Question: Network Analysis of Each Cluster of Protein Interaction Network
0
gravatar for hkarakurt
8 weeks ago by
hkarakurt100
hkarakurt100 wrote:

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.

python ppi network R • 138 views
ADD COMMENTlink modified 8 weeks ago by Shalu Jhanwar460 • written 8 weeks ago by hkarakurt100
1
gravatar for Jean-Karim Heriche
8 weeks ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

Take a look at the igraph package for R.

ADD COMMENTlink written 8 weeks ago by Jean-Karim Heriche23k

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.

ADD REPLYlink written 8 weeks ago by hkarakurt100

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).

ADD REPLYlink written 8 weeks ago by Jean-Karim Heriche23k
1
gravatar for Shalu Jhanwar
8 weeks ago by
Shalu Jhanwar460
Switzerland
Shalu Jhanwar460 wrote:

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.

ADD COMMENTlink written 8 weeks ago by Shalu Jhanwar460

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.

ADD REPLYlink written 8 weeks ago by hkarakurt100
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