This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 80 arm-level events and 12 clinical features across 278 patients, 2 significant findings detected with Q value < 0.25.
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3p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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3q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings detected.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
NUMBERPACKYEARSSMOKED |
NUMBER OF LYMPH NODES |
RACE | ETHNICITY | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
3p gain | 88 (32%) | 190 |
0.0608 (1.00) |
0.00896 (1.00) |
0.00124 (1.00) |
0.155 (1.00) |
0.00336 (1.00) |
0.818 (1.00) |
0.388 (1.00) |
0.238 (1.00) |
0.21 (1.00) |
9.73e-05 (0.0934) |
0.457 (1.00) |
0.329 (1.00) |
3q gain | 115 (41%) | 163 |
0.816 (1.00) |
0.0111 (1.00) |
0.00134 (1.00) |
0.424 (1.00) |
0.00065 (0.622) |
0.642 (1.00) |
1 (1.00) |
0.413 (1.00) |
0.529 (1.00) |
0.000158 (0.151) |
0.811 (1.00) |
1 (1.00) |
1p gain | 56 (20%) | 222 |
0.262 (1.00) |
0.302 (1.00) |
0.312 (1.00) |
0.977 (1.00) |
0.0571 (1.00) |
0.913 (1.00) |
0.504 (1.00) |
0.919 (1.00) |
0.23 (1.00) |
0.617 (1.00) |
0.304 (1.00) |
1 (1.00) |
1q gain | 82 (29%) | 196 |
0.182 (1.00) |
0.777 (1.00) |
0.0352 (1.00) |
0.622 (1.00) |
0.0719 (1.00) |
0.0415 (1.00) |
0.306 (1.00) |
0.93 (1.00) |
0.0979 (1.00) |
0.0759 (1.00) |
0.0904 (1.00) |
1 (1.00) |
2p gain | 66 (24%) | 212 |
0.217 (1.00) |
0.0769 (1.00) |
0.121 (1.00) |
0.84 (1.00) |
0.00602 (1.00) |
0.323 (1.00) |
0.0409 (1.00) |
0.723 (1.00) |
0.0381 (1.00) |
0.00477 (1.00) |
0.911 (1.00) |
0.589 (1.00) |
2q gain | 29 (10%) | 249 |
0.13 (1.00) |
0.856 (1.00) |
0.919 (1.00) |
0.837 (1.00) |
0.62 (1.00) |
0.509 (1.00) |
0.387 (1.00) |
0.819 (1.00) |
0.931 (1.00) |
0.368 (1.00) |
0.907 (1.00) |
1 (1.00) |
4p gain | 28 (10%) | 250 |
0.169 (1.00) |
0.941 (1.00) |
0.116 (1.00) |
0.0717 (1.00) |
0.176 (1.00) |
0.285 (1.00) |
0.181 (1.00) |
0.747 (1.00) |
0.996 (1.00) |
0.26 (1.00) |
0.721 (1.00) |
0.37 (1.00) |
4q gain | 17 (6%) | 261 |
0.407 (1.00) |
0.564 (1.00) |
0.0551 (1.00) |
0.098 (1.00) |
0.748 (1.00) |
0.652 (1.00) |
1 (1.00) |
0.593 (1.00) |
0.977 (1.00) |
0.389 (1.00) |
1 (1.00) |
0.256 (1.00) |
