title: Network Analysis Tools: from biological networks to clusters and pathways.
abstract: Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in approximately 1 h.
authors.affiliation: Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, Bruxelles, Belgium.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Brohée
authors.forename: Karoline
authors.initials: K
authors.lastname: Faust
authors.forename: Gipsi
authors.initials: G
authors.lastname: Lima-Mendez
authors.forename: Gilles
authors.initials: G
authors.lastname: Vanderstocken
authors.forename: Jacques
authors.initials: J
authors.lastname: van Helden
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D015398:Signal Transduction / Q000235:genetics*; D012984:Software; D049490:Systems Biology / Q000379:methods*