Classification of genes according to their pattern of gene expression divergence. The average log2 expression fold change between the alleles in the hybrids (F1) and between the parental strains (F0s) is plotted on the x- and y-axis, respectively. (A) Genes for which the expression levels have not diverged between the two strains are classified as conserved (colored black), while genes in which expression has diverged are classified as cis, trans, or cis and trans according to whether the divergence is explained by at least one regulatory variant acting in cis (colored yellow) or in trans (colored red), or by at least two regulatory variants, one in cis and one in trans (colored purple). (B) Subdivision of the cis and trans category. The regulatory variants can cause gene expression changes in the same direction with the regulatory variant in cis having a stronger effect on expression change than the regulatory variant in trans (blue), or the variant in trans having a stronger effect than the variant in cis (green). Expression changes can also be in opposite directions with the variant in cis having a stronger effect than the variant in trans (brown), or the variant in trans having a stronger effect than the variant in cis (orange).
