This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 75 arm-level events and 14 clinical features across 363 patients, 42 significant findings detected with Q value < 0.25.
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3p gain cnv correlated to 'GLEASON_SCORE'.
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3q gain cnv correlated to 'GLEASON_SCORE'.
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8p gain cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.
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8q gain cnv correlated to 'GLEASON_SCORE_PRIMARY'.
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9q gain cnv correlated to 'GLEASON_SCORE_PRIMARY' and 'GLEASON_SCORE'.
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4p loss cnv correlated to 'PATHOLOGY.N.STAGE', 'NUMBER.OF.LYMPH.NODES', 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
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4q loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.
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5p loss cnv correlated to 'GLEASON_SCORE_PRIMARY'.
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5q loss cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
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6p loss cnv correlated to 'GLEASON_SCORE_PRIMARY' and 'GLEASON_SCORE'.
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6q loss cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
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10p loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.
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10q loss cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_SECONDARY', and 'GLEASON_SCORE'.
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13q loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.
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15q loss cnv correlated to 'GLEASON_SCORE_PRIMARY'.
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16q loss cnv correlated to 'GLEASON_SCORE_PRIMARY'.
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17p loss cnv correlated to 'GLEASON_SCORE'.
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18p loss cnv correlated to 'GLEASON_SCORE'.
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18q loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.
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22q loss cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
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xq loss cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
Clinical Features |
Time to Death |
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 | logrank test | 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 | |
4p loss | 14 (4%) | 349 |
0.599 (1.00) |
0.333 (1.00) |
0.0347 (1.00) |
0.000151 (0.149) |
0.406 (1.00) |
0.00237 (1.00) |
2.31e-06 (0.00235) |
2.14e-06 (0.00218) |
0.000147 (0.145) |
0.00106 (1.00) |
2.2e-05 (0.0222) |
0.205 (1.00) |
0.536 (1.00) |
1 (1.00) |
5q loss | 12 (3%) | 351 |
0.698 (1.00) |
0.989 (1.00) |
0.0156 (1.00) |
0.0569 (1.00) |
1 (1.00) |
0.615 (1.00) |
0.0282 (1.00) |
6.02e-05 (0.06) |
5.46e-06 (0.00553) |
0.397 (1.00) |
4.18e-05 (0.042) |
0.403 (1.00) |
0.841 (1.00) |
1 (1.00) |
6q loss | 29 (8%) | 334 |
0.406 (1.00) |
0.439 (1.00) |
0.00985 (1.00) |
0.00335 (1.00) |
1 (1.00) |
0.0962 (1.00) |
0.000893 (0.857) |
2.98e-07 (0.000305) |
6.91e-06 (0.007) |
0.00273 (1.00) |
4.88e-08 (5.01e-05) |
0.634 (1.00) |
0.708 (1.00) |
0.125 (1.00) |
10q loss | 32 (9%) | 331 |