5p gain | 102 (37%) | 176 |
0.966 (1.00) |
0.949 (1.00) |
0.757 (1.00) |
0.464 (1.00) |
1 (1.00) |
0.0895 (1.00) |
0.267 (1.00) |
0.47 (1.00) |
0.57 (1.00) |
0.408 (1.00) |
0.125 (1.00) |
0.652 (1.00) |
5q gain | 34 (12%) | 244 |
0.932 (1.00) |
0.404 (1.00) |
0.505 (1.00) |
0.772 (1.00) |
0.351 (1.00) |
0.531 (1.00) |
0.415 (1.00) |
0.295 (1.00) |
0.299 (1.00) |
0.703 (1.00) |
0.928 (1.00) |
1 (1.00) |
6p gain | 41 (15%) | 237 |
0.962 (1.00) |
0.108 (1.00) |
0.241 (1.00) |
0.295 (1.00) |
0.683 (1.00) |
0.383 (1.00) |
0.707 (1.00) |
0.641 (1.00) |
0.0615 (1.00) |
0.773 (1.00) |
0.938 (1.00) |
1 (1.00) |
6q gain | 23 (8%) | 255 |
0.489 (1.00) |
0.285 (1.00) |
0.891 (1.00) |
0.713 (1.00) |
0.135 (1.00) |
0.436 (1.00) |
0.143 (1.00) |
0.17 (1.00) |
0.109 (1.00) |
0.875 (1.00) |
0.422 (1.00) |
1 (1.00) |
7p gain | 112 (40%) | 166 |
0.38 (1.00) |
0.0541 (1.00) |
0.157 (1.00) |
0.199 (1.00) |
0.0328 (1.00) |
0.972 (1.00) |
1 (1.00) |
0.659 (1.00) |
0.921 (1.00) |
0.241 (1.00) |
0.368 (1.00) |
0.651 (1.00) |
7q gain | 98 (35%) | 180 |
0.706 (1.00) |
0.0644 (1.00) |
0.0873 (1.00) |
0.0762 (1.00) |
0.00123 (1.00) |
0.387 (1.00) |
0.889 (1.00) |
0.487 (1.00) |
0.364 (1.00) |
0.0733 (1.00) |
0.124 (1.00) |
0.166 (1.00) |
8p gain | 55 (20%) | 223 |
0.0835 (1.00) |
0.488 (1.00) |
0.102 (1.00) |
0.623 (1.00) |
0.799 (1.00) |
0.504 (1.00) |
0.505 (1.00) |
0.825 (1.00) |
0.677 (1.00) |
0.183 (1.00) |
0.718 (1.00) |
1 (1.00) |
8q gain | 129 (46%) | 149 |
0.0914 (1.00) |
0.763 (1.00) |
0.301 (1.00) |
0.715 (1.00) |
0.381 (1.00) |
0.709 (1.00) |
0.893 (1.00) |
0.622 (1.00) |
0.233 (1.00) |
0.0791 (1.00) |
0.394 (1.00) |
1 (1.00) |
9p gain | 46 (17%) | 232 |
0.0198 (1.00) |
0.508 (1.00) |
0.538 (1.00) |
0.803 (1.00) |
0.195 (1.00) |
0.174 (1.00) |
0.371 (1.00) |
0.308 (1.00) |
0.52 (1.00) |
0.92 (1.00) |
0.269 (1.00) |
0.584 (1.00) |
9q gain | 36 (13%) | 242 |
0.124 (1.00) |
0.229 (1.00) |
0.016 (1.00) |
0.0754 (1.00) |
0.241 (1.00) |
0.0668 (1.00) |
0.692 (1.00) |
0.844 (1.00) |
0.122 (1.00) |
0.0512 (1.00) |
0.63 (1.00) |
1 (1.00) |
10p gain | 76 (27%) | 202 |
0.192 (1.00) |
0.864 (1.00) |
0.213 (1.00) |
0.794 (1.00) |
0.184 (1.00) |
0.869 (1.00) |
0.292 (1.00) |
0.68 (1.00) |
0.282 (1.00) |
0.423 (1.00) |
0.297 (1.00) |
1 (1.00) |
