Biological network and pathway Analysis
IPA (Ingenuity Pathway Analysis; Ingenuity Systems; Redwood City, CA www.qiagen.com/ingenuity) analysis (using trial version) was done on all expression value containing protein datasets. Uniprot IDs and respective gene names of proteins served as identifiers. IPA mapped protein IDs were used for core analysis. A threshold of 1.3 and p-value<0.05 (using in-built Fisher’s exact test) was constant throughout IPA analysis. Ingenuity Pathway Analysis Knowledge Base was the database against which major canonical pathways and protein networks were identified from the experimental dataset. The analysis parameters were specific for the organism and tissue used. IPA also predicted upstream regulator proteins for experimental datasets. IPA based analysis revealed the most significant canonical pathways, upstream regulator proteins, protein-protein networks and protein-process networks.