81e2b4c294447d686f055b2d794be7f0da11bbc9 kate Mon Apr 18 16:28:25 2016 -0700 More wordcrafting on GTEx announcement. Ready for Donna... diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index d287be1..9cc69e3 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -50,58 +50,65 @@ 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 <hr> <font color="#006666" size="4"><b>19 April 2016 - - New GTEx Gene Tissue Expression Track for hg19 and hg38</b></font> + - New GTEx Gene Expression Track for hg19 and hg38</b></font> <p> 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 + This track displays tissue-specific gene expression based on RNA-Seq in 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 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. + display — a bar graph! Each gene in the annotation includes a graph with colored bars depicting + the median expression level (in RPKM) of each tissue assayed by the GTEX project. + The bars are colored by tissue using GTEx conventions. To see the tissue and expression level, + mouseover a bar in the graph. + (You can also see the color legend from the + <a href="../../cgi-bin/hgTrackUi?db=hg19&g=gtexGene" target=_blank>track configuration page</a>, + which can be displayed alongside the track). + Below the bar graph is a line indicating the gene extent that was used to generate the annotation, colored + by gene class using GENCODE conventions (e.g. <span style='color: #0c0c78'>blue</span> for protein-coding, + <span style='color: #006400'>green</span> for non-coding). <p> <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://hgwdev.cse.ucsc.edu/goldenPath/help/examples/sessions/gtexAnnouncementSession" target=_blank> <center><img src="images/gtexAnnounceExample.png" width=75%></center></a> <p> - Notice how the bar graphs extend past the gene models underneath them? These gene - models represent the target of the RNA-Seq experiment, and the graph displays the RPKM levels - across many different tissues for the <em>entire</em> gene. In the + User alert: notice how the bar graphs sometimes extend past the gene itself? This is because all bar graphs in the + display are the same width (and have the same tissue ordering) to make it easy to compare. So in this screenshot, + and this <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://hgwdev.cse.ucsc.edu/goldenPath/help/examples/sessions/gtexAnnouncementSession" - target=_blank>example</a> above, the TCAP and NEUROD2 bar graphs actually extend past the - gene model, and traditionally the three large purple bars would be associated with the - intergenic region between the two genes. However, in this case those three purple bars indicate - that the entire TCAP 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 + target=_blank>example multi-region session</a> , + the three tall purple-spectrum bars in the TCAP annotation indicate this <em>entire</em> gene is highly expressed in + cardiac and skeletal muscle (not that there are expression peaks in the intergenic region beyond the gene). + + 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 of the methods used to generate the data. <p> Credit goes to Kate Rosenbloom and Christopher Lee for the implementation and testing of 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