This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 70 focal events and 10 clinical features across 949 patients, 40 significant findings detected with Q value < 0.25.
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AMP PEAK 4(3P26.1) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.T.STAGE'.
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AMP PEAK 5(3Q26.32) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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AMP PEAK 6(4Q13.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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AMP PEAK 8(6P23) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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AMP PEAK 9(6Q21) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.
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AMP PEAK 12(8Q24.21) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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AMP PEAK 13(10P15.1) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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AMP PEAK 15(11P13) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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AMP PEAK 18(12P13.33) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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AMP PEAK 23(15Q26.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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AMP PEAK 25(17Q23.1) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.T.STAGE' and 'GENDER'.
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AMP PEAK 27(19Q12) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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AMP PEAK 29(20Q13.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 1(1P36.13) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.T.STAGE'.
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DEL PEAK 2(1P22.1) MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.T.STAGE'.
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DEL PEAK 3(2Q37.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 4(3P14.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 5(4P16.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 6(4Q35.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 7(5Q11.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 8(5Q21.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 11(6Q27) MUTATION ANALYSIS cnv correlated to 'AGE'.
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DEL PEAK 12(7P22.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 14(8P23.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 16(9P23) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 17(9P21.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 19(9Q34.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 21(10Q26.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 28(13Q11) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 29(13Q14.2) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 30(14Q24.1) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 31(15Q13.1) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 32(16Q24.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 34(17Q21.31) MUTATION ANALYSIS cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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DEL PEAK 36(19P13.3) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 37(19Q13.32) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
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DEL PEAK 38(20P13) MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 70 focal events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 40 significant findings detected.
|
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBER OF LYMPH NODES |
||
| nCNV (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | t-test | |
| AMP PEAK 9(6Q21) MUTATION ANALYSIS | 178 (19%) | 771 |
0.0184 (1.00) |
0.364 (1.00) |
0.142 (1.00) |
9.41e-05 (0.0629) |
0.221 (1.00) |
0.932 (1.00) |
0.698 (1.00) |
1.24e-05 (0.00839) |
1 (1.00) |
0.418 (1.00) |
| AMP PEAK 25(17Q23 1) MUTATION ANALYSIS | 383 (40%) | 566 |
0.0903 (1.00) |
0.65 (1.00) |
0.0183 (1.00) |
0.000156 (0.103) |
0.414 (1.00) |
0.00302 (1.00) |
0.000107 (0.0712) |
0.00111 (0.722) |
