Nested effects do not explain the greater pleiotropy of trans-regulatory deletions relative to cis-regulatory deletions. (A) A copy of the schematic from figure 1A shows the effects of the trans-regulatory deletion (blue node) that may be due to indirect effects via a change in the expression of the focal gene (orange node). Recall that an arrow is shown from the trans-regulator to every gene whose expression was altered when the trans-regulator was deleted. Consequently, the two gray dots connected to the focal gene shown in pink in (A) did not show a change in expression in the trans-regulatory deletion of the focal gene shown in blue and were thus not part of the nested effects observed. (B) A copy of the schematic from figure 1A shows how nested effects were subtracted from the pleiotropic effects of the trans-regulators to estimate pleiotropic effects of trans-regulators that occur in parallel to the focal gene. (C) The median pleiotropic effects of trans-regulators occurring in parallel to the focal gene, calculated as the number of differentially expressed genes in the trans-regulatory deletion minus any nested effects, is plotted on the y-axis relative to the total pleiotropic effects of the cis-regulatory deletion plotted on the x-axis. An x = y line is shown.