81e2b4c294447d686f055b2d794be7f0da11bbc9
kate
  Mon Apr 18 16:28:25 2016 -0700
More wordcrafting on GTEx announcement.  Ready for Donna...

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                  <font size="4"><a name="TOC"></a><b>&nbsp; News</b></font><a href="http://www.twitter.com/GenomeBrowser" target="_blank"><img src="http://twitter-badges.s3.amazonaws.com/t_small-a.png" title="Follow &#64;GenomeBrowser on Twitter" alt="Follow &#64;GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a>
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           <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>
 
     <!-- start news -->
 <!-- Staged for later release
   <hr>
   <font color="#006666" size="4"><b>20 Apr 2016
   - Data from the Lens PatSeq Database Now Available</b></font>
   <p>
   We are pleased to announce the release of a set of tracks containing data from the
   <a href="https://www.lens.org/" target="_blank">Lens</a>
   PatSeq database in the UCSC Genome Browser. These tracks contain data from the
   <a href="https://www.lens.org/lens/bio" target="_blank">PatSeq</a>
   database mapped to the genome and then colored based on where the sequence appears in
   the patent document. Details pages contain the patent titles with links to the patents in the
   Lens database. The data from PatSeq is divided into two tracks, one includes those sequences
   that were submitted in bulk patents containing 100 or more sequences and the other containing
   all other sequences. These tracks are currently present on the human (hg19), mouse (mm10),
   and Ebola virus (eboVir3) genomes.
   </p>
 
   <p>
   Thanks to our collaborators at the Lens, Osmat Jefferson and Deniz Koellhofer, for providing the
   data and feedback on the visualization. Thank you to Max Haeussler and Matthew Speir, members of
   the UCSC Genome Browser team, for their efforts in creating these tracks.
   </p>
 -->
   <!-- Staging for Tuesday Announcement of GTEX track
   <hr>
   <font color="#006666" size="4"><b>19 April 2016
-  - New GTEx Gene Tissue Expression Track for hg19 and hg38</b></font>
+  - New GTEx Gene Expression Track for hg19 and hg38</b></font>
   <p>
   We are excited to announce the release of a new gene expression track based on data from the NIH
   <a href="http://commonfund.nih.gov/GTEx/index" TARGET = _BLANK> Genotype-Tissue Expression (GTEx)</a> project.  
-  This track displays tissue-specific expression based on RNA-Seq data of 53 tissues from 570 donors, obtained from
+  This track displays tissue-specific gene expression based on RNA-Seq in 53 tissues from 570 donors, obtained from
   the GTEx 'midpoint' data release (October 2015, V6).
   The original data for this 
   track can be found at the <a href="http://www.gtexportal.org/home" target = _blank>GTEX Portal</a> 
   hosted by the Broad Institute.
   <p>
   This track also features a new display method that extends the traditional Genome Browser 
-  display &mdash; a bar graph!  Each gene is represented by a graph with colored bars depicting the median expression 
-  level (in RPKM) of each tissue assayed by the GTEX project.
-  Note that the graph is a fixed width, and starts at the gene transcription start.
+  display &mdash; a bar graph!  Each gene in the annotation includes a graph with colored bars depicting 
+  the median expression level (in RPKM) of each tissue assayed by the GTEX project.  
+  The bars are colored by tissue using GTEx conventions. To see the tissue and expression level, 
+  mouseover a bar in the graph.
+  (You can also see the color legend from the 
+  <a href="../../cgi-bin/hgTrackUi?db=hg19&g=gtexGene" target=_blank>track configuration page</a>, 
+  which can be displayed alongside the track).
+  Below the bar graph is a line indicating the gene extent that was used to generate the annotation, colored
+  by gene class using GENCODE conventions (e.g. <span style='color: #0c0c78'>blue</span> for protein-coding, 
+  <span style='color: #006400'>green</span> for non-coding).
   <p>
   <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://hgwdev.cse.ucsc.edu/goldenPath/help/examples/sessions/gtexAnnouncementSession" 
   target=_blank>
   <center><img src="images/gtexAnnounceExample.png" width=75%></center></a>
   <p>
-  Notice how the bar graphs extend past the gene models underneath them? These gene
-  models represent the target of the RNA-Seq experiment, and the graph displays the RPKM levels
-  across many different tissues for the <em>entire</em> gene. In the
+  User alert: notice how the bar graphs sometimes extend past the gene itself?  This is because all bar graphs in the
+  display are the same width (and have the same tissue ordering) to make it easy to compare. So in this screenshot,
+  and this
   <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://hgwdev.cse.ucsc.edu/goldenPath/help/examples/sessions/gtexAnnouncementSession" 
-  target=_blank>example</a> above, the TCAP and NEUROD2 bar graphs actually extend past the 
-  gene model, and traditionally the three large purple bars  would be associated with the 
-  intergenic region between the two genes. However, in this case those three purple bars indicate 
-  that the entire TCAP gene is highly expressed in cardiac and skeletal muscle tissue. Clicking 
-  on the graph brings up a description page which displays a more detailed box and whisker plot of
+  target=_blank>example multi-region session</a> ,
+  the three tall purple-spectrum bars in the TCAP annotation indicate this <em>entire</em> gene is highly expressed in 
+  cardiac and skeletal muscle (not that there are expression peaks in the intergenic region beyond the gene).
+
+  Clicking on the graph brings up a description page which displays a more detailed box and whisker plot of
   the RPKM data, as well as a description of the methods used to generate the data. 
   <p>
   Credit goes to Kate Rosenbloom and Christopher Lee for the implementation and testing of this feature.
 -->
   <hr>
   <p>
   <font color="#006666" size="4"><b> 15 April 2016 -
   dbSNP 146 Available for hg19 and hg38</b></font>
   <p>
   We are pleased to announce the release of four tracks derived
   from NCBI <a href="http://www.ncbi.nlm.nih.gov/SNP/">
   dbSNP</a> Build 146 data, available on the two most
   recent human assemblies GRCh37/hg19 and GRCh38/hg38.
   NCBI's dbSNP database is a collection of &quot;simple nucleotide
   polymorphisms&quot; (SNPs), which are a class of genetic variations
   that include single nucleotide polymorphisms and small
   insertions/deletions (indels). This immense database contains over
   150 million such SNPs that cover the human genome.
   </p>
 
