Re: [Cytoscape-discuss] How to analyze the results of the network?

[piet molenaar]

Hi, 

I think this is slightly off topic for this discuss list that involves issues concerning Cytoscape as a graph visualization tool, not about graph topology itself which is a whole field of scientific study.

 

The meaning of some of the parameters is explained here; http://www.bioinformatics.org/aminonet/doc/formu.pdf

For other ones you can lookup wikipedia; like here: http://en.wikipedia.org/wiki/Betweenness_centrality 

Hope this helps,

Piet

On Mon, Nov 5, 2012 at 2:05 AM, Ash2ash Lee <wint...@gmail.com> wrote:

Thank you for developing the tool, cytoscape, for data integration and network visualization. I am a Chinese graduate student working on a biological issue, constructing several pieces of protein-protein-interaction network. But now I have some problems on this issue.

Firstly, I could not understand the meaning of the topological parameter( average clustering coefficient, betweenness centrality, closeness centrality, neighborhood connectivity, node degree distribution, shared neighbors, shortest length, stress centrality, topological coefficients), and after reading the "help" information, I still have no idea;

Another problem is that I have used the "Network analysis" plugin to analysis the network, and get several results, named average clustering coefficient distribution, betweenness centrality, closeness centrality, neighborhood connectivity distribution, node degree distribution, shared neighbors, shortest length, stress centrality distribution and topological coefficients. But I don't know whether distributions of such topological parameters in my network fit the distributions of them under the ideal conditions, and also I don't know the meaning of the distributions, as I have weak background of topology...

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

[giovanni scardoni]

Hi,
you can use the CentiScaPe plugin (for Cytoscape 2.8.3) to analyze the
topology of the network calculating
several centralitiy parameters. You can find the description and the
biological meaning of each parameter in the CentiScape
tutorial.
Download it and the tutorial here:
http://www.cbmc.it/~scardonig/centiscape/centiscape.php
Hope this helps,
Giovanni

2012/11/6 piet molenaar <piet...@gmail.com>:

Giovanni Scardoni
The Center for BioMedical Computing (CBMC)
www.cbmc.it
University of Verona
Strada le Grazie, 15 -37134
Verona -Italy