Bioinformatics Advance Access published online on March 13, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl081
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1 Division of Biomathematics and Bioinformatics, Rothamsted Research, AL5 2JQ, Harpenden, United Kingdom
Motivation: Assembling the relevant information needed to interpret the output from high throughput, genome scale, experiments such as gene expression microarrays is challenging. Analysis reveals genes that show statistically significant changes in expression levels, but more information is needed to determine their biological relevance. The challenge is to bring these genes together with biological information distributed across hundreds of databases or buried in the scientific literature (millions of articles). Software tools are needed to automate this task which at present is labour-intensive and requires considerable informatics and biological expertise. Results: This article describes ONDEX and how it can be applied to the task of interpreting gene expression results. ONDEX is a database system that combines the features of semantic database integration and text mining with methods for graph-based analysis. An overview of the ONDEX system is presented, concentrating on recently developed features for graph-based analysis and visualization. A case study is used to show how ONDEX can help to identify causal relationships between stress response genes and metabolic pathways from gene expression data. ONDEX also discovered functional annotations for most of the genes that emerged as significant in the microarray experiment, but were previously of unknown function. Availability: ONDEX is freely available under the GPL License and can be downloaded from SourceForge http://ondex.sourceforge.net/. Comment to the anonymous referees: the ONDEX frontend application, the integrated data for the application case and a tutorial that guides through the application case are included as supplementary material. The integrated data also includes subsets of commercial databases and may not be used for other purposes than reviewing this publication. The ONDEX front-end OVTK may be used and redistributed to not-for-profit organisations only.
Received January 4, 2006
Revised February 16, 2006
Accepted March 2, 2006
Article
Graph-based analysis and visualization of experimental results with ONDEX
Jacob Koehler 1 *,
Jan Baumbach 2,
Jan Taubert 2,
Michael Specht 2,
Andre Skusa 2,
Alexander Rueegg 2,
Chris Rawlings 1,
Paul Verrier 1,
and
Stephan Philippi 3
2 Faculty of Technology, Bielefeld University, Germany
3 University of Koblenz, Germany
Abstract
Associate Editor: Martin Bishop
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