f29825cc3b3ce2c55f8aeb5b4756aa960f9905b2 lrnassar Wed Jan 14 14:00:36 2026 -0800 Releasing and announcing the new ENCODE4 cCREs track, refs #34109 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 657815c1249..26f7818d408 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -1,78 +1,182 @@ <!DOCTYPE html> <!--#set var="TITLE" value="UCSC Genome Browser: News Archives" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <!--#include virtual="$ROOT/redmineWidget.html" --> <h1>News Archives</h1> <div class="container"> <div class="row"> <div class="col-sm-3"> <ul> + <li><a href="#2026">2026 News</a></li> <li><a href="#2025">2025 News</a></li> <li><a href="#2024">2024 News</a></li> <li><a href="#2023">2023 News</a></li> <li><a href="#2022">2022 News</a></li> - <li><a href="#2021">2021 News</a></li> </ul> </div> <div class="col-sm-3"> <ul> + <li><a href="#2021">2021 News</a></li> <li><a href="#2020">2020 News</a></li> <li><a href="#2019">2019 News</a></li> <li><a href="#2018">2018 News</a></li> <li><a href="#2017">2017 News</a></li> - <li><a href="#2016">2016 News</a></li> </ul> </div> <div class="col-sm-3"> <ul> + <li><a href="#2016">2016 News</a></li> <li><a href="#2015">2015 News</a></li> <li><a href="#2014">2014 News</a></li> <li><a href="#2013">2013 News</a></li> <li><a href="#2012">2012 News</a></li> - <li><a href="#2011">2011 News</a></li> </ul> </div> <div class="col-sm-3"> <ul> + <li><a href="#2011">2011 News</a></li> <li><a href="#2010">2010 News</a></li> <li><a href="#2009">2009 News</a></li> <li><a href="#2008">2008 News</a></li> - <li><a href="#2007">2007 News</a></li> - <li><a href="#2001">2001</a>-<a href="#2006">2006 News</a></li> + <li><a href="#2001">2001</a>-<a href="#2007">2007 News</a></li> </ul> </div> </div> </div> <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be found <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> +<!-- ============= 2025 archived news ============= --> +<a name="2026"></a> + +<a name="011526"></a> +<h2>Jan. 15, 2026 New ENCODE cCREs track available for human (hg38)</h2> +<p> +We are proud to announce a new <a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=cCREs&position=default" + target="_blank"> +ENCODE Registry of cCREs (candidate Cis-Regulatory Elements)</a> +container track for the hg38/GRCh38 genome as described in <a target="_blank" +href="https://www.nature.com/articles/s41586-025-09909-9"</a>Moore et al., <em>Nature</em> 2026</a>. +This container contains candidate Cis-Regulatory +Elements (cCREs) generated by the ENCODE Consortium during Phase 4 (ENCODE4) and Phase 3 (ENCODE3). +The previous "ENCODE3 cCREs" track is retained for archival purposes. The tracks include both integrated +(biosample-agnostic) and biosample-specific annotations derived from core epigenomic assays.</p> + +<div class="text-left"> +<a href="https://genome.ucsc.edu/s/Lou/HBBexample" target=_blank> +<img src="/images/encode4cCREsNews.png" width='75%'></a> +</div> +<p> +The new tracks include:</p> +<ul> +<li><b><a href="/cgi-bin/hgTrackUi?c=chr7&g=cCREregistry&position=default&db=hg38" target="_blank"> +ENCODE4 cCREs</a>:</b> This track presents the ENCODE Registry of 2,348,854 cCREs identified +and classified using data from all phases of the ENCODE Project (Phases 1–4). The registry +integrates chromatin accessibility and ChIP-seq signals across thousands of biosamples. All cCREs +are consolidated into a single, cell type-agnostic annotation track displayed here.</li> +<li><b><a href="/cgi-bin/hgTrackUi?c=chr7&g=coreCcres&position=default&db=hg38" target="_blank"> +ENCODE4 Core Collection</a>:</b> This track displays biosample-specific cCREs alongside +genome-wide epigenomic signals for the ENCODE4 Core Collection, consisting of 170 biosamples +comprehensively profiled using four core assays: DNase-seq, ChIP-seq for H3K4me3 and H3K27ac +(histone modifications), and ChIP-seq for CTCF. These data support detailed analysis of +regulatory activity in individual biosamples.