This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 78 arm-level results and 10 clinical features across 575 patients, 23 significant findings detected with Q value < 0.25.
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3q gain cnv correlated to 'Time to Death' and 'PATHOLOGICSPREAD(M)'.
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7p gain cnv correlated to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.
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7q gain cnv correlated to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.
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11p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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13q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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18p gain cnv correlated to 'PATHOLOGICSPREAD(M)'.
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20p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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20q gain cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
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Xq gain cnv correlated to 'PATHOLOGICSPREAD(M)'.
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2q loss cnv correlated to 'Time to Death'.
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3p loss cnv correlated to 'Time to Death'.
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14q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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17p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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18p loss cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
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18q loss cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
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22q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
GENDER |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | |
18q loss | 352 (61%) | 223 |
0.422 (1.00) |
0.32 (1.00) |
1.89e-07 (0.000146) |
0.731 (1.00) |
3.75e-14 (2.91e-11) |
0.231 (1.00) |
0.000363 (0.274) |
0.0028 (1.00) |
0.000242 (0.184) |
0.494 (1.00) |
3q gain | 53 (9%) | 522 |
0.000218 (0.165) |
0.644 (1.00) |
0.00881 (1.00) |
0.148 (1.00) |
0.0154 (1.00) |
0.952 (1.00) |
0.0296 (1.00) |
0.000283 (0.214) |
0.025 (1.00) |
0.198 (1.00) |
7p gain | 290 (50%) | 285 |
0.157 (1.00) |
0.631 (1.00) |
0.113 (1.00) |
1 (1.00) |
1.76e-05 (0.0135) |
0.923 (1.00) |
0.000378 (0.286) |
0.0472 (1.00) |
1.12e-05 (0.00859) |
