Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

Genome Research - Tập 13 Số 11 - Trang 2498-2504 - 2003
Paul Shannon1, Andrew Markiel1, Owen Ozier2, Nitin S. Baliga1, Jonathan T. Wang2, Daniel Ramage2, Nada Amin2, Benno Schwikowski1, Trey Ideker3,2
1Institute for Systems Biology, Seattle, Washington 98103, USA;
2Whitehead Institute for Biomedical Research Cambridge, Massachusetts 02142, USA
3Department of Bioengineering, University of California-San Diego, La Jolla, California 92093, USA

Tóm tắt

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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Genome Research

Tập 13 Số 11

2498-2504

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