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