0.505 (1.00) |
7q gain | 255 (44%) | 320 |
0.216 (1.00) |
0.615 (1.00) |
0.16 (1.00) |
0.866 (1.00) |
0.000112 (0.0855) |
0.898 (1.00) |
0.00972 (1.00) |
0.0213 (1.00) |
5.3e-05 (0.0404) |
0.519 (1.00) |
20q gain | 403 (70%) | 172 |
0.431 (1.00) |
0.88 (1.00) |
4.38e-05 (0.0335) |
0.362 (1.00) |
1.96e-15 (1.53e-12) |
0.221 (1.00) |
0.0403 (1.00) |
0.0328 (1.00) |
0.00152 (1.00) |
0.731 (1.00) |
18p loss | 324 (56%) | 251 |
0.607 (1.00) |
0.351 (1.00) |
2.12e-05 (0.0163) |
0.933 (1.00) |
1.18e-14 (9.14e-12) |
0.671 (1.00) |
0.00134 (0.995) |
0.00874 (1.00) |
0.00147 (1.00) |
0.738 (1.00) |
11p gain | 39 (7%) | 536 |
0.458 (1.00) |
0.031 (1.00) |
0.000607 (0.456) |
0.187 (1.00) |
0.000327 (0.247) |
0.0993 (1.00) |
0.377 (1.00) |
0.479 (1.00) |
0.327 (1.00) |
1 (1.00) |
13q gain | 314 (55%) | 261 |
0.29 (1.00) |
0.874 (1.00) |
0.0192 (1.00) |
0.45 (1.00) |
3.94e-09 (3.06e-06) |
0.788 (1.00) |
0.00123 (0.922) |
0.188 (1.00) |
0.00258 (1.00) |
0.521 (1.00) |
18p gain | 21 (4%) | 554 |
0.696 (1.00) |
0.931 (1.00) |
1 (1.00) |
1 (1.00) |
0.0799 (1.00) |
0.528 (1.00) |
0.00317 (1.00) |
1.41e-05 (0.0108) |
0.719 (1.00) |
0.286 (1.00) |
20p gain | 288 (50%) | 287 |
0.34 (1.00) |
0.564 (1.00) |
0.00146 (1.00) |
0.024 (1.00) |
8.79e-09 (6.81e-06) |
0.354 (1.00) |
0.366 (1.00) |
0.0171 (1.00) |
0.035 (1.00) |
1 (1.00) |
Xq gain | 17 (3%) | 558 |
0.0508 (1.00) |
0.469 (1.00) |
0.583 (1.00) |
0.628 (1.00) |
0.723 (1.00) |
0.232 (1.00) |
0.159 (1.00) |
1.67e-07 (0.000129) |
0.132 (1.00) |
1 (1.00) |
2q loss | 8 (1%) | 567 |
3.78e-07 (0.000292) |
0.809 (1.00) |
1 (1.00) |
0.73 (1.00) |
0.868 (1.00) |
0.893 (1.00) |
0.885 (1.00) |
0.658 (1.00) |
0.336 (1.00) |
1 (1.00) |
3p loss | 35 (6%) | 540 |
3.17e-05 (0.0243) |
0.909 (1.00) |
0.335 (1.00) |
0.163 (1.00) |
0.0365 (1.00) |
0.0472 (1.00) |
0.0698 (1.00) |
0.00361 (1.00) |
0.0391 (1.00) |
0.434 (1.00) |
14q loss | 143 (25%) | 432 |
0.382 (1.00) |
0.696 (1.00) |
0.0658 (1.00) |
1 (1.00) |
2.34e-05 (0.0179) |
0.506 (1.00) |
0.0125 (1.00) |
0.219 (1.00) |
0.597 (1.00) |
1 (1.00) |
17p loss | 252 (44%) | 323 |
0.429 (1.00) |
0.587 (1.00) |
0.0019 (1.00) |
0.614 (1.00) |
5.69e-07 (0.000439) |
0.648 (1.00) |
0.0436 (1.00) |
0.000879 (0.66) |
0.0196 (1.00) |
0.19 (1.00) |
22q loss | 122 (21%) | 453 |
0.143 (1.00) |
0.0712 (1.00) |
0.17 (1.00) |
0.262 (1.00) |
0.000204 (0.156) |
0.573 (1.00) |
0.013 (1.00) |
0.243 (1.00) |
0.0543 (1.00) |
0.101 (1.00) |
1p gain | 15 (3%) | 560 |
0.85 (1.00) |
0.658 (1.00) |
1 (1.00) |
0.61 (1.00) |
0.503 (1.00) |
0.903 (1.00) |
0.0439 (1.00) |
0.813 (1.00) |
0.578 (1.00) |
1 (1.00) |
