= 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