Hi,
I am hoping for some insight and suggestions :)
I am interested in the TFBSs of 3 TFs in all promoter sequences of the human genome (e.g. 1000bp upstream) - in particular, I am looking for co-occurring TFBSs of these 3 TFs. I have the motifs available through the JASPAR database.
I found following solutions:
FIMO (Meme Suite) & findMotifs.pl or scanMotifGenomeWide.pl (HOMER) offer a way of scanning for them using known motifs. Each motif is treated separately – I then computed the co-occurring ones in R.
MCAST (Meme Suite) offers to scan for clusters (however it gives any clusters not co-occurring specifically and very few results … and occasionally segmentation fault, so I dropped it). Is there another tool that scans for co-occurring TFBSs is particular?
JASPAR offers a pre-scanned genome based on FIMO and TFBS Perl module - so I subsetted with the predictions of TFs of interest and the regions of interest (promoters).
REMAP 2018: offers merged peaks across ChIP-seq experiments for many TFs. Assuming that most binding sites are shared in different cell types / conditions, one could use these - correct? Again, I subsetted with the peaks of TFs of interest and the regions of interest (promoters). Unfortunately, not all TFs I am interested in are in this database. Any other similar resources available?
I am grateful for any insight: remarks to my solutions, other tools, other solutions, reviews on this problem ... anything :)
Thanks,
I strongly disagree. TF binding is highly dynamic and depends on open chromatin regions, which again are highly dynamic and cell-type-specific, leave alone conditions, even more dynamic than gene expression.
Thank your for your comment. Isn't that more motif activity than the binding site? the binding sites should be fairly shared shouldn't they? If they are active however is a different issue and dependent on the system. Otherwise, the whole remap merged peaks would be nonsense, wouldn't it? Thank you for any insight.