Find genes of enriched known motif results in HOMER

Question

[Benn]

Hello,

I am using HOMER to find enriched known motifs in my differentially expressed gene lists (RNA-seq). I am using the findMotifs.pl tool. I get enriched motifs, and I would like to know now which genes have this motif. Is it possible to get these genes? I can't find it in the manual pages of HOMER, did I miss it? Does anyone has an idea how to get the target genes?

Ben

[rlbowman88]

Can you please point me to the relevant part of the manual? I had the same question in mind.

Answer 1

[Benn]

Sorry for posting this question, I found what I wanted in the manual pages section:

Finding Instances of Specific Motifs

Answer 2

[Benn]

If you go to:

http://homer.salk.edu/homer/microarray/index.html

You'll have to scroll down to: Finding Instances of Specific Motifs

You need the motif file from your analysis and the same settings, good luck!