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Bioinformatics Advance Access published online on March 3, 2005
Bioinformatics, 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@oupjournals.org
Received September 9, 2004
Revised February 21, 2005
Accepted February 23, 2005

Applications note

Gene Expression Omnibus integration and clustering tools in SeqExpress

John Boyle *

* To whom correspondence should be addressed.
John Boyle, E-mail: john{at}seqexpress.com


  Abstract

SeqExpress, a gene expression analysis suite, has been extended to offer a number of cluster generation, refinement and visualisation techniques. The cluster generation methods have been specialised 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 Maximisation to find a mixture of model based distributions within the data sets. Visualisations are provided both to explore and compare the results of the cluster generation algorithms.

Additionally, a tool has been developed which integrates SeqExpress with the Gene Expression Omnibus repository. The tool provides seamless access to the large number of experiment results in the repository, so that they can be visualised and analysed locally using SeqExpress.

Availability: SeqExpress is free to use, with no restrictions, by all. SeqExpress can be downloaded from http://www.seqexpress.com.


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