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'.
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amp_3q21.3 cnv correlated to 'GLEASON_SCORE'.
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amp_8q24.21 cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
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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'.
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del_5q11.2 cnv correlated to 'PATHOLOGY.N.STAGE', 'NUMBER.OF.LYMPH.NODES', 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
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del_5q13.2 cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
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del_6q14.3 cnv correlated to 'GLEASON_SCORE_COMBINED' and 'PSA_RESULT_PREOP'.
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del_12p13.1 cnv correlated to 'GLEASON_SCORE_PRIMARY'.
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del_15q21.3 cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
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del_16q22.3 cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
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del_16q24.1 cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE_PRIMARY'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 62 focal events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 31 significant findings detected.
|
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
Table S1. Gene #1: 'amp_1q21.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
| 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) |
Figure S1. Get High-res Image Gene #1: 'amp_1q21.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
P value = 0.000213 (Wilcoxon-test), Q value = 0.17
Table S2. Gene #1: 'amp_1q21.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
| 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) |
Figure S2. Get High-res Image Gene #1: 'amp_1q21.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
P value = 1.31e-05 (Wilcoxon-test), Q value = 0.01
Table S3. Gene #1: 'amp_1q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'
| 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) |
Figure S3. Get High-res Image Gene #1: 'amp_1q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'
P value = 0.000301 (Wilcoxon-test), Q value = 0.23
Table S4. Gene #2: 'amp_3q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'
| 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) |
Figure S4. Get High-res Image Gene #2: 'amp_3q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'
P value = 8.78e-07 (Wilcoxon-test), Q value = 7e-04
Table S5. Gene #8: 'amp_8q24.21' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
| 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) |
Figure S5. Get High-res Image Gene #8: 'amp_8q24.21' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
P value = 2.88e-06 (Wilcoxon-test), Q value = 0.0023
Table S6. Gene #8: 'amp_8q24.21' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
| 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) |
Figure S6. Get High-res Image Gene #8: 'amp_8q24.21' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
P value = 1.56e-05 (Wilcoxon-test), Q value = 0.012
Table S7. Gene #8: 'amp_8q24.21' versus Clinical Feature #10: 'GLEASON_SCORE'
| 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) |
Figure S7. Get High-res Image Gene #8: 'amp_8q24.21' versus Clinical Feature #10: 'GLEASON_SCORE'
P value = 8.76e-05 (Wilcoxon-test), Q value = 0.069
Table S8. Gene #9: 'amp_9q34.11' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'
| 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) |
Figure S8. Get High-res Image Gene #9: 'amp_9q34.11' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'
P value = 4.55e-07 (Wilcoxon-test), Q value = 0.00037
Table S9. Gene #9: 'amp_9q34.11' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
| 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) |
Figure S9. Get High-res Image Gene #9: 'amp_9q34.11' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
P value = 3.4e-06 (Wilcoxon-test), Q value = 0.0027
Table S10. Gene #9: 'amp_9q34.11' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
| 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) |
Figure S10. Get High-res Image Gene #9: 'amp_9q34.11' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
P value = 1.02e-06 (Wilcoxon-test), Q value = 0.00082
Table S11. Gene #9: 'amp_9q34.11' versus Clinical Feature #10: 'GLEASON_SCORE'
| 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) |
Figure S11. Get High-res Image Gene #9: 'amp_9q34.11' versus Clinical Feature #10: 'GLEASON_SCORE'
P value = 0.000257 (Wilcoxon-test), Q value = 0.2
Table S12. Gene #13: 'amp_14q21.1' versus Clinical Feature #10: 'GLEASON_SCORE'
| 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) |
Figure S12. Get High-res Image Gene #13: 'amp_14q21.1' versus Clinical Feature #10: 'GLEASON_SCORE'
P value = 2.39e-05 (Fisher's exact test), Q value = 0.019
Table S13. Gene #39: 'del_5q11.2' versus Clinical Feature #3: 'PATHOLOGY.N.STAGE'
| nPatients | 0 | 1 |
|---|---|---|
| ALL | 201 | 24 |
| DEL PEAK 10(5Q11.2) MUTATED | 23 | 12 |
| DEL PEAK 10(5Q11.2) WILD-TYPE | 178 | 12 |
Figure S13. Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #3: 'PATHOLOGY.N.STAGE'
P value = 7.88e-07 (Wilcoxon-test), Q value = 0.00063
