Fig. 1

Isoform eQTLs (ieQTLs) and gene eQTLs. A Genes and isoforms. Multiple isoforms can be expressed from a single gene. Gray boxes, solid line, and dotted lines indicate exons, introns, and splicing patterns, respectively. B Patterns of gene eQTLs (green) and ieQTLs (yellow and blue) by genotype (0, 1, and 2). Gene eQTLs are identified through the expression levels of entire genes, while ieQTLs are detected based on the expression levels of individual isoforms. The upper panels show a pattern in which one eQTL affects all isoforms of the gene and the overall gene expression. The lower panels display a pattern where one eQTL affects only one isoform, while the overall gene expression remains unaffected. This pattern is difficult to detect using conventional gene-based eQTL analysis. C Differential ieQTLs and opposite ieQTLs. Differential ieQTLs are ieQTLs that exhibit significantly different effects on distinct isoforms. Opposite ieQTLs are differential ieQTLs with contrary effects on different isoforms. D Venn diagram of the number of gene eQTLs and ieQTLs identified in this study