There are greater differences in TFBSs in cis-affected genes than trans-affected genes. (A) We identified TFBSs for the four immune-responsive transcription factors Dl, Rel, Srp, and CrebA in a 1-kb region upstream of 219 cis-affected genes and 199 trans-affected genes. Differences in total TFBS numbers between genotypes were calculated for each gene and plotted. We find that variance in the distribution of these differences is significantly greater in genes showing cis effects (F-test to compare distribution variances, Bonferroni-corrected). (B) For Dl TFBSs, there was not a significant difference in the width of the TFBS distribution between genes showing cis effects and trans effects. (C–E) For Rel, Srp, and CrebA TFBSs, there was a broader distribution of TFBS differences in genes with cis effects than in genes with trans effects. (F) A larger proportion of genes showing cis effects had a difference in total TFBSs than did genes showing trans effects, although the differences in these proportions were not significant.
