Fast Gene Ontology based clustering for microarray experiments.docVIP

BioData Mining BioMedCentral Software article Open Access Fast Gene Ontology based clustering for microarray experiments Kristian Ovaska, Marko Laakso and Sampsa Hautaniemi* Address: Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Program, Biomedicum Helsinki, University of Helsinki, PO Box 63 (Haartmaninkatu 8), 00014 UNIVERSITY OF HELSINKI, Finland Email: Kristian Ovaska - Kristian.Ovaska@Helsinki.FI; Marko Laakso - Marko.Laakso@Helsinki.FI; Sampsa Hautaniemi* - Sampsa.Hautaniemi@Helsinki.FI * Corresponding author Published: 21 November 2008 Received: 8 April 2008 Accepted: 21 November 2008 BioData Mining 2008, 1:11 doi:10.1186/1756-0381-1-11 This article is available from: /content/1/1/11 ? 2008 Ovaska et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Analysis of a microarray experiment often results in a list of hundreds of disease- associated genes. In order to suggest common biological processes and functions for these genes, Gene Ontology annotations with statistical testing are widely used. However, these analyses can produce a very large number of significantly altered biological processes. Thus, it is often challenging to interpret GO results and identify novel testable biological hypotheses. Results: We present fast software for advanced gene annotation using semantic similarity for Gene Ontology terms combined with clustering and heat map visualisation. The methodology allows rapid identification of genes sharing the same Gene Ontology cluster. Conclusion: Our R based semantic similarity open-source package has a speed advantage of over 2000-fold compared to existing implementations. From