Transcription factor binding site prediction program/algorithm

Question

[bharata1803]

Hello,

My supervisor asked me to predict transcription factor (TF) - target gene (TG) pair based on its binding site. Basically, what I must do is to make a pairwise comparison of TF binding region and TG binding site. I must check all pairwise comparison between all known TF and all known TG. We plan to develop another algorithm to narrow down the result and infer the functionality (inhibit or activate) later. So, currently, I focus on how to develop this pairwise comparison.

What I want to ask is, is this kind of database already exist? Predicted pair of TF-TG based on binding site? I think I have read several paper discussing about this but I forget which one. The only database I am familiar is Pazar but it is just a database for TF and the data come from literature, not prediction. I just search and I find PROMO but it is quite old. The published paper is 2003 so I want to ask here if someone know about well known database or algorithm or program to calculate this. Thank you very much.

Answer 1

[ATRX]

For human, go to UCSC and click output. This will provide you the predicted binding site or genomic loci and then you may use these genomic loci to find the nearest genes.

Software for TFBS prediction:

1. JasPar
2. Perl module
3. ChIP-Seq/ChIP-ChIP and Microarray
4. DBTSS

[bharata1803]

Thank you for the reply. Do you think ensembl database has this similar feature? Currently, I'm using ensembl as my reference. I'm afraid if I change to UCSC, the data or gene ID will be incompatible.

[ATRX]

Ensembl Regulatory Build; Here is the publication too