Question: GSEA analysis with Mouse (Please give some comments..)
0
gravatar for illinois.ks
3.8 years ago by
illinois.ks140
Korea, Republic Of
illinois.ks140 wrote:

Hello all,

I am doing GSEA analysis. I have done with human sucessfully. 

However, this time, I am trying to run with my mouse gene. .I realized that thse mSIG DB are annotated with only human.. I donwloaded the msigDB for mouse from genepattern website.

Howver, GSEA program didn't allow me to use this downloaded data for my analysis... 

Could you please someone help me with this?  T.T 

I am creating with my ***.rnk (rank file) for this analysis.. 

 

gsea; mouse; • 7.2k views
ADD COMMENTlink modified 16 months ago by AidanQuinn20 • written 3.8 years ago by illinois.ks140
1

I will try to capitalize all my mouse genes. Sometimes, it can fool the software to treat the mouse gene as human gene. If you want a even better approach, you can check the homology and convert the mouse to human. Usually capitalize are simple enough.

ADD REPLYlink written 3.8 years ago by Sam2.3k

Thnk you so much!

yEs. I will try.. :) 

ADD REPLYlink written 3.8 years ago by illinois.ks140
1
gravatar for igor
3.8 years ago by
igor7.6k
United States
igor7.6k wrote:

Jackson Lab has the Vertebrate Homology resource for converting between homologous human and mouse genes (most of the time, it's just adjusting the case).

ADD COMMENTlink written 3.8 years ago by igor7.6k
1
gravatar for AidanQuinn
16 months ago by
AidanQuinn20
United States
AidanQuinn20 wrote:

Generally I use Ensemble Biomart (but you can substitute your favorite gene ID conversion tool here) to convert all of the gene names in each gene signature in the *.gmx or *.gmt, from human to mouse. I then use the mouse IDs to make a custom *.gmx or *.gmt file.

It's convenient to do this in R if you know how but not necessary, it works perfectly well do to copy-paste into the web interface.

Word of warning: look out for genes that don't convert using automated tools. Often you will come across genes that actually do have mouse orthologs but are not annotated in Biomart. You can manually add these genes to the signatures by a quick Google search.

ADD COMMENTlink written 16 months ago by AidanQuinn20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1358 users visited in the last hour