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Perturbseq grit vs. perturbseq expression #10

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gwaybio opened this issue Jan 24, 2021 · 0 comments
Open

Perturbseq grit vs. perturbseq expression #10

gwaybio opened this issue Jan 24, 2021 · 0 comments

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@gwaybio
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gwaybio commented Jan 24, 2021

A question came up recently about how the gene expression patterns influenced position in UMAP space.

For many CRISPRi perturbations, we observe that grit really nicely tracks titration. For example, in HSPA5 we observe that with increasing relative activity (facets of the plot), we observe an increase in single cell grit.

GSE132080_HSPA5_singlecell_umap_grit

We are interested in how the measured expression of HSPA5 behaves in this space.

GSE132080_HSPA5_singlecell_umap_expression

For HSPA5, there does not appear to be a relationship.

(Note the UMAP coordinates are different from the last results - I reran UMAP after reprocessing in #9)

This lack of relationship is not universal. For example, here are the plots for HSPE1

GSE132080_HSPE1_singlecell_umap_grit

GSE132080_HSPE1_singlecell_umap_expression

See https://github.com/broadinstitute/grit-benchmark/blob/main/2.compare-metrics/perturb-seq/0.compare-activity-score.ipynb for all UMAP figures

cc @Avtar00

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