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Analyzing networks with VisANT
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Curr Protoc Bioinformatics (December 2004)

The VisANT tool, accessible from any recent Java-enabled browser, is a platform-independent, flexible, Web-enabled program for quick and simple construction, visualization, and analysis of molecular and higher order networks based on functional (e.g., expression profiles, phylogenetic profiles) and physical (e.g., yeast two-hybrid, chromatin-immunoprecipitation) relations from either the Predictome database or user-defined data sets. Analysis capabilities include identification of feed-forward and -back loops, shortest paths, and node degree distribution. Additionally, network constructs can be saved, accessed, and shared online. VisANT is able to develop and display meta-networks for meta-nodes that are structural complexes or pathways (soon including nodes representing any kind of dense cluster). Further, VisANT supports a growing number of standard exchange formats and database referencing standards, e.g., KEGG/KGML, BioPAX (in progress), GenBank, Gene Ontology. Multiple species are supported to the extent that computed or experimental evidence of interactions or associations are available (i.e., public datasets or Predictome database).
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