0.878 (1.00) |
0.169 (1.00) |
| DEL PEAK 34(17Q21 31) MUTATION ANALYSIS | 327 (34%) | 622 |
0.744 (1.00) |
0.000368 (0.243) |
0.146 (1.00) |
0.136 (1.00) |
0.0921 (1.00) |
0.173 (1.00) |
0.508 (1.00) |
1.53e-05 (0.0104) |
1 (1.00) |
0.482 (1.00) |
| AMP PEAK 4(3P26 1) MUTATION ANALYSIS | 192 (20%) | 757 |
0.00473 (1.00) |
0.537 (1.00) |
0.0598 (1.00) |
5.03e-05 (0.0338) |
0.0135 (1.00) |
0.0105 (1.00) |
0.696 (1.00) |
0.0013 (0.844) |
0.346 (1.00) |
0.794 (1.00) |
| AMP PEAK 5(3Q26 32) MUTATION ANALYSIS | 295 (31%) | 654 |
0.789 (1.00) |
0.276 (1.00) |
0.343 (1.00) |
0.00182 (1.00) |
0.544 (1.00) |
0.00884 (1.00) |
1 (1.00) |
1.61e-11 (1.12e-08) |
0.0724 (1.00) |
0.31 (1.00) |
| AMP PEAK 6(4Q13 3) MUTATION ANALYSIS | 146 (15%) | 803 |
0.0484 (1.00) |
0.384 (1.00) |
0.613 (1.00) |
0.0361 (1.00) |
0.486 (1.00) |
0.622 (1.00) |
0.657 (1.00) |
2.48e-05 (0.0168) |
0.464 (1.00) |
0.615 (1.00) |
| AMP PEAK 8(6P23) MUTATION ANALYSIS | 252 (27%) | 697 |
0.485 (1.00) |
0.119 (1.00) |
0.551 (1.00) |
0.016 (1.00) |
0.191 (1.00) |
0.772 (1.00) |
0.47 (1.00) |
2.13e-05 (0.0144) |
0.441 (1.00) |
0.25 (1.00) |
| AMP PEAK 12(8Q24 21) MUTATION ANALYSIS | 604 (64%) | 345 |
0.0665 (1.00) |
0.0354 (1.00) |
0.151 (1.00) |
0.00752 (1.00) |
0.498 (1.00) |
0.0228 (1.00) |
0.343 (1.00) |
2.3e-13 (1.6e-10) |
0.387 (1.00) |
0.336 (1.00) |
| AMP PEAK 13(10P15 1) MUTATION ANALYSIS | 269 (28%) | 680 |
0.147 (1.00) |
0.705 (1.00) |
0.201 (1.00) |
0.388 (1.00) |
0.688 (1.00) |
0.889 (1.00) |
0.298 (1.00) |
6.94e-09 (4.81e-06) |
0.276 (1.00) |
0.91 (1.00) |
| AMP PEAK 15(11P13) MUTATION ANALYSIS | 197 (21%) | 752 |
0.361 (1.00) |
0.397 (1.00) |
0.861 (1.00) |
0.708 (1.00) |
0.803 (1.00) |
0.769 (1.00) |
1 (1.00) |
1.03e-05 (0.00699) |
0.352 (1.00) |
0.254 (1.00) |
| AMP PEAK 18(12P13 33) MUTATION ANALYSIS | 246 (26%) | 703 |
0.95 (1.00) |
0.307 (1.00) |
0.235 (1.00) |
0.0053 (1.00) |
0.704 (1.00) |
0.467 (1.00) |
0.468 (1.00) |
7.17e-05 (0.0479) |
0.121 (1.00) |
0.868 (1.00) |
| AMP PEAK 23(15Q26 3) MUTATION ANALYSIS | 172 (18%) | 777 |
0.234 (1.00) |
0.00946 (1.00) |
0.475 (1.00) |
0.484 (1.00) |
0.942 (1.00) |
0.0464 (1.00) |
0.0891 (1.00) |
6.12e-05 (0.041) |
0.492 (1.00) |
0.941 (1.00) |
| AMP PEAK 27(19Q12) MUTATION ANALYSIS | 238 (25%) | 711 |
0.148 (1.00) |
0.205 (1.00) |
0.283 (1.00) |
0.644 (1.00) |
0.245 (1.00) |
0.0737 (1.00) |
0.28 (1.00) |
2.67e-05 (0.018) |
0.117 (1.00) |
0.27 (1.00) |
| AMP PEAK 29(20Q13 2) MUTATION ANALYSIS | 476 (50%) | 473 |
0.614 (1.00) |
0.224 (1.00) |
0.183 (1.00) |
0.0253 (1.00) |
0.00604 (1.00) |
0.0395 (1.00) |
0.108 (1.00) |
1.04e-13 (7.25e-11) |
0.0101 (1.00) |
0.909 (1.00) |
| DEL PEAK 1(1P36 13) MUTATION ANALYSIS | 392 (41%) | 557 |
0.146 (1.00) |
0.384 (1.00) |
0.0139 (1.00) |
1.22e-06 (0.000836) |
0.004 (1.00) |
0.212 (1.00) |
0.102 (1.00) |
0.0106 (1.00) |
0.701 (1.00) |
0.0726 (1.00) |
| DEL PEAK 2(1P22 1) MUTATION ANALYSIS | 314 (33%) | 635 |
0.00107 (0.699) |
0.162 (1.00) |
0.0107 (1.00) |
6.57e-06 (0.00448) |
0.00384 (1.00) |
0.438 (1.00) |
0.738 (1.00) |
0.0594 (1.00) |
0.335 (1.00) |
0.0608 (1.00) |
| DEL PEAK 3(2Q37 3) MUTATION ANALYSIS | 276 (29%) | 673 |
0.989 (1.00) |
0.668 (1.00) |
0.371 (1.00) |
0.00783 (1.00) |
0.255 (1.00) |
0.566 (1.00) |
0.732 (1.00) |
0.000233 (0.154) |
0.56 (1.00) |
0.204 (1.00) |
| DEL PEAK 4(3P14 3) MUTATION ANALYSIS | 291 (31%) | 658 |
0.0187 (1.00) |
0.000509 (0.336) |
0.674 (1.00) |
0.00287 (1.00) |
0.503 (1.00) |
0.375 (1.00) |
1 (1.00) |
5.79e-06 (0.00396) |
0.412 (1.00) |
0.699 (1.00) |
| DEL PEAK 5(4P16 3) MUTATION ANALYSIS | 292 (31%) | 657 |
0.876 (1.00) |
0.115 (1.00) |
0.249 (1.00) |
0.00127 (0.825) |
0.63 (1.00) |
0.591 (1.00) |
0.732 (1.00) |
3.05e-06 (0.00209) |
0.624 (1.00) |
0.793 (1.00) |
| DEL PEAK 6(4Q35 2) MUTATION ANALYSIS | 295 (31%) | 654 |
0.079 (1.00) |
0.856 (1.00) |
0.434 (1.00) |
0.00671 (1.00) |
0.797 (1.00) |
0.0298 (1.00) |
0.187 (1.00) |
1.3e-06 (0.000894) |
0.744 (1.00) |
0.689 (1.00) |
| DEL PEAK 7(5Q11 2) MUTATION ANALYSIS | 245 (26%) | 704 |
0.25 (1.00) |
0.0034 (1.00) |
0.301 (1.00) |
0.00644 (1.00) |
0.38 (1.00) |
0.284 (1.00) |
0.467 (1.00) |
1.26e-10 (8.76e-08) |
0.667 (1.00) |
0.205 (1.00) |
| DEL PEAK 8(5Q21 3) MUTATION ANALYSIS | 235 (25%) | 714 |
0.315 (1.00) |
0.00995 (1.00) |
0.111 (1.00) |
0.00272 (1.00) |
0.05 (1.00) |
0.443 (1.00) |
0.132 (1.00) |
4.71e-14 (3.29e-11) |
