Dear Anyuan, The data in the ENCODE Regulation Txn Factor ChIP Track is only a subset of the data included HAIB TFBS and Yale TFBS tracks. The HAIB TFBS and Yale TFBS tracks contain additional views such as "Raw Signal" and "Signal" whereas the Txn Factor ChIP Track utilizes data from only the "Peaks" view from the those tracks.
If you have further questions, please contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group Subject: inquire about UCSC Chip-seq data From: 郭安源 <[email protected]> Date: Thu, 09 Dec 2010 10:49:09 +0800 To: [email protected] Dear sir, Thanks for your great work about UCSC genome browser. I have a question about the human Chip-Seq data. At human hg18, under "Regulation" super tracks,there are tracks named "ENCODE Integrated Regulation Tracks-Txn Factor ChIP", "HAIB TFBS", "Yale TFBS". I want to know that whether the data in "ENCODE Integrated Regulation Tracks-Txn Factor ChIP" contains all the data in tracks "HAIB TFBS" and "Yale TFBS". Since I saw the following words on the track pages http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=174800793&c=chr1&g=wgEncodeRegTfbsClustered http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=174800793&c=chr1&g=wgEncodeHudsonalphaChipSeq http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=174800793&c=chr1&g=wgEncodeYaleChIPseq So if want a complete chip-seq data, need I download all these or just the Txn Factor ChIP track? Thanks very much. Anyuan Guo Description This track shows regions where transcription factors, proteins responsible for modulating gene transcription, bind to DNA as assayed by ChIP-seq (chromatin immunoprecipitation with antibodies specific to the transcription factor followed by sequencing of the precipitated DNA). Additional views of this data set and additional documentation on the methods used for this track are available at the Yale TFBS Track <http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeYaleChIPseq> and the HAIB TFBS Track <http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeHudsonalphaChipSeq> pages. The /Peaks / views in those pages are the basis for the clusters shown here, which combine data from the peaks from the different cell lines and different transcription factors in those pages. Credits This track shows data from the Myers Lab <http://myers.hudsonalpha.org/> at the HudsonAlpha Institute for Biotechnology <http://www.hudsonalpha.org/> and by the labs of Michael Snyder <http://snyderlab.stanford.edu/>, Mark Gerstein <http://bioinfo.mbb.yale.edu/> and Sherman Weissman <http://info.med.yale.edu/bcmm/SMW/SMWhome2.html> at Yale University; Peggy Farnham <http://www.genomecenter.ucdavis.edu/farnham/> at UC Davis; and Kevin Struhl <http://struhl.med.harvard.edu/> at Harvard. On the HAIB TFBS page, it shows "These data were provided by the Myers Lab <http://myers.hudsonalpha.org/> at the HudsonAlpha Institute for Biotechnology <http://www.hudsonalpha.org/>.". On the Yale TFBS track page, it shows "These data were generated and analyzed by the labs of Michael Snyder <http://www.yale.edu/snyder/>, Mark Gerstein <http://bioinfo.mbb.yale.edu/> and Sherman Weissman <http://info.med.yale.edu/bcmm/SMW/SMWhome2.html> at Yale University; Peggy Farnham <http://www.genomecenter.ucdavis.edu/farnham/> at UC Davis; and Kevin Struhl <http://struhl.med.harvard.edu/> at Harvard. Contact: the Gerstein lab <mailto:[email protected]>. ". _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
