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Bioinformatics Advance Access published online on February 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth096
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 16, 2003
Revised November 13, 2003
Accepted November 28, 2003

Applications note

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

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

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

* To whom correspondence should be addressed. E-mail: Florian.Sohler{at}bio.informatik.uni-muenchen.de.


  Abstract

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 to detect 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/.


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