![]() ![]() Online data import, network generation, interaction database Integrated analysis, functional module detection, graph analysisįinds clusters where member nodes show significant changes in expression levels Mines scientific literature to find publications related to search term and to create interaction network based on the search result Although some plugins come installed by default in the standard Cytoscape release, users optionally install most plugins to access the features they require ( Box 1).Įnrichment analysis, GO annotation, ontology analysisĬalculates overrepresented functions (GO terms) in the network and displays them as GO directed acyclic graphsĬlusters a given network on the basis of vertex weighting by local neighborhood density and outward traversal from a locally dense seed protein to isolate the dense regions Plugins provide a flexible means by which any researcher can bring new concepts in network and systems biology to a broad user base of life scientists. One of the most powerful consequences of this design is that, through the Cytoscape API, software developers can write extensions called plugins that link Cytoscape with new code and provide access to new or alternative features. To enable rapid prototyping and release of new methods, Cytoscape is implemented as an open-source software package with an accessible application programming interface (API) using the Java programming language. One of the major computational platforms for analyzing these networks is Cytoscape, a general-purpose and freely available software platform for integration, visualization and statistical modeling of molecular networks together with other systems-level data 1, 2. High-throughput technologies allow enormous amounts of data to be collected on biological networks, including protein-protein interactions, protein-DNA interactions, kinase-substrate interactions, genetic interactions, gene coexpression and other functional relationships. ![]()
0 Comments
Leave a Reply. |