This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 62 focal events and 13 clinical features across 271 patients, 31 significant findings detected with Q value < 0.25.
-
amp_1q21.3 cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
-
amp_3q21.3 cnv correlated to 'GLEASON_SCORE'.
-
amp_8q24.21 cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
-
amp_9q34.11 cnv correlated to 'NUMBER.OF.LYMPH.NODES', 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
-
amp_14q21.1 cnv correlated to 'GLEASON_SCORE'.
-
del_5q11.2 cnv correlated to 'PATHOLOGY.N.STAGE', 'NUMBER.OF.LYMPH.NODES', 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
-
del_5q13.2 cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
-
del_6q14.3 cnv correlated to 'GLEASON_SCORE_COMBINED' and 'PSA_RESULT_PREOP'.
-
del_12p13.1 cnv correlated to 'GLEASON_SCORE_PRIMARY'.
-
del_15q21.3 cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
-
del_16q22.3 cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
-
del_16q24.1 cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE_PRIMARY'.
Clinical Features |
AGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
HISTOLOGICAL TYPE |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
GLEASON SCORE COMBINED |
GLEASON SCORE PRIMARY |
GLEASON SCORE SECONDARY |
GLEASON SCORE |
PSA RESULT PREOP |
PSA VALUE |
RACE | ||
nCNV (%) | nWild-Type | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | |
del 5q11 2 | 38 (14%) | 233 |
0.324 (1.00) |
0.00095 (0.719) |
2.39e-05 (0.0189) |
1 (1.00) |
0.649 (1.00) |
7.88e-07 (0.000631) |
9.74e-07 (0.000777) |
3.59e-05 (0.0283) |
0.022 (1.00) |
7.36e-06 (0.00584) |
0.000363 (0.28) |
0.355 (1.00) |
0.438 (1.00) |
amp 9q34 11 | 25 (9%) | 246 |
0.286 (1.00) |
0.00747 (1.00) |
0.000887 (0.673) |
0.386 (1.00) |
0.775 (1.00) |
8.76e-05 (0.0686) |
4.55e-07 (0.000365) |
3.4e-06 (0.0027) |
0.0651 (1.00) |
1.02e-06 (0.000816) |
0.104 (1.00) |
0.147 (1.00) |
0.555 (1.00) |
amp 1q21 3 | 21 (8%) | 250 |
0.327 (1.00) |
0.0107 (1.00) |
0.436 (1.00) |
0.0497 (1.00) |
1 (1.00) |
0.401 (1.00) |
2.69e-05 (0.0212) |
0.000213 (0.166) |
0.0514 (1.00) |
1.31e-05 (0.0103) |
0.146 (1.00) |
0.182 (1.00) |
1 (1.00) |
amp 8q24 21 | 64 (24%) | 207 |
0.234 (1.00) |
0.00506 (1.00) |
0.09 (1.00) |
1 (1.00) |
0.716 (1.00) |
0.0859 (1.00) |
8.78e-07 (0.000702) |
2.88e-06 (0.00229) |
0.0528 (1.00) |
1.56e-05 (0.0123) |
0.13 (1.00) |
0.0512 (1.00) |
0.813 (1.00) |
del 5q13 2 | 37 (14%) | 234 |
0.859 (1.00) |
0.00151 (1.00) |
0.00572 (1.00) |
1 (1.00) |
0.823 (1.00) |
0.0024 (1.00) |
5.79e-07 (0.000464) |
6.31e-05 (0.0494) |
0.0106 (1.00) |
5.78e-05 (0.0454) |
0.0128 (1.00) |
0.218 (1.00) |
0.293 (1.00) |
del 15q21 3 | 30 (11%) | 241 |
0.983 (1.00) |
0.0582 (1.00) |
0.00857 (1.00) |
0.446 (1.00) |
