How to find TFs starting from promoter region

[Rosanna Di Tinco]

Hello, 

I am interested in finding a list of potential transcription factors that could bind the promoter region of a specific gene (CD274, human). Then, I would like to validate these results with ChIP-seq data. 

I never did it before, so Could anyone show me how to set up the research? Unfortunately, I am just a beginner in this field. 

Kind regards, 

Rosanna Di Tinco

[Anthony Mathelier]

Hi Rosanna,

I would suggest that you look at our UniBind database (https://unibind.uio.no/) since it stores precisely TFBSs found in ChIP-seq data. You can download the BED files to look for overlap in your region of interest. Or you can send to me (use my address anthony....@ncmm.uio.no) your region of interest and I'll intersect with our data.

Hope it helps.

Best

AM

[Rosanna Di Tinco]

Thanks for your reply. 

After opening the UniBind database what I have to do as I am not looking for a specific TF? 

Kind regards, 

Rosanna Di Tinco

[Anthony Mathelier]

As I wrote above, you can download the BED files to look for overlap in your region of interest. We now provide a tool for intersection as well, you can give it a try: https://unibind.uio.no/TFBS_extraction/