Network analysis tools: From biological networks to clusters and pathways

Sylvain Brohée, Karoline Faust, Gipsi Lima-Mendez, Gilles Vanderstocken, Jacques van Helden

Research output: Contribution to journalArticlepeer-review


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 ∼1 h.

Original languageEnglish
Pages (from-to)1616-1629
Number of pages14
JournalNature Protocols
Issue number10
Publication statusPublished - 2008
Externally publishedYes


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