10q gain | 25 (9%) | 253 |
0.261 (1.00) |
0.91 (1.00) |
0.243 (1.00) |
0.4 (1.00) |
0.0519 (1.00) |
0.58 (1.00) |
0.484 (1.00) |
0.423 (1.00) |
0.774 (1.00) |
0.142 (1.00) |
1 (1.00) |
1 (1.00) |
11p gain | 25 (9%) | 253 |
0.097 (1.00) |
0.993 (1.00) |
0.721 (1.00) |
0.187 (1.00) |
0.0382 (1.00) |
0.418 (1.00) |
0.0192 (1.00) |
0.857 (1.00) |
0.747 (1.00) |
0.926 (1.00) |
0.27 (1.00) |
0.396 (1.00) |
11q gain | 37 (13%) | 241 |
0.17 (1.00) |
0.0345 (1.00) |
0.558 (1.00) |
0.437 (1.00) |
0.0203 (1.00) |
0.161 (1.00) |
0.0166 (1.00) |
0.396 (1.00) |
0.657 (1.00) |
0.221 (1.00) |
0.173 (1.00) |
0.524 (1.00) |
12p gain | 77 (28%) | 201 |
0.827 (1.00) |
0.0464 (1.00) |
0.564 (1.00) |
0.383 (1.00) |
0.711 (1.00) |
0.239 (1.00) |
0.881 (1.00) |
0.825 (1.00) |
0.626 (1.00) |
0.249 (1.00) |
0.957 (1.00) |
1 (1.00) |
12q gain | 58 (21%) | 220 |
0.7 (1.00) |
0.451 (1.00) |
0.215 (1.00) |
0.152 (1.00) |
0.635 (1.00) |
0.102 (1.00) |
1 (1.00) |
0.651 (1.00) |
0.488 (1.00) |
0.196 (1.00) |
0.46 (1.00) |
1 (1.00) |
13q gain | 65 (23%) | 213 |
0.772 (1.00) |
0.182 (1.00) |
0.358 (1.00) |
0.842 (1.00) |
0.0108 (1.00) |
0.0726 (1.00) |
0.267 (1.00) |
0.964 (1.00) |
0.756 (1.00) |
0.0583 (1.00) |
0.0961 (1.00) |
0.342 (1.00) |
14q gain | 44 (16%) | 234 |
0.0651 (1.00) |
0.7 (1.00) |
0.475 (1.00) |
0.132 (1.00) |
0.971 (1.00) |
0.0302 (1.00) |
0.358 (1.00) |
0.69 (1.00) |
0.564 (1.00) |
0.651 (1.00) |
0.0133 (1.00) |
0.555 (1.00) |
15q gain | 22 (8%) | 256 |
0.866 (1.00) |
0.22 (1.00) |
0.862 (1.00) |
0.0679 (1.00) |
0.177 (1.00) |
0.106 (1.00) |
0.456 (1.00) |
0.296 (1.00) |
0.936 (1.00) |
0.524 (1.00) |
0.538 (1.00) |
1 (1.00) |
16p gain | 49 (18%) | 229 |
0.0605 (1.00) |
0.32 (1.00) |
0.183 (1.00) |
0.00643 (1.00) |
0.11 (1.00) |
0.0395 (1.00) |
0.602 (1.00) |
0.918 (1.00) |
0.276 (1.00) |
0.246 (1.00) |
0.475 (1.00) |
0.593 (1.00) |
16q gain | 54 (19%) | 224 |
0.49 (1.00) |
0.48 (1.00) |
0.572 (1.00) |
0.0151 (1.00) |
0.141 (1.00) |
0.0585 (1.00) |
0.313 (1.00) |
0.862 (1.00) |
0.93 (1.00) |
0.966 (1.00) |
0.321 (1.00) |
0.588 (1.00) |
17p gain | 39 (14%) | 239 |
0.0502 (1.00) |
0.105 (1.00) |
0.274 (1.00) |
0.643 (1.00) |
0.529 (1.00) |
0.345 (1.00) |
1 (1.00) |
0.348 (1.00) |
0.855 (1.00) |
0.93 (1.00) |
0.485 (1.00) |
