Ingenuity Pathway Analysis (IPA, www.Ingenuity.com) was performed using probe sets with an FDR ≤ 0.20 to examine Canonical Pathways. For all of our analyses the Ingenuity knowledge base was used as the reference set to insure all analyses used similar parameters. We analyzed the list of probe sets identified at FDR ≤ 0.20 from our study, the list of multiply identified genes described above, and the cell-type enriched sets of genes described above. We also carried out an IPA Upstream Regulator report to identify transcription factors, cytokines, and chemicals, etc. that are predicted to be activated or inactivated based on the direction of change in their downstream targets; a positive Z-score indicates likely activation and a negative Z-score indicates likely inactivation in alcoholics relative to the controls.
