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Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
Mukesh Bansal1, Giusy Della Gatta, Diego di Bernardo
1Telethon Institute of Genetics and Medicine, Via P. Castellino 111, 80131 Naples, Italy.
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@tigem.it SUPLEMENTARY INFORMATION: Supplementary data are available at http://dibernado.tigem.it
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