Incomplete genes in 22Q2 ccle_expression.csv and ccle_genecn.csv

Q&A
1

Hi all,

I am working on drug screens, particularly, looking at the drug’s AUC against the gene expression/copy number. Comparing the csv files in the download site with the depmap data explorer, the csv files only has 16383 genes whereas the depmap data explorer showed 19160 genes in total. Based on my analysis, among these 2, only 15573 genes intersect/overlap and there are 3587 extra genes in depmap data explorer. This happens in all 3: genecn.csv, expression.csv and expression_full.csv. Is there an explanation to this?

2

Hi!

Thanks for your feedback!
I am assuming you are downloading the csv files from the DepMap Public datasets. Do you mind going over how you are getting the genes in data explorer so I can reproduce this error and look into it? Screenshots would be very helpful. Thanks!

Simone