Hi All,
Is there a compiled list available somewhere with known transcription factor binding sites along with transcription factor name and type of transcription factors. I am particularly looking for transcriptional repressor binding sites in the exonic regions.
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Saad Murtaza Khan
ENCODE has a lot of ChIP-seq data, you can just use the peak bed file to intersect (bedtools) with the exon sequences to see what binds there.
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written
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Ming Tommy Tang
Another resource is the Ensembl FTP site.
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Ashutosh Pandey
You could take JASPAR PWMs and search with FIMO. This gives you positions for JASPAR TF binding sites, which you can map against ChIP-seq data, exons, or other constrained genomic regions taken from other annotation datasets, using BEDOPS tools like bedops --element-of or bedmap to do fast set operations.
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Alex Reynolds
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What standard are we using for "known". Do you just want places with apparent binding (in which case just go with the answer from tangming2005, or do you want known-functional binding?
The thing is that encode is cell line data and I am working with Blueprint data which has different cell types mostly blood cells. I needed to know which of the sites are most reliable and remain unchanged across different tissues/cell types. So even the predicted ones would do if they are well curated.