Tutorial:Power Graph Analysis with CyOog

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Slideshow Power_Graph_Analysis_with_CyOog (about ?? minutes)
Handout Power_Graph_Analysis_with_CyOog.pdf (?? pages)

Tutorial Sources
Tutorial Curators Anna Kuchinsky

Contents


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.

Procedure

  1. Load the CyOog plugin: http://www.biotec.tu-dresen.de/schroeder/group/powergraphs
  2. Load your network by loading one of the following session files.

File:Beyer.All.cys

File:Beyer.All2l.cys

Extract the power graph

  1. Click on the Extract Power Graph... button in the control panel of CyOog on the left hand side.
  2. 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.
  3. After extraction is finished, a new network view of a power graph appears on your Cytoscape desktop.
  4. Use the advantages of power graphs to find functional relationships of uncharacterized transcription factors to already well-characterized proteins.
    1. ALTERNATIVE: select node of interest or neighbors of selected nodes (twice) using board tools of Cytoscape.

Additional Information

Paper

The following is a link to a published paper about using Power Graph Analysis, "Unraveling Protein Networks with Power Graph Analysis."

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

Presentation

You can also look at the following PowerPoint presentation about using Power Graph Analysis in Cytoscape.

File:PowerGraph Presentation.pdf

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