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Bioinformatics Advance Access published online on January 17, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl003
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 16, 2005
Revised November 22, 2005
Accepted January 12, 2006

Article

Inference of gene regulatory networks and compound mode of action from time course gene expression profiles

Mukesh Bansal 1, Giusy Della Gatta 2, and Diego di Bernardo 1 *

1 Telethon Institute of Genetics and Medicine, Via P. Castellino 111, 80131 Naples, Italy; European School of Molecular Medicine (SEMM), Naples, Italy
2 Telethon Institute of Genetics and Medicine, Via P. Castellino 111, 80131 Naples, Italy; Seconda Universita degli Studi di Napoli, Naples, Italy

* To whom correspondence should be addressed.
Diego di Bernardo, E-mail: dibernardo{at}tigem.it


  Abstract

Motivation: Time series expression experiments are an increasingly popular method for studying a wide range of biological systems. Here we developed an algorithm that can infer the local network of gene-gene interactions surrounding a gene of interest. This is achieved by a perturbation of the gene of interest and subsequently measuring the gene expression profiles at multiple time points. We applied this algorithm to computer simulated data and to experimental data on a 9 gene network in Escherichia coli.

Results: In this paper we show that it is possible to recover the gene regulatory network from a time series data of gene expression following a perturbation to the cell. We show this both on simulated data and on a nine genes subnetwork part of the DNA-damage response pathway (SOS pathway) in the bacteria Escherichia coli.

Associate Editor: Satoru Miyano
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