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Table 2 Principal biological phenotypes identified as metagenes among TNBC

From: A clinically relevant gene signature in triple negative and basal-like breast cancer

Biological component Metagene name Correlation within metagene cluster # of probesets in metagene cluster Key markers Reference
Basal-like phenotype Basal-like 0.61 37 KRT-5,-6, -14, -17, SOX10, SFRP1, ELF5, EPHB3, GABRP [4]
Apocrine/androgen receptor signalling Apocrine 0.67 27 AR, FOXA1 [18, 19]
Immune system:      [4, 20, 21, 2325]
B-Cell B-Cell 0.87 48 IgG  
T-Cell T-Cell 0.84 27 TCR, LCK, ITK  
MHC class II MHC-2 0.83 14 HLA-DR, -DM, -DP, -DQ  
MHC class I MHC-1 0.84 17 HLA-A, -B, -C, -E, -F, -G  
Interferone response IFN 0.76 14 OAS1, OAS2, OAS3, MX1  
Stroma* Stroma 0.83 47 Decorin, Osteonectin, Fibronectin, COL5A1 [26, 27]
Claudin-CD24 signature Claudin-CD24 0.70 19 CLDN3, CLDN4, CD24, ELF3 [28, 29]
Proliferation Proliferation 0.74 47 BUB1, CDC2, STK6, BIRC5, TOP2A, [35]
Blood * Hemoglobin * 0.63 17 HBA1, HBA2, HBB [30]
Adipocytes Adipocyte 0.74 8 FABP4, PLIN, ADIPOQ, ADH1B [4]
Angiogenesis VEGF 0.57 7 VEGF, adrenomedullin, ANGPTL4 [34]
Inflammation IL-8 0.52 4 IL-8, CXCL1, CXCL2 [31, 32]
HOXA gene cluster HOXA 0.52 8 HOXA-4, -5, -7, -9, -10, -11 [64]
Histone gene cluster Histone 0.69 19 Histones H2A, H2B [65]
  1. * The Stroma and Hemoglobin metagenes displayed a bias between datasets related to different biopsy techniques (see Methods).