1q gain | 80 (14%) | 495 |
0.656 (1.00) |
0.838 (1.00) |
0.174 (1.00) |
0.148 (1.00) |
0.0623 (1.00) |
0.202 (1.00) |
0.176 (1.00) |
0.33 (1.00) |
0.0305 (1.00) |
1 (1.00) |
2p gain | 60 (10%) | 515 |
0.328 (1.00) |
0.924 (1.00) |
0.361 (1.00) |
0.173 (1.00) |
0.0437 (1.00) |
0.666 (1.00) |
0.3 (1.00) |
0.976 (1.00) |
0.155 (1.00) |
1 (1.00) |
2q gain | 59 (10%) | 516 |
0.384 (1.00) |
0.448 (1.00) |
0.169 (1.00) |
0.217 (1.00) |
0.0315 (1.00) |
0.871 (1.00) |
0.365 (1.00) |
0.9 (1.00) |
0.166 (1.00) |
1 (1.00) |
3p gain | 36 (6%) | 539 |
0.0324 (1.00) |
0.31 (1.00) |
0.0194 (1.00) |
0.301 (1.00) |
0.0545 (1.00) |
0.919 (1.00) |
0.608 (1.00) |
0.00172 (1.00) |
0.42 (1.00) |
0.444 (1.00) |
4p gain | 6 (1%) | 569 |
0.421 (1.00) |
0.885 (1.00) |
0.0537 (1.00) |
0.691 (1.00) |
0.199 (1.00) |
0.718 (1.00) |
0.323 (1.00) |
0.0446 (1.00) |
0.129 (1.00) |
1 (1.00) |
4q gain | 7 (1%) | 568 |
0.983 (1.00) |
0.758 (1.00) |
0.404 (1.00) |
1 (1.00) |
0.557 (1.00) |
0.581 (1.00) |
0.113 (1.00) |
0.179 (1.00) |
0.101 (1.00) |
1 (1.00) |
5p gain | 60 (10%) | 515 |
0.953 (1.00) |
0.356 (1.00) |
0.361 (1.00) |
1 (1.00) |
0.242 (1.00) |
0.904 (1.00) |
0.213 (1.00) |
0.777 (1.00) |
0.518 (1.00) |
0.24 (1.00) |
5q gain | 33 (6%) | 542 |
0.903 (1.00) |
0.867 (1.00) |
0.316 (1.00) |
0.592 (1.00) |
0.327 (1.00) |
0.817 (1.00) |
0.219 (1.00) |
0.416 (1.00) |
0.254 (1.00) |
1 (1.00) |
6p gain | 77 (13%) | 498 |
0.624 (1.00) |
0.48 (1.00) |
0.0769 (1.00) |
1 (1.00) |
0.0568 (1.00) |
0.628 (1.00) |
0.00301 (1.00) |
0.752 (1.00) |
0.0536 (1.00) |
0.107 (1.00) |
6q gain | 71 (12%) | 504 |
0.875 (1.00) |
0.874 (1.00) |
0.0866 (1.00) |
0.899 (1.00) |
0.0795 (1.00) |
0.892 (1.00) |
0.00864 (1.00) |
0.631 (1.00) |
0.0294 (1.00) |
0.307 (1.00) |
8p gain | 108 (19%) | 467 |
0.64 (1.00) |
0.516 (1.00) |
0.551 (1.00) |
0.831 (1.00) |
0.945 (1.00) |
0.468 (1.00) |
0.316 (1.00) |
0.832 (1.00) |
0.872 (1.00) |
1 (1.00) |
8q gain | 235 (41%) | 340 |
0.232 (1.00) |
0.125 (1.00) |
0.395 (1.00) |
0.396 (1.00) |
0.041 (1.00) |
0.207 (1.00) |
0.253 (1.00) |
0.29 (1.00) |
0.37 (1.00) |
0.744 (1.00) |
9p gain | 79 (14%) | 496 |
0.239 (1.00) |
0.339 (1.00) |
0.00178 (1.00) |
0.717 (1.00) |
0.0107 (1.00) |
0.87 (1.00) |
0.311 (1.00) |
0.674 (1.00) |
0.306 (1.00) |
0.619 (1.00) |
9q gain | 64 (11%) | 511 |
0.106 (1.00) |
0.197 (1.00) |
0.0386 (1.00) |
0.233 (1.00) |
0.194 (1.00) |
0.379 (1.00) |
0.321 (1.00) |
0.7 (1.00) |
0.205 (1.00) |
0.607 (1.00) |
10p gain | 28 (5%) | 547 |
0.0421 (1.00) |
0.165 (1.00) |
1 (1.00) |
0.252 (1.00) |
0.768 (1.00) |
0.103 (1.00) |
0.00549 (1.00) |
0.14 (1.00) |
0.191 (1.00) |