0.491 (1.00) |
0.00272 (1.00) |
8.7e-08 (7e-05) |
2.66e-06 (0.00211) |
0.0114 (1.00) |
4.01e-07 (0.000322) |
0.841 (1.00) |
0.279 (1.00) |
1 (1.00) |
del 16q22 3 | 93 (34%) | 178 |
0.118 (1.00) |
0.0301 (1.00) |
0.075 (1.00) |
1 (1.00) |
0.947 (1.00) |
0.0602 (1.00) |
0.000184 (0.144) |
6.02e-05 (0.0473) |
0.317 (1.00) |
0.000286 (0.222) |
0.139 (1.00) |
0.0637 (1.00) |
0.719 (1.00) |
del 6q14 3 | 85 (31%) | 186 |
0.0209 (1.00) |
0.322 (1.00) |
0.0119 (1.00) |
0.65 (1.00) |
0.0703 (1.00) |
0.00773 (1.00) |
0.000207 (0.162) |
0.000921 (0.698) |
0.161 (1.00) |
0.000964 (0.729) |
0.000213 (0.166) |
0.234 (1.00) |
0.579 (1.00) |
del 16q24 1 | 105 (39%) | 166 |
0.463 (1.00) |
0.00798 (1.00) |
0.125 (1.00) |
1 (1.00) |
0.965 (1.00) |
0.0906 (1.00) |
0.000215 (0.167) |
4.06e-05 (0.0319) |
0.419 (1.00) |
0.000547 (0.419) |
0.0757 (1.00) |
0.0982 (1.00) |
1 (1.00) |
amp 3q21 3 | 32 (12%) | 239 |
0.0192 (1.00) |
0.00797 (1.00) |
0.538 (1.00) |
1 (1.00) |
0.0259 (1.00) |
0.603 (1.00) |
0.00545 (1.00) |
0.00284 (1.00) |
0.599 (1.00) |
0.000301 (0.233) |
0.0138 (1.00) |
0.388 (1.00) |
0.659 (1.00) |
amp 14q21 1 | 14 (5%) | 257 |
0.0154 (1.00) |
0.554 (1.00) |
1 (1.00) |
0.235 (1.00) |
1 (1.00) |
0.827 (1.00) |
0.00371 (1.00) |
0.0806 (1.00) |
0.121 (1.00) |
0.000257 (0.199) |
0.336 (1.00) |
0.588 (1.00) |
1 (1.00) |
del 12p13 1 | 55 (20%) | 216 |
0.922 (1.00) |
0.0123 (1.00) |
0.12 (1.00) |
0.268 (1.00) |
0.614 (1.00) |
0.0908 (1.00) |
0.00799 (1.00) |
0.000203 (0.159) |
0.936 (1.00) |
0.00214 (1.00) |
0.0304 (1.00) |
0.219 (1.00) |
1 (1.00) |
amp 3q26 2 | 40 (15%) | 231 |
0.089 (1.00) |
0.021 (1.00) |
0.561 (1.00) |
0.553 (1.00) |
0.277 (1.00) |
0.507 (1.00) |
0.0113 (1.00) |
0.00323 (1.00) |
0.677 (1.00) |
0.00166 (1.00) |
0.0225 (1.00) |
0.326 (1.00) |
1 (1.00) |
amp 4q13 3 | 5 (2%) | 266 |
0.172 (1.00) |
0.146 (1.00) |
0.434 (1.00) |
1 (1.00) |
0.434 (1.00) |
0.544 (1.00) |
0.0402 (1.00) |
0.0695 (1.00) |
0.188 (1.00) |
0.0558 (1.00) |
0.117 (1.00) |
0.45 (1.00) |
1 (1.00) |
amp 5q33 3 | 8 (3%) | 263 |
0.0526 (1.00) |
0.0304 (1.00) |
0.205 (1.00) |
0.14 (1.00) |
1 (1.00) |
0.166 (1.00) |
0.0751 (1.00) |
0.0277 (1.00) |
0.831 (1.00) |
0.0035 (1.00) |
0.952 (1.00) |
0.627 (1.00) |
0.215 (1.00) |
amp 7p14 3 | 47 (17%) | 224 |
0.255 (1.00) |
0.166 (1.00) |
0.578 (1.00) |
0.591 (1.00) |
0.0747 (1.00) |
0.631 (1.00) |
0.0754 (1.00) |
0.155 (1.00) |
0.156 (1.00) |
0.0941 (1.00) |
0.104 (1.00) |
0.802 (1.00) |
1 (1.00) |
amp 8p11 23 | 26 (10%) | 245 |
0.087 (1.00) |
0.298 (1.00) |
0.72 (1.00) |
1 (1.00) |
0.919 (1.00) |
0.706 (1.00) |
0.00315 (1.00) |
0.00273 (1.00) |
0.241 (1.00) |
0.00752 (1.00) |
0.271 (1.00) |
0.526 (1.00) |
1 (1.00) |
amp 11q13 2 | 14 (5%) | 257 |
0.0874 (1.00) |
0.0023 (1.00) |
0.0371 (1.00) |
0.235 (1.00) |
