Stochastic model of yeast cell-cycle network

DOI10.1016/J.PHYSD.2006.05.009zbMATH Open1100.92017arXivq-bio/0605011OpenAlexW2117398609MaRDI QIDQ2500679FDOQ2500679

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)

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.

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

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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)

Cites Work

• Title not available (Why is that?)
• Potential in stochastic differential equations: novel construction
• Steady-state probabilities for attractors in probabilistic Boolean networks
• Metastability of exponentially perturbed Markov chains
• Numerical and theoretical studies of noise effects in the Kauffman model

Cited In (11)

• Derivation and experimental comparison of cell-division probability densities
• Dynamic properties of cell-cycle and life-cycle networks in budding yeast
• Logical analysis of the budding yeast cell cycle
• The stochastic model and metastability of the gene network
• Dimension reduction of large sparse AND-NOT network models
• Synchronization in Discrete-Time, Discrete-State Random Dynamical Systems
• Stochastic Petri net extension of a yeast cell cycle model
• Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle
• Two programmed replicative lifespans of \textit{Saccharomyces cerevisiae} formed by the endogenous molecular-cellular network
• Global dynamic properties of protein networks
• Synchronized dynamics and non-equilibrium steady states in a stochastic yeast cell-cycle net\-work

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