Question: Protein-protein interaction pathway analysis
0
gravatar for rida.rehman
9 months ago by
rida.rehman0 wrote:

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.

ADD COMMENTlink modified 11 weeks ago by zhao0330 • written 9 months ago by rida.rehman0
0
gravatar for Rodrigocout
11 weeks ago by
Rodrigocout0 wrote:

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

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by Rodrigocout0
0
gravatar for zhao03
11 weeks ago by
zhao0330
zhao0330 wrote:

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

ADD COMMENTlink written 11 weeks ago by zhao0330
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1720 users visited in the last hour