0.793 (1.00) |
0.0012 (0.782) |
| DEL PEAK 11(6Q27) MUTATION ANALYSIS | 319 (34%) | 630 |
0.105 (1.00) |
5.93e-06 (0.00405) |
0.381 (1.00) |
0.755 (1.00) |
0.0392 (1.00) |
0.0452 (1.00) |
0.509 (1.00) |
0.445 (1.00) |
0.423 (1.00) |
0.46 (1.00) |
| DEL PEAK 12(7P22 3) MUTATION ANALYSIS | 122 (13%) | 827 |
0.695 (1.00) |
0.306 (1.00) |
0.117 (1.00) |
0.317 (1.00) |
0.0512 (1.00) |
0.443 (1.00) |
0.626 (1.00) |
0.000285 (0.188) |
0.498 (1.00) |
0.0154 (1.00) |
| DEL PEAK 14(8P23 2) MUTATION ANALYSIS | 495 (52%) | 454 |
0.128 (1.00) |
0.774 (1.00) |
0.965 (1.00) |
0.0149 (1.00) |
0.102 (1.00) |
0.359 (1.00) |
0.346 (1.00) |
8.1e-09 (5.61e-06) |
0.449 (1.00) |
0.854 (1.00) |
| DEL PEAK 16(9P23) MUTATION ANALYSIS | 288 (30%) | 661 |
0.00104 (0.678) |
0.618 (1.00) |
0.0057 (1.00) |
0.00063 (0.414) |
0.00685 (1.00) |
0.0238 (1.00) |
0.181 (1.00) |
3.35e-05 (0.0225) |
0.412 (1.00) |
0.3 (1.00) |
| DEL PEAK 17(9P21 3) MUTATION ANALYSIS | 320 (34%) | 629 |
0.045 (1.00) |
0.867 (1.00) |
0.00776 (1.00) |
0.000739 (0.485) |
0.0115 (1.00) |
0.0982 (1.00) |
0.0955 (1.00) |
1.82e-08 (1.25e-05) |
0.472 (1.00) |
0.712 (1.00) |
| DEL PEAK 19(9Q34 2) MUTATION ANALYSIS | 255 (27%) | 694 |
0.835 (1.00) |
0.841 (1.00) |
0.0866 (1.00) |
0.054 (1.00) |
0.0503 (1.00) |
0.732 (1.00) |
0.0274 (1.00) |
1.13e-06 (0.000781) |
0.496 (1.00) |
0.0687 (1.00) |
| DEL PEAK 21(10Q26 3) MUTATION ANALYSIS | 276 (29%) | 673 |
0.0825 (1.00) |
0.808 (1.00) |
0.312 (1.00) |
0.258 (1.00) |
0.242 (1.00) |
0.319 (1.00) |
0.732 (1.00) |
0.000161 (0.107) |
0.56 (1.00) |
0.68 (1.00) |
| DEL PEAK 28(13Q11) MUTATION ANALYSIS | 376 (40%) | 573 |
0.478 (1.00) |
0.925 (1.00) |
0.775 (1.00) |
0.277 (1.00) |
0.267 (1.00) |
0.679 (1.00) |
0.748 (1.00) |
5.7e-05 (0.0382) |
0.589 (1.00) |
0.154 (1.00) |
| DEL PEAK 29(13Q14 2) MUTATION ANALYSIS | 430 (45%) | 519 |
0.0686 (1.00) |
0.436 (1.00) |
0.572 (1.00) |
0.0613 (1.00) |
0.383 (1.00) |
0.89 (1.00) |
0.362 (1.00) |
2.87e-05 (0.0194) |
0.94 (1.00) |
0.0513 (1.00) |
| DEL PEAK 30(14Q24 1) MUTATION ANALYSIS | 302 (32%) | 647 |
0.101 (1.00) |
0.232 (1.00) |
0.199 (1.00) |
0.00148 (0.96) |
0.142 (1.00) |
0.933 (1.00) |
0.734 (1.00) |
9.53e-09 (6.59e-06) |
0.466 (1.00) |
0.14 (1.00) |
| DEL PEAK 31(15Q13 1) MUTATION ANALYSIS | 325 (34%) | 624 |
0.269 (1.00) |
0.125 (1.00) |
0.215 (1.00) |
0.0267 (1.00) |
0.0613 (1.00) |
0.166 (1.00) |
0.743 (1.00) |
1.17e-05 (0.00798) |
0.0941 (1.00) |
0.754 (1.00) |
| DEL PEAK 32(16Q24 3) MUTATION ANALYSIS | 606 (64%) | 343 |
0.0846 (1.00) |
0.000607 (0.4) |
0.24 (1.00) |
0.262 (1.00) |
0.616 (1.00) |
0.183 (1.00) |
0.754 (1.00) |
2.62e-15 (1.84e-12) |
0.814 (1.00) |
0.566 (1.00) |
| DEL PEAK 36(19P13 3) MUTATION ANALYSIS | 317 (33%) | 632 |
0.184 (1.00) |
0.0154 (1.00) |
0.675 (1.00) |
0.288 (1.00) |
0.743 (1.00) |
0.489 (1.00) |
0.178 (1.00) |
3.37e-09 (2.34e-06) |
0.873 (1.00) |
0.0339 (1.00) |
| DEL PEAK 37(19Q13 32) MUTATION ANALYSIS | 187 (20%) | 762 |
0.612 (1.00) |
0.487 (1.00) |
0.432 (1.00) |
0.513 (1.00) |
0.0475 (1.00) |
0.323 (1.00) |
0.696 (1.00) |
6.92e-07 (0.000477) |
0.107 (1.00) |
0.5 (1.00) |
| DEL PEAK 38(20P13) MUTATION ANALYSIS | 139 (15%) | 810 |
0.0851 (1.00) |
0.156 (1.00) |
0.419 (1.00) |
0.614 (1.00) |
0.777 (1.00) |
0.429 (1.00) |
0.647 (1.00) |
0.000117 (0.0779) |
1 (1.00) |
0.67 (1.00) |
| AMP PEAK 1(1P22 3) MUTATION ANALYSIS | 209 (22%) | 740 |
0.889 (1.00) |
0.526 (1.00) |
0.412 (1.00) |
0.0154 (1.00) |
0.0821 (1.00) |
0.646 (1.00) |
1 (1.00) |
0.222 (1.00) |
0.855 (1.00) |
0.0494 (1.00) |
| AMP PEAK 2(1Q21 3) MUTATION ANALYSIS | 679 (72%) | 270 |
0.813 (1.00) |
0.752 (1.00) |
0.326 (1.00) |
0.0121 (1.00) |
0.794 (1.00) |
0.458 (1.00) |
0.482 (1.00) |
0.18 (1.00) |
0.209 (1.00) |
0.856 (1.00) |
| AMP PEAK 3(1Q44) MUTATION ANALYSIS | 677 (71%) | 272 |
0.0534 (1.00) |
0.567 (1.00) |
0.242 (1.00) |
0.00544 (1.00) |
0.572 (1.00) |
0.653 (1.00) |
1 (1.00) |
0.0243 (1.00) |
0.504 (1.00) |
0.874 (1.00) |
| AMP PEAK 7(5P15 33) MUTATION ANALYSIS | 340 (36%) | 609 |
0.0993 (1.00) |
0.203 (1.00) |
0.658 (1.00) |
0.357 (1.00) |
0.00416 (1.00) |
0.0706 (1.00) |
0.752 (1.00) |
0.139 (1.00) |
0.207 (1.00) |
0.88 (1.00) |
| AMP PEAK 10(8P11 23) MUTATION ANALYSIS | 360 (38%) | 589 |
0.0376 (1.00) |
0.131 (1.00) |
0.0595 (1.00) |
0.545 (1.00) |
0.21 (1.00) |
0.0384 (1.00) |
0.334 (1.00) |
0.638 (1.00) |
0.64 (1.00) |
