Subgraph for Cytoscape Usage

Subgraph

• Purpose: Functions for flexible subgraph creation, node identification, cycle finder, and path finder in directed and undirected graphs. It also has a function to select the p-neighborhood of a selected node or group of nodes which can be selected by pathway name, node type, or by a list in a file. This generates a set of plug-ins called: path and cycle finding, p-neighborhoods and subgraph selection.
• Cytoscape Version: 2.3, 2.4.1, 2.5
• Developers: Josette Etzel, Kyongryun Lee, Narasimha Rao Velagaleti
• Last Updated: October 2007

Usage Tutorial

Before starting the tutorial, please download and unzip the data files for this tutorial and put in the Cytoscape folder labeled "sampledata": MetNetSample.zip

1. Selecting a subgraph:
   • Download the sample data file given above.
   • Unzip the file and store in the sampleData folder in your Cytoscape Installation.
   • Start the Cytoscape application, select (on the top menu) File > Import Files > Network (multiple file types)
     
   • Select the button for Data Source Type: Local, then select your file from the sampleData folder and click on import.
     
   • After the data is loaded, you should see the display shown below. Select the close button. This is an arbitrary display of the nodes on a grid. Typically, it is not a good idea to display more than a few hundred nodes at one time on a small screen as it looks bad and is very difficult to decipher. The SubgraphCreator will help select data of interest.
     
   • Select the plugins menu and select the Create subgraph plugin. This plugin will create a subgraph using all nodes that are in the network that was just loaded or it can create a subgraph using only a pre-selected part of the graph.
     
2. Subgraph Selection: P- Neighborhood
   • Subgraphs may be selected in a variety of ways. In this case, select the by P neighborhood option (second from the top). This will give all nodes that are within P reaction steps of a subset of nodes.
     
   • This gives the p-neighborhood window. Select the Named Pathway button.
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   • Select Create subgraph now option. A window will open as shown below:
     
3. Subgraph Selection: List of Nodes
   • Subgraphs can also be created using lists of nodes. Examples of this may be a list of differentially expressed genes from a microarray experiment or metabolites present in a profiling experiment. Open the Create Subgraph plugin. Select the by P neighborhood creation method.
     
     
   • Select the Read from File option.
     
     
   • Select the Create subgraph now option. A window will open as shown below:
     
4. Importing Visual Styles
   • To color the nodes and reactions in a meaningful way, the Cytoscape VizMapper Tool must be used. The MetNet Style file was downloaded into the sampleData folder along with the pathway data. In Cytoscape, choose File->Import->Vizmap Property File. Select the file, FCMstyle.props. Then select "FCMStyle" from the drop-down menu on the right side of the Cytoscape toolbar to change the visual style.