This only works if you first imported the node atribute "URL".Ĭytoscape options. links to the Flybase gene page for the selected node. Shows all of the default gene attributes for the selected node.įlybase linkout. Adds all of the interactions for the selected node from DroID interaction data sets chosen by the user. Shows the number of interactions for the selected node in each of the different data sets in DroID.Įxpand node. In addition, DroID-Plugin enables several options from a contextual menu (right-click or CTRL-click on a node).Links to a web page with details about DroID. one example is BINGO, which calculate gene ontolgy term enrichment but requires CG Symbols. This option is useful when analyzing the network with plugins that don't recognize Flybase gene number Creates a copy of the current network with CG Symbol as the gene id. Clone current network with CG Symbol as ID.In addition to the default attributes that are automatically available, several additional interaction attributes can be imported, including references and experimental details specific for each interaction data set. If new interactions are added to a network manually or from a source other than DroID, this feature imports the gene attributes from DroID. In addition to the default attributes that are automatically available, several additional gene attributes can be imported, including Gene Ontology, protein domains, expression data, etc. A list of FBgns can be uploaded and used to search DroID. Build/add to interaction networks by searching DroID for interactions involving a user's list of genes. Add interactions for genes from user's list.DroID uses Flybase gene numbers (FBgn) from the Flybase database to uniquely identify each gene/protein, and pairs of FBgns to uniquely identify each interaction.
Cytoscape is a Java-based application that downloads to your local machine. These attributes can be used in Cytoscape's features for layouts, filtering, and coloring, and for other analyses. In the meantime, below is the help from the previous revision (Cytoscape 2.8). Interactions are retrieved from DroID along with a set of default gene (node) attributes and interaction (edge) attributes, including original data source, confidence score, and expression correlation value. Searches can be based on names, symbols, and a variety of other gene features (attributes). Build/add to interactome networks by searching DroID for Drosophila genes. You must have Cytoscape installed to use this plugin.
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To use it, download the plugin (,jar file) and put it into the Plugin folder in the Cytoscape application folder. DroID-Plugin provides access to the Drosophila Interactions Database (DroID) from within the Cytoscape environment.
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