What is my total number of genes in a hypergeometic distribution test?

Question

[connor.j.rogerson]

I'm working out the significance of an overlap of two RNAseqs experiments upon knockdown of two different transcription factors. I have read previous posts on phyper in R etc and they suggest total number of genes (I assume this is all genes). I have ChIP-seq data so I know what genes are bound by my transcription factors so is my total population ALL genes or just genes bound by either transcription factor?

Thanks in advance!

C

Answer 1

[Hussain Ather]

To find the significance of the overlap, you should use the total population of all genes.

Answer 2

[Prakash]

Have you tried BETA cistrome