0.0224 (1.00) |
| AMP PEAK 11(8P11 21) MUTATION ANALYSIS | 367 (39%) | 582 |
0.713 (1.00) |
0.117 (1.00) |
0.736 (1.00) |
0.886 (1.00) |
0.906 (1.00) |
0.432 (1.00) |
0.332 (1.00) |
0.0373 (1.00) |
0.0524 (1.00) |
0.759 (1.00) |
| AMP PEAK 14(10Q22 3) MUTATION ANALYSIS | 135 (14%) | 814 |
0.0833 (1.00) |
0.684 (1.00) |
0.203 (1.00) |
0.069 (1.00) |
0.479 (1.00) |
0.0975 (1.00) |
1 (1.00) |
0.0157 (1.00) |
0.194 (1.00) |
0.317 (1.00) |
| AMP PEAK 16(11Q13 3) MUTATION ANALYSIS | 352 (37%) | 597 |
0.453 (1.00) |
0.261 (1.00) |
0.681 (1.00) |
0.163 (1.00) |
0.816 (1.00) |
0.41 (1.00) |
0.186 (1.00) |
0.128 (1.00) |
0.876 (1.00) |
0.979 (1.00) |
| AMP PEAK 17(11Q14 1) MUTATION ANALYSIS | 234 (25%) | 715 |
0.353 (1.00) |
0.358 (1.00) |
0.319 (1.00) |
0.137 (1.00) |
0.195 (1.00) |
0.0454 (1.00) |
0.273 (1.00) |
0.0024 (1.00) |
0.792 (1.00) |
0.55 (1.00) |
| AMP PEAK 19(12Q15) MUTATION ANALYSIS | 242 (26%) | 707 |
0.146 (1.00) |
0.475 (1.00) |
0.1 (1.00) |
0.0205 (1.00) |
0.00523 (1.00) |
0.139 (1.00) |
0.00378 (1.00) |
0.0466 (1.00) |
0.795 (1.00) |
0.187 (1.00) |
| AMP PEAK 20(13Q12 3) MUTATION ANALYSIS | 129 (14%) | 820 |
0.0769 (1.00) |
0.287 (1.00) |
0.571 (1.00) |
0.138 (1.00) |
0.253 (1.00) |
0.0754 (1.00) |
0.634 (1.00) |
0.0236 (1.00) |
0.44 (1.00) |
0.954 (1.00) |
| AMP PEAK 21(13Q34) MUTATION ANALYSIS | 160 (17%) | 789 |
0.769 (1.00) |
0.0898 (1.00) |
0.237 (1.00) |
0.00886 (1.00) |
0.366 (1.00) |
0.0928 (1.00) |
0.228 (1.00) |
0.0172 (1.00) |
1 (1.00) |
0.49 (1.00) |
| AMP PEAK 22(14Q21 1) MUTATION ANALYSIS | 188 (20%) | 761 |
0.46 (1.00) |
0.0418 (1.00) |
0.0546 (1.00) |
0.00765 (1.00) |
0.0127 (1.00) |
0.313 (1.00) |
0.696 (1.00) |
0.17 (1.00) |
0.925 (1.00) |
0.0597 (1.00) |
| AMP PEAK 24(17Q12) MUTATION ANALYSIS | 301 (32%) | 648 |
0.159 (1.00) |
0.87 (1.00) |
0.485 (1.00) |
0.0578 (1.00) |
0.127 (1.00) |
0.302 (1.00) |
0.00226 (1.00) |
0.0063 (1.00) |
0.685 (1.00) |
0.9 (1.00) |
| AMP PEAK 26(19P13 12) MUTATION ANALYSIS | 196 (21%) | 753 |
0.831 (1.00) |
0.85 (1.00) |
0.76 (1.00) |
0.343 (1.00) |
0.65 (1.00) |
0.185 (1.00) |
0.0365 (1.00) |
0.00737 (1.00) |
0.0249 (1.00) |
0.325 (1.00) |
| AMP PEAK 28(19Q13 42) MUTATION ANALYSIS | 241 (25%) | 708 |
0.396 (1.00) |
0.099 (1.00) |
0.988 (1.00) |
0.485 (1.00) |
0.995 (1.00) |
0.00442 (1.00) |
0.134 (1.00) |
0.0241 (1.00) |
0.297 (1.00) |
0.838 (1.00) |
| DEL PEAK 9(6P25 3) MUTATION ANALYSIS | 180 (19%) | 769 |
0.536 (1.00) |
0.0119 (1.00) |
0.454 (1.00) |
0.125 (1.00) |
0.355 (1.00) |
0.286 (1.00) |
0.411 (1.00) |
0.115 (1.00) |
0.335 (1.00) |
0.17 (1.00) |
| DEL PEAK 10(6Q15) MUTATION ANALYSIS | 305 (32%) | 644 |
0.577 (1.00) |
0.0336 (1.00) |
0.221 (1.00) |
0.221 (1.00) |
0.0717 (1.00) |
0.405 (1.00) |
1 (1.00) |
0.44 (1.00) |
0.686 (1.00) |
0.159 (1.00) |
| DEL PEAK 13(7Q36 1) MUTATION ANALYSIS | 182 (19%) | 767 |
0.0757 (1.00) |
0.935 (1.00) |
0.775 (1.00) |
0.335 (1.00) |
0.341 (1.00) |
0.373 (1.00) |
1 (1.00) |
0.0137 (1.00) |
0.701 (1.00) |
0.893 (1.00) |
| DEL PEAK 15(8P11 21) MUTATION ANALYSIS | 180 (19%) | 769 |
0.0369 (1.00) |
0.302 (1.00) |
0.609 (1.00) |
0.133 (1.00) |
0.32 (1.00) |
0.398 (1.00) |
0.223 (1.00) |
0.0167 (1.00) |
1 (1.00) |
0.359 (1.00) |
| DEL PEAK 18(9Q21 11) MUTATION ANALYSIS | 258 (27%) | 691 |
0.441 (1.00) |
0.944 (1.00) |
0.287 (1.00) |
0.0794 (1.00) |
0.36 (1.00) |
0.331 (1.00) |
0.146 (1.00) |
0.000936 (0.613) |
0.61 (1.00) |
0.235 (1.00) |
| DEL PEAK 20(10Q23 31) MUTATION ANALYSIS | 271 (29%) | 678 |
0.746 (1.00) |
0.259 (1.00) |
0.321 (1.00) |
0.0721 (1.00) |
0.525 (1.00) |
0.3 (1.00) |
0.297 (1.00) |
0.000801 (0.525) |
0.316 (1.00) |
0.926 (1.00) |
| DEL PEAK 22(11P15 5) MUTATION ANALYSIS | 270 (28%) | 679 |
0.0909 (1.00) |
0.736 (1.00) |
0.33 (1.00) |
0.00757 (1.00) |
0.33 (1.00) |
0.89 (1.00) |
0.482 (1.00) |
0.00556 (1.00) |
1 (1.00) |
0.221 (1.00) |
| DEL PEAK 23(11Q13 1) MUTATION ANALYSIS | 201 (21%) | 748 |
0.219 (1.00) |
0.506 (1.00) |
0.304 (1.00) |
0.327 (1.00) |
0.211 (1.00) |
0.709 (1.00) |
0.449 (1.00) |
0.807 (1.00) |
0.517 (1.00) |
0.896 (1.00) |
| DEL PEAK 24(11Q23 2) MUTATION ANALYSIS | 473 (50%) | 476 |
0.36 (1.00) |
0.302 (1.00) |
0.2 (1.00) |
0.0729 (1.00) |
0.085 (1.00) |
0.427 (1.00) |
0.0634 (1.00) |
0.21 (1.00) |
1 (1.00) |
0.69 (1.00) |
| DEL PEAK 25(11Q25) MUTATION ANALYSIS | 441 (46%) | 508 |
0.261 (1.00) |
0.0226 (1.00) |
0.132 (1.00) |
