Power Graph Analysis with CyOog

Matthias Reimann

Biotechnology Center, Technische Universit├Ąt Dresden, Germany

reimann@biotec.tu-dresden.de

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

Do not change the options in the appearing Dialog and press Ok

The extraction takes a while. In case you run Cytoscape from a console you can check the progress there

After the extraction finished a new network view of a power graph appears on your Cytoscape desktop

Use the advantages of power graphs to find functional relationships of uncharacterized transcription factors to already well characterized proteins

ALTERNATIVE:

Select node of interest

Use board tools of Cytoscape

Select neighbors of the selected nodes (twice)

Use board tools of Cytoscape

Data / Session Files

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

Beyer.All2l.cys (https://www.biotec.tu-dresden.de/schroeder/group/powergraphs/examples/beyer/examples/beyer/Beyer.html)

Paper:

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

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

Presentation at ICSB 2008:

Oog.ICSB2008.pdf

Webstart:

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

It is still necessary to load one of the session files above!

CyOogPowerGraphAnalysisRecipe (last edited 2009-02-12 01:03:02 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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