Tutorial:Power Graph Analysis with CyOog
Slideshow Power_Graph_Analysis_with_CyOog (about ?? minutes)
Handout Power_Graph_Analysis_with_CyOog.pdf (?? pages)
Tutorial Curators Anna Kuchinsky
Power Graph Analysis with CyOog
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.
- Load the CyOog plugin: http://www.biotec.tu-dresen.de/schroeder/group/powergraphs
- Load your network by loading one of the following session files.
Extract the power graph
- Click on the Extract Power Graph... button 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 extraction is 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 or neighbors of selected nodes (twice) using board tools of Cytoscape.
The following is a link to a published paper about using Power Graph Analysis, "Unraveling Protein Networks with Power Graph Analysis."
You can also look at the following PowerPoint presentation about using Power Graph Analysis in Cytoscape.