MCODE User's Manual

TableOfContents()

Installation

To use the MCODE PlugIn, you must first obtain a copy of Cytoscape. The compatible MCODE and Cytoscape versions are outlined in the downloads section on the [:Software/MCODE: MCODE website]. The lastest MCODE, version 1.2, requires Cytoscape 2.3.2 or later.

• You can download a copy of Cytoscape from: http://www.cytsoscape.org.

Once you have downloaded Cytoscape and verified that it works, proceed with the next steps:

1. Copy the MCODE.jar file to your [Cytoscape_Home]/plugins directory.
2. Start Cytoscape. For example
   • On Unix/Linux or MacOS X, run: cytoscape.sh
   • On Windows, run: cytoscape.bat
3. Check that MCODE appears in the Plugins menu of Cytoscape
   • If it does not, then you likely placed the MCODE.jar file in the wrong directory. Repeat step one. You will have to restart Cytoscape to reload the plugin.

Running MCODE

MCODE is an extension for Cytoscape and can only be accessed through Cytoscape.

1. Start Cytoscape
2. Go to the Plugins Menu
3. Move the mouse over MCODE
4. Click Start MCODE
   • The main MCODE interface will appear as a tab in the left-hand panel of Cytoscape

Note: If MCODE does not appear in the Plugins Menu, then the installation of MCODE was not successfull. Please refer to the previous section of the User's Manual.

This menu provides two additional options:

• About MCODE
  • A quick reference to MCODE acknowledgements, citation information, and a link to the MCODE paper.
• Help
  • A link that will open the MCODE website at www.baderlab.org in your default browser for quick access to downloads, contact information, and the User's Manual with help and tutorials.

New to Version 1.2: MCODE can now be seen as a console for the underlying algorithm. It can be started independent of network loading. This provides for a more easily accessible, repeatable and modifyable analysis.

Getting Results

This section will cover some of the basic steps of running MCODE on a network.

1. LOAD THE NETWORK. To begin, make sure the network to be analyzed is loaded into Cytoscape. You can load as many networks as your computer system can handle, large or small. MCODE will recognize which network you wish to analyze either by noting which network view is on top or by your selection of the network in the Network Tab on the left-hand panel.

2. CHOOSE THE SCOPE. Cluster results can be reported in two fundamental ways with MCODE. This is referred to as the Scope of the process.

   1. Find Clusters in Whole Network
      • MCODE will find and report all clusters in the entire network.
   2. Find Clusters from Selection
      • Only those clusters including the selected node(s) as one of their members will be reported.
      • Selections can be made either in the view directly or in the node browser.
   3. The choice of scope is dependent on the your familiarity with the network in question and the desired outcome. Having a particular protein of interest within a network, for example, it may be appropriate to search for only those clusters involving such a protein. On the other hand, uniformed, exploratory work will most benefit from a whole network scope.

3. ANALYZE. Next, press Analyze. This will display a task monitor reporing the progress of the scoring, finding, and drawing steps, provided that the task is not too quick.

   • You may see several different messages at this step:
     1. The "No network" message
        • This means that MCODE failed to detect a loaded network for analysis. You must load a network, and make sure it is selected, before you can anaylze it.
     2. The "No selection" message
        • This message appears when the Selection Scope is used without an actual selection. You must select the desired node(s) before you MCODE can attempt to find clusters.
     3. The "Parameters unchanged" message
        • Parameters are discussed in detail in the following section. For now, you should know that if you attempt to analyze a network twice without changing any of the settings such as scope, MCODE will let you know that this analysis was previously conducted and will consequently display the previously attained results.
4. VIEW RESULTS. If everything goes to plan, a new tab will appear in the right-hand panel displaying the results as "Results 1"

   • Cluster Browser:

     • On the left side is a graphical representation of the cluster
       • Cluster members are coloured red.

       • The highest scoring node in the cluster is called the Seed. It is the node from which the cluster was derived and is represented as a square.

       • Other cluster members are circular.
       • Edges, representing interactions for example, are blue.
       • Edge directionality is represented by cyan arrows.
     • POST A PICTURE OF AN EXAMPLE CLUSTER
     • On the right side is a statisical summary of the cluster

       • Rank is based on the cluster's computed score and is used to refer to the clusters (for example, Cluster 1 is the highest ranked cluster in a given result set)

       • Nodes and Edges is a simple enumeration of the clusters members and their interconnections.

   • These results can be discarded at any time by pressing the Close button at the bottom of the results panel.

Fine-Tuning Results

Scoring Parameters

Finding Parameters

Exploring Results

Outputting Results

Tutorials

BiNGO Validation

Troubleshooting

General

• MCODE Does Not Appear in the Plugins Menu

Error Messages