NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.
The network analysis tools (NeAT) (http://rsat.ulb.ac.be/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.
Brohée
Sylvain
S
Laboratoire de Bioinformatique des Génomes et Réseaux (BiGRE), Université Libre de Bruxelles (ULB), Boulevard du Triomphe, CP263, B-1050 Bruxelles, Belgium. sylvain@scmbb.ulb.ac.be
Faust
Karoline
K
Lima-Mendez
Gipsi
G
Sand
Olivier
O
Janky
Rekin's
R
Vanderstocken
Gilles
G
Deville
Yves
Y
van Helden
Jacques
J
D016000:Cluster Analysis; D003196:Computer Graphics; D005786:Gene Expression Regulation; D020407:Internet; D053858:Metabolic Networks and Pathways; D020411:Oligonucleotide Array Sequence Analysis; D025941:Protein Interaction Mapping; D015398:Signal Transduction; D012984:Software