b7617abed29abc5f50b1a22b1d282e043ae77a52 gperez2 Mon Mar 31 15:35:38 2025 -0700 Announcing the release of the hg38 Pseudogenes track, refs #30563 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 6eeea20ca96..562b3320d42 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,71 @@ <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="033125"></a> +<h2>Mar. 31, 2025 New Pseudogenes track for hg38</h2> +<p> +We are happy to announce the release of the +<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=pseudogenes&position=default">Pseudogenes</a> +track for the hg38 (GRCh38) genome assembly. The composite track contains pseudogene predictions and +their corresponding parent genes, as identified by <a href="http://pseudogene.org/pseudopipe/" +target="_blank">PseudoPipe</a>, a homology-based computational pipeline that searches a mammalian +genome and identifies pseudogene sequences.</p> +<p> +This composite track consists of two subtracks: the <b>Pseudogene Parents</b> track and the +<b>Pseudogenes</b> track.</p> +<ul> + <li><b>Pseudogene Parents</b> – This track displays parent genes labeled with their HUGO + IDs, which were derived from Ensembl gene IDs provided by the Gerstein lab after dataset + creation. It includes indicators for pseudogenes, each linked to its corresponding entry + in the Pseudogenes track. <b><font color="#800080">Parent genes</font></b> are shown with + their associated pseudogenes represented as <b><font color="#A9A9A9">grey</font></b> + blocks. + <li><b>Pseudogenes</b> – This track displays pseudogenes labeled with their parent HUGO ID + and the pseudogenes are color-coded by pseudogene type: + <b><font color="#FF8C00">unspecified pseudogene</font></b>, <b><font + color="#0000FF">processed pseudogene</font></b>, and + <b><font color="#556B2F">unprocessed pseudogene</font></b>. +</ul> +<div class="text-center"> + <a href="https://genome.ucsc.edu/s/gperez2/Pseudogenes" target="_blank"> + <img src="../images/newsArchImages/Pseudogenes.jpg" alt="hg38 session + visualizing the Pseudogenes.jpg track" width='80%'></a> +</div> +<p> +More information on this composite track can be found on the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=pseudogenes&position=default#TRACK_HTML" target="_blank">track description</a> +page. +</p> +<p> +We would like to thank the Gerstein lab at Yale University for making this data available, and +Cristina Sisu for providing data in GTF format with parent annotations. We would also like to +thank Jeltje van Baren, Mark Diekhans, and Gerardo Perez for their efforts on this release. +</p> + <a name="031425"></a> <h2>Mar. 14, 2025 denovo-db tracks for hg19 now available</h2> <p> We are excited to announce the release of two <a href="/cgi-bin/hgTrackUi?db=hg19&c=chr7&g=denovoDbComposite" target="_blank">denovo-db V.1.6.1</a> tracks for the hg19/GRCh37 genome assembly. The <a href="https://denovo-db.gs.washington.edu/denovo-db/index.jsp" target="_blank">denovo-db (version 1.6.1)</a> is a curated database of germline de novo variants in the human genome, defined as variants present in children but absent in their parents. With advancements in whole-exome and whole-genome sequencing, denovo-db consolidates data from extensive genetic studies, including those on neurodevelopmental disorders, but is not restricted to specific phenotypes. This database provides essential resources for researchers investigating variant characteristics, mutability, and associated phenotypes.</p> <p> The denovo-db V.1.6.1 composite track contains <a href="https://www.sfari.org/resource/simons-simplex-collection/"