title: Analysis of host response to bacterial infection using error model based gene expression microarray experiments.
abstract: A key step in the analysis of microarray data is the selection of genes that are differentially expressed. Ideally, such experiments should be properly replicated in order to infer both technical and biological variability, and the data should be subjected to rigorous hypothesis tests to identify the differentially expressed genes. However, in microarray experiments involving the analysis of very large numbers of biological samples, replication is not always practical. Therefore, there is a need for a method to select differentially expressed genes in a rational way from insufficiently replicated data. In this paper, we describe a simple method that uses bootstrapping to generate an error model from a replicated pilot study that can be used to identify differentially expressed genes in subsequent large-scale studies on the same platform, but in which there may be no replicated arrays. The method builds a stratified error model that includes array-to-array variability, feature-to-feature variability and the dependence of error on signal intensity. We apply this model to the characterization of the host response in a model of bacterial infection of human intestinal epithelial cells. We demonstrate the effectiveness of error model based microarray experiments and propose this as a general strategy for a microarray-based screening of large collections of biological samples.
authors.affiliation: School of Biosciences, The University of Birmingham Birmingham B15 2TT, UK.
authors.forename: Dov J
authors.initials: DJ
authors.lastname: Stekel
authors.forename: Donatella
authors.initials: D
authors.lastname: Sarti
authors.forename: Victor
authors.initials: V
authors.lastname: Trevino
authors.forename: Lihong
authors.initials: L
authors.lastname: Zhang
authors.forename: Mike
authors.initials: M
authors.lastname: Salmon
authors.forename: Chris D
authors.initials: CD
authors.lastname: Buckley
authors.forename: Mark
authors.initials: M
authors.lastname: Stevens
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Pallen
authors.forename: Charles
authors.initials: C
authors.lastname: Penn
authors.forename: Francesco
authors.initials: F
authors.lastname: Falciani
mesh_terms: D001424:Bacterial Infections / Q000235:genetics* / Q000378:metabolism; D004927:Escherichia coli Infections / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D015233:Models, Statistical; D016328:NF-kappa B / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D016328:NF-kappa B