Abstract

Reverse engineering algorithms (REAs) aim at using gene expression data to reconstruct interactions in regulatory genetic networks. This may help to understand the basis of gene regulation, the core task of functional genomics. Collecting data for a number of environmental conditions is necessary to reengineer even the smallest regulatory networks with reasonable confidence. We systematically tested the requirements for the experimental design necessary for ranking alternative hypotheses about the structure of a given regulatory network. A genetic algorithm (GA) was used to explore the parameter space of a multistage discrete genetic network model with fixed connectivity and number of states per node. Our results show that it is not necessary to determine all parameters of the genetic network in order to rank hypotheses. The ranking process is easier the more experimental environmental conditions are used for the data set. During the ranking, the number of fixed parameters increases with the number of environmental conditions, while some errors in the hypothetical network structure may pass undetected, due to a maintained dynamical behaviour. (C) 2002 Elsevier Science Ireland Ltd. All rights reserved

Keywords

Reverse engineering; Genetic regulatory networks; Genetic algorithm; Gene expression data; Experimental design

Published in

BioSystems
2002, Volume: 66, number: 1-2, pages: 31-41
Publisher: ELSEVIER SCI LTD

SLU Authors

• Liljenström, Hans

  • Department of Energy and Technology, Swedish University of Agricultural Sciences
    
  • Agora for Biosystems

Publication identifier

DOI: https://doi.org/10.1016/S0303-2647(02)00019-9

Permanent link to this page (URI)

https://res.slu.se/id/publ/1960