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PMID:14597658
| Citation |
Shannon, P, Markiel, A, Ozier, O, Baliga, NS, Wang, JT, Ramage, D, Amin, N, Schwikowski, B and Ideker, T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498-504 |
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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. |
| Links |
PubMed PMC403769 Online version:10.1101/gr.1239303 |
| Keywords |
Algorithms; Archaeal Proteins/chemistry; Archaeal Proteins/metabolism; Bacteriophage lambda/physiology; Computational Biology/methods; Halobacterium/chemistry; Halobacterium/cytology; Halobacterium/physiology; Internet; Models, Biological; Neural Networks (Computer); Phenotype; Software/trends; Software Design; Stochastic Processes |
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Significance
Annotations
| Gene product | Qualifier | GO Term | Evidence Code | with/from | Aspect | Extension | Notes | Status |
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See also
References
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