743cce71f35609be0793fe89a87d93a22cc83a80 ccpowell Mon Jun 17 09:54:10 2019 -0700 Adding URL links and edits to the encode3 announcement, refs #23243 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index cc84a3b..8857fad 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,85 +39,86 @@ </div> <div class="col-sm-3"> <ul> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2019 archived news ============= --> <a name="2019"></a> -<a name="61319"></a> +<a name="061719"></a> <h2> Jun. 13, 2019 New ENCODE 3 transcription factor binding site track sets for human (<em>GRCh37/hg19, GRCh38/hg38</em>)</h2> <p> We are pleased to announce two new ENCODE 3 transcription factor binding site track sets for human (GRCh37/hg19, GRCh38/hg38). These track sets show regions of transcription factor binding derived from a large collection of ChIP-seq experiments performed by the ENCODE project between February 2011 and November 2018. </p> <p> The ENCODE TF ChIP-seq data were processed using the <a href="https://www.encodeproject.org/chip-seq/transcription_factor/" target="_blank" >ENCODE Transcription Factor ChIP-seq Processing Pipeline</a> to generate peaks of TF binding. Peaks from 1264 experiments (1256 in hg38) representing 338 transcription factors (340 in hg38) in 130 cell types (129 in hg38) were used to generate these two track sets.<br> <ul> - <li>The <b>ENCODE 3 TF ChIP Clusters track sets</b> are collections of ChIP-seq peaks consolidated into a + <li>The <b>ENCODE 3 TF ChIP Clusters tracks</b> are collections of ChIP-seq peaks consolidated into a summary display or ‘cluster’ showing occupancy regions for each factor. The cluster labels now include the count of cell types contributing to the cluster (those with ChIP-seq peaks in the region) and the total count of cell types tested for the factor. The new label feature can be disabled via a user option on the track configuration page. You can read more about the - TF ChIP Clusters track sets here: - <a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=encRegTfbsClustered" target="_blank">hg19</a>, - <a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=encRegTfbsClustered" target="_blank">hg38</a>.</li> + TF ChIP Clusters tracks here: + <a href="../cgi-bin/hgTrackUi?db=hg19&g=encRegTfbsClustered" target="_blank">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=encRegTfbsClustered" target="_blank">hg38</a>.</li> <li>The <b>ENCODE 3 TF ChIP Peaks track sets</b> are collections of the underlying ChIP-seq peak tracks which can be viewed individually or collectively by cell type or transcription factor. You can read more about the TF ChIP Peaks track sets here: - <a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=encTfChipPk" target="_blank">hg19</a>, - <a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=encTfChipPk" target="_blank">hg38</a>.</li> + <a href="../cgi-bin/hgTrackUi?db=hg19&g=encTfChipPk" target="_blank">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=encTfChipPk" target="_blank">hg38</a>.</li> </ul> </p> <p> An example of these two track sets is shown in the following sessions where CTCF binds to the MYC Proto-Oncogene -across more than 100 cell types. CTCF is a transcription factor identified as a repressor of MYC +across a few selected cell types. CTCF is a transcription factor identified as a repressor of MYC shown to inhibit cell growth (<a href="https://www.pnas.org/content/100/2/633" target="_blank">Qi et al., 2002</a>).<br> <ul> - <li><a href="https://genome.ucsc.edu/s/cocopow/hg19_myc%2Bctcf" target="_blank" + <li><a href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&wgEncodeReg=show&wgEncodeReg_hideKids=1&encTfChipPk=pack&encTfChipPk_hideKids=1&encTfChipPkENCFF535MZG=dense&encTfChipPkENCFF535MZG_sel=1&encTfChipPkENCFF579XTC=dense&encTfChipPkENCFF579XTC_sel=1&encTfChipPkENCFF574FIL=dense&encTfChipPkENCFF574FIL_sel=1&encTfChipPkENCFF560GGY=dense&encTfChipPkENCFF560GGY_sel=1&encTfChipPkENCFF552XDP=dense&encTfChipPkENCFF552XDP_sel=1&encTfChipPkENCFF540DVR=dense&encTfChipPkENCFF540DVR_sel=1&encRegTfbsClustered_sel=1&encRegTfbsClustered=full&encRegTfbsClustered.filterBy.name=CTCF&position=chr8%3A127736594-127740958&knownGene=full" +target="_blank" >CTCF