1 (1.00) |
17q gain | 92 (33%) | 186 |
0.0485 (1.00) |
0.344 (1.00) |
0.223 (1.00) |
0.529 (1.00) |
0.0631 (1.00) |
0.775 (1.00) |
0.888 (1.00) |
0.263 (1.00) |
0.567 (1.00) |
0.0539 (1.00) |
0.356 (1.00) |
0.656 (1.00) |
18p gain | 78 (28%) | 200 |
0.103 (1.00) |
0.496 (1.00) |
0.974 (1.00) |
0.37 (1.00) |
0.626 (1.00) |
0.201 (1.00) |
0.551 (1.00) |
0.029 (1.00) |
0.195 (1.00) |
0.901 (1.00) |
0.0537 (1.00) |
1 (1.00) |
18q gain | 40 (14%) | 238 |
0.101 (1.00) |
0.931 (1.00) |
1 (1.00) |
0.133 (1.00) |
0.941 (1.00) |
0.355 (1.00) |
0.706 (1.00) |
0.13 (1.00) |
0.558 (1.00) |
0.887 (1.00) |
0.0245 (1.00) |
0.545 (1.00) |
19p gain | 52 (19%) | 226 |
0.44 (1.00) |
0.632 (1.00) |
0.449 (1.00) |
0.436 (1.00) |
0.0734 (1.00) |
0.906 (1.00) |
0.493 (1.00) |
0.977 (1.00) |
0.865 (1.00) |
0.0593 (1.00) |
0.0327 (1.00) |
0.588 (1.00) |
19q gain | 88 (32%) | 190 |
0.226 (1.00) |
0.376 (1.00) |
0.459 (1.00) |
0.376 (1.00) |
0.211 (1.00) |
0.935 (1.00) |
0.886 (1.00) |
0.769 (1.00) |
0.448 (1.00) |
0.038 (1.00) |
0.82 (1.00) |
0.645 (1.00) |
20p gain | 132 (47%) | 146 |
0.642 (1.00) |
0.354 (1.00) |
0.256 (1.00) |
0.682 (1.00) |
0.0869 (1.00) |
0.308 (1.00) |
0.69 (1.00) |
0.389 (1.00) |
0.163 (1.00) |
0.129 (1.00) |
0.0864 (1.00) |
0.374 (1.00) |
20q gain | 154 (55%) | 124 |
0.688 (1.00) |
0.693 (1.00) |
0.653 (1.00) |
0.984 (1.00) |
0.256 (1.00) |
0.575 (1.00) |
1 (1.00) |
0.63 (1.00) |
0.416 (1.00) |
0.533 (1.00) |
0.303 (1.00) |
0.664 (1.00) |
21q gain | 77 (28%) | 201 |
0.397 (1.00) |
0.114 (1.00) |
0.669 (1.00) |
0.533 (1.00) |
0.14 (1.00) |
0.747 (1.00) |
0.232 (1.00) |
0.889 (1.00) |
0.898 (1.00) |
0.275 (1.00) |
0.843 (1.00) |
0.62 (1.00) |
22q gain | 36 (13%) | 242 |
0.741 (1.00) |
0.955 (1.00) |
0.461 (1.00) |
0.664 (1.00) |
1 (1.00) |
0.782 (1.00) |
0.842 (1.00) |
0.634 (1.00) |
0.959 (1.00) |
0.431 (1.00) |
0.629 (1.00) |
1 (1.00) |
xq gain | 29 (10%) | 249 |
0.174 (1.00) |
0.451 (1.00) |
0.912 (1.00) |
0.223 (1.00) |
0.897 (1.00) |
0.678 (1.00) |
0.387 (1.00) |
0.308 (1.00) |
0.991 (1.00) |
0.599 (1.00) |
0.694 (1.00) |
1 (1.00) |
1p loss | 19 (7%) | 259 |
0.756 (1.00) |
0.915 (1.00) |
0.965 (1.00) |
0.514 (1.00) |
0.713 (1.00) |
0.366 (1.00) |
0.111 (1.00) |
0.787 (1.00) |
0.179 (1.00) |
0.766 (1.00) |