1 (1.00) |
0.0127 (1.00) |
0.00359 (1.00) |
0.000371 (0.286) |
0.91 (1.00) |
0.00204 (1.00) |
0.174 (1.00) |
0.541 (1.00) |
0.349 (1.00) |
amp 12q23 1 | 10 (4%) | 261 |
0.975 (1.00) |
0.217 (1.00) |
0.00884 (1.00) |
1 (1.00) |
0.789 (1.00) |
0.00111 (0.835) |
0.00171 (1.00) |
0.0095 (1.00) |
0.379 (1.00) |
0.000659 (0.503) |
0.00267 (1.00) |
0.578 (1.00) |
1 (1.00) |
amp 13q12 11 | 12 (4%) | 259 |
0.00313 (1.00) |
0.148 (1.00) |
0.289 (1.00) |
0.204 (1.00) |
0.809 (1.00) |
0.312 (1.00) |
0.0707 (1.00) |
0.00746 (1.00) |
0.697 (1.00) |
0.243 (1.00) |
0.445 (1.00) |
0.383 (1.00) |
0.304 (1.00) |
amp 15q11 2 | 5 (2%) | 266 |
0.363 (1.00) |
0.707 (1.00) |
1 (1.00) |
1 (1.00) |
0.657 (1.00) |
0.49 (1.00) |
0.992 (1.00) |
0.159 (1.00) |
0.139 (1.00) |
0.404 (1.00) |
0.889 (1.00) |
0.772 (1.00) |
|
amp 16q11 2 | 13 (5%) | 258 |
0.0438 (1.00) |
0.0204 (1.00) |
1 (1.00) |
1 (1.00) |
0.375 (1.00) |
0.827 (1.00) |
0.00449 (1.00) |
0.00995 (1.00) |
0.267 (1.00) |
0.00565 (1.00) |
0.101 (1.00) |
0.106 (1.00) |
1 (1.00) |
amp 17q23 2 | 9 (3%) | 262 |
0.3 (1.00) |
0.306 (1.00) |
1 (1.00) |
0.156 (1.00) |
0.367 (1.00) |
0.937 (1.00) |
0.395 (1.00) |
0.627 (1.00) |
0.641 (1.00) |
0.119 (1.00) |
0.326 (1.00) |
0.463 (1.00) |
1 (1.00) |
amp 18q21 31 | 6 (2%) | 265 |
0.0476 (1.00) |
0.0515 (1.00) |
1 (1.00) |
0.107 (1.00) |
0.303 (1.00) |
0.394 (1.00) |
0.00141 (1.00) |
0.197 (1.00) |
0.00815 (1.00) |
0.00263 (1.00) |
0.21 (1.00) |
0.518 (1.00) |
1 (1.00) |
amp 19q13 43 | 5 (2%) | 266 |
0.186 (1.00) |
0.0134 (1.00) |
1 (1.00) |
0.0895 (1.00) |
1 (1.00) |
0.438 (1.00) |
0.0532 (1.00) |
0.159 (1.00) |
0.188 (1.00) |
0.00614 (1.00) |
0.214 (1.00) |
0.423 (1.00) |
1 (1.00) |
amp 20q13 2 | 14 (5%) | 257 |
0.0553 (1.00) |
0.00043 (0.33) |
0.373 (1.00) |
1 (1.00) |
0.2 (1.00) |
0.183 (1.00) |
0.00979 (1.00) |
0.00218 (1.00) |
0.627 (1.00) |
0.0118 (1.00) |
0.208 (1.00) |
0.268 (1.00) |
1 (1.00) |
amp xp22 2 | 8 (3%) | 263 |
0.653 (1.00) |
0.126 (1.00) |
0.601 (1.00) |
0.14 (1.00) |
0.736 (1.00) |
0.836 (1.00) |
0.108 (1.00) |
0.0116 (1.00) |
0.371 (1.00) |
0.16 (1.00) |
0.041 (1.00) |
0.5 (1.00) |
0.166 (1.00) |
amp xp22 11 | 9 (3%) | 262 |
0.852 (1.00) |
0.306 (1.00) |
1 (1.00) |
0.00934 (1.00) |
1 (1.00) |
0.937 (1.00) |
0.159 (1.00) |
0.151 (1.00) |
0.994 (1.00) |
0.229 (1.00) |
0.799 (1.00) |
0.944 (1.00) |
0.262 (1.00) |
amp xp22 11 | 9 (3%) | 262 |
0.389 (1.00) |
0.306 (1.00) |
1 (1.00) |
0.00934 (1.00) |
0.762 (1.00) |
0.937 (1.00) |
0.159 (1.00) |
0.0374 (1.00) |
0.562 (1.00) |
0.487 (1.00) |
0.114 (1.00) |
0.538 (1.00) |
0.216 (1.00) |
amp xp21 1 | 8 (3%) | 263 |
0.183 (1.00) |
0.126 (1.00) |
0.601 (1.00) |
0.00732 (1.00) |
0.765 (1.00) |
0.913 (1.00) |
0.31 (1.00) |
0.246 (1.00) |
0.899 (1.00) |
0.16 (1.00) |
0.293 (1.00) |