0.0064 (1.00) |
0.12 (1.00) |
0.606 (1.00) |
0.0514 (1.00) |
0.0609 (1.00) |
0.82 (1.00) |
0.759 (1.00) |
| DEL PEAK 26(12P13 1) MUTATION ANALYSIS | 162 (17%) | 787 |
0.831 (1.00) |
0.465 (1.00) |
0.311 (1.00) |
0.48 (1.00) |
0.786 (1.00) |
0.0294 (1.00) |
0.388 (1.00) |
0.00564 (1.00) |
0.841 (1.00) |
0.21 (1.00) |
| DEL PEAK 27(12Q24 31) MUTATION ANALYSIS | 169 (18%) | 780 |
0.242 (1.00) |
0.33 (1.00) |
0.674 (1.00) |
0.0829 (1.00) |
0.718 (1.00) |
0.803 (1.00) |
0.224 (1.00) |
0.0622 (1.00) |
0.555 (1.00) |
0.276 (1.00) |
| DEL PEAK 33(17P12) MUTATION ANALYSIS | 570 (60%) | 379 |
0.393 (1.00) |
0.00208 (1.00) |
0.648 (1.00) |
0.0971 (1.00) |
0.684 (1.00) |
0.897 (1.00) |
0.331 (1.00) |
0.00501 (1.00) |
0.877 (1.00) |
0.824 (1.00) |
| DEL PEAK 35(18Q23) MUTATION ANALYSIS | 307 (32%) | 642 |
0.0796 (1.00) |
0.46 (1.00) |
0.242 (1.00) |
0.0707 (1.00) |
0.181 (1.00) |
0.625 (1.00) |
0.735 (1.00) |
0.0113 (1.00) |
0.419 (1.00) |
0.513 (1.00) |
| DEL PEAK 39(21Q11 2) MUTATION ANALYSIS | 185 (19%) | 764 |
0.333 (1.00) |
0.386 (1.00) |
0.0134 (1.00) |
0.103 (1.00) |
0.00732 (1.00) |
0.464 (1.00) |
0.697 (1.00) |
0.00835 (1.00) |
0.39 (1.00) |
0.319 (1.00) |
| DEL PEAK 40(22Q11 1) MUTATION ANALYSIS | 400 (42%) | 549 |
0.524 (1.00) |
0.798 (1.00) |
0.822 (1.00) |
0.694 (1.00) |
0.462 (1.00) |
0.283 (1.00) |
0.532 (1.00) |
0.0386 (1.00) |
0.0265 (1.00) |
0.574 (1.00) |
| DEL PEAK 41(22Q13 31) MUTATION ANALYSIS | 434 (46%) | 515 |
0.446 (1.00) |
0.417 (1.00) |
0.835 (1.00) |
0.318 (1.00) |
0.631 (1.00) |
0.44 (1.00) |
0.526 (1.00) |
0.0372 (1.00) |
0.0483 (1.00) |
0.808 (1.00) |
P value = 5.03e-05 (Fisher's exact test), Q value = 0.034
Table S1. Gene #4: 'AMP PEAK 4(3P26.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
| nPatients | T1 | T2 | T3 | T4 |
|---|---|---|---|---|
| ALL | 247 | 551 | 113 | 35 |
| AMP PEAK 4(3P26.1) MUTATED | 31 | 131 | 16 | 13 |
| AMP PEAK 4(3P26.1) WILD-TYPE | 216 | 420 | 97 | 22 |
Figure S1. Get High-res Image Gene #4: 'AMP PEAK 4(3P26.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
P value = 1.61e-11 (Chi-square test), Q value = 1.1e-08
Table S2. Gene #5: 'AMP PEAK 5(3Q26.32) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| AMP PEAK 5(3Q26.32) MUTATED | 1 | 259 | 12 | 4 | 5 | 1 | 12 |
| AMP PEAK 5(3Q26.32) WILD-TYPE | 0 | 447 | 139 | 1 | 23 | 13 | 31 |
Figure S2. Get High-res Image Gene #5: 'AMP PEAK 5(3Q26.32) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 2.48e-05 (Chi-square test), Q value = 0.017
Table S3. Gene #6: 'AMP PEAK 6(4Q13.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| AMP PEAK 6(4Q13.3) MUTATED | 0 | 132 | 4 | 2 | 1 | 1 | 6 |
| AMP PEAK 6(4Q13.3) WILD-TYPE | 1 | 574 | 147 | 3 | 27 | 13 | 37 |
Figure S3. Get High-res Image Gene #6: 'AMP PEAK 6(4Q13.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 2.13e-05 (Chi-square test), Q value = 0.014
Table S4. Gene #8: 'AMP PEAK 8(6P23) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| AMP PEAK 8(6P23) MUTATED | 0 | 214 | 16 | 3 | 4 | 2 | 12 |
| AMP PEAK 8(6P23) WILD-TYPE | 1 | 492 | 135 | 2 | 24 | 12 | 31 |
Figure S4. Get High-res Image Gene #8: 'AMP PEAK 8(6P23) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 9.41e-05 (Fisher's exact test), Q value = 0.063
Table S5. Gene #9: 'AMP PEAK 9(6Q21) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
| nPatients | T1 | T2 | T3 | T4 |
|---|---|---|---|---|
| ALL | 247 | 551 | 113 | 35 |
| AMP PEAK 9(6Q21) MUTATED | 27 | 129 | 19 | 3 |
| AMP PEAK 9(6Q21) WILD-TYPE | 220 | 422 | 94 | 32 |
Figure S5. Get High-res Image Gene #9: 'AMP PEAK 9(6Q21) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
P value = 1.24e-05 (Chi-square test), Q value = 0.0084
Table S6. Gene #9: 'AMP PEAK 9(6Q21) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| AMP PEAK 9(6Q21) MUTATED | 1 | 152 | 12 | 3 | 1 | 0 | 9 |
| AMP PEAK 9(6Q21) WILD-TYPE | 0 | 554 | 139 | 2 | 27 | 14 | 34 |
Figure S6. Get High-res Image Gene #9: 'AMP PEAK 9(6Q21) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 2.3e-13 (Chi-square test), Q value = 1.6e-10
Table S7. Gene #12: 'AMP PEAK 12(8Q24.21) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| AMP PEAK 12(8Q24.21) MUTATED | 1 | 496 | 55 | 5 | 15 | 5 | 26 |
| AMP PEAK 12(8Q24.21) WILD-TYPE | 0 | 210 | 96 | 0 | 13 | 9 | 17 |
