Running MSigDB locally *without* expression data

Question

[Kasthuri]

Hi,

I understand GSEA is typically run with an expression dataset. If I have just a list of genes, I can run compute overlaps with the MSigDB database online:

http://software.broadinstitute.org/gsea/msigdb/annotate.jsp

However, I am wondering if I can compute overlaps in MSigDB datasets locally through a command line for a list of genes. I want to do this because I have tons of such datasets (only genes) which I need to query for overlaps with MSigDB. Has anyone done this?

Thanks.

Answer 1

[predeus]

What you need is an implementation of Fisher's exact test and some sort of matching algorithm.

I've never used it in a separate tool, but you probably can apply some of the code used to calculate GO enrichments, or just write it yourself - should be pretty easy.