SOS! how to search all the possible transcription binding site - (Jun/27/2005 )
We have identified a consesus binding site of a a transcription factor. Now I would like to know what other proteins are regularted by this transcription factor. But I don't know how to search it in the database. I tried blast, but it seemed that the input sequence is too short and no results.
Thank you all for your help.
En, here is my suggestions,
1. Got to know how long is your consensors, NCBI blast minimum word size allowed is 7, if you used default, should be 11, try lower it to 7. But I still a bit question about it, usually transcription factor binding site(TFBS) is not very strictly defined, have some degeneracy at certain positions, how can u use such consensors to blast is a problem, did you try to blast with all possible combinations?
2. Here is what I will do, first get all promoter regions of all genes, you can use pre-obtained promoter set which is here (http://arep.med.harvard.edu/labgc/adnan/hsmmupstream/ , an old version though), or use some program like EZRetrieve (http://siriusb.umdnj.edu:18080/EZRetrieve/index.jsp) to retrieve, say upstream 4kb of all genes. Then write a perl program to search your consensors with regular expression.
3. or after you have all promoter regions, you can use TESS, TFSearch, TRANSFAC to search all TFBSs, if you want to do whole genome scale, web version might not work you probably need to download and install a local version. The biology behind this is that usually TF work in concert, so identifying co-existing TFBS might provide insight into the regulation mechanism.
Hope these help. I have a list of links here you might want to check out:
Hope these help.
Thank you so much for your suggestions!
u r welcome! cheers!