Cytoscape: a software environment for integrated models of biomolecular interaction networks.
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.
Institute for Systems Biology, Seattle, Washington 98103, USA.
Paul
P
Shannon
Andrew
A
Markiel
Owen
O
Ozier
Nitin S
NS
Baliga
Jonathan T
JT
Wang
Daniel
D
Ramage
Nada
N
Amin
Benno
B
Schwikowski
Trey
T
Ideker
D000465:Algorithms; D019843:Archaeal Proteins / Q000737:chemistry / Q000378:metabolism; D010582:Bacteriophage lambda / Q000502:physiology; D019295:Computational Biology / Q000379:methods*; D006217:Halobacterium / Q000737:chemistry / Q000166:cytology / Q000502:physiology; D020407:Internet; D008954:Models, Biological; D016571:Neural Networks, Computer; D010641:Phenotype; D012984:Software / Q000639:trends*; D012985:Software Design; D013269:Stochastic Processes
D019843:Archaeal Proteins