0.196 (1.00) |
0.00776 (1.00) |
amp xq21 1 | 7 (3%) | 264 |
0.824 (1.00) |
0.518 (1.00) |
0.551 (1.00) |
1 (1.00) |
0.5 (1.00) |
0.723 (1.00) |
0.564 (1.00) |
0.612 (1.00) |
0.82 (1.00) |
0.531 (1.00) |
0.274 (1.00) |
0.386 (1.00) |
0.344 (1.00) |
amp xq21 1 | 5 (2%) | 266 |
0.435 (1.00) |
0.428 (1.00) |
0.0894 (1.00) |
1 (1.00) |
0.657 (1.00) |
0.0299 (1.00) |
0.331 (1.00) |
0.583 (1.00) |
0.482 (1.00) |
0.404 (1.00) |
0.093 (1.00) |
0.172 (1.00) |
0.0274 (1.00) |
amp xq21 31 | 5 (2%) | 266 |
0.265 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.659 (1.00) |
0.438 (1.00) |
0.234 (1.00) |
0.0235 (1.00) |
0.799 (1.00) |
0.692 (1.00) |
0.661 (1.00) |
0.135 (1.00) |
0.263 (1.00) |
amp xq25 | 4 (1%) | 267 |
0.1 (1.00) |
0.651 (1.00) |
1 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.49 (1.00) |
0.676 (1.00) |
0.287 (1.00) |
0.776 (1.00) |
0.751 (1.00) |
0.995 (1.00) |
0.216 (1.00) |
|
amp xq25 | 6 (2%) | 265 |
0.773 (1.00) |
0.719 (1.00) |
0.496 (1.00) |
1 (1.00) |
0.469 (1.00) |
0.681 (1.00) |
0.339 (1.00) |
0.895 (1.00) |
0.172 (1.00) |
0.541 (1.00) |
0.791 (1.00) |
0.394 (1.00) |
0.0188 (1.00) |
amp xq27 1 | 9 (3%) | 262 |
0.0965 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.766 (1.00) |
0.322 (1.00) |
0.794 (1.00) |
0.627 (1.00) |
0.476 (1.00) |
0.686 (1.00) |
0.627 (1.00) |
0.357 (1.00) |
0.424 (1.00) |
del 1p31 3 | 33 (12%) | 238 |
0.423 (1.00) |
0.153 (1.00) |
1 (1.00) |
1 (1.00) |
0.132 (1.00) |
0.938 (1.00) |
0.00719 (1.00) |
0.0855 (1.00) |
0.0323 (1.00) |
0.0179 (1.00) |
0.561 (1.00) |
0.0627 (1.00) |
0.199 (1.00) |
del 1p22 1 | 21 (8%) | 250 |
0.742 (1.00) |
0.579 (1.00) |
0.436 (1.00) |
1 (1.00) |
0.775 (1.00) |
0.413 (1.00) |
0.443 (1.00) |
0.364 (1.00) |
0.749 (1.00) |
0.603 (1.00) |
0.132 (1.00) |
0.343 (1.00) |
1 (1.00) |
del 1q42 2 | 22 (8%) | 249 |
0.0267 (1.00) |
0.415 (1.00) |
0.267 (1.00) |
1 (1.00) |
0.279 (1.00) |
0.253 (1.00) |
0.192 (1.00) |
0.189 (1.00) |
0.853 (1.00) |
0.0506 (1.00) |
0.045 (1.00) |
0.288 (1.00) |
0.556 (1.00) |
del 2p22 1 | 17 (6%) | 254 |
0.345 (1.00) |
0.201 (1.00) |
0.00438 (1.00) |
1 (1.00) |
0.339 (1.00) |
0.000819 (0.622) |
0.00664 (1.00) |
0.0994 (1.00) |
0.0168 (1.00) |
0.0136 (1.00) |
0.926 (1.00) |
0.375 (1.00) |
1 (1.00) |
del 2q22 1 | 37 (14%) | 234 |
0.000556 (0.424) |
0.807 (1.00) |
1 (1.00) |
1 (1.00) |
0.356 (1.00) |
0.701 (1.00) |
0.34 (1.00) |
0.0115 (1.00) |
0.155 (1.00) |
0.325 (1.00) |
0.583 (1.00) |
0.858 (1.00) |
0.416 (1.00) |
del 2q22 3 | 34 (13%) | 237 |
0.00413 (1.00) |
0.624 (1.00) |
1 (1.00) |
1 (1.00) |
0.494 (1.00) |
0.885 (1.00) |
0.669 (1.00) |
0.614 (1.00) |
0.328 (1.00) |
0.876 (1.00) |
0.723 (1.00) |
0.979 (1.00) |
1 (1.00) |
del 3p13 | 43 (16%) | 228 |
0.022 (1.00) |
0.735 (1.00) |
0.774 (1.00) |
0.18 (1.00) |
