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

Bioinformatics. 2006 Sep 1;22(17):2129-35. doi: 10.1093/bioinformatics/btl364. Epub 2006 Jul 15.


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.

Availability: Available from the authors upon request.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Animals
  • Computer Simulation
  • Drosophila Proteins / genetics
  • Drosophila Proteins / metabolism*
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / metabolism*
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation / physiology*
  • Models, Biological
  • Oligonucleotide Array Sequence Analysis / methods*
  • Signal Transduction / physiology*
  • Time Factors


  • Drosophila Proteins