Question: Where can I find mouse Gene MatriX file format (GMT)?
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gravatar for anu014
23 months ago by
anu014170
India
anu014170 wrote:

Hi Biostars!

I'm trying to do Gene set enrichment analysis (GSEA) using Broad Institute's GSEA tool itself (offline version). So, it is asking me to provide a GMT file in '-gmx' parameter. My organism is mouse. So where can I find GMT file for mouse. I'm getting human GO GMTs here but not for mouse : http://software.broadinstitute.org/gsea/downloads.jsp

Please help me out. Thank you :)

rna-seq biology next-gen gene • 1.7k views
ADD COMMENTlink modified 23 months ago by Santosh Anand5.0k • written 23 months ago by anu014170
1
gravatar for Santosh Anand
23 months ago by
Santosh Anand5.0k
Santosh Anand5.0k wrote:

The GMT files can be obtained from MSigDB Collections http://software.broadinstitute.org/gsea/msigdb

Click on gene-set you want, for example, Hallmark (H) http://software.broadinstitute.org/gsea/msigdb And there you'll find a link to dload that set in GMT format

Alternatively, you may use GenePattern online portal, which also provides the interface to GSEA as a module. In this online GSEA, you can just choose the names of gene-set without the need of any dload. https://genepattern.broadinstitute.org/gp/pages/index.jsf

ADD COMMENTlink written 23 months ago by Santosh Anand5.0k
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