Transcription Factor-gene regulations

Question

[bioinfo]

Hi

How to download curated human TF-gene regulations from the TRANSFAC database ?

Answer 1

[Alex Reynolds]

TRANSFAC comes with motif models you can convert to MEME format and use with FIMO to locate putative TF binding sites at your threshold of interest (e.g. 10^-4 or 10^-5), specific to FASTA sequence data for your genome of interest.

Once you have those binding sites, you can use set operations with bedops or bedmap to map binding sites to gene promoters (proximal, distal, etc.) or other regulatory regions from your gene annotations of interest, specific to your genome of interest, e.g. GENCODE, etc.

[bioinfo]

Thank you. I ll check it out.