Paper Info
Title
Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways.
Abstract
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.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 Ca(2+)/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.
Year
DOI
Venue
2008
10.1093/bioinformatics/btm560
Bioinformatics
Keywords
Field
DocType
regulation motif,information flow,complete data,process information,signal propagation dynamic,temporal information,camkii regulation pathway,signal propagation,regulation network,biological compounds yields information,petri net-based method,calmodulin,dynamic system,protein kinase,signaling pathway,petri net
Information flow (information theory),Protein kinase II,Petri net,Computer science,Ca2+/calmodulin-dependent protein kinase,Signal transduction,Cell signaling,Bioinformatics,Radio propagation,Dynamical system
Journal
Volume
Issue
ISSN
24
2
1367-4811
Citations 
PageRank 
References 
16
1.08
10
Authors
2
Name
Order
Citations
PageRank
Simon Hardy1433.67
Pierre N Robillard256865.22