What to do after finding differentially expressed genes?

[sazz]

Hello all,

Which programs do you use after finding the differentially expressed genes between 2 conditions? I assume, everyone first look at which GO terms are enriched. So far I have used DAVID, attempted to use GSEA (but did not work well, maybe I am doing something wrong). Also I will be happy if anyone can inform me how to arrange the files in GSEA for RNA-seq.

Thanks,
Erdem

[dpryan]

There's GOSeq, which is probably a bit more appropriate for RNAseq datasets than DAVID. Aside from that, it depends on the biological question.