Hi Some tracks are composed of many 'sub-tracks', which is the case for Yale. For any given region only a few of the sub-tracks may have any data.
In the table browser you can select the 'sub-track merge' option which appears further down the page after you choose 'Regulation tracks/Yale TFBS'. This opens a window where you can choose from all or a few of the tracks. If you do this, then you should see some data for your region. M On Fri, Aug 14, 2009 at 11:38 AM, Bhagwat, Medha (NIH/OD/ORS) [E]<[email protected]> wrote: > Hi Mike, > > I searched for a gene (hras) and wanted to see transcription factor binding > sites upstream of the gene. Hence, > > 1. I added regulation tracks such as TFBS conserved, Yale TFBS. > 2. zoomed out 3x so that I go to upstream sequence > 3. tried to download Tables to get information about which TF and their > binding site locations > > > If this is not correct way to what I am trying to do, let me know. If this > is the correct way, how do I download TFBS information for any gene? > > Thanks, > > Medha > > > > >> -----Original Message----- >> From: [email protected] [mailto:[email protected]] On Behalf Of >> Michael Pheasant >> Sent: Friday, August 14, 2009 1:49 PM >> To: Bhagwat, Medha (NIH/OD/ORS) [E] >> Cc: [email protected] >> Subject: Re: [Genome] Table download >> >> Hi Medha >> >> I have a few questions for you; >> >> *) what track(s) are you trying to download? >> - all "wgEncodeYaleChIPseqPeaks*", or some subset of peaks, or >> something else? >> - when I look at that region I see only one peak for HeLa Pol2 >> >> *) When you say you 'dont get the info' do you mean you get an page >> containing just the following text, or something else?: >> >> #bin chrom chromStart chromEnd name score strand >> signalValue >> pValue qValue peak >> # No results in given region. >> >> Cheers, >> >> Mike >> >> >> On Fri, Aug 14, 2009 at 7:41 AM, Bhagwat, Medha (NIH/OD/ORS) >> [E]<[email protected]> wrote: >> > Hi, >> > >> > I am going through UCSC browser and trying to download transcription >> factor binding sites information as Tables but not getting anywhere. >> > >> > I started with >> > >> > http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr11:523712- >> 524079&hgsid=139544794&wgEncodeYaleChIPseq=dense >> > >> > and then went to Tables to download, changed the group to regulation >> but don't get the info. >> > >> > Obviously there is some other way. Can you help? >> > >> > Thanks, >> > >> > Medha Bhagwat >> > NIH >> > >> > >> > >> > _______________________________________________ >> > Genome maillist - [email protected] >> > https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > >> >> >> >> -- >> Michael Pheasant >> Associate Project Scientist >> UCSC Genome Browser >> >> Email: [email protected] >> Skype: mpheasant >> Phone: +1-831-459-1424 >> >> Location: Engineering2 Room 515 >> Post: CBSE, UC Santa Cruz, MS:CBSE/ITI >> 1156 High Street >> Santa Cruz, CA 95064, USA > -- Michael Pheasant Associate Project Scientist UCSC Genome Browser Email: [email protected] Skype: mpheasant Phone: +1-831-459-1424 Location: Engineering2 Room 515 Post: CBSE, UC Santa Cruz, MS:CBSE/ITI 1156 High Street Santa Cruz, CA 95064, USA _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
