - anhydrase (CA) facilitates this secretion. There are multi -

      -
    • - Bicarbonate -
        -
      • Kristin Garcia
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    • - Bicarbonate -
        -
      • Mike Bada
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    -

    inhibitor

    -

    magnesium dichloride

    -
    -

    Text source name = 11604102.txt -

    ay, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Protease Inhibit -

      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose gradients in - 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for 2 hours at - 4°C. Fractions of 0.5 ml were collected from the bottom of the tubes and analyze -

      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    -

    messenger RNA

    -
    -

    Text source name = 11604102.txt -

    tting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family - in the regulation of mRNA translation is supported by lines of cir -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    lso interacts through its proline-rich domain with two microfilament-associated proteins profilin and Mena, which may - facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming - growth factor-β family that is required for generating dorsal mesoderm at the -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ressed later, in the cytoplasm of pachytene spermatocytes [5]. Genetic and biochemical studies suggest a role for the - DAZ family in the regulation of mRNA translation. Drosophila Boule mutants was defective in the translation - of the meiosis-specific CDC25 homologue, Twine [11], and DAZL was found to be -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    . Its predominant expression in testes suggests a role in spermatogenesis. Its subcellular localization indicates - that it is not directly involved in mRNA translation. - - Background - - Spermatogenesis is a complex developmental process in which male germ cells progress through mitotic proliferation, - meiotic -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, pre-mRNA - processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA translation is supporte -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the - alternative splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The - ability of Nova-1 to activate exon selection in neurons is antagonized by a seco -

      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    proteins may act together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be - involved in the transport of the mRNAs of the target genes of DAZL. Alternatively, DAZL and DAZAP1 may act - antagonistically to regulate the timing and the level of expression. Such an anta -

      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and characterized [16]. Prrp binds to a 340 nt - sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also int -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    mouse testes, DAZAP1 was found both in the nuclei and in the cytoplasm. Its absence from polyribosomes indicates - that it is not directly involved in mRNA translation. - - Materials and methods - - Isolation of mouse Dazap1 cDNA clones - - Dazap1 cDNA clones were isolated from a mouse testis cDNA library (#93730 -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ee-hybrid system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich - segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechanisms of its action, we - used a yeast two-hybrid s -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    and brain, and even less in other tissues. This pattern of expression is similar to that of the human DAZAP1 (14). - RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at embryonic day 15, similar to - Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted througho -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    r to that of the human DAZAP1 (14). RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at - embryonic day 15, similar to Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted - throughout testes development, in both the prenatal and postnatal periods. Dazl1 and Da -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    haracterization of the mouse Dazap1 gene and its protein product. The subcellular localization of DAZAP1 suggests - that it is not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 cDNA - - Mouse Dazap1 cDNA clones were isolated by library screening, and the 5' end of the -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its - proline-rich domain with two microfilament-associated proteins profilin and M -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA transcription, pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the - DAZ family in the regulation of mRNA translation is supported by lines of circumstantial evidence, including - the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from p -

      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    -

    metal cations

    -

    metals

    -
    -

    Text source name = 11604102.txt -

    at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were - prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with - Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antib -

      -
    • - metal -
        -
      • Kristin Garcia
        • -
      • class = metals
        • -
      • spans = 18346|18351
        • -
      -
    • - metal -
        -
      • Mike Bada
        • -
      • class = metal cations
        • -
      • spans = 18346|18351
        • -
      -
    -

    molecular entities

    -

    nucleotidyl groups

    -

    oligopeptides

    -
    -

    Text source name = 11604102.txt -

    was conjugated to KLH as carrier and injected into a goat. The anti-DAZAP1-P antibody thus produced was purified on - an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM Tris, pH - 8.0) -

      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 18831|18843
        • -
      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 18831|18843
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    on resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid residues of the mouse - DAZAP1 was synthesized in vitro using the services of Bethyl Laboratories (Montgomery, TX). Th -

      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 18509|18521
        • -
      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 18509|18521
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ntibody was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid residue at the - C-terminus. Both antibodies recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay ( -

      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 9799|9811
        • -
      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 9799|9811
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ntron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 - (starting from aa #197), was cloned in-fr -

      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 17939|17951
        • -
      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 17939|17951
        • -
      -
    -

    peptides

    -
    -

    Text source name = 11597317.txt -

    - - The second paper providing evidence, by Davies et al [26], is a biochemical study of the interaction between the - homologous recombinase RAD51 and a peptide consisting of one of the eight BRC repeats from human BRCA2. - Expression of a single BRC repeat (BRC4) had previously been reported to act as an inhib -

      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 7420|7427
        • -
      -
    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 7420|7427
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    on microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These - experiments raise the possibility that the full-length BRCA2 protein could act as a neg -

      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 8224|8231
        • -
      -
    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 8224|8231
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    t negative effect associated with expression of a single BRC repeat. DNA binding assays and electron microscopy - methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interact -

      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 8126|8133
        • -
      -
    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 8126|8133
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ge has occurred and factors required for 'productive' assembly of RAD51 at damaged sites are in place). As mentioned - previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction could reflect a role of - full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another pot -

      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 10885|10892
        • -
      -
    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 10885|10892
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ontaining the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the services of Bethyl - Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier and injected into a goat. The - anti-DAZAP1-P antibody thus produced was purified on an affinity column containing the -

      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 18673|18680
        • -
      -
    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 18673|18680
        • -
      -
    -

    phosphate(3-)

    -

    phosphates

    -
    -

    Text source name = 11532192.txt -

    ormalin fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 M phosphate buffer. All strains other than CBA/CaHN and C57BLKS/J - strains were evaluated. The eyes of CBA/CaJ and BALB/cJ mice were also fixed and processed for -

      -
    • - phosphate -
        -
      • Kristin Garcia
        • -
      • class = phosphates
        • -
      • spans = 38088|38097
        • -
      -
    • - phosphate -
        -
      • Mike Bada
        • -
      • class = phosphate(3-)
        • -
      • spans = 38088|38097
        • -
      -
    -

    pigment

    -

    potassium chloride

    -
    -

    Text source name = 11604102.txt -

    n at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose - gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for - 2 hours at 4°C. Fractions of 0.5 ml were collected from the bottom of the tu -

      -
    • - KCl -
        -
      • Kristin Garcia
        • -
      • class = potassium chloride
        • -
      • spans = 20325|20328
        • -
      -
    • - KCl -
        -
      • Mike Bada
        • -
      • class = potassium chloride
        • -
      • spans = 20325|20328
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    , Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Prot -

      -
    • - KCl -
        -
      • Kristin Garcia
        • -
      • class = potassium chloride
        • -
      • spans = 19828|19831
        • -
      -
    • - KCl -
        -
      • Mike Bada
        • -
      • class = potassium chloride
        • -
      • spans = 19828|19831
        • -
      -
    -

    proline

    -
    -

    Text source name = 11604102.txt -

    tion element (VLE) is sufficient for the migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. - Prrp also interacts through its proline-rich domain with two microfilament-associated proteins profilin and - Mena, which may facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The V -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 14405|14412
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 14405|14412
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    o acids only, with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% - identity with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly - conserved. They share 98% and 97% similarity and 97% and 92% identity, respectivel -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5681|5688
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5681|5688
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    e segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, - with 7 substitutions and two deleti -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5423|5430
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5423|5430
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two - RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the - testis. To understand the biological function of DAZAP1 and the significance of its -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 877|884
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 877|884
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    in, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody was raised against a recombinant - protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both ant -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 9724|9731
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 9724|9731
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA - binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% - similarity and 71% identity). There is an insertion of a 58 bp segment in Prrp cDNA that cau -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5950|5957
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5950|5957
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in testes. It encodes a protein - with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both - DAZ and DAZL in vitro. It also bound to RNA homopolymers. We now report our characte -

      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 4323|4330
        • -
      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 4323|4330
        • -
      -
    -

    proline residue

    -

    protease inhibitor

    -
    -

    Text source name = 11604102.txt -

    ontaining 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, - Madison, WI), and a mixture of 10 protease inhibitors provided in the Protease Inhibitors Set (Roche - Molecular Biochemicals, Indianapolis, IN). Homogenates were centrifuged at 1,000 × g for 10 minutes to -

      -
    • - protease inhibitors -
        -
      • Kristin Garcia
        • -
      • class = protease inhibitor
        • -
      • spans = 19941|19960
        • -
      -
    • - protease inhibitors -
        -
      • Mike Bada
        • -
      • class = protease inhibitor
        • -
      • spans = 19941|19960
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 - protease inhibitors provided in the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, IN). - Homogenates were centrifuged at 1,000 × g for 10 minutes to pellet cell debris and nuclei. Afte -

      -
    • - Protease Inhibitors -
        -
      • Kristin Garcia
        • -
      • class = protease inhibitor
        • -
      • spans = 19977|19996
        • -
      -
    • - Protease Inhibitors -
        -
      • Mike Bada
        • -
      • class = protease inhibitor
        • -
      • spans = 19977|19996
        • -
      -
    -

    proteins

    -
    -

    Text source name = 11597317.txt -

    sites are in place). As mentioned previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction - could reflect a role of full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another potential role for BRCA2 in promoting RAD51-dependent recombinational repair is a posi -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 10968|10975
        • -
      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 10968|10975
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its proline-rich domain - with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 mRNA - to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth fact -

      -
    • - proteins -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 14459|14467
        • -
      -
    • - proteins -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 14459|14467
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    y virtue of their expression of GFP. - - Moynahan et al [24] have used such a GFP recombination substrate to demonstrate that cells with defective BRCA2 protein - are deficient in their ability to repair the I-SceI-induced DSB through homologous recombination. Expression of - I-SceI resulted in 1 out of 1400 cell -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 4454|4461
        • -
      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 4454|4461
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    R1P and FXR2P, that were identified through their interaction with another polysomal-associated RNA-binding protein, - the fragile X mental retardation protein [21]. Both FXR1P and FXR2P are associated with the polyribosomes - [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 12395|12402
        • -
      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 12395|12402
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    tein product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins share 98% identity and their sequences are highly similar to the Xenopus orthologue - Prrp, especially in the RBDs. Dazap1 is expressed throughout test -

      -
    • - proteins -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 1338|1346
        • -
      -
    • - proteins -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 1338|1346
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    Both primer pairs annealed across intron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 ( -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 17904|17911
        • -
      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 17904|17911
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    se genomic DNA. The PCR primers span over introns and produce much larger (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti - DAZAP1-C antibody was raised against a recombinant protein containing the C-terminal pr -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 9569|9576
        • -
      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 9569|9576
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    mpletely independent of its defect in BRCA2. First, in the same study [24], recombination in a mouse ES cell line - that expresses only truncated BRCA2 protein was measured. This line was found to have lower recombination - efficiency than isogenic cells expressing full-length BRCA2 (the defect observed was ab -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 5648|5655
        • -
      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 5648|5655
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. This finding - is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardat -

      -
    • - proteins -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 12233|12241
        • -
      -
    • - proteins -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 12233|12241
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    em to isolate two human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed - predominantly in testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal - portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to R -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 4280|4287
        • -
      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 4280|4287
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    breaks (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with - the RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have b -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 2328|2335
        • -
      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 2328|2335
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    P and FXR2P are associated with the polyribosomes [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be defined. These proteins may act - together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be involved in the - transport of the mRNAs of -

      -
    • - proteins -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 12568|12576
        • -
      -
    • - proteins -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 12568|12576
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements - [5,6]. The sequence of this large protein (3418 amino acids) offers very little clue to its function, - although there are eight repeated segments (termed BRC repeats) in the middle of the prot -

      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 1330|1337
        • -
      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 1330|1337
        • -
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    nds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse testes, DAZAP1 w -

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    end of the cDNA was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region - (UTR), an open reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession - No: AF225910). The coding region shares 89% similarity with that of the human orth -

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    NA-binding domains (RBDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved - evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with X -

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    nts on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These experiments raise the - possibility that the full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA - interaction. - - The final experiment reported by Davies et al [26] is particularly importa -

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    he small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, consistent - with the fact that the truncation protein lacks a nuclear localization signal [28]. Davies et al showed - CAPAN-1 cells to be defective in nuclear localization of RAD51, raising the possibility -

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    , agenesis of the corpus callosum, and abnormalities other forebrain structure including widespread neocortical - ectopias [46, 47]. The MARCKS-related protein gene is expressed in the striatum during early brain - development in the rat [48]. - - The location of the QTL modulating striatal neuron number to the d -

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    em, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA binding domains and a proline - rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to RNA - homopolymers. We now report our characterization of the mouse Dazap1 gene and its pr -

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    ng dorsal mesoderm at the blastula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of - DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST search of - the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with -

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    illigrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on His-Bind metal chelation - resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid -

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    tein (3418 amino acids) offers very little clue to its function, although there are eight repeated segments (termed - BRC repeats) in the middle of the protein that are highly conserved among mammalian orthologs [7,8]. - - Breast cancer susceptibility genes and DNA repair - - Following the landmark discovery by Sc -

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    by centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by the - Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of tissue - extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-D -

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    Z gene family and to understanding the mechanisms of its action, we used a yeast two-hybrid system to isolate two - human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly - in testes. It encodes a protein with two RNA binding domains and a proline rich C-term -

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    ifferent from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction with another - polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both FXR1P and FXR2P - are associated with the polyribosomes [22]. - - The significance of the interaction -

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    e for direct RAD51 interaction. Cells lacking BRCA1/2 fail to form damage-induced subnuclear RAD51 foci with normal - efficiency, suggesting that these proteins are required for the formation of recombinase complexes at the - sites of DNA damage [20,21]. Finally, genetic measurements of recombination frequency -

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    ) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by - the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μ -

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    ed in CAPAN-1 cells, the same human tumor line examined by Moynahan et al [24]. It had been shown previously that the - small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, - consistent with the fact that the truncation protein lacks a nuclear localization signa -

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    acts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser degree in spleen, - liver, lung and brain (Figure 4). The protein was also present in the ovary. The expression of DAZAP1 during - germ cell development paralleled that of DAZL (Figure 5). It is present at a low level -

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    RI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences at the junctions were verified by DNA - sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on - His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with Fre -

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    t. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed by Western - blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translatio -

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    s a change of reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences betwee -

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    increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted with the anti-DAZAP1-P antibody. - - Figure 5 Western blot -

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    the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody - was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid r -

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    he two RBDs are especially highly conserved. They share 98% and 97% similarity and 97% and 92% identity, - respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA binding specificity. - The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% similarity and -

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    gene to be discovered, and was isolated through positional cloning using data from families with inherited breast - cancer [4]. Cells with mutant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate - gross chromosomal rearrangements [5,6]. The sequence of this large protein (3418 ami -

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    riginal URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast tw -

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    s recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting of mouse - tissue extracts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser - degree in spleen, liver, lung and brain (Figure 4). The protein was also present in t -

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    ential role for BRCA2 in promoting RAD51-dependent recombinational repair is a positive role in assembly of RAD51 at - damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to 'mediate' assembly of RAD51 - at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, includin -

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    ty of Nova-1 to activate exon selection in neurons is antagonized by a second RNA-binding protein, brPTB - (brain-enriched polypyrimidine tract-binding protein), which interacts with Nova-1 and inhibits its function - [24]. DAZAP1 could function in a similar manner by binding to DAZL and inhibiting its functio -

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    of DAZAP1 increased afterward, as the testes contained increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted -

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    striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the gene encoding the myristoylated - alanine-rich C kinase substrate (MARCKS protein). This molecule is important in cerebral development. - MARCKS-deficient mice have a high incidence of exencephaly, agenesis of the corpus callosum, an -

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    nal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in neurons is - antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding protein), - which interacts with Nova-1 and inhibits its function [24]. DAZAP1 could function in a -

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    erved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for - proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. T -

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    . Second, in an independent study, Powell was able to compare derivatives of CAPAN-1 that differed only in their - ability to express full-length BRCA2 protein (S. Powell, personal communication, 2001). In these experiments, - the derivative expressing full-length BRCA2 yielded 10-fold more recombinants than c -

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    ce, including the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from polyribosomes indicates - that it is not directly involved in protein synthesis. This finding is different from two RNA-binding - proteins, FXR1P and FXR2P, that were identified through their interaction with another poly -

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    AP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic interaction - between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding - protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNAs encoding neuron -

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    f expression. Such an antagonistic interaction between two interacting RNA-binding proteins is exemplified by the - neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of N -

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    titutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus - Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. They share - 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prr -

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    sophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and spermatogonia, an -

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    (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with the - RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have been indi -

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    via homologous recombination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of - BRCA2 on one homolog and codes for a protein truncated at amino acid 1981 on the other homolog. The authors - indicate that the level of I-SceI-induced recombination in CAPAN-1 is over 100-fold le -

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    logous recombination in vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the - easily detected green fluorescent protein), one of which contains a restriction site for I-SceI, a yeast - intron encoded endonuclease with an 18 base pair recognition site. Transient transfect -

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    mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast two-hybrid system through its - interaction with a putative male infertility factor, DAZ (Deleted in Azoospermi -

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    ation of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a R -

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    to the Xenopus orthologue Prrp, especially in the RBDs. Dazap1 is expressed throughout testis development. Western - blot detects a single 45 kD DAZAP1 protein that is most abundant in the testis. Although a majority of DAZAP1 - is present in the cytoplasmic fraction, they are not associated with polyribosomes -

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    share 85%, 90%, and 97% similarity with segments in the human 3' UTR, respectively. These segments probably contain - regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse -

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    infertility factor, DAZ (Deleted in Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ - and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a - proline-rich C-terminal portion, and is expressed most abundantly in the testis. To under -

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    n Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like - protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is - expressed most abundantly in the testis. To understand the biological function o -

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    Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s and the - Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and the mouse - sequences, and between the mouse and Xenopus sequences are marked by #'s and * -

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    ch domain with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 - mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth factor-β family that is - required for generating dorsal mesoderm at the blastula stage of Xenopus embryoge -

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    the level of expression. Such an antagonistic interaction between two interacting RNA-binding proteins is - exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative - splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. -

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    human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in - testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 - protein interacted with both DAZ and DAZL in vitro. It also bound to RNA homopolyme -

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    VLE that binds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse -

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    The 5' end of the cDNA was isolated by 5' RACE [15], using prdap11 (ttgcgggccatatccttg, #749–732) as the primer for - cDNA synthesis from mouse testis RNA, and prdap37 (ttgttgccacgtgggcg, #734–718) and an adaptor primer as the - primers for PCR amplification. The PCR products were cloned into a TA cloning -

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    BLAST search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, and possibly DAZAP1, may help to - identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolution -

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    mbers of Drosophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both - sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and -

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    article's original URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identifi -

