Question about gene ontology annotation: When analysing DE genes do we look for all DE or we separate over and under expression?

Question

[tiago211287]

I started doing gene ontology analysis and a doubt that came out was if I must look for the functional categories for over and under expressed genes separeted or together. I am trying to visuIize in cluego but I dont know if I can use the expression data in the network graph. Someone have some guidance for me ?

Answer 1

[Woa]

Check this thread:
"Separate enrichment analysis of pathways for up- and downregulated genes"

[tiago211287]

Thank you very much. This discussion will help me.