Inferring gene regulatory networks from time series data using the minimum description length principle

Wentao Zhao, Erchin Serpedin, Edward R. Dougherty

Research output: Contribution to journalArticle

116 Citations (Scopus)

Abstract

Motivation: A central question in reverse engineering of genetic networks consists in determining the dependencies and regulating relationships among genes. This paper addresses the problem of inferring genetic regulatory networks from time-series gene-expression profiles. By adopting a probabilistic modeling framework compatible with the family of models represented by dynamic Bayesian networks and probabilistic Boolean networks, this paper proposes a network inference algorithm to recover not only the direct gene connectivity but also the regulating orientations. Results: Based on the minimum description length principle, a novel network inference algorithm is proposed that greatly shrinks the search space for graphical solutions and achieves a good trade-off between modeling complexity and data fitting. Simulation results show that the algorithm achieves good performance in the case of synthetic networks. Compared with existing state-of-the-art results in the literature, the proposed algorithm exceptionally excels in efficiency, accuracy, robustness and scalability. Given a time-series dataset for Drosophila melanogaster, the paper proposes a genetic regulatory network involved in Drosophila's muscle development.

Original languageEnglish
Pages (from-to)2129-2135
Number of pages7
JournalBioinformatics
Volume22
Issue number17
DOIs
Publication statusPublished - 1 Sep 2006
Externally publishedYes

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ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

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