Bioinformatics Advance Access originally published online on November 22, 2007
Bioinformatics 2008 24(2):176-183; doi:10.1093/bioinformatics/btm562
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Analysis of a Gibbs sampler method for model-based clustering of gene expression data
1Department of Plant Systems Biology, VIB and 2Department of Molecular Genetics, UGent, Technologiepark 927, 9052 Gent, Belgium
*To whom correspondence should be addressed.
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Abstract |
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Motivation: Over the last decade, a large variety of clustering algorithms have been developed to detect coregulatory relationships among genes from microarray gene expression data. Model-based clustering approaches have emerged as statistically well-grounded methods, but the properties of these algorithms when applied to large-scale data sets are not always well understood. An in-depth analysis can reveal important insights about the performance of the algorithm, the expected quality of the output clusters, and the possibilities for extracting more relevant information out of a particular data set.
Results: We have extended an existing algorithm for model-based clustering of genes to simultaneously cluster genes and conditions, and used three large compendia of gene expression data for Saccharomyces cerevisiae to analyze its properties. The algorithm uses a Bayesian approach and a Gibbs sampling procedure to iteratively update the cluster assignment of each gene and condition. For large-scale data sets, the posterior distribution is strongly peaked on a limited number of equiprobable clusterings. A GO annotation analysis shows that these local maxima are all biologically equally significant, and that simultaneously clustering genes and conditions performs better than only clustering genes and assuming independent conditions. A collection of distinct equivalent clusterings can be summarized as a weighted graph on the set of genes, from which we extract fuzzy, overlapping clusters using a graph spectral method. The cores of these fuzzy clusters contain tight sets of strongly coexpressed genes, while the overlaps exhibit relations between genes showing only partial coexpression.
Availability: GaneSh, a Java package for coclustering, is available under the terms of the GNU General Public License from our website at http://bioinformatics.psb.ugent.be/software
Contact: yves.vandepeer{at}psb.ugent.be
Supplementary information: Supplementary data are available on our website at http://bioinformatics.psb.ugent.be/supplementary_data/anjos/gibbs
Associate Editor: Martin Bishop
Received on July 10, 2007; revised on October 31, 2007; accepted on November 6, 2007
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