0.753 (1.00) |
0.249 (1.00) |
0.0168 (1.00) |
0.0232 (1.00) |
1 (1.00) |
0.0375 (1.00) |
0.0128 (1.00) |
1.45e-06 (0.00148) |
0.000688 (0.667) |
0.000121 (0.12) |
2.03e-06 (0.00207) |
0.264 (1.00) |
0.814 (1.00) |
0.583 (1.00) |
22q loss | 32 (9%) | 331 |
0.534 (1.00) |
0.503 (1.00) |
0.00068 (0.66) |
0.026 (1.00) |
0.0969 (1.00) |
0.12 (1.00) |
0.018 (1.00) |
1.09e-05 (0.011) |
2.11e-05 (0.0213) |
0.0312 (1.00) |
3.01e-06 (0.00306) |
0.672 (1.00) |
0.207 (1.00) |
0.493 (1.00) |
xq loss | 29 (8%) | 334 |
0.428 (1.00) |
0.0944 (1.00) |
0.118 (1.00) |
0.157 (1.00) |
0.278 (1.00) |
0.518 (1.00) |
0.0747 (1.00) |
3.12e-06 (0.00316) |
1.26e-06 (0.00129) |
0.0689 (1.00) |
1.45e-05 (0.0146) |
0.0904 (1.00) |
0.376 (1.00) |
0.386 (1.00) |
8p gain | 48 (13%) | 315 |
0.976 (1.00) |
0.0169 (1.00) |
0.107 (1.00) |
1 (1.00) |
0.231 (1.00) |
0.102 (1.00) |
0.743 (1.00) |
7.1e-05 (0.0707) |
0.000667 (0.647) |
0.0555 (1.00) |
8.1e-05 (0.0806) |
0.016 (1.00) |
0.874 (1.00) |
0.658 (1.00) |
9q gain | 32 (9%) | 331 |
0.397 (1.00) |
0.0431 (1.00) |
0.00088 (0.845) |
0.0232 (1.00) |
0.0969 (1.00) |
0.237 (1.00) |
0.0088 (1.00) |
0.00127 (1.00) |
4.87e-05 (0.0487) |
0.505 (1.00) |
3.76e-05 (0.0379) |
0.0138 (1.00) |
0.722 (1.00) |
0.461 (1.00) |
4q loss | 10 (3%) | 353 |
0.669 (1.00) |
0.343 (1.00) |
0.0637 (1.00) |
0.0404 (1.00) |
0.309 (1.00) |
0.0691 (1.00) |
0.0257 (1.00) |
0.000144 (0.143) |
0.00168 (1.00) |
0.00939 (1.00) |
0.000174 (0.171) |
0.336 (1.00) |
0.107 (1.00) |
1 (1.00) |
6p loss | 15 (4%) | 348 |
0.617 (1.00) |
0.629 (1.00) |
0.028 (1.00) |
0.0114 (1.00) |
1 (1.00) |
0.25 (1.00) |
0.00591 (1.00) |
0.00177 (1.00) |
0.000106 (0.105) |
0.635 (1.00) |
0.000118 (0.117) |
0.84 (1.00) |
0.149 (1.00) |
0.306 (1.00) |
10p loss | 30 (8%) | 333 |
0.746 (1.00) |
0.0887 (1.00) |
0.00077 (0.742) |
0.0418 (1.00) |
1 (1.00) |
0.0452 (1.00) |
0.0247 (1.00) |
4e-05 (0.0402) |
0.000394 (0.385) |
0.00718 (1.00) |
4.46e-05 (0.0446) |
0.459 (1.00) |
0.612 (1.00) |
1 (1.00) |
13q loss | 53 (15%) | 310 |
0.222 (1.00) |
0.116 (1.00) |
0.0404 (1.00) |
0.0404 (1.00) |
0.701 (1.00) |
0.171 (1.00) |
0.0172 (1.00) |
1.05e-06 (0.00107) |
0.000305 (0.3) |
0.000421 (0.411) |
6.29e-08 (6.45e-05) |
0.0464 (1.00) |
0.456 (1.00) |
0.439 (1.00) |
18q loss | 71 (20%) | 292 |
0.635 (1.00) |
0.397 (1.00) |
0.0608 (1.00) |
0.00813 (1.00) |
1 (1.00) |
0.00037 (0.362) |
0.003 (1.00) |
5e-06 (0.00507) |
0.00164 (1.00) |
0.000358 (0.351) |
4.57e-07 (0.000468) |
0.212 (1.00) |
0.534 (1.00) |
0.753 (1.00) |
3p gain | 26 (7%) | 337 |
0.445 (1.00) |
0.00721 (1.00) |
0.0118 (1.00) |
0.377 (1.00) |
1 (1.00) |
0.304 (1.00) |
0.313 (1.00) |
0.0278 (1.00) |
0.00628 (1.00) |
0.618 (1.00) |
3.82e-05 (0.0384) |
0.596 (1.00) |
0.304 (1.00) |
0.527 (1.00) |
3q gain | 35 (10%) | 328 |
0.142 (1.00) |
0.0254 (1.00) |
0.00062 (0.603) |
0.289 (1.00) |
1 (1.00) |
0.24 (1.00) |
0.171 (1.00) |
0.0181 (1.00) |
0.000485 (0.472) |
0.968 (1.00) |
8.7e-05 (0.0865) |
0.0665 (1.00) |
0.157 (1.00) |
0.635 (1.00) |
8q gain | 78 (21%) | 285 |
0.667 (1.00) |
0.279 (1.00) |
0.0346 (1.00) |
0.703 (1.00) |
0.314 (1.00) |
0.489 (1.00) |
0.529 (1.00) |
0.00116 (1.00) |
2.75e-05 (0.0277) |
0.813 (1.00) |
0.00267 (1.00) |
0.065 (1.00) |
0.647 (1.00) |
0.731 (1.00) |
5p loss | 7 (2%) | 356 |
0.754 (1.00) |
0.807 (1.00) |
0.00877 (1.00) |
0.264 (1.00) |
1 (1.00) |
0.564 (1.00) |
0.352 (1.00) |
0.000492 (0.478) |
5.36e-05 (0.0535) |
0.236 (1.00) |
0.000929 (0.889) |
0.497 (1.00) |
0.867 (1.00) |
1 (1.00) |
15q loss | 22 (6%) | 341 |
0.485 (1.00) |
0.276 (1.00) |
