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Statistics and Computing

, Volume 22, Issue 6, pp 1257–1271 | Cite as

Reverse engineering gene regulatory networks using approximate Bayesian computation

  • Andrea Rau
  • Florence Jaffrézic
  • Jean-Louis Foulley
  • R. W. Doerge
Article

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.

Keywords

Approximate Bayesian computation Gene regulatory networks Longitudinal gene expression Markov chain Monte Carlo 

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Andrea Rau
    • 1
    • 2
  • Florence Jaffrézic
    • 2
  • Jean-Louis Foulley
    • 2
  • R. W. Doerge
    • 1
    • 3
  1. 1.Department of StatisticsPurdue UniversityWest LafayetteUSA
  2. 2.UMR 1313 GABIINRAJouy-en-JosasFrance
  3. 3.Department of AgronomyPurdue UniversityWest LafayetteUSA

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