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

DOI10.1016/J.JTBI.2009.11.017MaRDI QIDQ1715328zbMATH OpenOpenAlexWikidataFDO

Authors Berkin Malkoç, Duygu Balcan, Ayşe Erzan

Publication date 4 February 2019

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

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

zbMATH Keywords

combinatoricsemergencesystems biologystochastic modeling

Mathematics Subject Classification ID

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

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.

Recommendations

• Gene regulatory networks: a discrete model of dynamics and topological evolution
• Inferring the topology of gene regulatory networks: an algebraic approach to reverse engineering
• scientific article; zbMATH DE number 5032055
• Research on modeling of genetic networks based on information measurement
• A survey of models for inference of gene regulatory networks
• The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks

Cites work

• scientific article; zbMATH DE number 3150484 (Why is no real title available?)
• scientific article; zbMATH DE number 3168330 (Why is no real title available?)
• scientific article; zbMATH DE number 1179517 (Why is no real title available?)
• Analytical solution of a stochastic content-based network model
• Bioinformatic principles underlying the information content of transcription factor binding sites
• Content-based networks: A pedagogical overview
• Emergence of Scaling in Random Networks
• Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization.
• Long- and short-range correlations in genome organization
• Mersenne twister
• Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics
• Statistical mechanics of complex networks
• Theory of probability and random processes.

Cited in

(1)

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

Describes a project that uses

Uses Software

• FANMOD
• RegulonDB
• MersenneTwister

This page was built for publication: Information content based model for the topological properties of the gene regulatory network of \textit{Escherichia coli}

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q1715328)