Running GSEA on CRISPR Screen Data

[Zahra Sheybani]

Dear GSEA Team,

I have a question regarding the analysis of CRISPR screening data. I have a ranked gene list that includes both enriched (positively selected) and dropped out (negatively selected) genes. For running GSEA, should I analyze the entire ranked list as a whole, or is it better to separate the enriched and dropped out genes and run them independently?

I would appreciate your guidance on the best practice for this type of analysis.

Kind regards,

Zahra

[Anthony Castanza]

Hi Zahra,

For GSEA you generally want to run the entire ranked list, and not separate runs for up and down components.

That said, there may be other quirks of running CRISPR data through GSEA that we aren't aware of, as it's a data type we can't specifically vouch for.

Do let us know if you encounter any other issues or oddities in your GSEA results.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

[Zahra Sheybani]

Hi Anthony,

Thank you so much for your prompt reply.

Very helpful!

Best regards,

Zahra

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