What are the common approaches used in protein-protein interaction network analysis?

Question

[Diwan]

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.

Thanks
Diwan

Answer 1

[Giovanni M Dall'Olio]

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.

Answer 2

[favrin]

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.