e7880ea3badaf9e449dbded588a77d3154ea335c brianlee Fri Apr 18 16:10:21 2014 -0700 Removing links to AWG hub in news release as creates a unique issue with new TF ChIP-seq track Motifs refs # 12259 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index b59f10e..eca770c 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,131 +1,129 @@ <!-- 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> 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 + found in the Analysis Working Group Hub, 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 & 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> <!-- 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 & 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> <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> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>