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Analyzing and reconstructing gene regulatory networks

Part 3. Proteomics

3.8. Systems Biology

Specialist Review

  1. J. Jeremy Rice,
  2. Aaron Kershenbaum,
  3. Gustavo Stolovitzky

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g308212

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Rice, J. J., Kershenbaum, A. and Stolovitzky, G. 2005. Analyzing and reconstructing gene regulatory networks. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.8:109.

Author Information

  1. IBM T.J. Watson Research Center, Yorktown Heights, NY, USA

Publication History

  1. Published Online: 15 APR 2005

Abstract

The study of networks is becoming an increasingly important area of biological research. This chapter starts with a general discussion of network properties, and then focuses on the transcriptional control network of Escherichia coli, a gene regulatory network that is better characterized than in most other organisms. This network is analyzed in terms of distinct layers that show short paths from higher, input to lower, output levels. This structure suggests that short temporal delays are favored over additional information integration that might be achieved with more levels of processing. Repeating structures, termed motifs, were discovered including triangle-, square-, and tree-shaped motifs. In an example shown, discovered motifs suggest that functional modules may be inferred from such topological analyses. Other topological structures such as redundant pathways and negative feedback loops are not found, perhaps indicating that simple feed-forward designs are favored over more complex systems that might improve cellular robustness. Current gene regulatory networks are reconstructed by combining data from many experiments and many labs using hypothesis-driven approaches, but there is a growing effort to infer biological networks from high-throughput and genome-wide data sets. While sufficient data is generally lacking for fully detailed kinetic reconstructions, efforts to reconstruct network topology have shown promise. We review some of these reconstruction methods in light of an eventual goal of reconstructing whole regulatory networks.

Keywords:

  • networks;
  • topology;
  • transcriptional regulation;
  • gene regulation;
  • network inference;
  • reconstruction;
  • pathways;
  • gene expression data;
  • E. coli