1c249a4b1bdb700c68999bff5724a1cdfa75ac02 gperez2 Wed Sep 6 17:25:50 2023 -0700 Staging and releasing the new GENCODE Known Gene tracks V44 and VM33, refs #30840 #30841 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 70594a7..dcc29d9 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,76 @@ </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> <!-- ============= 2023 archived news ============= --> <a name="2023"></a> +<a name="090723"></a> +<h2>Sep. 07, 2023 GENCODE Genes V44 for human (hg38) and VM33 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 V44 (hg38)</a> +and the +<a href="/cgi-bin/hgTrackUi?db=mm39&g=knownGene&c=chrX">GENCODE VM33 (mm39)</a> tracks. +The track description pages for these tracks contain options +for configuring the display such as also showing non-coding genes, splice variants, and pseudogenes. +Different tags and labels may also be toggled.</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 v44 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>19,396</td><td>Protein-coding transcripts</td><td>89,067</td></tr> +<tr align=left><td>Long non-coding RNA genes</td><td>19,922</td><td><font size="-1">- full length protein-coding</font></td><td>63,968</td></tr> +<tr align=left><td>Small non-coding RNA genes</td><td>7,566</td><td><font size="-1">- partial length protein-coding</font></td><td>25,099</td></tr> +<tr align=left><td>Pseudogenes</td><td>14,735</td><td>Nonsense mediated decay transcripts</td><td>21,384</td></tr> +<tr align=left><td>Immunoglobulin/T-cell receptor gene segments</td><td>647</td><td>Long non-coding RNA loci transcripts</td><td>58,246</td></tr> +<tr align=left><td>Total No of distinct translations</td><td>65,342</td><td>Genes that have more than one distinct translations</td><td>13,594</td></tr> +</table><BR> +</p> +<p> +<table class="stdTbl"> +<tr><th COLSPAN=4>GENCODE VM33 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>21,403</td><td>Protein-coding transcripts</td><td>58,750</td></tr> +<tr align=left><td>Long non-coding RNA genes</td><td>14,842</td><td><font size="-1">- full length protein-coding</font></td><td>45,112</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>13,638</td></tr> +<tr align=left><td>Pseudogenes</td><td>13,809</td><td>Nonsense mediated decay transcripts</td><td>7,218</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>26,564</td></tr> +<tr align=left><td>Total No of distinct translations</td><td>44,993</td><td>Genes that have more than one distinct translations</td><td>10,893</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="081823"></a> <h2>Aug. 18, 2023 New GENCODE gene tracks: Human V44 (hg19/hg38) - Mouse VM33 (mm39)</h2> <p> We are pleased to announce new GENCODE Gene annotation tracks, which correspond to <a href="https://www.ensembl.info/2023/07/17/ensembl-110-has-been-released/" target="_blank">Ensembl 110</a>, for three assemblies: <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=wgEncodeGencodeV44lift37">hg19/GRCh37</a>, <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=wgEncodeGencodeV44">hg38/GRCh38</a>, and <a target="_blank" href="/cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM33">mm39/GRCm39</a>. For human, the GENCODE V44 annotations were mapped to hg38/GRCh38 and then back-mapped to the hg19/GRCh37 assembly. For all three assemblies, the gene sets contain the following tracks:</p> <ul>