0.146 (1.00) |
0.644 (1.00) |
0.285 (1.00) |
0.573 (1.00) |
0.512 (1.00) |
0.2 (1.00) |
0.389 (1.00) |
0.779 (1.00) |
1 (1.00) |
del 3q29 | 16 (6%) | 255 |
0.177 (1.00) |
0.851 (1.00) |
0.389 (1.00) |
0.264 (1.00) |
0.107 (1.00) |
0.27 (1.00) |
0.477 (1.00) |
0.857 (1.00) |
0.337 (1.00) |
0.615 (1.00) |
0.239 (1.00) |
0.897 (1.00) |
1 (1.00) |
del 4q28 1 | 24 (9%) | 247 |
0.0284 (1.00) |
0.0985 (1.00) |
0.476 (1.00) |
0.373 (1.00) |
0.22 (1.00) |
0.651 (1.00) |
0.0837 (1.00) |
0.0595 (1.00) |
0.581 (1.00) |
0.0583 (1.00) |
0.95 (1.00) |
0.292 (1.00) |
0.299 (1.00) |
del 5q21 1 | 45 (17%) | 226 |
0.113 (1.00) |
0.567 (1.00) |
0.162 (1.00) |
1 (1.00) |
1 (1.00) |
0.148 (1.00) |
0.0697 (1.00) |
0.00264 (1.00) |
0.52 (1.00) |
0.0776 (1.00) |
0.207 (1.00) |
0.0264 (1.00) |
0.733 (1.00) |
del 7q31 33 | 13 (5%) | 258 |
0.437 (1.00) |
1 (1.00) |
0.332 (1.00) |
1 (1.00) |
0.551 (1.00) |
0.345 (1.00) |
0.629 (1.00) |
0.205 (1.00) |
0.516 (1.00) |
0.773 (1.00) |
0.968 (1.00) |
0.848 (1.00) |
1 (1.00) |
del 8p21 3 | 146 (54%) | 125 |
0.401 (1.00) |
0.00038 (0.293) |
0.0799 (1.00) |
1 (1.00) |
0.869 (1.00) |
0.0568 (1.00) |
0.138 (1.00) |
0.00259 (1.00) |
0.278 (1.00) |
0.359 (1.00) |
0.00176 (1.00) |
0.139 (1.00) |
0.728 (1.00) |
del 8p11 21 | 82 (30%) | 189 |
0.433 (1.00) |
0.199 (1.00) |
1 (1.00) |
0.64 (1.00) |
0.00597 (1.00) |
0.876 (1.00) |
0.753 (1.00) |
0.233 (1.00) |
0.359 (1.00) |
0.773 (1.00) |
0.0882 (1.00) |
0.17 (1.00) |
0.191 (1.00) |
del 9p23 | 24 (9%) | 247 |
0.695 (1.00) |
0.271 (1.00) |
0.0799 (1.00) |
1 (1.00) |
0.758 (1.00) |
0.0745 (1.00) |
0.0112 (1.00) |
0.022 (1.00) |
0.258 (1.00) |
0.0428 (1.00) |
0.691 (1.00) |
0.484 (1.00) |
1 (1.00) |
del 10q23 31 | 84 (31%) | 187 |
0.809 (1.00) |
0.00707 (1.00) |
0.0119 (1.00) |
1 (1.00) |
0.333 (1.00) |
0.012 (1.00) |
0.00882 (1.00) |
0.0519 (1.00) |
0.0871 (1.00) |
0.00313 (1.00) |
0.615 (1.00) |
0.00244 (1.00) |
0.236 (1.00) |
del 11p11 2 | 12 (4%) | 259 |
0.714 (1.00) |
0.509 (1.00) |
0.0994 (1.00) |
1 (1.00) |
0.117 (1.00) |
0.0576 (1.00) |
0.448 (1.00) |
0.308 (1.00) |
0.903 (1.00) |
0.302 (1.00) |
0.539 (1.00) |
0.649 (1.00) |
0.0403 (1.00) |
del 11q23 2 | 27 (10%) | 244 |
0.194 (1.00) |
0.00164 (1.00) |
0.728 (1.00) |
0.411 (1.00) |
0.398 (1.00) |
0.748 (1.00) |
0.0331 (1.00) |
0.0701 (1.00) |
0.218 (1.00) |
0.0225 (1.00) |
0.224 (1.00) |
0.0858 (1.00) |
1 (1.00) |
del 12q24 31 | 20 (7%) | 251 |
0.928 (1.00) |
0.213 (1.00) |
0.436 (1.00) |
0.32 (1.00) |
1 (1.00) |
0.522 (1.00) |
0.0341 (1.00) |
0.12 (1.00) |
0.295 (1.00) |
0.0365 (1.00) |
0.699 (1.00) |
0.367 (1.00) |
1 (1.00) |
del 13q14 13 | 116 (43%) | 155 |
0.0514 (1.00) |
0.357 (1.00) |
0.195 (1.00) |
0.0732 (1.00) |
0.0269 (1.00) |
0.173 (1.00) |
0.0256 (1.00) |
0.0431 (1.00) |
0.345 (1.00) |
