f75be6cdc179d7ce11539664b23406306976052d
gperez2
  Tue May 21 12:27:38 2024 -0700
Staging and releasing the new GENCODE Known Gene tracks V46 and VM35, refs #33080 #33083

diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html
index b825546..87093f0 100755
--- src/hg/htdocs/goldenPath/newsarch.html
+++ src/hg/htdocs/goldenPath/newsarch.html
@@ -51,30 +51,80 @@
 </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 
 <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 <a
 href="https://github.com/ucscGenomeBrowser/kent/commits/master"
 target=_blank>our GitHub page</a>.</p>
 
 <!-- ============= 2024 archived news ============= -->
 <a name="2024"></a>
 
+<a name="052224"></a>
+<h2>May. 22, 2024 &nbsp;&nbsp; New GENCODE &quot;KnownGene&quot; V46 for human (hg38) and VM35 for mouse (mm39)</h2>
+<p>
+We are pleased to announce the release of the
+<a href="/cgi-bin/hgTrackUi?db=hg38&g=knownGene&c=chrX">GENCODE V46 (hg38)</a>
+and the
+<a href="/cgi-bin/hgTrackUi?db=mm39&g=knownGene&c=chrX">GENCODE VM35 (mm39)</a> gene tracks.
+The GENCODE &quot;KnownGene&quot; V46 and VM35 gene tracks were built using a UCSC
+pipeline (KnownGene) and the GENCODE comprehensive gene set to generate high-quality manual
+annotations merged with evidence-based automated annotations. The GENCODE &quot;KnownGene&quot;
+tracks are our default gene tracks, which have extensive associations to external sources. This
+allows for additional metadata on every item as well as external links. The track description pages
+contain options for configuring the display, such as showing non-coding genes, splice variants, and
+pseudogenes. The track description pages for these tracks contain options for configuring the
+display such as also showing non-coding genes, splice variants, and pseudogenes.</p>
+
+<p>
+Below is a summary of the contents found in each release. For more details visit the <a target="_blank"
+href="https://www.gencodegenes.org/">GENCODE site</a>.</p>
+<p>
+<table class="stdTbl">
+<tr><th COLSPAN=4>GENCODE v46 Release Stats</th></tr>
+<tr align=left><th>Genes</th><th>Observed</th><th>Transcripts</th><th>Observed</th></tr>
+<tr align=left><td>Protein-coding genes</td><td>19,411</td><td>Protein-coding transcripts</td><td>89,581</td></tr>
+<tr align=left><td>Long non-coding RNA genes</td><td>20,310</td><td><font size="-1">- full length protein-coding</font></td><td>64,695</td></tr>
+<tr align=left><td>Small non-coding RNA genes</td><td>7,565</td><td><font size="-1">- partial length protein-coding</font></td><td>24,886</td></tr>
+<tr align=left><td>Pseudogenes</td><td>14,716</td><td>Nonsense mediated decay transcripts</td><td>21,774</td></tr>
+<tr align=left><td>Immunoglobulin/T-cell receptor gene segments</td><td>648</td><td>Long non-coding RNA loci transcripts</td><td>59,927</td></tr>
+<tr align=left><td>Total No of distinct translations</td><td>65,650</td><td>Genes that have more than one distinct translations</td><td>13,620</td></tr>
+</table><BR>
+</p>
+<p>
+<table class="stdTbl">
+<tr><th COLSPAN=4>GENCODE VM35 Release Stats</th></tr>
+<tr align=left><th>Genes</th><th>Observed</th><th>Transcripts</th><th>Observed</th></tr>
+<tr align=left><td>Protein-coding genes</td><td>21,423</td><td>Protein-coding transcripts</td><td>58,457</td></tr>
+<tr align=left><td>Long non-coding RNA genes</td><td>15,126</td><td><font size="-1">- full length protein-coding</font></td><td>44,851</td></tr>
+<tr align=left><td>Small non-coding RNA genes</td><td>6,105</td><td><font size="-1">- partial length protein-coding</font></td><td>13,606</td></tr>
+<tr align=left><td>Pseudogenes</td><td>13,756</td><td>Nonsense mediated decay transcripts</td><td>7,243</td></tr>
+<tr align=left><td>Immunoglobulin/T-cell receptor gene segments</td><td>701</td><td>Long non-coding RNA loci transcripts</td><td>27,096</td></tr>
+<tr align=left><td>Total No of distinct translations</td><td>44,819</td><td>Genes that have more than one distinct translations</td><td>10,833</td></tr>
+</table><BR>
+</p>
+<p>
+We would like to thank the <a target="_blank"
+href="https://www.gencodegenes.org/pages/gencode.html">GENCODE project</a> for providing these
+annotations. We would also like to thank Jonathan Casper and Gerardo Perez for the development and
+release of these tracks.</p>
+
+
 <a name="042524"></a>
 <h2>Apr. 25, 2024 &nbsp;&nbsp; New AbSplice Prediction Scores track for hg19</h2>
 <p>
 We are excited to announce the release of the
 <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=abSplice" target="_blank">AbSplice scores track</a>
 that was previously only on
 <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=abSplice" target="_blank">GRCh38/hg38</a>
 and is now also available on the human GRCh37/hg19 genome assembly. AbSplice is a method that
 predicts aberrant splicing across human tissues, as described in <a href="https://doi.org/10.1038/s41588-023-01373-3"
 target="_blank">Wagner, &Ccedil;elik et al., 2023</a>. This track consists of an aberrant splicing
 benchmark dataset that spans over 8.8 million rare variants in 49 human tissues from the
 <a target="_blank" href="https://www.gtexportal.org/home/samplingSitePage">Genotype-Tissue
 Expression (GTEx) dataset</a> and displays precomputed AbSplice scores for all possible
 single-nucleotide variants genome-wide. The AbSplice score is a probability estimate of how likely
 aberrant splicing of some sort takes place in a given tissue. Aberrant splicing predictions for