MCODE Plugin Demo Recipe

Gary Bader

University of Toronto

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!).


Cytoscape version: Version number (2.6)

Plugins to Load: MCODE

GUI steps:

Describe each step (story), the GUI action to take, and probable remarks




Building the annotated network

Start Cytoscape and load in the interaction network, the prediction score, and the functional annotation- The latter two should be loaded as node attributes.

or start with a session that has this

Find a suitable layout

run the plugin

Use MCODE to identify potential protein complexes in the network using the default settings.

How many complexes does the MCODE algorithm identify?

Visualize the nucleolus scores on the MCODE results

Highlight the proteins with a high nucleolus prediction score with the vizMapper.

Change the node attribute setting, so it uses the functional description as attribute. Look through MCODE complexes with a score above 2.5 by selecting the nodes in a complex (clicking on the MCODE output-window) and transfer them to a new network.

find complexes where three or more proteins have high prediction scores and they seem to have a similar functional description. How likely is this to be at random?

Data / Session Files: Attach (preferably) a session file or else the data files used in the workflow

Presentation: Attach your presentation

Webstart: Attach a webstart

Video: Attach a video link

McodePluginRecipe (last edited 2009-02-12 01:03:12 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

MoinMoin Appliance - Powered by TurnKey Linux