Question: GSEA Positional Gene sets for mouse chromosomes
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gravatar for mmalumbresm
7 days ago by
mmalumbresm0 wrote:

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,

ADD COMMENTlink modified 7 days ago by Gordon Smyth1.7k • written 7 days ago by mmalumbresm0

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

ADD REPLYlink written 7 days ago by igor11k

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.

ADD REPLYlink modified 7 days ago • written 7 days ago by Gordon Smyth1.7k

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.

ADD REPLYlink written 7 days ago by igor11k
0
gravatar for Gordon Smyth
7 days ago by
Gordon Smyth1.7k
Australia
Gordon Smyth1.7k wrote:

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/

ADD COMMENTlink modified 5 days ago • written 7 days ago by Gordon Smyth1.7k

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

ADD REPLYlink written 2 days ago by mmalumbresm0
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