Power Graph Analysis with CyOog

Matthias Reimann

Biotechnology Center, Technische Universität Dresden, Germany

Biological Use Case:

General: Analysis of gigantic biological networks like protein interaction networks, sequence homology networks, or regulatory networks. The information you are looking for in such networks is hidden by a big mass of edges -- inside a 'fur ball' or 'hairy monster'. Instead of loosing valuable details in the networks by coarse-graining them using clustering techniques, Power Graph Analysis can be used. A power graph is a compressed version of a normal graph. The used transformation is completely reversible.

Example described here: Finding functional relationships among transcription factors in a huge regulatory network.

Recipe

Cytoscape version: Version number (2.6)

Plugins to Load: CyOog: http://www.biotec.tu-dresden.de/schroeder/group/powergraphs

GUI steps:

Story	Action	Remarks
Load your network	Load the session file attached to this page
Extract power graph	Click on the button 'Extract Power Graph ...' in the control panel of CyOog on the left hand side	This operation takes a while. In case you run Cytoscape from a console you can check the progress there

Data / Session Files:

attachment:Beyer.All.cys (https://www.biotec.tu-dresden.de/schroeder/group/powergraphs/examples/beyer/examples/beyer/Beyer.html)

Paper:

Royer L, Reimann M, Andreopoulos B, Schroeder M (2008) Unraveling Protein Networks with Power Graph Analysis. PLoS Comput Biol 4(7): e1000108

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000108

Webstart:

http://www.biotec.tu-dresden.de/schroeder/group/powergraphs/download_cyplugin.html

It is still necessary to load session file separately!

CyOogPowerGraphAnalysisRecipe

Power Graph Analysis with CyOog