Next, we evaluated differences in the proportion of genes that contain the “NF-κB”- or “p50 homodimer”-subtypes of κB elements in 10 kb promoter region between upregulated, downregulated and control genes (Figure 5C, D; Table S4). There was a significant difference in the frequency of occurrence of genes with each “NF-κB”- or “p50 homodimer”- subtype of κB elements between up- and down regulated genes and control genes (Chi-square test, df = 2: χ2 = 8.30, P<0.05; χ2 = 7.75, P<0.05). The frequency of each subtype of binding sites in the downregulated genes was lower compared to the upregulated genes (Chi-square test, df = 1: χ2 = 4.72, P<0.05; χ2 = 4.94, P<0.05) and control genes (Chi-square test, df = 1: χ2 = 8.23, P<0.01; χ2 = 7.75, P<0.01) (Figure 5 C, D). Thus, genes with κB elements were generally upregulated in the PFC in alcoholics; these genes may be derepressed due to decreased activity of the p50 homodimer, an inhibitor of transcription and a dominant κB binding factor.
