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In Silico Biology 6, 0001 (2006); ©2006, Bioinformation Systems e.V.  



Simulation-based validation of the p53 transcriptional activity with hybrid functional Petri net

Atsushi Doi1, Masao Nagasaki1, Hiroshi Matsuno2* and Satoru Miyano1

1 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
2 Faculty of Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512, Japan

* Corresponding author
   Email: matsuno@sci.yamaguchi-u.ac.jp


Edited by E. Wingender; received September 20, 2005; revised December 03; accepted December 04, 2005; published January 04, 2006


Abstract

MDM2 and p19ARF are essential proteins in cancer pathways forming a complex with protein p53 to control the transcriptional activity of protein p53. It is confirmed that protein p53 loses its transcriptional activity by forming the functional dimer with protein MDM2. However, it is still unclear that protein p53 keeps its transcriptional activity when it forms the trimer with proteins MDM2 and p19ARF. We have observed mutual behaviors among genes p53, MDM2, p19ARF and their products on a computational model with hybrid functional Petri net (HFPN) which is constructed based on information described in the literature. The simulation results suggested that protein p53 should have the transcriptional activity in the forms of the trimer of proteins p53, MDM2, and p19ARF. This paper also discusses the advantages of HFPN based modeling method in terms of pathway description for simulations.


Keywords: hybrid functional Petri net, p53, biological pathway, simulation