Is there any web tool to use where you can insert the gene ID of Your Favourite Gene, and the result is a list of putative/validated TF binding the promoter of YFG? Without having to search for the promoter sequence first, then paste it in a software which queries for consensus sequences in there.
Hi, You can search your gene here "http://www.grnpedia.org/trrust/Network_search_form.php". Or search like this way "https://slowkow.com/notes/tftargets/". or you can search in these two files which we have created using literature search and from ENCODE.
But remember all these methods may have error. You may want to cross check by yourself before using the result/methods. Hope this helps.
This is a context specific question. For example, if you want to predict nuclear receptor response elements, you can go for NUBIscan.
If you're interested in embryonic stem cell epigenetics, check out the BindDB tool on the web or direct link from the meshorerlab website.
You can also use the UCSC genome browser (if working with Human / mouse, hg19 / mm9 genome versions) and use the ENCODE tracks for TF binding sites. Then you search for your gene genomic location by entering its name and see if there is any putative binding site in its promoter. All TFs have not been looked for in all cell types, but you might be lucky and find something interesting. Data are more complete for human, but even if you work with another species, there is a fair chance that the regulators are conserved, even if the binding site(s) would not be at the same location. It's worth a look, but I don't think you can skip the in silico search for motifs, meaning you have to start from your promoter sequence... Good luck!
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