Table 1

Publicly available gene expression data from breast cancer studies

Dataset symbol

Number of arrays

Institution

Reference(s)

Platform

Data source

Number of GeneIDs


Genomic platforms

NKI

337

Nederlands Kanker Instituut (Amsterdam, The Netherlands)

[19,20]

Agilent

Author's website

13,120

EMC

286

Erasmus Medical Center (Rotterdam, The Netherlands)

[21]

Affymetrix U133A

GEO: GSE2034

11,837

UPP

249

Karolinksa Institute (Uppsala, Sweden)

[3,11]

Affymetrix U133A,B

GEO: GSE4922

15,684

STOCK

159

Karolinska Institute (Stockholm, Sweden)

[3,13]

Affymetrix U133A,B

GEO: GSE1456

15,684

DUKE

171

Duke University (Durham, NC, USA)

[8]

Affymetrix U95Av2

Author's website

8,149

UCSF

161 + 8

University of California at San Francisco (USA)

[9]

cDNA

Author's website

6,178

UNC

143 + 10

University of North Carolina (Chapel Hill, NC, USA)

[7]

Agilent HuA1

Author's website

13,784

NCH

135

Nottingham City Hospital (Nottingham, UK)

[12]

Agilent HuA1

AE: E-UCON-1

13,784

STNO

115 + 7

Stanford University (Palo Alto, CA, USA)/Norwegian Radium Hospital (Oslo, Norway)

[16]

cDNA

Author's website

5,614

JRH1

99

John Radcliffe Hospital (Oxford, UK)

[17]

cDNA

Journal's website

4,112

JRH2

61

John Radcliffe Hospital

[18]

Affymetrix U133A

GEO: GSE2990

11,837

MGH

60

Massachusetts General Hospital (Boston, MA, USA)

[10]

Agilent

GEO: GSE1379

11,421

expO

239

International Genomic Consortium

[41]

Affymetrix U133v2

GEO: GSE2109

16,634

TGIF1

49

EORTC trial 10994

[5]

Affymetrix U133A

GEO: GSE1561

11,837

BWH

40 + 7

Brigham and Women's Hospital (Boston, MA, USA)

[14]

Affymetrix U133v2

GEO: GSE3744

16,634

Small diagnostic platforms

TRANSBIG

253

TRANSBIG Consortium

[2]

Agilent

AE: E-TABM-77

1,052

EMC2

180

Erasmus Medical Center

[6]

Affymetrix (custom)

GSE3453

86

HPAZ

96

Hospital La Paz (Madrid, Spain)

[4]

RT-PCR

Appendix of [4]

61

Total

2,865 = 2,833 carcinomas + 32 nonmalignant breast tissues

Number of the union of all GeneIDs:

17,198

Number of GeneIDs common to genomic platforms:

1,963


Datasets UNC, STNO, UCSF, and BWH include a small number of normal breast or fibroadenoma tissue samples. AE, ArrayExpress (accession); Affymetrix, Affymetrix, Inc., Santa Clara, CA, USA; Agilent, Agilent Technologies, Inc., Santa Clara, CA, USA; EORTC, European Organization for Research and Treatment of Cancer; GEO, Gene Expression Omnibus (accession); RT-PCR, reverse transcription-polymerase chain reaction.

Wirapati et al. Breast Cancer Research 2008 10:R65   doi:10.1186/bcr2124

Open Data