Inferring parameters of gene regulatory networks via particle filtering

Abstract

Gene regulatory networks are highly complex dynamical systems comprising biomolecular components which interact with each other and through those interactions determine gene expression levels, that is, determine the rate of gene transcription. In this paper, a particle filter with Markov Chain Monte Carlo move step is employed for the estimation of reaction rate constants in gene regulatory networks modeled by chemical Langevin equations. Simulation studies demonstrate that the proposed technique outperforms previously considered methods while being computationally more efficient. Dynamic behavior of gene regulatory networks averaged over a large number of cells can be modeled by ordinary differential equations. For this scenario, we compute an approximation to the Cramer-Rao lower bound on the mean-square error of estimating reaction rates and demonstrate that, when the number of unknown parameters is small, the proposed particle filter can be nearly optimal. Copyright © 2010 Xiaohu Shen and Haris Vikalo.