Cytoscape plugins - GeneMania and CentiScape
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Cytoscape is an open source software platform. It provides features for data integration, analysis and visualization. Additional features are available in the form of apps (plugins). These apps can be used for network analyses, molecular scripting and connection with databases.These apps are available in Cytoscape App Store.
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- 1. GeneMANIA & CentiScaPe Nixon Mendez Department of Bioinformatics
- 2. CYTOSCAPE Cytoscape is an open source software platform which was initially made public in July 2002 (v0.8) Cytoscape is funded and maintained by the U.S. National Institute of General Medicinal Sciences (NIGMS). It can be used for visualizing complex networks and integrating these with any type of attribute data. The software is written in Java code, we can write our own Apps in Java codes.
- 3. CYTOSCAPE Cytoscape supports a lot of standard file formats : SIF, SBML, delimited text file and MS Excel. It provides features for data integration, analysis and visualization. Additional features are available in the form of apps (plugins). These apps can be used for network analyses, molecular scripting and connection with databases. These apps are available in Cytoscape App Store. Eg: MiMI, ClusterONE, Network Analysis etc.,
- 4. GeneMANIA
- 5. GeneMANIA Imports interaction networks from public databases from a list of genes with their annotations and putative functions.
- 6. GeneMANIA identifies the most related genes to a query gene set using a guilt-by- association approach. The plugin uses a large database of functional interaction networks from multiple organisms and each related gene is traceable to the source network used to make the prediction. Users may add their own interaction networks and expression profile data to complement or override the default data.
- 7. Features Number of query genes is limited only by the amount of memory available. Powerful command line tools to automate basic and advanced analysis not available via the website Users can add their own organisms Integration with the popular Cytoscape network visualization and analysis platform so Cytoscape networks can be imported into GeneMANIA and GeneMANIA results can be used in other Cytoscape analysis. Also, results can be saved in Cytoscape session files for later work, backup or sharing with colleagues.
- 8. CentiScaPe
- 9. CentiScaPe Find the most important nodes in a network, calculating centrality parameters for each node.
- 10. How it works? Centiscape computes specific centrality parameters describing the network topology. Here we use Dijkstra algorithm. The centrality parameters aid the users to find the most significant nodes in a complex network. The plugin computation generates both numerical and graphical output making easy to find the key nodes also in large networks.
- 11. CentiScaPe computes: Network parameters: Diameter Average Distance Node parameters and their min, max and average values: Eccentricity Closeness Betweenness Stress Centroid Radiality Degree Eigenvector Bridging centrality Edge parameters and their min, max and average values: Edge Betweenness
- 12. Features Centralities for directed networks (the edges can have a direction as in metabolic and signal transduction networks) Centralities for weighted networks (use experimental data set as weight for the edges of the network) New centralities added.
- 13. THANK YOU