Pathway enrichment analysis

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!

degs pathway-enrichment

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updated 3.0 years ago by liux.bio

• written 4.8 years ago by BioQueen •

2 answers

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.

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written 4.8 years ago by ATpoint

Try EnrichMiner

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written 3.0 years ago by liux.bio

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