Pathway enrichment analysis

Question

[BioQueen]

Hi! I have found DEGs. What do I use for the pathway enrichment analysis; all DEGs or separate between up and down?

Also is it normal to only choose a subset like the top 50 up-reg genes or would I like to take all the up-reg genes I found in the enrichment analysis in KEGG or Reactome for an instance?

Thanks so much!

Answer 1

[ATpoint]

See answer/comments from me and Papyrus in this related thread:

Enrichr input genes, up, down, or both at once

Also is it normal to only choose a subset like the top 50 up-reg genes or would I like to take all the up-reg genes I found in the enrichment analysis in KEGG or Reactome for an instance?

I would take all, and then see if anything interesting is in there. Many smaller changes can also drive a phenotype, it does not need to be the top ones, regardless of the metric you choose for the ranking.

Answer 2

[liux.bio]

Try EnrichMiner