Analysis of TFBS Enrichment.

ProbeSets differentially expressed between strains/lines or showing AHR-dependent effects were identified using linear models. The promoter regions for these genes were extracted from UCSC build rn4 of the rat genome and analyzed for transcription-factor binding-site (TFBS) enrichment using a library of 123 position-weight matrices. Statistical significance was estimated using five separate tests, and only those matrices enriched in at least four of the five are reported here. The Motif ID is the identifier given in the JASPAR library, and the numeric columns correspond to the p-value for enrichment (close to zero) or depletion (closer to one) of that motif in each contrast. The p-values reported here are from 1,000 permutations of a background dataset of hepatically expressed genes (see Methods). NS, not significant (p<0.05).