I have expression data from 65 patient. I am interested in creating protein-protein interaction network based on known interaction (STRINGdb) and expression (RNA-seq). My main purpose is to identify what interactions are present in tumor vs normal cell, as I have expression data for both. I am focusing on respiration pathway genes only. Could anyone guide me what would be a better way using Cytoscape or if not what is a better alternative?
Thanks so much!