717a49525e045cc82ee02b8cd9f906f97e8f348e gperez2 Wed Oct 23 14:05:35 2024 -0700 Staging and releasing the new GENCODE Known Gene tracks V47 and VM36, refs #34219 #34218 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index acc1f37..70bee39 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -54,30 +54,78 @@ <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> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> + +<a name="102324"></a> +<h2>Oct. 23, 2024 New GENCODE "KnownGene" V47 for human (hg38) and VM36 for mouse (mm39)</h2> +<p> +We are pleased to announce the release of the +<a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=knownGene">GENCODE V47 (hg38)</a> +and the +<a href="/cgi-bin/hgTrackUi?db=mm39&position=default&g=knownGene">GENCODE VM36 (mm39)</a> gene tracks. +The GENCODE "KnownGene" V47 and VM36 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.</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 v47 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>19,433</td><td>Protein-coding transcripts</td><td>89,832</td></tr> +<tr align=left><td>Long non-coding RNA genes</td><td>35,934</td><td><font size="-1">- full length protein-coding</font></td><td>64,988</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>24,844</td></tr> +<tr align=left><td>Pseudogenes</td><td>14,703</td><td>Nonsense mediated decay transcripts</td><td>21,873</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>191,106</td></tr> +<tr align=left><td>Total No of distinct translations</td><td>65,809</td><td>Genes that have more than one distinct translations</td><td>13,646</td></tr> +</table><BR> +</p> +<p> +<table class="stdTbl"> +<tr><th COLSPAN=4>GENCODE VM36 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>21,470</td><td>Protein-coding transcripts</td><td>58,547</td></tr> +<tr align=left><td>Long non-coding RNA genes</td><td>36,172</td><td><font size="-1">- full length protein-coding</font></td><td>44,949</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>13,598</td></tr> +<tr align=left><td>Pseudogenes</td><td>13,769</td><td>Nonsense mediated decay transcripts</td><td>7,247</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>156,135</td></tr> +<tr align=left><td>Total No of distinct translations</td><td>44,888</td><td>Genes that have more than one distinct translations</td><td>10,840</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="100924"></a> <h2>Oct. 9, 2024 CADD v1.7 and ClinGen CSpec tracks for hg19 and hg38</h2> <p> We are excited to announce two new tracks available for human assemblies hg38/GRCh38 and hg19/GRCh37.</p> <h3>Clingen CSpec Variant Interpretation VCEP Specifications</h3> <p> The <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=clinGenComp">ClinGen VCEP Specifications track</a> identifies loci that have <a target="_blank" href="https://cspec.genome.network/cspec/ui/svi/">ClinGen criteria Specification (CSpec)</a> information. This is used and applied by ClinGen Variant Curation Expert Panels (VCEPs) and biocurators in the classification of variants.</p> <p>