title: Construction of regulatory networks using expression time-series data of a genotyped population.
abstract: The inference of regulatory and biochemical networks from large-scale genomics data is a basic problem in molecular biology. The goal is to generate testable hypotheses of gene-to-gene influences and subsequently to design bench experiments to confirm these network predictions. Coexpression of genes in large-scale gene-expression data implies coregulation and potential gene-gene interactions, but provide little information about the direction of influences. Here, we use both time-series data and genetics data to infer directionality of edges in regulatory networks: time-series data contain information about the chronological order of regulatory events and genetics data allow us to map DNA variations to variations at the RNA level. We generate microarray data measuring time-dependent gene-expression levels in 95 genotyped yeast segregants subjected to a drug perturbation. We develop a Bayesian model averaging regression algorithm that incorporates external information from diverse data types to infer regulatory networks from the time-series and genetics data. Our algorithm is capable of generating feedback loops. We show that our inferred network recovers existing and novel regulatory relationships. Following network construction, we generate independent microarray data on selected deletion mutants to prospectively test network predictions. We demonstrate the potential of our network to discover de novo transcription-factor binding sites. Applying our construction method to previously published data demonstrates that our method is competitive with leading network construction algorithms in the literature.
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
authors.forename: Ka Yee
authors.initials: KY
authors.lastname: Yeung
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Dombek
authors.forename: Kenneth
authors.initials: K
authors.lastname: Lo
authors.forename: John E
authors.initials: JE
authors.lastname: Mittler
authors.forename: Jun
authors.initials: J
authors.lastname: Zhu
authors.forename: Eric E
authors.initials: EE
authors.lastname: Schadt
authors.forename: Roger E
authors.initials: RE
authors.lastname: Bumgarner
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Raftery
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D001665:Binding Sites / Q000235:genetics; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D014644:Genetic Variation; D016015:Logistic Models; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008954:Models, Biological; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics; D015003:Yeasts
chemical_list: D014157:Transcription Factors
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