Bioinformatics Original Paper Inference of Gene Regulatory Networks and Compound Mode of Action from Time Course Gene Expression Profiles

Motivation: Time series expression experiments are an increasingly popular method for studying a wide range of biological systems. Here wedevelopedanalgorithmthatcan infer the localnetworkofgene–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 theDNA-damage response pathway (SOS pathway) in the bacteria E. coli. Contact: dibernardo@tigem.it Supplementary information: Supplementary data are available at http://dibernado.tigem.it

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