g a Branson 450 sonifier. Supernatant was trans ferred to fresh microcentrifuge tubes and incubated with rabbit IgG and anti AhR overnight at 4 C under gentle agitation. ChIP samples were washed and the DNA was isolated Sorafenib as pre viously described. For ChIP chip experiments, immunoprecipitated DNA isolated following immuno precipitation with anti AhR of liver extracts from TCDD treated mice was linearly amplified using a whole genome amplification kit according to the manu facturers instructions. Linearly amplified DNA was fragmented by limited DNAseI digestion and hybridized to Affymetrix GeneChip mouse 2. 0R tiling arrays as previously described. The hybridization Inhibitors,Modulators,Libraries and washing steps were performed according to the manufacturers proto col at the Centre for Applied Genomics.

Data were normalized and analyzed using Cis Genome and mapped against mouse genome version mm9. Enriched regions with a false discovery rate of 1. 0% were determined by comparing tri plicate samples of AhRTCDD to triplicate IgGTCDD using a moving average approach with default settings in TileMap v2. Regions were merged if the gap between Inhibitors,Modulators,Libraries them was 300 bp and the number of probes failing to reach the cut off was 5. Regions were dis carded if they were 120 bp or did not contain at least 5 continuous probes above the cut off. ChIPed DNA was purified using the PCR purification kit from BioBa sic Inc. and quantified Inhibitors,Modulators,Libraries using quantita tive real time PCR. Fold enrichment values were calculated relative to IgG controls. ChIP PCR primer sequences are provided in Additional File 14.

ChIP chip Location Analysis The mouse genomic assembly and associated annotation within the refGene and refLink databases were downloaded from the UCSC Genome Browser. Individual segments of a gene region Inhibitors,Modulators,Libraries for each mature gene encoding reference sequence were determined using the genomic coordinates within the refGene data bases. Intragenic DNA regions within the genomes were computationally identified by merging overlapping gene regions from both strands of the genome, and the DNA between adjacent intragenic regions are defined as the non transcribed intergenic DNA regions. AhR enrich ment densities were calculated based on the number of significant enriched regions occurring in an interrogated Drug_discovery region divided by the total sum of the region length. Gene annotation asso ciated with each RefSeq sequence was derived from the refLink database in the UCSC Genome Browser.

Transcription Factor Motif Analysis The locations of AhR enrichment were compared against 5 GCGTG 3 DRE core sequence locations in the mouse genome. Identification of TF motifs over represented in regions containing a DRE core were performed using the default parameter settings thoroughly in RegionMiner, a program within the Genomatix suite of applications that contains an extensive database of TF binding motifs. Identified module families and individual matrices with z scores 3 were considered significant. De novo motif discovery was performed using the Gibbs moti