</li> +</ul> +<p> +The cCREs are colored by their putative functional assignment based on biochemical +signatures and genomic context:</p> +<div class="text-left"> +<p> +<img src="/images/encode4cCREs.png" width='35%'> +</div> +<p> +This results in the following classifications:</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;">Classification criteria</th> + </tr> +<tr><td style='background-color: #FF0000;'> </td><td>red</td> + <td>promoter</td> + <td>promoter-like signature</td> + <td>within 200 bp of TSS, high chromatin accessibility and H3K4me3</td></tr> +<tr><td style='background-color: #FFA700;'> </td><td>orange</td> + <td>proximal enhancer</td> + <td>TSS-proximal enhancer-like signature</td> + <td>high chromatin accessibility and H3K27ac, within 2 kb of TSS; if within 200 bp of TSS, must have low H3K4me3</td></tr> +<tr><td style='background-color: #FFCD00;'> </td><td>yellow</td> + <td>distal enhancer</td> + <td>TSS-distal enhancer-like signature</td> + <td>high chromatin accessibility and H3K27ac, >2 kb from TSS</td></tr> +<tr><td style='background-color: #FFAAAA;'> </td><td>pink</td> + <td>CA-H3K4me3</td> + <td>chromatin accessibility + H3K4me3</td> + <td>high chromatin accessibility and H3K4me3, low H3K27ac, not within 200 bp of TSS</td></tr> +<tr><td style='background-color: #00B0F0;'> </td><td>blue</td> + <td>CA-CTCF</td> + <td>chromatin accessibility + CTCF</td> + <td>high chromatin accessibility and CTCF, low H3K4me3 and H3K27ac</td></tr> +<tr><td style='background-color: #800080;'> </td><td>dark purple</td> + <td>CA-TF</td> + <td>chromatin accessibility + transcription factor</td> + <td>high chromatin accessibility, low H3K4me3, H3K27ac, and CTCF, bound by transcription factor</td></tr> +<tr><td style='background-color: #06B050;'> </td><td>green</td> + <td>CA</td> + <td>chromatin accessibility</td> + <td>high chromatin accessibility, low H3K4me3, H3K27ac, and CTCF</td></tr> +<tr><td style='background-color: #CC99FF;'> </td><td>light purple</td> + <td>TF</td> + <td>transcription factor</td> + <td>low chromatin accessibility, low H3K4me3, H3K27ac, and CTCF, bound by transcription factor</td></tr> +</table> + +<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 Mingshi Gao, Zhiping Weng, and Jill Moore 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.</p> +<p> +For more details on this track and data, see the <a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=cCREs&position=default" +target="_blank">track description page</a>, as well as +Moore <em>et al</em>. <a href="https://www.nature.com/articles/s41586-025-09909-9" target="_blank"> +An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation</a> +. <em>Nature</em>. 2026 January 7. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39763870" +target="_blank">39763870</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11703161/" +target="_blank">PMC11703161</a>. +</p> + <!-- ============= 2025 archived news ============= --> <a name="2025"></a> <a name="121925"></a> <h2>Dec. 19, 2025 EVA SNP release 8 for 41 assemblies</h2> <p> We are pleased to announce the release of the EVA SNP Release 8 tracks for 41 assemblies. These tracks contain mappings of single nucleotide variants and small insertions and deletions (indels) — collectively Simple Nucleotide Variants (SNVs) — from the European Variation Archive (<a href="https://www.ebi.ac.uk/eva/" target="_blank">EVA</a>) Release 8. The full list of assemblies that contain the EVA SNP release 8 track is below:</p> <p> <div class="container"> <div class="row">