Hi all, merry Christmas. I have just done a chip-seq with a protein product of novel gene that possibly acts as a TF (it translocates into nuclear upon some challenges during oncogenesis). At the end, the program returned me ~1500 peaks and possible motifs. About a quarter of these peaks were associated with genes (390 genes). Since this is a novel gene, I totally have no clue about its binding sites, so for all those genes and motifs I have to perform verification experiments. As a start, I plan to choose some most-promising genes to test their expression response to this gene.
Now comes my question: are those genes that associated with more PEAKS are most possible target of this gene?? Or are those genes that contain sequences showing highest homology with MOTIFS are most promising candidate of such target? Any suggestion are greatly appreiciated. Yiqiang