38efe73ca469fb8bff5206559a713488a4561ba0 jnavarr5 Thu Jun 18 16:25:41 2020 -0700 Adding the announcement for the ENCODE cCREs track for human and mouse, refs #24668 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 728307d..595987b 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,98 @@ </div> <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <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> <!-- ============= 2020 archived news ============= --> <a name="2020"></a> +<a name="061820"></a> +<h2>Jun. 18, 2020 New ENCODE cCREs track available for human and mouse (hg38 and mm10) +</h2> +<p> +We are pleased to announce the <em>ENCODE Registry of candidate cis-Regulatory Elements</em> (cCREs) +track for the human and mouse genomes +(<a href="../../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=encodeCcreCombined" +target="_blank">GRCh37/hg19</a> and +<a href="../../cgi-bin/hgTrackUi?db=mm10&c=chrX&g=encodeCcreCombined" +target="_blank">GRCm38/mm10</a>). +cCREs are the subset of representative DNase hypersensitive sites across ENCODE and Roadmap +Epigenomics samples that are supported by either histone modifications (H3K4me3 and H3K27ac) or +CTCF-binding data. The Registry of cCREs is one of the core components of the integrative level of +the <a href="https://www.encodeproject.org/" target="_blank">ENCODE Encyclopedia of DNA +Elements</a>. A total of 926,535 elements for human and 339,815 elements for mouse were identified +and classified by the ENCODE Data Analysis Center according to biochemical signatures.</p> + +<a href="http://genome.ucsc.edu/s/Kate/hg38%20ENCODE%20cCRE%20announcement%20largeprint" +target="_blank"> +<img style="margin-left" width="950px" src="../images/ccreAnnouncementScreenshot.png"></a> + +<p> +CCREs are colored and labeled according to classification by regulatory signature: +<p> +<table cellpadding='2'> + + <tr> + <th style="border-bottom: 2px solid;">Color</th> + <th style="border-bottom: 2px solid;"></th> + <th style="border-bottom: 2px solid;">UCSC label</th> + <th style="border-bottom: 2px solid;">ENCODE classification</th> + <th style="border-bottom: 2px solid;">ENCODE label</th> + </tr> + </thead> + +<tr><td style='background-color: #FF0000;'></td><td>red</td> + <td>prom</td> + <td>promoter-like signature</td> + <td>PLS</td></tr> +<tr><td style='background-color: #FFA700;'></td><td>orange</td> + <td>enhP</td> + <td>proximal enhancer-like signature</td> + <td>pELS</td></tr> +<tr><td style='background-color: #FFCD00;'></td><td>yellow</td> + <td>enhD</td> + <td>distal enhancer-like signature</td> + <td>dELS</td></tr> +<tr><td style='background-color: #FFAAAA;'></td><td>pink</td> + <td>K4m3</td> + <td>DNase-H3K4me3</td> + <td>DNase-H3K4me3</td></tr> +<tr><td style='background-color: #00B0F0;'</td><td>blue</td> + <td>CTCF</td> + <td>CTCF-only</td> + <td>CTCF-only</td></tr> +</table> +</p> + +<p> +This dataset was produced by the ENCODE Data Analysis Center +(<a href="https://www.umassmed.edu/zlab/" target="_blank">Zlab</a> at UMass Medical Center). Thanks +to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI for providing this data and +initial version of the track. Thanks also to the ENCODE Consortium, the ENCODE production +laboratories, and the ENCODE Data Coordination Center for generating and processing the datasets +used here. Thanks to Kate Rosenbloom and Jairo Navarro for the development and release of these +tracks.</p> + + <a name="052720"></a> <h2>May 26, 2020 New video on the Browser's YouTube channel</h2> <p> We have released a new video to the Browser's <a href = "https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" target = _blank>YouTube channel</a>. </p> <p> <b> Browser Basics, Part Three — Configuring the Browser + DNA navigation </b> </p>