d0e054ad7c3474a8aee0497ae4506a4f2649577c kate Mon Apr 18 14:23:00 2016 -0700 Tweaks to intro paragraph of GTEx announcement. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index ca02c37..988ec6c 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -47,59 +47,60 @@ <a href="https://www.lens.org/lens/bio" target="_blank">PatSeq</a> database mapped to the genome and then colored based on where the sequence appears in the patent document. Details pages contain the patent titles with links to the patents in the Lens database. The data from PatSeq is divided into two tracks, one includes those sequences that were submitted in bulk patents containing 100 or more sequences and the other containing all other sequences. These tracks are currently present on the human (hg19), mouse (mm10), and Ebola virus (eboVir3) genomes. </p> <p> Thanks to our collaborators at the Lens, Osmat Jefferson and Deniz Koellhofer, for providing the data and feedback on the visualization. Thank you to Max Haeussler and Matthew Speir, members of the UCSC Genome Browser team, for their efforts in creating these tracks. </p> --> - <!-- Staging for Tuesday Announcement of GTEX track + <!-- 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> + - New GTEx Gene 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 original data for this + We are excited to announce the release of a new gene expression track based on data from the NIH + <a href="http://commonfund.nih.gov/GTEx/index" TARGET = _BLANK> Genotype-Tissue Expression (GTEx)</a> project. + This track displays tissue-specific expression based on RNA-Seq data of 53 tissues from 570 donors, obtained from + the GTEx 'midpoint' data release (October 2015, V6). + The original 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 - vertical location in the browser! + display — a bar graph! Each gene is represented by a graph with colored bars depicting the median expression + level (in RPKM) of each tissue assayed by the GTEX project. + Note that the graph is a fixed width, and starts at the gene transcription start. <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 + Notice how the blue gene-model underneath the graph shown here 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 across many different tissues for the <em>entire</em> gene. Traditionally the 3 purple bars would be associated with the intron of TCAP gene, in this case those three bars indicate that the entire gene is highly expressed in cardiac and skeletal muscle tissue. Clicking on the graph brings up a description page which displays a more detailed box and whisker plot of the RPKM - data, as well as a description about all the methods used in the generation of the data. + data, as well as a description of the methods used to generate the data. <p> - Credit goes to Kate Rosenbloom for implementing this feature. - --> + Credit goes to Kate Rosenbloom for implementing and Christopher Lee for quality reviewing this feature. + <--> <hr> <p> <font color="#006666" size="4"><b> 15 April 2016 - dbSNP 146 Available for hg19 and hg38</b></font> <p> We are pleased to announce the release of four tracks derived from NCBI <a href="http://www.ncbi.nlm.nih.gov/SNP/"> dbSNP</a> Build 146 data, available on the two most recent human assemblies GRCh37/hg19 and GRCh38/hg38. NCBI's dbSNP database is a collection of "simple nucleotide polymorphisms" (SNPs), which are a class of genetic variations that include single nucleotide polymorphisms and small insertions/deletions (indels). This immense database contains over 150 million such SNPs that cover the human genome. </p>