We analyzed RNA extracted from the hippocampi of 20 alcoholics and 19 controls (6 females in each group) using Affymetrix Gene 1.0 ST microarrays. Supplemental Table S1 describes the samples. Subject age and RNA integrity (RIN) did not significantly differ between alcoholics and controls (all p > 0.4). The single factor that most affects microarray measurement of gene expression from post mortem brain tissue is the pH (Atz et al., 2007); pH (mean 6.5, SD 0.3) did not significantly differ between alcoholics and controls. A total of 22,987 probe sets (80% of the core probe sets on the Affymetrix Gene 1.0 ST array) were expressed (detected above background) in at least 1 of the 2 groups (alcoholics or controls). A 3-way ANOVA using factors for phenotype (alcoholic/control), sex, and microarray-processing batch detected 743 probe sets that significantly differed between alcoholics and controls at a False Discovery Rate (FDR) ≤ 0.20. This represented 639 named genes (46 of which were measured twice) plus 58 unnamed probe sets (Supplemental Table S2). Among the significant probe sets, 50% (52% of the named genes) showed absolute fold changes ≥ 1.2 (Figure 1). Slightly over half the changes (53%) reflected lower expression in the alcoholics.