Table S14. Gene #39: 'del_5q11.2' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'
| 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) |
Figure S14. Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'
P value = 9.74e-07 (Wilcoxon-test), Q value = 0.00078
Table S15. Gene #39: 'del_5q11.2' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
| 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) |
Figure S15. Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
P value = 3.59e-05 (Wilcoxon-test), Q value = 0.028
Table S16. Gene #39: 'del_5q11.2' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
| 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) |
Figure S16. Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
P value = 7.36e-06 (Wilcoxon-test), Q value = 0.0058
Table S17. Gene #39: 'del_5q11.2' versus Clinical Feature #10: 'GLEASON_SCORE'
| 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) |
Figure S17. Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #10: 'GLEASON_SCORE'
P value = 5.79e-07 (Wilcoxon-test), Q value = 0.00046
Table S18. Gene #40: 'del_5q13.2' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
| 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) |
Figure S18. Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
P value = 6.31e-05 (Wilcoxon-test), Q value = 0.049
Table S19. Gene #40: 'del_5q13.2' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
| 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) |
Figure S19. Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
P value = 5.78e-05 (Wilcoxon-test), Q value = 0.045
Table S20. Gene #40: 'del_5q13.2' versus Clinical Feature #10: 'GLEASON_SCORE'
| 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) |
Figure S20. Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #10: 'GLEASON_SCORE'
P value = 0.000207 (Wilcoxon-test), Q value = 0.16
Table S21. Gene #42: 'del_6q14.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
| 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) |
Figure S21. Get High-res Image Gene #42: 'del_6q14.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
P value = 0.000213 (Wilcoxon-test), Q value = 0.17
Table S22. Gene #42: 'del_6q14.3' versus Clinical Feature #11: 'PSA_RESULT_PREOP'
| 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) |
Figure S22. Get High-res Image Gene #42: 'del_6q14.3' versus Clinical Feature #11: 'PSA_RESULT_PREOP'
P value = 0.000203 (Wilcoxon-test), Q value = 0.16
Table S23. Gene #50: 'del_12p13.1' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
| 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) |
Figure S23. Get High-res Image Gene #50: 'del_12p13.1' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
P value = 8.7e-08 (Wilcoxon-test), Q value = 7e-05
Table S24. Gene #54: 'del_15q21.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
| 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) |
Figure S24. Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
P value = 2.66e-06 (Wilcoxon-test), Q value = 0.0021
Table S25. Gene #54: 'del_15q21.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
| 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) |
Figure S25. Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
P value = 4.01e-07 (Wilcoxon-test), Q value = 0.00032
Table S26. Gene #54: 'del_15q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'
| 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) |
Figure S26. Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'
P value = 0.000184 (Wilcoxon-test), Q value = 0.14
Table S27. Gene #55: 'del_16q22.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
| 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) |
Figure S27. Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
P value = 6.02e-05 (Wilcoxon-test), Q value = 0.047
Table S28. Gene #55: 'del_16q22.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
| 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) |
Figure S28. Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
P value = 0.000286 (Wilcoxon-test), Q value = 0.22
Table S29. Gene #55: 'del_16q22.3' versus Clinical Feature #10: 'GLEASON_SCORE'
| 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) |
Figure S29. Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #10: 'GLEASON_SCORE'
P value = 0.000215 (Wilcoxon-test), Q value = 0.17
Table S30. Gene #56: 'del_16q24.1' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
| 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) |
Figure S30. Get High-res Image Gene #56: 'del_16q24.1' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'
P value = 4.06e-05 (Wilcoxon-test), Q value = 0.032
Table S31. Gene #56: 'del_16q24.1' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
| 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) |
Figure S31. Get High-res Image Gene #56: 'del_16q24.1' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'
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Copy number data file = transformed.cor.cli.txt
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Clinical data file = PRAD-TP.merged_data.txt
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Number of patients = 271
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Number of significantly focal cnvs = 62
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Number of selected clinical features = 13
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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.