Information content based model for the topological properties of the gene regulatory network of \textit{Escherichia coli}

DOI10.1016/J.JTBI.2009.11.017zbMATH Open1406.92248arXiv0912.5381OpenAlexW2124590058WikidataQ44712230 ScholiaQ44712230MaRDI QIDQ1715328FDOQ1715328

Duygu Balcan, Ayşe Erzan, Berkin Malkoç

Publication date: 4 February 2019

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: Gene regulatory networks (GRN) are being studied with increasingly precise quantitative tools and can provide a testing ground for ideas regarding the emergence and evolution of complex biological networks. We analyze the global statistical properties of the transcriptional regulatory network of the prokaryote Escherichia coli, identifying each operon with a node of the network. We propose a null model for this network using the content-based approach applied earlier to the eukaryote Saccharomyces cerevisiae. (Balcan et al., 2007) Random sequences that represent promoter regions and binding sequences are associated with the nodes. The length distributions of these sequences are extracted from the relevant databases. The network is constructed by testing for the occurrence of binding sequences within the promoter regions. The ensemble of emergent networks yields an exponentially decaying in-degree distribution and a putative power law dependence for the out-degree distribution with a flat tail, in agreement with the data. The clustering coefficient, degree-degree correlation, rich club coefficient and k-core visualization all agree qualitatively with the empirical network to an extent not yet achieved by any other computational model, to our knowledge. The significant statistical differences can point the way to further research into non-adaptive and adaptive processes in the evolution of the E. coli GRN.

Full work available at URL: https://arxiv.org/abs/0912.5381

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zbMATH Keywords

combinatoricsemergencesystems biologystochastic modeling

Mathematics Subject Classification ID

Applications of graph theory (05C90) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Cites Work

• Mersenne twister
• Statistical mechanics of complex networks
• Emergence of Scaling in Random Networks
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• Theory of probability and random processes.
• Long- and short-range correlations in genome organization
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• Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics
• Bioinformatic principles underlying the information content of transcription factor binding sites
• Analytical solution of a stochastic content-based network model
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Cited In (1)

• Gene regulatory networks: a discrete model of dynamics and topological evolution

Uses Software

• MersenneTwister
• RegulonDB
• FANMOD

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