comprehensive analysis of gene-environmental interactions with temporal gene expression profiles in pseudomonas aeruginosa综合分析gene-environmental交互时序基因表达谱在铜绿假单胞菌.pdfVIP

Comprehensive Analysis of Gene-Environmental Interactions with Temporal Gene Expression Profiles in Pseudomonas aeruginosa 1 2 2 3 4 Kangmin Duan , William M. McCullough , Michael G. Surette , Tony Ware , Jiuzhou Song * 1 Department of Oral Biology; Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada, 2 Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada, 3 Department of Mathematics and Statistics, University of Calgary, Calgary, Canada, 4 Department of Animal and Avian Science, Animal Science Center, University of Maryland, College Park, Maryland, United States of America 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 understan