0.659 (1.00) |
1 (1.00) |
1q loss | 20 (7%) | 258 |
0.465 (1.00) |
0.872 (1.00) |
0.699 (1.00) |
0.654 (1.00) |
0.698 (1.00) |
0.702 (1.00) |
0.605 (1.00) |
0.876 (1.00) |
0.0631 (1.00) |
0.685 (1.00) |
1 (1.00) |
1 (1.00) |
2p loss | 30 (11%) | 248 |
0.346 (1.00) |
0.861 (1.00) |
0.758 (1.00) |
0.346 (1.00) |
0.702 (1.00) |
0.866 (1.00) |
0.196 (1.00) |
0.466 (1.00) |
0.271 (1.00) |
0.679 (1.00) |
0.62 (1.00) |
0.421 (1.00) |
2q loss | 61 (22%) | 217 |
0.357 (1.00) |
0.814 (1.00) |
0.583 (1.00) |
0.957 (1.00) |
0.0832 (1.00) |
0.845 (1.00) |
1 (1.00) |
0.137 (1.00) |
0.983 (1.00) |
0.151 (1.00) |
0.656 (1.00) |
0.289 (1.00) |
3p loss | 36 (13%) | 242 |
0.541 (1.00) |
0.267 (1.00) |
0.903 (1.00) |
0.647 (1.00) |
0.397 (1.00) |
0.837 (1.00) |
0.114 (1.00) |
0.467 (1.00) |
0.374 (1.00) |
0.773 (1.00) |
0.131 (1.00) |
0.48 (1.00) |
3q loss | 15 (5%) | 263 |
0.536 (1.00) |
0.517 (1.00) |
0.871 (1.00) |
0.804 (1.00) |
0.529 (1.00) |
0.39 (1.00) |
1 (1.00) |
0.206 (1.00) |
0.801 (1.00) |
0.449 (1.00) |
0.69 (1.00) |
1 (1.00) |
4p loss | 91 (33%) | 187 |
0.292 (1.00) |
0.374 (1.00) |
0.197 (1.00) |
0.245 (1.00) |
0.0308 (1.00) |
0.657 (1.00) |
0.394 (1.00) |
0.936 (1.00) |
0.0873 (1.00) |
0.0668 (1.00) |
0.0763 (1.00) |
1 (1.00) |
4q loss | 89 (32%) | 189 |
0.923 (1.00) |
0.0728 (1.00) |
0.439 (1.00) |
0.316 (1.00) |
0.336 (1.00) |
0.462 (1.00) |
1 (1.00) |
0.417 (1.00) |
0.671 (1.00) |
0.322 (1.00) |
0.407 (1.00) |
1 (1.00) |
5p loss | 42 (15%) | 236 |
0.528 (1.00) |
0.0911 (1.00) |
0.338 (1.00) |
0.972 (1.00) |
0.639 (1.00) |
0.47 (1.00) |
0.454 (1.00) |
0.367 (1.00) |
0.466 (1.00) |
0.664 (1.00) |
0.818 (1.00) |
1 (1.00) |
5q loss | 105 (38%) | 173 |
0.708 (1.00) |
0.102 (1.00) |
0.0935 (1.00) |
0.809 (1.00) |
0.0286 (1.00) |
0.0313 (1.00) |
0.784 (1.00) |
0.00816 (1.00) |
0.402 (1.00) |
0.0597 (1.00) |
0.294 (1.00) |
0.368 (1.00) |
6p loss | 65 (23%) | 213 |
0.675 (1.00) |
0.845 (1.00) |
0.0919 (1.00) |
0.0148 (1.00) |
0.0525 (1.00) |
0.633 (1.00) |
0.53 (1.00) |
0.699 (1.00) |
0.399 (1.00) |
0.15 (1.00) |
0.311 (1.00) |
0.0871 (1.00) |
6q loss | 101 (36%) | 177 |
0.632 (1.00) |
0.912 (1.00) |
0.112 (1.00) |
0.511 (1.00) |
0.0505 (1.00) |
0.576 (1.00) |
0.268 (1.00) |
0.157 (1.00) |
0.532 (1.00) |
0.0285 (1.00) |
