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Deposited research article

Reverse engineering of gene regulatory networks: a finite state linear model

Alvis Brazma and Thomas Schlitt*

Author Affiliations

EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom

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Genome Biology 2003, 4:P5 doi:10.1186/gb-2003-4-6-p5

Published: 29 April 2003

Abstract

We propose a new model for describing gene regulatory networks that can capture discrete (Boolean) and continuous (differential) aspects of gene regulation. After giving some illustrations of the model, we study the problem of the reverse engineering of such networks, i.e., how to construct a network from gene expression data. We prove that for our model there exists an algorithm finding a network compatible with the given data. We demonstrate the model by simulating lambda-phage. We also describe some generalizations of the model, discuss their relevance to the real-world gene networks and formulate a number of open problems.

Keywords:
gene regulation; regulatory networks; regulatory circuits; dynamic systems; finite state automata; reverse engineering