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

115 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

Fingerprint

Gene Regulatory Networks
Gene Regulatory Network
Time Series Data
Time series
Genes
Genetic Regulatory Networks
Drosophilidae
Gene
Probabilistic Modeling
Reverse Genetics
Dynamic Bayesian Networks
Boolean Networks
Data Fitting
Genetic Network
Gene Expression Profile
Excel
Muscle Development
Reverse engineering
Reverse Engineering
Bayesian networks

ASJC Scopus subject areas

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

Cite this

Inferring gene regulatory networks from time series data using the minimum description length principle. / Zhao, Wentao; Serpedin, Erchin; Dougherty, Edward R.

In: Bioinformatics, Vol. 22, No. 17, 01.09.2006, p. 2129-2135.

Research output: Contribution to journalArticle

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