V15: search for tracks, search for KEGG pathway

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Friday, March 1, 2013


Version 15 of WashU Genome Browser enables you to search for tracks by keyword. In the case of human, mouse, fruit fly, you can easily identify your target experimental assay tracks from our vast collection.

With help from KEGG support team, we've brought back KEGG pathway query. For all genomes hosted by our Browser, user can search for pathways curated by KEGG with keyword, and run Gene set view by selecting a pathway.

To get the source code of this version use the links below:

https://www.dropbox.com/sh/kyosquasf4rr4f4/QShHggjiKx

http://epigenomegateway.wustl.edu/info/source/subtleKnife.v15.tgz

Track search

To search for tracks by keyword, go to the small Toolbox panel and click "Tracks", then "Experimental assay tracks", the native track selection panel is shown.

V15- search for tracks, search for KEGG pathway 2 1.png

Enter keyword in the text field on top of the panel and press Find to get a list of experimental assay tracks matching your query:

V15- search for tracks, search for KEGG pathway 3 1.png

Keyword is case insensitive. If you enter "dnase hypersensitivity" and it will be treated as one keyword.

Track either matching by name or description will all be shown. In above example, we intend to search for "DNase hypersensitivity" tracks but the first one is an RNA-Seq track, that's because the detailed information of this track contains the word "DNase".

To performed a search by combining multiple keywords, use AND operator (you must use upper case but not lower case "and"):

V15- search for tracks, search for KEGG pathway 4 1.png

KEGG pathway

At toolbox panel click "Apps" then "Gene set view" to open this panel:

V15- search for tracks, search for KEGG pathway 5 1.png

Click the button "KEGG pathway" to show the options:

V15- search for tracks, search for KEGG pathway 6 1.png

Search for keyword "glyco" will get following hits for the human genome:

V15- search for tracks, search for KEGG pathway 7 1.png

Each green button is one pathway, select one and click to launch gene set view with it:

V15- search for tracks, search for KEGG pathway 8 1.png

After you run gene set view on the human glycolysis pathway genes, a table is displayed showing list of genes in this pathway. Gene name are in a blue button where the width of dark fill indicates the length of this gene in respect to the whole set. In this case gene "HK1" is the longest.