MCODE Plugin Demo Recipe

Chris Workman

DTU-Systems Biology

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: Plugins and urls

GUI steps:

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

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