0.26 (1.00) |
0.061 (1.00) |
7p loss | 10 (4%) | 268 |
0.387 (1.00) |
0.716 (1.00) |
0.534 (1.00) |
0.82 (1.00) |
0.117 (1.00) |
0.49 (1.00) |
0.293 (1.00) |
0.729 (1.00) |
0.657 (1.00) |
0.16 (1.00) |
1 (1.00) |
1 (1.00) |
7q loss | 15 (5%) | 263 |
0.68 (1.00) |
0.6 (1.00) |
0.758 (1.00) |
0.664 (1.00) |
0.383 (1.00) |
0.729 (1.00) |
0.249 (1.00) |
0.729 (1.00) |
0.0236 (1.00) |
0.565 (1.00) |
0.835 (1.00) |
0.241 (1.00) |
8p loss | 125 (45%) | 153 |
0.948 (1.00) |
0.126 (1.00) |
0.00558 (1.00) |
0.63 (1.00) |
0.0278 (1.00) |
0.00269 (1.00) |
0.894 (1.00) |
0.151 (1.00) |
0.138 (1.00) |
0.0501 (1.00) |
0.0703 (1.00) |
0.388 (1.00) |
8q loss | 22 (8%) | 256 |
0.92 (1.00) |
0.181 (1.00) |
0.202 (1.00) |
0.00198 (1.00) |
0.0458 (1.00) |
0.0926 (1.00) |
1 (1.00) |
0.79 (1.00) |
0.244 (1.00) |
0.0113 (1.00) |
1 (1.00) |
1 (1.00) |
9p loss | 116 (42%) | 162 |
0.792 (1.00) |
0.104 (1.00) |
0.426 (1.00) |
0.969 (1.00) |
0.587 (1.00) |
0.747 (1.00) |
0.418 (1.00) |
0.294 (1.00) |
0.304 (1.00) |
0.869 (1.00) |
0.839 (1.00) |
1 (1.00) |
9q loss | 110 (40%) | 168 |
0.42 (1.00) |
0.211 (1.00) |
0.647 (1.00) |
0.592 (1.00) |
0.71 (1.00) |
0.716 (1.00) |
0.411 (1.00) |
0.586 (1.00) |
0.0109 (1.00) |
0.88 (1.00) |
0.521 (1.00) |
1 (1.00) |
10p loss | 49 (18%) | 229 |
0.681 (1.00) |
0.672 (1.00) |
0.81 (1.00) |
0.921 (1.00) |
0.462 (1.00) |
0.452 (1.00) |
1 (1.00) |
0.923 (1.00) |
0.0249 (1.00) |
0.356 (1.00) |
0.00281 (1.00) |
1 (1.00) |
10q loss | 87 (31%) | 191 |
0.845 (1.00) |
0.135 (1.00) |
0.59 (1.00) |
0.546 (1.00) |
0.699 (1.00) |
0.371 (1.00) |
1 (1.00) |
0.156 (1.00) |
0.634 (1.00) |
0.653 (1.00) |
0.288 (1.00) |
0.638 (1.00) |
11p loss | 113 (41%) | 165 |
0.459 (1.00) |
0.0457 (1.00) |
0.0188 (1.00) |
0.274 (1.00) |
0.103 (1.00) |
0.104 (1.00) |
0.892 (1.00) |
0.26 (1.00) |
0.407 (1.00) |
0.033 (1.00) |
0.131 (1.00) |
1 (1.00) |
11q loss | 81 (29%) | 197 |
0.961 (1.00) |
0.639 (1.00) |
0.672 (1.00) |
0.624 (1.00) |
0.123 (1.00) |
0.685 (1.00) |
0.305 (1.00) |
0.535 (1.00) |
0.644 (1.00) |
0.629 (1.00) |
0.183 (1.00) |
0.327 (1.00) |
12p loss | 33 (12%) | 245 |
0.929 (1.00) |
0.712 (1.00) |
0.222 (1.00) |
0.812 (1.00) |
0.0957 (1.00) |
0.379 (1.00) |
0.836 (1.00) |
0.699 (1.00) |
0.0561 (1.00) |
0.0367 (1.00) |
