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.