title: Comprehensive analysis of gene-environmental interactions with temporal gene expression profiles in Pseudomonas aeruginosa.
abstract: To explore gene-environment interactions, based on temporal gene expression information, we analyzed gene and treatment information intensively and inferred interaction networks accordingly. The main idea is that gene expression reflects the response of genes to environmental factors, assuming that variations of gene expression occur under different conditions. Then we classified experimental conditions into several subgroups based on the similarity of temporal gene expression profiles. This procedure is useful because it allows us to combine diverse gene expression data as they become available, and, especially, allowing us to lay the regulatory relationships on a concrete biological basis. By estimating the activation points, we can visualize the gene behavior, and obtain a consensus gene activation order, and hence describe conditional regulatory relationships. The estimation of activation points and building of synthetic genetic networks may result in important new insights in the ongoing endeavor to understand the complex network of gene regulation.
authors.affiliation: Department of Oral Biology, Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
authors.forename: Kangmin
authors.initials: K
authors.lastname: Duan
authors.forename: William M
authors.initials: WM
authors.lastname: McCullough
authors.forename: Michael G
authors.initials: MG
authors.lastname: Surette
authors.forename: Tony
authors.initials: T
authors.lastname: Ware
authors.forename: Jiuzhou
authors.initials: J
authors.lastname: Song
mesh_terms: D030541:Databases, Genetic; D004777:Environment; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks / Q000235:genetics; D059647:Gene-Environment Interaction; D005798:Genes, Bacterial / Q000235:genetics; D017930:Genes, Reporter / Q000235:genetics; D010363:Pattern Recognition, Automated; D011550:Pseudomonas aeruginosa / Q000235:genetics*; D012984:Software; D013997:Time Factors; D015533:Transcriptional Activation / Q000235:genetics