5A for statistical significance; Fig. 5B for enrichment). Processes that pertain to oxidation–reduction were commonly dysregulated in L-E, H/W, LnA, and LnC rats but not in F344 and Wis rats, perhaps implying different mechanisms that animals possess for handling TCDD. By contrast toxin metabolic processes were significantly enriched across all

six strains, and many core TCDD-responsive genes (e.g. Cyp1a1) lie within this highly enriched category. In order to gain additional insight into the functional processes of the candidate genes, we performed RedundancyMiner analysis. Redundant GO categories were eliminated and parent categories were weighted to prevent over-representation. Redundant TSA HDAC molecular weight GO terms were collapsed into groups; GO categories that were recognized as statistically significant from GOMiner analysis were also significant after application of RedundancyMiner. Oxidoreductase activity and toxin metabolic process showed significant enrichment before and after RedundancyMiner analysis (FDR < 0.01),

indicating the robustness of the results (Fig. 5C). To provide additional mechanistic insight into how this functional diversity of TCDD responses is generated, we hypothesized that a small number of transcriptional regulators were at play. We therefore analyzed the occurrence of transcription factor binding sites (TFBSs) in TCDD-responsive genes using enrichment analysis as previously described (Boutros et al., 2011). We plotted the number of occurrences and the maximal conservation scores of each motif CP-868596 cost against the number of rat strains in which the gene was affected by TCDD treatment. AHRE-I has been found to reside on common

AHR-regulated genes such as Cyp1a1 where it binds the ligand–AHR–ARNT complex and enhances transcription. More recently, several studies have revealed that the AHRE-II motif aids transcription of Cyp1a2 and some other TCDD-responsive genes ( Boutros et al., 2004 and Sogawa et al., 2004). We analyzed the number and conservation of each motif across the strains ( Figs. 6A–D). AHRE-I motifs were conserved within genes that were significantly altered across all six strains, whereas Palmatine AHRE-II motifs were not conserved across the rat strains that we tested. Finally, to examine potential roles of the selected genes in mediating TCDD toxicity and to check whether the responsiveness of these genes is regulated in a time- or dose-dependent way, we conducted PCR analysis on six genes across 152 animals (84 H/W rats and 68 L-E rats) in both time-course (from 0 to 384 h) and dose–response experiments (from 0 to 3000 μg/kg). Experiments involving different time points were used to determine whether the genes exhibit acute or downstream effects; dose–response experiments were used to observe patterns of expression with increasing dose that might relate to doses that evoke hepatic toxicity.