c9cebe93b5e6f403757fa5d67566f828b2728bfc
brianlee
  Fri Apr 18 15:58:41 2014 -0700
Adding news about Genome Segmentations and Switch to TF ChIP-seq track with new Motifs refs # 12259
diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html
index f32bddd..b59f10e 100755
--- src/hg/htdocs/indexNews.html
+++ src/hg/htdocs/indexNews.html
@@ -1,122 +1,131 @@
 <!-- News Section ============================================- -->  
 <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1">
     <TR><TD>        
     <TABLE BGCOLOR="#fffee8" WIDTH="100%"  BORDER="0" CELLSPACING="0" CELLPADDING="0">
         <TR><TD>        
         <TABLE BGCOLOR="#D9E4F8" BACKGROUND="images/hr.gif" WIDTH="100%" BORDER=0>
             <TR><TD>
             <!--cheap trick to get background on row to be continuous-->
             <TABLE CELLPADDING=0 CELLSPACING=0 WIDTH="100%">
                 <TR><TD ALIGN="left">
                  <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" alt="Follow GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a></TD>
                 <TD ALIGN="right"><A HREF="goldenPath/newsarch.html"><IMG 
                 SRC="images/news.jpg" ALT="" ALIGN="right" BORDER=0></A>
             </TD></TR></TABLE>
         </TD></TR></TABLE>
         <TABLE BGCOLOR="#fffee8" WIDTH="100%" CELLPADDING=0>
           <TR><TH HEIGHT=3></TH></TR>
           <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.</P>
 
     <!-- start news -->
 
         <hr>
         <p>
+        <font face="courier" size="3"><b> 18 April 2014 - 
+        New Motif Displays for Transcription Factor ChIP-seq Track and New Genome Segmentations from ENCODE</b></font>
+        <p>
+        The browser's default displayed Transcription Factor ChIP-seq track is updating to the
+        <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3">latest data release</a>,
+        which has been enhanced with the display of Factorbook motifs.  Within a cluster, a green
+        highlight indicates the highest scoring site of a Factorbook-identified canonical motif for the
+        corresponding factor. Upon clicking a transcription factor's cluster with a motif, the details page
+        now displays the motif's sequence logo, alignment and underlying Positional Weight Matrix. Also,
+        the track configuration page now enables the filtering of factors.
+        </p>
+        <p>
+        The newly added <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeAwgSegmentation">
+        Genome Segmentations from ENCODE</a> tracks display multivariate genome-segmentation performed on
+        <a target=ucscVocab href="http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?term=GM12878,H1-hESC,K562,HeLa-S3,HepG2,HUVEC">six human cell types</a>
+        (GM12878, K562, H1-hESC, HeLa-S3, HepG2, and HUVEC), integrating ChIP-seq data for
+        <a target=ucscVocab href="http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?term=CTCF,H3K4me1,H3K4me2,H3K4me3,H3K27ac,H3K9ac,H3K36me3,H4K20me1,H3K27me3,Pol2,Input">
+        eight chromatin marks, RNA Polymerase II, the CTCF transcription factor and input data</a>. In total,
+        twenty-five states were used to segment the genome, and these states were then grouped and colored to
+        highlight predicted functional elements. These Genome Segmentations are the same data as
+        found in the
+        <a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=hub_4607_genomeSegmentation&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt"
+        target="_blank">Analysis Working Group Hub</a>, but are now hosted natively in the browser with enhanced
+        filtering capability where desired segmented states can be selected using the
+        'Filter by Segment Type' control on the track configuration page.
+        </p>
+
+        <hr>
+        <p>
         <font face="courier" size="3"><b>15 April 2014 -
         New Minke Whale (balAcu1) Assembly Now Available in the Genome Browser</b></font>
         <p>
         A Genome Browser is now available for the minke whale (Balaenoptera acutorostrata scammoni)
         assembly released October 2013 by the <A HREF="http://eng.kiost.ac/kordi_eng/main/" TARGET="_BLANK">
         Korea Ocean Research &amp; Development Institute</A> (KORDI version BalAcu1.0, UCSC version balAcu1).
         For more information and statistics about this assembly, see the NCBI assembly record for
         <A HREF="http://www.ncbi.nlm.nih.gov/assembly/78761" TARGET="_BLANK">BalAcu1.0</A>. There are
         10,776 scaffolds with a total size of 2,431,687,698 bases.
         </p>
 