0.00135 (1.00) |
0.2 (1.00) |
0.563 (1.00) |
0.86 (1.00) |
0.198 (1.00) |
0.000939 (0.897) |
4.37e-05 (0.0438) |
0.516 (1.00) |
0.00216 (1.00) |
0.493 (1.00) |
0.39 (1.00) |
1 (1.00) |
16q loss | 69 (19%) | 294 |
0.768 (1.00) |
0.569 (1.00) |
0.102 (1.00) |
0.842 (1.00) |
1 (1.00) |
0.646 (1.00) |
0.826 (1.00) |
0.00332 (1.00) |
0.000216 (0.213) |
0.519 (1.00) |
0.00565 (1.00) |
0.0543 (1.00) |
0.303 (1.00) |
1 (1.00) |
17p loss | 53 (15%) | 310 |
0.248 (1.00) |
0.509 (1.00) |
0.00584 (1.00) |
0.015 (1.00) |
0.701 (1.00) |
0.166 (1.00) |
0.00745 (1.00) |
0.000311 (0.305) |
0.000355 (0.349) |
0.176 (1.00) |
0.000205 (0.202) |
0.211 (1.00) |
0.211 (1.00) |
0.7 (1.00) |
18p loss | 48 (13%) | 315 |
0.325 (1.00) |
0.497 (1.00) |
0.0978 (1.00) |
0.484 (1.00) |
0.685 (1.00) |
0.0512 (1.00) |
0.35 (1.00) |
0.00078 (0.751) |
0.00507 (1.00) |
0.0192 (1.00) |
4.6e-05 (0.046) |
0.411 (1.00) |
0.903 (1.00) |
0.702 (1.00) |
1p gain | 11 (3%) | 352 |
0.71 (1.00) |
0.177 (1.00) |
0.00147 (1.00) |
0.64 (1.00) |
1 (1.00) |
0.669 (1.00) |
0.627 (1.00) |
0.025 (1.00) |
0.0329 (1.00) |
0.259 (1.00) |
0.00253 (1.00) |
0.0102 (1.00) |
0.829 (1.00) |
1 (1.00) |
1q gain | 17 (5%) | 346 |
0.59 (1.00) |
0.498 (1.00) |
0.00862 (1.00) |
0.711 (1.00) |
0.47 (1.00) |
0.717 (1.00) |
0.559 (1.00) |
0.0219 (1.00) |
0.00393 (1.00) |
0.655 (1.00) |
0.00501 (1.00) |
0.0261 (1.00) |
0.604 (1.00) |
1 (1.00) |
2p gain | 7 (2%) | 356 |
0.703 (1.00) |
0.354 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.511 (1.00) |
0.412 (1.00) |
0.188 (1.00) |
0.139 (1.00) |
0.98 (1.00) |
0.368 (1.00) |
0.411 (1.00) |
0.025 (1.00) |
|
2q gain | 5 (1%) | 358 |
0.777 (1.00) |
0.267 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.419 (1.00) |
0.479 (1.00) |
0.173 (1.00) |
0.063 (1.00) |
0.821 (1.00) |
0.521 (1.00) |
0.59 (1.00) |
0.082 (1.00) |
|
4p gain | 6 (2%) | 357 |
0.707 (1.00) |
0.0924 (1.00) |
0.453 (1.00) |
0.599 (1.00) |
1 (1.00) |
0.745 (1.00) |
0.312 (1.00) |
0.832 (1.00) |
0.753 (1.00) |
0.553 (1.00) |
0.743 (1.00) |
0.274 (1.00) |
0.38 (1.00) |
1 (1.00) |
4q gain | 5 (1%) | 358 |
0.72 (1.00) |
0.0456 (1.00) |
0.442 (1.00) |
1 (1.00) |
1 (1.00) |
0.697 (1.00) |
0.357 (1.00) |
0.647 (1.00) |
0.489 (1.00) |
0.923 (1.00) |
0.232 (1.00) |
0.203 (1.00) |
0.185 (1.00) |
|
5p gain | 15 (4%) | 348 |
0.627 (1.00) |
0.0105 (1.00) |
0.00126 (1.00) |
0.0356 (1.00) |
0.428 (1.00) |
0.15 (1.00) |
0.00748 (1.00) |
0.0469 (1.00) |
0.00646 (1.00) |
0.972 (1.00) |
0.00031 (0.305) |
0.085 (1.00) |
0.0633 (1.00) |
|
5q gain | 8 (2%) | 355 |
0.722 (1.00) |
0.00214 (1.00) |
0.0394 (1.00) |
0.0917 (1.00) |
1 (1.00) |
0.0982 (1.00) |
0.0351 (1.00) |
0.289 (1.00) |
0.357 (1.00) |
0.536 (1.00) |
0.0231 (1.00) |
0.118 (1.00) |
0.00213 (1.00) |
|
6p gain | 5 (1%) | 358 |
0.0893 (1.00) |
0.601 (1.00) |
0.443 (1.00) |
0.151 (1.00) |
0.168 (1.00) |
0.311 (1.00) |
0.108 (1.00) |
0.0469 (1.00) |
0.0274 (1.00) |
0.604 (1.00) |
0.234 (1.00) |
0.505 (1.00) |
0.426 (1.00) |
|
6q gain | 4 (1%) | 359 |
0.686 (1.00) |
0.121 (1.00) |
0.661 (1.00) |
0.463 (1.00) |
0.136 (1.00) |
0.417 (1.00) |
0.508 (1.00) |
0.078 (1.00) |
0.0382 (1.00) |
0.665 (1.00) |
0.35 (1.00) |
0.906 (1.00) |
0.902 (1.00) |
|
7p gain | 68 (19%) | 295 |
0.183 (1.00) |
0.0225 (1.00) |
0.166 (1.00) |
1 (1.00) |
0.476 (1.00) |
0.0148 (1.00) |
0.9 (1.00) |
0.0171 (1.00) |
0.0247 (1.00) |
0.125 (1.00) |
0.00229 (1.00) |
0.184 (1.00) |
0.519 (1.00) |
1 (1.00) |
7q gain | 62 (17%) | 301 |
0.2 (1.00) |
0.036 (1.00) |
0.366 (1.00) |
0.136 (1.00) |
0.705 (1.00) |
0.0122 (1.00) |
