Hello, my name is Hamid, I have constructed a condition independent gene co-expression network. There are some transcription factors in modules of this network. The function of these transcription factors are in accordance with the module function, but their binding sites were not over represented in that module. I would be very happy if somebody help me to find an explanation for this problem?
Vertebrates known transcription factor binding motifs were downloaded from the JASPAR database. Overrepresentation of known transcription factor binding motifs in the CIS regions of the genes within each module was performed using Clover.
Thanks in Advance