Cytoscape

Category Cross-Omics>Pathway Analysis/Tools

Abstract Cytoscape is an open-source bioinformatics software platform that enables researchers to form a visual map of complex biological networks increasing their understanding of molecular pathways and the biological causes of disease. Cytoscape allows you to visualize molecular interaction networks and integrates these interactions with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged.

Cytoscape supports the following features/capabilities:

Input --

• 1) Input and construct molecular interaction networks from raw interaction files [Simple Interaction Format (SIF) format] containing lists of protein-protein and/or protein-DNA interaction pairs. For yeast and other model organisms, large sources of pairwise interactions are available through the Biomolecular Interaction Network Database (BIND) and Gene Transcription Factor Database (TRANSFAC) databases. User-defined interaction types are also supported.
• 2) Load and save previously-constructed interaction networks in the Graph Markup Language (GML) format.
• 3) Load and save networks and node/edge attributes in an eXtensible Markup Language (XML) document format called XGMML (eXtensible Graph Markup and Modeling Language).
• 4) Input mRNA expression profiles from tab- or space-delimited text files.
• 5) Load and save arbitrary attributes on nodes and edges. For example, input a set of custom annotation terms for your proteins; create a set of confidence values for your protein-protein interactions; etc.
• 6) Import gene functional annotations from the Gene Ontology (GO) and KEGG databases.
• 7) Directly import GO Terms and annotations from Open Biomedical Ontologies (OBO) and Gene Association files.
• 8) Load and save the 'state' of the Cytoscape session in a Cytoscape Session (.cys) file. The Cytoscape Session file includes networks, attributes (for node/edge/network), Desktop states (selected/hidden nodes and edges, window sizes), Properties, and Visual Styles.

Visualization --

• 1) Customize network data displays using advanced visual styles.
• 2) View a superposition of gene expression ratios and p-values on the network. Expression data can be mapped to node color, label, border thickness, or border color, etc. according to user-configurable colors and visualization schemes.
• 3) Layout networks in two (2) dimensions. A variety of layout algorithms are available, including cyclic and spring-embedded layouts.
• 4) Zoom in/out and pan while browsing the network.
• 5) Use the network manager to organize multiple networks. The structure created by the network manager can also be saved in a session file.
• 6) Use the 'bird's eye' view to navigate large networks.
• 7) Navigate large networks (100,000+ nodes and edges) created by our efficient rendering engine.

Analysis --

Plugins that are available for network and molecular profile analysis. For example:

1) Filter the network to select subsets of nodes and/or interactions based on the current data. For instance, users may select nodes involved in a threshold number of interactions, nodes that share a particular GO annotation, or nodes whose gene expression levels change significantly in one or more conditions according to p-values loaded with the gene expression data.

2) Find active subnetworks/pathway modules. The network is screened against gene expression data to identify connected sets of interactions, i.e. interaction subnetworks, whose genes show particularly high levels of differential expression. The interactions contained in each subnetwork provide hypotheses for the regulatory and signaling interactions in control of the observed expression changes.

3) Find clusters (highly interconnected regions) in any network loaded into Cytoscape. Depending on the type of network, clusters may mean different things. For instance, clusters in a protein-protein interaction network have been shown to be protein complexes and parts of pathways. Clusters in a protein similarity network represent protein families.

More info about Plugins --

Cytoscape includes a flexible Plugin architecture that enables developers to add extra functionality beyond that provided in the core. Plugins also provide a convenient place for testing out new Cytoscape features.

Current plugins are categorized into five (5) sections:

• 1) Analysis Plugins - Used for analyzing existing networks.
• 2) Network and Attribute I/O Plugins - Used for importing networks and attributes in different file formats.
• 3) Network Inference Plugins - Used for inferring new networks.
• 4) Functional Enrichment Plugins - Used for functional enrichment of networks.
• 5) Communication/Scripting Plugins - Used for communicating with or scripting Cytoscape.

System Requirements

Cytoscape is a Java application (Java SE 5 or 6 only) verified to run on Linux, Windows, and Mac OS X. Although not officially supported, other UNIX platforms such as Solaris or FreeBSD may run Cytoscape if Java version 5 or later is available for the platform.

The system requirements for Cytoscape depend on the size of the networks the user wants to load, view and manipulate.

Small NetworkVisualization

• 1 GHz processor
• 512 MB memory
• On board video graphics card
• XGA (1024x768) monitor

Large Network Analysis/Visualization

• 1 GHz processor as fast as possible
• 2 GB+ memory
• High end graphics card
• Wide or dual monitor

Manufacturer

The Cytoscape project is an ongoing collaboration between:

• The Institute for Systems Biology
• University of California at San Diego
• Memorial Sloan Kettering Cancer Center
• Institut Pasteur
• Agilent Technologies
• University of California at San Francisco

Manufacturer Web Site Cytoscape project

Price Freely available for download from http://www.cytoscape.org/ as an open source Java application.

G6G Abstract Number 20092

G6G Manufacturer Number 100709