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GSEA Positional Gene sets for mouse chromosomes

I am trying to analyze enrichment of gene expression (preranked GSEA) based on the position of each gene in the mouse genome. I found a gene set (gmt) file that contains the list of genes for each human chromosome and each cytogenetic band (GSEA/MSigDB; https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp) but did not find a similar file for the mouse genome. Does anyone know whether such a file exists for the mouse genome? Thanks,

gsea geneset mouse chromosome cytogenetic band
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updated by Gordon Smyth Gordon Smyth • written by mmalumbresm • mmalumbresm

None of the old discussion answers OPs question however. The old discussion only advises how to map human genes to mouse orthologs, which will not help OP getting genes for mouse cytobands.

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written by Gordon Smyth Gordon Smyth

It was only a comment. It would be appropriate for the non-positional gene sets, which is related. The link was to all the gene sets, not just positional.

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written by igor igor

1 answer

The Broad Institute only provides human molecular signatures. We created a mouse verson of the MSigDB, including gene sets for mouse cytobands, for our use with all gene set collections in R format. It is publicly available from http://bioinf.wehi.edu.au/MSigDB/

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written by Gordon Smyth Gordon Smyth

Wooww! That's a fantastic resource. Many thanks for the link!

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written by mmalumbresm • mmalumbresm

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