b41b698689dc47edacdc76d7ccb85d6399f8ebd0 donnak Fri Apr 29 13:17:04 2016 -0700 Incorporated feedback from paired review, refs #17219. Did some minor editing of Lens PatSeq announcement. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index c7d4aa4..b94b9c9 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,150 +1,152 @@

News

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22 Apr 2016 - Data from the Lens PatSeq Database Now Available

- We are pleased to announce the release of a set of tracks containing data from the - Lens - PatSeq database in the UCSC Genome Browser. These tracks contain data from the - PatSeq - 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), + We are pleased to announce the release of a set of tracks showing the genomic mapping of + biomedical sequences submitted as part of patent application documents worldwide. The sequence + data, mappings and associated patent information were obtained from the + PatSeq database provided by + The Lens. The PatSeq data are + mapped to the genome, and the individual sequence features within the tracks are then + color-coded to indicate their status within the associated patent documents. + Track details pages show information about the patent documents in which the sequences + are referenced, and provide a link to The Lens PatSeq Analyzer tool for the given chromosome + range. The PatSeq data are divided into two tracks: a bulk patent track for sequences affiliated + with patents in which more than 100 sequences were submitted, and a non-bulk patent track + for all other sequences. These tracks are currently present on the human (hg19), mouse (mm10), and Ebola virus (eboVir3) genomes.

- Thanks to our collaborators at the Lens, Osmat Jefferson and Deniz Koellhofer, for providing the + 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.

20 April 2016 - New GTEx Gene Expression Track for hg19 and hg38

We are excited to announce the release of a new gene expression track based on data from the NIH Genotype-Tissue Expression (GTEx) project. This track displays tissue-specific gene expression based on RNA-seq in 53 tissues from 570 donors obtained from the GTEx 'midpoint' data release (V6, October 2015). The original data for this track can be found at the GTEX Portal hosted by the Broad Institute.

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. + and can also be popped up for viewing alongside the track using the right-click menu. 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! + the three tall bars in the annotation of the TCAP gene indicate that 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 + 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.

15 April 2016 - dbSNP 146 Available for hg19 and hg38: We are pleased to announce the release of four tracks derived from NCBI dbSNP Build 146 data. Read more.

15 April 2016 - Genome Browsers for Gorilla, Rhesus, and Crab-Eating Macacque Now Available. Read more.