Cluster analysis identified two groups among the 36 neural cell lines: 17 in a low-expression Cluster 1 and 19 in a high-expression Cluster 2. There was a significant association between cluster membership and GABRA2 rs279858 genotype (χ2= 9.9, df=2, p=0.007): Cluster 1 cell lines had a greater frequency of C alleles than those in Cluster 2 (0.76 vs. 0.34; χ2= 12.9, df=1, p=0.003) (Table 2). Scatter plots comparing RNA levels for GABRA2 to those for GABRG1, GABRA4, or GABRB1 RNA, Figure 2, illustrate group differences in chr4p12 GABAA subunit gene expression levels between the two clusters (Figure 2 A–C). Mixed-effects models identified significant differences in RNA expression between Cluster 1 and Cluster 2 for each of the chr4p12 GABAA genes (Figure 3 A–D) (GABRG1 F=44.6, df=1,34, p<0.001, GABRA2 F=44.5, df=1,34, p<0.001, GABRA4 F=45.9, df=1,34, p<0.001, GABRB1 F=82.7, df=1,34, p<0.001). There was no between-cluster difference in RNA levels for GABRD (Figure 3E; F=0.034, df=1,30, p=0.86) or RBFOX3 (Figure 3F; F=0.41, df=1,29, p=0.53).
