Reverse engineering gene regulatory networks using approximate Bayesian computation

DOI10.1007/S11222-011-9309-1zbMATH Open1252.62113arXiv1109.1402OpenAlexW2008737153MaRDI QIDQ693367FDOQ693367

Authors: Andrea Rau, Florence Jaffrezic, Jean-Louis Foulley Error creating thumbnail:

Publication date: 7 December 2012

Published in: Statistics and Computing (Search for Journal in Brave)

Abstract: Gene regulatory networks are collections of genes that interact with one other and with other substances in the cell. By measuring gene expression over time using high-throughput technologies, it may be possible to reverse engineer, or infer, the structure of the gene network involved in a particular cellular process. These gene expression data typically have a high dimensionality and a limited number of biological replicates and time points. Due to these issues and the complexity of biological systems, the problem of reverse engineering networks from gene expression data demands a specialized suite of statistical tools and methodologies. We propose a non-standard adaptation of a simulation-based approach known as Approximate Bayesian Computing based on Markov chain Monte Carlo sampling. This approach is particularly well suited for the inference of gene regulatory networks from longitudinal data. The performance of this approach is investigated via simulations and using longitudinal expression data from a genetic repair system in Escherichia coli.

Full work available at URL: https://arxiv.org/abs/1109.1402

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zbMATH Keywords

Markov chain Monte Carlolongitudinal gene expressions

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Computational methods for problems pertaining to biology (92-08) Cell biology (92C37)

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Cited In (3)

• Computational Science and Its Applications – ICCSA 2004
• Reverse Engineering Galactose Regulation in Yeast through Model Selection
• Statistical Reconstruction of Transcription Factor Activity Using Michaelis–Menten Kinetics

Uses Software

• ebdbNet

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