find / score transcription factors based on motifs

Question

[Jessica]

Hi all,

I got a list of motifs of interest from MSigDB. Is there a way to find / score transcription factors that potentially bind to those motifs? Thank you very much.

Jessica

Answer 1

[Alex Reynolds]

If you don't have PWMs, you might try to map a motif list to models in JASPAR, TRANSFAC, UniPROBE or other TF databases. Once you have PWMs, you could use a tool like FIMO to search for putative binding sites across your genome of interest; each binding site will have an associated p-value under some threshold you specify for the search.