Question: Where can I find mouse Gene MatriX file format (GMT)?
0
gravatar for anu014
2.9 years ago by
anu014180
India
anu014180 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 • 2.9k views
ADD COMMENTlink modified 5 months ago by Gordon Smyth2.0k • written 2.9 years ago by anu014180

Hey!

I am using the online GSEA as well and my model is mouse too. Did you find out which GMT file is for mouse only? Is there any way to segregate the mouse and humans after using the .GMT available? Also, in the offline version, what did you use as your phenotype labels?

Thanking you.

ADD REPLYlink written 9 months ago by shweta.johari130

Hi, since I spend some time to understand this, I would like to try to explain this in case somebody needs it:

If you use GSEA with a ranked list from e.g. a DESeq2 output, which is basically a two-column table with gene name and the adjusted p-value, you have to use the the tool in the software called "Run GSEAPreranked". Here you do not need the phenotype lables.

Otherwise, the input has more than 2 columns, with one column per sample and you enter a cls file which tells the program which column belongs to what sample group, like WT vs KO of a gene.

ADD REPLYlink modified 9 months ago • written 9 months ago by caggtaagtat1.3k
2
gravatar for Santosh Anand
2.9 years ago by
Santosh Anand5.2k
Santosh Anand5.2k 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 2.9 years ago by Santosh Anand5.2k
0
gravatar for Gordon Smyth
5 months ago by
Gordon Smyth2.0k
Australia
Gordon Smyth2.0k wrote:

The Broad Institute's MSigDB itself is only for human. We created a mouse version of the MSigDB at http://bioinf.wehi.edu.au/MSigDB/.

ADD COMMENTlink modified 5 months ago • written 5 months ago by Gordon Smyth2.0k
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