Cis-regulatory deletions are less pleiotropic than trans-regulatory deletions. (A) A copy of the schematic shown in figure 1A shows the pleiotropic effects (purple) of a trans-regulatory deletion (blue node) to the focal gene (orange node). The pleiotropic effects include all genes differentially expressed in the deletion of the trans-regulator, excluding the focal gene and the trans-regulator itself. Note 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 did not show a change in expression in the trans-regulatory deletion of the focal gene shown in blue, and are not considered pleiotropic effects of the trans-regulatory deletion. (B) The number of differentially expressed genes in the deletion of PTR2 (pleiotropy of its cis-regulatory deletion, green line) is smaller than the median (black line) number of differentially expressed genes for all trans-regulatory deletions to PTR2 (histogram). (C) For all focal genes, the log10 median pleiotropy of all deletions that act in trans to that gene is plotted on the y-axis and the log10 pleiotropy of the deletion that acts in cis to that gene is plotted on the x-axis. An x = y line is shown. (D) A histogram of differences between cis-regulatory pleiotropy and the median trans-regulatory pleiotropy for all focal genes included in the study is shown. The median difference (red line) is significantly greater than zero (black line) (P-value = 3 × 10−165, one-sided t-test).
