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NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways

Brohée, Sylvain, Faust, Karoline, Lima-Mendez, Gipsi, Sand, Olivier, Janky, Rekin's, Vanderstocken, Gilles, Deville, Yves, van Helden, Jacques
Nucleic acids research 2008 v.36 no.suppl_2 pp. W444
Internet, data collection, databases, genes, mass spectrometry, metabolism, microarray technology, nucleic acids
The network analysis tools (NeAT) ( provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources.