Pathways & Networks

BioPAX

BioPax is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge.

Pathway Commons

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes.

Cytoscape

Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating 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.

MEMo

MEMo (Mutually Exclusive Modules) is a method for identifying mutually exclusive driver networks in cancer. The method uses correlation analysis and statistical tests to identify network modules by three criteria: (1) Member genes are recurrently altered across a set of tumor samples; (2) member genes are known to or are likely to participate in the same biological process; and (3) alteration events within the modules are mutually exclusive. The method is freely available below as a Java-based command line tool.

NetBox 1.0 Software

NetBox is a Java-based software tool for performing network analysis on human interaction networks. It is pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map. It currently supports a command line interface for connecting genes into a network, identifying statistically significant “linker” genes, partitioning the network into modules, and executing two random background models. Results are then made available to the end user as an HTML web page and a series of network and attribute files, which can be loaded into Cytoscape for visualization and further analysis.

Pathguide

Pathguide is a comprehensive directory of biological pathway and molecular interaction resources.

Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C., Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011 Jan. [Abstract]

Ciriello G, Cerami E, Sander C, Schultz N., Mutual exclusivity analysis identifies oncogenic network modules. Genome Res. 2012 Feb. [Abstract]