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Neural network model of gene expression

JIÍ VOHRADSK

Institute of Microbiology, CAS,142 20 Prague, Czech Republic

¹Correspondence: Institute of Microbiology, CAS, Videská 1083, CZ-14220 Prague, Czech Republic. E-mail: vohr{at}biomed.cas.cz

Many natural processes consist of networks of interacting elements that, over time, affect each other’s state. Their dynamics depend on the pattern of connections and the updating rules for each element. Genomic regulatory networks are networks of this sort. In this paper we use artificial neural networks as a model of the dynamics of gene expression. The significance of the regulatory effect of one gene product on the expression of other genes of the system is defined by a weight matrix. The model considers multigenic regulation including positive and/or negative feedback. The process of gene expression is described by a single network and by two linked networks where transcription and translation are modeled independently. Each of these processes is described by different network controlled by different weight matrices. Methods for computing the parameters of the model from experimental data are discussed. Results computed by means of the model are compared with experimental observations. Generalization to a ‘black box’ concept, where the molecular processes occurring in the cell are considered as signal processing units forming a global regulatory network, is discussed.—Vohradsk, J. Neural network model of gene expression.

Key Words: genetic network • regulation of gene expression • mathematical modeling

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