1 (1.00) |
10q gain | 13 (2%) | 562 |
0.431 (1.00) |
0.0098 (1.00) |
0.762 (1.00) |
0.4 (1.00) |
0.603 (1.00) |
0.292 (1.00) |
0.0309 (1.00) |
0.494 (1.00) |
0.137 (1.00) |
1 (1.00) |
11q gain | 39 (7%) | 536 |
0.414 (1.00) |
0.00274 (1.00) |
0.0272 (1.00) |
1 (1.00) |
0.0125 (1.00) |
0.191 (1.00) |
0.478 (1.00) |
0.751 (1.00) |
0.0946 (1.00) |
1 (1.00) |
12p gain | 93 (16%) | 482 |
0.659 (1.00) |
0.0189 (1.00) |
0.801 (1.00) |
0.91 (1.00) |
0.951 (1.00) |
0.528 (1.00) |
0.00985 (1.00) |
0.409 (1.00) |
0.081 (1.00) |
0.644 (1.00) |
12q gain | 78 (14%) | 497 |
0.834 (1.00) |
0.00427 (1.00) |
0.344 (1.00) |
0.393 (1.00) |
0.729 (1.00) |
0.676 (1.00) |
0.0409 (1.00) |
0.443 (1.00) |
0.036 (1.00) |
0.617 (1.00) |
14q gain | 19 (3%) | 556 |
0.313 (1.00) |
0.908 (1.00) |
0.61 (1.00) |
1 (1.00) |
0.759 (1.00) |
0.366 (1.00) |
0.469 (1.00) |
0.0266 (1.00) |
0.446 (1.00) |
0.263 (1.00) |
15q gain | 7 (1%) | 568 |
0.91 (1.00) |
0.405 (1.00) |
1 (1.00) |
0.71 (1.00) |
0.208 (1.00) |
0.872 (1.00) |
0.875 (1.00) |
0.714 (1.00) |
0.797 (1.00) |
1 (1.00) |
16p gain | 96 (17%) | 479 |
0.689 (1.00) |
0.342 (1.00) |
0.618 (1.00) |
1 (1.00) |
0.0208 (1.00) |
0.842 (1.00) |
0.00671 (1.00) |
0.371 (1.00) |
0.00407 (1.00) |
0.178 (1.00) |
16q gain | 96 (17%) | 479 |
0.853 (1.00) |
0.215 (1.00) |
0.454 (1.00) |
1 (1.00) |
0.0172 (1.00) |
0.809 (1.00) |
0.000484 (0.364) |
0.312 (1.00) |
0.000404 (0.305) |
0.178 (1.00) |
17p gain | 13 (2%) | 562 |
0.163 (1.00) |
0.669 (1.00) |
0.531 (1.00) |
0.78 (1.00) |
0.533 (1.00) |
0.55 (1.00) |
0.862 (1.00) |
0.00171 (1.00) |
0.65 (1.00) |
1 (1.00) |
17q gain | 67 (12%) | 508 |
0.0443 (1.00) |
0.51 (1.00) |
0.772 (1.00) |
0.3 (1.00) |
0.121 (1.00) |
0.877 (1.00) |
0.983 (1.00) |
0.0163 (1.00) |
0.387 (1.00) |
1 (1.00) |
18q gain | 12 (2%) | 563 |
0.639 (1.00) |
0.596 (1.00) |
1 (1.00) |
0.398 (1.00) |
0.32 (1.00) |
0.105 (1.00) |
0.0996 (1.00) |
0.826 (1.00) |
0.976 (1.00) |
0.174 (1.00) |
19p gain | 52 (9%) | 523 |
0.575 (1.00) |
0.37 (1.00) |
0.259 (1.00) |
0.884 (1.00) |
0.0798 (1.00) |
0.936 (1.00) |
0.882 (1.00) |
0.724 (1.00) |
0.985 (1.00) |
1 (1.00) |
19q gain | 61 (11%) | 514 |
0.279 (1.00) |
0.351 (1.00) |
0.367 (1.00) |
0.499 (1.00) |
0.363 (1.00) |
0.848 (1.00) |
0.982 (1.00) |
0.992 (1.00) |
0.883 (1.00) |
0.608 (1.00) |
21q gain | 19 (3%) | 556 |
0.262 (1.00) |
0.607 (1.00) |
0.292 (1.00) |
0.644 (1.00) |
0.669 (1.00) |
0.146 (1.00) |
0.145 (1.00) |
0.741 (1.00) |
0.227 (1.00) |
1 (1.00) |
22q gain | 7 (1%) | 568 |
0.487 (1.00) |
0.542 (1.00) |
0.0201 (1.00) |
0.71 (1.00) |
0.071 (1.00) |
1 (1.00) |
0.161 (1.00) |
0.179 (1.00) |
