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Bioinformatics Advance Access published online on April 20, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn197
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Comparative conservation analysis of the human mitotic phosphoproteome

Rainer Malik *, Erich A. Nigg and Roman Körner

Department of Cell Biology, Max Planck Institute of Biochemistry, Martinsried D-82152, Germany.

*To whom correspondence should be addressed. Dr. Rainer Malik, E-mail: malik{at}biochem.mpg.de


  Abstract

Motivation: A key challenge in phosphoproteomic studies is to distinguish functionally relevant phosphorylation sites from potentially "silent" phosphorylation. Considering that relevant phosphorylation sites are expected to be better conserved during evolution than overall Serine, Threonine, and Tyrosine (S/T/Y) residues, we asked whether this can be directly demonstrated through statistic analysis, using a large experimental dataset.

Results: Analyzing phosphoproteomic data derived from the human mitotic spindle apparatus, we found that 95.2 % of 1744 phosphorylation sites are conserved in at least one of six other vertebrate species. Using a new score, termed CZ-Score, we demonstrate that phosphorylation sites are significantly better conserved than other S/T/Y sites, a conclusion validated from several kinase consensus motifs. Most importantly, phosphorylation sites with experimentally verified biological functions were significantly better conserved than other phosphorylation sites, indicating that analysis utilizing evolutionary conservation may constitute a powerful basis for the development of improved phosphorylation site predictors.

Contact: malik{at}biochem.mpg.de

Associate Editor: Prof. Burkhard Rost

Received on February 6, 2008; revised on April 17, 2008; accepted on April 17, 2008

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