A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series

  • Oliver Stegle
  • Katherine Denby
  • David L. Wild
  • Zoubin Ghahramani
  • Karsten M. Borgwardt
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5541)


Understanding the regulatory mechanisms that are responsible for an organism’s response to environmental changes is an important question 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 time points. In classification experiments our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.


Gaussian Process Reference Dataset Expectation Propagation Gaussian Process Regression Gaussian Process Model 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Oliver Stegle
    • 1
  • Katherine Denby
    • 2
  • David L. Wild
    • 2
  • Zoubin Ghahramani
    • 1
  • Karsten M. Borgwardt
    • 1
    • 3
  1. 1.University of CambridgeUK
  2. 2.University of WarwickUK
  3. 3.Max-Planck-Institutes for Developmental Biology and Biological CyberneticsTübingenGermany

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