4a137c940e730eeddf1fd887dd56c101ba0bb2f8 katrina Tue Aug 24 15:10:21 2010 -0700 added Donna's regulation track announcement, minimized the most recentannouncement and removed the oldest announcement diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index e75b0a2..b2e86ef 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -25,62 +25,70 @@ TARGET=_blank>genome-announce</A> mailing list.</P> <!-- start news --> - <P> - <FONT FACE="courier" SIZE="3"><B>18 August 2010 - Cat Genome Browser Available</B></FONT> + <FONT FACE="courier" SIZE="3"><B>20 August 2010 - +New ENCODE Integrated Regulation Super-track Released</B></FONT> + <P> + We are pleased to announce the release of the ENCODE Integrated + Regulation super-track, a collection of regulatory tracks containing + state-of-the-art information about the mechanisms that turn genes on and + off at the transcription level. Individual tracks within the set show + enrichment of histone modifications suggestive of enhancer and promoter + activity, DNAse clusters indicating open chromatin, regions of + transcription factor binding, and transcription levels. When viewed in + combination, the complementary nature of the data within these tracks + has the potential to greatly facilitate our understanding of regulatory + DNA. </P> - We have released a Genome Browser for the latest assembly of Cat (<em>Felis catus</em>). - The GTB V17E assembly (December 2008, UCSC version felCat4) was produced by the NHGRI - Genome Technology Branch and NIH Intramural Sequencing Center, Maryland; Agencourt - Bioscience Corporation, Massachusetts; NCI Laboratory of Genomic Diversity, Maryland; - and Hill's Pet Nutrition, Inc, Kansas. The mitochondrial genome was sequenced by NCI - Laboratory of Genomic Diversity. For detailed sequencing and assembly information, see - the NCBI Felis catus - <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=10703" - TARGET=_blank>assembly page</a>. - </p> - - <p> - Downloads of the Cat data and annotations may be obtained from the - <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/felCat4/">UCSC FTP site</A> - or - <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#cat">Downloads</A> - page. These data have been freely provided for use in the UCSC Genome Browser - with specific conditions for use. - </p> - - <p> - Many thanks to NHGRI, Agencourt Bioscience Corporation, NCI and Hill's Pet Nutrition - for providing these data. The felCat4 annotation tracks were generated by UCSC and - its collaborators. We'd also like to acknowledge the UCSC Cat browser team: Chin Li, - Antonio Coelho, Mary Goldman and Donna Karolchik. See the - <A HREF="goldenPath/credits.html#cat_credits">Credits</A> - page for a detailed list of the organizations and individuals who contributed to - this release. - </p> - - + <P> + The data comprising these tracks were generated from hundreds of + experiments on multiple cell lines conducted by labs participating in + the Encyclopedia of DNA Elements (ENCODE) project, and were submitted to + the UCSC ENCODE Data Coordination Center for display on the Genome + Browser. + </P> + <P> + Faced with the problem of how to display such a large amount of data + in a manner facilitating analysis, UCSC has developed new visualization + methods that cluster and overlay the data, and then display the + resulting tracks on a single screen. Each of the cell lines in a track + is associated with a particular color. Light, saturated colors are used + to produce the best transparent overlay. + </P> + <P><TABLE ALIGN = CENTER><TR><TD ALIGN = CENTER > + <A HREF="http://tiny.cc/aqtyt"><img src="/images/encodeRegShot.gif" + alt="ENCODE Regulatory track screenshot" ALIGN=CENTER></A></TD></TABLE> + </P> + <P> + The data in the ENCODE Regulation super-track, as with all data from the + production phase of the ENCODE project, have genome-wide coverage. In + general, Genome Browser tracks that show ENCODE-generated data can be + identified by the double-helix icon preceding the name in the track + list. Currently, the ENCODE Regulation data are available only on the + March 2006 (NCBI Build 36, UCSC version hg18) assembly of the human + genome. + </P> + <P> + For a detailed description of the datasets contained in this super-track + and a discussion of how the tracks can be used synergistically to + examine regions of regulatory functionality within the genome, see the + <A HREF="http://tiny.cc/ntvjk">track description</A> page. </P><HR> - <P> - <FONT FACE="courier" SIZE="3"><B>23 July 2010 - BigBed/BigWig Paper Published:</b></FONT> - We are pleased to announce that we have published a paper on the BigBed and BigWig - format. <A HREF="goldenPath/newsarch.html#072310">Read more</A>. - <BLOCKQUOTE> - Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. - <A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq351" - TARGET=_blank>BigWig and BigBed: enabling browsing of large distributed data sets.</A> - <EM>Bioinformatics</EM>. 2010 July 17. Published online in advance of print. - </BLOCKQUOTE> - + <FONT FACE="courier" SIZE="3"><B>18 August 2010 - +Cat Genome Browser Available:</B></FONT> + We have released a Genome Browser for the latest assembly of Cat (<em>Felis catus</em>). + <A HREF="goldenPath/newsarch.html#081810">Read more</A>. </P><HR> - <P> - <FONT FACE="courier" SIZE="3"><B>15 July 2010 - Conservation - track available for zebrafish (danRer6): </b></FONT> - We are pleased to announce the release of a new Conservation track based - on the zebrafish (danRer6) assembly. - <A HREF="goldenPath/newsarch.html#071510">Read more</A>. + <FONT FACE="courier" SIZE="3"><B>23 July 2010 - BigBed/BigWig Paper Published:</b></FONT> + We are pleased to announce that we have published a paper on + the BigBed and BigWig format. + <A HREF="goldenPath/newsarch.html#072310">Read more</A>. + Kent WJ <em>et al</em>. <A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq351" + TARGET=_blank>BigWig and BigBed: enabling browsing of + large distributed data sets.</A> <EM>Bioinformatics</EM>. + 2010 July 17. Published online in advance of print. </P> </TD><TD WIDTH=15>