Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Genome Res. 2003 Nov;13(11):2498-504.

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

Author information

  • 1Institute for Systems Biology, Seattle, Washington 98103, USA.

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.

PMID:
14597658
[PubMed - indexed for MEDLINE]
PMCID:
PMC403769
Free PMC Article

Images from this publication.See all images (5)Free text

Figure 2
Figure 1
Figure 3
Figure 4
Figure 5
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Write to the Help Desk