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) | 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) | Affymetrix U133A,B | GEO: GSE4922 | 15,684 | |
STOCK | 159 | Karolinska Institute (Stockholm, Sweden) | 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 | |||||