DESCRIPTION:
LncRNA and protein-coding gene (PCG) expressions in the NAc from 41 subjects with alcohol dependence (AD) and 41 controls were assessed via a regression model. Weighted gene coexpression network analysis was used to identify lncRNA and PCG networks (i.e., modules) significantly correlated with AD. Within the significant modules, key network genes (i.e., hubs) were also identified. The lncRNA and PCG hubs were correlated via Pearson correlations to elucidate the potential biological functions of lncRNA. The lncRNA and PCG hubs were further integrated with GWAS data to identify expression quantitative trait loci (eQTL). A significant genotype/disease interaction for a SNP/gene pair indicates that the effect of genotype on expression is significantly different in AD cases versus controls. At FDR of 10%, we identified 93 eQTL with significant (SNP × AD) interaction terms that mediate the expression of 24 PCG hubs and 69 lncRNA hubs. The most significantly interacting PCG eQTL was between FK506 binding protein 51 (FKBP5) and rs2766532 (Fig. 6 A,B), whereas the most significantly interacting lncRNA eQTL was between G006838 and rs12142153 (Fig. 7 A,B). Data shown here are PCG hubs that were associated with/ affected by eQTLs at FDR p<0.10 that had a significant interaction between SNP and AD status (Table S10A,B).
LABEL:
PCG NAc eQTL associations sig. SNP x AD interaction in cases vs. controls, FDR p<0.10
SCORE TYPE:
Binary
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