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
