Protein-protein interaction pathway analysis

Question

[rida.rehman]

I am interested in doing pathway analysis on my protein expression data but I am not sure from where should I being. I did study some basics and understood the science behind it but now I have protein expression data from arrays which I used LIMMA package to process. Now I want to do pathway analysis for which I need some guidance. I was thinking of using GSEA for which I think gene expression data (gene annotation and all) is required but again I have protein expression data ( phosphorylated proteins after stimulus) so I'm kind of confused, lost and not sure what to do. What i would like to see is which pathway my deferentially expressed proteins belong to and how they might be interacting with eachother or which pathway they probably are activating.

Answer 1

[Rodrigocout]

I think you could use STRING. You can do a protein-protein interaction followed by pathway enrichment analysis.

Answer 2

[zhao03]

you can try to use clusterProfiler, a R package for enrichment