DroID-Plugin for Cytoscape.
Compatible with Cytoscape v 2.8
DroID-Plugin provides access to the Drosophila Interactions Database (DroID) from within the Cytoscape environment. To use it, download the plugin (,jar file) and put it into the Plugin folder in the Cytoscape application folder. You must have Cytoscape installed to use this plugin. To obtain Cytoscape go here.
The plugin offers the following options:
- Add interactions. Build/add to interactome networks by searching DroID for Drosophila genes. Searches can be based on names, symbols, and a variety of other gene features (attributes). 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. These attributes can be used in Cytoscape's features for layouts, filtering, and coloring, and for other analyses. 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.
- Add interactions for genes from user's list. Build/add to interaction networks by searching DroID for interactions involving a user's list of genes. A list of FBgns can be uploaded and used to search DroID.
- Import node attributes. 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. If new interactions are added to a network manually or from a source other than DroID, this feature imports the gene attributes from DroID.
- Import edge attributes. 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.
- Clone current network with CG Symbol as ID. Creates a copy of the current network with CG Symbol as the gene id. This option is useful when analyzing the network with plugins that don't recognize Flybase gene number (FBgn) as a gene id. one example is BINGO, which calculate gene ontolgy term enrichment but requires CG Symbols.
- About database. Links to a web page with details about DroID.
- In addition, DroID-Plugin enables several options from a contextual menu (right-click or CTRL-click on a node). These include:
Number of interactions. Shows the number of interactions for the selected node in each of the different data sets in DroID.
Expand node. Adds all of the interactions for the selected node from DroID interaction data sets chosen by the user.
Show attributes. Shows all of the default gene attributes for the selected node.
Flybase linkout. links to the Flybase gene page for the selected node. This only works if you first imported the node atribute "URL".
Cytoscape options. These include other linkouts, options fo rchanging the visual characteristics of the node, hiding the node, and features of other plugins.
Comments and suggestions are welcome. E-mail to email@example.com.