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Protein-protein interaction pathway analysis

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.

pathway analysis protein expression data
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updated by zhao03 • zhao03 • written by rida.rehman • rida.rehman

2 answers

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

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written by Rodrigocout • Rodrigocout

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

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written by zhao03 • zhao03

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