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Bioinformatics Advance Access published online on November 30, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti169
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 18, 2004
Revised October 15, 2004
Accepted November 18, 2004

Article

Generalized Venn diagrams: a new method of visualizing complex genetic set relations

Hans A. Kestler 1*, André Müller 2, Thomas M. Gress 2, and Malte Buchholz 2

1 Neuroinformatics, University of Ulm, 89069 Ulm, Germany; Internal Medicine I, University Hospital Ulm, Robert-Koch-Str. 8, 89081 Ulm, Germany
2 Internal Medicine I, University Hospital Ulm, Robert-Koch-Str. 8, 89081 Ulm, Germany

* To whom correspondence should be addressed.
Hans A. Kestler, E-mail: hans.kestler{at}medizin.uni-ulm.de


  Abstract

Motivation: Microarray experiments generate vast amounts of data. The unknown or only partially known functional context of differentially expressed genes may be assessed by querying the Gene Ontology database via GOMiner. Resulting tree representations are difficult to interpret and are not suited for visualization of this type of data. Methods are needed to effectively visualize these complex set relationships.

Results: We present a visualization approach for set relationships based on Venn diagrams. The proposed extension enhances the usual notion of Venn diagrams by incorporating set size information. The cardinality of the sets and intersection sets is represented by their corresponding circle (polygon) sizes. To avoid local minima, solutions to this problem are sought by evolutionary optimization. This generalized Venn diagram approach has been implemented as an interactive Java application (VennMaster) specifically designed for the use with GOMiner in the context of the Gene Ontology database.

Availability: VennMaster is platform independent (Java 1.4.2) and has been tested on Windows (XP, 2000), Mac OS X, and Linux. Supplementary information and the software (free for non-commercial use) are available at http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/vennm together with a user documentation.


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