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OCRA_DEG_Pathways.r
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###### Pathway analysis of OCRA RNASeq comparisons ######
library(magrittr)
library(clusterProfiler)
# Load DEEG Objects from ocra_rnaseq.R script
load("~/OCRA/DEG_Objects_OCRA.Rda")
res # OvCancer vs Normal #
res <- na.omit(res)
norm.can.path <- res[res$padj < 0.05, ]$log2FoldChange
## Name for each gene need to be in entrezid
library(biomaRt)
mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
genes.mart <-
getBM(attributes = c("ensembl_gene_id", "entrezgene_id"),
values = substr(rownames(res[res$padj < 0.05, ]),1,15), mart = mart)
res$entrezid <- genes.mart$entrezgene_id[match(substr(rownames(res),1,15), genes.mart$ensembl_gene_id)]
names(norm.can.path) <- res[res$padj < 0.05,]$entrezid
gene.df <- bitr(names(norm.can.path), fromType = "ENTREZID",
toType = c("ENSEMBL", "SYMBOL"),
OrgDb = org.Hs.eg.db)
gene.df <- gene.df[gene.df$ENSEMBL %in% substr(rownames(res),1,15),]
aux <- res[substr(rownames(res),1,15) %in% gene.df$ENSEMBL, ]
gene.df$FC <- aux$log2FoldChange[match(substr(rownames(aux),1,15), gene.df$ENSEMBL)]
ego <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
head(ego)
ego.mf <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "MF",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
ego.cc <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "CC",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
norn.can.kk <- enrichKEGG(gene = gene.df$ENTREZID,
organism = 'hsa',
pvalueCutoff = 0.05, qvalueCutoff = 1)
#geneList = sort(norm.can.path, decreasing = TRUE)
e.go.bp <- setReadable(ego, 'org.Hs.eg.db', 'ENSEMBL')
e.go.mf <- setReadable(ego.mf, 'org.Hs.eg.db', 'ENSEMBL')
e.go.cc <- setReadable(ego.cc, 'org.Hs.eg.db', 'ENSEMBL')
write.table(e.go.bp, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/NormalvsOvCancer_GO_ORA_BP_table.tsv")
write.table(e.go.mf, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/NormalvsOvCancer_GO_ORA_MF_table.tsv")
write.table(e.go.cc, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/NormalvsOvCancer_GO_ORA_CC_table.tsv")
library(enrichplot)
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_NormalsvsCancer_GOBP.pdf", 17, 15)
dotplot(ego, showCategory=50, title = "ORA - Normal vs Ovarian Cancer , GO BP")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_NormalsvsCancer_GOMF.pdf", 17, 15)
dotplot(ego.mf, showCategory=50, title = "ORA - Normal vs Ovarian Cancer , GO MF")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_NormalsvsCancer_GOCC.pdf", 17, 15)
dotplot(ego.cc, showCategory = 50, title = "ORA - Normal vs Ovarian Cancer , GO CC")
dev.off()
#Goplots
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_NormalsvsCancer_GOBP.pdf", 20, 15)
goplot(ego, showCategory=20, title = "ORA - Normals vs ovCancer , GO BP")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_NormalsvsCancer_GOMF.pdf", 20, 15)
goplot(ego.mf, showCategory=20, title = "ORA - Normals vs ovCancer , GO MF")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_NormalsvsCancer_GOCC.pdf", 20, 15)
goplot(ego.cc, showCategory=20, title = "ORA - Normals vs ovCancer , GO CC")
dev.off()
# HGSOC vs FTSEC #
res2
res2 <- na.omit(res2)
hg.ft.path <- res2[res2$padj < 0.05, ]$log2FoldChange
## Name for each gene need to be in entrezid
#mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
genes.mart <-
getBM(attributes = c("ensembl_gene_id", "entrezgene_id"),
values = substr(rownames(res2[res2$padj < 0.05, ]),1,15), mart = mart)
res2$entrezid <- genes.mart$entrezgene_id[match(substr(rownames(res2),1,15), genes.mart$ensembl_gene_id)]
names(hg.ft.path) <- res2[res2$padj < 0.05,]$entrezid
gene.df <- bitr(names(hg.ft.path), fromType = "ENTREZID",
toType = c("ENSEMBL", "SYMBOL"),
OrgDb = org.Hs.eg.db)
# gene.df <- gene.df[gene.df$ENSEMBL %in% substr(rownames(res),1,15),]
# aux <- res[substr(rownames(res),1,15) %in% gene.df$ENSEMBL, ]
# gene.df$FC <- aux$log2FoldChange[match(substr(rownames(aux),1,15), gene.df$ENSEMBL)]
hg.ft.ego.bp <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
