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Table 1 Datasets used in this analysis

From: BreastMark: An Integrated Approach to Mining Publicly Available Transcriptomic Datasets Relating to Breast Cancer Outcome

GEO Accession Number

Reference

Data Format

Sample Number

Platform Type (probe number)

GSE7849

Anders et al., 2008 [51]

Processed only

78

Affymetrix Human Genome U95 Version 2 Array (12,625 probes)

GSE3143

Bild et al., 2006 [52]

Raw .CEL files

158

Affymetrix Human Genome U95 Version 2 Array (12,625 probes)

GSE12276

Bos et al., 2009 [53]

Raw .CEL files

204

Affymetrix U133 Plus 2.0 (54,675 probes)

GSE22219

Buffa et al., 2011 [44]

Raw Data files

216

Illumina humanRef-8 v1.0 expression beadchip

GSE10510

Calabro et al., 2009 [54]

Raw .gpr files

152

DKFZ Division of Molecular Genome Analysis Human Operon 4.0 oligo Array 35 k (36,486 probes)

NA

Chang et al., 2005 [31]

Processed only

295

Agilent 21 K oligo array (22,575 probes)

NA

Chin et al., 2006 [55]

Processed only

118

Affymetrix U133AAofAv2 (22,944 probes)

GSE9893

Chanrion et al., 2008 [56]

Raw data available

155

MLRG Human 21 K V12.0 (22,656 probes)

GSE7390

Desmedt et al., 2007 [57]

Raw .CEL files

198

Affymetrix U133A (22,283 probes)

GSE16391

Desmedt et al., 2009 [58]

Raw .CEL files

48

Affymetrix U133 Plus 2.0 (54,675 probes)

GSE25055

Hatzis et al., 2011 [59]

Raw .CEL files

508

Affymetrix U133A (22,283 probes)

GSE24450

Heikkinen et al., 2011 [60]

Raw Data files

183

Illumina HumanHT-12 V3.0 expression beadchip

GSE1992

Hu et al., 2006 [27]

Processed only

99

Agilent 21 K oligo array (22,575 probes)

GSE20685

Kao et al., 2011 [61]

Raw .CEL files

327

Affymetrix U133 Plus 2.0 (54,675 probes)

NA

Kok et al., 2009 [62]

Processed only

109

Agilent 44 K oligo array (54,675 probes)

GSE9195

Loi et al., 2008 [63]

Raw .CEL files

77

Affymetrix U133 Plus 2.0 (54,675 probes)

GSE6532

Loi et al., 2008 [63]

Raw .CEL files

265

Affymetrix U133A/B (22,283/22,645 probes) and U133 Plus 2.0

GSE1378, GSE 1379

Ma et al., 2004 [64]

Processed only

60

Custom 22 K oligo array (22,575 probes)

GSE3494

Miller et al., 2005 [65]

Raw .CEL files

251

Affymetrix U133A/B (22,283/22,645 probes)

GSE45255

Nagalla et l., 2013 [66]

Raw .CEL files

139

Affymetrix U133A (22,283 probes)

GSE1456

Pawitan et l., 2005 [67]

Raw .CEL files

159

Affymetrix U133A/B (22,283/22,645 probes)

GSE21653

Sabatier et al., 2010 [68]

Raw .CEL files

266

Affymetrix U133 Plus 2.0 (54,675 probes)

GSE11121

Schmidt et al., 2008 [69]

Raw .CEL files

200

Affymetrix U133A (22,283 probes)

GSE17907

Sircoulomb et al., 2010 [70]

Raw .CEL files

51

Affymetrix U133 Plus 2.0 (54,675 probes)

GSE2034

Wang et al., 2006 [71]

Raw .CEL files

286

Affymetrix U133A (22,283 probes)

GSE12093

Zhang et al., 2008 [72]

Raw .CEL files

136

Affymetrix U133A (22,283 probes)

 

Total

 

4738

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