title: Structural modeling and analysis of signaling pathways based on Petri nets.
abstract: The purpose of this paper is to discuss how to model and analyze signaling pathways by using Petri net. Firstly, we propose a modeling method based on Petri net by paying attention to the molecular interactions and mechanisms. Then, we introduce a new notion "activation transduction component" in order to describe an enzymic activation process of reactions in signaling pathways and shows its correspondence to a so-called elementary T-invariant in the Petri net models. Further, we design an algorithm to effectively find basic enzymic activation processes by obtaining a series of elementary T-invariants in the Petri net models. Finally, we demonstrate how our method is practically used in modeling and analyzing signaling pathway mediated by thrombopoietin as an example.
authors.affiliation: Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan. li@ib.sci.yamaguchi-u.ac.jp
authors.forename: Chen
authors.initials: C
authors.lastname: Li
authors.forename: Shunichi
authors.initials: S
authors.lastname: Suzuki
authors.forename: Qi-Wei
authors.initials: QW
authors.lastname: Ge
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Nakata
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Matsuno
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D000465:Algorithms; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D008954:Models, Biological; D016571:Neural Networks, Computer; D009716:Numerical Analysis, Computer-Assisted; D015398:Signal Transduction / Q000502:physiology*; D009626:Terminology as Topic