Structural modeling and analysis of signaling pathways based on Petri nets.
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.
Li
Chen
C
Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan. li@ib.sci.yamaguchi-u.ac.jp
Suzuki
Shunichi
S
Ge
Qi-Wei
QW
Nakata
Mitsuru
M
Matsuno
Hiroshi
H
Miyano
Satoru
S
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