Question: What are the common approaches used in protein-protein interaction network analysis?
gravatar for Diwan
5.4 years ago by
United States
Diwan560 wrote:

Hello all,

I have a generic question and would appreciate your input. I have a list of proteins involved in a disease (eg. proteins involved in liver cancer) and would like to identify other unknown proteins related to the disease.  I can map the list proteins to PPI (biogrid etc) and extract sub-networks of closely related proteins. Is this too trivial? Are there other more useful methods (that makes use of some statistics) that will give new information?

(or) What are the methods/approaches that you will use for protein-protein interaction analysis?

Note: I am curious because in case of gene expression analysis there are some standard set of approaches: differential expression, clustering, GO-term enrichment, pathway enrichment that is commonly done. 



ADD COMMENTlink modified 3.8 years ago by favrin20 • written 5.4 years ago by Diwan560
gravatar for Giovanni M Dall'Olio
5.4 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

I would start with getting the subnetwork of closely interacting proteins. It's better to start with the simple things first, and then you may eventually go to more advanced analysis afterwards.

I would also suggest you to have a look at Cytoscape, and at its App Store. It contains many plugins that will be useful for the pathway and interactions analysis.

ADD COMMENTlink written 5.4 years ago by Giovanni M Dall'Olio26k
gravatar for favrin
3.8 years ago by
favrin20 wrote:

I find that esyN is very effective for the network analysis. 

It allows to study the what are the central genes in your network - and what happens when you delete them - and importantly what drugs interact with the genes in your network. 


ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by favrin20
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