P value of enriched lineages

Hi,
On overview of PTBP1, it presents an module of enriched lineages, where listed P value of 3 cell lines, such as glioma. May I know how to calculate this value?
Thanks!

Hi, which tab are you seeing this in? Could you paste a snapshot of what you’re looking at? -thanks

image
The P value is shown in parentheses. How to calculate this value?
Thanks!

Hello,

The reported p-value is an uncorrected p-value from performing a t-test.

The two groups being compared are the gene effect of those lines annotated as that disease (ie: Kidney) vs the gene effect for all other lines. The annotations for which lines are annotated for which diseases can be found in the sample info file.

Thanks,
Phil

Hello,

Can you confirm that these lineage enrichments are still calculated via t-test of gene effect scores from “within lineage” cell lines vs. “other lineage” cell lines? I tried to reproduce this using the CRISPR_gene_effect.csv file, but am seeing different values than what is shown in the DepMap interface.

Specifically, for a given gene and lineage combination (e.g. SOX10 + skin), I would take the column from CRISPR_gene_effect.csv that corresponds to SOX10 Chronos values. I map the DepMap_ID’s to their lineages using the sample_info.csv file. I then break the SOX10 Chronos values into skin vs. all other lineages … and run a t-test comparing these groups. I get a p-value of about 5e-21 for SOX10 in skin, whereas the value shown in DepMap is 2.4e-154 (SOX10 DepMap Gene Summary). Can you advise if I am approaching this p-value calculation incorrectly?

Thanks!