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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%
  1. ER+ estrogen-receptor-positive, Her2+ human epidermal growth factor receptor 2-positive, BasalL basal-like intrinsic subtype, Her2E Her2-enriched intrinsic subtype, LumA luminal A intrinsic subtype, LumB luminal B intrinsic subtype, NormaL normal-like intrinsic subtype, RNA-seq RNA sequencing, METABRIC Molecular Taxonomy of Breast Cancer International Consortium, TCGA The Cancer Genome Atlas