GSEA Positional Gene sets for mouse chromosomes

Question

[mmalumbresm]

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,

[igor]

Related discussion: GSEA analysis with Mouse (Please give some comments..)

[Gordon Smyth]

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.

[igor]

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.

Answer 1

[Gordon Smyth]

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/

[mmalumbresm]

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