Open Access Highly Accessed Research article

Integrating multiple oestrogen receptor alpha ChIP studies: overlap with disease susceptibility regions, DNase I hypersensitivity peaks and gene expression

Adam E Handel12*, Geir K Sandve3, Giulio Disanto1, Lahiru Handunnetthi1, Gavin Giovannoni2 and Sreeram V Ramagopalan12

Author Affiliations

1 Medical Research Council Functional Genomics Unit and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK

2 Blizard Institute, Queen Mary University of London, Barts and The London School of Medicine and Dentistry, London, UK

3 Department of Informatics, University of Oslo, Blindern, Norway

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BMC Medical Genomics 2013, 6:45  doi:10.1186/1755-8794-6-45

Published: 30 October 2013

Additional files

Additional file 1:

We have included the following additional files.Table S1. Characteristics of included studies; Table S2. ESR1 binding sites overlapping with blacklisted regions; Table S3. Genomic location of ESR1 binding sites relative to the number of shared datasets; Table S4. Frequency of ESR1 binding sites possessing at least one JASPAR ESR1 motif (MA0112.2); Table S5. ESR1 enrichment within genomic regions associated with diseases/traits (O/E = observed/expected); Table S6. ESR1 enrichment within genomic regions associated with diseases/traits for central 200 bps of each interval (O/E = observed/expected); Table S7. GWAS SNPs or those in LD (r^2 ≥ 0.8) within ESR1 binding sites; Table S8. ESR1 enrichment within DNase I hypersensitivity peaks and estradiol differentially expressed genes (n.d. = not done); Table S9. ESR1 with and without motifs or DNase I hypersensitivity peaks enrichment within genomic regions associated with diseases/traits for central 200 bps of each interval (O/E = observed/expected; DHS = DNase I hypersensitivity peaks); and Table S10. Overlap of ESR1 ChIP-seq binding sites from primary cancer samples (O/E = observed/expected).

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Additional file 2: Figure S1:

MEME-identified motifs within ESR1 binding sites for individual datasets. E-values are shown for each motif along with TOMTOM similarity to known motifs (JASPAR (upper case) and uniprobe mouse (lower case) with E-value <10). Study details show the first author, tissue type, cell type and length of estradiol treatment.

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Additional file 3: Figure S2:

ESR1-like DREME-identified motifs within ESR1 binding sites for individual datasets. E-values are shown for each motif along with TOMTOM similarity to known motifs (JASPAR (upper case) and uniprobe mouse (lower case) with E-value <10). The motif shown is the top motif by E-value for all except Carroll et al. (second top) and Need et al. (third top). Study details show the first author, tissue type, cell type and length of estradiol treatment.

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Additional file 4: Figure S3:

MEME- and DREME- identified motifs within ESR1 binding sites without classical ESR1 recognition motifs. E-values are shown for each motif along with TOMTOM similarity to known motifs (JASPAR (upper case) and uniprobe mouse (lower case) with E-value <10).

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