Hello Gaurav, Thank you while for your patience while we gathered information concerning your request.
The short answer is that a definitive set of all mappings does not exist, however there are tracks/analysis methods that you might be interested in. I am forwarding you the reply from one of the TFBS track authors who is very knowledgeable about this datatype. For any external data found, the option of adding it to the UCSC browser as a custom track is always possible. The overall idea would be to find TFB Sites and map to genes (if needed) using the Table browser and Galaxy. http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser Best wishes, Jennifer > Please suggest our conserved binding site track "TFBS Conserved". > Of course, these are simply computational predictions, so > there will of course have plenty of false positives and false negatives. > The track also only include conserved binding sites and many functional > binding sites are not conserved in Conservation (MAF) alignments. > > The user may also way to check out the PReMod database, which uses a > more advanced method to detect conserved binding sites: > > http://genomequebec.mcgill.ca/PReMod/welcome.do > > As far as I know, there is currently no really good method for > globally predicting TF binding sites (its a hard problem afterall!) > > Here's a good review on the topic: > http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS0-4GCX06C-2&_user=994540&_coverDate=08/31/2005&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050024&_version=1&_urlVersion=0&_userid=994540&md5=47ddfad2167a2834e1d2e88b99db89eb > > Anyways, hopefully this helps. > Matt ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Gaurav Arora" <[email protected]> wrote: > From: "Gaurav Arora" <[email protected]> > To: [email protected] > Cc: "Gaurav Arora" <[email protected]> > Sent: Monday, February 1, 2010 11:40:14 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Transcription Factors and the genes they target > > Hi there, > > I am trying to identify potential target genes for known transcription > factors. I am aware that this information is available as matrix, > however is there a way that I can track each transcription factor to > their target genes. > > I have been looking at your archives, however I haven't found any > definite answer. Let me know if there is a way to match any tables > available on your website. > > Thanks, > Gaurav > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