0.114 (1.00) |
0.0611 (1.00) |
0.0737 (1.00) |
0.231 (1.00) |
0.0114 (1.00) |
0.201 (1.00) |
0.237 (1.00) |
1 (1.00) |
9p gain | 19 (5%) | 344 |
0.496 (1.00) |
0.0219 (1.00) |
0.0112 (1.00) |
0.154 (1.00) |
0.143 (1.00) |
0.186 (1.00) |
0.0923 (1.00) |
0.0721 (1.00) |
0.0207 (1.00) |
0.813 (1.00) |
0.00146 (1.00) |
0.00721 (1.00) |
0.908 (1.00) |
0.346 (1.00) |
10p gain | 9 (2%) | 354 |
0.649 (1.00) |
0.505 (1.00) |
0.393 (1.00) |
0.322 (1.00) |
0.282 (1.00) |
0.425 (1.00) |
0.357 (1.00) |
0.682 (1.00) |
0.732 (1.00) |
0.436 (1.00) |
0.0282 (1.00) |
0.878 (1.00) |
0.929 (1.00) |
1 (1.00) |
10q gain | 10 (3%) | 353 |
0.613 (1.00) |
0.665 (1.00) |
0.306 (1.00) |
0.622 (1.00) |
0.309 (1.00) |
0.467 (1.00) |
0.362 (1.00) |
0.661 (1.00) |
0.56 (1.00) |
0.889 (1.00) |
0.0556 (1.00) |
0.433 (1.00) |
0.0786 (1.00) |
1 (1.00) |
11p gain | 13 (4%) | 350 |
0.55 (1.00) |
0.39 (1.00) |
0.0658 (1.00) |
0.0765 (1.00) |
1 (1.00) |
0.102 (1.00) |
0.0934 (1.00) |
0.0136 (1.00) |
0.007 (1.00) |
0.229 (1.00) |
0.00152 (1.00) |
0.795 (1.00) |
0.469 (1.00) |
0.263 (1.00) |
11q gain | 15 (4%) | 348 |
0.528 (1.00) |
0.358 (1.00) |
0.0678 (1.00) |
0.124 (1.00) |
1 (1.00) |
0.102 (1.00) |
0.182 (1.00) |
0.00317 (1.00) |
0.00138 (1.00) |
0.202 (1.00) |
0.000381 (0.373) |
0.425 (1.00) |
0.963 (1.00) |
0.262 (1.00) |
12p gain | 8 (2%) | 355 |
0.675 (1.00) |
0.0384 (1.00) |
0.0393 (1.00) |
0.0403 (1.00) |
1 (1.00) |
0.0117 (1.00) |
0.0166 (1.00) |
0.00836 (1.00) |
0.00746 (1.00) |
0.267 (1.00) |
0.000719 (0.695) |
0.115 (1.00) |
0.222 (1.00) |
|
12q gain | 8 (2%) | 355 |
0.659 (1.00) |
0.104 (1.00) |
0.0388 (1.00) |
0.0403 (1.00) |
1 (1.00) |
0.00124 (1.00) |
0.0166 (1.00) |
0.00836 (1.00) |
0.000899 (0.861) |
0.607 (1.00) |
0.000719 (0.695) |
0.0976 (1.00) |
0.222 (1.00) |
|
13q gain | 5 (1%) | 358 |
0.63 (1.00) |
0.73 (1.00) |
1 (1.00) |
1 (1.00) |
0.168 (1.00) |
0.695 (1.00) |
0.412 (1.00) |
0.11 (1.00) |
0.908 (1.00) |
0.019 (1.00) |
0.802 (1.00) |
0.904 (1.00) |
0.317 (1.00) |
|
14q gain | 8 (2%) | 355 |
0.0682 (1.00) |
0.11 (1.00) |
1 (1.00) |
0.264 (1.00) |
0.255 (1.00) |
0.0825 (1.00) |
0.192 (1.00) |
0.0399 (1.00) |
0.0211 (1.00) |
0.607 (1.00) |
0.0061 (1.00) |
0.406 (1.00) |
0.588 (1.00) |
|
15q gain | 5 (1%) | 358 |
0.765 (1.00) |
0.443 (1.00) |
1 (1.00) |
0.541 (1.00) |
1 (1.00) |
0.695 (1.00) |
0.683 (1.00) |
0.541 (1.00) |
0.561 (1.00) |
0.604 (1.00) |
0.166 (1.00) |
0.698 (1.00) |
0.615 (1.00) |
|
16p gain | 20 (6%) | 343 |
0.506 (1.00) |
0.281 (1.00) |
0.0042 (1.00) |
0.0786 (1.00) |
0.527 (1.00) |
0.731 (1.00) |
0.0714 (1.00) |
0.0119 (1.00) |
0.000879 (0.845) |
0.54 (1.00) |
0.00177 (1.00) |
0.785 (1.00) |
0.181 (1.00) |
1 (1.00) |
16q gain | 7 (2%) | 356 |
0.81 (1.00) |
0.0254 (1.00) |
0.319 (1.00) |
0.541 (1.00) |
1 (1.00) |
0.772 (1.00) |
0.788 (1.00) |
0.188 (1.00) |
0.0765 (1.00) |
0.98 (1.00) |
0.104 (1.00) |
0.5 (1.00) |
0.717 (1.00) |
1 (1.00) |
17p gain | 5 (1%) | 358 |
0.791 (1.00) |
0.652 (1.00) |
0.138 (1.00) |
0.151 (1.00) |
1 (1.00) |
0.697 (1.00) |
0.0638 (1.00) |
0.369 (1.00) |
0.063 (1.00) |
0.821 (1.00) |
0.428 (1.00) |
0.997 (1.00) |
0.212 (1.00) |
|
17q gain | 6 (2%) | 357 |
0.759 (1.00) |
0.888 (1.00) |
0.119 (1.00) |
0.0403 (1.00) |
1 (1.00) |
0.745 (1.00) |
0.00875 (1.00) |
0.232 (1.00) |
0.0436 (1.00) |
0.93 (1.00) |
0.295 (1.00) |
0.529 (1.00) |
0.372 (1.00) |
|
18p gain | 12 (3%) | 351 |
0.655 (1.00) |
0.0626 (1.00) |
0.0321 (1.00) |
0.16 (1.00) |
1 (1.00) |
1 (1.00) |
0.156 (1.00) |
0.191 (1.00) |
0.494 (1.00) |
0.397 (1.00) |
0.298 (1.00) |
0.254 (1.00) |
0.908 (1.00) |
