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Table 1 Publicly available gene expression data from breast cancer studies

From: Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures

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
  1. 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.