0.0359 (1.00) |
1 (1.00) |
1p loss | 68 (12%) | 507 |
0.054 (1.00) |
0.932 (1.00) |
0.774 (1.00) |
0.52 (1.00) |
0.281 (1.00) |
0.716 (1.00) |
0.0533 (1.00) |
0.185 (1.00) |
0.0962 (1.00) |
1 (1.00) |
1q loss | 25 (4%) | 550 |
0.717 (1.00) |
0.179 (1.00) |
0.651 (1.00) |
0.312 (1.00) |
0.876 (1.00) |
0.758 (1.00) |
0.164 (1.00) |
0.631 (1.00) |
0.346 (1.00) |
0.332 (1.00) |
2p loss | 10 (2%) | 565 |
0.311 (1.00) |
0.324 (1.00) |
0.151 (1.00) |
0.758 (1.00) |
0.247 (1.00) |
0.836 (1.00) |
0.748 (1.00) |
0.855 (1.00) |
0.968 (1.00) |
1 (1.00) |
3q loss | 17 (3%) | 558 |
0.0355 (1.00) |
0.121 (1.00) |
0.791 (1.00) |
0.0815 (1.00) |
0.00183 (1.00) |
0.598 (1.00) |
0.746 (1.00) |
0.169 (1.00) |
0.164 (1.00) |
0.238 (1.00) |
4p loss | 122 (21%) | 453 |
0.028 (1.00) |
0.29 (1.00) |
0.304 (1.00) |
0.475 (1.00) |
0.0198 (1.00) |
0.81 (1.00) |
0.00971 (1.00) |
0.0151 (1.00) |
0.00857 (1.00) |
0.101 (1.00) |
4q loss | 113 (20%) | 462 |
0.417 (1.00) |
0.288 (1.00) |
0.00866 (1.00) |
0.674 (1.00) |
0.00132 (0.988) |
0.743 (1.00) |
0.0763 (1.00) |
0.518 (1.00) |
0.149 (1.00) |
0.0795 (1.00) |
5p loss | 34 (6%) | 541 |
0.508 (1.00) |
0.66 (1.00) |
0.845 (1.00) |
0.481 (1.00) |
0.177 (1.00) |
0.804 (1.00) |
0.0599 (1.00) |
0.974 (1.00) |
0.114 (1.00) |
0.0941 (1.00) |
5q loss | 60 (10%) | 515 |
0.533 (1.00) |
0.659 (1.00) |
0.0672 (1.00) |
0.891 (1.00) |
0.046 (1.00) |
0.461 (1.00) |
0.045 (1.00) |
0.769 (1.00) |
0.439 (1.00) |
0.00908 (1.00) |
6p loss | 18 (3%) | 557 |
0.401 (1.00) |
0.889 (1.00) |
1 (1.00) |
0.813 (1.00) |
0.126 (1.00) |
1 (1.00) |
0.567 (1.00) |
0.605 (1.00) |
0.725 (1.00) |
1 (1.00) |
6q loss | 33 (6%) | 542 |
0.0672 (1.00) |
0.211 (1.00) |
0.543 (1.00) |
1 (1.00) |
0.0943 (1.00) |
0.683 (1.00) |
0.0842 (1.00) |
0.000881 (0.66) |
0.471 (1.00) |
1 (1.00) |
7q loss | 3 (1%) | 572 |
0.191 (1.00) |
0.0213 (1.00) |
0.6 (1.00) |
0.0106 (1.00) |
0.679 (1.00) |
0.757 (1.00) |
0.924 (1.00) |
0.55 (1.00) |
1 (1.00) |
|
8p loss | 145 (25%) | 430 |
0.948 (1.00) |
0.996 (1.00) |
0.00687 (1.00) |
0.0831 (1.00) |
0.00148 (1.00) |
0.812 (1.00) |
0.0373 (1.00) |
0.19 (1.00) |
0.269 (1.00) |
0.0493 (1.00) |
8q loss | 12 (2%) | 563 |
0.765 (1.00) |
0.117 (1.00) |
1 (1.00) |
0.154 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.2 (1.00) |
0.0709 (1.00) |
1 (1.00) |
9p loss | 39 (7%) | 536 |
0.0253 (1.00) |
0.271 (1.00) |
0.712 (1.00) |
1 (1.00) |
0.748 (1.00) |
0.204 (1.00) |
0.758 (1.00) |
0.83 (1.00) |
0.484 (1.00) |
1 (1.00) |
9q loss | 37 (6%) | 538 |
0.287 (1.00) |
0.00981 (1.00) |
1 (1.00) |
0.395 (1.00) |
0.53 (1.00) |
0.111 (1.00) |
0.634 (1.00) |
