Background set for GO enrichment analysis

[yvan.wenger]

Hello,

I determined that out of ~70'000 transcripts, ~15'000 are spatially regulated (I used the LRT method in DESeq2). The patterns of these 15'000 transcripts clustered into 15 groups.

I would like now to perform a GO gene set enrichment analysis for the transcripts in each cluster. It seems more logical to me that my "background" annotation will comprise the 15'000 transcripts, not the 70'000. Is it correct?

Many thanks !

Yvan

[sdriscoll]

I'd agree with that whereas if you were interested in GO enrichment of the 15,000 genes you'd then use the 70,000 as the background.