Tutorial:MCODE Plugin Demo
Tutorial:MCODE Plugin Demo
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!).
Procedure
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)....
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For this example, load nucleolus_exercise.sif.
Find a suitable layout.
Click Plugins>MCODE>Start MCODE.
In the MCODE tab in the Control Panel, select in Whole Network and click Analyze.
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Tutorial:MCODE Plugin Demo
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.
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Tutorial:MCODE Plugin Demo
Additional Information
The MCODE users manual is available through the following link: http:/ / baderlab. org/ Software/ MCODE/
UsersManual
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Article Sources and Contributors
Article Sources and Contributors
Tutorial:MCODE Plugin Demo Source: http://opentutorials.rbvi.ucsf.edu/index.php?oldid=551 Contributors: AnnaKuchinsky
Image Sources, Licenses and Contributors
File:nucleolus_exercise.sif Source: http://opentutorials.rbvi.ucsf.edu/index.php?title=File:Nucleolus_exercise.sif License: unknown Contributors: AnnaKuchinsky
File:nucleolus.noa Source: http://opentutorials.rbvi.ucsf.edu/index.php?title=File:Nucleolus.noa License: unknown Contributors: AnnaKuchinsky
File:protein_description.noa Source: http://opentutorials.rbvi.ucsf.edu/index.php?title=File:Protein_description.noa License: unknown Contributors: AnnaKuchinsky
File:mcode_analyze.png Source: http://opentutorials.rbvi.ucsf.edu/index.php?title=File:Mcode_analyze.png License: unknown Contributors: AnnaKuchinsky
File:subnetwork.png Source: http://opentutorials.rbvi.ucsf.edu/index.php?title=File:Subnetwork.png License: unknown Contributors: AnnaKuchinsky
License
Attribution-Noncommercial-Share Alike 3.0 Unported
http:/ / creativecommons. org/ licenses/ by-nc-sa/ 3. 0/
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