1 (1.00) |
18q gain | 5 (1%) | 358 |
0.775 (1.00) |
0.124 (1.00) |
0.141 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.357 (1.00) |
0.462 (1.00) |
0.908 (1.00) |
0.255 (1.00) |
0.55 (1.00) |
0.712 (1.00) |
0.746 (1.00) |
|
19p gain | 6 (2%) | 357 |
0.697 (1.00) |
0.443 (1.00) |
0.0133 (1.00) |
1 (1.00) |
1 (1.00) |
0.512 (1.00) |
0.939 (1.00) |
0.022 (1.00) |
0.0145 (1.00) |
0.246 (1.00) |
0.0317 (1.00) |
0.0089 (1.00) |
0.966 (1.00) |
|
19q gain | 6 (2%) | 357 |
0.649 (1.00) |
0.337 (1.00) |
0.013 (1.00) |
1 (1.00) |
1 (1.00) |
0.511 (1.00) |
0.939 (1.00) |
0.022 (1.00) |
0.0436 (1.00) |
0.0844 (1.00) |
0.0317 (1.00) |
0.0156 (1.00) |
0.834 (1.00) |
1 (1.00) |
20p gain | 13 (4%) | 350 |
0.582 (1.00) |
0.207 (1.00) |
0.139 (1.00) |
0.0991 (1.00) |
1 (1.00) |
0.545 (1.00) |
0.0585 (1.00) |
0.018 (1.00) |
0.0346 (1.00) |
0.111 (1.00) |
0.00377 (1.00) |
0.858 (1.00) |
0.928 (1.00) |
|
20q gain | 16 (4%) | 347 |
0.51 (1.00) |
0.0623 (1.00) |
0.0146 (1.00) |
0.261 (1.00) |
1 (1.00) |
0.302 (1.00) |
0.169 (1.00) |
0.0334 (1.00) |
0.0122 (1.00) |
0.417 (1.00) |
0.00122 (1.00) |
0.152 (1.00) |
0.843 (1.00) |
1 (1.00) |
21q gain | 13 (4%) | 350 |
0.496 (1.00) |
0.00894 (1.00) |
0.141 (1.00) |
0.409 (1.00) |
0.383 (1.00) |
0.184 (1.00) |
0.405 (1.00) |
0.151 (1.00) |
0.0346 (1.00) |
0.792 (1.00) |
0.0023 (1.00) |
0.277 (1.00) |
0.253 (1.00) |
1 (1.00) |
xq gain | 4 (1%) | 359 |
0.761 (1.00) |
0.264 (1.00) |
0.188 (1.00) |
1 (1.00) |
1 (1.00) |
0.0259 (1.00) |
0.412 (1.00) |
0.149 (1.00) |
0.0382 (1.00) |
0.8 (1.00) |
0.0527 (1.00) |
0.473 (1.00) |
0.776 (1.00) |
|
1p loss | 13 (4%) | 350 |
0.532 (1.00) |
0.542 (1.00) |
0.139 (1.00) |
0.701 (1.00) |
1 (1.00) |
0.65 (1.00) |
0.45 (1.00) |
0.00139 (1.00) |
0.00134 (1.00) |
0.111 (1.00) |
0.00182 (1.00) |
0.505 (1.00) |
0.053 (1.00) |
1 (1.00) |
2p loss | 9 (2%) | 354 |
0.575 (1.00) |
0.0528 (1.00) |
0.193 (1.00) |
0.368 (1.00) |
1 (1.00) |
0.809 (1.00) |
0.213 (1.00) |
0.293 (1.00) |
0.258 (1.00) |
0.559 (1.00) |
0.687 (1.00) |
0.352 (1.00) |
0.561 (1.00) |
|
2q loss | 10 (3%) | 353 |
0.575 (1.00) |
0.127 (1.00) |
0.112 (1.00) |
0.367 (1.00) |
1 (1.00) |
0.672 (1.00) |
0.188 (1.00) |
0.197 (1.00) |
0.186 (1.00) |
0.517 (1.00) |
0.526 (1.00) |
0.54 (1.00) |
0.561 (1.00) |
|
3p loss | 6 (2%) | 357 |
0.616 (1.00) |
0.602 (1.00) |
0.457 (1.00) |
0.207 (1.00) |
1 (1.00) |
0.224 (1.00) |
0.12 (1.00) |
0.00178 (1.00) |
0.0436 (1.00) |
0.0029 (1.00) |
0.000447 (0.435) |
0.279 (1.00) |
0.265 (1.00) |
|
3q loss | 4 (1%) | 359 |
0.644 (1.00) |
0.297 (1.00) |
0.66 (1.00) |
1 (1.00) |
1 (1.00) |
0.416 (1.00) |
0.412 (1.00) |
0.0236 (1.00) |
0.0916 (1.00) |
0.0497 (1.00) |
0.00486 (1.00) |
0.259 (1.00) |
0.65 (1.00) |
|
8p loss | 121 (33%) | 242 |
0.986 (1.00) |
0.856 (1.00) |
0.00134 (1.00) |
0.233 (1.00) |
1 (1.00) |
0.882 (1.00) |
0.163 (1.00) |
0.736 (1.00) |
0.0167 (1.00) |
0.0534 (1.00) |
0.887 (1.00) |
0.611 (1.00) |
0.103 (1.00) |
0.162 (1.00) |
8q loss | 19 (5%) | 344 |
0.0021 (1.00) |
0.944 (1.00) |
0.00503 (1.00) |
0.00726 (1.00) |
1 (1.00) |
0.0964 (1.00) |
0.000703 (0.681) |
0.0285 (1.00) |
0.015 (1.00) |
0.376 (1.00) |
0.029 (1.00) |
0.661 (1.00) |
0.405 (1.00) |
1 (1.00) |
9p loss | 15 (4%) | 348 |
0.592 (1.00) |
0.504 (1.00) |
0.0694 (1.00) |
0.0478 (1.00) |
1 (1.00) |
0.765 (1.00) |
0.0159 (1.00) |
0.0128 (1.00) |
0.0294 (1.00) |
0.101 (1.00) |
0.00199 (1.00) |
0.922 (1.00) |
0.83 (1.00) |
1 (1.00) |
9q loss | 6 (2%) | 357 |
0.741 (1.00) |
0.466 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.761 (1.00) |
0.0322 (1.00) |
