0497d2117545f7ce8b6caaf452c9b1e10dbc2ed4 lrnassar Fri May 16 10:45:34 2025 -0700 News release for the pext track and the exon relevance RTS, refs #35116 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 6c764658dfc..dfcb6902639 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,79 @@ <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="2025"></a> +<a name="051425"></a> +<h2>May 14, 2025 Exon Relevance RTS and gnomAD pext track for hg38</h2> +<p> +We are pleased to share our latest <a href="#022222">Recommended Track Set (RTS)</a>, +<b>Exon Relevance</b>, and a new track, +<a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadPext" target="_blank">gnomAD Proportion +Expression Across Transcript Scores (pext)</a> for GRCh38/hg38.</p> + +<h3>Exon Relevance RTS</h3> +<p> +The Exon Relevance track set can be found in the blue bar menu (<b>Genome Browser</b> +> <b>Recommended Track Sets</b>) on both the hg19 and hg38 browsers. This track set +can assist in variant interpretation by evaluating if the variant is present in an exon +required for function of the expressed gene product.</p> + +<div class="text-center"> + <img src="../images/exonRelevanceNewsImage.png" alt="New Exon Relevance track set" width='40%'> +</div> + +<h3>gnomAD Proportion Expression Across Transcript Scores (pext) for GRCh38/hg38</h3> + +<p> +The hg38 gnomAD super track now includes +the gnomAD pext datasets. This track displays isoform +expression levels across 50 tissues from +the Genotype Tissue Expression (GTEx) v10 dataset, showing a comprehensive +view of the expression of exons across +a gene using the proportion expression across transcripts, or pext metric, a +transcript-level annotation metric which quantifies isoform expression for variants. +</p> +<p> +This is especially useful for those interested in alternative splicing and +clinical assessment of variants. For more +information, see the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadPext" target="_blank">track description page</a> and +the <a href="https://www.nature.com/articles/s41586-020-2329-2" target="_blank">associated +publication</a>.</p> + +<div class="text-center"> + <a href="https://genome.ucsc.edu/s/Lou/hg38pextNews" target="_blank"><img src="../images/hg38pextTrackNewsImage.png" +alt="Image of TRDN gene showing variants primarily expressed in heart tissue." width='80%'></a> +</div> + +<p> +We would like to thank the gnomAD team and the UCSC Genome Browser team members +Jeltje van Baren, Max Haeussler, Lou Nassar, and Anna Benet-Pages for developing and +releasing this track, as well as making the Exon Relevance RTS. +</p> + <a name="050525"></a> <h2>May 5, 2025 VISTA Enhancers track update for Human and Mouse</h2> <p> We are happy to announce an update to the VISTA Enhancers tracks for human (<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=vistaEnhancersBb">GRCh38/hg38</a> and <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=vistaEnhancersBb">GRCh37/hg19</a>) and mouse (<a target="_blank" href="/cgi-bin/hgTrackUi?db=mm39&position=default&g=vistaEnhancersBb">GRCm39/mm39</a> and <a target="_blank" href="/cgi-bin/hgTrackUi?db=mm10&position=default&g=vistaEnhancersBb">GRCm38/mm10</a>) genome assemblies. The track shows potential enhancers whose activity was experimentally validated in transgenic mice. With this update, the tracks now include over 1,900 new entries for the human assemblies and over 2,500 new entries for the mouse assemblies. Hovering over an enhancer annotation