Trascription factor binding site prediction

Question

[Eisuan]

Hello everyone! I would like to ask adiveces for trascription factor binding site prediction.

My co-supervisor asked me to check if a particular human gene promoter has potential binding site for a TF.

I have tried solving out this problem by coding a matlab code based upon information theory but I have found problems with defining a method in order to determine significance level of my result (since Σf*I values don't give any information by themselfs). I have tried one but it has failed to make positive predictions for a consensus site in promoters chosen as "positive controls". Therefore, I would like to change the approach and looking for some online predictors.

Have you got any advice?

I have tried using JASPAR on Genome Broswer but it seems to be not so much convenient since I am not able to download the analysis (and it means I have to check each TF name on the screen, because I cannot use the search function).

Thank you for your support!

Answer 1

[husensofteng]

If you are looking for an online tool where you can upload a list of genomic coordinates and get the overlapping TF motifs, I would suggest our developed resource called: funMotifs. It also provides tissue-type specific annotations. Alternatively, you could use regulomeDB

However, if you are looking to identify motif instances of a particular TF in a particular sequence then you could use FIMO.

Answer 2

[Alex Reynolds]

Some answers I've written on searching promoters for TFBS using FIMO:

TFBS enrichiment analysis

https://bioinformatics.stackexchange.com/questions/2467/where-to-download-jaspar-tfbs-motif-bed-file/2491#2491

Adjust for your organism, assembly, and TF databases of interest.