Power Graph Analysis in Cytoscape with CyOog

Matthias Reimann

Biotechnology Center, Technische Universit├Ąt Dresden, Germany




Networks play a crucial role in biology and are often used as a way to represent experimental results. Yet, their analysis and representation is still an open problem. Recent experimental and computational progress yields networks of increased size and complexity. There are for example small and large scale interaction networks, regulatory networks, genetic networks, protein-ligand interaction networks, and homology networks analyzed and published regularly. A common way to access the information in a network is though direct visualization, but this fails as it often just results in "fur balls" from which little insight can be gathered. On the other hand, clustering techniques manage to avoid the problems caused by the large number of nodes and even larger number of edges by coarse-graining the networks and thus abstracting details. But these fail too since, in fact, much of the biology lies in the details. Power Graph Analysis is a novel methodology for analyzing and representing networks. Power Graphs are a lossless representation of networks which reduces network complexity by explicitly representing re-occurring network motifs. Moreover, power graphs can be clearly visualized: Power Graphs compress up to 90% of the edges in biological networks and are applicable to all types of networks such as protein interaction, regulatory, or homology networks.
We implemented a powerful plugin for Cytoscape, named CyOog, that allows to extract Power Graphs from Networks and visualize them. Furthermore, CyOog provides filtering tools based on the properties of Power Graphs, like interactive edge filtering.

CytoscapeRetreat2008/Matthias (last edited 2009-02-12 01:03:49 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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