59ee91e2829e1f6d33d83b5272de6bf12ba84922 dschmelt Tue May 26 10:51:40 2020 -0700 Announcing GENCODE and GTEx #25130 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 63330cd..29a5f2d 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -80,44 +80,44 @@ <li>2-way Pseudogenes - pseudogenes predicted by both the Yale Pseudopipe and UCSC Retrofinder pipelines.</li> <li>PolyA - polyA signals and sites manually annotated on the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of transcripts containing at least 3 A's not matching the genome.</li></ul> <p> Details on each release can be found on the <a target="_blank" href="https://www.gencodegenes.org/">GENCODE site</a>. This includes <a target="_blank" href="https://www.gencodegenes.org/human/stats.html">statistics on each release</a>. <p>We would like to thank the <a target="_blank" href="https://www.gencodegenes.org/pages/gencode.html">GENCODE project</a> for providing these annotations. We would also like to thank Mark Diekhans and Daniel Schmelter for the development and release of these tracks.</p> -<h3>Updated GTEx V8 gene transcript expression from RNA-seq of 54 tissues</h3> +<h3>GTEx V8 gene transcript expression from RNA-seq of 54 tissues</h3> <a name="052220a"></a> <p>We are excited to announce an update to the GTEx V8 for the gene expression track based on data from the <a target="_blank" href="http://commonfund.nih.gov/GTEx/index"> NIH Genotype-Tissue Expression (GTEx) project</a>. This track displays tissue-specific gene expression based on RNA-seq in 54 tissues from 948 donors released in August 2019. The original data for this track can be found at <a target="_blank" href="https://www.gtexportal.org/">the GTEX Portal</a> hosted by the Broad Institute. This track features a horizontal bar chart for each GENCODE gene, resulting in colored bars which show median tissue expression values assayed by the GTEx project in RPKM. Mouse over the bar in the graph shows a tissue specific expression value, while clicking on a chart -shows a much larger box-and-wiskers graph for that transcript. The complete tissue color legend +shows a much larger box-and-whiskers graph for that transcript. The complete tissue color legend and filters are shown on the <a target="_blanK" a href="/cgi-bin/hgGtexTrackSettings?db=hg38&g=gtexGeneV8">GTEx track configuration page</a>. Below the bar graph, a line is shown indicating the gene extent that was used to generate the annotation, colored by gene class using GENCODE conventions (e.g. blue for protein-coding, green for non-coding). </p> <p> <a href = "/cgi-bin/hgGtexTrackSettings?db=hg38&g=gtexGeneV8" target = _blank> <img src = "../images/GTExV8.png" WIDTH = 750 HEIGHT = 432> </a> </p> <p>