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    coding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in - neurons is antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding - protein), which interacts with Nova-1 and inhibits its function [24]. DAZAP1 coul -

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    with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity - with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. - They share 98% and 97% similarity and 97% and 92% identity, respectively, betwee -

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    erved. They share 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These - proteins may therefore have a similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 - and Prrp are less conserved (81% similarity and 71% identity). There is an insert -

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    DAZL and DAZAP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic - interaction between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear - RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNA -

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    communication). The genomic structure of Dazap1, delineated here, should facilitate the generating of Dazap1 null - mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of -

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    ressed most abundantly in the testis. - - Figure 3 Developmental expression of Dazap1 and Dazl in mouse testes. RT-PCR was performed on total testicular RNAs - isolated from day 15 (El 5) and day 17 (El 7) embryos, new born mice (Day 0), and mice at various days after birth. - Wv/Wv testes contain diminished g -

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    rose gradient. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed - by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localiz -

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    ch fractions was analyzed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA -

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    finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both - FXR1P and FXR2P are associated with the polyribosomes [22]. - - The significance of -

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    stula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of DAZAP1 and Prrp suggests that - these proteins may bind to similar RNA sequences. However, a BLAST search of the GenBank for the 340 nt VLE - sequence failed to identify any mammalian sequences with significant homology. F -

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    n with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and - DAZL in vitro. It also bound to RNA homopolymers. We now report our characterization of the mouse Dazap1 gene - and its protein product. The subcellular localization of DAZAP1 suggests th -

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    97% similarity with segments in the human 3' UTR, respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human pr -

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    es [12]. The absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. - This finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their - interaction with another polysomal-associated RNA-binding protein, the fragile -

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    BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-lik -

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    nction difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; ssDNA = - single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like - protein.. Cell. 19 -

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    recruited into a functional repair complex when damage occurs. For example, previous studies indicated that RAD51 - shows little binding preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This - result could mean that regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA in -

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    d to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional form. Alternatively, or - in addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to - the regions of ssDNA that form during normal DNA replication. BRCA2 may thus prom -

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    nctional repair complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding - preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that - regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA interacti -

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    al form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might be important for preventing - RAD51 from binding to the regions of ssDNA that form during normal DNA replication. BRCA2 may thus promote - RAD51 assembly into recombinational repair complexes via a negative regulatory mechan -

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    sodium chloride

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    urified on an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of deb -

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    sodium dodecyl sulfate

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    -

    Text source name = 11604102.txt -

    etermined by the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of - tissue extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-DAZAP1-C - antibody (at a 1/2,000 dilution) or the anti-DAZAP1-P antibody (at a 1/5,000 dilution). -

      -
    • - SDS -
        -
      • Kristin Garcia
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 19342|19345
        • -
      -
    • - SDS -
        -
      • Mike Bada
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 19342|19345
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    taining the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 -

      -
    • - SDS -
        -
      • Kristin Garcia
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 18969|18972
        • -
      -
    • - SDS -
        -
      • Mike Bada
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 18969|18972
        • -
      -
    -

    sodium phosphates

    -
    -

    Text source name = 11319941.txt -

    ply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, 0.5-1.0 ml ip) and perfused - through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) followed by 1.25% - glutaraldehyde/1.0% paraformaldehyde in 0.1 M PB (pH 7.40) over a period of 2 to 4 min. An additional -

      -
    • - sodium phosphate -
        -
      • Kristin Garcia
        • -
      • class = sodium phosphates
        • -
      • spans = 26402|26418
        • -
      -
    • - sodium phosphate -
        -
      • Mike Bada
        • -
      • class = sodium phosphates
        • -
      • spans = 26402|26418
        • -
      -
    -

    sucrose

    -
    -

    Text source name = 11604102.txt -

    se gradient analyses of the post- mitochondria fraction showed that, unlike DAZL, DAZAP1 did not co-sediment with - polyribosomes (Figure 6). - - Figure 6 Sucrose gradient analyses shows that DAZAP1 is not associated with polyribosomes. The - post-mitochondrial supernatant of mouse testis extracts was analyzed on -

      -
    • - Sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11395|11402
        • -
      -
    • - Sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11395|11402
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    analyses shows that DAZAP1 is not associated with polyribosomes. The post-mitochondrial supernatant of mouse testis - extracts was analyzed on a 15–45% sucrose gradient. Sedimentation was from left to right. The presence of - DAZAP1 and DAZL in each fractions was analyzed by Western blotting. - - Discussion - - RNA- -

      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11562|11569
        • -
      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11562|11569
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    [12]. Similar analyses showed that a majority of DAZAP1 in adult mouse testes was also present in the cytoplasmic - fraction (data not shown). However, sucrose gradient analyses of the post- mitochondria fraction showed that, - unlike DAZL, DAZAP1 did not co-sediment with polyribosomes (Figure 6). - - Figure 6 Su -

      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11240|11247
        • -
      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11240|11247
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    uclei. After an additional centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the - supernatant were applied to 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged - in a Beckman SW41 rotor at 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were -

      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 20285|20292
        • -
      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 20285|20292
        • -
      -
    -

    terpenes

    -
    -

    Text source name = 11532192.txt -

    esia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and wood - shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in wood - shavings alters drug resistance and decreases the effect of anesthetic agents in both ra -

      -
    • - Terpene -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25559|25566
        • -
      -
    • - Terpene -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25559|25566
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    of anesthesia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and - wood shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in - wood shavings alters drug resistance and decreases the effect of anesthetic agents i -

      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25549|25557
        • -
      -
    • - terpenes -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25549|25557
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    may be important. We use wood shavings for bedding and wood shavings expose the mice to terpenes. Terpene - administration or environmental exposure to terpenes in wood shavings alters drug resistance and decreases - the effect of anesthetic agents in both rats and mice [40-45]. - - Risk factors for increased IOP - -

      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
      -
    • - terpenes -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
      -
    -

    tert-pentyl group

    -
    -

    Text source name = 11319941.txt -

    lution digital images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% g -

      -
    • - tert-pentyl -
        -
      • Kristin Garcia
        • -
      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    • - tert-pentyl -
        -
      • Mike Bada
        • -
      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    -

    tris

    -
    -

    Text source name = 11604102.txt -

    oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of - debris by centrifugation at 10,000 × g for 10 m -

      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to - 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at - 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were collected from the bott -

      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ham Pharmacia Biotech, Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors -

      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    -

    uracil-1-yl group

    -

    uridyl groups

    -

    water

    -
    -

    Text source name = 11532192.txt -

    containing white pine bedding and covered with polyester filters. For most experiments, the mice were fed NIH31 (6 % - fat) chow ad libitum, and their water was acidified to pH 2.8 to 3.2. B6 mice develop diet induced diabetes - when maintained on a high fat diet [76]. To ensure that we were analyzing the e -

      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    f sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, - 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) - followed by 1.25% glutaraldehyde/1.0 -

      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    +Each concept that was considered a match is shown in the text that it was found in. The matching annotations from the other concept sets are also shown. For more detailed documentation on Iaa please see the Iaa documentation. + +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    • +
      • Mike Bada
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16449
      • spanCollection = sgenic [21540, 21547]
    • +
      • Mike Bada
      • class = CHEBI:32441
      • spanCollection = sgenic [21540, 21547]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = Dazap1 [4323, 4330]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = Dazap1 [4323, 4330]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = and the [5950, 5957]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = and the [5950, 5957]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = the tra [14405, 14412]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = the tra [14405, 14412]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = inserti [5681, 5688]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = inserti [5681, 5688]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = y and 9 [5423, 5430]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = y and 9 [5423, 5430]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nthesiz [9724, 9731]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nthesiz [9724, 9731]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nomic s [877, 884]
    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nomic s [877, 884]
    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    • +
      • Mike Bada
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    • +
      • Mike Bada
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:32484
      • spanCollection = on on gen [21235, 21244]
    • +
      • Mike Bada
      • class = CHEBI:14321
      • spanCollection = on on gen [21235, 21244]
    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    • +
      • Mike Bada
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ral [22890, 22893]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ral [22890, 22893]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = es [38583, 38586]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = es [38583, 38586]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = rie [30232, 30235]
    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = rie [30232, 30235]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    +

    CHEBI_15377

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    +

    CHEBI_16670

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    +

    CHEBI_17544

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    +

    CHEBI_17992

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    +

    CHEBI_23367

    +

    CHEBI_25213

    +

    CHEBI_25613

    +

    CHEBI_25676

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    +

    CHEBI_26020

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26020
      • spanCollection = he anteri [38088, 38097]
    • +
      • Mike Bada
      • class = CHEBI:18367
      • spanCollection = he anteri [38088, 38097]
    +

    CHEBI_26710

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    +

    CHEBI_27594

    +

    CHEBI_30879

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    +

    CHEBI_32588

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    +

    CHEBI_33521

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33521
      • spanCollection = ng th [18346, 18351]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25213
      • spanCollection = ng th [18346, 18351]
    +

    CHEBI_33708

    +

    CHEBI_33709

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = imilar RNA [5527, 5538]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = imilar RNA [5527, 5538]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = p1 genomic [6273, 6283]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = p1 genomic [6273, 6283]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = served amon [1344, 1355]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = served amon [1344, 1355]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = (BRCA2+) h [4797, 4807]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = (BRCA2+) h [4797, 4807]
    +

    CHEBI_35186

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    +

    CHEBI_36080

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    +

    CHEBI_37586

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    +

    CHEBI_6636

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    +

    CHEBI_8984

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    +

    CHEBI_9754

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    diff --git a/src/test/resources/iaa_test_project/iaa/Span matcher.matches.Mike Bada.html b/src/test/resources/iaa_test_project/iaa/Span matcher.matches.Mike Bada.html index f9885d5e..80f2c24f 100644 --- a/src/test/resources/iaa_test_project/iaa/Span matcher.matches.Mike Bada.html +++ b/src/test/resources/iaa_test_project/iaa/Span matcher.matches.Mike Bada.html @@ -2,4339 +2,847 @@ Matches for Mike Bada

    Matches for Mike Bada

    -Each annotation that was considered a match is shown in the text that it was found in. The matching annotations from the -other annotation sets are also shown. For more detailed documentation on IAA please see the IAA documentation. - -

    5'-cytidylyl group

    -

    5'-guanylyl group

    -

    5'-uridylyl group

    -

    acid

    -
    -

    Text source name = 11532192.txt -

    e at the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered w -

      -
    • - acid -
        -
      • Mike Bada
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    • - acid -
        -
      • Kristin Garcia
        • -
      • class = acid
        • -
      • spans = 37924|37928
        • -
      -
    -

    adenine group

    -

    alanine

    -

    alanine residue

    -
    -

    Text source name = 11319941.txt -

    y down-regulate synaptic activity in the striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the - gene encoding the myristoylated alanine-rich C kinase substrate (MARCKS protein). This molecule is important - in cerebral development. MARCKS-deficient mice have a high incidence of exenceph -

      -
    • - alanine -
        -
      • Mike Bada
        • -
      • class = alanine residue
        • -
      • spans = 21540|21547
        • -
      -
    • - alanine -
        -
      • Kristin Garcia
        • -
      • class = alanine
        • -
      • spans = 21540|21547
        • -
      -
    -

    alcohols

    -
    -

    Text source name = 11319941.txt -

    al images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% glutarald -

      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 26319|26326
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    the time of IOP measurement. - - Histological analysis - - Eyes from at least 2 mice of the listed strains were fixed (4% paraformaldehyde or Fekete's acid-alcohol-formalin - fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 -

      -
    • - alcohol -
        -
      • Mike Bada
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    • - alcohol -
        -
      • Kristin Garcia
        • -
      • class = alcohols
        • -
      • spans = 37929|37936
        • -
      -
    -

    amino acids

    -

    amino-acid residues

    -
    -

    Text source name = 11604102.txt -

    reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and -

      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 6273|6283
        • -
      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 6273|6283
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    Text source name = 11597317.txt -

    ein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements [5,6]. The - sequence of this large protein (3418 amino acids) offers very little clue to its function, although there are - eight repeated segments (termed BRC repeats) in the middle of the protein that are highl -

      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 1344|1355
        • -
      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 1344|1355
        • -
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    Text source name = 11597317.txt -

    bination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of BRCA2 on one homolog and - codes for a protein truncated at amino acid 1981 on the other homolog. The authors indicate that the level of - I-SceI-induced recombination in CAPAN-1 is over 100-fold less than that seen using -

      -
    • - amino acid -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 4797|4807
        • -
      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 4797|4807
        • -
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    -
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    Text source name = 11604102.txt -

    BDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved evolutionarily. The mouse - and the human proteins differ in 9 amino acids only, with 7 substitutions and two deletions/insertions. The - mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for proline -

      -
    • - amino acids -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 5527|5538
        • -
      -
    • - amino acids -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 5527|5538
        • -
      -
    -

    anaesthetic

    -
    -

    Text source name = 11532192.txt -

    parate group of the same age. - - Anesthesia protocol avoids IOP alteration and allows detection of diurnal differences - - All IOPs were assessed using an anesthetic regime of 99 mg/kg ketamine and 9 mg/kg xylazine (defined as 1X). - Initial experiments suggested that an almost identical dose (100 mg/kg ketamine and -

      -
    • - anesthetic -
        -
      • Mike Bada
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    • - anesthetic -
        -
      • Kristin Garcia
        • -
      • class = anaesthetic
        • -
      • spans = 12466|12476
        • -
      -
    -

    canonical nucleoside residues

    -

    carbon

    -

    carboxy group

    -

    cytidyl groups

    -

    cytosin-1-yl group

    -

    deoxyribonucleic acids

    -
    -

    Text source name = 11597317.txt -

    1 and BRCA2 are involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during - the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of repair of - spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either B -

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    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1955|1958
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    97), was cloned in-frame into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences - at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 18230|18233
        • -
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    Text source name = 11597317.txt -

    and homologous recombination - - Abstract - - Two recent papers provide new evidence relevant to the role of the breast cancer susceptibility gene BRCA2 in - DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in homology-dependent - (recombinational) repair of DNA double-strand br -

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    • - DNA -
        -
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        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
      -
    • - DNA -
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      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 322|325
        • -
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    Text source name = 11597317.txt -

    subnuclear RAD51 foci with normal efficiency, suggesting that these proteins are required for the formation of - recombinase complexes at the sites of DNA damage [20,21]. Finally, genetic measurements of recombination - frequency have shown that Brca1-/- embryonic stem (ES) cells are deficient in recombin -

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        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
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    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2773|2776
        • -
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    Text source name = 11597317.txt -

    ia the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - interactions. BRCA2–Rad51 int -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19529|19532
        • -
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    -
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    Text source name = 11597317.txt -

    ole in assembly of RAD51 at damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to - 'mediate' assembly of RAD51 at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, - including XRCC2, XRCC3, RAD51B, RAD51C and RAD51D, may function as a complex that actively p -

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    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 11281|11284
        • -
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    -
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    Text source name = 11597317.txt -

    ty gene BRCA2 in DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in - homology-dependent (recombinational) repair of DNA double-strand breaks. The second paper, by Davies et al, - begins to address the mechanism through which BRCA2 makes its contribution to recombinationa -

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    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
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    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 455|458
        • -
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    Text source name = 11597317.txt -

    BRCA2 as grey bars. (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to - suppress RAD51–BRCA2 interactions until DNA damage is present. When damage occurs, Rad51 is recruited to - damaged sites where is polymerizes into nucleoprotein filaments. In this model, BRCA2 is -

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        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
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    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19746|19749
        • -
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    Text source name = 11597317.txt -

    r by Davies et al, data provide evidence for a plausible mechanism of the dominant negative effect associated with - expression of a single BRC repeat. DNA binding assays and electron microscopy methods were used to show that - a BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8045|8048
        • -
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    -
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    Text source name = 11597317.txt -

    event a substantial fraction of Rad51 from being sequestered in a nonfunctional form. In a BRCA2-defective cell, - mutant Rad51 becomes associated with DNA at random sites and is therefore not readily recruited to sites of - damage. (b) Positive regulation. BRCA2 is proposed to be required for Rad51 to ass -

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    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
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    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 20128|20131
        • -
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    Text source name = 11597317.txt -

    ognition site. Transient transfection of an I-SceI expression vector results in the production of a DSB in the first - mutated copy of GFP. One or both DNA ends formed by the break invade(s) the homologous sequence in the second - mutant GFP copy, resulting in repair of the DSB via a homology-mediated gene -

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        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
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    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3918|3921
        • -
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    Text source name = 11597317.txt -

    es of DNA damage. Chromosomal DNA is shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. - (a) Prevention of nonproductive DNA interactions. BRCA2–Rad51 interaction is proposed to suppress RAD51–BRCA2 - interactions until DNA damage is present. When damage occurs, Rad51 is recr -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19649|19652
        • -
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    Text source name = 11597317.txt -

    clear sites with BRCA1 [9], a number of additional results have provided evidence that both BRCA1 and BRCA2 are - involved in recombinational repair of DNA damage. BRCA1 and BRCA2 form discrete nuclear foci during the S - phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably si -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 1859|1862
        • -
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    Text source name = 11597317.txt -

    gene conversion occurs via the synthesis-dependent annealing mechanism. - - Figure 2 Potential roles of BRCA2 in promoting assembly of Rad51 at sites of DNA damage. Chromosomal DNA is - shown as pairs of straight lines, Rad51 as open circles, and BRCA2 as grey bars. (a) Prevention of nonproductive DNA - inter -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 19505|19508
        • -
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    Text source name = 11604102.txt -

    gaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment from - mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics (Hunt -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16713|16716
        • -
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    Text source name = 11597317.txt -

    clear foci during the S phase and after exposure to DNA damaging agents [9,10,11]. These foci are probably sites of - repair of spontaneous and induced DNA damage [12,13,14]. Cell lines defective in either BRCA1 or BRCA2 are - sensitive to damaging agents that form double-strand breaks (DSBs), as are other -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 2053|2056
        • -
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    Text source name = 11597317.txt -

    ve cells - - Pierce et al have designed a set of recombination substrates for measuring the level of homologous recombination in - vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the easily detected - green fluorescent protein), one of which contains a restriction site -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3543|3546
        • -
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    Text source name = 11604102.txt -

    tgtctgaag) were designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment - from mouse but not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse - chromosome fragments in a hamster background were purchased from Research Genetics -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 16708|16711
        • -
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    Text source name = 11597317.txt -

    ing of one of the eight BRC repeats from human BRCA2. Expression of a single BRC repeat (BRC4) had previously been - reported to act as an inhibitor of DNA repair by Chen et al [27]. These investigators showed that expression - of constructs containing the BRC4 repeat in MCF-7 cells enhances the radiosensi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 7585|7588
        • -
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    Text source name = 11597317.txt -

    s and electron microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to - assemble into oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA - interaction. These experiments raise the possibility that the full-length BRCA2 protein co -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8212|8215
        • -
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    Text source name = 11604102.txt -

    l population due to a mutated W (White spotted) gene. GC1 and MT4 are mouse germ cell and Sertoli cell lines, - respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger (if - any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two a -

