785fe0f558efddc86b461d5538071f3820d101a2 chmalee Fri Apr 15 16:01:01 2016 -0700 Staging gtex announcement, refs #15645 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 937c460..a15c46f 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -116,31 +116,57 @@ Macaca_fascicularis_5.0</A> in the NCBI Assembly database. There are 7,625 scaffolds with a total size of 2,946,843,737 bases. </p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/macFas5/">FTP server</a> or the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#crab-eating_macaque">Downloads</a> page. Please observe the <a href="credits.html#crab-eating_macaque_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="credits.html#crab-eating_macaque_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> --> - + <!-- Staging for Tuesday Announcement of GTEX track + <hr> + <font color="#006666" size="4"><b>19 April 2016 + - New Genotyping Tissue Expression Track for hg19 and hg38!</b></font> + <p> + We are excited to announce the release of a new track based on data from the + <a href="http://commonfund.nih.gov/GTEx/index" TARGET = _BLANK> + Genotyping Tissue Expression Consortium</a> V6 data freeze. This track displays tissue-specific + gene expression for a single gene based on RNA-Seq data. The data for this + track can be found at the <a href="http://www.gtexportal.org/home" target = _blank>GTEX Portal</a> + hosted by the Broad Institute. + <p> + This track also features a new display method that extends the traditional Genome Browser + display — a bar graph! Each bar graph depicts the expression level (in RPKM) of the + various tissues assayed by the GTEX Consortium, and is specific to each gene, not the graph's + location in the browser! + <p> + <center><img src="images/gtexAnnounceExample.png"></center> + <p> + Notice how the blue gene-model underneath the graph extends past the end of the graph? This gene + model represents the target of the RNA-Seq experiment, and the graph displays the RPKM levels + from across many different tissues for the <em>entire</em> gene. Clicking on the graph through + to the details page displays a more detailed box and whisker plot of the RPKM data, as well + as information as a description about all the methods used in the generation of the data. + <p> + Credit goes to Kate Rosenbloom for implementing this feature. + --> <hr> <font color="#006666" size="4"><b>4 Apr 2016 - New video shows how to obtain sequence or coordinates for exons. </b></font> <p> We have released a new <A HREF = "http://genome.ucsc.edu/training/vids/index.html#vid08" TARGET = _BLANK>video</A> to our YouTube channel. This newest installment in our effort to share the capabilities of the Genome Browser shows how to use the Table Browser to obtain either the sequences or the coordinates for exons in the genes from a chosen region of the genome. </p> <p> We also want to take this opportuinty to remind you that we offer on-site <A HREF = "http://genome.ucsc.edu/training/index.html" TARGET =