Evaluation of AHR binding: presence and effects. A higher fraction of genes that were significantly affected by AHR-status across multiple tissues were found to possess AHRE-I (Full) motifs in the upstream 5′-regulatory region, compared to genes that were AHR-status independent (A). At several count thresholds, the fractions of significant and non-significant genes were contrasted for the presence of both AHRE-I (Full) and AHRE-II motifs (B). Similar to findings of the transcription factor binding site analysis, a higher fraction of genes significantly altered across multiple tissues were found to exhibit AHR binding in vitro (C). The AHR appears to largely exert an upregulating effect on genes in rat liver in the absence of exogenous ligands, but a smaller fraction of downregulation is present as well (D). Genes that were differentially-abundant in the constitutive condition were also observed to be altered in greater proportions following TCDD-induced AHR activation in the mouse liver (E) and rat liver (F).