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    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9430|9433
        • -
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    Text source name = 11597317.txt -

    addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to the regions - of ssDNA that form during normal DNA replication. BRCA2 may thus promote RAD51 assembly into recombinational - repair complexes via a negative regulatory mechanism (i.e. by blocking RAD51– -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 10554|10557
        • -
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    Text source name = 11319941.txt -

    al forebrain [27, 50]. - - Brain volume and neuron number - - It has previously been shown that differences in brain weight are proportional to total brain DNA content and - consequently to total CNS cell number [51, 52]. For this reason, brain weight has been suggested to be a good - surrogate measure for total -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 22890|22893
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 22890|22893
        • -
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    Text source name = 11597317.txt -

    onal DSB repair [22,23]. The similarity between phenotypes associated with BRCA1 and BRCA2 deficiency, together with - data showing a similar effect of DNA damage on distribution of BRCA1 and BRCA2 in repair-proficient cells, - led to the hypothesis that BRCA2, like BRCA1, is required for efficient recombi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 3079|3082
        • -
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    Text source name = 11597317.txt -

    BRC3 peptide interferes with the ability of RAD51 to assemble into oligomeric filaments on DNA. A BRC4 peptide was - also reported to inhibit the RAD51–DNA interaction. These experiments raise the possibility that the - full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8271|8274
        • -
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    Text source name = 11532192.txt -

    d as they contain most ocular structures. - - Analysis of Myoc - - Exons and the proximal promoter of the mouse Myoc gene were amplified from mouse genomic DNA using the - following combinations of primers: - - Exon 1: 5'-cttgcaggagaactttccagaa-3' and 5'-atctcgaaggagattgttatagg-3' - - 5'-gaccagctggagacccaaaccag-3' a -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 38583|38586
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 38583|38586
        • -
      -
    -
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    Text source name = 11319941.txt -

    ure was .81 (P < .05), which is similar to the reliability seen in previous estimates of neuron number [39, 40]. - - Genotyping and QTL Mapping - - Genomic DNA was extracted from spleens of F2 animals using a high-salt procedure [63]. A set of 82 - microsatellite loci distributed across all autosomes and the X -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 30232|30235
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 30232|30235
        • -
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    Text source name = 11597317.txt -

    –DNA interaction. These experiments raise the possibility that the full-length BRCA2 protein could act as a negative - regulator of inappropriate RAD51–DNA interaction. - - The final experiment reported by Davies et al [26] is particularly important with respect to understanding the - mechanism(s) through whi -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 8420|8423
        • -
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    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
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      • spans = 8420|8423
        • -
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    Text source name = 11597317.txt -

    gure 2 are not mutually exclusive. BRCA2 could prevent inappropriate RAD51 assembly in the absence of damage and - promote functional RAD51 assembly at DNA lesions during the damage response. Further experiments are clearly - required to clarify the functional interactions between BRCA2 and RAD51 during re -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 12046|12049
        • -
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    Text source name = 11604102.txt -

    li cell lines, respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and produce much larger - (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C - antibody was raised against a -

      -
    • - DNA -
        -
      • Mike Bada
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = deoxyribonucleic acids
        • -
      • spans = 9525|9528
        • -
      -
    -

    double-stranded DNA

    -
    -

    Text source name = 11597317.txt -

    cluding the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. -

      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12909|12914
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    mage occurs. For example, previous studies indicated that RAD51 shows little binding preference for single-strand DNA - (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as BRCA2, - are required to suppress RAD51–dsDNA interactions to prevent sequestration of -

      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10196|10201
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    the large size of BRCA2, promise to make biochemical characterization of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involv -

      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 12917|12934
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    air complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding preference - for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory - factors, such as BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestra -

      -
    • - double-strand DNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    • - double-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10177|10194
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    rand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that regulatory factors, such as - BRCA2, are required to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional - form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might b -

      -
    • - dsDNA -
        -
      • Mike Bada
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    • - dsDNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 10305|10310
        • -
      -
    -

    drug

    -

    glutamate residue

    -

    glutamate(1-)

    -

    glutamate(2-)

    -
    -

    Text source name = 11319941.txt -

    l portion of Chr 10 in proximity with a number of genes known to affect brain development. One of these is Grk2, a - member of the family of ionotropic glutamate receptor genes that is thought to play a role in modulating - Huntington disease [44]. In the mouse, members of this receptor type act to indirectly do -

      -
    • - glutamate -
        -
      • Mike Bada
        • -
      • class = glutamate(2-)
        • -
      • spans = 21235|21244
        • -
      -
    • - glutamate -
        -
      • Kristin Garcia
        • -
      • class = glutamate residue
        • -
      • spans = 21235|21244
        • -
      -
    -

    glycine

    -
    -

    Text source name = 11604102.txt -

    d by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate - exon selection in neurons is antagonized by a second RNA-binding protein, brPTB (brain- -

      -
    • - glycine -
        -
      • Mike Bada
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    • - glycine -
        -
      • Kristin Garcia
        • -
      • class = glycine
        • -
      • spans = 13102|13109
        • -
      -
    -

    guanine group

    -

    guanosyl groups

    -

    histidine

    -
    -

    Text source name = 11604102.txt -

    equences at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins - were mixed with Freund's adjuvant and injected into rabbits to generate the anti-DAZ -

      -
    • - His -
        -
      • Mike Bada
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    • - His -
        -
      • Kristin Garcia
        • -
      • class = histidine
        • -
      • spans = 18337|18340
        • -
      -
    -

    hydrogencarbonate

    -
    -

    Text source name = 11532192.txt -

    derstanding of the molecular mechanisms controlling diurnal rhythms of IOP and that may be relevant to glaucoma. - - Car2 deficiency does not alter IOP - - Bicarbonate formation is important for aqueous humor secretion from the ciliary processes and carbonic - anhydrase (CA) facilitates this secretion. There are multi -

      -
    • - Bicarbonate -
        -
      • Mike Bada
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    • - Bicarbonate -
        -
      • Kristin Garcia
        • -
      • class = hydrogencarbonate
        • -
      • spans = 31251|31262
        • -
      -
    -

    inhibitor

    -

    magnesium dichloride

    -
    -

    Text source name = 11604102.txt -

    ay, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Protease Inhibit -

      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 19838|19843
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose gradients in - 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for 2 hours at - 4°C. Fractions of 0.5 ml were collected from the bottom of the tubes and analyze -

      -
    • - MgCl2 -
        -
      • Mike Bada
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    • - MgCl2 -
        -
      • Kristin Garcia
        • -
      • class = magnesium dichloride
        • -
      • spans = 20338|20343
        • -
      -
    -

    messenger RNA

    -
    -

    Text source name = 11604102.txt -

    Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and characterized [16]. Prrp binds to a 340 nt - sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also int -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14232|14236
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    tting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family - in the regulation of mRNA translation is supported by lines of cir -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11845|11849
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ee-hybrid system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich - segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechanisms of its action, we - used a yeast two-hybrid s -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3973|3977
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    and brain, and even less in other tissues. This pattern of expression is similar to that of the human DAZAP1 (14). - RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at embryonic day 15, similar to - Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted througho -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8222|8226
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    proteins may act together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be - involved in the transport of the mRNAs of the target genes of DAZL. Alternatively, DAZL and DAZAP1 may act - antagonistically to regulate the timing and the level of expression. Such an anta -

      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 12718|12723
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    . Its predominant expression in testes suggests a role in spermatogenesis. Its subcellular localization indicates - that it is not directly involved in mRNA translation. - - Background - - Spermatogenesis is a complex developmental process in which male germ cells progress through mitotic proliferation, - meiotic -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 1919|1923
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    mouse testes, DAZAP1 was found both in the nuclei and in the cytoplasm. Its absence from polyribosomes indicates - that it is not directly involved in mRNA translation. - - Materials and methods - - Isolation of mouse Dazap1 cDNA clones - - Dazap1 cDNA clones were isolated from a mouse testis cDNA library (#93730 -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 15477|15481
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA transcription, pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the - DAZ family in the regulation of mRNA translation is supported by lines of circumstantial evidence, including - the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from p -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11954|11958
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, pre-mRNA - processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA translation is supporte -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 11828|11832
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    lso interacts through its proline-rich domain with two microfilament-associated proteins profilin and Mena, which may - facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming - growth factor-β family that is required for generating dorsal mesoderm at the -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14529|14533
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient for the - migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its - proline-rich domain with two microfilament-associated proteins profilin and M -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 14328|14332
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    haracterization of the mouse Dazap1 gene and its protein product. The subcellular localization of DAZAP1 suggests - that it is not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 cDNA - - Mouse Dazap1 cDNA clones were isolated by library screening, and the 5' end of the -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 4623|4627
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ressed later, in the cytoplasm of pachytene spermatocytes [5]. Genetic and biochemical studies suggest a role for the - DAZ family in the regulation of mRNA translation. Drosophila Boule mutants was defective in the translation - of the meiosis-specific CDC25 homologue, Twine [11], and DAZL was found to be -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 3555|3559
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the - alternative splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The - ability of Nova-1 to activate exon selection in neurons is antagonized by a seco -

      -
    • - mRNAs -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    • - mRNAs -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 13067|13072
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    r to that of the human DAZAP1 (14). RT-PCR analyses showed that Dazap1 mRNA was already present in fetal testes at - embryonic day 15, similar to Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 persisted - throughout testes development, in both the prenatal and postnatal periods. Dazl1 and Da -

      -
    • - mRNA -
        -
      • Mike Bada
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    • - mRNA -
        -
      • Kristin Garcia
        • -
      • class = messenger RNA
        • -
      • spans = 8301|8305
        • -
      -
    -

    metal cations

    -
    -

    Text source name = 11604102.txt -

    at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were - prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with - Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antib -

      -
    • - metal -
        -
      • Mike Bada
        • -
      • class = metal cations
        • -
      • spans = 18346|18351
        • -
      -
    • - metal -
        -
      • Kristin Garcia
        • -
      • class = metals
        • -
      • spans = 18346|18351
        • -
      -
    -

    metals

    -

    molecular entities

    -

    nucleotidyl groups

    -

    oligopeptides

    -
    -

    Text source name = 11604102.txt -

    on resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid residues of the mouse - DAZAP1 was synthesized in vitro using the services of Bethyl Laboratories (Montgomery, TX). Th -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 18509|18521
        • -
      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 18509|18521
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ntron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 - (starting from aa #197), was cloned in-fr -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 17939|17951
        • -
      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 17939|17951
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ntibody was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid residue at the - C-terminus. Both antibodies recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay ( -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 9799|9811
        • -
      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 9799|9811
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    was conjugated to KLH as carrier and injected into a goat. The anti-DAZAP1-P antibody thus produced was purified on - an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM Tris, pH - 8.0) -

      -
    • - oligopeptide -
        -
      • Mike Bada
        • -
      • class = oligopeptides
        • -
      • spans = 18831|18843
        • -
      -
    • - oligopeptide -
        -
      • Kristin Garcia
        • -
      • class = oligopeptides
        • -
      • spans = 18831|18843
        • -
      -
    -

    peptides

    -
    -

    Text source name = 11597317.txt -

    t negative effect associated with expression of a single BRC repeat. DNA binding assays and electron microscopy - methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interact -

      -
    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 8126|8133
        • -
      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 8126|8133
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ontaining the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the services of Bethyl - Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier and injected into a goat. The - anti-DAZAP1-P antibody thus produced was purified on an affinity column containing the -

      -
    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 18673|18680
        • -
      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 18673|18680
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    - - The second paper providing evidence, by Davies et al [26], is a biochemical study of the interaction between the - homologous recombinase RAD51 and a peptide consisting of one of the eight BRC repeats from human BRCA2. - Expression of a single BRC repeat (BRC4) had previously been reported to act as an inhib -

      -
    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 7420|7427
        • -
      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 7420|7427
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    ge has occurred and factors required for 'productive' assembly of RAD51 at damaged sites are in place). As mentioned - previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction could reflect a role of - full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another pot -

      -
    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 10885|10892
        • -
      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 10885|10892
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    on microscopy methods were used to show that a BRC3 peptide interferes with the ability of RAD51 to assemble into - oligomeric filaments on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These - experiments raise the possibility that the full-length BRCA2 protein could act as a neg -

      -
    • - peptide -
        -
      • Mike Bada
        • -
      • class = peptides
        • -
      • spans = 8224|8231
        • -
      -
    • - peptide -
        -
      • Kristin Garcia
        • -
      • class = peptides
        • -
      • spans = 8224|8231
        • -
      -
    -

    phosphate(3-)

    -
    -

    Text source name = 11532192.txt -

    ormalin fixative) processed, paraffin embedded and sectioned as previously reported [15,79], except that the - paraformaldehyde was buffered with 0.1 M phosphate buffer. All strains other than CBA/CaHN and C57BLKS/J - strains were evaluated. The eyes of CBA/CaJ and BALB/cJ mice were also fixed and processed for -

      -
    • - phosphate -
        -
      • Mike Bada
        • -
      • class = phosphate(3-)
        • -
      • spans = 38088|38097
        • -
      -
    • - phosphate -
        -
      • Kristin Garcia
        • -
      • class = phosphates
        • -
      • spans = 38088|38097
        • -
      -
    -

    phosphates

    -

    pigment

    -

    potassium chloride

    -
    -

    Text source name = 11604102.txt -

    , Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Prot -

      -
    • - KCl -
        -
      • Mike Bada
        • -
      • class = potassium chloride
        • -
      • spans = 19828|19831
        • -
      -
    • - KCl -
        -
      • Kristin Garcia
        • -
      • class = potassium chloride
        • -
      • spans = 19828|19831
        • -
      -
    -
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    Text source name = 11604102.txt -

    n at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose - gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for - 2 hours at 4°C. Fractions of 0.5 ml were collected from the bottom of the tu -

      -
    • - KCl -
        -
      • Mike Bada
        • -
      • class = potassium chloride
        • -
      • spans = 20325|20328
        • -
      -
    • - KCl -
        -
      • Kristin Garcia
        • -
      • class = potassium chloride
        • -
      • spans = 20325|20328
        • -
      -
    -

    proline

    -

    proline residue

    -
    -

    Text source name = 11604102.txt -

    tion element (VLE) is sufficient for the migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. - Prrp also interacts through its proline-rich domain with two microfilament-associated proteins profilin and - Mena, which may facilitate the anchoring of Vg1 mRNA to the vegetal cortex. The V -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 14405|14412
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 14405|14412
        • -
      -
    -
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    Text source name = 11604102.txt -

    interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two - RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the - testis. To understand the biological function of DAZAP1 and the significance of its -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 877|884
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 877|884
        • -
      -
    -
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    Text source name = 11604102.txt -

    e segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, - with 7 substitutions and two deleti -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5423|5430
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5423|5430
        • -
      -
    -
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    Text source name = 11604102.txt -

    and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA - binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% - similarity and 71% identity). There is an insertion of a 58 bp segment in Prrp cDNA that cau -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5950|5957
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5950|5957
        • -
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    -
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    Text source name = 11604102.txt -

    in, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody was raised against a recombinant - protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both ant -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 9724|9731
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 9724|9731
        • -
      -
    -
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    Text source name = 11604102.txt -

    o acids only, with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% - identity with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly - conserved. They share 98% and 97% similarity and 97% and 92% identity, respectivel -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 5681|5688
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 5681|5688
        • -
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    -
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    Text source name = 11604102.txt -

    associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in testes. It encodes a protein - with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both - DAZ and DAZL in vitro. It also bound to RNA homopolymers. We now report our characte -

      -
    • - proline -
        -
      • Mike Bada
        • -
      • class = proline residue
        • -
      • spans = 4323|4330
        • -
      -
    • - proline -
        -
      • Kristin Garcia
        • -
      • class = proline
        • -
      • spans = 4323|4330
        • -
      -
    -

    protease inhibitor

    -
    -

    Text source name = 11604102.txt -

    ontaining 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, - Madison, WI), and a mixture of 10 protease inhibitors provided in the Protease Inhibitors Set (Roche - Molecular Biochemicals, Indianapolis, IN). Homogenates were centrifuged at 1,000 × g for 10 minutes to -

      -
    • - protease inhibitors -
        -
      • Mike Bada
        • -
      • class = protease inhibitor
        • -
      • spans = 19941|19960
        • -
      -
    • - protease inhibitors -
        -
      • Kristin Garcia
        • -
      • class = protease inhibitor
        • -
      • spans = 19941|19960
        • -
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    Text source name = 11604102.txt -

    KCl, 5 mM MgCl2, 0.3% NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 - protease inhibitors provided in the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, IN). - Homogenates were centrifuged at 1,000 × g for 10 minutes to pellet cell debris and nuclei. Afte -

      -
    • - Protease Inhibitors -
        -
      • Mike Bada
        • -
      • class = protease inhibitor
        • -
      • spans = 19977|19996
        • -
      -
    • - Protease Inhibitors -
        -
      • Kristin Garcia
        • -
      • class = protease inhibitor
        • -
      • spans = 19977|19996
        • -
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    proteins

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    Text source name = 11597317.txt -

    sites are in place). As mentioned previously, the ability of a BRC peptide to repress the RAD51–BRCA2 interaction - could reflect a role of full-length protein in suppressing unwanted RAD51–BRCA2 interactions. - - Yet another potential role for BRCA2 in promoting RAD51-dependent recombinational repair is a posi -

      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 10968|10975
        • -
      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 10968|10975
        • -
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    -
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    Text source name = 11604102.txt -

    absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. This finding - is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardat -

      -
    • - proteins -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 12233|12241
        • -
      -
    • - proteins -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 12233|12241
        • -
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    Text source name = 11597317.txt -

    tein (3418 amino acids) offers very little clue to its function, although there are eight repeated segments (termed - BRC repeats) in the middle of the protein that are highly conserved among mammalian orthologs [7,8]. - - Breast cancer susceptibility genes and DNA repair - - Following the landmark discovery by Sc -

      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 1483|1490
        • -
      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 1483|1490
        • -
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    Text source name = 11604102.txt -

    titutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus - Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. They share - 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prr -

      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 5706|5713
        • -
      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 5706|5713
        • -
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    Text source name = 11604102.txt -

    P and FXR2P are associated with the polyribosomes [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be defined. These proteins may act - together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be involved in the - transport of the mRNAs of -

