Obtaining gene sets from KEGG or other sources

Question

[jleehan]

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?

[Fatima]

Are you interested in MetaCyc pathways too?

[jleehan]

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

[Fatima]

Fun4me packages uses Minpath that provides you with pathway information from MetaCyc. You can download the package from here:

https://sourceforge.net/p/fun4me/code/ci/master/tree/data/

For more information:

https://link.springer.com/protocol/10.1007/978-1-4939-7015-5_3

Feel free to let me know if you have any questions regarding the pipeline.

Answer 1

[jared.andrews07]

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)

[jleehan]

That was immensely helpful. Thank you very much!