Tutorial:MCODE Plugin Demo

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Slideshow MCODE_Plugin_Demo (about ?? minutes)
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Tutorial Sources
Tutorial Curators Anna Kuchinsky

Tutorial: MCODE Plugin

Finding complexes in the nucleolus

In this exercise we will integrate functional information with protein-protein interaction network in a 'real life' case study for the human nucleolus. The nucleolus is an ill-defined substructure found in the nucleus and little is known about it. However, it is known to be involved in ribosome biogenesis.

Based on a proteomics study an external collaborator has made a mass-spec-based purification of proteins found in the human nucleolus. This data is unfortunately a mixture of true nucleolus proteins and contaminants (proteins that are not in the nucleolus). You are now faced with the challenge of identifying true nucleolus-located protein complexes (if there are any!).


  1. Start by loading the MCODE Plugin by going to Plugins->Manage Plugins->Analysis->MCODE.

Building the annotated network

  1. Start Cytoscape and load a network. Go to File->Import->Network (multiple file types)....
    1. File:Nucleolus exercise.sif
    2. File:Nucleolus.noa
    3. File:Protein description.noa
  2. For this example, load nucleolus_exercise.sif.
  3. Find a suitable layout.
  4. Click Plugins>MCODE>Start MCODE.
  5. In the MCODE tab in the Control Panel, select in Whole Network and click Analyze.

Analysis with MCODE

Visualize the nucleolus scores on the MCODE results

The following instructions assume that the network contains the prediction score and the functional annotation as attributes.

  1. Proteins with a high nucleolus prediction score are highlighted in increasing shades of red.
  2. Select the first the first complex in the MCODE Cluster Browser. Note that the corresponding nodes are selected in the network window.
  3. Click Create sub-network to transfer the selected cluster to a new network.

MCODE Sub-Network

Additional Information

The MCODE users manual is available through the following link: http://baderlab.org/Software/MCODE/UsersManual