CentiScaPe, Centralities for Cytoscape                     

A Cytoscape plug-in for calculating network centralities with numerical and graphical output

Complex biological networks, such as intracellular signaling networks, are modeled by the evolution to accomplish a variety of different regulatory functions. This is achieved by controlling the overall topology of the network which, then, affects its dynamic behavior. Biological networks are hierarchichal, scale-free, modular structure in which few nodes, the hubs, play a particularly relevant topological role and this may reflect a critical role at biological level. However, also nodes with no or lower hub role may have critical regulatory role in certain biological phenomena. This could reflect node-specific topological properties. Thus, it is of interest to categorize every nodes in a network by means of topological parameters allowing scoring of the nodes according to their individual topological relevance. Computation of centrality indexes may accomplish this goal. The centrality indexes are topological parameters allowing a node-by-node quantification of the reciprocal relationship between the nodes. This provides a classification of the nodes according to their capability to influence the function of other nodes in the network. Combination of this analysis with experimental data (node attributes) may help to identify critical nodes and regulatory circuits in a context-specific manner.

 

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Cytoscape 3.0

Click to Download CentiScaPe (for Cytoscape 3.0):

  • Works for directed and undirected networks (edges can have directions)

  • Works for weighted networks (a numeric value can be assigned to edges. It will be considered in computation of centralities)

 

Cytoscape 2.8.x

Click here to Download CentiScaPe (for Cytoscape 2.8.x)

 

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If you publish result using CentiScaPe please cite:

"Analyzing biological network parameters with CentiScaPe"
Giovanni Scardoni; Michele Petterlini; Carlo Laudanna. Bioinformatics 2009;
doi:10.1093/bioinformatics/btp517

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