Cytoscape Wiki
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!).
Recipe
Cytoscape version: Version number (2.6)
Plugins to Load: MCODE http://www.cbs.dtu.dk/courses/27041/exercises/Ex2/nucleolus_exercise.sif http://www.cbs.dtu.dk/courses/27041/exercises/Ex2/nucleolus_prediction.noa http://www.cbs.dtu.dk/courses/27041/exercises/Ex2/protein_description.noa
GUI steps:
Describe each step (story), the GUI action to take, and probable remarks
Story |
Action |
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