Hello Shuli, For any of our tracks you can find information as you describe on the track description page. For this particular track you will find the description page here:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClustered <http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClustered> To see the description for any track you can click on the gray bar to the left of the track in the main display or click on the track title above its configuration pulldown menu. In general to find the description page for a track associated with a table you can use our track search feature. You can get to track search by clicking on the "track search" button below the assembly pulldowns on the gateway page (http://genome.ucsc.edu/cgi-bin/hgGateway) or below the main browser display. Once in track search click the "Advanced" tab and from the pulldown that reads "Antibody or target protein" select the category "Table name at UCSC". In the "contains" field paste in "wgEncodeRegTfbsClustered" and click "search". This should find your track of interest. You can read the track description by clicking on the track name, or you can view it in the browser by clicking the checkbox to the left of the search result and "View in Browser". Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 4/10/12 5:25 PM, Shuli Kang wrote: > Hi Vanessa, > > Thanks for your explanation. I'm also compiling a TFBS dataset by using > the Chip-Seq data from ENCODE project. I have tried to combine the data > from the five major groups, but it's not an easy task for me. > > I have found a set of clustered TFBSs from Kent's lab on the website ( > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegTfbsClustered/). > Seem this is exactly what I need. Could you please tell me where I can > find detailed description of this dataset, such as how the TFBSs > clustered, what's the meaning of the scores in the bed file, etc ? > > Thanks, > Shuli > > On 04/10/2012 10:30 AM, Vanessa Kirkup Swing wrote: >> Hi Anyuan, >> >> The additional tracks that you seeing in the table browser are in the >> genome browser and are grouped under the ENC TF Binding Super-track ( >> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeTfBindingSuper >> ) >> >> To see all the available tracks on the genome browser there is a tool >> called Track Search. You can get to track search from the gateway page ( >> http://genome.ucsc.edu/cgi-bin/hgGateway). Select the assembly you are >> interested in and then click on "track search". >> >> With regards to intersecting data between experiments, we are are unable to >> give you advice on that. >> >> From the track description page for the hg19 TFBS Conserved Track ( >> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=tfbsConsSite) >> here is what was done that is different from hg18: >> >> "These data were obtained by running the program tfloc (Transcription >> Factor binding site LOCater) on multiz46way alignments, restricting only to >> the July 2007 (mm9) mouse genome assembly, the November 2004 rat assembly >> (rn4), and the February 2009 human genome assembly (hg19). Transcription >> factor information was culled from the Transfac Factor database, version >> 7.0." >> >> Here is what is different for the hg18 TFBS Conserved Track ( >> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&c=chr21&g=tfbsConsSites): >> >> "These data were obtained by running the program tfloc (Transcription >> Factor binding site LOCater) on multiz alignments of the February 2006 >> (mm8) mouse genome assembly and the November 2004 rat assembly (rn4) to the >> March 2006 human genome assembly (hg18.) Transcription factor information >> was culled from the Transfac Factor database, version 7.0." >> >> These differences would explain why there are larger amounts of data for >> hg19. >> >> I hope that answers your questions. If you have further questions, please >> email the list: [email protected]. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> ---------- Forwarded message ---------- >> From: 郭安源<[email protected]> >> Date: 2012/4/10 >> Subject: [Genome] ask about the CHIP-seq and tfbs data for human hg19 >> To: [email protected] >> >> >> Dear Sir/Madam, >> I am trying to use the human CHIP-seq data on UCSC and now I have >> several questions about it. >> From the hg19 browser page, the only one chip-seq data in the >> regulation tracks is the "ENCODE regulation tracks", which includes the >> "Txn Factor ChIP" track. However, from the Table browser download page, we >> can find several other CHIP TFBS tracks, such as HAIB TFBS and UTA TFBS etc. >> Is it because that the Txn Factor ChIP track includes all the data of >> others? So if I need the most comprehensive CHIP data, should I donwload >> only the Txn Factor ChIP track data or also download other TFBS data in the >> table browser page? >> I noticed that one track has many experiments for the same TF, such as >> for the Nrsf TF in the HAIB TFBS track, there are the following >> experiments. For these, should I use the intersection data to reduce false >> positve for the Nrsf tfbs? >> wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep1.broadPeak >> wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep2.broadPeak >> wgEncodeHaibTfbsH1hescNrsfV0416102PkRep1.broadPeak >> wgEncodeHaibTfbsH1hescNrsfV0416102PkRep2.broadPeak >> wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep1.broadPeak >> wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep2.broadPeak >> wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep1.broadPeak >> wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep2.broadPeak >> wgEncodeHaibTfbsK562NrsfV0416102PkRep1.broadPeak >> wgEncodeHaibTfbsK562NrsfV0416102PkRep2.broadPeak >> wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep1.broadPeak >> wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep2.broadPeak >> wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep1.broadPeak >> wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep2.broadPeak >> wgEncodeHaibTfbsSknshNrsfPcr2xPkRep1.broadPeak >> wgEncodeHaibTfbsSknshNrsfPcr2xPkRep2.broadPeak >> wgEncodeHaibTfbsU87NrsfPcr2xPkRep1.broadPeak >> wgEncodeHaibTfbsU87NrsfPcr2xPkRep2.broadPeak >> >> For the conserved TFBS prediction in the "TFBS Conserved" track, I noticed >> ther are much more data than the data downloaded from hg18 previously. >> However, the description page of this track ( >> http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=255151677&c=chr21&g=tfbsConsSites), >> it seem no different from the hg18 page, which said using the TransFac 7.0 >> matrix and the same program. If that, why much more tfbs were predicted? I >> guess you use the new version of TransFac matrix but didn't update the >> description page, right? >> These data are very important for us. I am looking forward for your reply. >> Thanks very much. >> Best, >> Anyuan Guo >> _______________________________________________ >> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