head(hg.ft.ego.bp)
hg.ft.ego.mf <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "MF",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
hg.ft.ego.cc <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "CC",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
hg.ft.kk <- enrichKEGG(gene = gene.df$ENTREZID,
organism = 'hsa',
pvalueCutoff = 0.05, qvalueCutoff = 1)
#geneList = sort(norm.can.path, decreasing = TRUE)
e.hg.ft.ego.bp <- setReadable(hg.ft.ego.bp, 'org.Hs.eg.db', 'ENSEMBL')
e.hg.ft.ego.mf <- setReadable(hg.ft.ego.mf, 'org.Hs.eg.db', 'ENSEMBL')
e.hg.ft.ego.cc <- setReadable(hg.ft.ego.cc, 'org.Hs.eg.db', 'ENSEMBL')
e.gh.ft.kk <- setReadable(hg.ft.kk, 'org.Hs.eg.db', 'ENTREZID')
write.table(e.hg.ft.ego.bp, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/HGSOCvsFTSEC_GO_ORA_BP_table.tsv")
write.table(e.hg.ft.ego.mf, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/HGSOCvsFTSEC_GO_ORA_MF_table.tsv")
write.table(e.hg.ft.ego.cc, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/HGSOCvsFTSEC_GO_ORA_CC_table.tsv")
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_HGSOCvsFTSEC_GOBP.pdf", 17, 15)
dotplot(hg.ft.ego.bp, showCategory=50, title = "ORA - HGSOC vs FTSEC , GO BP")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_HGSOCvsFTSEC_GOMF.pdf", 17, 15)
dotplot(hg.ft.ego.mf, showCategory=50, title = "ORA - HGSOC vs FTSEC , GO MF")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_HGSOCvsFTSEC_GOCC.pdf", 17, 15)
dotplot(hg.ft.ego.cc, showCategory=50, title = "ORA - HGSOC vs FTSEC , GO CC")
dev.off()
#Goplots
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_HGSOCvsFTSEC_GOBP.pdf", 20, 15)
goplot(hg.ft.ego.bp, showCategory=20, title = "ORA - HGSOC vs FTSEC , GO BP")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_HGSOCvsFTSEC_GOMF.pdf", 20, 15)
goplot(hg.ft.ego.mf, showCategory=20, title = "ORA - HGSOC vs FTSEC , GO MF")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_HGSOCvsFTSEC_GOCC.pdf", 20, 15)
goplot(hg.ft.ego.cc, showCategory=20, title = "ORA - HGSOC vs FTSEC , GO CC")
dev.off()
# IOSE vs HGSOC #
res3
res3 <- na.omit(res3)
io.hg.path <- res3[res3$padj < 0.05, ]$log2FoldChange
## Name for each gene need to be in entrezid
#mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
genes.mart <-
getBM(attributes = c("ensembl_gene_id", "entrezgene_id"),
values = substr(rownames(res3[res3$padj < 0.05, ]),1,15), mart = mart)
res3$entrezid <- genes.mart$entrezgene_id[match(substr(rownames(res3),1,15), genes.mart$ensembl_gene_id)]
names(io.hg.path) <- res3[res3$padj < 0.05,]$entrezid
gene.df <- bitr(names(io.hg.path), fromType = "ENTREZID",
toType = c("ENSEMBL", "SYMBOL"),
OrgDb = org.Hs.eg.db)
# gene.df <- gene.df[gene.df$ENSEMBL %in% substr(rownames(res),1,15),]
# aux <- res[substr(rownames(res),1,15) %in% gene.df$ENSEMBL, ]
# gene.df$FC <- aux$log2FoldChange[match(substr(rownames(aux),1,15), gene.df$ENSEMBL)]
io.hg.ego.bp <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
head(io.hg.ego.bp)
io.hg.ego.mf <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "MF",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
io.hg.ego.cc <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "CC",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
io.hg.kk <- enrichKEGG(gene = gene.df$ENTREZID,
organism = 'hsa',
pvalueCutoff = 0.05, qvalueCutoff = 1)
#geneList = sort(norm.can.path, decreasing = TRUE)
e.io.hg.ego.bp <- setReadable(io.hg.ego.bp, 'org.Hs.eg.db', 'ENSEMBL')
e.io.hg.ego.mf <- setReadable(io.hg.ego.mf, 'org.Hs.eg.db', 'ENSEMBL')
e.io.hg.ego.cc <- setReadable(io.hg.ego.cc, 'org.Hs.eg.db', 'ENSEMBL')
e.io.hg.kk <- setReadable(io.hg.kk, 'org.Hs.eg.db', 'ENTREZID')
write.table(e.io.hg.ego.bp, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/IOSEvsHGSOC_GO_ORA_BP_table.tsv")
write.table(e.io.hg.ego.mf, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/IOSEvsHGSOC_GO_ORA_MF_table.tsv")
write.table(e.io.hg.ego.cc, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/IOSEvsHGSOC_GO_ORA_CC_table.tsv")
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_IOSEvsHGSOC_GOBP.pdf", 17, 15)
