Hello, Biostars. I want to look for over-represented transcription factor binding sites for a given set of genes. I have learned a lot from similar questions in Biostar and papers. But I still have a problem and can't find the precise answer. According to papers, the promoter region contains 5'UTR, INTROS, upstream or downstream of TSS. For the uptream or downstream, I don't know how many bps should I take(the specie is Mouse). In papers, it's different one from another and I didn't find the basic principles to do it. Could you give me some suggestions or give me some reference? Thanks.