So I'm analysing human ChIP-seq data, and have made genelists of genes with enrichment at their promoters in two samples - each sample has about 3000 genes enriched, with ~1500 in common. I wanted to do some gene ontology analysis to see what kinds of enriched genes I am getting, and as a GO newbie I used DAVID which is a bit clunky but OK.
So now I have a heap of tables downloaded from DAVID of the enriched GO terms (for BP & MF 1,2,3 and FAT) in each cell line - is there a framework available for comparing the two samples enrichments robustly? I'd like to explore which GO terms overlap and which differ.
Additionally, I have a second ChIP-seq set of data for these two samples, so in the future I want to split each genelist into whether this second factor is present as well, and see if that stratifies out any particular biological groupings of genes.
Any help/pointers appreciated! I've only sunk a bit of time into DAVID so I'm more than happy to try something else (if it takes refseq mrna IDs) - I'm quite intimate with the NGS side of R/Bioconductor but haven't looked at any of its GO packages.