Stochastic model of yeast cell-cycle network

DOI10.1016/J.PHYSD.2006.05.009MaRDI QIDQ2500679zbMATH OpenOpenAlexFDO

Authors Qi Ouyang, Minghua Deng, Fangting Li, Chao Tang, Yuping Zhang, Minping Qian

Publication date 17 August 2006

Published in Physica D (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/q-bio/0605011

zbMATH Keywords

Markov chainstationary distributionprobabilistic Boolean networkcell division cycleprotein network

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Biochemistry, molecular biology (92C40) Markov chains (discrete-time Markov processes on discrete state spaces) (60J10) Cell biology (92C37)

Abstract: Biological functions in living cells are controlled by protein interaction and genetic networks. These molecular networks should be dynamically stable against various fluctuations which are inevitable in the living world. In this paper, we propose and study a stochastic model for the network regulating the cell cycle of the budding yeast. The stochasticity in the model is controlled by a temperature-like parameter $$. Our simulation results show that both the biological stationary state and the biological pathway are stable for a wide range of "temperature". There is, however, a sharp transition-like behavior at $$, below which the dynamics is dominated by noise. We also define a pseudo energy landscape for the system in which the biological pathway can be seen as a deep valley.

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Cites work

• scientific article; zbMATH DE number 3236503 (Why is no real title available?)
• Metastability of exponentially perturbed Markov chains
• Numerical and theoretical studies of noise effects in the Kauffman model
• Potential in stochastic differential equations: novel construction
• Steady-state probabilities for attractors in probabilistic Boolean networks

Cited in

(14)

• Dimension reduction of large sparse AND-NOT network models
• Two programmed replicative lifespans of \textit{Saccharomyces cerevisiae} formed by the endogenous molecular-cellular network
• Derivation and experimental comparison of cell-division probability densities
• Synchronized dynamics and non-equilibrium steady states in a stochastic yeast cell-cycle net\-work
• Superstability of the yeast cell-cycle dynamics: ensuring causality in the presence of biochemical stochasticity
• Signal propagation in small-world biological networks with weak noise
• Stochastic Petri net extension of a yeast cell cycle model
• Dynamic properties of cell-cycle and life-cycle networks in budding yeast
• Logical analysis of the budding yeast cell cycle
• Synchronization in Discrete-Time, Discrete-State Random Dynamical Systems
• Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle
• The stochastic model and metastability of the gene network
• Effects of stochasticity in models of the cell cycle: from quantized cycle times to noise-induced oscillations
• Global dynamic properties of protein networks

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