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Bioinformatics Advance Access published online on April 10, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl129
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received August 19, 2005
Revised March 28, 2006
Accepted March 30, 2006

Applications note

ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles

Ryo Yoshida 1 *, Tomoyuki Higuchi 2, Seiya Imoto 1, and Satoru Miyano 1

1 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
2 Research Organization of Information and Systems, The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106-8569, Japan

* To whom correspondence should be addressed.
Ryo Yoshida, E-mail: yoshidar{at}ims.u-tokyo.ac.jp


  Abstract

Summary: One of the significant challenges in gene expression analysis is to find unknown subtypes of several diseases at the molecular levels. This task can be addressed by grouping gene expression patterns of the collected samples on the basis of a large number of genes. Application of commonly used clustering methods to such a dataset however are likely to fail due to over-learning, because the number of samples to be grouped is much smaller than the data dimension which is equal to the number of genes involved in the dataset. To overcome such difficulty, we developed a novel model-based clustering method, referred to as the mixed factors analysis. The ArrayCluster is a freely available software to perform the mixed factors analysis. It provides us some analytic tools for clustering DNA microarray experiments, data visualization and an automatic detector for module transcriptional of genes that are relevant to the calibrated molecular subtypes and so on.

Availability: The ArrayCluster can be used free of charge for non-commercial and academic use and downloaded from http://www.ism.ac.jp/~higuchi/arraycluster.htm.

Associate Editor: Alvis Brazma
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