0.315 (1.00) |
0.469 (1.00) |
12q loss | 34 (12%) | 244 |
0.793 (1.00) |
0.165 (1.00) |
0.0461 (1.00) |
0.789 (1.00) |
0.0183 (1.00) |
0.293 (1.00) |
0.415 (1.00) |
0.862 (1.00) |
0.178 (1.00) |
0.019 (1.00) |
0.27 (1.00) |
1 (1.00) |
13q loss | 52 (19%) | 226 |
0.358 (1.00) |
0.622 (1.00) |
0.884 (1.00) |
0.782 (1.00) |
0.333 (1.00) |
0.444 (1.00) |
0.303 (1.00) |
0.493 (1.00) |
0.528 (1.00) |
0.791 (1.00) |
0.125 (1.00) |
1 (1.00) |
14q loss | 77 (28%) | 201 |
0.544 (1.00) |
0.238 (1.00) |
0.235 (1.00) |
0.908 (1.00) |
0.0295 (1.00) |
0.808 (1.00) |
0.37 (1.00) |
0.788 (1.00) |
0.23 (1.00) |
0.131 (1.00) |
0.767 (1.00) |
0.614 (1.00) |
15q loss | 93 (33%) | 185 |
0.694 (1.00) |
0.348 (1.00) |
0.377 (1.00) |
0.233 (1.00) |
0.987 (1.00) |
0.00902 (1.00) |
0.777 (1.00) |
0.182 (1.00) |
0.398 (1.00) |
0.432 (1.00) |
0.0226 (1.00) |
0.336 (1.00) |
16p loss | 68 (24%) | 210 |
0.292 (1.00) |
0.962 (1.00) |
0.446 (1.00) |
0.127 (1.00) |
0.659 (1.00) |
0.00812 (1.00) |
0.877 (1.00) |
0.834 (1.00) |
0.683 (1.00) |
0.996 (1.00) |
0.0933 (1.00) |
0.602 (1.00) |
16q loss | 63 (23%) | 215 |
0.798 (1.00) |
0.717 (1.00) |
0.898 (1.00) |
0.647 (1.00) |
0.242 (1.00) |
0.0043 (1.00) |
0.523 (1.00) |
0.516 (1.00) |
0.853 (1.00) |
0.299 (1.00) |
0.555 (1.00) |
0.329 (1.00) |
17p loss | 117 (42%) | 161 |
0.655 (1.00) |
0.15 (1.00) |
0.881 (1.00) |
0.895 (1.00) |
0.382 (1.00) |
0.684 (1.00) |
0.786 (1.00) |
0.631 (1.00) |
0.462 (1.00) |
0.787 (1.00) |
0.614 (1.00) |
0.652 (1.00) |
17q loss | 26 (9%) | 252 |
0.602 (1.00) |
0.547 (1.00) |
0.489 (1.00) |
0.355 (1.00) |
0.0828 (1.00) |
0.32 (1.00) |
0.49 (1.00) |
0.555 (1.00) |
0.99 (1.00) |
0.347 (1.00) |
0.00959 (1.00) |
1 (1.00) |
18p loss | 67 (24%) | 211 |
0.299 (1.00) |
0.989 (1.00) |
0.156 (1.00) |
0.295 (1.00) |
0.2 (1.00) |
0.148 (1.00) |
0.278 (1.00) |
0.0676 (1.00) |
0.808 (1.00) |
0.109 (1.00) |
0.828 (1.00) |
0.0871 (1.00) |
18q loss | 96 (35%) | 182 |
0.0701 (1.00) |
0.814 (1.00) |
0.348 (1.00) |
0.386 (1.00) |
0.653 (1.00) |
0.494 (1.00) |
0.778 (1.00) |
0.672 (1.00) |
0.773 (1.00) |
0.274 (1.00) |
0.962 (1.00) |
0.34 (1.00) |
19p loss | 68 (24%) | 210 |
0.00457 (1.00) |
0.0838 (1.00) |
0.0383 (1.00) |
0.0212 (1.00) |
0.0146 (1.00) |
0.0688 (1.00) |
0.756 (1.00) |
