Ingenuity Pathways Analysis (IPA) of genes with FDR ≤ 0.20 revealed many canonical pathways that differed between alcoholics and controls (Table 2). Signaling pathways predominated, along with stress or immune responses. Acute phase response signaling, IL-6 signaling, IL-8 signaling, IL-10 signaling, LPS/IL-1 mediated inhibition of RXR function, mTOR signaling, hypoxia signaling, p38 MapK signaling, EIF2 signaling (eukaryotic translation initiation factor 2), and glucocorticoid signaling were up. GADD45 (growth arrest and DNA-damage-inducible) signaling, p38 signaling, and Her2 signaling, were mixed or down. Many of the pathways shared key genes. ATM (ataxia telangiectasia mutated; down 20%) is in 39 of the 60 pathways and AKT1 (v-akt murine thymoma viral oncogene homolog 1; increased 8%) is in 32 of the pathways. TRAF6, PRKD1, MAP2K3, RHOB and RHOC, CREB1, CCND, and the guanine binding proteins GNAI1, GNB2, and GNG5 were each in at least 12 of the pathways.
