ToPNet

 

Software:

ToPNet has been exclusively licensed to BioSolveIT . Commercial use of ToPNet requires a license from BioSolveIT. The ToPNet package is available free of charge to academic institutions and can be downloaded at the BioSolveIT-website.

The ToPNet program enables biological experts to interactively interpret expression data in the context of biological networks of various kinds (e.g. metabolic, regulatory or text-mining networks).

Description

The sensible analysis of gene expression data poses a great challenge to bioinformatics today. With present microarrays, the expression level of several thousands of genes in a biological sample can be estimated simultaneously. However, usually only few such large scale measurements are conducted in one experimental setup. As the measurement process is subject to noise, sensible analysis is hard without any prior biological knowledge. Biological networks (e.g. metabolic, regulatory or interaction networks) are a rich source of such prior knowledge. The ToPNet program enables biological experts to interactively interpret expression data in the context of these biological networks.

Methods

ToPNet provides the means to load several kinds of biological networks and visualize (parts of) the network with associated annotation information (e.g. gene expression data or Gene Ontology information). Besides this visualization options, ToPNet facilitates restriction of networks to interesting regions in the light of currently loaded experimaental data. The restricted network provide a good starting point for the formulation of biological hypotheses.