0.571 (1.00) |
0.825 (1.00) |
0.466 (1.00) |
0.00483 (1.00) |
0.596 (1.00) |
19q loss | 40 (14%) | 238 |
0.0198 (1.00) |
0.465 (1.00) |
0.712 (1.00) |
0.0424 (1.00) |
0.431 (1.00) |
0.0813 (1.00) |
0.849 (1.00) |
0.306 (1.00) |
0.624 (1.00) |
0.907 (1.00) |
0.0953 (1.00) |
1 (1.00) |
20p loss | 21 (8%) | 257 |
0.841 (1.00) |
0.151 (1.00) |
0.237 (1.00) |
0.164 (1.00) |
0.54 (1.00) |
0.703 (1.00) |
0.453 (1.00) |
0.497 (1.00) |
0.145 (1.00) |
0.314 (1.00) |
0.344 (1.00) |
1 (1.00) |
20q loss | 9 (3%) | 269 |
0.0459 (1.00) |
0.434 (1.00) |
0.528 (1.00) |
1 (1.00) |
0.56 (1.00) |
0.461 (1.00) |
0.711 (1.00) |
0.439 (1.00) |
0.509 (1.00) |
0.502 (1.00) |
0.269 (1.00) |
1 (1.00) |
21q loss | 44 (16%) | 234 |
0.123 (1.00) |
0.381 (1.00) |
0.178 (1.00) |
0.732 (1.00) |
0.0114 (1.00) |
0.199 (1.00) |
0.717 (1.00) |
0.291 (1.00) |
0.525 (1.00) |
0.677 (1.00) |
0.641 (1.00) |
1 (1.00) |
22q loss | 106 (38%) | 172 |
0.311 (1.00) |
0.271 (1.00) |
0.0373 (1.00) |
0.201 (1.00) |
0.0712 (1.00) |
0.00053 (0.508) |
1 (1.00) |
0.273 (1.00) |
0.758 (1.00) |
0.0496 (1.00) |
0.214 (1.00) |
0.0708 (1.00) |
xq loss | 54 (19%) | 224 |
0.465 (1.00) |
0.866 (1.00) |
0.809 (1.00) |
0.822 (1.00) |
0.545 (1.00) |
0.909 (1.00) |
0.612 (1.00) |
0.567 (1.00) |
0.584 (1.00) |
0.898 (1.00) |
0.844 (1.00) |
0.226 (1.00) |
P value = 9.73e-05 (Wilcoxon-test), Q value = 0.093
Table S1. Gene #5: '3p gain' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 219 | 2.2 (7.6) |
3P GAIN MUTATED | 66 | 4.2 (12.6) |
3P GAIN WILD-TYPE | 153 | 1.3 (3.7) |
Figure S1. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
![](D5V10.png)
P value = 0.000158 (Wilcoxon-test), Q value = 0.15
Table S2. Gene #6: '3q gain' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 219 | 2.2 (7.6) |
3Q GAIN MUTATED | 90 | 3.6 (11.0) |
3Q GAIN WILD-TYPE | 129 | 1.2 (3.6) |
Figure S2. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
![](D6V10.png)
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = BLCA-TP.merged_data.txt
-
Number of patients = 278
-
Number of significantly arm-level cnvs = 80
-
Number of selected clinical features = 12
-
Exclude regions 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 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.