0.395 (1.00) |
0.0159 (1.00) |
0.00525 (1.00) |
0.671 (1.00) |
0.452 (1.00) |
1 (1.00) |
11p loss | 3 (1%) | 360 |
0.0871 (1.00) |
0.297 (1.00) |
1 (1.00) |
1 (1.00) |
0.286 (1.00) |
0.479 (1.00) |
0.255 (1.00) |
0.0521 (1.00) |
0.646 (1.00) |
0.321 (1.00) |
0.472 (1.00) |
0.489 (1.00) |
||
12p loss | 31 (9%) | 332 |
0.376 (1.00) |
0.843 (1.00) |
0.17 (1.00) |
0.0623 (1.00) |
0.613 (1.00) |
0.29 (1.00) |
0.0732 (1.00) |
0.00176 (1.00) |
0.00116 (1.00) |
0.132 (1.00) |
0.00304 (1.00) |
0.449 (1.00) |
0.0467 (1.00) |
1 (1.00) |
12q loss | 13 (4%) | 350 |
0.607 (1.00) |
0.789 (1.00) |
0.201 (1.00) |
0.0991 (1.00) |
1 (1.00) |
0.571 (1.00) |
0.101 (1.00) |
0.0312 (1.00) |
0.007 (1.00) |
0.463 (1.00) |
0.0219 (1.00) |
0.757 (1.00) |
0.69 (1.00) |
1 (1.00) |
14q loss | 18 (5%) | 345 |
0.373 (1.00) |
0.774 (1.00) |
0.0157 (1.00) |
0.304 (1.00) |
0.49 (1.00) |
0.283 (1.00) |
0.336 (1.00) |
0.00359 (1.00) |
0.00408 (1.00) |
0.168 (1.00) |
0.00349 (1.00) |
0.032 (1.00) |
0.283 (1.00) |
1 (1.00) |
16p loss | 21 (6%) | 342 |
0.464 (1.00) |
0.948 (1.00) |
1 (1.00) |
0.33 (1.00) |
1 (1.00) |
0.695 (1.00) |
0.224 (1.00) |
0.397 (1.00) |
0.116 (1.00) |
0.794 (1.00) |
0.24 (1.00) |
0.703 (1.00) |
0.731 (1.00) |
1 (1.00) |
17q loss | 12 (3%) | 351 |
0.596 (1.00) |
0.741 (1.00) |
0.222 (1.00) |
1 (1.00) |
1 (1.00) |
0.0937 (1.00) |
0.506 (1.00) |
0.0368 (1.00) |
0.0231 (1.00) |
0.446 (1.00) |
0.15 (1.00) |
0.978 (1.00) |
0.344 (1.00) |
1 (1.00) |
19p loss | 13 (4%) | 350 |
0.569 (1.00) |
0.0552 (1.00) |
0.375 (1.00) |
1 (1.00) |
1 (1.00) |
0.65 (1.00) |
0.912 (1.00) |
0.0235 (1.00) |
0.0162 (1.00) |
0.415 (1.00) |
0.072 (1.00) |
0.261 (1.00) |
0.186 (1.00) |
1 (1.00) |
19q loss | 13 (4%) | 350 |
0.569 (1.00) |
0.0552 (1.00) |
0.376 (1.00) |
1 (1.00) |
1 (1.00) |
0.649 (1.00) |
0.912 (1.00) |
0.0235 (1.00) |
0.0162 (1.00) |
0.415 (1.00) |
0.072 (1.00) |
0.261 (1.00) |
0.186 (1.00) |
1 (1.00) |
20p loss | 13 (4%) | 350 |
0.0861 (1.00) |
0.518 (1.00) |
0.0387 (1.00) |
0.198 (1.00) |
1 (1.00) |
1 (1.00) |
0.151 (1.00) |
0.992 (1.00) |
0.109 (1.00) |
0.0657 (1.00) |
0.807 (1.00) |
0.132 (1.00) |
0.642 (1.00) |
0.346 (1.00) |
20q loss | 7 (2%) | 356 |
0.752 (1.00) |
0.0504 (1.00) |
0.0431 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.803 (1.00) |
0.188 (1.00) |
0.0139 (1.00) |
0.473 (1.00) |
0.269 (1.00) |
0.152 (1.00) |
0.726 (1.00) |
1 (1.00) |
21q loss | 14 (4%) | 349 |
0.616 (1.00) |
0.718 (1.00) |
0.0339 (1.00) |
0.0256 (1.00) |
0.406 (1.00) |
0.651 (1.00) |
0.00896 (1.00) |
0.000704 (0.681) |
0.00153 (1.00) |
0.0762 (1.00) |
0.00079 (0.76) |
0.0893 (1.00) |
0.394 (1.00) |
1 (1.00) |
P value = 3.82e-05 (Wilcoxon-test), Q value = 0.038
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
3P GAIN MUTATED | 26 | 8.3 (1.0) |
3P GAIN WILD-TYPE | 337 | 7.5 (0.9) |
P value = 8.7e-05 (Wilcoxon-test), Q value = 0.086
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
3Q GAIN MUTATED | 35 | 8.1 (1.0) |
3Q GAIN WILD-TYPE | 328 | 7.4 (0.9) |
P value = 7.1e-05 (Wilcoxon-test), Q value = 0.071
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.4 (0.9) |
8P GAIN MUTATED | 48 | 7.9 (0.9) |
8P GAIN WILD-TYPE | 315 | 7.4 (0.9) |
P value = 8.1e-05 (Wilcoxon-test), Q value = 0.081
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
8P GAIN MUTATED | 48 | 8.0 (1.0) |
8P GAIN WILD-TYPE | 315 | 7.4 (0.9) |
P value = 2.75e-05 (Wilcoxon-test), Q value = 0.028
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.6 (0.6) |
8Q GAIN MUTATED | 78 | 3.9 (0.6) |
8Q GAIN WILD-TYPE | 285 | 3.5 (0.6) |
