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Bioinformatics Advance Access originally published online on May 24, 2005
Bioinformatics 2005 21(15):3201-3212; doi:10.1093/bioinformatics/bti517
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Computational cluster validation in post-genomic data analysis

Julia Handl *, Joshua Knowles and Douglas B. Kell

School of Chemistry, University of Manchester Faraday Building, Sackville Street, PO Box 88,Manchester M60 1QD, UK

*To whom correspondence should be addressed.

Motivation: The discovery of novel biological knowledge from the ab initio analysis of post-genomic data relies upon the use of unsupervised processing methods, in particular clustering techniques. Much recent research in bioinformatics has therefore been focused on the transfer of clustering methods introduced in other scientific fields and on the development of novel algorithms specifically designed to tackle the challenges posed by post-genomic data. The partitions returned by a clustering algorithm are commonly validated using visual inspection and concordance with prior biological knowledge—whether the clusters actually correspond to the real structure in the data is somewhat less frequently considered. Suitable computational cluster validation techniques are available in the general data-mining literature, but have been given only a fraction of the same attention in bioinformatics.

Results: This review paper aims to familiarize the reader with the battery of techniques available for the validation of clustering results, with a particular focus on their application to post-genomic data analysis. Synthetic and real biological datasets are used to demonstrate the benefits, and also some of the perils, of analytical clustervalidation.

Availability: The software used in the experiments is available at http://dbkweb.ch.umist.ac.uk/handl/clustervalidation/

Contact: J.Handl{at}postgrad.manchester.ac.uk

Supplementary information: Enlarged colour plots are provided in the Supplementary Material, which is available at http://dbkweb.ch.umist.ac.uk/handl/clustervalidation/

Received on March 24, 2005; revised on May 24, 2005; accepted on May 24, 2005

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