Network Analysis of Each Cluster of Protein Interaction Network

Question

[hkarakurt]

Hello, I have a really big PPI network and I clustered the network. Is there a way to analyze each cluster to find metrics of each cluster such as closeness, degree etc. I want to treat each cluster as an independent network but I have 56 cluster so an automated library would be great. I searched but could not find such a library. Is there a way to do it?

I can use R, Python or Cytoscape for this task.

Thank you in advance.

Answer 1

[Jean-Karim Heriche]

Take a look at the igraph package for R.

[hkarakurt]

Thank you for your answer. I am already using igraph but as I know it does not have a function to extract and analyze the subset of main graph. I can try with a for loop.

[Jean-Karim Heriche]

There's no function that will do everything you ask for in one go if that's what you mean. Otherwise, you can extract a subgraph corresponding to a list of nodes with the subgraph() function then indeed operate on the subgraphs in a loop (or in parallel).

Answer 2

[Shalu Jhanwar]

Have a look at Cytoscape Analyzer http://manual.cytoscape.org/en/stable/Network_Analyzer.html. From the GUI of Cytoscape, it's very easy to run this functionality either on an entire or subset of the network. It computes different network properties including Node Degree Distribution, Betweenness Centrality, Closeness Centrality etc.

[hkarakurt]

Thank you for your answer. I can use Cytoscape to analyze a subset of nodes but as I mentioned for more than 50 cluster (can go up to 350) it would be really time consuming activity. I am more like looking for a way to analyze each cluster with single function.