= Power Graph Analysis with CyOog =
'''Matthias Reimann '''

''Biotechnology Center, Technische Universität 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__'''

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

[[attachment: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__''':

[[attachment: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!''