db93d1ac9ffd179e8e70e2c98999c98fbb9efd5d markd Wed Apr 17 21:12:30 2024 -0700 added missing or outdated ENCODE files from the rr diff --git src/hg/htdocs/ENCODE/news_archive.html src/hg/htdocs/ENCODE/news_archive.html index 84b64f6..1800097 100755 --- src/hg/htdocs/ENCODE/news_archive.html +++ src/hg/htdocs/ENCODE/news_archive.html @@ -1,133 +1,133 @@ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN"> <HTML> <HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1"> <META name="description" content="ENCODE Project at UCSC - News Archives"> <META name="keywords" content="ENCODE, project, ENCODE project, genome, genome browser, human genome, Blat, UCSC, bioinformatics, gene prediction, SNP, EST, mRNA, NHGRI, NISC"> <TITLE>ENCODE Project at UCSC: News Archives</TITLE> <LINK REL="STYLESHEET" HREF="../style/HGStyle.css"> </HEAD> <BODY BGCOLOR="FFF9D2" LINK="0000CC" VLINK="#330066" ALINK="#6600FF"> <A NAME="TOP"></A> <!-- Header Images and links --> <TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH="100%"> <TR> <TH COLSPAN=2 ALIGN="left"> <A HREF="http://www.genome.gov/10005107" TARGET=_BLANK><IMG SRC="../images/encodelogo.gif" height=50 ALT="ENCODE Project at NHGRI"></A> <A HREF="/ENCODE/"><IMG SRC="../images/encodeDcc.jpg" ALT="ENCODE Data Coordination Center at UCSC"></A> </TH> </TR> <TR><TD COLSPAN=2 HEIGHT=40><!--#include virtual="../inc/encode.topbar.html"--></TD></TR> <!--Content Tables-------------------------------------------------------> <TR><TD COLSPAN=2 CELLPADDING=10> <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDERCOLOR="888888" BORDER=1> <TR><TD> <TABLE BGCOLOR="D9E4F8" BACKGROUND="../images/hr.gif" WIDTH="100%"> <TR><TD> <FONT SIZE="4"><B> News Archives </B></FONT> </TD></TR> </TABLE> <TABLE BGCOLOR="fffee8" WIDTH=100% CELLPADDING=0> <TH HEIGHT=10></TH> <TR><TD WIDTH=10></TD><TD> <UL> <LI><A CLASS="toc" HREF="#2007">2008 News</A></LI> <LI><A HREF="newsarch.html">Pilot Phase News Archive</A> </UL> <HR> <!- Begin 2008 news items --> <A NAME="2008"></A> <P> There are currently no news items in this archive. <!-- <A NAME="100407"></A> <FONT SIZE=4 COLOR="#006666">4 Oct. 2007 - ENCODE Genome Browser Released for hg18 Assembly</B></FONT><BR> <P> The ENCODE browser for UCSC human genome assembly hg18 (NCBI Build 36) is now available. You can access the browser directly at <A HREF="encode.hg18.html">http://genome.ucsc.edu/ENCODE/encode.hg18.html</A> or by clicking the ENCODE link on the Genome Browser <A HREF="../index.html">home page</A>, then selecting the Regions (hg18) item in the sidebar menu on the ENCODE portal page.</P> <P> The hg18 ENCODE browser includes 540 data tables in 59 browser tracks that were migrated from the hg17 browser. The hg17 data coordinates were converted to hg18 coordinates using the UCSC liftOver process.</P> <P> To improve the accessibility of the data, related ENCODE tracks have been gathered into new configuration groupings ("super-tracks") that can be displayed or hidden using a single visiblity control. We have also reduced the number of track groups and have modified some of the group names for clarity. </P> <P> The following table summarizes the data currently present in the hg18 ENCODE browser: <BR><BR> <TABLE BORDER=1 BORDERCOLOR="#aaaaaa" WIDTH="100%"> <TR> <TD nowrap><FONT color="#006666"><B>Group</B></FONT></TD> <TD nowrap><FONT color="#006666"><B>Super-tracks</B></FONT></TD> <TD nowrap><FONT color="#006666"><B>Tracks</B></FONT></TD> <TD nowrap><FONT color="#006666"><B>Tables</B></FONT></TD> </TR> <TR><TD>Regions and Genes</TD><TD>2</TD><TD>12</TD><TD>73</TD></TR> <TR><TD>Transcription</TD><TD>2</TD><TD>11</TD><TD>67</TD></TR> <TR><TD>Chromatin Immunoprecipitation</TD><TD>8</TD><TD>28</TD><TD>349</TD></TR> <TR><TD>Chromatin Structure</TD><TD>2</TD><TD>8</TD><TD>51</TD></TR> </TABLE></P> <P> Note that the Variation and Comparative Genomics data were not lifted during this migration; instead, they will be replaced by new data. The first ENCODE MSA alignment for hg18 (TBA) is currently in progress on the UCSC - <A HREF="http://hgwdev.soe.ucsc.edu/ENCODE/">development + <A HREF="http://hgwdev.cse.ucsc.edu/ENCODE/">development server</A>. <P> During the migration, ENCODE tracks with whole-genome data were moved into the standard browser track groups. These include the GIS PET and UCSD/LI TAF1 tracks. Future submissions of whole-genome ENCODE data will be loaded directly into the standard track groups. </P> <P> We have expanded the ENCODE downloads site to include original data for all "wiggle" datasets. These data files now have filename extensions indicating the wiggle input format (fixed step, variable step, or bedGraph).</P> <P> You can find a description of the migration project and full details of the tables, tracks, and super-tracks available at the UCSC ENCODE portal on the UCSC <A HREF="http://genomewiki.ucsc.edu/index.php/ENCODE_Hg18_Migration" TARGET=_BLANK> genomeWiki</A>.</P> <P> The UCSC team members who contributed to this effort were: Andy Pohl (data conversion and database loading), Ting Wang and Donna Karolchik (super-track documentation), Bob Kuhn (portal updates), Brooke Rhead, Kayla Smith, and Ann Zweig (quality assurance), and Kate Rosenbloom (super-track development, project management). <P> <HR> --> <BR><BR> </TD><TD WIDTH=15></TD></TR> </TABLE> </TD></TR> </TABLE> </TD></TR> </TABLE> </BODY></HTML>