What to do after finding differentially expressed genes?

sazz · 07-15-2013, 10:44 AM

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 · 07-15-2013, 11:39 AM

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

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07-15-2013, 10:44 AM	#1
sazz Member Location: Istanbul, Turkey Join Date: Oct 2012 Posts: 28	What to do after finding differentially expressed genes? 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

07-15-2013, 11:39 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	There's GOSeq, which is probably a bit more appropriate for RNAseq datasets than DAVID. Aside from that, it depends on the biological question.