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    • - proteins -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 12568|12576
        • -
      -
    • - proteins -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 12568|12576
        • -
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    Text source name = 11604102.txt -

    the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody - was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid r -

      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 9690|9697
        • -
      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 9690|9697
        • -
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    Text source name = 11597317.txt -

    y virtue of their expression of GFP. - - Moynahan et al [24] have used such a GFP recombination substrate to demonstrate that cells with defective BRCA2 protein - are deficient in their ability to repair the I-SceI-induced DSB through homologous recombination. Expression of - I-SceI resulted in 1 out of 1400 cell -

      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 4454|4461
        • -
      -
    • - protein -
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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 4454|4461
        • -
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    Text source name = 11597317.txt -

    mpletely independent of its defect in BRCA2. First, in the same study [24], recombination in a mouse ES cell line - that expresses only truncated BRCA2 protein was measured. This line was found to have lower recombination - efficiency than isogenic cells expressing full-length BRCA2 (the defect observed was ab -

      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 5648|5655
        • -
      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 5648|5655
        • -
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    Text source name = 11319941.txt -

    striatum [45]. Another gene that falls into the Bsc10a interval is Macs, the gene encoding the myristoylated - alanine-rich C kinase substrate (MARCKS protein). This molecule is important in cerebral development. - MARCKS-deficient mice have a high incidence of exencephaly, agenesis of the corpus callosum, an -

      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 21580|21587
        • -
      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 21580|21587
        • -
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    Text source name = 11604102.txt -

    mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast two-hybrid system through its - interaction with a putative male infertility factor, DAZ (Deleted in Azoospermi -

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    • - Protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 549|556
        • -
      -
    • - Protein -
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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 549|556
        • -
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    Text source name = 11597317.txt -

    via homologous recombination in the human pancreatic tumor cell line CAPAN-1. CAPAN-1 cells carry a deletion of - BRCA2 on one homolog and codes for a protein truncated at amino acid 1981 on the other homolog. The authors - indicate that the level of I-SceI-induced recombination in CAPAN-1 is over 100-fold le -

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    • - protein -
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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 4776|4783
        • -
      -
    • - protein -
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      • Kristin Garcia
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      • class = proteins
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      • spans = 4776|4783
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    Text source name = 11604102.txt -

    t. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed by Western - blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translatio -

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    • - proteins -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 11727|11735
        • -
      -
    • - proteins -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 11727|11735
        • -
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    Text source name = 11604102.txt -

    by centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by the - Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of tissue - extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-D -

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    • - Protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 19243|19250
        • -
      -
    • - Protein -
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      • Kristin Garcia
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      • class = proteins
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      • spans = 19243|19250
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    Text source name = 11319941.txt -

    , agenesis of the corpus callosum, and abnormalities other forebrain structure including widespread neocortical - ectopias [46, 47]. The MARCKS-related protein gene is expressed in the striatum during early brain - development in the rat [48]. - - The location of the QTL modulating striatal neuron number to the d -

      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 21850|21857
        • -
      -
    • - protein -
        -
      • Kristin Garcia
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      • class = proteins
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      • spans = 21850|21857
        • -
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    Text source name = 11597317.txt -

    e for direct RAD51 interaction. Cells lacking BRCA1/2 fail to form damage-induced subnuclear RAD51 foci with normal - efficiency, suggesting that these proteins are required for the formation of recombinase complexes at the - sites of DNA damage [20,21]. Finally, genetic measurements of recombination frequency -

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    • - proteins -
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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 2692|2700
        • -
      -
    • - proteins -
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      • Kristin Garcia
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      • class = proteins
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      • spans = 2692|2700
        • -
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    Text source name = 11604102.txt -

    sophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and spermatogonia, an -

      -
    • - proteins -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 3183|3191
        • -
      -
    • - proteins -
        -
      • Kristin Garcia
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      • class = proteins
        • -
      • spans = 3183|3191
        • -
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    Text source name = 11604102.txt -

    R1P and FXR2P, that were identified through their interaction with another polysomal-associated RNA-binding protein, - the fragile X mental retardation protein [21]. Both FXR1P and FXR2P are associated with the polyribosomes - [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be -

      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 12395|12402
        • -
      -
    • - protein -
        -
      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 12395|12402
        • -
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    Text source name = 11597317.txt -

    ed in CAPAN-1 cells, the same human tumor line examined by Moynahan et al [24]. It had been shown previously that the - small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, - consistent with the fact that the truncation protein lacks a nuclear localization signa -

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    • - protein -
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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 8808|8815
        • -
      -
    • - protein -
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      • Kristin Garcia
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      • class = proteins
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      • spans = 8808|8815
        • -
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    Text source name = 11604102.txt -

    em, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA binding domains and a proline - rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to RNA - homopolymers. We now report our characterization of the mouse Dazap1 gene and its pr -

      -
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        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 4367|4374
        • -
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    • - protein -
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      • Kristin Garcia
        • -
      • class = proteins
        • -
      • spans = 4367|4374
        • -
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    Text source name = 11604102.txt -

    riginal URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast tw -

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      • class = proteins
        • -
      • spans = 442|449
        • -
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      • class = proteins
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      • spans = 442|449
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    Text source name = 11604102.txt -

    he two RBDs are especially highly conserved. They share 98% and 97% similarity and 97% and 92% identity, - respectively, between DAZAP1 and Prrp. These proteins may therefore have a similar RNA binding specificity. - The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved (81% similarity and -

      -
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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 5872|5880
        • -
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    • - proteins -
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      • Kristin Garcia
        • -
      • class = proteins
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      • spans = 5872|5880
        • -
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    Text source name = 11604102.txt -

    se genomic DNA. The PCR primers span over introns and produce much larger (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti - DAZAP1-C antibody was raised against a recombinant protein containing the C-terminal pr -

      -
    • - protein -
        -
      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 9569|9576
        • -
      -
    • - protein -
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      • Kristin Garcia
        • -
      • class = proteins
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      • spans = 9569|9576
        • -
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    Text source name = 11604102.txt -

    infertility factor, DAZ (Deleted in Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ - and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a - proline-rich C-terminal portion, and is expressed most abundantly in the testis. To under -

      -
    • - protein -
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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 809|816
        • -
      -
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      • Kristin Garcia
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      • class = proteins
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      • spans = 809|816
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    Text source name = 11597317.txt -

    . Second, in an independent study, Powell was able to compare derivatives of CAPAN-1 that differed only in their - ability to express full-length BRCA2 protein (S. Powell, personal communication, 2001). In these experiments, - the derivative expressing full-length BRCA2 yielded 10-fold more recombinants than c -

      -
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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 5979|5986
        • -
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      • Kristin Garcia
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      • class = proteins
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      • spans = 5979|5986
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    Text source name = 11604102.txt -

    NA-binding domains (RBDS) and a C-terminal portion that is rich in proline (Figure 1). It is highly conserved - evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with X -

      -
    • - proteins -
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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 5506|5514
        • -
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      • Kristin Garcia
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      • class = proteins
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      • spans = 5506|5514
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    Text source name = 11604102.txt -

    tein product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins share 98% identity and their sequences are highly similar to the Xenopus orthologue - Prrp, especially in the RBDs. Dazap1 is expressed throughout test -

      -
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      • Mike Bada
        • -
      • class = proteins
        • -
      • spans = 1338|1346
        • -
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    • - proteins -
        -
      • Kristin Garcia
        • -
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    nal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in neurons is - antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding protein), - which interacts with Nova-1 and inhibits its function [24]. DAZAP1 could function in a -

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    ng dorsal mesoderm at the blastula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of - DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST search of - the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with -

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    to the Xenopus orthologue Prrp, especially in the RBDs. Dazap1 is expressed throughout testis development. Western - blot detects a single 45 kD DAZAP1 protein that is most abundant in the testis. Although a majority of DAZAP1 - is present in the cytoplasmic fraction, they are not associated with polyribosomes -

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    f expression. Such an antagonistic interaction between two interacting RNA-binding proteins is exemplified by the - neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the - pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of N -

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    s a change of reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse - DAZAP1s and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences betwee -

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    s recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting of mouse - tissue extracts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser - degree in spleen, liver, lung and brain (Figure 4). The protein was also present in t -

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    ation of BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a R -

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    of DAZAP1 increased afterward, as the testes contained increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted -

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    nds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse testes, DAZAP1 w -

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    share 85%, 90%, and 97% similarity with segments in the human 3' UTR, respectively. These segments probably contain - regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse -

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    RI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). Sequences at the junctions were verified by DNA - sequencing. Milligrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on - His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed with Fre -

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    he small amount of truncated BRCA2 protein expressed by CAPAN-1 cells was mislocalized to the cytoplasm, consistent - with the fact that the truncation protein lacks a nuclear localization signal [28]. Davies et al showed - CAPAN-1 cells to be defective in nuclear localization of RAD51, raising the possibility -

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    acts detected a 45 kD protein that was present most abundantly in the testis, and to a lesser degree in spleen, - liver, lung and brain (Figure 4). The protein was also present in the ovary. The expression of DAZAP1 during - germ cell development paralleled that of DAZL (Figure 5). It is present at a low level -

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    ce, including the association of DAZL with polyribosomes [12]. The absence of DAZAP1 from polyribosomes indicates - that it is not directly involved in protein synthesis. This finding is different from two RNA-binding - proteins, FXR1P and FXR2P, that were identified through their interaction with another poly -

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    clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its proline-rich domain - with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 mRNA - to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth fact -

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    (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with the - RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have been indi -

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    illigrams of fusion proteins between thioredoxin and DAZAP1 were prepared and purified on His-Bind metal chelation - resins (Novagen, Madison, WI). The proteins were mixed with Freund's adjuvant and injected into rabbits to - generate the anti-DAZAPl-C antibody. An oligopeptide containing the last 19 ammo acid -

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    ifferent from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction with another - polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both FXR1P and FXR2P - are associated with the polyribosomes [22]. - - The significance of the interaction -

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    ty of Nova-1 to activate exon selection in neurons is antagonized by a second RNA-binding protein, brPTB - (brain-enriched polypyrimidine tract-binding protein), which interacts with Nova-1 and inhibits its function - [24]. DAZAP1 could function in a similar manner by binding to DAZL and inhibiting its functio -

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    em to isolate two human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed - predominantly in testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal - portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to R -

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    Both primer pairs annealed across intron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide - synthesized in vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 ( -

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    erved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 substitutions and two - deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with Xenopus Prrp (for - proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. T -

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    end of the cDNA was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region - (UTR), an open reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession - No: AF225910). The coding region shares 89% similarity with that of the human orth -

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    Z gene family and to understanding the mechanisms of its action, we used a yeast two-hybrid system to isolate two - human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly - in testes. It encodes a protein with two RNA binding domains and a proline rich C-term -

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    increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various - tissue extracts were applied to a 10% SDS-polyacrylamide gel and western blotted with the anti-DAZAP1-P antibody. - - Figure 5 Western blot -

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    gene to be discovered, and was isolated through positional cloning using data from families with inherited breast - cancer [4]. Cells with mutant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate - gross chromosomal rearrangements [5,6]. The sequence of this large protein (3418 ami -

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    AP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic interaction - between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding - protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNAs encoding neuron -

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    logous recombination in vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the - easily detected green fluorescent protein), one of which contains a restriction site for I-SceI, a yeast - intron encoded endonuclease with an 18 base pair recognition site. Transient transfect -

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    ential role for BRCA2 in promoting RAD51-dependent recombinational repair is a positive role in assembly of RAD51 at - damaged sites (Fig. 2b). Several proteins that interact with RAD51 are thought to 'mediate' assembly of RAD51 - at sites of DNA damage (reviewed in [30]). RAD51 paralogs in particular, includin -

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    ) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by - the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μ -

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    breaks (DSBs), as are other cell lines defective in recombinational repair (reviewed in [15]). BRCA2 interacts with - the RAD51 recombinase via direct protein-protein contacts [16,17,18,19]. Biochemical analysis also showed - interaction between BRCA1 and RAD51, although these detected interactions may have b -

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    ant BRCA2 protein are, like many cancer cells, genetically unstable and accumulate gross chromosomal rearrangements - [5,6]. The sequence of this large protein (3418 amino acids) offers very little clue to its function, - although there are eight repeated segments (termed BRC repeats) in the middle of the prot -

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    nts on DNA. A BRC4 peptide was also reported to inhibit the RAD51–DNA interaction. These experiments raise the - possibility that the full-length BRCA2 protein could act as a negative regulator of inappropriate RAD51–DNA - interaction. - - The final experiment reported by Davies et al [26] is particularly importa -

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    ribonucleic acids

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    BLAST search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, and possibly DAZAP1, may help to - identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolution -

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    article's original URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility - factors DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identifi -

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    ch domain with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring of Vg1 - mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth factor-β family that is - required for generating dorsal mesoderm at the blastula stage of Xenopus embryoge -

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    erved. They share 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These - proteins may therefore have a similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 - and Prrp are less conserved (81% similarity and 71% identity). There is an insert -

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    DAZL and DAZAP1 may act antagonistically to regulate the timing and the level of expression. Such an antagonistic - interaction between two interacting RNA-binding proteins is exemplified by the neuron-specific nuclear - RNA-binding protein, Nova-1. Nova-1 regulates the alternative splicing of the pre-mRNA -

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    ressed most abundantly in the testis. - - Figure 3 Developmental expression of Dazap1 and Dazl in mouse testes. RT-PCR was performed on total testicular RNAs - isolated from day 15 (El 5) and day 17 (El 7) embryos, new born mice (Day 0), and mice at various days after birth. - Wv/Wv testes contain diminished g -

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    • - RNAs -
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      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 9119|9123
        • -
      -
    • - RNAs -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 9119|9123
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    communication). The genomic structure of Dazap1, delineated here, should facilitate the generating of Dazap1 null - mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 13965|13968
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 13965|13968
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    coding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability of Nova-1 to activate exon selection in - neurons is antagonized by a second RNA-binding protein, brPTB (brain-enriched polypyrimidine tract-binding - protein), which interacts with Nova-1 and inhibits its function [24]. DAZAP1 coul -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 13225|13228
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 13225|13228
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    human genes encoding DAZ associated proteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in - testes. It encodes a protein with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 - protein interacted with both DAZ and DAZL in vitro. It also bound to RNA homopolyme -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 4297|4300
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 4297|4300
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s and the - Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and the mouse - sequences, and between the mouse and Xenopus sequences are marked by #'s and * -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 6368|6371
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 6368|6371
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    n with two RNA binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and - DAZL in vitro. It also bound to RNA homopolymers. We now report our characterization of the mouse Dazap1 gene - and its protein product. The subcellular localization of DAZAP1 suggests th -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 4436|4439
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 4436|4439
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    VLE that binds Prrp, and possibly DAZAP1, may help to identify the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. - Its predominant expression in testes suggests a role in spermatogenesis. In mouse -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 15181|15184
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 15181|15184
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    es [12]. The absence of DAZAP1 from polyribosomes indicates that it is not directly involved in protein synthesis. - This finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their - interaction with another polysomal-associated RNA-binding protein, the fragile -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 12221|12224
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12221|12224
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    rose gradient. Sedimentation was from left to right. The presence of DAZAP1 and DAZL in each fractions was analyzed - by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localiz -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 11715|11718
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 11715|11718
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    mbers of Drosophila[7], C. elegans[8], and Xenopus[9] also affect the fertility in either males, females, or both - sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL - are expressed in the nucleus and cytoplasm of primordial germ cells and -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 3171|3174
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 3171|3174
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    the level of expression. Such an antagonistic interaction between two interacting RNA-binding proteins is - exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the alternative - splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 12985|12988
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12985|12988
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    stula stage of Xenopus embryogenesis [25]. Sequence conservation between the RBDs of DAZAP1 and Prrp suggests that - these proteins may bind to similar RNA sequences. However, a BLAST search of the GenBank for the 340 nt VLE - sequence failed to identify any mammalian sequences with significant homology. F -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 14837|14840
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 14837|14840
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    n Azoospermia). In vitro, DAZAP1 interacts with both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like - protein, DAZL. DAZAP1 contains two RNA-binding domains (RBDs) and a proline-rich C-terminal portion, and is - expressed most abundantly in the testis. To understand the biological function o -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 844|847
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 844|847
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    The 5' end of the cDNA was isolated by 5' RACE [15], using prdap11 (ttgcgggccatatccttg, #749–732) as the primer for - cDNA synthesis from mouse testis RNA, and prdap37 (ttgttgccacgtgggcg, #734–718) and an adaptor primer as the - primers for PCR amplification. The PCR products were cloned into a TA cloning -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 15847|15850
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 15847|15850
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified through their interaction - with another polysomal-associated RNA-binding protein, the fragile X mental retardation protein [21]. Both - FXR1P and FXR2P are associated with the polyribosomes [22]. - - The significance of -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 12341|12344
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 12341|12344
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    97% similarity with segments in the human 3' UTR, respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human pr -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 5355|5358
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 5355|5358
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ch fractions was analyzed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 11805|11808
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 11805|11808
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    with 7 substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity - with Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. - They share 98% and 97% similarity and 97% and 92% identity, respectively, betwee -

      -
    • - RNA -
        -
      • Mike Bada
        • -
      • class = ribonucleic acids
        • -
      • spans = 5694|5697
        • -
      -
    • - RNA -
        -
      • Kristin Garcia
        • -
      • class = ribonucleic acids
        • -
      • spans = 5694|5697
        • -
      -
    -

    single-stranded DNA

    -
    -

    Text source name = 11597317.txt -

    BRCA2 function difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; - ssDNA = single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-lik -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 12990|12995
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 12990|12995
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    d to suppress RAD51–dsDNA interactions to prevent sequestration of RAD51 in a nonfunctional form. Alternatively, or - in addition, suppression of RAD51–ssDNA interaction might be important for preventing RAD51 from binding to - the regions of ssDNA that form during normal DNA replication. BRCA2 may thus prom -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10435|10440
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10435|10440
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    nction difficult. - - Abbreviations - - DSB = double-strand break; dsDNA = double-strand DNA; ES = embryonic stem; GFP = green fluorescent protein; ssDNA = - single-strand DNA. - - References - - 1. Shinohara A, Ogawa H, Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like - protein.. Cell. 19 -

      -
    • - single-strand DNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 12998|13015
        • -
      -
    • - single-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 12998|13015
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    recruited into a functional repair complex when damage occurs. For example, previous studies indicated that RAD51 - shows little binding preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This - result could mean that regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA in -

      -
    • - single-strand DNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10146|10163
        • -
      -
    • - single-strand DNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10146|10163
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    nctional repair complex when damage occurs. For example, previous studies indicated that RAD51 shows little binding - preference for single-strand DNA (ssDNA) over double-strand DNA (dsDNA) [3,29]. This result could mean that - regulatory factors, such as BRCA2, are required to suppress RAD51–dsDNA interacti -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10165|10170
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10165|10170
        • -
      -
    -
    -

