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          Institute: MPI für Entwicklungsbiologie     Collection: Abteilung 6 - Molecular Biology (D. Weigel)     Display Documents



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ID: 561638.0, MPI für Entwicklungsbiologie / Abteilung 6 - Molecular Biology (D. Weigel)
A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series
Authors:Stegle, O.; Denby, K. J.; Cooke, E. J.; Wild, D. L.; Ghahramani, Z.; Borgwardt, K. M.
Date of Publication (YYYY-MM-DD):2010-03
Title of Journal:Journal of Computational Biology
Volume:17
Issue / Number:3
Start Page:355
End Page:367
Review Status:not specified
Audience:Not Specified
Abstract / Description:Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answer the question whether a gene is differentially expressed, they do not explicitly address the question when a gene is differentially expressed, although this information may provide insights into the course and causal structure of regulatory programs. In this article, we propose a two-sample test for identifying intervals of differential gene expression in microarray time series. Our approach is based on Gaussian process regression, can deal with arbitrary numbers of replicates, and is robust with respect to outliers. We apply our algorithm to study the response of Arabidopsis thaliana genes to an infection by a fungal pathogen using a microarray time series dataset covering 30,336 gene probes at 24 observed time points. In classification experiments, our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.
Free Keywords:differential gene expression; gaussian processes; microarray time series; gaussian process; regression; profiles; networks
External Publication Status:published
Document Type:Article
Affiliations:MPI für Entwicklungsbiologie/Abteilung 6 - Molekulare Biologie (Detlef Weigel)
External Affiliations:Max Planck Inst Biol Cybernet, Interdept Bioinformat Grp, Max Planck Inst Dev Biol, Spemannstr 38, D-72076 Tubingen, Germany Max Planck Inst Biol Cybernet, Interdept Bioinformat Grp, Max Planck Inst Dev Biol, Spemannstr 38, D-72076 Tubingen, Germany Max Planck Inst Biol Cybernet, Interdept Bioinformat Grp, Max Planck Inst Dev Biol, D-72076 Tubingen, Germany Warwick HRI & Warwick Syst Biol, Wellesbourne, Warks, England Univ Warwick, MOAC Doctoral Training Ctr, Coventry CV4 7AL, W Midlands, England Univ Warwick, Warwick Syst Biol Ctr, Coventry CV4 7AL, W Midlands, England Univ Cambridge, Dept Engn, Cambridge CB2 1PZ, England %G English
Identifiers:ISSN:1066-5277 %R DOI 10.1089/cmb.2009.0175 [ID No:1]
ISI:000279271600011 [ID No:2]
ISI:000279271600011 [ID No:3]
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