A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics

A stochastic genetic toggle switch model that consists of two identical, mutually repressive genes is built using the Gillespie algorithm with time delays as an example of a simple stochastic gene regulatory network. The stochastic kinetics of this model is investigated, and it is found that the delays for the protein productions can highly weaken the global fluctuations for the expressions of the two genes, making the two mutually repressive genes coexist for a long time. Starting from this model, we propose a practical modeling strategy for more complex gene regulatory networks. Unlike previous applications of the Gillespie algorithm to simulate specific genetic networks dynamics, this modeling strategy is proposed for an ensemble approach to study the dynamical properties of these networks. The model allows any combination of gene expression products, forming complex multimers, and each one of the multimers is assigned to a randomly chosen gene promoter site as an activator or inhi...

• Type: Journal
• Year: 2006
• Where: JCB
• Authors: Andre Ribeiro, Rui Zhu, Stuart A. Kauffman
• Keywords: Gene Regulatory Networks, Gillespie Algorithm, JCB 2006, Stochastic Genetic Toggle