    Text source name = 11597317.txt -

    al form. Alternatively, or in addition, suppression of RAD51–ssDNA interaction might be important for preventing - RAD51 from binding to the regions of ssDNA that form during normal DNA replication. BRCA2 may thus promote - RAD51 assembly into recombinational repair complexes via a negative regulatory mechan -

      -
    • - ssDNA -
        -
      • Mike Bada
        • -
      • class = single-stranded DNA
        • -
      • spans = 10524|10529
        • -
      -
    • - ssDNA -
        -
      • Kristin Garcia
        • -
      • class = single-stranded DNA
        • -
      • spans = 10524|10529
        • -
      -
    -

    sodium chloride

    -
    -

    Text source name = 11604102.txt -

    urified on an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of deb -

      -
    • - NaCl -
        -
      • Mike Bada
        • -
      • class = sodium chloride
        • -
      • spans = 18936|18940
        • -
      -
    • - NaCl -
        -
      • Kristin Garcia
        • -
      • class = sodium chloride
        • -
      • spans = 18936|18940
        • -
      -
    -

    sodium dodecyl sulfate

    -
    -

    Text source name = 11604102.txt -

    taining the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 -

      -
    • - SDS -
        -
      • Mike Bada
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 18969|18972
        • -
      -
    • - SDS -
        -
      • Kristin Garcia
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 18969|18972
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    etermined by the Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of - tissue extracts were separated on 10% SDS-polyacrylamide gels and blotted with either the anti-DAZAP1-C - antibody (at a 1/2,000 dilution) or the anti-DAZAP1-P antibody (at a 1/5,000 dilution). -

      -
    • - SDS -
        -
      • Mike Bada
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 19342|19345
        • -
      -
    • - SDS -
        -
      • Kristin Garcia
        • -
      • class = sodium dodecyl sulfate
        • -
      • spans = 19342|19345
        • -
      -
    -

    sodium phosphates

    -
    -

    Text source name = 11319941.txt -

    ply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, 0.5-1.0 ml ip) and perfused - through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) followed by 1.25% - glutaraldehyde/1.0% paraformaldehyde in 0.1 M PB (pH 7.40) over a period of 2 to 4 min. An additional -

      -
    • - sodium phosphate -
        -
      • Mike Bada
        • -
      • class = sodium phosphates
        • -
      • spans = 26402|26418
        • -
      -
    • - sodium phosphate -
        -
      • Kristin Garcia
        • -
      • class = sodium phosphates
        • -
      • spans = 26402|26418
        • -
      -
    -

    sucrose

    -
    -

    Text source name = 11604102.txt -

    analyses shows that DAZAP1 is not associated with polyribosomes. The post-mitochondrial supernatant of mouse testis - extracts was analyzed on a 15–45% sucrose gradient. Sedimentation was from left to right. The presence of - DAZAP1 and DAZL in each fractions was analyzed by Western blotting. - - Discussion - - RNA- -

      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11562|11569
        • -
      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11562|11569
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    uclei. After an additional centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the - supernatant were applied to 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged - in a Beckman SW41 rotor at 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were -

      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 20285|20292
        • -
      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 20285|20292
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    se gradient analyses of the post- mitochondria fraction showed that, unlike DAZL, DAZAP1 did not co-sediment with - polyribosomes (Figure 6). - - Figure 6 Sucrose gradient analyses shows that DAZAP1 is not associated with polyribosomes. The - post-mitochondrial supernatant of mouse testis extracts was analyzed on -

      -
    • - Sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11395|11402
        • -
      -
    • - Sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11395|11402
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    [12]. Similar analyses showed that a majority of DAZAP1 in adult mouse testes was also present in the cytoplasmic - fraction (data not shown). However, sucrose gradient analyses of the post- mitochondria fraction showed that, - unlike DAZL, DAZAP1 did not co-sediment with polyribosomes (Figure 6). - - Figure 6 Su -

      -
    • - sucrose -
        -
      • Mike Bada
        • -
      • class = sucrose
        • -
      • spans = 11240|11247
        • -
      -
    • - sucrose -
        -
      • Kristin Garcia
        • -
      • class = sucrose
        • -
      • spans = 11240|11247
        • -
      -
    -

    terpenes

    -
    -

    Text source name = 11532192.txt -

    esia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and wood - shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in wood - shavings alters drug resistance and decreases the effect of anesthetic agents in both ra -

      -
    • - Terpene -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25559|25566
        • -
      -
    • - Terpene -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25559|25566
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    may be important. We use wood shavings for bedding and wood shavings expose the mice to terpenes. Terpene - administration or environmental exposure to terpenes in wood shavings alters drug resistance and decreases - the effect of anesthetic agents in both rats and mice [40-45]. - - Risk factors for increased IOP - -

      -
    • - terpenes -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25611|25619
        • -
      -
    -
    -

    Text source name = 11532192.txt -

    of anesthesia in rats [38,39]. The type of bedding used also may be important. We use wood shavings for bedding and - wood shavings expose the mice to terpenes. Terpene administration or environmental exposure to terpenes in - wood shavings alters drug resistance and decreases the effect of anesthetic agents i -

      -
    • - terpenes -
        -
      • Mike Bada
        • -
      • class = terpenes
        • -
      • spans = 25549|25557
        • -
      -
    • - terpenes -
        -
      • Kristin Garcia
        • -
      • class = terpenes
        • -
      • spans = 25549|25557
        • -
      -
    -

    tert-pentyl group

    -
    -

    Text source name = 11319941.txt -

    lution digital images of sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in - water, 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH - 7.4) followed by 1.25% g -

      -
    • - tert-pentyl -
        -
      • Mike Bada
        • -
      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    • - tert-pentyl -
        -
      • Kristin Garcia
        • -
      • class = tert-pentyl group
        • -
      • spans = 26307|26318
        • -
      -
    -

    tris

    -
    -

    Text source name = 11604102.txt -

    oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM - Tris, pH 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of - debris by centrifugation at 10,000 × g for 10 m -

      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 18980|18984
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    centrifugation at 10,000 × g for 10 minutes to pellet the mitochondria, aliquots of the supernatant were applied to - 15–45% sucrose gradients in 20 mM Tris, 100 mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at - 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml were collected from the bott -

      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 20312|20316
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    ham Pharmacia Biotech, Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% - NP-40, 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors -

      -
    • - Tris -
        -
      • Mike Bada
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    • - Tris -
        -
      • Kristin Garcia
        • -
      • class = tris
        • -
      • spans = 19807|19811
        • -
      -
    -

    uracil-1-yl group

    -

    uridyl groups

    -

    water

    -
    -

    Text source name = 11532192.txt -

    containing white pine bedding and covered with polyester filters. For most experiments, the mice were fed NIH31 (6 % - fat) chow ad libitum, and their water was acidified to pH 2.8 to 3.2. B6 mice develop diet induced diabetes - when maintained on a high fat diet [76]. To ensure that we were analyzing the e -

      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 34648|34653
        • -
      -
    -
    -

    Text source name = 11319941.txt -

    f sections from all cases are available at . - - Mice were anesthetized deeply with Avertin (1.25% 2,2,2-tribromoethanol and 0.8% tert-pentyl alcohol in water, - 0.5-1.0 ml ip) and perfused through the left ventricle with 0.9% sodium phosphate buffered (PB) saline (pH 7.4) - followed by 1.25% glutaraldehyde/1.0 -

      -
    • - water -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    • - water -
        -
      • Kristin Garcia
        • -
      • class = water
        • -
      • spans = 26330|26335
        • -
      -
    +Each concept that was considered a match is shown in the text that it was found in. The matching annotations from the other concept sets are also shown. For more detailed documentation on Iaa please see the Iaa documentation. + +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:14321
      • spanCollection = on on gen [21235, 21244]
    • +
      • Kristin Garcia
      • class = CHEBI:32484
      • spanCollection = on on gen [21235, 21244]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    • +
      • Kristin Garcia
      • class = CHEBI:15428
      • spanCollection = ct-bind [13102, 13109]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = neg [8212, 8215]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = tes [11281, 11284]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19529, 19532]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19746, 19749]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ote [8420, 8423]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ina [12046, 12049]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ond [322, 325]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = C- [9525, 9528]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ed [18230, 18233]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [1859, 1862]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ye [3543, 3546]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = DN [8045, 8048]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ar [1955, 1958]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = efe [2053, 2056]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [20128, 20131]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = e g [9430, 9433]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = A2 [455, 458]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ven [3918, 3921]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19649, 19652]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = of [16708, 16711]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ir. [3079, 3082]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = +Th [8271, 8274]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = ls [7585, 7588]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = use [16713, 16716]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = es [38583, 38586]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = es [38583, 38586]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = 2 i [10554, 10557]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = ral [22890, 22893]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ral [22890, 22893]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = rie [30232, 30235]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = rie [30232, 30235]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = epa [2773, 2776]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    • +
      • Kristin Garcia
      • class = CHEBI:16991
      • spanCollection = [19505, 19508]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:18367
      • spanCollection = he anteri [38088, 38097]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26020
      • spanCollection = he anteri [38088, 38097]
    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    • +
      • Kristin Garcia
      • class = CHEBI:27570
      • spanCollection = co [18337, 18340]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    • +
      • Kristin Garcia
      • class = CHEBI:30360
      • spanCollection = nessee by D [26307, 26318]
    +

    +

    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32441
      • spanCollection = sgenic [21540, 21547]
    • +
      • Kristin Garcia
      • class = CHEBI:16449
      • spanCollection = sgenic [21540, 21547]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = inserti [5681, 5688]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = inserti [5681, 5688]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = the tra [14405, 14412]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = the tra [14405, 14412]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = and the [5950, 5957]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = and the [5950, 5957]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nthesiz [9724, 9731]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nthesiz [9724, 9731]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = nomic s [877, 884]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = nomic s [877, 884]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = y and 9 [5423, 5430]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = y and 9 [5423, 5430]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:32874
      • spanCollection = Dazap1 [4323, 4330]
    • +
      • Kristin Garcia
      • class = CHEBI:26271
      • spanCollection = Dazap1 [4323, 4330]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ted [9119, 9123]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nes [11805, 11808]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = an [12341, 12344]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ke [430, 433]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = nce [14837, 14840]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = d c [13965, 13968]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n t [15181, 15184]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = te [12985, 12988]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = e m [4297, 4300]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = Ds [5355, 5358]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = on [14565, 14568]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = , C [15847, 15850]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = a 5 [5694, 5697]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = equ [5910, 5913]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = by [13225, 13228]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = gly [12918, 12921]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tio [3171, 3174]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = tei [15012, 15015]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = The [4436, 4439]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = n a [844, 847]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = y [ [11715, 11718]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = ac [6368, 6371]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    • +
      • Kristin Garcia
      • class = CHEBI:33697
      • spanCollection = 1]. [12221, 12224]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = pren [8222, 8226]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = fin [1919, 1923]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = anch [14328, 14332]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = rtio [3973, 3977]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = g th [11845, 11849]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = in t [8301, 8305]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ryog [14529, 14533]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = h do [14232, 14236]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = (bra [13067, 13072]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = vide [11828, 11832]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = two i [12718, 12723]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = sing [15477, 15481]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = 5910 [4623, 4627]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = ich [3555, 3559]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    • +
      • Kristin Garcia
      • class = CHEBI:33699
      • spanCollection = is [11954, 11958]
    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    • +
      • Kristin Garcia
      • class = CHEBI:37527
      • spanCollection = + +Fo [37924, 37928]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = bris and nuclei. Af [19941, 19960]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    • +
      • Kristin Garcia
      • class = CHEBI:37670
      • spanCollection = centrifugation at [19977, 19996]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    • +
      • Kristin Garcia
      • class = CHEBI:38867
      • spanCollection = (n = 12) w [12466, 12476]
    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = ation of RAD51 in [10177, 10194]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = trate [12909, 12914]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = for [10305, 10310]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = sed for assaying [12917, 12934]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = nonf [10196, 10201]
    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ssemb [10435, 10440]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = mutant GFP (SceGF [12998, 13015]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = ent s [10165, 10170]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = nteractions to pr [10146, 10163]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = hin t [12990, 12995]
    +

    +

    • +
      • Mike Bada
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    • +
      • Kristin Garcia
      • class = CHEBI:9160
      • spanCollection = eEven [10524, 10529]
    +

    CHEBI_15377

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = Strom [26330, 26335]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_15377
      • spanCollection = +Mate [34648, 34653]
    +

    CHEBI_16670

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = tern bl [18673, 18680]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = e exper [8126, 8133]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = NA repa [7420, 7427]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ulator [8224, 8231]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_16670
      • spanCollection = ential [10885, 10892]
    +

    CHEBI_17544

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17544
      • spanCollection = r more deta [31251, 31262]
    +

    CHEBI_17992

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = found t [11562, 11569]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = Sedime [11395, 11402]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = ws that [11240, 11247]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_17992
      • spanCollection = of the [20285, 20292]
    +

    CHEBI_23367

    +

    CHEBI_25213

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25213
      • spanCollection = ng th [18346, 18351]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33521
      • spanCollection = ng th [18346, 18351]
    +

    CHEBI_25613

    +

    CHEBI_25676

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = 0.2 g tissu [18831, 18843]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = ed to KLH as [18509, 18521]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = blotting of [9799, 9811]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_25676
      • spanCollection = I sites of a [17939, 17951]
    +

    CHEBI_26020

    +

    CHEBI_26710

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_26710
      • spanCollection = 0 × [18936, 18940]
    +

    CHEBI_27594

    +

    CHEBI_30879

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = most s [37929, 37936]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_30879
      • spanCollection = . Riche [26319, 26326]
    +

    CHEBI_32588

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = cul [19828, 19831]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_32588
      • spanCollection = tti [20325, 20328]
    +

    CHEBI_33521

    +

    CHEBI_33708

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = (BRCA2+) h [4797, 4807]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = (BRCA2+) h [4797, 4807]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = imilar RNA [5527, 5538]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = imilar RNA [5527, 5538]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = p1 genomic [6273, 6283]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = p1 genomic [6273, 6283]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = served amon [1344, 1355]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = served amon [1344, 1355]
    +

    CHEBI_33709

    +

    CHEBI_35186

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = d in de [25559, 25566]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = we stud [25549, 25557]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_35186
      • spanCollection = fect dur [25611, 25619]
    +

    CHEBI_36080

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ptor α2 [12930, 12938]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = and in [15193, 15200]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = site w [12981, 12988]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = espect [8355, 8362]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Prrp are [5610, 5618]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tive ro [10968, 10975]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = offers [1190, 1197]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ent in [5706, 5713]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of Daz [13297, 13304]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = y act t [12395, 12402]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = l that [1483, 1490]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = antibo [9690, 9697]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = contai [4916, 4923]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = avies e [8808, 8815]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = screen [4367, 4374]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = o DAZL [13237, 13244]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ti DAZA [9569, 9576]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d most [549, 556]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ein) [1 [5334, 5341]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = protein [809, 816]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng XRCC2 [11192, 11200]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = The BR [2336, 2343]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ther map [14808, 14816]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ed for g [14459, 14467]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = transla [3183, 3191]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Alterna [12568, 12576]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 51 is n [8923, 8930]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = P1 was s [18397, 18405]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = wn that [2692, 2700]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = I-SceI [3645, 3652]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ng GFP [4454, 4461]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = tion. + + [1555, 1562]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = +Conclus [1338, 1346]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = the DAZ [5872, 5880]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ZAP1 du [10037, 10044]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = eparate [19142, 19149]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = of DAZA [10628, 10635]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ction i [12997, 13004]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = hat see [4776, 4783]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ization [4184, 4192]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ice whi [10165, 10172]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ns [43] [21580, 21587]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = g prote [12167, 12174]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = dy. + +Fi [10573, 10580]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = DAZL. D [442, 449]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = le for t [11727, 11735]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = xpressi [5979, 5986]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = are hig [1330, 1337]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ect [9] [2328, 2335]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cloned [17904, 17911]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = d into r [18267, 18275]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ay there [5506, 5514]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = old to [5648, 5655]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = cteriza [4280, 4287]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 1P and F [12233, 12241]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = 000 dil [19243, 19250]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = e in mo [21850, 21857]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = Z remai [12353, 12360]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = ing mous [6259, 6267]
    +

    CHEBI_37586

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_37586
      • spanCollection = in age from 35 [26402, 26418]
    +

    CHEBI_6636

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = hemic [19838, 19843]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_6636
      • spanCollection = wledg [20338, 20343]
    +

    CHEBI_8984

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = ish [19342, 19345]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_8984
      • spanCollection = cen [18969, 18972]
    +

    CHEBI_9754

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = y we [20312, 20316]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = of t [18980, 18984]
    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_9754
      • spanCollection = itor [19807, 19811]
    diff --git a/src/test/resources/iaa_test_project/iaa/Span matcher.nonmatches.Kristin Garcia.html b/src/test/resources/iaa_test_project/iaa/Span matcher.nonmatches.Kristin Garcia.html index 0437dabd..2c8ac0f5 100644 --- a/src/test/resources/iaa_test_project/iaa/Span matcher.nonmatches.Kristin Garcia.html +++ b/src/test/resources/iaa_test_project/iaa/Span matcher.nonmatches.Kristin Garcia.html @@ -2,144 +2,78 @@ Non-matches for Kristin Garcia

    Non-matches for Kristin Garcia

    -Each annotation that was considered a non-match is shown in the text that it was found in. Overlapping annotations from -the other annotation sets are also shown. For more detailed documentation on IAA please see the IAA documentation. +Each concept that was considered a non-match is shown in the text that it was found in. Overlapping annotations from the other concept sets are also shown. For more detailed documentation on Iaa please see the Iaa documentation. -

    5'-cytidylyl group

    -

    5'-guanylyl group

    -

    5'-uridylyl group

    -

    acid

    -

    adenine group

    -

    alanine

    -

    alanine residue

    -

    alcohols

    -

    amino acids

    -
    -

    Text source name = 11604102.txt -

    was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region (UTR), an open - reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession No: AF225910). - The coding region shares 89% similarity with that of the human orthologue. The 3' UTR -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 4931|4941
        • -
      -
    • - amino acid residues -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 4931|4950
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    nant protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both antibodies recognized in vitro - synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting -

