The Journal of Biological Physics and Chemistry


Volume 7, Number 2, p.p. 37-43

Checking consistency between expression data and large scale regulatory networks: a case study

Carito Guziolowski,1,* Philippe Veber,1 Michel Le Borgne,2 Ovidiu Radulescu1,3 and Anne Siegel4

1IRISA, INRIA, Rennes, France
2IRISA, Université de Rennes 1, Rennes, France
3IRMAR, Université de Rennes 1, Rennes, France
4IRISA, CNRS, Rennes, France

We have previously proposed a qualitative approach to check the compatibility between models of interactions and gene expression data. The purpose of the present work is to validate this methodology in a real-life setting. We study the response of the E. coli regulatory network to nutritional stress, and compare it to publicly available DNA microarray experiments. We show how the incompatibilities we found reveal missing interactions in the network, as well as observations in contradiction with some of available literature.

Keywords: qualitative modeling, systems biology, transcriptional networks

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