Open Access Highly Accessed Research article

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

Oli MV Grober1, Margherita Mutarelli1, Giorgio Giurato1, Maria Ravo12, Luigi Cicatiello1, Maria Rosaria De Filippo1, Lorenzo Ferraro1, Giovanni Nassa12, Maria Francesca Papa1, Ornella Paris1, Roberta Tarallo12, Shujun Luo3, Gary P Schroth3, Vladimir Benes4 and Alessandro Weisz12*

Author Affiliations

1 Department of General Pathology, Second University of Naples, vico L. De Crecchio 7, 80138 Napoli, Italy

2 Molecular Medicine Laboratory, University of Salerno, via Allende, 84081 Baronissi, Italy

3 Illumina, Inc., Hayward, 94545 California, USA

4 Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg 69117, Germany

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BMC Genomics 2011, 12:36  doi:10.1186/1471-2164-12-36

Published: 14 January 2011

Additional files

Additional File 1:

Grober_ER-alpha_Binding_Sites ERα binding sites. The UCSC genome BED formatted file lists the chromosome, start coordinate, stop coordinate and identifier of the ERα binding sites.

Format: BED Size: 222KB Download file

Open Data

Additional File 2:

Grober_ER-beta_Binding_Sites ERβ binding sites. The UCSC genome BED formatted lists the chromosome, start coordinate, stop coordinate and identifier of the ERβ binding sites.

Format: BED Size: 359KB Download file

Open Data

Additional File 3:

Sheet 1: Additional Table S1 Differentially Regulated Genes. Overview of the 921 genes differentially regulated by E2 in ERβ+ vs ERβ- cells, containing the following additional information: gene set membership, symbol, Entrez ID, gene name and expression values (fold-change). Sheet 2: Additional Table S2 TFBS enrichment matrix. The worksheet shows the over-representation values for the TF binding matrices from ERE- binding sites. Sheet 3: Additional Table S3 Primary ERβ target genes, showing ERβ binding sites within 10 kb of the TU. Overview of the 424 putative ERβ primary gene targets containing the following additional information: gene set membership, category of ERβ binding sites, Symbol, Entrez ID, Gene Name, TU Coordinates, ERα Binding Sites Coordinates and ERβ Binding Sites Coordinates. Sheet 4: Additional Table S4 Primary ERα target genes, showing ERα binding sites within 10 kb of the TU in ERβ- cells. Overview of the 228 putative ERα primary gene targets containing the following additional information: Symbol, Entrez ID, Gene Name, TU Coordinates.

Format: XLS Size: 440KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional File 4:

GO analysis of primary ERβ target genes. Containing the following information: Biological process, Gene Ontology term, Name, Count in total GO population, Count in selected genes, % genes and p-value.

Format: DOC Size: 112KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional File 5:

GO analysis of primary ERα target genes. Containing the following information: Biological process, Gene Ontology term, Name, Count in total GO population, Count in selected genes, % genes and p-value.

Format: DOC Size: 88KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional File 6:

ERβ binding sites in proximity of miRNA loci. Containing the following information: miRNA name, ID of ER-β binding site upstream, Distance from the closest ERβ binding site upstream, ID of ER-β binding site downstream and Distance from the closest ERβ binding site downstream.

Format: DOC Size: 118KB Download file

This file can be viewed with: Microsoft Word Viewer

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