4003ca71c92462fbcc997ae1e9bddd0b55ff5e05 chmalee Wed Apr 20 17:07:10 2016 -0700 Fixing links to gtex session, refs #15645 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 5eeafc9..5593e3c 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -76,39 +76,39 @@ This track also features a new gene expression display method that extends the traditional Genome Browser display — a horizontal bar graph. Every gene is annotated by a graph with colored bars, each of which corresponds to a specific tissue assayed by the GTEx project. Within a graph, the bar color indicates the tissue type, using GTEx conventions, and the bar height depicts the median expression level (in RPKM). To quickly view the tissue and expression level represented by a bar in the tracks display, mouse over the bar in the graph. The complete tissue color legend is shown on the track configuration page, and can also be popped up for viewing alongside the track. 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).

-

User alert: In the figure above, do you notice how the bar graph sometimes extends past the righthand end of the associated gene annotation? This is because all bar graphs in the display are the same width (and have the same tissue ordering) to facilitate comparison. For example, in this figure (which may also be viewed - here), the three tall bars in the TCAP annotation indicate this entire gene is highly expressed in cardiac and skeletal muscle. It does not indicate that there are expression peaks in the intergenic region beyond the gene!

Similar to other Genome Browser track displays, clicking on the graph will bring up a description page that shows a detailed box and whiskers plot of the RPKM data, as well as a description of the methods used to generate the data.

Credit goes to Kate Rosenbloom and Christopher Lee for the implementation and testing of this feature.