Gain and loss of phosphorylation sites in human cancer
1School of Informatics, Indiana University, 901 East Tenth Street, Bloomington, IN 47408, 2Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 West Tenth Street, Suite 5000, Indianapolis, IN 46202, 3Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 and 4Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
*To whom correspondence should be addressed.
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Abstract |
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Motivation: Coding-region mutations in human genes are responsible for a diverse spectrum of diseases and phenotypes. Among lesions that have been studied extensively, there are insights into several of the biochemical functions disrupted by disease-causing mutations. Currently, there are more than 60 000 coding-region mutations associated with inherited disease catalogued in the Human Gene Mutation Database (HGMD, August 2007) and more than 70 000 polymorphic amino acid substitutions recorded in dbSNP (dbSNP, build 127). Understanding the mechanism and contribution these variants make to a clinical phenotype is a formidable problem.
Results: In this study, we investigate the role of phosphorylation in somatic cancer mutations and inherited diseases. Somatic cancer mutation datasets were shown to have a significant enrichment for mutations that cause gain or loss of phosphorylation when compared to our control datasets (putatively neutral nsSNPs and random amino acid substitutions). Of the somatic cancer mutations, those in kinase genes represent the most enriched set of mutations that disrupt phosphorylation sites, suggesting phosphorylation target site mutation is an active cause of phosphorylation deregulation. Overall, this evidence suggests both gain and loss of a phosphorylation site in a target protein may be important features for predicting cancercausing mutations and may represent a molecular cause of disease for a number of inherited and somatic mutations.
Contact: sdmooney{at}iupui.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
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