   <p>
   There are four SNP tracks available as part of this release.
   One is a track containing all mappings of reference SNPs
   to the human assembly, labeled &quot;All SNPs (146)&quot;.
   The other three tracks are subsets of this track
   and show interesting and easily defined subsets of dbSNP:
   </p>
 
   <ul>
   <li>Common SNPs (146): uniquely mapped variants that appear
   in at least 1% of the population or are 100% non-reference.</li>
   <li>Flagged SNPs (146): uniquely mapped variants, excluding
   Common SNPs, that have been flagged by dbSNP as
   &quot;clinically associated&quot;.</li>
   <li>Mult. SNPs (146): variants that have been mapped to more
   than one genomic location. This track has been shrinking over
   the course of the last few releases as dbSNP now excludes most
   SNPs whose flanking sequences map to multiple locations in
   the genome.</li>
   </ul>
 
   <p>
   By default, only the Common SNPs (146) are visible;
   other tracks must be made visible using the track controls.
   You will find the other SNPs (146) tracks on both
   of GRCh37/hg19 and GRCh38/hg38 browsers in the &quot;Variation&quot; group.
   </p>
   <p>
   The tracks were produced at UCSC by Angie Hinrichs and
   Matthew Speir. We'd like to thank the dbSNP group at
   NCBI for providing access to these data.
   </p>
 
   <hr>
   <a name="041516"></a>
   <p>
   <font color="#006666" size="4"><b> 15 April 2016 -
   Three New Assemblies Now Available in the Genome Browser</b></font>
   <p>
   A Genome Browser is now available for the gorilla (<em>Gorilla gorilla gorilla</em>)
   assembly released December 2014 by the Wellcome Trust Sanger Institute. 
   For more information and statistics about this assembly, see the NCBI assembly record
   for <a href="http://www.ncbi.nlm.nih.gov/assembly/503571" target="_blank">gorGor4</a>.  
   There are 25 complete chromosomes alongside 40,667 scaffolds with a total size of
   3,063,362,754 bases.
   </p>
 
   <p>
   Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
   <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/gorGor4/">FTP server</a> or the
   <a href="http://hgdownload.soe.ucsc.edu/downloads.html#gorilla">Downloads</a> page.
   Please observe the <a href="goldenPath/credits.html#gorilla_use">conditions for use</a> when
   accessing and using these data sets.  The annotation tracks for this browser were
   generated by UCSC and collaborators worldwide.  See the <a
   href="goldenPath/credits.html#gorilla_credits">Credits</a> page for a detailed list of the
   organizations and individuals who contributed to this release.
   </p>
   - - -
   <p>
   A Genome Browser is now available for the rhesus monkey (<em>Macaca mulatta</em>)
   assembly released November 2015 by the 
   <A HREF="https://www.hgsc.bcm.edu/non-human-primates/rhesus-monkey-genome-project"
   TARGET="_blank">Baylor College of Medicine Human Genome Sequencing Center</A>. 
   For more information and statistics about this assembly, see the NCBI assembly record
   for <a href="http://www.ncbi.nlm.nih.gov/assembly/2715158" target="_blank"> Mmul_8.0.1</a>.  
   There are 23 complete chromosomes alongside 284,705 scaffolds with a total size of
   3,236,224,332 bases.
   </p>
 