0.0192 (1.00) |
0.43 (1.00) |
0.333 (1.00) |
0.00389 (1.00) |
del 13q22 1 | 89 (33%) | 182 |
0.0324 (1.00) |
0.0689 (1.00) |
0.117 (1.00) |
0.176 (1.00) |
0.273 (1.00) |
0.114 (1.00) |
0.00393 (1.00) |
0.0391 (1.00) |
0.0779 (1.00) |
0.000387 (0.298) |
0.149 (1.00) |
0.911 (1.00) |
0.00034 (0.263) |
del 17p13 1 | 69 (25%) | 202 |
0.507 (1.00) |
0.00644 (1.00) |
0.0145 (1.00) |
1 (1.00) |
0.884 (1.00) |
0.0105 (1.00) |
0.000411 (0.316) |
0.000656 (0.5) |
0.177 (1.00) |
0.000441 (0.338) |
0.593 (1.00) |
0.326 (1.00) |
0.822 (1.00) |
del 17q21 31 | 53 (20%) | 218 |
0.802 (1.00) |
0.811 (1.00) |
1 (1.00) |
0.587 (1.00) |
0.385 (1.00) |
0.703 (1.00) |
0.867 (1.00) |
0.584 (1.00) |
0.935 (1.00) |
0.888 (1.00) |
0.652 (1.00) |
0.64 (1.00) |
0.763 (1.00) |
del 18q22 1 | 68 (25%) | 203 |
0.743 (1.00) |
0.267 (1.00) |
0.458 (1.00) |
0.602 (1.00) |
0.283 (1.00) |
0.331 (1.00) |
0.0106 (1.00) |
0.0377 (1.00) |
0.222 (1.00) |
0.0121 (1.00) |
0.566 (1.00) |
0.918 (1.00) |
0.136 (1.00) |
del 19q13 2 | 24 (9%) | 247 |
0.094 (1.00) |
0.178 (1.00) |
0.15 (1.00) |
1 (1.00) |
0.121 (1.00) |
0.106 (1.00) |
0.00607 (1.00) |
0.00105 (0.793) |
0.581 (1.00) |
0.00517 (1.00) |
0.501 (1.00) |
0.328 (1.00) |
1 (1.00) |
del 21q22 2 | 26 (10%) | 245 |
0.25 (1.00) |
0.129 (1.00) |
0.011 (1.00) |
0.398 (1.00) |
0.73 (1.00) |
0.00315 (1.00) |
0.8 (1.00) |
0.947 (1.00) |
0.679 (1.00) |
0.965 (1.00) |
0.854 (1.00) |
0.33 (1.00) |
0.0765 (1.00) |
del 21q22 3 | 77 (28%) | 194 |
0.759 (1.00) |
0.0281 (1.00) |
0.00154 (1.00) |
0.625 (1.00) |
0.197 (1.00) |
0.000773 (0.588) |
0.169 (1.00) |
0.3 (1.00) |
0.346 (1.00) |
0.275 (1.00) |
0.306 (1.00) |
0.16 (1.00) |
0.0792 (1.00) |
P value = 2.69e-05 (Wilcoxon-test), Q value = 0.021
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
AMP PEAK 1(1Q21.3) MUTATED | 21 | 8.0 (0.9) |
AMP PEAK 1(1Q21.3) WILD-TYPE | 250 | 7.2 (0.8) |
P value = 0.000213 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 3.5 (0.6) |
AMP PEAK 1(1Q21.3) MUTATED | 21 | 3.9 (0.4) |
AMP PEAK 1(1Q21.3) WILD-TYPE | 250 | 3.5 (0.6) |
P value = 1.31e-05 (Wilcoxon-test), Q value = 0.01
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
AMP PEAK 1(1Q21.3) MUTATED | 21 | 8.1 (0.9) |
AMP PEAK 1(1Q21.3) WILD-TYPE | 250 | 7.3 (0.8) |
P value = 0.000301 (Wilcoxon-test), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
AMP PEAK 2(3Q21.3) MUTATED | 32 | 7.8 (1.0) |
AMP PEAK 2(3Q21.3) WILD-TYPE | 239 | 7.3 (0.8) |
P value = 8.78e-07 (Wilcoxon-test), Q value = 7e-04
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
AMP PEAK 8(8Q24.21) MUTATED | 64 | 7.7 (0.9) |
AMP PEAK 8(8Q24.21) WILD-TYPE | 207 | 7.1 (0.7) |
P value = 2.88e-06 (Wilcoxon-test), Q value = 0.0023
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 3.5 (0.6) |
