Inference of gene networks from temporal gene expression profiles.
Genes interact with each other in complex networks that enable the processing of information and the metabolism of nutrients inside the cell. A novel inference algorithm based on linear ordinary differential equations is proposed. The algorithm can infer the local network of gene-gene interactions surrounding a gene of interest from time-series gene expression profiles. The performance of the algorithm has been tested on in silico simulated gene expression data and on a nine gene subnetwork part of the DNA-damage response pathway (SOS pathway) in the bacteria Escherichia coli. This approach can infer regulatory interactions even when only a small number of measurements is available.
Bansal
M
M
Telethon Institute of Genetics and Medicine, Via P. Castellino 111, Naples 80131, Italy. bansal@tigem.it
di Bernardo
D
D
D003198:Computer Simulation; D004926:Escherichia coli / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D013014:SOS Response, Genetics / Q000502:physiology*; D015398:Signal Transduction / Q000502:physiology*; D013997:Time Factors
D029968:Escherichia coli Proteins