7ec5f6b170c7eee12739e419d7890daa4a331fcb jnavarr5 Wed Nov 27 16:37:42 2019 -0800 Announcing the EPD track for human and mouse, refs #23881 and #23888 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 9a99d09..35bf828 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -38,30 +38,69 @@ </ul> </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="112719a"></a> +<h2>Nov. 27, 2019 New EPD TSS track for human and mouse</h2> +<p> +We are pleased to announce the release of the new EPDnew Promoters track for human +(<a href="../../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=epdNew" target="_blank">hg38</a> and +<a href="../../cgi-bin/hgTrackUi?db=hg19&c=chrX&g=epdNew" target="_blank">hg19</a>) +and mouse (<a href="../../cgi-bin/hgTrackUi?db=mm10&c=chrX&g=epdNew" target="_blank">mm10</a>) +assemblies. These tracks represent the experimentally validated promoters generated by the +<a href="https://epd.epfl.ch/" target="_blank">Eukaryotic Promoter Database</a>, based on gene +transcript models obtained from multiple sources (HGNC, GENCODE, Ensembl, RefSeq), then validated +using data from CAGE and RAMPAGE experimental studies obtained from FANTOM 5, UCSC, and ENCODE. Peak +calling, clustering and filtering based on relative expression were applied to identify the most +expressed promoters and those present in the largest number of samples.</p> +<p> +We would like to thanks Philipp Bucher and the EPD team at the Swiss Bioinformatics Institute for +providing this data, and Kate Rosenbloom and Jairo Navarro at UCSC for creating and reviewing these +tracks.</p> + +<a name="112719b"></a> +<h2>Nov. 27, 2019 New ENCODE Enhancer-Gene Interactions for mouse</h2> +<p> +We are pleased to announce a new +<a href="../../cgi-bin/hgTrackUi?db=mm10&c=chrX&g=encode3RenEnhancerEpdNewPromoter" +target="_blank">Enhancer-Gene Map</a> for the mouse mm10 assembly. This track set presents +enhancer-promoter interactions predicted from correlation of enhancer-associated chromatin signals +and gene expression across tissue stages, based on histone modification (ChIP-seq) and transcription +(RNA-seq) assays and analysis performed in the ENCODE project as part of the Mouse Developmental +Series (part of ENCODE phase 3). Data underlying this track are presented in the Histone +Modifications and Chromatin State tracks, part of the ENCODE Regulation supertrack. The promoters +in this track were derived from experimentally validated promoters provided by the Eukaryotic +Promoter Database (EPDNew). A more complete presentation of this annotation can be found in the +EPDnew Promoters track.</p> +<p> +We would like to thank Iros Barozzi and colleagues in the Environmental Genomics and Systems Biology +Division at the Lawrence Berkeley Laboratory, and David Gorkin and Yanxiao Zhang at the Ren lab +(UCSD/Ludwig Institute for Cancer Research) and the ENCODE Consortium for providing these data +and assisting with track development at UCSC. We also thank Kate Rosenbloom and Jairo Navarro at +UCSC for creating and reviewing these tracks.</p> + <a name="112519"></a> <h2> Nov. 25, 2019 LOVD track split to separate long and short variants for human</h2> <p> We are glad to announce an update to the <a href="../../cgi-bin/hgTrackUi?db=hg19&c=chrX&g=lovdComp" target="_blank">LOVD track</a> for human (GRCh37/hg19). The LOVD track is now a composite track with the following two subtracks:</p> <ul> <li>LOVD Variants <= 100bp</li> <li>LOVD Variants > 100bp</li> </ul> <p> With this new update, the option is now available to only show the short variants and exclude the long variants, or vice versa.</p> <p>