      -
    • - amino acid -
        -
      • Kristin Garcia
        • -
      • class = amino acids
        • -
      • spans = 9835|9845
        • -
      -
    • - amino acid residue -
        -
      • Mike Bada
        • -
      • class = amino-acid residues
        • -
      • spans = 9835|9853
        • -
      -
    -

    amino-acid residues

    -

    anaesthetic

    -

    canonical nucleoside residues

    -

    carbon

    -

    carboxy group

    -

    cytidyl groups

    -

    cytosin-1-yl group

    -

    deoxyribonucleic acids

    -

    double-stranded DNA

    -
    -

    Text source name = 11597317.txt -

    ty gene BRCA2 in DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in - homology-dependent (recombinational) repair of DNA double-strand breaks. The second paper, by Davies et al, - begins to address the mechanism through which BRCA2 makes its contribution to recombinationa -

      -
    • - DNA -
        -
      • Kristin Garcia
        • -
      • class = double-stranded DNA
        • -
      • spans = 455|458
        • -
      -
    -

    drug

    -

    glutamate residue

    -

    glutamate(1-)

    -

    glutamate(2-)

    -

    glycine

    -

    guanine group

    -

    guanosyl groups

    -

    histidine

    -

    hydrogencarbonate

    -

    inhibitor

    -

    magnesium dichloride

    -

    messenger RNA

    -

    metal cations

    -

    metals

    -

    molecular entities

    -

    nucleotidyl groups

    -

    oligopeptides

    -

    peptides

    -

    phosphate(3-)

    -

    phosphates

    -

    pigment

    -

    potassium chloride

    -

    proline

    -

    proline residue

    -

    protease inhibitor

    -

    proteins

    -
    -

    Text source name = 11604102.txt -

    nteraction with DAZ and DAZL, we isolated and characterized the mouse Dazap1 gene, and studied its expression and the - subcellular localization of its protein product. +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Kristin Garcia
      • class = CHEBI:4705
      • spanCollection = A2 [455, 458]
    +

    +

    CHEBI_15377

    +

    CHEBI_16670

    +

    CHEBI_17544

    +

    CHEBI_17992

    +

    CHEBI_23367

    +

    CHEBI_25213

    +

    CHEBI_25613

    +

    CHEBI_25676

    +

    CHEBI_26020

    +

    CHEBI_26710

    +

    CHEBI_27594

    +

    CHEBI_30879

    +

    CHEBI_32588

    +

    CHEBI_33521

    +

    CHEBI_33708

    +

    CHEBI_33709

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = tected a 4 [9835, 9845]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = tected a 45 kD pro [9835, 9853]
    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33709
      • spanCollection = tory eleme [4931, 4941]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = tory elements. - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 prot -
          -
        • - protein -
            -
          • Kristin Garcia
            • -
          • class = proteins
            • -
          • spans = 1185|1192
            • -
          -
        • - protein product -
            -
          • Mike Bada
            • -
          • class = proteins
            • -
          • spans = 1185|1200
            • -
          -
        -

        ribonucleic acids

        -

        single-stranded DNA

        -

        sodium chloride

        -

        sodium dodecyl sulfate

        -

        sodium phosphates

        -

        sucrose

        -

        terpenes

        -

        tert-pentyl group

        -

        tris

        -

        uracil-1-yl group

        -

        uridyl groups

        -

        water

        +The [4931, 4950]
    +

    CHEBI_35186

    +

    CHEBI_36080

    +

    +

    • +
      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = n that [1185, 1192]
    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = n that is most [1185, 1200]
    +

    CHEBI_37586

    +

    CHEBI_6636

    +

    CHEBI_8984

    +

    CHEBI_9754

    diff --git a/src/test/resources/iaa_test_project/iaa/Span matcher.nonmatches.Mike Bada.html b/src/test/resources/iaa_test_project/iaa/Span matcher.nonmatches.Mike Bada.html index 2be9f629..e8b74166 100644 --- a/src/test/resources/iaa_test_project/iaa/Span matcher.nonmatches.Mike Bada.html +++ b/src/test/resources/iaa_test_project/iaa/Span matcher.nonmatches.Mike Bada.html @@ -2,1500 +2,270 @@ Non-matches for Mike Bada

    Non-matches for Mike Bada

    -Each annotation that was considered a non-match is shown in the text that it was found in. Overlapping annotations from -the other annotation sets are also shown. For more detailed documentation on IAA please see the IAA documentation. - -

    5'-cytidylyl group

    -
    -

    Text source name = 11604102.txt -

    [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = 5'-cytidylyl group
        • -
      • spans = 3904|3905
        • -
      -
    -

    5'-guanylyl group

    -
    -

    Text source name = 11604102.txt -

    should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = 5'-guanylyl group
        • -
      • spans = 14030|14031
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    estes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family an -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = 5'-guanylyl group
        • -
      • spans = 3899|3900
        • -
      -
    -

    5'-uridylyl group

    -
    -

    Text source name = 11604102.txt -

    eated here, should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = 5'-uridylyl group
        • -
      • spans = 14019|14020
        • -
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    with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid - system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich segment - in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the funct -

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    ZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) stretches interspersed - by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechan -

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    acid

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    he insertion allele. The other allele was identical to the published sequence [22]. The insertion allele also had a - previously reported substitution (A to G, Thr164Ala) in exon 1 and several other single base changes in the - promoter region [22]. The presence or absence of this allele does not associa -

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    e proteins were mixed with Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antibody. An - oligopeptide containing the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the - services of Bethyl Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier -

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    nant protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an - oligopeptide containing the last 19 amino acid residue at the C-terminus. Both antibodies recognized in vitro - synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western blotting of mouse -

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    was isolated by 5' RACE [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region (UTR), an open - reading frame for a protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession No: AF225910). - The coding region shares 89% similarity with that of the human orthologue. The 3' UTR sequence -

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    tely thirty 3 to 4 month old mice were analyzed at each dose and time B-D. Scatter-plots demonstrating no change in - IOP over the 12 minutes following anesthetic administration in three relatively unrelated mouse strains. All - strains consisted of males and females that ranged from 3 to 6 months of age. The sex -

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    me). The greater the dose the greater the decrease in IOP. At the 5 minute measurement, however, IOP was the same - using all doses suggesting that the anesthetic effect on IOP had not yet occurred. To identify any early - window when it may be possible to assess IOP without an obvious anesthetic effect, 195 mice -

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    tic dose within 12 minutes of administration. A Mean IOP ± SD is shown for C57BL/6J mice at 5 and 25 minutes after - administration of various doses of anesthetic. The 1X dose consisted of 99 mg/kg ketamine and 9 mg/kg - xylazine. All doses decreased IOP by 25 minutes. At all doses the IOP at 5 minutes was the sa -

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    he mice to terpenes. Terpene administration or environmental exposure to terpenes in wood shavings alters drug - resistance and decreases the effect of anesthetic agents in both rats and mice [40-45]. - - Risk factors for increased IOP - - Some epidemiological studies implicate factors such as diabetes, vascular hypertensio -

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    do not immediately identify them as likely glaucoma candidates. - - No effect of anesthetic protocol on IOP during a 12 minute measurement window - - Many anesthetic agents including xylazine lower IOP. Ketamine usually appears to increase IOP [31-33], but - there are reports of ketamine having no effect on IOP or even red -

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    ronments may contribute to these differences. The relationship between the IOPs we measure and those in conscious - mice depends upon the effect of our anesthetic protocol (intraperitoneal injection of 99 mg/kg ketamine and 9 - mg/kg xylazine). An anesthetic effect could potentially alter IOP and mask genetically -

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    s (Figure 6). In these experiments, IOP measurements were made between 5 and 12 minutes after administration of - anesthesia. - - Figure 5 No effect of 1X anesthetic dose within 12 minutes of administration. A Mean IOP ± SD is shown for - C57BL/6J mice at 5 and 25 minutes after administration of various doses of ane -

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    those in conscious mice depends upon the effect of our anesthetic protocol (intraperitoneal injection of 99 mg/kg - ketamine and 9 mg/kg xylazine). An anesthetic effect could potentially alter IOP and mask genetically - determined differences in IOP. Therefore, it is very important to understand this effect. Her -

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    minutes after administration. Thus, to avoid effects of anesthesia on IOP, all measurements should be made within a - window of up to 12 minutes after anesthetic administration. - - Similarities and differences to rat studies - - Our results agree with the time course of cardiovascular depression caused by intraperi -

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    own functions do not suggest that they affect aqueous humor dynamics or do not immediately identify them as likely - glaucoma candidates. - - No effect of anesthetic protocol on IOP during a 12 minute measurement window - - Many anesthetic agents including xylazine lower IOP. Ketamine usually appears to increase IOP -

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    canonical nucleoside residues

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    12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) - stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA - [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understan -

