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 New GENCODE "KnownGene" 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 "KnownGene" 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 "KnownGene" +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 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, Çelik 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