4340f42241e6c5840fb5327e5190efe1b62ba639
chmalee
  Mon Apr 18 15:37:45 2016 -0700
Editing gtex announcement, refs #15645

diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html
index c288805..d287be1 100755
--- src/hg/htdocs/indexNews.html
+++ src/hg/htdocs/indexNews.html
@@ -47,62 +47,65 @@
   <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-->
+  <!-- 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>
   <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
   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.
   <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 blue gene-model underneath the graph shown here extends past the end of the graph? This gene
-  model represents the target of the RNA-Seq experiment, and the graph displays the RPKM levels
-  across many different tissues for the <em>entire</em> gene. Traditionally the 3 purple bars 
-  would be associated with the intron of TCAP gene, in this case those three bars indicate that 
-  the entire 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 the RPKM 
-  data, as well as a description of the methods used to generate the data. 
+  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
+  <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
+  the RPKM data, as well as a description of the methods used to generate the data. 
   <p>
-  Credit goes to Kate Rosenbloom for implementing and Christopher Lee for quality reviewing this feature.
-  <-->
+  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>