Hi,

I am trying to find cis nature of regulatory regions. Currently, I have used a hypergeometric test for checking targets affected in the cis window versus the rest of the Genome. I have also looked at null distributions.

Is there any other approach you might be aware of to increase the sensitivity while checking whether a region has cis-regulation of nearby genes or not?

(I have expression information of all the genes when the region is knockdown)

Thanks a ton!