Identical KEGG pathways enriched by up- and down-regulated genes

Question

[ashwing.kofficial]

Hello everyone.

I have some pathways of a dataset from kegg which has been upregulated and downregulated. Why does it happen? Is it okay for it to occur? If so, what is the explanation for it, If not, should I discard it.

This question has been asked in the platform before but the answer was not a satisificatory one. Posting a link of that too. Same KEGG pathways enriched by up- and down-regulated genes]1

Answer 1

[boczniak767]

I think it is possible and mean that some elements of pathway are downregulated and some upregulated. Both in quantity enough to give significant p-value.

In the end it make interpretation difficult. Maybe you could see if activation/inhibition involve specific parts of a pathway?

[ashwing.kofficial]

Thanks for your advice , it gave a unique perspective at how I looked at the problem. I will try to get back to you if I get a solution. Cheers!!