Figure S7. Get High-res Image Gene #12: 'AMP PEAK 12(8Q24.21) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 6.94e-09 (Chi-square test), Q value = 4.8e-06
Table S8. Gene #13: 'AMP PEAK 13(10P15.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| AMP PEAK 13(10P15.1) MUTATED | 1 | 234 | 17 | 4 | 4 | 0 | 8 |
| AMP PEAK 13(10P15.1) WILD-TYPE | 0 | 472 | 134 | 1 | 24 | 14 | 35 |
Figure S8. Get High-res Image Gene #13: 'AMP PEAK 13(10P15.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.03e-05 (Chi-square test), Q value = 0.007
Table S9. Gene #15: 'AMP PEAK 15(11P13) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| AMP PEAK 15(11P13) MUTATED | 1 | 168 | 12 | 3 | 1 | 2 | 10 |
| AMP PEAK 15(11P13) WILD-TYPE | 0 | 538 | 139 | 2 | 27 | 12 | 33 |
Figure S9. Get High-res Image Gene #15: 'AMP PEAK 15(11P13) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 7.17e-05 (Chi-square test), Q value = 0.048
Table S10. Gene #18: 'AMP PEAK 18(12P13.33) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| AMP PEAK 18(12P13.33) MUTATED | 1 | 203 | 21 | 4 | 8 | 1 | 8 |
| AMP PEAK 18(12P13.33) WILD-TYPE | 0 | 503 | 130 | 1 | 20 | 13 | 35 |
Figure S10. Get High-res Image Gene #18: 'AMP PEAK 18(12P13.33) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 6.12e-05 (Chi-square test), Q value = 0.041
Table S11. Gene #23: 'AMP PEAK 23(15Q26.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| AMP PEAK 23(15Q26.3) MUTATED | 0 | 151 | 6 | 2 | 4 | 3 | 5 |
| AMP PEAK 23(15Q26.3) WILD-TYPE | 1 | 555 | 145 | 3 | 24 | 11 | 38 |
Figure S11. Get High-res Image Gene #23: 'AMP PEAK 23(15Q26.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 0.000156 (Fisher's exact test), Q value = 0.1
Table S12. Gene #25: 'AMP PEAK 25(17Q23.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
| nPatients | T1 | T2 | T3 | T4 |
|---|---|---|---|---|
| ALL | 247 | 551 | 113 | 35 |
| AMP PEAK 25(17Q23.1) MUTATED | 71 | 249 | 45 | 16 |
| AMP PEAK 25(17Q23.1) WILD-TYPE | 176 | 302 | 68 | 19 |
Figure S12. Get High-res Image Gene #25: 'AMP PEAK 25(17Q23.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
P value = 0.000107 (Fisher's exact test), Q value = 0.071
Table S13. Gene #25: 'AMP PEAK 25(17Q23.1) MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
| nPatients | FEMALE | MALE |
|---|---|---|
| ALL | 939 | 10 |
| AMP PEAK 25(17Q23.1) MUTATED | 373 | 10 |
| AMP PEAK 25(17Q23.1) WILD-TYPE | 566 | 0 |
Figure S13. Get High-res Image Gene #25: 'AMP PEAK 25(17Q23.1) MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
P value = 2.67e-05 (Chi-square test), Q value = 0.018
Table S14. Gene #27: 'AMP PEAK 27(19Q12) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| AMP PEAK 27(19Q12) MUTATED | 0 | 197 | 21 | 5 | 5 | 2 | 8 |
| AMP PEAK 27(19Q12) WILD-TYPE | 1 | 509 | 130 | 0 | 23 | 12 | 35 |
Figure S14. Get High-res Image Gene #27: 'AMP PEAK 27(19Q12) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.04e-13 (Chi-square test), Q value = 7.2e-11
Table S15. Gene #29: 'AMP PEAK 29(20Q13.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| AMP PEAK 29(20Q13.2) MUTATED | 1 | 408 | 37 | 1 | 10 | 1 | 18 |
| AMP PEAK 29(20Q13.2) WILD-TYPE | 0 | 298 | 114 | 4 | 18 | 13 | 25 |
Figure S15. Get High-res Image Gene #29: 'AMP PEAK 29(20Q13.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.22e-06 (Fisher's exact test), Q value = 0.00084
Table S16. Gene #30: 'DEL PEAK 1(1P36.13) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
| nPatients | T1 | T2 | T3 | T4 |
|---|---|---|---|---|
| ALL | 247 | 551 | 113 | 35 |
| DEL PEAK 1(1P36.13) MUTATED | 73 | 255 | 40 | 23 |
| DEL PEAK 1(1P36.13) WILD-TYPE | 174 | 296 | 73 | 12 |
Figure S16. Get High-res Image Gene #30: 'DEL PEAK 1(1P36.13) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
P value = 6.57e-06 (Fisher's exact test), Q value = 0.0045
Table S17. Gene #31: 'DEL PEAK 2(1P22.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
| nPatients | T1 | T2 | T3 | T4 |
|---|---|---|---|---|
| ALL | 247 | 551 | 113 | 35 |
| DEL PEAK 2(1P22.1) MUTATED | 57 | 203 | 33 | 21 |
| DEL PEAK 2(1P22.1) WILD-TYPE | 190 | 348 | 80 | 14 |
Figure S17. Get High-res Image Gene #31: 'DEL PEAK 2(1P22.1) MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
P value = 0.000233 (Chi-square test), Q value = 0.15
Table S18. Gene #32: 'DEL PEAK 3(2Q37.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 3(2Q37.3) MUTATED | 0 | 232 | 20 | 2 | 9 | 3 | 9 |
