Rasmussen, Carl Edward, De la Cruz, Bernard J., Ghahramani, Zoubin and Wild, David L.. (2009) Modeling and visualizing uncertainty in gene expression clusters using Dirichlet process mixtures. IEEE - ACM Transactions on Computational Biology and Bioinformatics, Vol.6 (No.4). pp. 615-628. ISSN 1545-5963

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Abstract

Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data, little attention has been paid to uncertainty in the results obtained. Dirichlet process mixture (DPM) models provide a nonparametric Bayesian alternative to the bootstrap approach to modeling uncertainty in gene expression clustering. Most previously published applications of Bayesian model-based clustering methods have been to short time series data. In this paper, we present a case study of the application of nonparametric Bayesian clustering methods to the clustering of high-dimensional nontime series gene expression data using full Gaussian covariances. We use the probability that two genes belong to the same cluster in a DPM model as a measure of the similarity of these gene expression profiles. Conversely, this probability can be used to define a dissimilarity measure, which, for the purposes of visualization, can be input to one of the standard linkage algorithms used for hierarchical clustering. Biologically plausible results are obtained from the Rosetta compendium of expression profiles which extend previously published cluster analyses of this data.

Item Type:	Journal Article
Subjects:	Q Science > QA Mathematics Q Science > QH Natural history > QH426 Genetics
Divisions:	Faculty of Science > Centre for Systems Biology
Library of Congress Subject Headings (LCSH):	Bioinformatics, Gaussian distribution, Stochastic processes, Statistics -- Data processing, Monte Carlo method, Probability measures, Bayesian statistical decision theory
Journal or Publication Title:	IEEE - ACM Transactions on Computational Biology and Bioinformatics
Publisher:	IEEE
ISSN:	1545-5963
Date:	October 2009
Volume:	Vol.6
Number:	No.4
Page Range:	pp. 615-628
Identification Number:	10.1109/TCBB.2007.70269
Status:	Peer Reviewed
Access rights to Published version:	Open Access
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URI:	http://wrap.warwick.ac.uk/id/eprint/2694

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