c0e990a37bac39f6d5c8d22512d6232d299050fd gperez2 Wed Mar 5 10:39:28 2025 -0800 Announcing the release of the Splicing Impact super track and the SpliceVarDB track, refs #34823 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 1c087a8bd3d..f097443be12 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,68 @@ </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="2025"></a> + +<a name="030525"></a> +<h2>Mar. 05, 2025 New Splicing Impact Prediction Scores super track (hg19/hg38) and SpliceVarDB track for hg38</h2> +<p> +We are excited to announce the new Splicing Impact Prediction Scores and Databases super track for +the +<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=spliceImpactSuper&position=default">hg38/GRCh38</a> +and <a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg19&g=spliceImpactSuper&position=default">hg19/GRCh37</a> human assemblies. +This super track includes the +<a target="_blank" href="newsarch.html#042524">AbSplice Scores</a>, +<a target="_blank" href="newsarch.html#081224">SpliceAI</a>, and, for hg38, the new +<a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&g=spliceImpactSuper&position=default">SpliceVarDB track</a>. +<a target="_blank" href="https://splicevardb.org/">SpliceVarDB</a> +is an online database consolidating over 50,000 variants assayed for their effects on +splicing in over 8,000 human genes. The SpliceVarDB authors evaluated over 500 published data +sources and established a spliceogenicity scale to standardize, harmonize, and consolidate variant +validation data generated by a range of experimental protocols. SpliceVarDB data is displayed as +lollipop plots, color-coded by score value. A score of <b>3</b> indicates a +<span style="color: rgb(219,61,61);">Splice-altering</span></li> variant, +<b>2</b> represents a <span style="color: rgb(128,82,160);">Low-frequency</span> variant, +<b>1</b> is classified as <span style="color: rgb(57,135,204);">Normal</span>, and +<b>0</b> denotes <span style="color: rgb(140,140,140);">Conflicting</span> data. +</p> + +<div class="text-center"> + <a href="https://genome.ucsc.edu/s/gperez2/SpliceVarDB" target="_blank"> + <img src="../images/newsArchImages/SpliceVarDB.jpg" alt="hg38 session + visualizing the SpliceVarDB track" width='70%'></a> +</div> + +<p> +We would like to thank the SpliceVarDB team for providing the data to UCSC. We would also like to +thank Jeltje van Baren, Max Haeussler, Luis Nassar, Jairo Navarro, and Gerardo Perez for their +efforts on this release. +</p> + <a name="030325"></a> <h2>Mar. 03, 2025 New highlight features for track hubs now available</h2> <p> We are happy to announce the release of new highlight features for track hubs. These settings follow exactly the same syntax and functionality as the <code>filter</code> trackDb settings, except instead of items being excluded from the display, items are striped with a colored background to appear "highlighted" compared to the other items in the display. The full list of highlight trackDb settings is available on the <a href="/goldenPath/help/trackDb/trackDbHub.html#highlight">trackDb definitions</a> page. </p> <p> Please note that at this time, only one higlight color is available per track, and if multiple highlight settings are present on the same track, only items that pass ALL highlight settings will be highlighted.</p> <p>