Fig. 3

Classification of genes according to the expression pattern of purebreed and hybrid data sets. Consider the male brain a and the female brain b of cross 2, for example (for the other groups, see Additional file). Each point represents a single gene and is color-coded according to its regulatory category. The coordinate position shows the average log2 expression fold-change between the alleles in the hybrids (y-axis) and between the two purebreeds (x-axis). The proportion of each category is summarized in the bar graph c, where we removed the conserved and ambiguous genes, and further subdivided the cis + trans category genes into two categories, based on whether the cis and trans variants acted in the same direction or in opposite directions. The number above the bar represents the proportion of genes in the regulatory category, and the number on the bar represents the gene count of the category