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Bioinformatics Advance Access originally published online on November 22, 2007
Bioinformatics 2008 24(2):209-217; doi:10.1093/bioinformatics/btm560
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways

Simon Hardy * and Pierre N. Robillard

Department of Computer Engineering, École Polytechnique de Montréal, P.O. Box 6079, Station Centre-Ville, Montréal, H3C 3A7, Canada

*To whom correspondence should be addressed.


  Abstract

Motivation: Cellular signaling networks are dynamic systems that propagate and process information, and, ultimately, cause phenotypical responses. Understanding the circuitry of the information flow in cells is one of the keys to understanding complex cellular processes. The development of computational quantitative models is a promising avenue for attaining this goal. Not only does the analysis of the simulation data based on the concentration variations of biological compounds yields information about systemic state changes, but it is also very helpful for obtaining information about the dynamics of signal propagation.

Results: This article introduces a new method for analyzing the dynamics of signal propagation in signaling pathways using Petri net theory. The method is demonstrated with the Ca2+/calmodulin-dependent protein kinase II (CaMKII) regulation network. The results constitute temporal information about signal propagation in the network, a simplified graphical representation of the network and of the signal propagation dynamics and a characterization of some signaling routes as regulation motifs.

Contact: simon.hardy{at}polymtl.ca

Supplementary information: Complete data of the Petri net model of the CaMKII regulation pathway available at http://www.polymtl.ca/rgl/Downloads.php

Associate Editor: Martin Bishop

Received on July 8, 2007; revised on October 9, 2007; accepted on November 5, 2007

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