Is there a way to Find cut vertices or articulation points in PPI networks by cytoscape?

[azad jafarnezhad]

Hi everybody I Want to find articulation points in PPI networks by cytoscape,Is there a plugin for it? any suggestion or point is helpful. Thank you. Azadeh

[giovanni scardoni]

Hi Azadeh,

the Interference plugin can be used to this goal. 

Interference is based on removing a node and calculating the variation on the centrality values. 

As "side effect" of the computation, the plugin give you a message when the removal of the selected node  
results in one or more disconnected component. 

Use the Interference plugin in this way:

-select the nodes you want to verify (all the nodes if needed)

-select one or more centralities

-select the "single nodes" option

This will remove one by one all the nodes and give you a message when a removal results in disconnected components.

Interference is not written to find articulation point, so the computation could take a lot of time if the network is large and you 

have to write by hand the name of the nodes when the message appear.

But if you need something more informative you can use the interference plugin with the betweenness centralities.

for each node you will find its "area of influence" i.e. the set of nodes that are more affected by the removal of the node

(measured as variation on betweenness). It is a virtual knock-out experiment on the network.

Here you find the plugin, the tutorial and some examples:

http://www.cbmc.it/~scardonig/interference/Interference.php

hope this help,

Giovanni

2011/10/15 azad jafarnezhad <jafarne...@yahoo.com>

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Giovanni Scardoni
The Center for BioMedical Computing (CBMC)

www.cbmc.it
University of Verona
Strada le Grazie, 15 -37134
Verona -Italy