Hello Amanda, One of our scientists reminded me of a few other excellent sources for TFBS data:
Yale TFBS - ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard HAIB TFBS - ENCODE Transcription Factor Binding Sites by ChIP-seq from HudsonAlpha Institute Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "Amanda Formosa" <[email protected]> > Cc: [email protected] > Sent: Thursday, January 21, 2010 11:19:29 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] how to find Transcription Factor Binding Sites > > Hello, > > The track group "Regulation" would contain annotation like this. > Some tracks to start with in the Human Mar. 2006 Assembly (hg18) are: > > TFBS - HMR Conserved Transcription Factor Binding Sites. > SwitchGear TSS - SwitchGear Genomics Transcription Start Sites > > (The Human GRCh37 Assembly (hg19) is still undergoing development for > tracks such as these, so use hg18.) > > You can set the position in the browser for your region to view the > data. Or, use the Table Browser to extract the data. > > Some help with examples that provide many details: > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GetStarted > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#FineTuning > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser > > We hope this helps to get you started, > Jennifer > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Amanda Formosa" <[email protected]> wrote: > > > From: "Amanda Formosa" <[email protected]> > > To: [email protected] > > Sent: Thursday, January 21, 2010 3:00:29 AM GMT -08:00 US/Canada > Pacific > > Subject: [Genome] how to find Transcription Factor Binding Sites > > > > Dear UCSC, > > > > I would like to know how to search for Transcription Factor Binding > > Sites and likely promoter regions with your program. > > > > For example, I have a region of interest on chromosome 17, - strand, > > coordinates 1899670-1909378. I would like to know if there any > > sub-regions within that region that are likely to have Transcription > > Factor Binding activity and/or promoter activity. > > > > How can I do this? (Please explain step by step since I'm knew to > > this) > > > > Thank you > > > > Amanda Formosa > > > > PhD candidate, The University of Rome, Tor Vergata, Department of > > Internal Medicine. > > > > > > > > __________________________________________________________________ > > Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark > > your favourite sites. Download it now > > http://ca.toolbar.yahoo.com. > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