| DEL PEAK 3(2Q37.3) WILD-TYPE | 1 | 474 | 131 | 3 | 19 | 11 | 34 |
Figure S18. Get High-res Image Gene #32: 'DEL PEAK 3(2Q37.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 5.79e-06 (Chi-square test), Q value = 0.004
Table S19. Gene #33: 'DEL PEAK 4(3P14.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 4(3P14.3) MUTATED | 0 | 251 | 25 | 2 | 4 | 0 | 9 |
| DEL PEAK 4(3P14.3) WILD-TYPE | 1 | 455 | 126 | 3 | 24 | 14 | 34 |
Figure S19. Get High-res Image Gene #33: 'DEL PEAK 4(3P14.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 3.05e-06 (Chi-square test), Q value = 0.0021
Table S20. Gene #34: 'DEL PEAK 5(4P16.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 5(4P16.3) MUTATED | 1 | 246 | 22 | 3 | 6 | 0 | 14 |
| DEL PEAK 5(4P16.3) WILD-TYPE | 0 | 460 | 129 | 2 | 22 | 14 | 29 |
Figure S20. Get High-res Image Gene #34: 'DEL PEAK 5(4P16.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.3e-06 (Chi-square test), Q value = 0.00089
Table S21. Gene #35: 'DEL PEAK 6(4Q35.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 6(4Q35.2) MUTATED | 1 | 251 | 24 | 3 | 4 | 0 | 11 |
| DEL PEAK 6(4Q35.2) WILD-TYPE | 0 | 455 | 127 | 2 | 24 | 14 | 32 |
Figure S21. Get High-res Image Gene #35: 'DEL PEAK 6(4Q35.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.26e-10 (Chi-square test), Q value = 8.8e-08
Table S22. Gene #36: 'DEL PEAK 7(5Q11.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 7(5Q11.2) MUTATED | 1 | 217 | 8 | 4 | 4 | 1 | 9 |
| DEL PEAK 7(5Q11.2) WILD-TYPE | 0 | 489 | 143 | 1 | 24 | 13 | 34 |
Figure S22. Get High-res Image Gene #36: 'DEL PEAK 7(5Q11.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 4.71e-14 (Chi-square test), Q value = 3.3e-11
Table S23. Gene #37: 'DEL PEAK 8(5Q21.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 8(5Q21.3) MUTATED | 1 | 211 | 4 | 5 | 4 | 0 | 9 |
| DEL PEAK 8(5Q21.3) WILD-TYPE | 0 | 495 | 147 | 0 | 24 | 14 | 34 |
Figure S23. Get High-res Image Gene #37: 'DEL PEAK 8(5Q21.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 5.93e-06 (t-test), Q value = 0.004
Table S24. Gene #40: 'DEL PEAK 11(6Q27) MUTATION STATUS' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 946 | 58.5 (13.2) |
| DEL PEAK 11(6Q27) MUTATED | 318 | 55.9 (12.5) |
| DEL PEAK 11(6Q27) WILD-TYPE | 628 | 59.9 (13.3) |
Figure S24. Get High-res Image Gene #40: 'DEL PEAK 11(6Q27) MUTATION STATUS' versus Clinical Feature #2: 'AGE'
P value = 0.000285 (Chi-square test), Q value = 0.19
Table S25. Gene #41: 'DEL PEAK 12(7P22.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 12(7P22.3) MUTATED | 0 | 112 | 3 | 0 | 2 | 0 | 5 |
| DEL PEAK 12(7P22.3) WILD-TYPE | 1 | 594 | 148 | 5 | 26 | 14 | 38 |
Figure S25. Get High-res Image Gene #41: 'DEL PEAK 12(7P22.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 8.1e-09 (Chi-square test), Q value = 5.6e-06
Table S26. Gene #43: 'DEL PEAK 14(8P23.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 14(8P23.2) MUTATED | 1 | 408 | 45 | 3 | 10 | 3 | 24 |
| DEL PEAK 14(8P23.2) WILD-TYPE | 0 | 298 | 106 | 2 | 18 | 11 | 19 |
Figure S26. Get High-res Image Gene #43: 'DEL PEAK 14(8P23.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 3.35e-05 (Chi-square test), Q value = 0.023
Table S27. Gene #45: 'DEL PEAK 16(9P23) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 16(9P23) MUTATED | 0 | 244 | 19 | 2 | 8 | 5 | 10 |
| DEL PEAK 16(9P23) WILD-TYPE | 1 | 462 | 132 | 3 | 20 | 9 | 33 |
Figure S27. Get High-res Image Gene #45: 'DEL PEAK 16(9P23) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.82e-08 (Chi-square test), Q value = 1.3e-05
Table S28. Gene #46: 'DEL PEAK 17(9P21.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 17(9P21.3) MUTATED | 1 | 271 | 18 | 4 | 10 | 5 | 11 |
| DEL PEAK 17(9P21.3) WILD-TYPE | 0 | 435 | 133 | 1 | 18 | 9 | 32 |
Figure S28. Get High-res Image Gene #46: 'DEL PEAK 17(9P21.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.13e-06 (Chi-square test), Q value = 0.00078
Table S29. Gene #48: 'DEL PEAK 19(9Q34.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 19(9Q34.2) MUTATED | 0 | 219 | 16 | 4 | 5 | 3 | 7 |
| DEL PEAK 19(9Q34.2) WILD-TYPE | 1 | 487 | 135 | 1 | 23 | 11 | 36 |
Figure S29. Get High-res Image Gene #48: 'DEL PEAK 19(9Q34.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 0.000161 (Chi-square test), Q value = 0.11
