GSEA with mouse RNAseq data

Question

[Alex Gibbs]

Hi everyone,

I have had RNAseq performed on mouse samples (12 samples, 4 groups) and have the results ready to plug into Gene Set Enrichment Analysis (GSEA) software.

I notice that there are plenty of human gene sets available on MSigDB, but not many for mouse. I would like to run GSEA with 6 signalling pathway gene sets, but the only ones I can find are for human. Does anyone know if the human signalling pathways are exactly the same as mouse signalling pathways? Or is there a mouse database that I can go onto to download mouse specific signalling pathway gene sets?

Thank you in advance!

Alex

[igor]

MSigDB pathways are presented as human symbols, but are based on multiple species.

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

Answer 1

[Gordon Smyth]

We created a mouse version of the MSigDB, available from http://bioinf.wehi.edu.au/MSigDB/

Our version is designed for use with R so the gene sets are provided as native R objects.

[Alternative]

Why don't you provide them in ".gmt" format for direct download/load on GSEA?

[Kevin Blighe]

It works just as well as they are. You can easily output the data objects in GMT format, if you wish.

Answer 2

[Buffo]

You can use webgestalt, it has a list of organisms (including mouse)

Answer 3

[Kevin Blighe]

Another answer: you can retrieve these gene sets automatically via msigdbr, too: https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html

Kevin