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 | Â | 0.023 (1/22 CpGs) | Â | N.S. | Â | 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) |  |