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A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series

2009

Conference Paper

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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.

Author(s): Stegle, O. and Denby, K. and Wild, DL. and Ghahramani, Z. and Borgwardt, KM.
Book Title: Research in Computational Molecular Biology
Journal: Research in Computational Molecular Biology: 13th Annual International Conference (RECOMB 2009)
Pages: 201-216
Year: 2009
Month: May
Day: 0
Editors: Batzoglou, S.
Publisher: Springer

Department(s): Empirical Inference
Bibtex Type: Conference Paper (inproceedings)

DOI: 10.1007/978-3-642-02008-7_14
Event Name: 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009)
Event Place: Tucson, AZ, USA

Address: Berlin, Germany
Digital: 0
ISBN: 978-3-642-02008-7
Language: en
Organization: Max-Planck-Gesellschaft
School: Biologische Kybernetik

Links: Web

BibTex

@inproceedings{5665,
  title = {A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series},
  author = {Stegle, O. and Denby, K. and Wild, DL. and Ghahramani, Z. and Borgwardt, KM.},
  journal = {Research in Computational Molecular Biology: 13th Annual International Conference (RECOMB 2009)},
  booktitle = {Research in Computational Molecular Biology},
  pages = {201-216},
  editors = {Batzoglou, S. },
  publisher = {Springer},
  organization = {Max-Planck-Gesellschaft},
  school = {Biologische Kybernetik},
  address = {Berlin, Germany},
  month = may,
  year = {2009},
  month_numeric = {5}
}