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Gene Regulatory Networks: A Primer in Biological Processes and Statistical Modelling

  • Olivia Angelin-Bonnet
  • Patrick J. Biggs
  • Matthieu VignesEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1883)

Abstract

Modelling gene regulatory networks requires not only a thorough understanding of the biological system depicted, but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to familiarize the reader with the biological processes and molecular factors at play in the process of gene expression regulation. We first describe the different interactions controlling each step of the expression process, from transcription to mRNA and protein decay. In the second section, we provide statistical tools to accurately represent this biological complexity in the form of mathematical models. Among other considerations, we discuss the topological properties of biological networks, the application of deterministic and stochastic frameworks, and the quantitative modelling of regulation. We particularly focus on the use of such models for the simulation of expression data that can serve as a benchmark for the testing of network inference algorithms.

Key words

Gene expression regulation Regulatory network modelling Systems biology data simulation Post-transcriptional regulation Post-translational regulation Deterministic and stochastic models Molecular regulatory interactions 

Notes

Acknowledgements

We are very grateful for enriching discussions and suggestions on this manuscript made by Samantha Baldwin and Susan Thomson (Plant and Food Research, Lincoln, New Zealand). We would like to thank the reviewers of this chapter for their useful comments. MV was partly supported by a visiting professor scholarship from Aix-Marseille University.

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Copyright information

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Authors and Affiliations

  • Olivia Angelin-Bonnet
    • 1
    • 2
  • Patrick J. Biggs
    • 1
    • 2
  • Matthieu Vignes
    • 1
    • 2
    Email author
  1. 1.Institute of Fundamental SciencesPalmerston NorthNew Zealand
  2. 2.School of Veterinary ScienceMassey UniversityPalmerston NorthNew Zealand

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