Hi, First of all, my apology that the question might be a little confusing. I'll try to explain. I did a ChIP-seq experiment on a novel protein and got some nice peaks. MEME motif analysis wasn't very informative (this is not a sequence-specific TF). Since there is not much known about this protein, I am thinking about correlating it with public datasets (ChIP-seqs, RNA-seqs, etc). In another word, to find what other protein/histone modifications have similar binding patterns to this protein. This will potentially tell me what are the cofactors of my protein. However, I am not able to process all the public datasets, so I am looking for such tools.

I already have .bed files with coordinates of the protein binding sites generated by MACS2. My specific question is, is there a tool that can compare this bed file with public datasets, and output factors/histone modifications that have similar binding patterns? Thanks!