#Cytoscape pathway analysis manual#

It can be freely downloaded from the Cytoscape homepage and allows the user to view the communication between nodes and interact with them in a user-friendly manner ( Merico, Gfeller, & Bader, 2009 Shannon et al., 2003). George Priya Doss, in Advances in Protein Chemistry and Structural Biology, 2018 3.1 CytoscapeĬytoscape ( ) ( Shannon et al., 2003) is one of the most widely used open source network visualization tools for analyzing protein interactions as well as expression and metabolic profiles. Other exciting new plugins include clusterMaker, for creating and viewing clusters within Cytoscape networks. This powerful, detailed view is made possible by the BioPax data specification (BioPax: Biological Pathway Exchange, ) that is capable of containing protein interaction data (like PSI-MI) but has further depth, allowing it to describe biological pathways. Edges are colored to indicate multiple relationship types between these entities. A multipartite graph representation is used to represent proteins, complexes, and small molecules as distinct node types. Advanced users may then move on to explore the many plugin functionalities.įor instance, Pathway Commons incorporates data from both primary interaction and pathway databases.

#Cytoscape pathway analysis manual#

A manual and tutorials make it easy for the novice to get started. At the time of writing, the list of Cytoscape plugins cover everything from data retrieval from source databases, integration and analysis of gene expression data, text-mining, and visual layout (compartments, complex viewing), to analysis of over-represented gene-ontology annotation in a subgraph of interactions. Cytoscape also allows for independent development of extended functionalities by third-party developers as “plugins”. Cytoscape is maintained by an active set of developers that oversee maintenance and upgrades of the core functionality. Donaldson, in Handbook of Cell Signaling (Second Edition), 2010 CytoscapeĬytoscape is a free, open-source, visual interface for importing, visually exploring, and analyzing graphical data.