Inquiry regarding Gene Content (lncRNA/miRNA) in MSigDB Collections (C2, C5)

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I am currently conducting GSEA analysis using the C2 and C5 collections and have a question regarding gene biotype inclusion.(RNA_seq)

Specifically, my questions are:
1. For C2 and C5 collections, is it sufficient to include only protein-coding genes in the ranked gene list?

2. If lncRNAs and miRNAs are excluded from the input gene list when using C2, would this significantly affect the results?

Thank you for your time and I look forward to your response.

[Anthony Castanza]

Hello,

MSigDB itself is not specifically filtered to include only protein coding genes, however, the ncRNA component is generally quite small across most sets.

The largest impact will actually be in the gene distribution that GSEA uses to compute rankings, where filtering these genes out will change the underlying differential expression distribution.

I can't speak specifically to how much the impact will be, it is extremely variable from dataset to dataset. That said, it is not inherently incorrect to do so if you are interested in just the protein coding components.

Let me know if you have any other questions,

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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