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    BMC Genomics. 2001; 2: 6. - PubMed ID: 11604102 - - Copyright © 2001 Dai et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and - redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along - with the article's original URL. - - -------------------------------------------------------------------- - - Characterization of the mouse Dazap1 gene encoding an RNA-binding protein that interacts with infertility factors - DAZ and DAZL - - Abstract - - Background - - DAZAP1 (DAZ Associated Protein 1) was originally identified by a yeast two-hybrid system through its interaction - with a putative male infertility factor, DAZ (Deleted in Azoospermia). In vitro, DAZAP1 interacts with both the Y - chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding domains - (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the testis. To understand the - biological function of DAZAP1 and the significance of its interaction with DAZ and DAZL, we isolated and - characterized the mouse Dazap1 gene, and studied its expression and the subcellular localization of its protein - product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins share 98% identity and their sequences are highly similar to the Xenopus orthologue Prrp, - especially in the RBDs. Dazap1 is expressed throughout testis development. Western blot detects a single 45 kD - DAZAP1 protein that is most abundant in the testis. Although a majority of DAZAP1 is present in the cytoplasmic - fraction, they are not associated with polyribosomes. - - Conclusions - - DAZAP1 is evolutionarily highly conserved. Its predominant expression in testes suggests a role in spermatogenesis. - Its subcellular localization indicates that it is not directly involved in mRNA translation. - - Background - - Spermatogenesis is a complex developmental process in which male germ cells progress through mitotic proliferation, - meiotic division and dramatic morphological changes to form mature sperm. This process is vital for the propagation - of a species, and involves a large portion of the genome of an organism to ensure the quality and quantity of the - final products. It is estimated that mutations in up to 11% of all genes in Drosophila might lead to male sterility - [1]. This is likely to be true for humans also, considering the extremely high incidence (4–5%) of infertility in - men [2]. Among the genes associated with male infertility is the DAZ (Deleted in Azoospermia) gene family. The - family includes the Y-linked DAZ genes that are present only in great apes and old world monkeys [3], and the - autosomal DAZL1 (DAZ-like 1) and BOULE genes [4,5] in all mammals. Deletion of the DAZ genes is found in about 10% - of infertile males with idiopathic azoospermia [2], and disruption of Dazl1 causes infertility in both male and - female mice [6]. Mutations in the DAZ family members of Drosophila[7], C. elegans[8], and Xenopus[9] also affect the - fertility in either males, females, or both sexes. - - The DAZ gene family encodes RNA binding proteins that are expressed specifically in germ cells. DAZ and DAZL are - expressed in the nucleus and cytoplasm of primordial germ cells and spermatogonia, and in the cytoplasm of meiotic - spermatocytes [6,10]. BOULE is expressed later, in the cytoplasm of pachytene spermatocytes [5]. Genetic and - biochemical studies suggest a role for the DAZ family in the regulation of mRNA translation. Drosophila Boule - mutants was defective in the translation of the meiosis-specific CDC25 homologue, Twine [11], and DAZL was found to - be associated with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast - three-hybrid system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich - segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechanisms of its action, we - used a yeast two-hybrid system to isolate two human genes encoding DAZ associated proteins (DAZAPs) [14]. One of - them, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA binding domains and a proline - rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL in vitro. It also bound to RNA - homopolymers. We now report our characterization of the mouse Dazap1 gene and its protein product. The subcellular - localization of DAZAP1 suggests that it is not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 cDNA - - Mouse Dazap1 cDNA clones were isolated by library screening, and the 5' end of the cDNA was isolated by 5' RACE - [15]. The near fall length cDNA consists of a 53 bp 5' untranslated region (UTR), an open reading frame for a - protein of 405 amino acid residues, and a 362 bp 3' UTR (GenBank Accession No: AF225910). The coding region shares - 89% similarity with that of the human orthologue. The 3' UTR sequence is remarkably conserved. It contains three - segments of 35 bp, 133 bp and 90 bp that share 85%, 90%, and 97% similarity with segments in the human 3' UTR, - respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline (Figure - 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids only, with 7 - substitutions and two deletions/insertions. The mammalian proteins shares 89% similarity and 81% identity with - Xenopus Prrp (for proline-rich RNA binding protein) [16]. The two RBDs are especially highly conserved. They share - 98% and 97% similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore - have a similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved - (81% similarity and 71% identity). There is an insertion of a 58 bp segment in Prrp cDNA that causes a change of - reading frame and results in a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s - and the Xenopus Prrp are compared. The two RNA binding domains are boxed. Differences between the human and the - mouse sequences, and between the mouse and Xenopus sequences are marked by #'s and *'s, respectively. - - Genomic structure of Dazap1 and chromosomal mapping - - Several overlapping lambda clones containing mouse Dazap1 genomic sequences were isolated. The locations of exons - were determined by PCR amplification across exon-intron boundaries following by sequencing. All but the first exon - were isolated and mapped. The genomic structure of the human DAZAP1 gene was also determined by blasting the human - genome sequence at National Center for Biotechnology Information with the human DAZAP1 cDNA sequence. The mouse and - the human genes have very similar structures, consisting of 12 exons spanning about 28 kb. All intron insertion - sites are conserved (Table 1). The two RBDs are encoded by exons 1–4 and 5–8, respectively. - - Table 1 Exon-intron Organization of the Mouse and Human DAZAP1 genes - - A pair of PCR primers was designed from Dazap1 intronic sequences that amplified mouse but not hamster genomic - sequences. Using a panel of mouse-hamster radiation hybrids, the mouse Dazap1 gene was mapped to chromosome 10 - placed 27.84 cR from D10Mit260 (lod > 3.0) (data not shown). This region is syntenic to human 19p13.3 where the - human DAZAP1 gene is located [14,17]. It contains no known mutant alleles that are associated with infertility. - - Expression of Dazap1 - - Northern analyses of adult mouse tissues showed the presence of two Dazap1 transcripts of 1.75 kb and 2.4 kb, - respectively (Figure 2). Only the shorter transcript has been isolated in cDNA clones. Dazap1 was expressed most - abundantly in the testis, much less in liver, heart and brain, and even less in other tissues. This pattern of - expression is similar to that of the human DAZAP1 (14). RT-PCR analyses showed that Dazap1 mRNA was already present - in fetal testes at embryonic day 15, similar to Dazl1 mRNA (Figure 3). The expression of both Dazl1 and Dazap1 - persisted throughout testes development, in both the prenatal and postnatal periods. Dazl1 and Dazap1 transcripts - were also present in the testes of Wv/Wv mutant mice which contained diminished number of germ cells [18]. However, - only Dazap1 was expressed in a mouse germ cell line GCl-spg [19] and a Sertoli cell line MT4. The results suggest - that Dazap1 is expressed in both somatic and germ cells in the testis. - - Figure 2 Expression of Dazap1 in adult mouse tissues. A mouse multiple-tissue Northern blot was hybridized with a - Dazap1 cDNA probe, stripped, and rehybridized with a β-actin probe. Dazap1 is expressed most abundantly in the - testis. - - Figure 3 Developmental expression of Dazap1 and Dazl in mouse testes. RT-PCR was performed on total testicular RNAs - isolated from day 15 (El 5) and day 17 (El 7) embryos, new born mice (Day 0), and mice at various days after birth. - Wv/Wv testes contain diminished germ cell population due to a mutated W (White spotted) gene. GC1 and MT4 are mouse - germ cell and Sertoli cell lines, respectively, and gDNA is mouse genomic DNA. The PCR primers span over introns and - produce much larger (if any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C - antibody was raised against a recombinant protein containing the C-terminal proline-rich portion, and the anti - DAZAP1-P antibody was raised against an oligopeptide containing the last 19 amino acid residue at the C-terminus. - Both antibodies recognized in vitro synthesized DAZAP1 in an immunoprecipitation assay (data not shown). Western - blotting of mouse tissue extracts detected a 45 kD protein that was present most abundantly in the testis, and to a - lesser degree in spleen, liver, lung and brain (Figure 4). The protein was also present in the ovary. The expression - of DAZAP1 during germ cell development paralleled that of DAZL (Figure 5). It is present at a low level in the - testes of 6 days old mice which contained only primitive type A spermatogonia. The expression of DAZAP1 increased - afterward, as the testes contained increasing number of proliferating and meiotic germ cells. - - Figure 4 Expression of the DAZAP1 protein in adult mouse tissues. Equal amounts of total protein from various tissue - extracts were applied to a 10% SDS-polyacrylamide gel and western blotted with the anti-DAZAP1-P antibody. - - Figure 5 Western blot analyses of the expression of DAZAP1 and DAZL in mouse testes during postnatal development. - - Subcellular localization of DAZAP1 - - Our previous fractionation of mouse testis extracts showed that most DAZL were present in the post mitochondrial - fraction, and some of them were associated with polyribosomes [12]. Similar analyses showed that a majority of - DAZAP1 in adult mouse testes was also present in the cytoplasmic fraction (data not shown). However, sucrose - gradient analyses of the post- mitochondria fraction showed that, unlike DAZL, DAZAP1 did not co-sediment with - polyribosomes (Figure 6). - - Figure 6 Sucrose gradient analyses shows that DAZAP1 is not associated with polyribosomes. The post-mitochondrial - supernatant of mouse testis extracts was analyzed on a 15–45% sucrose gradient. Sedimentation was from left to - right. The presence of DAZAP1 and DAZL in each fractions was analyzed by Western blotting. - - Discussion - - RNA-binding proteins have been found to participate in many cellular functions, including RNA transcription, - pre-mRNA processing, mRNA transport, localization, translation and stability [20]. A role for the DAZ family in the - regulation of mRNA translation is supported by lines of circumstantial evidence, including the association of DAZL - with polyribosomes [12]. The absence of DAZAP1 from polyribosomes indicates that it is not directly involved in - protein synthesis. This finding is different from two RNA-binding proteins, FXR1P and FXR2P, that were identified - through their interaction with another polysomal-associated RNA-binding protein, the fragile X mental retardation - protein [21]. Both FXR1P and FXR2P are associated with the polyribosomes [22]. - - The significance of the interaction between DAZAP1 and DAZL/DAZ remains to be defined. These proteins may act - together to facilitate the expression of a set of genes in germ cells. For example, DAZAP1 could be involved in the - transport of the mRNAs of the target genes of DAZL. Alternatively, DAZL and DAZAP1 may act antagonistically to - regulate the timing and the level of expression. Such an antagonistic interaction between two interacting - RNA-binding proteins is exemplified by the neuron-specific nuclear RNA-binding protein, Nova-1. Nova-1 regulates the - alternative splicing of the pre-mRNAs encoding neuronal inhibitory glycine receptor α2 (GlyR α2) [23]. The ability - of Nova-1 to activate exon selection in neurons is antagonized by a second RNA-binding protein, brPTB - (brain-enriched polypyrimidine tract-binding protein), which interacts with Nova-1 and inhibits its function [24]. - DAZAP1 could function in a similar manner by binding to DAZL and inhibiting its function. Comparing the phenotypes - of Dazl1 and Dazap1 single and double knock-out mice may provide some clues to the significance of their - interaction. Dazl1 knock-out mice have already been generated and studied [6]. The spermatogenic defect in the male - becomes apparent only after day 7 post partum when the germ cells are committing to meiosis (H. Cooke, personal - communication). The genomic structure of Dazap1, delineated here, should facilitate the generating of Dazap1 null - mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural substrates - have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and characterized [16]. - Prrp binds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization element (VLE) is sufficient - for the migration and clustering of Vg1 mRNA to the vegetal cortex of mature oocyte. Prrp also interacts through its - proline-rich domain with two microfilament-associated proteins profilin and Mena, which may facilitate the anchoring - of Vg1 mRNA to the vegetal cortex. The Vg1 RNA encodes a member of the transforming growth factor-β family that is - required for generating dorsal mesoderm at the blastula stage of Xenopus embryogenesis [25]. Sequence conservation - between the RBDs of DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST - search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, and possibly DAZAP1, may help to identify - the natural substrates of DAZAP1. - - Conclusions - - DAZAP1 is an evolutionarily conserved RNA-binding protein. It is present at variable levels in many tissues. Its - predominant expression in testes suggests a role in spermatogenesis. In mouse testes, DAZAP1 was found both in the - nuclei and in the cytoplasm. Its absence from polyribosomes indicates that it is not directly involved in mRNA - translation. - - Materials and methods - - Isolation of mouse Dazap1 cDNA clones - - Dazap1 cDNA clones were isolated from a mouse testis cDNA library (#937308, Stratagene, La Jolla, CA) using a human - DAZAP1 cDNA as a probe. The 5' end of the cDNA was isolated by 5' RACE [15], using prdap11 (ttgcgggccatatccttg, - #749–732) as the primer for cDNA synthesis from mouse testis RNA, and prdap37 (ttgttgccacgtgggcg, #734–718) and an - adaptor primer as the primers for PCR amplification. The PCR products were cloned into a TA cloning vector - pCR2.1-TOPO (Invitrogen, Carlsbad CA). Dazap1 clones were identified by colony hybridization and sequenced. The 5' - RACE clone with the longest 5' UTR region and the cDNA clone P21 were ligated together through a unique PmlI site at - # 722 to generate a cDNA clone (Dazap1-C) with a near full-length insert. - - Chromosomal mapping of Dazap1 - - Dazap1 genomic clones were isolated from a mouse 129SV genomic library (#946305, Stragagene), and sequences flanking - each exons were determined. PCR primers (prdap25: cacctccaggatgtgttagc and prdazp26:gtcaccaagggtgtctgaag) were - designed from intronic sequences flanking Dazap1 exon 8. These primers amplified a 271 bp fragment from mouse but - not hamster genomic DNA. DNA samples of a panel of 100 radiation hybrids containing mouse chromosome fragments in a - hamster background were purchased from Research Genetics (Huntsville, AL). The presence of mouse Dazap1 in the - radiation hybrids was determined by PCR and the results were sent to the MIT server for computerized physical - mapping of the gene. - - Expression of Dazap1 transcripts - - Northern hybridization was carried out according to standard procedures [26] using a mouse Multiple Tissue Northern - Blot #7762–1 from Clontech (Palo Alto, CA). The blot was hybridized sequentially with DAZAP1 and β-actin cDNA - probes, with stripping of the bound probes in between. - - Reverse transcription-polymerase chain reaction (RT-PCR) was carried out as preciously described using an annealing - temperature of 54°C [27]. The primers were prdap35: agctcagggagtacttcaaga and prdap24 :ggagcttgattcttgctgtcc for - Dazap1 which generated a product of 211 bp, and prdaz71: atcgaactggtgtgtcgaagg and prdaz72: ggaggctgcatgtaagtctca - for Dazl1 which generated a product of 245 bp. Both primer pairs annealed across intron insertion sites. - - Generation of anti-DAZAP1 antibodies - - Antibodies were generated against both a recombinant protein produced in E. coli and an oligopeptide synthesized in - vitro. The insert of a Dazap1 cDNA clone P21, which encoded the C-terminal portion of DAZAP1 (starting from aa - #197), was cloned in-frame into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, WI). - Sequences at the junctions were verified by DNA sequencing. Milligrams of fusion proteins between thioredoxin and - DAZAP1 were prepared and purified on His-Bind metal chelation resins (Novagen, Madison, WI). The proteins were mixed - with Freund's adjuvant and injected into rabbits to generate the anti-DAZAPl-C antibody. An oligopeptide containing - the last 19 ammo acid residues of the mouse DAZAP1 was synthesized in vitro using the services of Bethyl - Laboratories (Montgomery, TX). The peptide was conjugated to KLH as carrier and injected into a goat. The - anti-DAZAP1-P antibody thus produced was purified on an affinity column containing the oligopeptide antigen. - - Western blotting - - Mouse tissues were homogenized in the RIPA lysis buffer (150 mM NaCl, 1.0% NP-40, 0.5% DOC, 0.1% SDS, 50 mM Tris, pH - 8.0) at a concentration of 0.2 g tissue per ml of buffer. The homogenized samples were cleared of debris by - centrifugation at 10,000 × g for 10 minutes. Protein concentration of the tissue extracts was determined by the - Bradford method using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA). About 50 μg of tissue extracts were - separated on 10% SDS-polyacrylamide gels and blotted with either the anti-DAZAP1-C antibody (at a 1/2,000 dilution) - or the anti-DAZAP1-P antibody (at a 1/5,000 dilution). After incubation with horseradish peroxidase-conjugated - secondary antibodies, the binding of antibodies was detected using the ECL Western Blotting System (Amersham - Pharmacia Biotech, Piscataway, NJ). - - Fractionation of mouse testicular extracts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, - 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors provided in - the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, IN). Homogenates were centrifuged at 1,000 - × g for 10 minutes to pellet cell debris and nuclei. After an additional centrifugation at 10,000 × g for 10 minutes - to pellet the mitochondria, aliquots of the supernatant were applied to 15–45% sucrose gradients in 20 mM Tris, 100 - mM KCl and 5 mM MgCl2 and centrifuged in a Beckman SW41 rotor at 39,000 rpm for 2 hours at 4°C. Fractions of 0.5 ml - were collected from the bottom of the tubes and analyzed by western blotting. - - Acknowledgments - - We thank Gary Kuo for his involvement in the construction of Dazap1 expression vectors, and Ron Swerdloff's group - for helpful discussion. The work was supported by grants from the National Institutes of Health (HD28009 and - HD36347). Y. Vera was supported by an NIH grant (GM56902) on Initiative for Minority Student Development. - - References - - 1. Hackstein JHP, Hochstenbach R, Pearson PL. Towards an understanding of the genetics of human male infertility.. - TIG. 2000;16:565-572. doi: 10.1016/S0168-9525(00)02140-5 - - 2. De Kretser DM. Male infertility.. Lancet. 1997;349:787-790. doi: 10.1016/S0140-6736(96)08341-9 - - 3. Reijo R, Lee T-Y, Salo P, Allagappan R, Brown LG, Rosenberg M, Rozen S, Jaffe T, Straus D, Hovatta O, de la - Chapelle A, Silber S, Page DC. Diverse spermatogenic defects in humans caused by Y chromosome deletions encompassing - a novel RNA-binding protein gene.. Nat Genet. 1995;10:383-393. doi: 10.1038/ng0895-383 - - 4. Cooke HJ, Lee M, Kerr S, Ruggiu M. A murine homologue of the human DAZ gene is autosomal and expressed only in - male and female gonads.. Hum Mol Genet. 1996;5:513-516. doi: 10.1093/hmg/5.4.513 - - 5. Xu EY, Moore FL, Pera RAR. A gene family required for human germ cell development evolved from an ancient meiotic - gene conserved in metazoans.. PNAS. 2001;98:7414-7419. doi: 10.1073/pnas.131090498 - - 6. Ruggiu M, Speed R, Taggart M, McKay SJ, Kilanowski F, Saunders P, Dorin J, Cooke HJ. The mouse DAZLA gene encodes - a cytoplasmic protein essential for gametogenesis.. Nature. 1997;389:73-77. doi: 10.1038/37987 - - 7. Eberhar CG, Maines JZ, Wasserman SA. Meiotic cell cycle requirement for a fly homologue of human Deleted in - Azoospermia.. Nature. 1996;381:783-785. doi: 10.1038/381783a0 - - 8. Karashima T, Sugimoto A, Yamamoto M. Caenorhabditis elegans homologue of the human azoospermia factor DAZ is - required for oogenesis but not for spermatogenesis.. Development. 2000;127:1069-1079. - - 9. Houston DW, Zhang J, Maines JZ, Wasserman SA, King ML. A Xenopus DAZ-like gene encodes an RNA component of germ - plasm and is a functional homologue of Drosophila boule.. Development. 1998;125:171-180. - - 10. Reijo RA, Dorfman DM, Slee R, Renshaw AA, Laughlin KR, Cooke H, Page DC. DAZ family proteins exist through male - germ cell development and transit from nucleus to cytoplasm at meiosis in humans and mice.. Biol Reprod. - 2000;63:1490-1496. - - 11. Maines JZ, Wasserman SA. Post-transcriptional regulation of the meiotic Cdc25 protein Twine by the Daz1 - orthologue Boule.. Nat Cell Biol. 1999;1:171-174. doi: 10.1038/11091 - - 12. Tsui S, Dai T, Warren ST, Salido EC, Yen PH. Association of the infertility factor DAZL1 with actively - translating polyribosomes.. Biol Reprod. 2000;62:1655-1660. - - 13. Venables JP, Ruggiu M, Cooke HJ. The RNA-binding specificity of the mouse Daz1 protein.. Nucl Acids Res. - 2001;29:2479-2483. doi: 10.1093/nar/29.12.2479 - - 14. Tsui S, Dai T, Roettger S, Schempp W, Salido EC, Yen PY. Identification of two novel proteins that interact with - germ-cell specific RNA-binding proteins DAZ and DAZL1.. Genomics. 2000;65:266-273. doi: 10.1006/geno.2000.6169 - - 15. Frohman MA, Dush MK, Martin GR. Rapid production of full-length cDNAs from rare transcripts: amplification using - a single gene-specific oligonucleotide primer.. PNAS. 1988;85:8998-9002. - - 16. Zhao W, Jiang C, Kroll TT, Huber PW. proline-rich protein binds to the localization element of Xenopus Vg1 mRNA - and to ligands involved in actin polymerization.. EMBO J. 2001;20:2315-2325. doi: 10.1093/emboj/20.9.2315 - - 17. DeBry RW, Seldin MF. Human/mouse homology relationships.. Genomics. 1996;33:337-351. doi: 10.1006/geno.1996.0209 - - 18. Fleischman RA. From white spots to stem cells: The role of the Kit receptor in mammalian development.. Trends - Genet. 1993;9:285-290. doi: 10.1016/0168-9525(93)90015-A - - 19. Hofmann MC, Narisawa S, Hess RA, Millan JL. Immortalization of germ cells and somatic testicular cells using the - SV40 large T antigen.. Exp Cell Res. 1992;201:417-435. doi: 90291-F - - 20. Siomi H, Dreyfuss G. RNA-binding proteins as regulators of geneexpression.. Cur Opin Genet Develop. - 1997;7:345-353. doi: 10.1016/S0959-437X(97)80148-7 - - 21. Zhang Y, O'Connor JP, Siomi MC, Srinivasan S, Dutra A, Nussbaum RL, Dreyfuss G. The fragile X mental retardation - syndrome protein interacts with novel homologs FXR1 and FXR2.. EMBO J. 1995;14:5358-5366. - - 22. Siomi MC, Zhang Y, Siomi H, Dreyfuss G. Specific sequences in the fragile X syndrome protein FMR1 and the FXR2 - proteins mediate their binding to 60S ribosomal subunits and the interactions among them.. Mol Cell Biol. - 1996;16:3825-3832. - - 23. Jensen KB, Dredge BK, Stefani G, Zhong R, Buckanovich RJ, Okano HJ, Yang YY, Darnell RB. Nova-1 regulates - neuron-specific alternative splicing and is essential for neuronal viability.. Neuron. 2000;25:359-371. doi: - 10.1016/S0896-6273(00)80900-9 - - 24. Polydorides AD, Okano HJ, Yang YY, Stefani G, Darnell RB. A brain-enriched polypyrimidine tract-binding protein - antagonizes the ability of Nova to regulate neuron-specific alternative splicing.. PNAS. 2000;97:6350-6355. doi: - 10.1073/pnas.110128397 - - 25. Thomson GH, Melton DA. Processed Vg1 protein is an axial mesoderm inducer in Xenopus.. Cell. 1993;74:433-441. - doi: 10.1016/0092-8674(93)80045-G - - 26. Sambrook J, Fritsch EF, Maniatis T. null. Molecular Cloning: A Laboratory Manual 2nd ed, Cold Spring Harbor - Laboratory Press, Cold Spring Harbor,. 1989;null:null-null. - - 27. Salido EC, Yen PH, Mohandas TK, Shapiro LJ. Expression of the X-inactivation-associated gene XIST during - spermatogenesis.. Nat Genet. 1992;2:196-199. doi: 10.1038/ng1192-196 - - -

      -
    • -
        -
      • Mike Bada
        • -
      • class = canonical nucleoside residues
        • -
      • spans =
        • -
      -
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    carbon

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    Text source name = 11532192.txt -

    ins. Most tested strains exhibit a diurnal rhythm with IOP being the highest during the dark period of the day. - Homozygosity for a null allele of the carbonic anhydrase II gene (Car2n) does not alter IOP while - homozygosity for a mutation in the leptin receptor gene (Leprdb) that causes obesity and diabetes -

      -
    • - carbonic -
        -
      • Mike Bada
        • -
      • class = carbon
        • -
      • spans = 1189|1197
        • -
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    Text source name = 11532192.txt -

    evant to glaucoma. - - Car2 deficiency does not alter IOP - - Bicarbonate formation is important for aqueous humor secretion from the ciliary processes and carbonic - anhydrase (CA) facilitates this secretion. There are multiple forms of CA and the CAII isoform is reported to be the - predominant form in the ciliary -

      -
    • - carbonic -
        -
      • Mike Bada
        • -
      • class = carbon
        • -
      • spans = 31345|31353
        • -
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    Text source name = 11532192.txt -

    rified and sequenced as described [22]. - - Abbreviations - - Intraocular pressure (IOP), C57BL/6J (B6), chromosome (Chr), polymerase chain reaction (PCR), carbonic - anhydrase (CA) - - Acknowledgments - - We thank Norma Buckley, Felicia Farley and Jennifer Smith for their assistance with data entry, references, and figu -

      -
    • - carbonic -
        -
      • Mike Bada
        • -
      • class = carbon
        • -
      • spans = 39453|39461
        • -
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    Text source name = 11532192.txt -

    ± SD; db/db 422 ± 110 mg/dl ; db/+ 147 ± 19 mg/dl; Anthony Nicholson, The Jackson Laboratory, personal communication) - - Car2 - - To test if deficiency of carbonic anhydrase II leads to decreased IOP, we analyzed mice of a B6 background - that were genetically similar but with normal or mutant alleles of the Car2 -

      -
    • - carbonic -
        -
      • Mike Bada
        • -
      • class = carbon
        • -
      • spans = 19152|19160
        • -
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    carboxy group

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    Text source name = 11604102.txt -

    nst both a recombinant protein produced in E. coli and an oligopeptide synthesized in vitro. The insert of a Dazap1 - cDNA clone P21, which encoded the C-terminal portion of DAZAP1 (starting from aa #197), was cloned in-frame - into the EcoRI/XhoI sites of an expression vector pET32b (Novagen, Madison, W -

      -
    • - C -
        -
      • Mike Bada
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      • class = carboxy group
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      • spans = 18031|18032
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    Text source name = 11604102.txt -

    e C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised against an oligopeptide containing the - last 19 amino acid residue at the C-terminus. Both antibodies recognized in vitro synthesized DAZAP1 in an - immunoprecipitation assay (data not shown). Western blotting of mouse tissue e -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
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      • spans = 9861|9862
        • -
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    Text source name = 11604102.txt -

    oteins (DAZAPs) [14]. One of them, DAZAP1, is expressed predominantly in testes. It encodes a protein with two RNA - binding domains and a proline rich C-terminal portion. The DAZAP1 protein interacted with both DAZ and DAZL - in vitro. It also bound to RNA homopolymers. We now report our characterizatio -

      -
    • - C -
        -
      • Mike Bada
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      • class = carboxy group
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      • spans = 4336|4337
        • -
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    Text source name = 11604102.txt -

    AZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti DAZAP1-C antibody was raised against a - recombinant protein containing the C-terminal proline-rich portion, and the anti DAZAP1-P antibody was raised - against an oligopeptide containing the last 19 amino acid residue at the C-t -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = carboxy group
        • -
      • spans = 9713|9714
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    Text source name = 11604102.txt -

    identity). There is an insertion of a 58 bp segment in Prrp cDNA that causes a change of reading frame and results in - a shorter Prrp with a different C-terminal end sequence. - - Figure 1 Evolutionary conservation of the DAZAP1 proteins. The amino acid sequences of the human and mouse DAZAP1s - and the Xe -

      -
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      • class = carboxy group
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      • spans = 6184|6185
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    Text source name = 11604102.txt -

    similarity and 97% and 92% identity, respectively, between DAZAP1 and Prrp. These proteins may therefore have a - similar RNA binding specificity. The C-terminal proline-rich portions of DAZAP1 and Prrp are less conserved - (81% similarity and 71% identity). There is an insertion of a 58 bp segment in P -

      -
    • - C -
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      • Mike Bada
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      • class = carboxy group
        • -
      • spans = 5939|5940
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    Text source name = 11604102.txt -

    any) fragments from genomic DNA. - - To study the expression of the DAZAP1 protein, two antibodies against mouse DAZAP1 were generated. The anti - DAZAP1-C antibody was raised against a recombinant protein containing the C-terminal proline-rich portion, - and the anti DAZAP1-P antibody was raised against a -

