Cytoscape

Cytoscape integrates and visualizes biomolecular interaction networks and high-throughput molecular-state data to enable exploration of protein-protein, protein-DNA, and genetic interactions and their relationships to gene expression and phenotypes.

Key Features:

• Network layout and querying: Layout and query intricate interaction networks to represent and navigate complex biomolecular relationships.
• Data integration: Merge high-throughput gene expression profiles, phenotypes, and other molecular states with network structures for combined analysis.
• Functional annotation linking: Link network nodes and edges to external databases of functional annotations to contextualize interactions.
• Support for interaction types and organisms: Handle large datasets of protein-protein interactions, protein-DNA interactions, and genetic interactions for humans and various model organisms.
• Extensible architecture: Extensible plug-in system enabling development and incorporation of additional computational analyses and analytical features.
• Pathway and complex analysis: Identify interaction pathways that correlate with gene expression changes and analyze protein complexes involved in cellular responses such as DNA damage.
• Network inference: Infer combined physical and functional interaction networks for organisms, exemplified by applications to Halobacterium.
• Model interfacing: Interface with detailed stochastic and kinetic models of gene regulation for integrated analysis.

Scientific Applications:

• Pathway identification: Identify interaction pathways that correlate with changes in gene expression.
• Protein complex analysis: Investigate protein complexes involved in cellular responses to DNA damage.
• Network inference in non-model organisms: Infer combined physical/functional interaction networks for organisms such as Halobacterium.
• Gene-regulatory model integration: Integrate network data with stochastic or kinetic models of gene regulation.

Methodology:

Computational methods include network layout and querying, visual integration of gene expression profiles, phenotypes, and other molecular states with networks, linking to databases of functional annotations, an extensible plug-in architecture for additional analyses, and interfaces to stochastic and kinetic gene-regulatory models.