Table 1 Characteristics of the breast cancer datasets used in this study
From: Detecting gene signature activation in breast cancer in an absolute, single-patient manner
Dataset | Training/validation | Platform | Number of samples | ER+ | Her2+ | BasalL | Her2 E | LumA | LumB | NormaL |
|---|---|---|---|---|---|---|---|---|---|---|
expO Bittner M. (www.intgen.org) | Training | Affymetrix (U133 Plus 2.0) | 312 | 65.7% | 28.1% | 21.2% | 16.3% | 31.4% | 18.9% | 12.2% |
Lu et al. Breast Cancer Res Treat 2008 [40] | Training | Affymetrix (U133 Plus 2.0) | 127 | 58.3% | 23.6% | 26.8% | 17.3% | 37.0% | 16.5% | 2.4% |
Li et al. Nat Med 2010 [41] | Training | Affymetrix (U133 Plus 2.0) | 115 | 60.9% | 31.3% | 27.0% | 16.5% | 36.5% | 18.3% | 1.7% |
Parker et al. J Clin Oncol 2009 [25] | Training | Agilent | 226 | 58.2% | 12.4% | 31.0% | 12.4% | 33.2% | 16.4% | 7.1% |
Curtis et al. Nature 2012 (METABRIC) [13] | Training | Illumina (HT-12 v3) | 1992 | 76.2% | 12.5% | 20.5% | 16.0% | 26.7% | 22.8% | 14.0% |
Guedj et al. Oncogene 2012 [42] | Training | Affymetrix (U133 Plus 2.0) | 537 | 75.9% | 13.0% | 16.2% | 17.1% | 24.8% | 24.2% | 17.7% |
TCGA Nature 2012 [23] | Training | Agilent | 233 | 79.3% | 21.9% | 22.3% | 15.5% | 30.9% | 21.0% | 10.3% |
Miller et al. PNAS 2005 [43] | Training | Affymetrix (U133AB) | 251 | 86.2% | 13.1% | 15.9% | 18.3% | 25.1% | 20.3% | 20.3% |
Pawitan et al. Breast Cancer Res 2005 [44] | Training | Affymetrix (U133AB) | 159 | N/A | 13.8% | 12.6% | 13.8% | 28.3% | 27.7% | 17.6% |
TCGA Nature 2012 [23] | Training | RNA-seq (Illumina) | 558 | 77.9% | 24.2% | 19.2% | 12.9% | 30.5% | 22.2% | 15.2% |
McGill [12] | Validation | Affymetrix Gene ST | 429 | 78.1% | 18.5% | 20.5% | 17.4% | 37.6% | 16.2% | 8.1% |
TCGA Nature 2012 [23] | Validation | RNA-seq (Illumina) | 313 | 72.6% | 11.9% | 19.2% | 13.4% | 35.8% | 15.3% | 16.3% |