A model of gene expression based on random dynamical systems reveals modularity properties of gene regulatory networks
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Publication:299391
DOI10.1016/J.MBS.2016.03.008zbMATH Open1341.92044arXiv1309.0765OpenAlexW1680277005WikidataQ50675999 ScholiaQ50675999MaRDI QIDQ299391FDOQ299391
Authors: Fernando Antoneli, Renata C. Ferreira, Marcelo R. S. Briones 
Publication date: 22 June 2016
Published in: Mathematical Biosciences (Search for Journal in Brave)
Abstract: Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node is modeled by a RDS. The main virtues of this approach are the following: (i) it provides a natural way to obtain arbitrarily large networks by coupling together simple basic pieces, thus revealing the modularity of regulatory networks; (ii) the assumptions about the stochastic processes used in the modeling are fairly general, in the sense that the only requirement is stationarity; (iii) there is a well developed mathematical theory, which is a blend of smooth dynamical systems theory, ergodic theory and stochastic analysis that allows one to extract relevant dynamical and statistical information without solving the system; (iv) one may obtain the classical rate equations form the corresponding stochastic version by averaging the dynamic random variables (small noise limit). It is important to emphasize that unlike the deterministic case, where coupling two equations is a trivial matter, coupling two RDS is non-trivial, specially in our case, where the coupling is performed between a state variable of one gene and the switching stochastic process of another gene and, hence, it is not a priori true that the resulting coupled system will satisfy the definition of a random dynamical system. We shall provide the necessary arguments that ensure that our coupling prescription does indeed furnish a coupled regulatory network of random dynamical systems. Finally, the fact that classical rate equations are the small noise limit of our stochastic model ensures that any validation or prediction made on the basis of the classical theory is also a validation or prediction of our model.
Full work available at URL: https://arxiv.org/abs/1309.0765
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gene expressioncoupled stochastic systemsgene regulatory network (GRN)random dynamical systems (RDS)
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- RANDOM SHUFFLING OF SWITCHING PARAMETERS IN A MODEL OF GENE EXPRESSION REGULATORY NETWORK
- Mathematical aspects of the regulation of gene transcription by promoters
- Stability and structural properties of gene regulation networks with coregulation rules
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