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


Anatomy & Physiology: Current Research

Author(s): Bansal M, Della Gatta G, di Bernardo D

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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 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: [email protected] SUPLEMENTARY INFORMATION: Supplementary data are available at This article was published in Bioinformatics and referenced in Anatomy & Physiology: Current Research

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