P value = 4.87e-05 (Wilcoxon-test), Q value = 0.049
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.6 (0.6) |
9Q GAIN MUTATED | 32 | 4.0 (0.6) |
9Q GAIN WILD-TYPE | 331 | 3.6 (0.6) |
P value = 3.76e-05 (Wilcoxon-test), Q value = 0.038
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
9Q GAIN MUTATED | 32 | 8.2 (0.9) |
9Q GAIN WILD-TYPE | 331 | 7.5 (0.9) |
P value = 0.000151 (Fisher's exact test), Q value = 0.15
nPatients | 0 | 1 |
---|---|---|
ALL | 263 | 44 |
4P LOSS MUTATED | 6 | 8 |
4P LOSS WILD-TYPE | 257 | 36 |
P value = 2.31e-06 (Wilcoxon-test), Q value = 0.0023
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 303 | 0.3 (1.3) |
4P LOSS MUTATED | 14 | 1.3 (1.6) |
4P LOSS WILD-TYPE | 289 | 0.3 (1.3) |
P value = 2.14e-06 (Wilcoxon-test), Q value = 0.0022
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.4 (0.9) |
4P LOSS MUTATED | 14 | 8.6 (0.7) |
4P LOSS WILD-TYPE | 349 | 7.4 (0.9) |
P value = 0.000147 (Wilcoxon-test), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.6 (0.6) |
4P LOSS MUTATED | 14 | 4.2 (0.4) |
4P LOSS WILD-TYPE | 349 | 3.6 (0.6) |
P value = 2.2e-05 (Wilcoxon-test), Q value = 0.022
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
4P LOSS MUTATED | 14 | 8.6 (0.8) |
4P LOSS WILD-TYPE | 349 | 7.5 (0.9) |
P value = 0.000144 (Wilcoxon-test), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.4 (0.9) |
4Q LOSS MUTATED | 10 | 8.6 (0.8) |
4Q LOSS WILD-TYPE | 353 | 7.4 (0.9) |
P value = 0.000174 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
4Q LOSS MUTATED | 10 | 8.7 (0.8) |
4Q LOSS WILD-TYPE | 353 | 7.5 (0.9) |
P value = 5.36e-05 (Wilcoxon-test), Q value = 0.053
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.6 (0.6) |
5P LOSS MUTATED | 7 | 4.7 (0.5) |
5P LOSS WILD-TYPE | 356 | 3.6 (0.6) |
P value = 6.02e-05 (Wilcoxon-test), Q value = 0.06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.4 (0.9) |
5Q LOSS MUTATED | 12 | 8.5 (0.8) |
5Q LOSS WILD-TYPE | 351 | 7.4 (0.9) |
P value = 5.46e-06 (Wilcoxon-test), Q value = 0.0055
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.6 (0.6) |
5Q LOSS MUTATED | 12 | 4.5 (0.5) |
5Q LOSS WILD-TYPE | 351 | 3.6 (0.6) |
P value = 4.18e-05 (Wilcoxon-test), Q value = 0.042
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
5Q LOSS MUTATED | 12 | 8.7 (0.8) |
5Q LOSS WILD-TYPE | 351 | 7.5 (0.9) |
P value = 0.000106 (Wilcoxon-test), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.6 (0.6) |
6P LOSS MUTATED | 15 | 4.2 (0.4) |
6P LOSS WILD-TYPE | 348 | 3.6 (0.6) |
P value = 0.000118 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
6P LOSS MUTATED | 15 | 8.5 (0.8) |
6P LOSS WILD-TYPE | 348 | 7.5 (0.9) |
P value = 2.98e-07 (Wilcoxon-test), Q value = 3e-04
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.4 (0.9) |
6Q LOSS MUTATED | 29 | 8.3 (0.9) |
6Q LOSS WILD-TYPE | 334 | 7.4 (0.9) |
P value = 6.91e-06 (Wilcoxon-test), Q value = 0.007
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.6 (0.6) |
6Q LOSS MUTATED | 29 | 4.1 (0.6) |
6Q LOSS WILD-TYPE | 334 | 3.6 (0.6) |
P value = 4.88e-08 (Wilcoxon-test), Q value = 5e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
6Q LOSS MUTATED | 29 | 8.5 (0.9) |
6Q LOSS WILD-TYPE | 334 | 7.4 (0.9) |
P value = 4e-05 (Wilcoxon-test), Q value = 0.04
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.4 (0.9) |
10P LOSS MUTATED | 30 | 8.2 (1.0) |
10P LOSS WILD-TYPE | 333 | 7.4 (0.9) |
P value = 4.46e-05 (Wilcoxon-test), Q value = 0.045
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
10P LOSS MUTATED | 30 | 8.2 (1.0) |
10P LOSS WILD-TYPE | 333 | 7.4 (0.9) |
