Quick question, is there a place where one can download BED files for the binding motifs of certain transcription factors. In my case, I'm looking for a BED file for the genomic regions (enhancers) where TET2 binds to genome-wide. I'm looking to examine the DNA methylation levels in those regions.
Thank You!
The UCSC Genome Browser offers a JASPAR track, which you could download as BED and do basic set operations upon. However, it does not appear to include TET2 binding sites, so you'll need to look elsewhere.
You might be better off running a FIMO scan against TRANSFAC or other databases (which you may need to obtain separately).
Here's a post I wrote on Bioinformatics SE about doing a whole-genome FIMO search for TFBS of factors in JASPAR:
If you were to follow these instructions, you would replace the JASPAR database with TRANSFAC, UniPROBE, or other TF databases that have TET2 position weight matrices (MEME-formatted, or with the ability to be converted to MEME format).
Once you have the whole genome scanned, you would get the TET2 hits and then do bedmap or other mapping steps to get DNA methylation signal over those hits.
The advantage of a whole-genome scan is the ability to come back to look at other TFs of interest, which you might find have tangential regulatory relationships with TET2 or other TFs.
Another advantage of using FIMO is control over statistical aspects of the TF scan. Other tools may hide these details for simplicity. While simplicity can be useful, it can also be useful to have control or know what those details are.
Transcription factors bind to different regions in the genome depending on the tissue type. The best would be for you to look for a TET2 Chip-seq data on GEO data in your tissue / cell type. If you cannot find any, I would try and find the closest tissue for TET2 Chip-seq..
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