PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series
Oliver Stegle, Katherine Denby, Zoubin Ghahramani, David Wild and Karsten Borgwardt
RECOMB 2009 2008.

Abstract

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 {\it whether} a gene is differentially expressed, they do not explicitly address the question {\it 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 {\it 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 {\it 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.

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EPrint Type:Article
Project Keyword:Project Keyword UNSPECIFIED
Subjects:Learning/Statistics & Optimisation
ID Code:4954
Deposited By:Karsten Borgwardt
Deposited On:24 March 2009