P value = 1.45e-06 (Wilcoxon-test), Q value = 0.0015
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.4 (0.9) |
10Q LOSS MUTATED | 32 | 8.2 (1.0) |
10Q LOSS WILD-TYPE | 331 | 7.4 (0.9) |
P value = 0.000121 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.9 (0.6) |
10Q LOSS MUTATED | 32 | 4.3 (0.6) |
10Q LOSS WILD-TYPE | 331 | 3.8 (0.6) |
P value = 2.03e-06 (Wilcoxon-test), Q value = 0.0021
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
10Q LOSS MUTATED | 32 | 8.3 (1.0) |
10Q LOSS WILD-TYPE | 331 | 7.4 (0.9) |
P value = 1.05e-06 (Wilcoxon-test), Q value = 0.0011
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.4 (0.9) |
13Q LOSS MUTATED | 53 | 8.1 (1.0) |
13Q LOSS WILD-TYPE | 310 | 7.3 (0.9) |
P value = 6.29e-08 (Wilcoxon-test), Q value = 6.4e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
13Q LOSS MUTATED | 53 | 8.2 (1.0) |
13Q LOSS WILD-TYPE | 310 | 7.4 (0.9) |
P value = 4.37e-05 (Wilcoxon-test), Q value = 0.044
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.6 (0.6) |
15Q LOSS MUTATED | 22 | 4.1 (0.6) |
15Q LOSS WILD-TYPE | 341 | 3.6 (0.6) |
P value = 0.000216 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.6 (0.6) |
16Q LOSS MUTATED | 69 | 3.9 (0.6) |
16Q LOSS WILD-TYPE | 294 | 3.5 (0.6) |
P value = 0.000205 (Wilcoxon-test), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
17P LOSS MUTATED | 53 | 7.9 (0.9) |
17P LOSS WILD-TYPE | 310 | 7.4 (0.9) |
P value = 4.6e-05 (Wilcoxon-test), Q value = 0.046
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
18P LOSS MUTATED | 48 | 8.1 (1.0) |
18P LOSS WILD-TYPE | 315 | 7.4 (0.9) |
P value = 5e-06 (Wilcoxon-test), Q value = 0.0051
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.4 (0.9) |
18Q LOSS MUTATED | 71 | 7.9 (1.0) |
18Q LOSS WILD-TYPE | 292 | 7.3 (0.9) |
P value = 4.57e-07 (Wilcoxon-test), Q value = 0.00047
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
18Q LOSS MUTATED | 71 | 8.1 (1.0) |
18Q LOSS WILD-TYPE | 292 | 7.4 (0.9) |
P value = 1.09e-05 (Wilcoxon-test), Q value = 0.011
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.4 (0.9) |
22Q LOSS MUTATED | 32 | 8.2 (1.0) |
22Q LOSS WILD-TYPE | 331 | 7.4 (0.9) |
P value = 2.11e-05 (Wilcoxon-test), Q value = 0.021
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.6 (0.6) |
22Q LOSS MUTATED | 32 | 4.1 (0.6) |
22Q LOSS WILD-TYPE | 331 | 3.6 (0.6) |
P value = 3.01e-06 (Wilcoxon-test), Q value = 0.0031
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
22Q LOSS MUTATED | 32 | 8.3 (0.9) |
22Q LOSS WILD-TYPE | 331 | 7.4 (0.9) |
P value = 3.12e-06 (Wilcoxon-test), Q value = 0.0032
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.4 (0.9) |
XQ LOSS MUTATED | 29 | 8.2 (0.9) |
XQ LOSS WILD-TYPE | 334 | 7.4 (0.9) |
P value = 1.26e-06 (Wilcoxon-test), Q value = 0.0013
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 3.6 (0.6) |
XQ LOSS MUTATED | 29 | 4.1 (0.5) |
XQ LOSS WILD-TYPE | 334 | 3.6 (0.6) |
P value = 1.45e-05 (Wilcoxon-test), Q value = 0.015
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 363 | 7.5 (1.0) |
XQ LOSS MUTATED | 29 | 8.2 (0.9) |
XQ LOSS WILD-TYPE | 334 | 7.4 (0.9) |
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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 = 363
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Number of significantly arm-level cnvs = 75
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Number of selected clinical features = 14
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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.