I have list of homer results. For example:

CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer

I usually extract the first letters using pattern - CTCF.

But there are several others where I cannot readily extract the gene ID. For example:

GATA(Zf),IR3/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer

Is there a way to convert all these homer motif results into gene ID so that I can easily overlay fpkm values or differential expression of genes into homer results?

I am interested in selecting motifs whose gene is expressed.

Thanks!