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Bioinformatics Advance Access originally published online on January 17, 2006
Bioinformatics 2006 22(7):815-822; 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

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

Mukesh Bansal 1,2, Giusy Della Gatta 1,3 and Diego di Bernardo 1,2,*

1Telethon Institute of Genetics and Medicine Via P. Castellino 111, 80131 Naples, Italy
2European School of Molecular Medicine (SEMM) Naples, Italy
3Seconda Universita degli Studi di Napoli Naples, Italy

*To whom correspondence should be addressed.

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 nine 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 gene subnetwork part of the DNA-damage response pathway (SOS pathway) in the bacteria E. coli.

Contact: dibernardo{at}tigem.it

Supplementary information: Supplementary data are available at http://dibernado.tigem.it

Received on June 16, 2005; revised on November 22, 2005; accepted on January 12, 2006

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