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Bioinformatics Advance Access originally published online on February 12, 2004
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Bioinformatics 20(9) © Oxford University Press 2004; all rights reserved.

Applications Note

ToPNet—an application for interactive analysis of expression data and biological networks

Daniel Hanisch 1, Florian Sohler 2,* and Ralf Zimmer 2

1 Institute for Algorithms and Scientific Computing (SCAI), Fraunhofer Gesellschaft, Schloss Birlinghoven, 53754 Sankt Augustin, Germany and 2 Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstrasse 17, 80333 München, Germany

Received on July 16, 2003; revised on November 13, 2003; accepted on November 28, 2003
Advance Access Publication February 12, 2004

Summary: ToPNet is a new tool for the combined visualization and exploration of gene networks and expression data. ToPNet provides various ways of restricting, manipulating and combining biological networks according to annotation data (e.g. Gene Ontology terms) and presents results to the user via different visualization procedures and hyperlinks to the underlying data sources. To easily identify relevant parts of the network, ToPNet provides a method of detecting significant subnetworks with respect to expression measurements. As ToPNet is a pure JAVA application with additional scripting capabilities, it is well-suited as a test-bed for algorithm development and exploratory biological data analysis alike.

Availability: ToPNet is freely available for academic institutions at http://www.biosolveit.de/ToPNet/

Contact: Florian.Sohler{at}bio.ifi.lmu.de

* To whom correspondence should be addressed.


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