We compared GABAB1 gene expression levels between alcoholic and control subjects using whole transcriptome libraries (Figure 5). Reads per kilobase of exon model per million mapped reads (RPKM) is most commonly used for RNA-seq expression studies and is calculated for transcripts considering known exons (29). However, we discovered unknown splice junctions at introns and intergenic regions, and many reads were also mapped there. Thus, RPGM was introduced to consider these regions. In the genome wide study, RPGM allowed calculation of expression levels from each gene as well as any small interesting regions within the gene model.
