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


BACKGROUND
dibernardo@tigem.it SUPLEMENTARY INFORMATION: Supplementary data are available at http://dibernado.tigem.it
Bansal
Mukesh
M
Telethon Institute of Genetics and Medicine, Via P. Castellino 111, 80131 Naples, Italy.
Della Gatta
Giusy
G
di Bernardo
Diego
D
D000465:Algorithms; D001499:Bayes Theorem; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D015233:Models, Statistical; D013997:Time Factors