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

      Genome research

      Stochastic Processes, Software Design, trends, Software, Phenotype, Neural Networks (Computer), Models, Biological, Internet, physiology, cytology, chemistry, Halobacterium, methods, Computational Biology, Bacteriophage lambda, metabolism, Archaeal Proteins, Algorithms

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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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          Journal
          10.1101/gr.1239303
          14597658
          403769

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