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Allows for biological network analysis and module discovery. GraphWeb provides methods to: (i) integrate heterogeneous and multispecies data for constructing directed and undirected, weighted and unweighted networks; (ii) discover network modules using a variety of algorithms and topological filters and (iii) interpret modules using functional knowledge of the Gene Ontology (GO) and pathways, as well as regulatory features such as binding motifs and microRNA targets. GraphWeb is designed to analyse individual or multiple merged networks, search for conserved features across multiple species, mine large biological networks for smaller modules, discover novel candidates and connections for known pathways and compare results of high-throughput datasets. The GraphWeb is freely available online.

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GraphWeb classification

GraphWeb specifications

Web user interface
Input data:
A combined biological network of a selected species, consisting of genes, proteins or microarray probesets as nodes and corresponding associations as edges.
Programming languages:
C++, Perl
Restrictions to use:
Output data:
A table containing one row for each graph module found, with the following columns containing links to results: node name conversion, number of nodes, list nodes, list edges, zoom in, label distribution, score, g:Profiler annotations, visualisations.
Computer skills:

GraphWeb support



  • Jaak Vilo <>


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University of Tartu, Institute of Computer Science, Tartu, Estonia; EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; University of Tartu, Institute of Molecular and Cell Biology, Tartu, Estonia; QureTec Ltd. Ulikooli, Tartu, Estonia

Funding source(s)

This work has been supported by the EU FP6 grants ENFIN LSHG-CT-2005-518254 and COBRED LSHB-CT-2007-037730, Estonian Science Foundation grant ETF7437, and funding from the Marie Curie Biostar program and the Tiger University program of the Estonian Information Technology Foundation.

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