Cytoscape: A software environment for integrated models of biomolecular interaction networks

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other Molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in Conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to Visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional Computational analyses and features. Several case Studies of Cytoscape plug-ins are Surveyed, including a search for interaction pathways correlating with changes in gene expression, a Study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.