0dcc1250b62a45b62e7121597073e023ceafe81f jnavarr5 Wed Aug 20 15:31:22 2025 -0700 Announcing the MaveDB track for hg38, refs #31812 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 7dcaafc1fb3..00a74c81408 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,65 @@ <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="082125"></a> +<h2>Aug. 21, 2025 MaveDB Experiment Heatmaps and Alignment track for hg38</h2> +<p> +We are excited to announce the release of the <a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=mavedb_maps">MaveDB Experiment Heatmaps and +Alignment</a> track for hg38. This release provides heatmaps of <b>m</b>ultiplexed <b>a</b>ssays of +<b>v</b>ariant <b>e</b>ffects (MAVE) from <a target="_blank" href="https://mavedb.org/">MaveDB</a>. +Each heatmap presents the results of an experiment where many small substitutions were tested within +a gene to examine their functional consequences. Accompanying tracks display alignments of each +experiment sequence to the genome. +</p> +<p> +Please note that only a subset of MaveDB experiments could be displayed as heatmaps; the sequence +alignments in this track only cover those experiments.</p> + +<div class="text-center"> + <a href="https://genome.ucsc.edu/s/view/MaveDB_BRCA1"> + <img src="../images/newsArchImages/MaveDB_BRCA1_exon_19.png" + alt="MaveDB heatmap and alignment tracks for the BRCA1 exon 19" width='75%'> + <p class="gbsCaption"> + <em>Genome Browser screenshot of BRCA1 exon 19 showing the alignment and heatmap tracks.</em> + </p></a> +</div> +<p> +Hover-over each item in the heatmap to see the consequence of substituting invididual amino acids +within the genome with alternatives. Score ranges vary among experiments, but each is presented +with the highest scores in <span style="color: #FF0000; font-weight: bold;">red</span>, the lowest +scores in <span style="color: #0000FF; font-weight: bold;">blue</span>, and scores at the midpoint +between the two in <span style="color: #C0C0C0; font-weight: bold;">silver</span>. Higher scores +correspond to a higher enrichment level for that variant compared to others in the experiment set. +</p> +<p> +We would like to thank MaveDB for making this data publicly available. We would also like to thank +Jonathan Casper and Jairo Navarro for the creation and release of the Genome Browser tracks.</p> + <a name="081125"></a> <h2>Aug. 11, 2025 CLS Long-read RNA transcripts track for hg38 and mm10</h2> <p> New Capture long-seq (CLS) long-read lncRNAs tracks are available for <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=clsLongReadRnaTrack" target="_blank">hg38</a> and <a href="/cgi-bin/hgTrackUi?db=mm10&position=default&g=clsLongReadRnaTrack" target="_blank">mm10</a>. These tracks represent the results of targeted long-read RNA sequencing aimed at identifying lowly expressed lncRNAs. The data is comprised of the capture target regions, the reads, and transcript models organized in the following way:</p> <ul> <li><b>Targets:</b> Targeted RNA capture regions</li> <li><b>Models:</b> Transcript models generated from reads and merging</li> <li><b>Sample models:</b> Transcript models by sample in which they were observed</li> <li><b>Per-experiment reads:</b> Read mappings per experiment</li> <li><b>Per-experiment Models:</b> Transcript models generated from the experiments</li> </ul>