Interpreting Two-sided Fishers For Directional Regulation of Genes

Question

[Anthony]

Hello,

I'm having a tough time conceptualizing what the output of a fisher's exact test would imply for comparing the directional relations of genes that overlap between two gene sets.

This exact test returns a significant p-value which I think means the proportions are different. Or am I completely misunderstanding the point of this test?

Thank you for any insight you can provide.

Answer 1

[Asaf]

Yes, you are correct. The significant p-value suggests that the genes up and down in A are biased also in B, genes going down in A are observed going down in B as well more than expected at random (based on the distribution of up/down in B for genes going up in A)