transcription factor binding to MYC on hg19</a></li> - <li><a href="https://genome.ucsc.edu/s/cocopow/hg38_myc%2Bctcf" target="_blank" + <li><a href="../cgi-bin/hgTracks?db=hg19&hideTracks=1&wgEncodeReg=show&wgEncodeReg_hideKids=1&encRegTfbsClustered_sel=1&encRegTfbsClustered=full&encRegTfbsClustered.filterBy.name=CTCF&wgEncodeTfBindingSuper=show&wgEncodeTfBindingSuper_hideKids=1&encTfChipPk=dense&encTfChipPk_hideKids=1&encTfChipPkENCFF003YLJ=dense&encTfChipPkENCFF003YLJ_sel=1&position=chr8%3A128748315-128753680&knownGene=full&encTfChipPkENCFF016EUX=dense&encTfChipPkENCFF016EUX_sel=1&encTfChipPkENCFF030BPR=dense&encTfChipPkENCFF030BPR_sel=1&encTfChipPkENCFF032DEW=dense&encTfChipPkENCFF032DEW_sel=1&encTfChipPkENCFF777TZZ=dense&encTfChipPkENCFF777TZZ_sel=1" target="_blank" >CTCF transcription factor binding to MYC on hg38</a></li> </ul> </p> <p> Thanks to the <a href="https://www.encodeproject.org/" target="_blank">ENCODE Consortium</a>, the ENCODE ChIP-seq production laboratories, and the ENCODE Data Coordination Center for generating and processing the TF ChIP-seq datasets. The ENCODE accession numbers of the constituent datasets are available on the peak details page as links in the Clusters tracks and in the track title for the Peaks tracks. Special thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI, at the <a href="https://www.umassmed.edu/zlab/" target="_blank">ENCODE Data Analysis Center (ZLab at UMass Medical Center)</a> for providing the peak datasets, metadata, and guidance developing these track sets. Thanks to Kate Rosenbloom and Conner Powell of the UCSC Genome Browser group for their work in creating and releasing these track sets. </p> -<a name="60619"></a> +<a name="060619"></a> <h2>June 6, 2019 New Genome Browser: Chinese Hamster Ovary (CHO) cell line, criGriChoV2 (<em>Cricetulus griseus</em>)</h2> <p> A genome browser is now available for the <em>Chinese Hamster Ovary cell line</em> assembly released in June 2017 by the <a href="https://www.eaglegenomics.com/eagle-case-studies/horizon-case-study/" target="_blank">Eagle Genomics Ltd</a> (CHOK1S_HZDv1). <h3>About the assembly:</h3> <ul> <li><b>UCSC Genome Browser assembly ID:</b> <a href=../cgi-bin/hgTracks?db=criGriChoV2>criGriChoV2</a></li> <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.eaglegenomics.com/" target="_blank"> Eagle Genomics Ltd</a></li> <li><b>Assembly date:</b> June 2017</li> <li><b>Accession ID:</b> GCA_900186095.1</li> <li><b>NCBI Genome information:</b><a href="https://www.ncbi.nlm.nih.gov/genome/2791" target="_blank" > 2791</a> <em>(Cricetulus griseus)</em></li> <li><b>NCBI Assembly information:</b><a href="https://www.ncbi.nlm.nih.gov/assembly/1422381" target="_blank" > 1422381</a></li> @@ -131,31 +132,31 @@ target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#chinese_hamster_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV2/" target="_blank" >FTP</a></li> <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#chinese_hamster" target="_blank" >Downloads page</a></li> </ul> </p> -<a name="52119"></a> +<a name="052119"></a> <h2>May 21, 2019 New Genome Browser: Cat, felCat9 (<em>Felis catus</em>)</h2> <p> A genome browser is now available for the <em>Felis catus</em> assembly released in November 2017 by the <a href="https://www.genome.wustl.edu/" target="_blank">Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine</a> (Felis_catus_9.0). <h3>About the assembly:</h3> <ul> <li><b>UCSC Genome Browser assembly ID:</b> felCat9</li> <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.genome.wustl.edu/" target="_blank"> Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine</a></li> <li><b>Assembly date:</b> November 2017</li> <li><b>Accession ID:</b> GCF_000181335.3</li> <li><b>NCBI Genome information:</b><a href="https://www.ncbi.nlm.nih.gov/genome/78" target="_blank" > 78</a> <em>(Felis catus)</em></li> <li><b>NCBI Assembly information:</b><a href="https://www.ncbi.nlm.nih.gov/assembly/1448961" target="_blank" > 1448961 </a></li>