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Table 1 Clinicopathological features of the TCGA breast adenocarcinomas

From: Large-scale analysis of DFNA5 methylation reveals its potential as biomarker for breast cancer

Clinicopathological parameter Methylation (N = 668) Expression–microarray (N = 476) Expression–RNA-seq (N = 666)
Number (%) P value (range) Number (%) P value Number (%) P value
ER   2.2 × 10−22–0.049 (20/22 CpGs)   0.038   3.3 × 10− 3
 ER+ 490 (73.3)   362 (76.0)   488 (73.3)  
 ER− 142 (21.3)   107 (22.5)   142 (21.3)  
 Unknown 36 (5.4)   7 (1.5)   36 (5.4)  
PR   9.7 × 10−15–3.0 × 10−3 (15/22 CpGs)   N.S.   N.S.
 PR+ 428 (64.1)   310 (65.1)   427 (64.1)  
 PR− 201 (30.1)   158 (33.2)   200 (30.0)  
 Unknown 39 (5.8)   8 (1.7)   39 (5.9)  
HER2   0.023 (1/22 CpGs)   N.S.   N.S.
HER2+ 32 (4.8)   45 (9.4)   32 (4.8)  
HER2 195 (29.2)   166 (34.9)   195 (29.3)  
 Unknown 441 (66.0)   265 (55.7)   439 (65.9)  
Tumor stage   1.9 × 10−4–0.020 (5/22 CpGs)   N.S.   N.S.
 I 109 (16.3)   83 (17.5)   107 (16.1)  
 II 378 (56.6)   269 (56.5)   378 (56.8)  
 III 166 (24.9)   99 (20.8)   166 (24.9)  
 IV 9 (1.3)   12 (2.5)   9 (1.3)  
 Unknown 6 (0.9)   13 (2.7)   6 (0.9)  
Histological diagnosis   1.0 × 10−4–0.038 (10/22 CpGs)   4.2 × 10−4   3.2 × 10−4
 Ductal 496 (74.3)   435 (91.4)   494 (74.2)  
 Lobular 172 (25.7)   41 (8.6)   172 (25.8)  
  1. Important clinicopathological parameters, such as ER status, PR status, HER2 status, tumor stage (I–IV), and histological diagnosis are reported for the breast adenocarcinomas. The numbers of adenocarcinomas in each category are reported for the methylation and expression (both microarray and RNA-seq) dataset. The significant p values for the association analysis with either DFNA5 methylation, DFNA5 microarray expression, or DFNA5 RNA-seq expression are reported
  2. N.S. not significant