Finally, transcriptome-wide expression correlation analysis showed that expression of PHF3 and PTP4A1 transcripts in brain was significantly correlated with expression of many alcoholism-related genes (Table S2) (although some associations between these genes and alcoholism have not yet been well replicated so far). Interestingly, many of these genes were those top-ranked genes identified by previous GWASs on alcoholism [5], [6], [16], including the GWAS in German sample that was different from the datasets we used. These top-ranked gene included NRD1, PDE4B, OLFM3, NXPH2, PECR, PPARG, SH3BP5, BBX, PCDH7, LOC91431, IPO11, CAST, ERAP1, PPP2R2B, FAM44B, ANKS1A, EPHA7, NAP1L4, CARS, CCDC41, PCDH9, CDH8 and CDH13 (see Table S2). Additionally, some genes co-expressed with PHF3 and PTP4A1 were from the dopaminergic (DRD2, DRD4 and TH) [17], serotoninergic (HTR2A, HTR3B and SLC6A4) [18], GABAergic (GABRA1, GABRA2, GABRB1, GABRB2 and GABRG2) [19], glutamatergic (GAD1) [6], histaminergic (HNMT) [20] and endocannabinoid (CNR1) [21] systems (α = 3.4×10−6).
