Exploratory Analysis of Biological Networks through Visualization, Clustering, and Functional Annotation in Cytoscape.  The visualization procedure described here relies on the open-source network visualization software Cytoscape and includes detailed instructions on formatting and loading the data, clustering networks, and overlaying functional annotations.
Cytoscape
Cold Spring Harbor protocols
D019295:Computational Biology; D053263:Gene Regulatory Networks; D060066:Protein Interaction Maps; D012441:Saccharomyces cerevisiae; D049490:Systems Biology
Baryshnikova Anastasia A 0000-0002-0123-2052