Dear Ahmed Eltokhi ,

This is a very broad discussion. But I'd rather put whole list and then see how many have upregulated and dowregulated. And so I infer what is the "direction" of the pathway.

https://www.researchgate.net/post/While_doing_Gene_Set_Enrichment_Analysis_should_one_separate_up-and_down-regulated_genes

https://www.biostars.org/p/100123/

https://www.biostars.org/p/155501/

Best,

Leite

Thanks a lot. This was very helpful