What’s The Answer? (compare gene lists)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

I highlight this week’s question because I think it’s something people may increasingly have to solve–what to do to compare across gene lists. There are tools that can take up lists and explore the specific features of that list–like DAVID, which we like–but comparing lists with each other is more difficult.

Question: Gene set enrichment test tool that can compare multiple gene lists

I received some excellent recommendations of enrichment test tools for testing single gene sets here at Biostars in the past. I am hoping someone will have something similar to offer for my latest query.

I have three gene lists (~1600 genes) that are not ranked in any particular way and have no expression data (they were obtained based on the Fst of SNPs within them – I have dealt with linkage disequilibrium to the best extent I am able, so not too worried about this). I would like to compare these three gene lists for enrichment of biological processes, in particular I am interested to see if they are enriched for immunological function.

I have become familiar with DAVID, but the issue I am finding is that I have to run the three tests separately and the enrichment scores obtained for gene functional classification seem to be only internally meaningful (that is to say comparing one gene list to another isn’t a simple matter of side by side comparison in terms of enrichment scores).

Does anyone know of a test that can run all three lists side by side and statistically compare them?

confusedious

Check out the suggested answers–but also be sure to add your favorite tools for this as well if you’ve found a solution for this issue.