0.925 (1.00) |
0.343 (1.00) |
1 (1.00) |
10p loss | 40 (7%) | 535 |
0.566 (1.00) |
0.0105 (1.00) |
0.043 (1.00) |
0.511 (1.00) |
0.0111 (1.00) |
0.722 (1.00) |
0.353 (1.00) |
0.595 (1.00) |
0.185 (1.00) |
0.48 (1.00) |
10q loss | 46 (8%) | 529 |
0.346 (1.00) |
0.0151 (1.00) |
0.00307 (1.00) |
1 (1.00) |
0.00268 (1.00) |
0.841 (1.00) |
0.73 (1.00) |
0.829 (1.00) |
0.532 (1.00) |
0.53 (1.00) |
11p loss | 40 (7%) | 535 |
0.377 (1.00) |
0.969 (1.00) |
0.00589 (1.00) |
0.743 (1.00) |
0.00128 (0.959) |
0.94 (1.00) |
0.216 (1.00) |
0.962 (1.00) |
0.0417 (1.00) |
0.48 (1.00) |
11q loss | 51 (9%) | 524 |
0.74 (1.00) |
0.821 (1.00) |
0.00745 (1.00) |
0.378 (1.00) |
0.00239 (1.00) |
0.702 (1.00) |
0.152 (1.00) |
0.981 (1.00) |
0.469 (1.00) |
0.0377 (1.00) |
12p loss | 33 (6%) | 542 |
0.0704 (1.00) |
0.986 (1.00) |
0.316 (1.00) |
0.0481 (1.00) |
0.12 (1.00) |
0.0526 (1.00) |
0.0182 (1.00) |
0.511 (1.00) |
0.19 (1.00) |
0.415 (1.00) |
12q loss | 28 (5%) | 547 |
0.103 (1.00) |
0.578 (1.00) |
1 (1.00) |
0.252 (1.00) |
0.303 (1.00) |
0.259 (1.00) |
0.0259 (1.00) |
0.29 (1.00) |
0.096 (1.00) |
1 (1.00) |
13q loss | 12 (2%) | 563 |
0.874 (1.00) |
0.864 (1.00) |
0.329 (1.00) |
1 (1.00) |
0.304 (1.00) |
0.394 (1.00) |
0.0251 (1.00) |
0.426 (1.00) |
0.511 (1.00) |
1 (1.00) |
15q loss | 156 (27%) | 419 |
0.531 (1.00) |
0.64 (1.00) |
0.0113 (1.00) |
0.851 (1.00) |
0.000516 (0.388) |
0.393 (1.00) |
0.289 (1.00) |
0.365 (1.00) |
0.208 (1.00) |
0.263 (1.00) |
16p loss | 15 (3%) | 560 |
0.993 (1.00) |
0.548 (1.00) |
0.379 (1.00) |
0.123 (1.00) |
0.26 (1.00) |
0.951 (1.00) |
0.673 (1.00) |
0.985 (1.00) |
0.832 (1.00) |
1 (1.00) |
16q loss | 17 (3%) | 558 |
0.455 (1.00) |
0.852 (1.00) |
0.00999 (1.00) |
0.628 (1.00) |
0.0229 (1.00) |
0.885 (1.00) |
0.179 (1.00) |
0.972 (1.00) |
0.652 (1.00) |
0.238 (1.00) |
17q loss | 45 (8%) | 530 |
0.52 (1.00) |
0.854 (1.00) |
0.39 (1.00) |
0.877 (1.00) |
0.278 (1.00) |
0.602 (1.00) |
0.112 (1.00) |
0.922 (1.00) |
0.459 (1.00) |
0.152 (1.00) |
19p loss | 20 (3%) | 555 |
0.758 (1.00) |
0.538 (1.00) |
0.454 (1.00) |
0.111 (1.00) |
0.519 (1.00) |
0.577 (1.00) |
0.775 (1.00) |
0.56 (1.00) |
0.619 (1.00) |
1 (1.00) |
19q loss | 18 (3%) | 557 |
0.957 (1.00) |
0.166 (1.00) |
0.598 (1.00) |
0.235 (1.00) |
0.698 (1.00) |
0.62 (1.00) |
0.76 (1.00) |
0.404 (1.00) |
0.945 (1.00) |
1 (1.00) |
20p loss | 47 (8%) | 528 |
0.39 (1.00) |
0.814 (1.00) |
0.304 (1.00) |
0.761 (1.00) |
0.327 (1.00) |
0.418 (1.00) |
0.777 (1.00) |
0.731 (1.00) |
0.596 (1.00) |
1 (1.00) |
21q loss | 114 (20%) | 461 |
0.35 (1.00) |
0.956 (1.00) |
0.00967 (1.00) |
0.403 (1.00) |
0.00996 (1.00) |
