922b1992e052b8e7ae1673c51fb723f8917cf98b donnak Wed May 25 16:15:52 2011 -0700 Added news item about mm9 UCSC Genes. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 5875636..7bb4d18 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -15,141 +15,71 @@ </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="https://lists.soe.ucsc.edu/mailman/listinfo/genome-announce" TARGET=_blank>genome-announce</A> mailing list.</P> <!-- start news --> - <!-- ENCODE usability survey --> <P> - <FONT FACE="courier" SIZE="3"><B>1 May 2011 - ENCODE User's Guide and Usability Survey</B></FONT> + <FONT FACE="courier" SIZE="3"><B>26 May 2011 - New +Release of UCSC Genes for Mouse</B></FONT> </P> <P> + We've released an updated set of UCSC Genes for the mm9 + (NCBI Build 37) mouse Genome Browser. This version of the + gene set was generated using the same computational + pipeline as the previous mm9 UCSC Genes, but is based on + more recent GenBank data. + <P> + The new release has 55,419 total transcripts, compared with + 49,409 in the previous version. The total number of canonical + genes has increased from 27,389 to 28,661. + <P> + Comparing the new gene set with the previous version: + <UL> + <LI>33,977 transcripts did not change between versions + <LI>69 transcripts were not carried forward to the new version + <LI>13,701 transcripts are "compatible" with those in the + previous set + <LI>1,662 transcripts overlap with those in the previous set + </UL> + </P> + <HR> + + <!-- ENCODE usability survey --> + <P> + <FONT FACE="courier" SIZE="3"><B>1 May 2011 - ENCODE +User's Guide and Usability Survey: </B></FONT> The ENCODE project has just published an overview of their ongoing large-scale efforts to interpret the human genome sequence in the journal PLoS Biology. <a target=_blank href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001046 "> A Users Guide to the Encyclopedia of DNA Elements</a>, highlights the scope of data production, and provides guidance for locating - and using the data. With the vast amount of data now available, the ENCODE Data Coordination Center - at UCSC continues to focus on improving the accessiblity and usability of this valuable resource. - We invite all current and prospective users of ENCODE data to participate in the - <a target=_blank href="http://www.surveymonkey.com/s/5YYTRWQ">2011 ENCODE Usability Survey</a>. - Your input will help us to make this data more accessible to the scientific community. Thank you! + and using the data. + <A HREF="goldenPath/newsarch.html#050111">Read more</A>. </P> - <HR> <!-- hg19 snp132 release --> <P> - <FONT FACE="courier" SIZE="3"><B>18 April 2011 - dbSNP 132 Available for hg19</B></FONT> - </P> - <P> + <FONT FACE="courier" SIZE="3"><B>18 April 2011 - +dbSNP 132 Available for hg19: </B></FONT> We are pleased to announce the release of four tracks derived from <a href="http://www.ncbi.nlm.nih.gov/projects/SNP/" target=_blank>dbSNP</a> build 132, available on the human assembly (GRCh37/hg19). - dbSNP build 132 is available at NCBI. The new tracks contain - additional annotation data not included in previous dbSNP tracks, - with corresponding coloring and filtering options in the Genome - Browser. - </P> - <P> - As for prior builds of dbSNP, there is a track that contains all - mappings of reference SNPs to the human assembly; it is now labeled - "All SNPs (132)". Three new tracks have been added to show - interesting and easily defined subsets of dbSNP: - </P> - <ul> - <li> Common SNPs (132): uniquely mapped variants that appear in at - least 1% of the population</li> - - <li>Flagged SNPs (132): uniquely mapped variants, excluding Common - SNPs, that have been flagged by dbSNP as "clinically associated"</li> - - <li>Mult. SNPs (132): variants that have been mapped to more than one - genomic location</li> - </ul> - <P> - By default, only the Common SNPs (132) are visible; other tracks must - be made visible using the track controls. - </P> - <P> - The counts of distinct reference SNPs and their mappings to hg19 - differ greatly among the tracks: - </P> - <BLOCKQUOTE> - <table border="1" cellpadding="3"> - <tr> - <th>Track</th> - <th>Reference SNPs</th> - <th>Mappings to hg19</th> - </tr> - <tr> - <td>Common SNPs (132)</td> - <td>13,842,381</td> - <td>14,024,295 *</td> - </tr> - <tr> - <td>Flagged SNPs (132)</td> - <td>17,899</td> - <td>18,084 *</td> - </tr> - <tr> - <td>Mult. SNPs (132)</td> - <td>1,114,599</td> - <td>3,568,988</td> - </tr> - <tr> - <td>All SNPs (132)</td> - <td>30,030,754</td> - <td>33,026,121</td> - </tr> - </table> - </BLOCKQUOTE> - <P> - - * The Common and Flagged tracks have more mappings than SNPs due to the - alternate haplotype sequences and the pseudoautosomal regions on X and Y. - SNPs are considered uniquely mapped if they map only once to a haploid - reference genome. These regions add non-haploid sequence to the reference - genome; therefore, multiple mappings involving these regions are still - considered unique. - </P> - <P> - You will find the four SNPs (132) tracks on the Human Feb. 2009 - (GRCh37/hg19) browser in the "Variation and Repeats" group. + dbSNP build 132 is available at NCBI. + <A HREF="goldenPath/newsarch.html#041811.2">Read more</A>. </P> - <P> - Many thanks to dbSNP at NCBI for the data, and to - <a href="http://www.gs.washington.edu/faculty/king.htm" - target=_blank>Mary-Claire King</a> - at the University of Washington for helpful comments that motivated - us to enhance our dbSNP annotations. The tracks were produced at UCSC - by Angie Hinrichs, Brooke Rhead, Bob Kuhn, and Jim Kent. - </P> - - <hr> - <p><FONT FACE="courier" SIZE="3"><B>18 April 2011 - Sheep Browser Released:</B></FONT> - We are happy to announce a Genome Browser for - the initial release of the sheep (<em>Ovis aries</em>) genome. - <A HREF="goldenPath/newsarch.html#041811.1">Read more</A> - </p> - - <p><FONT FACE="courier" SIZE="3"><B>04 March 2011 - The Meaning of Red: Consensus on color scheme for CNVs: </B></FONT> - Consensus was reached on color standards to represent CNV loss (red) - and gain (blue) in genomics databases by DGV, NCBI, DECIPHER, UCSC and ISCA - during the 1st annual ISCA Scientific Conference. - <A HREF="goldenPath/newsarch.html#030411">Read more</A> - </p> ==> <a href="goldenPath/newsarch.html">News Archives</a> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>