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Application of Petri net based analysis techniques to signal transduction pathways.

Sackmann, Andrea; Heiner, Monika; Koch, Ina

In: Journal BMC Bioinformatics 7, pages 482-500. 2006.

Abstract: We apply Petri net theory to model and analyse signal transduction pathways first qualitatively before continuing with quantitative analyses. This paper demonstrates how to build systematically a discrete model, which reflects provably the qualitative biological behaviour without any knowledge of kinetic parameters. The mating pheromone response pathway in Saccharomyces cerevisiae serves as case study. Results: We propose an approach for model validation of signal transduction pathways, based on the network structure only. For this purpose, we introduce the new notion of feasible t-invariants, which represent minimal self-contained subnets being active under a given input situation. Each of these subnets stands for a signal flow in the system. We define maximal common transition sets (MCT-sets), which can be used for t-invariant examination and net decomposition into smallest biologically meaningful functional units.

Keywords: place/transition Petri nets; biochemical networks; signal transduction networks; transition invariants, net decomposition, case study.

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