To see whether the alcoholics differed in expression of genes enriched in particular cell types, we examined the sets of genes whose expression is known to be enriched in astrocytes, oligodendrocytes, or neurons (Cahoy et al., 2008), noted in Supplemental Table S2. The vast majority of these cell-enriched genes were not differentially expressed: about 95% have FDR > 0.20. However, for those genes that were differentially expressed, the fraction up and down was skewed compared to the overall results. Eighty-three percent of the differentially expressed transcripts enriched in oligodendrocytes were expressed at lower levels in alcoholics (p = 3.9 × 10−9), as were 83% of the differentially expressed transcripts in neurons (p = 2.1 × 10−4), whereas only 53% of the total probe sets were down. The differentially expressed genes expressed in astrocytes demonstrated the opposite trend, with 61% at higher levels in alcoholics (p = 0.003), including hypoxia response genes.