0.651 (1.00) |
0.0763 (1.00) |
0.843 (1.00) |
0.214 (1.00) |
0.695 (1.00) |
Xq loss | 11 (2%) | 564 |
0.386 (1.00) |
0.251 (1.00) |
0.151 (1.00) |
1 (1.00) |
0.291 (1.00) |
0.744 (1.00) |
0.337 (1.00) |
0.402 (1.00) |
0.549 (1.00) |
1 (1.00) |
P value = 0.000218 (logrank test), Q value = 0.17
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 444 | 60 | 0.1 - 135.5 (7.0) |
3Q GAIN MUTATED | 38 | 10 | 0.2 - 60.0 (5.7) |
3Q GAIN WILD-TYPE | 406 | 50 | 0.1 - 135.5 (7.6) |
P value = 0.000283 (Chi-square test), Q value = 0.21
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 435 | 71 | 9 | 1 | 49 |
3Q GAIN MUTATED | 32 | 8 | 3 | 1 | 8 |
3Q GAIN WILD-TYPE | 403 | 63 | 6 | 0 | 41 |
P value = 1.76e-05 (Fisher's exact test), Q value = 0.014
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
7P GAIN MUTATED | 184 | 15 | 87 | 2 |
7P GAIN WILD-TYPE | 172 | 39 | 56 | 11 |
P value = 1.12e-05 (Fisher's exact test), Q value = 0.0086
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
7P GAIN MUTATED | 46 | 78 | 99 | 52 |
7P GAIN WILD-TYPE | 51 | 129 | 67 | 29 |
P value = 0.000112 (Fisher's exact test), Q value = 0.085
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
7Q GAIN MUTATED | 161 | 14 | 77 | 1 |
7Q GAIN WILD-TYPE | 195 | 40 | 66 | 12 |
P value = 5.3e-05 (Fisher's exact test), Q value = 0.04
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
7Q GAIN MUTATED | 42 | 67 | 88 | 46 |
7Q GAIN WILD-TYPE | 55 | 140 | 78 | 35 |
P value = 0.000327 (Fisher's exact test), Q value = 0.25
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
11P GAIN MUTATED | 18 | 0 | 21 | 0 |
11P GAIN WILD-TYPE | 338 | 54 | 122 | 13 |
P value = 3.94e-09 (Fisher's exact test), Q value = 3.1e-06
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
13Q GAIN MUTATED | 199 | 12 | 96 | 2 |
13Q GAIN WILD-TYPE | 157 | 42 | 47 | 11 |
P value = 1.41e-05 (Chi-square test), Q value = 0.011
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 435 | 71 | 9 | 1 | 49 |
18P GAIN MUTATED | 15 | 2 | 0 | 1 | 2 |
18P GAIN WILD-TYPE | 420 | 69 | 9 | 0 | 47 |
P value = 8.79e-09 (Fisher's exact test), Q value = 6.8e-06
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
20P GAIN MUTATED | 176 | 11 | 93 | 2 |
20P GAIN WILD-TYPE | 180 | 43 | 50 | 11 |
P value = 4.38e-05 (Fisher's exact test), Q value = 0.033
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
20Q GAIN MUTATED | 269 | 131 |
20Q GAIN WILD-TYPE | 143 | 28 |
P value = 1.96e-15 (Fisher's exact test), Q value = 1.5e-12
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
20Q GAIN MUTATED | 251 | 16 | 125 | 4 |
