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| ''Biotechnology Center, Dresden University of Technology (BIOTEC, TU Dresden)'' | ''Biotechnology Center, Technische Universität Dresden, Germany'' |
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| '''__Biological Use Case__''': Describe a real biological problem. |
'''__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. |
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| ''__Cytoscape version__'': Version number (2.6) | ''__Cytoscape version__'': Version number (2.6) |
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| ''__Plugins to Load__'': Plugins and urls | ''__Plugins to Load__'': CyOog: http://www.biotec.tu-dresden.de/schroeder/group/powergraphs |
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| ''__GUI steps__'': |
''__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 || |
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Describe each step (story), the GUI action to take, and probable remarks || ''Story'' || ''Action'' || ''Remarks'' || || || || || |
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| '''__Data / Session Files__''': Attach (preferably) a session file or else the data files used in the workflow | '''__Data / Session Files__''': |
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| '''__Presentation__''': Attach your presentation | attachment:'''Beyer.All.cys''' (https://www.biotec.tu-dresden.de/schroeder/group/powergraphs/examples/beyer/examples/beyer/Beyer.html) |
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| '''__Webstart__''': Attach a webstart | '''__Paper__''': |
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| '''__Video__''': Attach a video link |
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!'' |
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!