STRUCTURAL MODELING AND ANALYSIS OF SIGNALING PATHWAYS BASED ON PETRI NETS

CHEN LI, SHUNICHI SUZUKI, QI-WEI GE, MITSURU NAKATA, HIROSHI MATSUNO, SATORU MIYANO
2006 Journal of Bioinformatics and Computational Biology  
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
more » ... ithm 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.
doi:10.1142/s021972000600234x pmid:17099944 fatcat:qo7d6mz6ejge7aakdl77ubpfcu