Gene Set Database Comparison

[Arko Samad]

Hi

If my expression dataset is compiled of Mouse Ensembl Gene ID's, is it still productive to use a human collection for my gene set database?

Or should I use one of the mouse collections available on GSEA?

[Anthony Castanza]

The Human collections are generally more comprehensive than the Mouse collections, however if you are interested in the more "canonical" collections like GO, Reactome, etc. I'd probably recommend doing the analysis in the native mouse-gene space.

The specific gene ID type doesn't really matter, we offer CHIP files for both analysis in the native gene-space, and for ortholog mapping to the cross-species analysis.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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