Gene Ontology (GO) terms that are more enriched in down-regulated genes are under-represented terms?

[Franelizabethgalvez]

Discussed in #516

^{Originally posted by Franelizabethgalvez February 13, 2025}
I have performed enrichment analysis for up- and down-regulated gene sets with the topGO library based on GO annotations.
In writing up these results, I have questions such as: is it OK to describe the more enriched GO terms (higher number of significant annotated genes) of the up-regulated genes as over-represented, and conversely, is it OK to describe the more enriched GO terms of the down-regulated gene sets as under-represented or under-enriched?

Any clarification is helpful.
Thank you!!

[suzialeksander]

Hi @Franelizabethgalvez,

This is a good question. More-enriched terms would be described as more/over enriched, regardless of if you're looking at a set of down-regulated or up-regulated genes.

So,

is it OK to describe the more enriched GO terms (higher number of significant annotated genes) of the up-regulated genes as over-represented,

Yes, this is correct

and conversely, is it OK to describe the more enriched GO terms of the down-regulated gene sets as under-represented or under-enriched?

No, these are also OE

[Franelizabethgalvez]

Thank you @suzialeksander for your clear and quick reply!!
It is difficult to clarify the over-representation for up-regulated genes and the over-representation for down-regulated genes.
I will have to review the literature, once I have a clarification I will post to close this question ;)