Open Access Research article

Integration of Genome-Wide Computation DRE Search, AhR ChIP-chip and Gene Expression Analyses of TCDD-Elicited Responses in the Mouse Liver

Edward Dere1, Raymond Lo2, Trine Celius2, Jason Matthews2 and Timothy R Zacharewski13*

Author Affiliations

1 Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA

2 Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada

3 Center for Integrative Toxicology, Michigan State University, East Lansing, MI, 48824, USA

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BMC Genomics 2011, 12:365  doi:10.1186/1471-2164-12-365

Published: 15 July 2011

Additional files

Additional file 1:

Genomic location, gene annotation and enrichment values of significant (FDR < 0.01) TCDD-induced AhR enrichment at 2 hrs. Detailed results of the AhR ChIP-chip analysis that include the genomic location and TCDD-induced enrichment values, and the gene annotation of enrichment peaks located within the 10 kb upstream and transcribed region of a gene.

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Additional file 2:

Genomic location, gene annotation and enrichment values of significant (FDR < 0.01) TCDD-induced AhR enrichment at 24 hrs. Detailed results of the AhR ChIP-chip analysis that include the genomic location and TCDD-induced enrichment values, and the gene annotation of enrichment peaks located within the 10 kb upstream and transcribed region of a gene.

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Additional file 3:

Definitions of various genomic regions used to map regions of AhR enrichment. A) Genomic locations from the UCSC Genome Browser refGene database were used to obtain sequences for 10 kb region upstream of the TSS, the 5' and 3' UTRs, and the CDS of every known human, mouse and rat RefSeq sequence. A gene region is defined as the sequence spanning the region 10 kb upstream of a TSS through to the end of the 3' UTR. B) Intragenic DNA regions in a genome were determined by combining the non-overlapping gene regions. For example, gene regions of tissue specific isoforms of a gene that have different TSS positions were merged to determine the longest spanning range (genes C & C' and genes E & E'). Additionally, overlapping genes on both strands of the genome were also merged (genes B + E + E'). Non-transcribed DNA segments that span the regions between adjacent intragenic regions are defined as the intergenic DNA regions.

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Additional file 4:

TCDD-induced AhR enrichment (FDR < 0.01) density across the mouse genome at 2 hrs. The density of significant AhR enrichment (per Mbp) at 2 hrs were calculated for each of the defined genomic regions across the individual chromosomes.

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Additional file 5:

TCDD-induced AhR enrichment (FDR < 0.01) density across the mouse genome at 24 hrs. The density of significant AhR enrichment (per Mbp) at 24 hrs were calculated for each of the defined genomic regions across the individual chromosomes.

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Additional file 6:

Transcription factor binding site analysis of significant TCDD-induced AhR enrichment (FDR < 0.01) at 2 hrs. DNA sequences for the regions of significant AhR enrichment at 2 hrs were analyzed for transcription factor (TF) binding site motif over-representation using RegionMiner. The results list the TF matrices and their corresponding over-representation and z-score value.

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Additional file 7:

Transcription factor binding site analysis of significant TCDD-induced AhR enrichment (FDR < 0.01) at 24 hrs. DNA sequences for the regions of significant AhR enrichment at 24 hrs were analyzed for transcription factor (TF) binding site motif over-representation using RegionMiner. The results list the TF matrices and their corresponding over-representation and z-score value.

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Additional file 8:

Over-representation of transcription factor binding motifs located proximally (10-50 bp) of a DRE in a significantly AhR enriched region (FDR < 0.01). DNA sequences for the regions of significant AhR enrichment at 2 and 24 hrs possessing a DRE core sequence (5'-GCGTG-3') were analyzed for transcription factor (TF) binding site motif over-representation using RegionMiner. The results list the TF matrices and their corresponding over-representation and z-score value.

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Additional file 9:

Repetitive sequence elements identified in the de novo motif analysis of significant intragenic and intergenic AhR enriched regions (FDR < 0.01) lacking a DRE core. The repetitive over-represented motifs from each region are shown with their consensus and reverse complement sequence, and the Gibbs motif sampler score.

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Additional file 10:

Pathway analysis of genes associated with DRE-containing regions of AhR enrichment (FDR < 0.01) at 2 hrs. List of the most significant Bio-Functions (p < 0.01) identified using Ingenuity Pathway Analysis for the genes associated with a significant AhR enriched region (FDR < 0.01) containing a DRE core (5'-GCGTG-3') at 2 hrs.

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Additional file 11:

Pathway analysis of genes associated with DRE-containing regions of AhR enrichment (FDR < 0.01) at 24 hrs. List of the most significant Bio-Functions (p < 0.01) identified using Ingenuity Pathway Analysis for the genes associated with a significant AhR enriched region (FDR < 0.01) containing a DRE core (5'-GCGTG-3') at 24 hrs.

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Additional file 12:

Circos plots integrating DRE analysis, AhR enrichment (2 hrs; FDR < 0.01) and heatmaps for hepatic differential gene expression responses (|fold change| ≥ 1.5 and P1(t) > 0.999) induced by TCDD across the genome. Circos plots illustrate the ideograms for each individual chromosome and the entire genome and integrate the results of the DRE, ChIP-chip and gene expression analyses.

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Additional file 13:

Pathway analysis of differentially regulated genes (|fold change| ≥ 1.5 and P1(t) > 0.999) associated with regions of AhR enrichment (FDR < 0.01) at 2 hrs. List of the most significant Bio-Functions (p < 0.01) identified using Ingenuity Pathway Analysis for TCDD-elicited gene expression responses (|fold change| ≥ 1.5 and P1(t) > 0.999) associated with a significant AhR enriched region (FDR < 0.01) containing a DRE core (5'-GCGTG-3') at 24 hrs.

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Additional file 14:

Primer sequences used to verify 2 hr ChIP-chip responses. QRTPCR primers used to verify AhR enriched regions isolated from the 2 hr ChIP-chip.

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