RNAseq Enrichment analysis

Question

[kimmitzka]

Hi all,

I have multiple treatment groups and one contort group. I already got the differential expression gene list. Should I compare one by one or merge all the list and perform enrichment analysis？

Thanks

[ATpoint]

Unclear. Enrichment for what?

Answer 1

[shiyang_bio]

It depends on the goal of your study. If you want to know the difference between each treatment and control, you should perform enrichment analysis one by one. If you want to know the overall difference between treatment and control, you should do differential gene expression analysis again, using (all treatment samples vs all control samples). Then do enrichment analysis.

[kimmitzka]

I see, thanks for your reply