Connection and difference between cells from various tissues

Q&A
1

Dear DEPMAP community,

Thank you very much for sharing your data! I have encountered a question at the beginning of my project while using DEPMAP. I am utilizing the gene dependency file and gene effect file databases to explore the connections and differences between cells from various tissues, such as lung, kidney, and others. However, when I directly used the columns from these files as cell signatures, I did not observe any significant clustering results among the cells.

I would greatly appreciate it if you could provide regarding which file I should use or how to handle the data more effectively. I am seeking to uncover meaningful insights and patterns related to the different tissues.

Thank you in advance for your guidance and support.

Best regards,
Asher

2

I also attempted to utilize the effect scores of high variance genes as cellular signatures in order to improve the clustering results. While the clustering figure showed some improvement, it was not quite satisfactory or acceptable.

3

While it sounds like you’re doing a specific analysis which is not one I can comment on, I think you are looking on the correct files to do an analysis on gene essentiality in different tissues.

I’ll also offer while that it’s common for dependencies to be enriched in specific lineages, I’m not sure that dependencies would naturally cluster with tissue type. I’d expect expression to do a better job of distinguishing cell types.

Thanks,
Phil

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