Nucleic Acids Research Advance Access originally published online on June 4, 2008
Nucleic Acids Research 2008 36(Web Server issue):W444-W451; doi:10.1093/nar/gkn336
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W444-W451
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
1Laboratoire de Bioinformatique des Génomes et Réseaux (BiGRE), Université Libre de Bruxelles (ULB), Boulevard du Triomphe, CP263, B-1050 Bruxelles and 2Department of Computing Science and Engineering, Université catholique de Louvain (UCL), Place Sainte Barbe, 2. B-1348 Louvain-la-Neuve, Belgium
*To whom correspondence should be addressed. Tel: +32 02 6505434; Fax: +32 02 6505425; Email: sylvain{at}scmbb.ulb.ac.be
Received January 31, 2008. Revised April 24, 2008. Accepted May 10, 2008.
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.
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