a37997b9cc519202c89d2b66ae0ec69b86e392f6 ccpowell Tue Jun 11 16:10:16 2019 -0700 Editing newarch for encode 3 tfbs tracks announcements, refs #23243 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 20751c0..b552894 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -48,41 +48,60 @@ </div> </div> <!-- ============= 2019 archived news ============= --> <a name="2019"></a> <a name="061319"></a> <h2> Jun. 16, 2019 New ENCODE 3 transcription factor binding site tracks for human (<em>GRCh37/hg19, GRCh38/hg38</em>)</h2> <p> We are pleased to announce two new ENCODE 3 transcription factor binding site tracks for human (GRCh37/hg19, GRCh38/hg38) assemblies. These tracks 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 following two sessions express where the CTCF Binding factor binds to the MYC Proto-Oncogene +across more than 100 cell types. CTCF is a transcription factor identified as a repressor of MYC +shown to cause cell growth inhibition (<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" + >CTCF transcription factor bidning to MYC on hg19</a></li> + <li><a href="https://genome.ucsc.edu/s/cocopow/hg38_myc%2Bctcf" target="_blank" + >CTCF transcription factor bidning to MYC on hg38</a></li> +</ul> +</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 compiled in order to -generate these two tracks. The peaks were grouped together to produce a summary display showing -occupancy regions for each factor, seen here in the TF ChIP Clusters tracks: -<a href="https://genome.ucsc.edu/s/cocopow/hg19_tf_clusters" target="_blank">hg19</a>, -<a href="https://genome.ucsc.edu/s/cocopow/hg38_tf_clusters" target="_blank">hg38</a><br> -The underlying ChIP-seq peak data are available from the ENCODE 3 TF ChIP Peaks tracks: -<a href="https://genome.ucsc.edu/s/cocopow/hg19_tf_peaks" target="_blank">hg19</a>, -<a href="https://genome.ucsc.edu/s/cocopow/hg38_tf_peaks" target="_blank">hg38</a> +<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 compiled in order to generate these two tracks.<br> +<ul> + <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 include + the count of cell types contributing to the cluster (those with a ChIP-seq peaks in the region), and + the total count of cell types tested for the factor. This label can be disabled via a user option on + the track configuration page. You can read more about the TF ChIP Clusters tracks 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> + <li>The <b>ENCODE 3 TF ChIP Peaks tracks</b> are collections of the underlying ChIP-seq peak tracks + which are available collectively or individually. You can read more about the TF ChIP Peaks composite tracks 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> +</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 used here. The ENCODE accession numbers of the constituent datasets are available from the peak details page. 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 this track. Thanks to Kate Rosenbloom and Conner Powell of the UCSC Genome Browser group for their work in creating and releasing these tracks. </p> <a name="60619"></a> <h2>June 6, 2019 New Genome Browser: Chinese Hamster Ovary (CHO) cell line, criGriChoV2 (<em>Cricetulus griseus</em>)</h2>