8f54eba62d6f5805969fe36a58e1a4c970903a64 chmalee Thu Jun 30 13:41:06 2016 -0700 Announcing UCSC Genes release, refs #15315 and #10968 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 5601873..3e4cf82 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -26,63 +26,87 @@ <TR><TD WIDTH=10></TD> <TD> <P> To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the <A HREF="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en" TARGET=_blank>genome-announce</A> mailing list. Please see our <a href="http://genome.ucsc.edu/blog" target=_blank>blog</a> for posts about Genome Browser tools, features, projects and more. </p> <hr> <!-- start news --> - <! -- staging gencode genes (hg38) and ucsc genes (mm10) announcment <font color="#006666" size="4"><b>30 June 2016 - Updated Gene Tracks Available for the Human (hg38) and Mouse (mm10) Assemblies</b></font> <p> We are pleased to announce the release of an updated GENCODE Genes track for the Human (GRCh38/hg38) assembly. The GENCODE v24 gene set has 197,782 total transcripts, compared with 195,178 in the previous version. The total number of canonical genes has increased from 49,534 to 49,948. Comparing the new gene set with the previous version: </p> <p> <ul> <li>193,647 transcripts did not change.</li> <li>128 transcripts were not carried forward to the new version.</li> <li>997 transcripts are "compatible" with those in the previous set, meaning that the two transcripts show consistent splicing. In most cases, the old and new transcripts differ in the lengths of their UTRs.</li> <li>406 transcripts overlap with those in the previous set, but do not show consistent splicing (i.e., they contain overlapping introns with - differing splice sites)</li> + differing splice sites).</li> </ul> <p> More details about the GENCODE Genes track can be found on the <a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene"> GENCODE v24 track description page</a>. </p> + <p> + Many thanks to Brian Raney and Luvina Guruvadoo for their work on this track! + </p> + --- + <p> + We are pleased to announce the release of an updated UCSC Genes track for the + Mouse (GRCm38/mm10) assembly. + The new release has 63,759 total transcripts, compared with 63,244 + in the previous version. The total number of canonical genes has increased from 32,958 + to 33,079. Comparing the new gene set with the previous version: + <ul> + <li>60,827 transcripts did not change between versions.</li> + <li>148 transcripts were not carried forward to the new version.</li> + <li>1,929 transcripts are "compatible" with those in the previous set, meaning + that the two transcripts show consistent splicing. In most cases, the old and new + transcripts differ in the lengths of their UTRs.</li> + <li>340 transcripts overlap with those in the previous set, but do not show consistent + splicing (i.e., they contain overlapping introns with differing splice sites).</li> + </ul> + </p> + <p> + More details about the new UCSC Genes track can be found on the + <a href="../cgi-bin/hgTrackUi?db=mm10&g=knownGene">UCSC Genes track + description page</a>. + </p> + <p> + Many thanks to Jonathan Casper and Christopher Lee for their work on this track! + </p> <hr> - --> - - <font color="#006666" size="4"><b>27 June 2016 - New Way to Share Sessions - Public Sessions!</b></font> <p> We are excited to announce the release of the <a href="cgi-bin/hgPublicSessions">Public Sessions</a> page, the newest way to share your UCSC Genome Browser snapshots with your colleagues and the world. The Public Sessions page collects sessions that users have elected to share publicly. Sessions on this page can be filtered based on assembly, name, or a phrase from the description. Sessions can also be sorted based on their popularity or creation date. To add your own sessions to this Public Sessions page, just check the box under "post in public listing" on the session management page. </p> <p> @@ -143,30 +167,38 @@ that our three supported sites are offline. </p> <p> We wish to express our special thanks to Dr. Hideya Kawaji at the <a href="http://www.riken.jp/en/research/labs/accc/" target="_blank">RIKEN Advanced Center for Computing and Communication</a> for making this possible. We would also like to acknowledge the following members of the UCSC Genome Browser team for their efforts: Galt Barber, Robert Kuhn, Jorge Garcia, and Luvina Guruvadoo. </p> <hr> <!-- start archives --> <!--staged for future release <p> + <font color="#006666" size="4"><b>30 June 2016 - Updated Gene Tracks Available for + the Human (hg38) and Mouse (mm10) Assemblies </b> </font> + We are pleased to announce the release of updated GENCODE Genes and UCSC Genes tracks + for the Human (GRCh38/hg38) and Mouse (GRCm38/mm10) assemblies. + <a href="goldenPath/newsarch.html#063016">Read more</a>. + </p> + + <p> <font color="#006666" size="4"><b>27 June 2016 - New Way to Share Sessions - Public Sessions!</b> </font> We are excited to announce the release of the <a href="cgi-bin/hgPublicSessions">Public Sessions</a> page, the newest way to share your UCSC Genome Browser snapshots with your colleagues and the world. <a href="goldenPath/newsarch.html#062816">Read more</a>. </p> <p> <font color="#006666" size="4"><b>15 June 2016 - New Official Asian Mirror Released</b>: </font> We are pleased to announce the introduction of a new supported Genome Browser mirror to serve our users in Asia. <a href="goldenPath/newsarch.html#061516">Read more</a>. </p> -->