KEGG gene set

[Jazmin Machuca Machuca]

Dear MSigDB Support Team,

I am currently conducting KEGG pathway enrichment analysis in RStudio and am looking to download the appropriate gene set collection for Mus musculus. I came across the M2 collection (curated gene sets, 2733 sets) and wanted to confirm if this includes the C2:CP:KEGG gene sets mapped to mouse genes.

If not, could you please advise whether KEGG gene sets specific to Mus musculus are available for download, or if they must be derived from the human sets using ortholog mapping?

Thank you for your assistance.

Best regards,
Jaz

[Anthony Castanza]

Hi Jaz

Unfortunately neither the KEGG:Legacy (an old version of the full KEGG before their licensing terms changed), nor KEGG:Medicus (a modern version of KEGG licensed under permissive terms, but more limited in scope) are available directly in the Mouse collections. In order to use them with mouse data you would need to use the human version of this collection with our ortholog mapping chip files to map your mouse gene data to human gene symbols.

Sorry I couldn't be of more assistance here, but please let us know if you have any additional questions

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego