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.