Linear mapping approximation of gene regulatory networks with stochastic dynamics

Zhixing Cao and Ramon Grima ()
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Zhixing Cao: the University of Edinburgh
Ramon Grima: the University of Edinburgh

Nature Communications, 2018, vol. 9, issue 1, 1-15

Abstract: Abstract The presence of protein–DNA binding reactions often leads to analytically intractable models of stochastic gene expression. Here we present the linear-mapping approximation that maps systems with protein–promoter interactions onto approximately equivalent systems with no binding reactions. This is achieved by the marriage of conditional mean-field approximation and the Magnus expansion, leading to analytic or semi-analytic expressions for the approximate time-dependent and steady-state protein number distributions. Stochastic simulations verify the method’s accuracy in capturing the changes in the protein number distributions with time for a wide variety of networks displaying auto- and mutual-regulation of gene expression and independently of the ratios of the timescales governing the dynamics. The method is also used to study the first-passage time distribution of promoter switching, the sensitivity of the size of protein number fluctuations to parameter perturbation and the stochastic bifurcation diagram characterizing the onset of multimodality in protein number distributions.

Date: 2018
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DOI: 10.1038/s41467-018-05822-0

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