AMP PEAK 8(8Q24.21) MUTATED | 64 | 3.8 (0.6) |
AMP PEAK 8(8Q24.21) WILD-TYPE | 207 | 3.4 (0.5) |
P value = 1.56e-05 (Wilcoxon-test), Q value = 0.012
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
AMP PEAK 8(8Q24.21) MUTATED | 64 | 7.8 (1.0) |
AMP PEAK 8(8Q24.21) WILD-TYPE | 207 | 7.2 (0.7) |
P value = 8.76e-05 (Wilcoxon-test), Q value = 0.069
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 223 | 0.2 (1.2) |
AMP PEAK 9(9Q34.11) MUTATED | 23 | 1.1 (3.1) |
AMP PEAK 9(9Q34.11) WILD-TYPE | 200 | 0.1 (0.6) |
P value = 4.55e-07 (Wilcoxon-test), Q value = 0.00037
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
AMP PEAK 9(9Q34.11) MUTATED | 25 | 8.0 (0.9) |
AMP PEAK 9(9Q34.11) WILD-TYPE | 246 | 7.2 (0.8) |
P value = 3.4e-06 (Wilcoxon-test), Q value = 0.0027
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 3.5 (0.6) |
AMP PEAK 9(9Q34.11) MUTATED | 25 | 4.0 (0.5) |
AMP PEAK 9(9Q34.11) WILD-TYPE | 246 | 3.4 (0.6) |
P value = 1.02e-06 (Wilcoxon-test), Q value = 0.00082
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
AMP PEAK 9(9Q34.11) MUTATED | 25 | 8.0 (0.8) |
AMP PEAK 9(9Q34.11) WILD-TYPE | 246 | 7.3 (0.8) |
P value = 0.000257 (Wilcoxon-test), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
AMP PEAK 13(14Q21.1) MUTATED | 14 | 8.1 (0.8) |
AMP PEAK 13(14Q21.1) WILD-TYPE | 257 | 7.3 (0.8) |
P value = 2.39e-05 (Fisher's exact test), Q value = 0.019
nPatients | 0 | 1 |
---|---|---|
ALL | 201 | 24 |
DEL PEAK 10(5Q11.2) MUTATED | 23 | 12 |
DEL PEAK 10(5Q11.2) WILD-TYPE | 178 | 12 |
P value = 7.88e-07 (Wilcoxon-test), Q value = 0.00063
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 223 | 0.2 (1.2) |
DEL PEAK 10(5Q11.2) MUTATED | 35 | 0.9 (2.6) |
DEL PEAK 10(5Q11.2) WILD-TYPE | 188 | 0.1 (0.6) |
P value = 9.74e-07 (Wilcoxon-test), Q value = 0.00078
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
DEL PEAK 10(5Q11.2) MUTATED | 38 | 7.9 (1.0) |
DEL PEAK 10(5Q11.2) WILD-TYPE | 233 | 7.2 (0.7) |
P value = 3.59e-05 (Wilcoxon-test), Q value = 0.028
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 3.5 (0.6) |
DEL PEAK 10(5Q11.2) MUTATED | 38 | 3.8 (0.6) |
DEL PEAK 10(5Q11.2) WILD-TYPE | 233 | 3.4 (0.5) |
P value = 7.36e-06 (Wilcoxon-test), Q value = 0.0058
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
DEL PEAK 10(5Q11.2) MUTATED | 38 | 7.9 (1.0) |
DEL PEAK 10(5Q11.2) WILD-TYPE | 233 | 7.2 (0.8) |
P value = 5.79e-07 (Wilcoxon-test), Q value = 0.00046
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
DEL PEAK 11(5Q13.2) MUTATED | 37 | 7.9 (0.9) |
DEL PEAK 11(5Q13.2) WILD-TYPE | 234 | 7.2 (0.7) |
P value = 6.31e-05 (Wilcoxon-test), Q value = 0.049
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 3.5 (0.6) |
DEL PEAK 11(5Q13.2) MUTATED | 37 | 3.8 (0.6) |
