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Table 1 Published signatures included in the analysis

From: Genes and functions from breast cancer signatures

Full name Short namea gene # Extract # Cov %b Used forc Platformd Purposee
Prognosis Predict Subtyping
70-gene signature [1] Mamma 70 66 100 ER+ Agilent Hu25K yes yes no
21-gene signature [4] RS 16 16 100 ER+ RT-PCR yes yes no
97-gene genomic grade index [15] GGI97 97 94 100 ER+ Affymetrix U133A yes yes no
8-gene genomic grade index [27] GGI8 4 4 100 ER+ qRT-PCR yes yes no
EndoPredict assay [33] Endo 8 8 100 ER+ qRT-PCR yes yes no
Breast cancer index [21] BCI 7 7 100 ER+ qRT-PCR yes yes no
HOXB13:IL17 BR ratio [14] HI 2 2 100 ER+ Agilent Arcturus 22 k yes yes no
IHC4 Score [32] IHC4 4 4 100 ER+ IHC yes yes no
14-gene metastasis score [23] MS14 14 14 100 ER+ RT-PCR yes no no
8-gene score [29] SMS 8 8 100 ER+ qRT-PCR yes no no
PAM50 assay [3] PAM50 50 50 100 BC Agilent human 1Av2 yes yes yes
76-gene signature [10] Wang 76 71 100 BC Affymetrix U133A yes yes no
64-gene expression signature [9] Pawitan 64 48 75 BC Affymetrix U133 yes yes no
32-gene p53 status signature [7] p53 32 21 100 BC Affymetrix U133 A or B yes yes yes
Cell cycle pathway signature [20] CCPS 26 26 100 BC Affymetrix U95 Av2 or U133 yes no no
127-gene classifier [24] Robust 127 127 100 BC Affymetrix microarray yes no no
26-gene stroma-derived prognostic predictor [19] SDPP 26 26 100 BC Agilent 44 k yes no no
54-gene lung metastasis signature [8] LM 54 54 100 BC Affymetrix U133A yes no no
186-invasivenessgene signature [17] IGS 186 186 100 BC Affymetrix U133 A or B yes no no
92-gene predictor [2] Chang 92 86 100 BC Affymetrix U95 Av2 no yes no
85-gene signature [6] Iwao 85 73 100 BC ATAC-PCR no yes no
512-gene signature [16] Olaf 512 355 69 BC Human Oligo set 2.1 no yes no
7-gene immune response module [18] IR7 7 7 100 ER- Agilent and Affymetrix microarray yes no yes
T-cell metagene [26] Tcell 50 50 100 ER- Affymetrix U133A yes no no
Multigene HRneg/Tneg signature [31] Multigene 14 14 100 TNBC Affymetrix U133A yes no no
26-gene signature [35] Novel1 26 20 100 TNBC Affymetrix U133 yes yes no
264-gene signature [35] Novel2 264 225 100 TNBC Affymetrix U133 yes no no
B-cell:IL8 ratio [41] Bcell 22 20 100 100 TNBC Affymetrix U133A or U133 Plus 2.0 yes no no
MAGE-A [38] MAGEA 2 2 100 TNBC Affymetrix U133 yes no no
368-gene medullary breast cancer like signature [36] MBC 368 368 100 TNBC Affymetrix or Agilent aaray yes no yes
158-gene HER2-derived prognostic predictor [30] HDPP 158 158 100 HER2+ SWEGENE H_v2.1.1 55 K yes no yes
GCNs of MET and HGF [39] GCN 2 2 100 HER2+ Fluorescence in situ hybridisation (FISH) no yes No
28-gene expression profile [28] Vegran 28 27 100 HER2+ Affymetrix microarray no yes no
  1. aThe short name for the full name used in this paper
  2. bFor some signatures with 100% coverage (all signature genes were found in data set), the extracted gene No (Extract# column) is less than the reported gene No (gene# column) because some genes are duplicated with different probe names within a signature
  3. cThe subtype the signatures are developed for: ER+, the signature is used for ER-positive breast cancer; ER-, the signature is used for ER-negative breast cancer; uc-BC, the signature is used for un-classified breast cancer with mixed subtypes; TNBC, the signature is used for TNBC or basal breast cancer; HER2+, the signature is used for HER2-positive breast cancer
  4. dThe experimental platform used for developing the signatures
  5. eThe clinical purpose of these signatures: prognosis, the signature can be used for prognosis; prediction, the signature can be used for predicting the response to treatment or drug; subtyping, the signature can be used for further subtyping breast cancers