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

Stegle, O., Denby, K., Wild, D., Ghahramani, Z., & Borgwardt, K. (2009). A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. In S. Batzoglou (Ed.), Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009, Tucson, AZ, USA, May 18-21, 2009 (pp. 201-216). Berlin, Germany: Springer.

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 Creators:
Stegle, O, Author              
Denby , K, Author
Wild, Dl, Author
Ghahramani, Z, Author
Borgwardt, KM1, 2, Author              
Affiliations:
1Former Research Group Machine Learning and Computational Biology, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_2528696              
2Max Planck Institute for Biological Cybernetics, Max Planck Society, Spemannstrasse 38, 72076 Tübingen, DE, ou_1497794              

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 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 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.

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 Dates: 2009-05
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1007/978-3-642-02008-7_14
BibTex Citekey: 5665
 Degree: -

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Title: 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009)
Place of Event: Tucson, AZ, USA
Start-/End Date: 2009-05-18 - 2009-05-21

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Title: Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009, Tucson, AZ, USA, May 18-21, 2009
Source Genre: Proceedings
 Creator(s):
Batzoglou, S, Editor
Affiliations:
-
Publ. Info: Berlin, Germany : Springer
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: 201 - 216 Identifier: ISBN: 978-3-642-02008-7

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Title: Lecture Notes in Computer Science
Source Genre: Series
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Pages: - Volume / Issue: 5541 Sequence Number: - Start / End Page: - Identifier: -