      -
    • - C -
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      • class = carboxy group
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      • spans = 9646|9647
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    Text source name = 11604102.txt -

    system (Bio-Rad, Hercules, CA). About 50 μg of tissue extracts were separated on 10% SDS-polyacrylamide gels and - blotted with either the anti-DAZAP1-C antibody (at a 1/2,000 dilution) or the anti-DAZAP1-P antibody (at a - 1/5,000 dilution). After incubation with horseradish peroxidase-conjugated secon -

      -
    • - C -
        -
      • Mike Bada
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      • class = carboxy group
        • -
      • spans = 19406|19407
        • -
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    Text source name = 11604102.txt -

    h both the Y chromosome-encoded DAZ and an autosome-encoded DAZ-like protein, DAZL. DAZAP1 contains two RNA-binding - domains (RBDs) and a proline-rich C-terminal portion, and is expressed most abundantly in the testis. To - understand the biological function of DAZAP1 and the significance of its interac -

      -
    • - C -
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      • class = carboxy group
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      • spans = 890|891
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    Text source name = 11604102.txt -

    he human 3' UTR, respectively. These segments probably contain regulatory elements. - - The DAZAP1 protein contains two RNA-binding domains (RBDS) and a C-terminal portion that is rich in proline - (Figure 1). It is highly conserved evolutionarily. The mouse and the human proteins differ in 9 amino acids -

      -
    • - C -
        -
      • Mike Bada
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      • class = carboxy group
        • -
      • spans = 5388|5389
        • -
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    cytidyl groups

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    Text source name = 11604102.txt -

    [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = cytidyl groups
        • -
      • spans = 3904|3905
        • -
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    cytosin-1-yl group

    -
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    Text source name = 11604102.txt -

    [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to -

      -
    • - C -
        -
      • Mike Bada
        • -
      • class = cytosin-1-yl group
        • -
      • spans = 3904|3905
        • -
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    deoxyribonucleic acids

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    double-stranded DNA

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    drug

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    Text source name = 11532192.txt -

    ng this period in any analyzed strain. Environmental differences may be important. Cage cleanliness, changing - frequency and housing density can alter drug metabolism and the effect of anesthesia in rats [38,39]. The - type of bedding used also may be important. We use wood shavings for bedding and wood sh -

      -
    • - drug -
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      • class = drug
        • -
      • spans = 25369|25373
        • -
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    vings for bedding and wood shavings expose the mice to terpenes. Terpene administration or environmental exposure to - terpenes in wood shavings alters drug resistance and decreases the effect of anesthetic agents in both rats - and mice [40-45]. - - Risk factors for increased IOP - - Some epidemiological studies -

      -
    • - drug -
        -
      • Mike Bada
        • -
      • class = drug
        • -
      • spans = 25644|25648
        • -
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    glutamate residue

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    glutamate(1-)

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    Text source name = 11319941.txt -

    l portion of Chr 10 in proximity with a number of genes known to affect brain development. One of these is Grk2, a - member of the family of ionotropic glutamate receptor genes that is thought to play a role in modulating - Huntington disease [44]. In the mouse, members of this receptor type act to indirectly do -

      -
    • - glutamate -
        -
      • Mike Bada
        • -
      • class = glutamate(1-)
        • -
      • spans = 21235|21244
        • -
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    -

    glutamate(2-)

    -

    glycine

    -

    guanine group

    -
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    Text source name = 11604102.txt -

    should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanine group
        • -
      • spans = 14030|14031
        • -
      -
    -
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    Text source name = 11604102.txt -

    estes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family an -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanine group
        • -
      • spans = 3899|3900
        • -
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    Text source name = 11532192.txt -

    sertion allele. The other allele was identical to the published sequence [22]. The insertion allele also had a - previously reported substitution (A to G, Thr164Ala) in exon 1 and several other single base changes in the - promoter region [22]. The presence or absence of this allele does not associate wi -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanine group
        • -
      • spans = 16993|16994
        • -
      -
    -

    guanosyl groups

    -
    -

    Text source name = 11604102.txt -

    estes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to - oligo(U) stretches interspersed by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C - mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family an -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanosyl groups
        • -
      • spans = 3899|3900
        • -
      -
    -
    -

    Text source name = 11604102.txt -

    should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds -

      -
    • - G -
        -
      • Mike Bada
        • -
      • class = guanosyl groups
        • -
      • spans = 14030|14031
        • -
      -
    -

    histidine

    -

    hydrogencarbonate

    -

    inhibitor

    -
    -

    Text source name = 11597317.txt -

    ptide consisting of one of the eight BRC repeats from human BRCA2. Expression of a single BRC repeat (BRC4) had - previously been reported to act as an inhibitor of DNA repair by Chen et al [27]. These investigators showed - that expression of constructs containing the BRC4 repeat in MCF-7 cells enhances the rad -

      -
    • - inhibitor -
        -
      • Mike Bada
        • -
      • class = inhibitor
        • -
      • spans = 7572|7581
        • -
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    -
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    Text source name = 11604102.txt -

    cts - - Adult mouse testes were homogenized in a buffer containing 20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP-40, - 40 U/ml of Rnasin ribonuclase inhibitor (Promega, Madison, WI), and a mixture of 10 protease inhibitors - provided in the Protease Inhibitors Set (Roche Molecular Biochemicals, Indianapolis, -

      -
    • - inhibitor -
        -
      • Mike Bada
        • -
      • class = inhibitor
        • -
      • spans = 19887|19896
        • -
      -
    -

    magnesium dichloride

    -

    messenger RNA

    -

    metal cations

    -

    metals

    -

    molecular entities

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    -

    Text source name = 11532192.txt -

    hese risk factors. - - IOP is increased during the dark period of the day - - Diurnal variation in IOP is common in humans and laboratory animals [53]. The molecular mechanisms underlying - the diurnal rhythm are not defined but increased aqueous humor production or flow occurs during the period of - increased IOP in -

      -
    • - molecular -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 29448|29457
        • -
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    Text source name = 11319941.txt -

    d Not genes. Vax1 is localized during development to the anterior ventral forebrain, and is expressed in the striatum - during embryogenesis [28]. This molecule also has an important role in axon guidance: both the anterior - portion of the corpus callosum and the optic chiasm are malformed or absent in Vax1 kn -

      -
    • - molecule -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 22409|22417
        • -
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    Text source name = 11319941.txt -

    rior portion of the corpus callosum and the optic chiasm are malformed or absent in Vax1 knockout mice [49]. In - addition, Vax1 interacts with several molecules including sonic hedgehog,Pax2, Pax6, and Rx that are known to - be important during development of the basal forebrain [27, 50]. - - Brain volume and neur -

      -
    • - molecules -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 22626|22635
        • -
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    Text source name = 11532192.txt -

    accurate and rapid enough to allow large scale genetic studies of factors determining IOP. Mice have great potential - for helping to characterize the molecular mechanisms affecting IOP. - - Materials and Methods - - Animal husbandry - - All experiments were performed in compliance with the ARVO statement for use of a -

      -
    • - molecular -
        -
      • Mike Bada
        • -
      • class = molecular entities
        • -
      • spans = 34211|34220
        • -
      -
    -

    nucleotidyl groups

    -
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    Text source name = 11532192.txt -

    OP in mouse strains, we analyzed the gene in an assortment of strains with different IOPs. Two alleles were - identified. One of these alleles had a 12 nucleotide insertion in the promoter region (ccagagcagggt, between - positions -340 and -341) compared to the previously published sequence and is called the inse -

      -
    • - nucleotide -
        -
      • Mike Bada
        • -
      • class = nucleotidyl groups
        • -
      • spans = 16685|16695
        • -
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    Text source name = 11604102.txt -

    ral substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. Prrp binds to a 340 nt sequence in the 3' UTR of Xenopus Vg1 mRNA. This Vg1 localization - element (VLE) is sufficient for the migration and clustering of Vg1 mRNA to the veg -

      -
    • - nt -
        -
      • Mike Bada
        • -
      • class = nucleotidyl groups
        • -
      • spans = 14191|14193
        • -
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    Text source name = 11604102.txt -

    etween the RBDs of DAZAP1 and Prrp suggests that these proteins may bind to similar RNA sequences. However, a BLAST - search of the GenBank for the 340 nt VLE sequence failed to identify any mammalian sequences with significant - homology. Further mapping of the RNA sequence within VLE that binds Prrp, an -

      -
    • - nt -
        -
      • Mike Bada
        • -
      • class = nucleotidyl groups
        • -
      • spans = 14903|14905
        • -
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    oligopeptides

    -

    peptides

    -

    phosphate(3-)

    -

    phosphates

    -

    pigment

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    Text source name = 11532192.txt -

    nt with this result, mice with albino eyes that are homozygous for tyrosinase or pink eye dilution mutations have - altered diurnal rhythms compared to pigmented mice [75]. Albinism by itself is either not sufficient to alter - the diurnal rhythm of IOP or alters it in different ways depending upon genetic backg -

      -
    • - pigmented -
        -
      • Mike Bada
        • -
      • class = pigment
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      • spans = 33044|33053
        • -
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    -

    Text source name = 11532192.txt -

    these abnormalities affect mammalian IOP. Here, we show increased IOP in mice lacking tyrosinase activity compared to - otherwise genetically identical pigmented B6 mice. Additionally, IOP differences between the light and dark - period of the day were detected in the pigmented but not the albino B6 mice. Thus, -

      -
    • - pigmented -
        -
      • Mike Bada
        • -
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      -
    -
    -

    Text source name = 11532192.txt -

    to otherwise genetically identical pigmented B6 mice. Additionally, IOP differences between the light and dark period - of the day were detected in the pigmented but not the albino B6 mice. Thus, albinism can affect the diurnal - pattern of IOP changes. In agreement with this result, mice with albino eyes that a -

      -
    • - pigmented -
        -
      • Mike Bada
        • -
      • class = pigment
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      -
    -

    potassium chloride

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    proline

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    -
    -

    Text source name = 11604102.txt -

    in interacted with both DAZ and DAZL in vitro. It also bound to RNA homopolymers. We now report our characterization - of the mouse Dazap1 gene and its protein product. The subcellular localization of DAZAP1 suggests that it is - not involved directly in mRNA translation. - - Results - - Characterization of the mouse Dazap1 -

      -
    • - protein product -
        -
      • Mike Bada
        • -
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      -
    -
    -

    Text source name = 11604102.txt -

    nteraction with DAZ and DAZL, we isolated and characterized the mouse Dazap1 gene, and studied its expression and the - subcellular localization of its protein product. - - Results - - The human and mouse genes have similar genomic structures and map to syntenic chromosomal regions. The mouse and - human DAZAP1 proteins sha -

      -
    • - protein product -
        -
      • Mike Bada
        • -
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        • -
      -
    • - protein -
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      • Kristin Garcia
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      -
    -

    ribonucleic acids

    -

    single-stranded DNA

    -

    sodium chloride

    -

    sodium dodecyl sulfate

    -

    sodium phosphates

    -

    sucrose

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    terpenes

    -

    tert-pentyl group

    -

    tris

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    uracil-1-yl group

    -
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    Text source name = 11604102.txt -

    eated here, should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. -

      -
    • - U -
        -
      • Mike Bada
        • -
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    Text source name = 11604102.txt -

    with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid - system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich segment - in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the funct -

      -
    • - U -
        -
      • Mike Bada
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    Text source name = 11604102.txt -

    ZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) stretches interspersed - by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechan -

      -
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      • Mike Bada
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    -
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    Text source name = 11604102.txt -

    eated here, should facilitate the generating of Dazap1 null mutation. - - DAZAP1 was shown to bind RNA homopolymers in vitro, with a preference for poly U and poly G. Its natural - substrates have not been identified. Recently, the Xenopus orthologue of DAZAP1, Prrp, was identified and - characterized [16]. -

      -
    • - U -
        -
      • Mike Bada
        • -
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    Text source name = 11604102.txt -

    ZL was shown both in vitro and in a yeast three-hybrid system to bind specifically to oligo(U) stretches interspersed - by G or C residues, including a U-rich segment in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the function of the DAZ gene family and to understanding the mechan -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uridyl groups
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    Text source name = 11604102.txt -

    with polyribosomes in mouse testes [12]. More recently, DAZL was shown both in vitro and in a yeast three-hybrid - system to bind specifically to oligo(U) stretches interspersed by G or C residues, including a U-rich segment - in the 5' UTR of mouse Cdc25C mRNA [13]. - - In an attempt to elucidate the funct -

      -
    • - U -
        -
      • Mike Bada
        • -
      • class = uridyl groups
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    water

    -
    -

    Text source name = 11532192.txt -

    ariation in IOP is common in humans and laboratory animals [53]. The molecular mechanisms underlying the diurnal - rhythm are not defined but increased aqueous humor production or flow occurs during the period of increased - IOP in both rabbits and humans [63-65]. Small changes in the resistance to aqueous hum -

      -
    • - aqueous -
        -
      • Mike Bada
        • -
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    Text source name = 11532192.txt -

    important approaches as they may allow the association of genes with IOP and glaucoma whose currently known functions - do not suggest that they affect aqueous humor dynamics or do not immediately identify them as likely glaucoma - candidates. - - No effect of anesthetic protocol on IOP during a 12 minute measure -

      -
    • - aqueous -
        -
      • Mike Bada
        • -
      • class = water
        • -
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      -
    -
    -

    Text source name = 11532192.txt -

    sed aqueous humor production or flow occurs during the period of increased IOP in both rabbits and humans [63-65]. - Small changes in the resistance to aqueous humor drainage may also contribute to diurnal differences in IOP - [66,67]. We first suspected IOP changes with time of day when the IOP of a group of -

      -
    • - aqueous -
        -
      • Mike Bada
        • -
      • class = water
        • -
      • spans = 29675|29682
        • -
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    +Each concept that was considered a non-match is shown in the text that it was found in. Overlapping annotations from the other concept sets are also shown. For more detailed documentation on Iaa please see the Iaa documentation. + +

    +

    +

    +

    +

    +

    +

    +

    • +
      • Mike Bada
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    +

    +

    • +
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    • +
      • Mike Bada
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    • +
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    +

    +

    +

    • +
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    • +
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    +

    • +
      • Mike Bada
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    +

    +

    • +
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    +

    • +
      • Mike Bada
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    +

    • +
      • Mike Bada
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    +

    +

    +

    • +
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    +

    +

    +

    • +
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    +

    • +
      • Mike Bada
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    +

    • +
      • Mike Bada
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    +

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    • +
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    +

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    • +
      • Mike Bada
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    +

    • +
      • Mike Bada
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    +

    +

    +

    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:33791
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    +

    +

    • +
      • Mike Bada
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    +

    • +
      • Mike Bada
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      • spanCollection = tivity of [7572, 7581]
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    +

    +

    +

    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = able infor [22370, 22380]
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    • +
      • Mike Bada
      • class = CHEBI:38867
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    • +
      • Mike Bada
      • class = CHEBI:38867
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    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = y anesthet [22840, 22850]
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    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = ask geneti [23386, 23396]
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    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = be important. Ca [25688, 25705]
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    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = he effects [13227, 13237]
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    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = s doses of [14779, 14789]
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    +

    • +
      • Mike Bada
      • class = CHEBI:38867
      • spanCollection = producibility als [22441, 22458]
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    • +
      • Mike Bada
      • class = CHEBI:38867
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    • +
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    • +
      • Mike Bada
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    • +
      • Mike Bada
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    CHEBI_15377

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    +

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      • Mike Bada
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    • +
      • Mike Bada
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    • +
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      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_23367
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    CHEBI_25213

    +

    CHEBI_25613

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      • Mike Bada
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    CHEBI_25676

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      • Mike Bada
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    CHEBI_30879

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    CHEBI_32588

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      • spanCollection = tected a 4 [9835, 9845]
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    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
      • spanCollection = to a goat. The ant [18545, 18563]
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    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_33708
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    • +
      • Kristin Garcia
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    CHEBI_33709

    +

    CHEBI_35186

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    CHEBI_36080

    +

    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = n that is most [1185, 1200]
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      • Kristin Garcia
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
      • spanCollection = n that [1185, 1192]
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    +

    • +
      • Mike Bada
      • class = http://www.owl-ontologies.com/unnamed.owl#CHEBI_36080
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    CHEBI_37586

    +

    CHEBI_6636

    +

    CHEBI_8984

    +

    CHEBI_9754

    diff --git a/src/test/resources/iaa_test_project/iaa/index.html b/src/test/resources/iaa_test_project/iaa/index.html index 3f08fd3e..ba1e57ee 100644 --- a/src/test/resources/iaa_test_project/iaa/index.html +++ b/src/test/resources/iaa_test_project/iaa/index.html @@ -1,7 +1,7 @@ - -Inter-Annotator Agreement - -
      -
    • Class matcher
      • -
    • Span matcher
      • -
    • Class and span matcher
      • +Inter-Profile Agreement + + diff --git a/src/test/resources/import_test_project1/Annotations/d1.xml b/src/test/resources/import_test_project1/Annotations/d1.xml new file mode 100644 index 00000000..7af151f1 --- /dev/null +++ b/src/test/resources/import_test_project1/Annotations/d1.xml @@ -0,0 +1,9 @@ + + + + + + a + + + diff --git a/src/test/resources/import_test_project1/Articles/d1.txt b/src/test/resources/import_test_project1/Articles/d1.txt new file mode 100644 index 00000000..b0883f38 --- /dev/null +++ b/src/test/resources/import_test_project1/Articles/d1.txt @@ -0,0 +1 @@ +abcdefghijklmnopqrstuvwxyz diff --git a/src/test/resources/import_test_project1/import_test_project1.knowtator b/src/test/resources/import_test_project1/import_test_project1.knowtator new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/import_test_project2/Annotations/d1.xml b/src/test/resources/import_test_project2/Annotations/d1.xml new file mode 100644 index 00000000..c3edd335 --- /dev/null +++ b/src/test/resources/import_test_project2/Annotations/d1.xml @@ -0,0 +1,13 @@ + + + + + + a + + + + a + + + diff --git a/src/test/resources/import_test_project2/Articles/d1.txt b/src/test/resources/import_test_project2/Articles/d1.txt new file mode 100644 index 00000000..b0883f38 --- /dev/null +++ b/src/test/resources/import_test_project2/Articles/d1.txt @@ -0,0 +1 @@ +abcdefghijklmnopqrstuvwxyz diff --git a/src/test/resources/import_test_project2/import_test_project2.knowtator b/src/test/resources/import_test_project2/import_test_project2.knowtator new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/import_test_project3/Annotations/d1.xml b/src/test/resources/import_test_project3/Annotations/d1.xml new file mode 100644 index 00000000..3af8697c --- /dev/null +++ b/src/test/resources/import_test_project3/Annotations/d1.xml @@ -0,0 +1,9 @@ + + + + + + a + + + diff --git a/src/test/resources/import_test_project3/import_test_project3.knowtator b/src/test/resources/import_test_project3/import_test_project3.knowtator new file mode 100644 index 00000000..e69de29b