         <p>
         Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
         <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/balAcu1/">FTP server</A> or the
         <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#minke_whale">Downloads</A> page. Please
         observe the <A HREF="goldenPath/credits.html#minke_whale_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#minke_whale_credits">Credits</A>
         page for a detailed list of the organizations and individuals who contributed to this release.
         </p>
-
-        <hr>
-        <p>
-        <font face="courier" size="3"><b>11 April 2014 -
-        New UCSC Genes Track Released for GRCm38/mm10</b></font>
-        <p>
-        We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10
-        mouse Genome Browser.  The new release has 61,642 total transcripts, compared with 59,121
-        in the previous version.  The total number of canonical genes has increased from 31,469
-        to 32,408.  Comparing the new gene set with the previous version:
-        <ul>
-          <li>54,714 transcripts did not change between versions.</li>
-          <li>19 transcripts were not carried forward to the new version.</li>
-          <li>3,866 transcripts are &quot;compatible&quot; 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>522 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>
         <hr>
 
         <!-- staged for archive use
 
         <p>
+        <font face="courier" size="3"><b>18 April 2014 - 
+        New Motif Displays and New Genome Segmentations from ENCODE</b></font>
+        The browser's default displayed 
+        <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3">Transcription Factor ChIP-seq track</a>
+        updated to the latest release, enhanced with the display of Factorbook motifs. And the browser added
+        <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeAwgSegmentation">Genome
+        Segmentations from ENCODE</a> tracks, which segment the genome into twenty-five states that were then grouped
+        and colored to highlight predicted functional elements.
+        <a href="goldenPath/newsarch.html#041814">Read more</a>.
+        </p>
+
+        <p>
         <font face="courier" size="3"><b>15 April 2014 -
         New Minke Whale (balAcu1) Assembly Now Available in the
         Genome Browser</b></font>
         A Genome Browser is now available for the minke whale
         (Balaenoptera acutorostrata scammoni) assembly released 
         October 2013 by the Korea Ocean Research &amp; Development Institute.
         <a href="goldenPath/newsarch.html#041514">Read more</a>.
         </p>
 
+                -->
+        <!-- start archives -->
+
         <p>
         <font face="courier" size="3"><b>11 April 2014 -
         New UCSC Genes Track Released for GRCm38/mm10</b></font>
         </p>
         We're happy to announce the release of an updated UCSC Genes
         track for the GRCm38/mm10 mouse Genome Browser.
         <a href="goldenPath/newsarch.html#041114">Read more</a>.
         </p>
 
-                -->
-        <!-- start archives -->
+
 	<p>
         <font face="courier" size="3"><b>06 March 2014 -
         The new GRCh38 Human Genome Browser is here!</b></font>
         In the final days of 2013, the Genome Reference Consortium (GRC)
         released the eagerly awaited GRCh38 human genome assembly, the
         first major revision of the human genome in more than four years.
         <a href="goldenPath/newsarch.html#030614">Read more</a>.
         </p>
 
-        <p>
-        <font face="courier" size="3"><b>04 March 2014 - 
-        Introducing Genome Browser highlight feature:</b></font>
-        We are excited to announce a new highlight feature in the UCSC
-        Genome Browser. Using drag-and-select, you can now highlight a
-        region or gene of interest.
- 	<a href="goldenPath/newsarch.html#030414">Read more</a>.
-	</p>
-
             </TD><TD WIDTH=15>
          </TD></TR></TABLE>
     <BR></TD></TR></TABLE>
 </TD></TR></TABLE>