Saturday, March 30, 2013

cBioPortal -- rapid access to numerous cancer genomics sets


Today's issue of Science and Science signaling have a special emphasis on Cancer Genomics.  Most of the articles, unfortunately, won't be available to actually read for a couple of days, but I did manage to find something interesting.  The cBioPortal at MSK is a database that looks through a large number of published genomics data sets and gives you information on whether your gene(s) of interest have been previously implicated in any forms of cancer.
For example, a study that  I did during one of my postdoctoral fellowship implicated a novel phosphorylation site on integrin alpha 4 (ITGA4) in the mechanism of action of a proprietary drug we were working with.  Input ITGA4 into cBioPortal and you get this nifty chart:

This shows that ITGA4 mutations, amplifications, and deletions have all been implicated in these forms of cancer.  This would have been a great slide for our monthly progress reports!  At least we have access to this great database now!  You can find more on it (and a tutorial) at the MSK website.


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