A schematic diagram of eQTL studies. Suppose the eQTL is captured by marker Z with allele A and B. We code Z as 0 or 1 if the inherited allele is A or B, respectively. (a) 1D-trait mapping: conventional eQTL mapping compares one gene expression profile against one marker genotype profile to find significant differential expression. (b) 2D-trait mapping: co-expression trait mapping aims at the detection of changes in the co-regulation pattern by comparing two genes' expression profiles against one marker genotype profile. (c) Two genes are co-up-regulated under allele B(Z = 1). (d) The expression of one gene has a shift in the marginal distribution, detectable by 1D mapping. (e) The expression of both genes are shifted in the marginal distributions, detectable by 1D mapping. Only (b) and (c) are detectable by our 2D-trait mapping method.