Selected Papers from International Conference on Bioinformatics 2005 (InCoB 2005)No Access

STRUCTURAL MODELING AND ANALYSIS OF SIGNALING PATHWAYS BASED ON PETRI NETS

CHEN LI

Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan

Search for more papers by this author

SHUNICHI SUZUKI

Tokyo Head Office, TIS System Service Inc., Toyo Center Bldg., 29-15, Toyo-cho 5-chome, Koto-ku, Tokyo 135-0016, Japan

Search for more papers by this author

QI-WEI GE

Faculty of Education, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan

Search for more papers by this author

MITSURU NAKATA

Faculty of Education, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan

Search for more papers by this author

HIROSHI MATSUNO

Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8512, Japan

Search for more papers by this author

, and

SATORU MIYANO

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan

Search for more papers by this author

https://doi.org/10.1142/S021972000600234XCited by:25 (Source: Crossref)

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.

Keywords:

References

V. N. Reddy, M. N. Liebman and M. L. Mavrovouniotis, Comput. Biol. Med. 26(1), 9 (1996), DOI: 10.1016/0010-4825(95)00042-9. Crossref, Medline, Google Scholar
V. N. Reddy, M. L. Mavrovouniotis and M. N. Liebman, Petri net representations in metabolic pathways, Proc. Int. Conf. Intell. Syst. Mol. Biol.1 (1993) pp. 328–336. Google Scholar
M. Heiner, I. Koch and J. Will, Biosystems 75(1–3), 15 (2004), DOI: 10.1016/j.biosystems.2004.03.003. Crossref, Medline, Google Scholar
J. Peccoud, Medicine Sciences 14(8–9), 991 (1998). Google Scholar
H. Matsunoet al., Towards biopathway modeling and simulation, Proc. 24th ICATPN, Lecture Notes in Computer Science 2679 (2003) pp. 3–22. Google Scholar
H. Matsunoet al., In Silico Biol. 3(3), 389 (2003). Medline, Google Scholar
H. J. Genrich, R. Küffner and K. Voss, International Journal on Software Tools for Technology Transfer 3(4), 394 (2001). Crossref, Google Scholar
D. Y. Leeet al., Metabolic Engineering 8(2), 112 (2006), DOI: 10.1016/j.ymben.2005.10.001. Crossref, Medline, Google Scholar
K. Voss, H. Monika and I. Koch, In Silico Biol. 3(3), 367 (2003). Medline, Google Scholar
R Hofestädt and S. Thelen, In Silico Biol. 1(1), 39 (1998). Medline, Google Scholar
I. Zevedei-Oancea and S. Schuster, In Silico Biol. 3(3), 323 (2003). Medline, Google Scholar
S. Schusteret al., Structural Analysis of Metabolic Networks: Elementary Flux Mode, Analogy to Petri Nets, and Application to Mycoplasma Pneumoniae, German Conference on Bioinformatics 2000 (2000) pp. 115–120. Google Scholar
S. Schuster, T. Dandekar and D. A. Fell, Trends Biotechnol. 17(2), 53 (1999), DOI: 10.1016/S0167-7799(98)01290-6. Crossref, Medline, Google Scholar
S. Schuster, D. A. Fell and T. Dandekar, Nature Biotechnol. 18(3), 326 (2000), DOI: 10.1038/73786. Crossref, Google Scholar
J. Peterson , Petri net theory and the modeling of systems ( Prectice-Hall , Englewood Cliffs, NJ , 1981 ) . Google Scholar
R. Hofestädt, Syst. Anal. Mod. Simul. 16, 113 (1994). Google Scholar
T. Takai-Igarashi and R. Mizoguchi, In Silico Biol. 4(1), 81 (2004). Medline, Google Scholar
Q. W. Ge, T. Tanida and K. Onaga, Construction of a T-base and design of a periodic firing sequence of a Petri net, Proc. 8th Mathematical Programming Symposium (1987) pp. 51–57. Google Scholar
Araki T., Tanida T., Watanabe T., Onaga K., A linear programming-based algorithm for successively enumerating elementary invariants of Petri nets, Technical Report of IEICE, 125–132 (CAS89–89), 1989 . Google Scholar
D. Avis and K. Fukuda, Discrete Comput. Geom. 8, 295 (1992), DOI: 10.1007/BF02293050. Crossref, Google Scholar
J. Martinez and M. Silva, A simple and fast algorithm to obtain all invariants of a generalized Petri nets, Proc. Second European Workshop on Application and Theory of Petri Nets, Informatik-Fachberichte 52 (Springer-Verlag, 1982) pp. 301–310. Google Scholar
K. Takanoet al., IEICE Trans on Fundamentals E84-A(11), 2871 (2001). Google Scholar
Q. W. Ge, T. Fukunaga and M. Nakata, On generating elementary T-invariants of Petri nets by linear programming, Proc. ISCAS2005 (2005) pp. 168–171, http://genome.ib.sci.yamaguchi-u.ac.jp/~pnp/papers/gqw-iscas2005.pdf. Google Scholar
A. E. Geddis, H. M. Linden and K. Kaushansky, Cytokine Growth Factor Rev. 13, 61 (2002), DOI: 10.1016/S1359-6101(01)00030-2. Crossref, Medline, Google Scholar
H. Schulzeet al., Experimental Hematology 28, 294 (2000), DOI: 10.1016/S0301-472X(99)00154-X. Crossref, Medline, Google Scholar
W. S. Alexander, IJBCB 31, 1027 (1999). Google Scholar