Table S30. Gene #50: 'DEL PEAK 21(10Q26.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 21(10Q26.3) MUTATED | 0 | 228 | 25 | 4 | 5 | 1 | 12 |
| DEL PEAK 21(10Q26.3) WILD-TYPE | 1 | 478 | 126 | 1 | 23 | 13 | 31 |
Figure S30. Get High-res Image Gene #50: 'DEL PEAK 21(10Q26.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 5.7e-05 (Chi-square test), Q value = 0.038
Table S31. Gene #57: 'DEL PEAK 28(13Q11) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 28(13Q11) MUTATED | 1 | 310 | 37 | 2 | 11 | 1 | 13 |
| DEL PEAK 28(13Q11) WILD-TYPE | 0 | 396 | 114 | 3 | 17 | 13 | 30 |
Figure S31. Get High-res Image Gene #57: 'DEL PEAK 28(13Q11) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 2.87e-05 (Chi-square test), Q value = 0.019
Table S32. Gene #58: 'DEL PEAK 29(13Q14.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 29(13Q14.2) MUTATED | 0 | 352 | 47 | 4 | 10 | 2 | 14 |
| DEL PEAK 29(13Q14.2) WILD-TYPE | 1 | 354 | 104 | 1 | 18 | 12 | 29 |
Figure S32. Get High-res Image Gene #58: 'DEL PEAK 29(13Q14.2) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 9.53e-09 (Chi-square test), Q value = 6.6e-06
Table S33. Gene #59: 'DEL PEAK 30(14Q24.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 30(14Q24.1) MUTATED | 1 | 261 | 23 | 4 | 3 | 1 | 8 |
| DEL PEAK 30(14Q24.1) WILD-TYPE | 0 | 445 | 128 | 1 | 25 | 13 | 35 |
Figure S33. Get High-res Image Gene #59: 'DEL PEAK 30(14Q24.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.17e-05 (Chi-square test), Q value = 0.008
Table S34. Gene #60: 'DEL PEAK 31(15Q13.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 31(15Q13.1) MUTATED | 1 | 270 | 30 | 4 | 8 | 1 | 10 |
| DEL PEAK 31(15Q13.1) WILD-TYPE | 0 | 436 | 121 | 1 | 20 | 13 | 33 |
Figure S34. Get High-res Image Gene #60: 'DEL PEAK 31(15Q13.1) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 2.62e-15 (Chi-square test), Q value = 1.8e-12
Table S35. Gene #61: 'DEL PEAK 32(16Q24.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 32(16Q24.3) MUTATED | 0 | 433 | 135 | 2 | 19 | 1 | 16 |
| DEL PEAK 32(16Q24.3) WILD-TYPE | 1 | 273 | 16 | 3 | 9 | 13 | 27 |
Figure S35. Get High-res Image Gene #61: 'DEL PEAK 32(16Q24.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 0.000368 (t-test), Q value = 0.24
Table S36. Gene #63: 'DEL PEAK 34(17Q21.31) MUTATION STATUS' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 946 | 58.5 (13.2) |
| DEL PEAK 34(17Q21.31) MUTATED | 326 | 56.4 (13.4) |
| DEL PEAK 34(17Q21.31) WILD-TYPE | 620 | 59.7 (12.9) |
Figure S36. Get High-res Image Gene #63: 'DEL PEAK 34(17Q21.31) MUTATION STATUS' versus Clinical Feature #2: 'AGE'
P value = 1.53e-05 (Chi-square test), Q value = 0.01
Table S37. Gene #63: 'DEL PEAK 34(17Q21.31) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 34(17Q21.31) MUTATED | 0 | 268 | 27 | 4 | 10 | 1 | 16 |
| DEL PEAK 34(17Q21.31) WILD-TYPE | 1 | 438 | 124 | 1 | 18 | 13 | 27 |
Figure S37. Get High-res Image Gene #63: 'DEL PEAK 34(17Q21.31) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 3.37e-09 (Chi-square test), Q value = 2.3e-06
Table S38. Gene #65: 'DEL PEAK 36(19P13.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 36(19P13.3) MUTATED | 1 | 270 | 16 | 4 | 7 | 4 | 14 |
| DEL PEAK 36(19P13.3) WILD-TYPE | 0 | 436 | 135 | 1 | 21 | 10 | 29 |
Figure S38. Get High-res Image Gene #65: 'DEL PEAK 36(19P13.3) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 6.92e-07 (Chi-square test), Q value = 0.00048
Table S39. Gene #66: 'DEL PEAK 37(19Q13.32) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 37(19Q13.32) MUTATED | 0 | 166 | 6 | 3 | 4 | 3 | 4 |
| DEL PEAK 37(19Q13.32) WILD-TYPE | 1 | 540 | 145 | 2 | 24 | 11 | 39 |
Figure S39. Get High-res Image Gene #66: 'DEL PEAK 37(19Q13.32) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 0.000117 (Chi-square test), Q value = 0.078
Table S40. Gene #67: 'DEL PEAK 38(20P13) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 706 | 151 | 5 | 28 | 14 | 43 |
| DEL PEAK 38(20P13) MUTATED | 1 | 122 | 8 | 2 | 2 | 0 | 4 |
| DEL PEAK 38(20P13) WILD-TYPE | 0 | 584 | 143 | 3 | 26 | 14 | 39 |
Figure S40. Get High-res Image Gene #67: 'DEL PEAK 38(20P13) MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = BRCA-TP.clin.merged.picked.txt
-
Number of patients = 949
-
Number of significantly focal cnvs = 70
-
Number of selected clinical features = 10
-
Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.