![]() Interactions in an organism) high-level (outlining relationships among pathway components without detailed information on Interactions and states are well matched, in that both data types are global (providing information for all components or High-throughput data pertaining to molecular 2001) may be quantified with mass spectrometry, NMR, and other advanced techniques. 2001), and metabolite concentrations ( Griffin et al. 1999), protein phosphorylation state ( Zhou et al. 1997), whereas changes in protein abundance ( Gygi et al. For instance, global changes in gene expressionĪre measured with DNA microarrays ( DeRisi et al. States induced by pathway interactions under different experimental conditions. To complement these data, a second set of high-throughput methods are available to characterize the molecular and cellular 2002), and genetic interactions ( Tong et al. ![]() Models are now being supplemented with global data gathered for an entire cell or organism, by use of two complementary approaches.įirst, recent technological developments have made it feasible to measure pathway structure systematically, using high-throughput Typically, models are directed toward a cellular process or disease pathway of interest ( Gilman and Arkin 2002) and are built by formulating existing literature as a system of differential and/or stochastic equations. Verify knowledge of a pathway (2) manage the immense complexity of hundreds or potentially thousands of cellular componentsĪnd interactions and (3) reveal emergent properties and unanticipated consequences of different pathway configurations. Such models promise to transform biological research by providing a framework to (1) systematically interrogate and experimentally A variety of modeling environments haveīeen developed to simulate biochemical reactions and gene transcription kinetics ( Endy and Brent 2001), cellular physiology ( Loew and Schaff 2001), and metabolic control ( Mendes 1997). Interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.Ĭomputer-aided models of biological networks are a cornerstone of systems biology. SeveralĬase studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in geneĮxpression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional The Core is extensible throughĪ straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Cytoscape's software Core providesīasic functionality to layout and query the network to visually integrate the network with expression profiles, phenotypes,Īnd other molecular states and to link the network to databases of functional annotations. Although applicable to any system of molecular componentsĪnd interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA,Īnd genetic interactions that are increasingly available for humans and model organisms. Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expressionĭata and other molecular states into a unified conceptual framework.
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