Could any of you help me to explain the steps in creating backbone network or the steps in validating the same in Cytoscape?

Question

[sasmbi06]

I am doing my work in protein protein interaction network and I have constructed PPI using STRING database and Cytoscape software. But i need to create backbone of the network using nodes with high degree and high BC and the test netowrk also..pls help me to find the accuracy in creating backbone and validating the network.

Thank you

Answer 1

[xanderpico]

I don't know precisely what you mean by "backbone", but you can readily measer degree, betweeenness centrality and other network properties in Cytoscape. You can then use the distribution of those properties to choose cutoffs to define your backbone I suppose. Here are two approaches I would recommend:

1. New Analyzer app for Cytoscape: http://apps.cytoscape.org/apps/analyzer. See instructions for how to invoke Analyzer and even plot results using CyCharts.

2. CentiScape app for Cytoscape: http://apps.cytoscape.org/apps/centiscape. Again, the app page provides instrutions and links to tutorials, etc.

The graph analysis category of apps is a good place in general to find apps to do these sorts of things: http://apps.cytoscape.org/apps/with_tag/graphanalysis