Question: What is my total number of genes in a hypergeometic distribution test?
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gravatar for connor.j.rogerson
14 months ago by
connor.j.rogerson10 wrote:

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

statistics rna-seq chip-seq R • 462 views
ADD COMMENTlink modified 14 months ago by Prakash740 • written 14 months ago by connor.j.rogerson10
0
gravatar for Hussain Ather
14 months ago by
Hussain Ather910
National Institutes of Health, Bethesda, MD
Hussain Ather910 wrote:

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

ADD COMMENTlink written 14 months ago by Hussain Ather910
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gravatar for Prakash
14 months ago by
Prakash740
India
Prakash740 wrote:

Have you tried BETA cistrome

ADD COMMENTlink written 14 months ago by Prakash740
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