DEL PEAK 11(5Q13.2) WILD-TYPE | 234 | 3.4 (0.5) |
P value = 5.78e-05 (Wilcoxon-test), Q value = 0.045
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
DEL PEAK 11(5Q13.2) MUTATED | 37 | 7.8 (1.0) |
DEL PEAK 11(5Q13.2) WILD-TYPE | 234 | 7.2 (0.8) |
P value = 0.000207 (Wilcoxon-test), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
DEL PEAK 13(6Q14.3) MUTATED | 85 | 7.5 (0.8) |
DEL PEAK 13(6Q14.3) WILD-TYPE | 186 | 7.2 (0.8) |
P value = 0.000213 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 269 | 10.4 (11.0) |
DEL PEAK 13(6Q14.3) MUTATED | 85 | 13.3 (12.3) |
DEL PEAK 13(6Q14.3) WILD-TYPE | 184 | 9.0 (10.1) |
P value = 0.000203 (Wilcoxon-test), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 3.5 (0.6) |
DEL PEAK 21(12P13.1) MUTATED | 55 | 3.7 (0.6) |
DEL PEAK 21(12P13.1) WILD-TYPE | 216 | 3.4 (0.5) |
P value = 8.7e-08 (Wilcoxon-test), Q value = 7e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
DEL PEAK 25(15Q21.3) MUTATED | 30 | 8.1 (0.9) |
DEL PEAK 25(15Q21.3) WILD-TYPE | 241 | 7.2 (0.7) |
P value = 2.66e-06 (Wilcoxon-test), Q value = 0.0021
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 3.5 (0.6) |
DEL PEAK 25(15Q21.3) MUTATED | 30 | 4.0 (0.6) |
DEL PEAK 25(15Q21.3) WILD-TYPE | 241 | 3.4 (0.5) |
P value = 4.01e-07 (Wilcoxon-test), Q value = 0.00032
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
DEL PEAK 25(15Q21.3) MUTATED | 30 | 8.1 (1.0) |
DEL PEAK 25(15Q21.3) WILD-TYPE | 241 | 7.2 (0.8) |
P value = 0.000184 (Wilcoxon-test), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
DEL PEAK 26(16Q22.3) MUTATED | 93 | 7.5 (0.9) |
DEL PEAK 26(16Q22.3) WILD-TYPE | 178 | 7.2 (0.7) |
P value = 6.02e-05 (Wilcoxon-test), Q value = 0.047
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 3.5 (0.6) |
DEL PEAK 26(16Q22.3) MUTATED | 93 | 3.7 (0.6) |
DEL PEAK 26(16Q22.3) WILD-TYPE | 178 | 3.4 (0.5) |
P value = 0.000286 (Wilcoxon-test), Q value = 0.22
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
DEL PEAK 26(16Q22.3) MUTATED | 93 | 7.6 (0.9) |
DEL PEAK 26(16Q22.3) WILD-TYPE | 178 | 7.2 (0.7) |
P value = 0.000215 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 7.3 (0.8) |
DEL PEAK 27(16Q24.1) MUTATED | 105 | 7.5 (0.9) |
DEL PEAK 27(16Q24.1) WILD-TYPE | 166 | 7.1 (0.7) |
P value = 4.06e-05 (Wilcoxon-test), Q value = 0.032
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 271 | 3.5 (0.6) |
DEL PEAK 27(16Q24.1) MUTATED | 105 | 3.7 (0.6) |
DEL PEAK 27(16Q24.1) WILD-TYPE | 166 | 3.4 (0.5) |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = PRAD-TP.merged_data.txt
-
Number of patients = 271
-
Number of significantly focal cnvs = 62
-
Number of selected clinical features = 13
-
Exclude genes that fewer than K tumors have mutations, K = 3
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.