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      Cytoscape: a software environment for integrated models of biomolecular interaction networks.

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          Abstract

          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.

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          Author and article information

          Journal
          Genome Res
          Genome research
          Cold Spring Harbor Laboratory
          1088-9051
          1088-9051
          Nov 2003
          : 13
          : 11
          Affiliations
          [1 ] Institute for Systems Biology, Seattle, Washington 98103, USA.
          Article
          13/11/2498
          10.1101/gr.1239303
          403769
          14597658
          227491f1-692c-418a-8f3d-c3c4d38131e0
          History

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