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?