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

cell division cycleMarkov chainprobabilistic Boolean networkprotein networkstationary distribution

Mathematics Subject Classification ID

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

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.

Review text

The gene-protein interaction in the four-phase cell division cycle is modeled by a probabilistic Boolean network for a yeast cell. The interaction is described by a graph with 11 nodes. Each node corresponds to some protein or protein complex. The nodes can be in active (1) or inactive (0) state. The interaction is represented by oriented vertexes which correspond to activation (positive interaction), repression (negative interaction) and self degradation (loop vertexes). The cell state is described by a combination of node states i.e., there are \(2^{11}\) different cell states. The transitions between the cell states are described by a Markov chain in which transitions for node states are conditionally independent given the previous cell state. Their probabilities are described by a kind of logistic function. The authors investigate the stationary distribution of the obtained Markov chain for different values of parameters via simulations. It is demonstrated that for low levels of noise the biological pathway is stable.

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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)

• Logical analysis of the budding yeast cell cycle
• Signal propagation in small-world biological networks with weak noise
• Stochastic Petri net extension of a yeast cell cycle model
• Effects of stochasticity in models of the cell cycle: from quantized cycle times to noise-induced oscillations
• Superstability of the yeast cell-cycle dynamics: ensuring causality in the presence of biochemical stochasticity
• 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
• Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle
• Dimension reduction of large sparse AND-NOT network models
• Synchronization in Discrete-Time, Discrete-State Random Dynamical Systems
• Dynamic properties of cell-cycle and life-cycle networks in budding yeast
• The stochastic model and metastability of the gene network
• Global dynamic properties of protein networks

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