This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Obtaining gene sets from KEGG or other sources

I am trying to obtain gene sets to perform gene set enrichment analysis and I am struggling to find gene sets for my organism, Bacillus subtilis. I've read in peer-reviewed papers that people working with my organism have been able to perform gene set enrichment analysis and some said they obtained gene sets from KEGG. I've looked through KEGG and haven't really been able to figure out how to find gene sets that are compatible with GSEA. I'm aware of MsigDB, but this appears to only provide gene sets for a small number of model, primarily eukaryotic, organisms.

Can anyone assist me in obtaining gene sets for Bacillus subtilis?

gsea gene sets kegg
• 1,875 views • link
updated by jared.andrews07 jared.andrews07 • written by jleehan • jleehan

Are you interested in MetaCyc pathways too?

• 0 views • link
written by Fatima Fatima

Sure, anything helps. The data set I'm working with has been particularly tricky and frustrating.

• 0 views • link
written by jleehan • jleehan

1 answer

You can view the available genesets for that organism on the KEGG website. There are a few different ways to pull them down in R, but I've found the easiest to be the kegg.gsets function from the GAGE package:

library(gage)
bs <- kegg.gsets(species = "bsu", id.type = "kegg", check.new=FALSE)
• 0 views • link
written by jared.andrews07 jared.andrews07

That was immensely helpful. Thank you very much!

• 0 views • link
written by jleehan • jleehan

Log in to answer this question.

More posts like this