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Bioinformatics. 2004 Jun 12;20(9):1470-1. Epub 2004 Feb 12.

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

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  • 1Institute for Algorithms and Scientific Computing (SCAI), Fraunhofer Gesellschaft, Schloss Birlinghoven, 53754 Sankt Augustin, Germany.



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.


ToPNet is freely available for academic institutions at

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