dotplot(io.hg.ego.bp, showCategory=50, title = "ORA - IOSE vs HGSOC , GO BP")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_IOSECvsHGSOC_GOMF.pdf", 17, 15)
dotplot(io.hg.ego.mf, showCategory=50, title = "ORA - IOSE vs HGSOC , GO MF")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_IOSEvsHGSOC_GOCC.pdf", 17, 15)
dotplot(io.hg.ego.cc, showCategory=50, title = "ORA - IOSE vs HGSOC , GO CC")
dev.off()
#Goplots
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_IOSEvsHGSOC_GOBP.pdf", 20, 15)
goplot(io.hg.ego.bp, showCategory=20, title = "ORA - IOSE vs FTSEC , GO BP")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_IOSEvsHGSOC_GOMF.pdf", 20, 15)
goplot(io.hg.ego.mf, showCategory=20, title = "ORA - IOSE vs HGSOC , GO BP")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_IOSEvsHGSOC_GOCC.pdf", 20, 15)
goplot(io.hg.ego.cc, showCategory=20, title = "ORA - IOSE vs HGSOC , GO BP")
dev.off()
# IOSE vs FTSEC #
res4
res4 <- na.omit(res4)
io.ft.path <- res4[res4$padj < 0.05, ]$log2FoldChange
## Name for each gene need to be in entrezid
#mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
genes.mart <-
getBM(attributes = c("ensembl_gene_id", "entrezgene_id"),
values = substr(rownames(res4[res4$padj < 0.05, ]),1,15), mart = mart)
res4$entrezid <- genes.mart$entrezgene_id[match(substr(rownames(res4),1,15), genes.mart$ensembl_gene_id)]
names(io.ft.path) <- res4[res4$padj < 0.05,]$entrezid
gene.df <- bitr(names(io.ft.path), fromType = "ENTREZID",
toType = c("ENSEMBL", "SYMBOL"),
OrgDb = org.Hs.eg.db)
# gene.df <- gene.df[gene.df$ENSEMBL %in% substr(rownames(res),1,15),]
# aux <- res[substr(rownames(res),1,15) %in% gene.df$ENSEMBL, ]
# gene.df$FC <- aux$log2FoldChange[match(substr(rownames(aux),1,15), gene.df$ENSEMBL)]
io.ft.ego.bp <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
io.ft.ego.mf <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "MF",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
io.ft.ego.cc <- enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Hs.eg.db,
keyType = 'ENSEMBL',
ont = "CC",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05)
io.ft.kk <- enrichKEGG(gene = gene.df$ENTREZID,
organism = 'hsa',
pvalueCutoff = 0.05, qvalueCutoff = 1)
#geneList = sort(norm.can.path, decreasing = TRUE)
e.io.ft.ego.bp <- setReadable(io.ft.ego.bp, 'org.Hs.eg.db', 'ENSEMBL')
e.io.ft.ego.mf <- setReadable(io.ft.ego.mf, 'org.Hs.eg.db', 'ENSEMBL')
e.io.ft.ego.cc <- setReadable(io.ft.ego.cc, 'org.Hs.eg.db', 'ENSEMBL')
e.io.ft.kk<- setReadable(io.ft.kk, 'org.Hs.eg.db', 'ENTREZID')
write.table(e.io.ft.ego.bp, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/IOSEvsFTSEC_GO_ORA_BP_table.tsv")
write.table(e.io.ft.ego.mf, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/IOSEvsFTSEC_GO_ORA_MF_table.tsv")
write.table(e.io.ft.ego.cc, quote =F, row.names = F, sep = "\t",
file = "~/Documents/OCRA_Files/Pathway_Analysis/IOSEvsFTSEC_GO_ORA_CC_table.tsv")
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_IOSEvsFTSEC_GOBP.pdf", 17, 15)
dotplot(io.ft.ego.bp, showCategory=50, title = "ORA - IOSE vs FTSEC , GO BP")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_IOSECvsFTSEC_GOMF.pdf", 17, 15)
dotplot(io.ft.ego.mf, showCategory=50, title = "ORA - IOSE vs FTSEC , GO MF")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_DotPlot_IOSEvsFTSEC_GOCC.pdf", 17, 15)
dotplot(io.ft.ego.cc, showCategory=50, title = "ORA - IOSE vs FTSEC , GO CC")
dev.off()
#Goplots
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_IOSEvsFTSEC_GOBP.pdf", 20, 15)
goplot(io.ft.ego.bp, showCategory=20, title = "ORA - IOSE vs FTSEC , GO BP")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_IOSEvsFTSEC_GOMF.pdf", 20, 15)
goplot(io.ft.ego.mf, showCategory=20, title = "ORA - IOSE vs FTSEC , GO MF")
dev.off()
pdf("~/Documents/OCRA_Files/Pathway_GOPlot_IOSEvsFTSEC_GOCC.pdf", 20, 15)
goplot(io.ft.ego.cc, showCategory=20, title = "ORA - IOSE vs FTSEC , GO CC")
dev.off()
###
aux <- read_excel("~/Documents/OCRA_Files/Plummer_OCRA_SciAdv_Suppl_2021.xlsx", sheet = 21, skip = 1)