Table 1 |
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|
Publicly available gene expression data from breast cancer studies |
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| Dataset symbol |
Number of arrays |
Institution |
Reference(s) |
Platform |
Data source |
Number of GeneIDs |
|
|
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| Genomic platforms |
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| 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 |
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| 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. |
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|
Wirapati et al. Breast Cancer Research 2008 10:R65 doi:10.1186/bcr2124 |
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