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Bioinformatics Advance Access originally published online on March 3, 2005
Bioinformatics 2005 21(10):2550-2551; doi:10.1093/bioinformatics/bti355
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Gene-Expression Omnibus integration and clustering Tools in SeqExpress

John Boyle

Holbeck George Street, Cambridge CB4 1AJ, UK

Summary: SeqExpress, a gene-expression analysis suite, has been extended to offer a number of cluster generation, refinement and visualization techniques. The cluster generation methods have been specialized to deal with aspects of the sparseness and extreme values that occur within microarray data. The results of such cluster analysis can then be refined using either: a functional enrichment based procedure, which examines each cluster to see if it possesses an unusually high or low concentration of ontology terms; or by using Expectation–Maximization to find a mixture of model based distributions within the datasets. Visualizations are provided both to explore and compare the results of the cluster generation algorithms. In addition, a tool has been developed which integrates SeqExpress with the Gene-Expression Omnibus repository. The tool provides seamless access to the large number of experimental results in the repository, so that they can be visualized and analysed locally using SeqExpress.

Availability: SeqExpress is available as a 6 MB download from http://www.seqexpress.com and runs under Windows. A server-based version is available and is required for the GEO integration. SeqExpress is not affiliated with any academic institution, funding body or commercial organization and is free to use by all.

Contact: john{at}seqexpress.com


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