20Q GAIN WILD-TYPE | 105 | 38 | 18 | 9 |
P value = 1.67e-07 (Chi-square test), Q value = 0.00013
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 435 | 71 | 9 | 1 | 49 |
XQ GAIN MUTATED | 10 | 4 | 0 | 1 | 1 |
XQ GAIN WILD-TYPE | 425 | 67 | 9 | 0 | 48 |
P value = 3.78e-07 (logrank test), Q value = 0.00029
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 444 | 60 | 0.1 - 135.5 (7.0) |
2Q LOSS MUTATED | 5 | 1 | 0.3 - 1.0 (1.0) |
2Q LOSS WILD-TYPE | 439 | 59 | 0.1 - 135.5 (7.3) |
P value = 3.17e-05 (logrank test), Q value = 0.024
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 444 | 60 | 0.1 - 135.5 (7.0) |
3P LOSS MUTATED | 21 | 5 | 0.3 - 14.5 (4.0) |
3P LOSS WILD-TYPE | 423 | 55 | 0.1 - 135.5 (7.3) |
P value = 2.34e-05 (Fisher's exact test), Q value = 0.018
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
14Q LOSS MUTATED | 90 | 3 | 48 | 0 |
14Q LOSS WILD-TYPE | 266 | 51 | 95 | 13 |
P value = 5.69e-07 (Fisher's exact test), Q value = 0.00044
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
17P LOSS MUTATED | 156 | 7 | 79 | 6 |
17P LOSS WILD-TYPE | 200 | 47 | 64 | 7 |
P value = 2.12e-05 (Fisher's exact test), Q value = 0.016
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
18P LOSS MUTATED | 209 | 112 |
18P LOSS WILD-TYPE | 203 | 47 |
P value = 1.18e-14 (Fisher's exact test), Q value = 9.1e-12
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
18P LOSS MUTATED | 201 | 7 | 107 | 5 |
18P LOSS WILD-TYPE | 155 | 47 | 36 | 8 |
P value = 1.89e-07 (Fisher's exact test), Q value = 0.00015
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
18Q LOSS MUTATED | 225 | 124 |
18Q LOSS WILD-TYPE | 187 | 35 |
P value = 3.75e-14 (Fisher's exact test), Q value = 2.9e-11
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
18Q LOSS MUTATED | 214 | 10 | 114 | 9 |
18Q LOSS WILD-TYPE | 142 | 44 | 29 | 4 |
P value = 0.000242 (Fisher's exact test), Q value = 0.18
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
18Q LOSS MUTATED | 50 | 112 | 112 | 62 |
18Q LOSS WILD-TYPE | 47 | 95 | 54 | 19 |
P value = 0.000204 (Fisher's exact test), Q value = 0.16
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
22Q LOSS MUTATED | 80 | 1 | 36 | 4 |
22Q LOSS WILD-TYPE | 276 | 53 | 107 | 9 |
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = COADREAD-TP.clin.merged.picked.txt
-
Number of patients = 575
-
Number of significantly arm-level cnvs = 78
-
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 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 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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.