   <p>
   Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
   <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac8/">FTP server</a> or the
   <a href="http://hgdownload.soe.ucsc.edu/downloads.html#rhesus">Downloads</a> page.
   Please observe the <a href="goldenPath/credits.html#rhesus_use">conditions for use</a> when
   accessing and using these data sets.  The annotation tracks for this browser were
   generated by UCSC and collaborators worldwide.  See the <a
   href="goldenPath/credits.html#rhesus_credits">Credits</a> page for a detailed list of the
   organizations and individuals who contributed to this release.
   </p>
   - - -
   <p>
   A Genome Browser is now available for the crab-eating macaque (<em>Macaca fascicularis</em>)
   assembly released June 2013 by the 
   <A HREF="http://genome.wustl.edu/genomes/detail/macaca-fascicularis/"
   TARGET=_blank>Genome Sequencing Center at Washington University, St. Louis</A>.
   For more information about this assembly, see
   <A HREF="http://www.ncbi.nlm.nih.gov/assembly/704988"
   TARGET="_blank">Macaca_fascicularis_5.0</A> in the NCBI Assembly database. There are 
   22 complete chromosomes alongside 7,579 scaffolds with a total size of 2,946,843,737 bases.
   </p>
 
   <p>
   Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
   <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/macFas5/">FTP server</a> or the
   <a href="http://hgdownload.soe.ucsc.edu/downloads.html#crab-eating_macaque">Downloads</a> page.
   Please observe the <a href="goldenPath/credits.html#crab-eating_macaque_use">conditions for use</a> when
   accessing and using these data sets.  The annotation tracks for this browser were
   generated by UCSC and collaborators worldwide.  See the <a
   href="goldenPath/credits.html#crab-eating_macaque_credits">Credits</a> page for a detailed list of the
   organizations and individuals who contributed to this release.
   </p>
 
   <hr>
   <font color="#006666" size="4"><b>4 Apr 2016
   - New video shows how to obtain sequence or coordinates for exons. </b></font>
   <p>
   We have released a new <A HREF =
   "http://genome.ucsc.edu/training/vids/index.html#vid08" TARGET =
   _BLANK>video</A> to our YouTube channel.  This newest installment in our effort
   to share the capabilities of the Genome Browser shows how to
   use the Table Browser to obtain either the sequences or the coordinates for
   exons in the genes from a chosen region of the genome.
   </p>
 
   <p>
   We also want to take this opportuinty to remind you that we offer
   on-site <A HREF = "http://genome.ucsc.edu/training/index.html" TARGET =
   _BLANK>workshops</A> to help you and your colleagues make the most out
   of the Genome Browser.
   </p>
   <hr>
 
 <!-- start archives -->
 <!--staged for future release
         <p>
 	<font color="#006666" size="4"><b>20 Apr 2016
 	- Data from the Lens PatSeq Database Now Available</b>: </font>
 	We are pleased to announce the release of a set of tracks containing data from the
 	<a href="https://www.lens.org/" target="_blank">Lens</a>
 	PatSeq database in the UCSC Genome Browser.
 	<a href="goldenPath/newsarch.html#042016">Read more</a>.
 
         <p>
         <font color="#006666" size="4"><b>19 April 2016
         - New Genotyping Tissue Expression Track for hg19 and hg38!</b></font>
         <p>
         We are excited to announce the release of a new track based on data from the 
         <a href="http://commonfund.nih.gov/GTEx/index" TARGET = _BLANK>
         Genotyping Tissue Expression Consortium</a> V6 data freeze. This track displays tissue-specific
         gene expression for a single gene based on RNA-Seq data, as well as a new display 
         method that extends the traditional Genome Browser display &mdash; a bar graph! Each bar graph 
         depicts the expression level (in RPKM) of the various tissues assayed by the GTEX Consortium, 
         and is specific to each gene, not the graph's vertical location in the browser! 
 	<a href="goldenPath/newsarch.html#04192016">Read more</a>.
 
         <p>
 	<font color="#006666" size="4"><b> 15 April 2016 -
 	dbSNP 146 Available for hg19 and hg38</b>: </font>
 	We are pleased to announce the release of four tracks derived
 	from NCBI <a href="http://www.ncbi.nlm.nih.gov/SNP/">
 	dbSNP</a> Build 146 data.
 	<a href="goldenPath/newsarch.html#041516_2">Read more</a>.
 	</p>
 
 	<p>
 	<font color="#006666" size="4"><b>15 April 2016
 	- Genome Browsers for Gorilla, Rhesus, and Crab-Eating Macacque Now Available.</b></font>
 	<a href="goldenPath/newsarch.html#041516_1">Read more</a>.
 	</p>
 	
 	<p>
 	<font color="#006666" size="4"><b>4 Apr 2016
         - New video shows how to obtain sequence or coordinates for exons. </b></font>
 	<a href="goldenPath/newsarch.html#040416">Read more</a>.
 	</p>
 
 -->
 	<p>
 	<font color="#006666" size="4"><b>1 Apr 2016
 	- Going Back to Our Roots!</b></font>
 	<a href="goldenPath/newsarch.html#040116">Read more</a>.
 	</p>
 
 	<p>
 	<font color="#006666" size="4"><b>21 Mar 2016
 	- Genome Browsers for <i>C. elegans</i> and Brown Kiwi Now Available.</b></font>
 	<a href="goldenPath/newsarch.html#032116">Read more</a>.
 	</p>
 
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