This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 78 arm-level events and 12 clinical features across 439 patients, 20 significant findings detected with Q value < 0.25.
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7p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.N.STAGE'.
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13q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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20p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'HISTOLOGICAL.TYPE'.
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20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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4p loss cnv correlated to 'PATHOLOGY.M.STAGE'.
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5q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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14q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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17p loss cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.N.STAGE', 'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.
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18p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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18q loss cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.N.STAGE', 'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.
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19p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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22q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
RACE | ||
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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | |
17p loss | 230 (52%) | 209 |
0.099 (1.00) |
0.0534 (1.00) |
7e-05 (0.0647) |
0.645 (1.00) |
0.0001 (0.092) |
0.00419 (1.00) |
0.0555 (1.00) |
9.99e-06 (0.00926) |
0.25 (1.00) |
0.0372 (1.00) |
8.56e-06 (0.00794) |
0.833 (1.00) |
18q loss | 264 (60%) | 175 |
0.871 (1.00) |
0.0108 (1.00) |
7e-05 (0.0647) |
0.851 (1.00) |
0.00013 (0.119) |
0.0015 (1.00) |
0.329 (1.00) |
7.48e-09 (6.97e-06) |
0.279 (1.00) |
0.107 (1.00) |
0.000114 (0.105) |
0.908 (1.00) |
7p gain | 242 (55%) | 197 |
0.985 (1.00) |
0.0835 (1.00) |
6e-05 (0.0556) |
0.333 (1.00) |
9e-05 (0.0829) |
0.0608 (1.00) |
1 (1.00) |
0.0358 (1.00) |
0.256 (1.00) |
0.286 (1.00) |
0.000331 (0.302) |
0.413 (1.00) |
20p gain | 236 (54%) | 203 |
0.267 (1.00) |
0.396 (1.00) |
0.0001 (0.092) |
0.756 (1.00) |
0.196 (1.00) |
0.00198 (1.00) |
0.125 (1.00) |
0.000215 (0.197) |
0.253 (1.00) |
0.0626 (1.00) |
0.0871 (1.00) |
0.797 (1.00) |
13q gain | 250 (57%) | 189 |
0.91 (1.00) |
0.603 (1.00) |
0.00049 (0.443) |
0.989 (1.00) |
0.00331 (1.00) |
0.0017 (1.00) |
0.385 (1.00) |
8.48e-07 (0.000789) |
0.263 (1.00) |
0.03 (1.00) |
0.0124 (1.00) |
0.178 (1.00) |
20q gain | 311 (71%) | 128 |
0.699 (1.00) |
0.212 (1.00) |
0.00205 (1.00) |
0.305 (1.00) |
0.0162 (1.00) |
0.0136 (1.00) |
0.248 (1.00) |
9.99e-07 (0.000929) |
0.559 (1.00) |
0.091 (1.00) |
0.0172 (1.00) |
0.467 (1.00) |
4p loss | 129 (29%) | 310 |
0.028 (1.00) |
0.786 (1.00) |
0.00192 (1.00) |
0.314 (1.00) |
0.00304 (1.00) |
0.00026 (0.238) |
1 (1.00) |
0.0131 (1.00) |
0.025 (1.00) |
0.0267 (1.00) |
0.000573 (0.518) |
0.881 (1.00) |
5q loss | 74 (17%) | 365 |
0.0224 (1.00) |
0.163 (1.00) |
0.0189 (1.00) |
0.555 (1.00) |
0.0003 (0.274) |
0.0217 (1.00) |
0.251 (1.00) |
0.351 (1.00) |
0.075 (1.00) |
0.646 (1.00) |
6.4e-05 (0.0592) |
0.33 (1.00) |
14q loss | 133 (30%) | 306 |
0.596 (1.00) |
0.343 (1.00) |
0.207 (1.00) |
0.331 (1.00) |
0.144 (1.00) |
0.019 (1.00) |
1 (1.00) |
6.05e-06 (0.00562) |
0.557 (1.00) |
0.638 (1.00) |
0.173 (1.00) |
0.927 (1.00) |
18p loss | 247 (56%) | 192 |
0.937 (1.00) |
0.0163 (1.00) |
0.00044 (0.399) |
0.937 (1.00) |
0.00451 (1.00) |
0.00037 (0.336) |
0.441 (1.00) |
2.29e-09 (2.14e-06) |
0.26 (1.00) |
0.027 (1.00) |
0.00127 (1.00) |
0.951 (1.00) |
19p loss | 39 (9%) | 400 |
0.0479 (1.00) |
0.222 (1.00) |
0.018 (1.00) |
1 (1.00) |
0.00294 (1.00) |
0.00386 (1.00) |
0.868 (1.00) |
0.327 (1.00) |
0.244 (1.00) |
0.286 (1.00) |
7.31e-05 (0.0674) |
0.74 (1.00) |
22q loss | 139 (32%) | 300 |
0.0671 (1.00) |
0.581 (1.00) |
0.0017 (1.00) |
0.443 (1.00) |
0.00032 (0.292) |
0.00726 (1.00) |
0.919 (1.00) |
0.00261 (1.00) |
1 (1.00) |
0.414 (1.00) |
0.000191 (0.175) |
0.522 (1.00) |
1p gain | 32 (7%) | 407 |
0.705 (1.00) |
0.295 (1.00) |
0.787 (1.00) |
0.948 (1.00) |
0.485 (1.00) |
0.22 (1.00) |
0.717 (1.00) |
0.6 (1.00) |
0.204 (1.00) |
0.18 (1.00) |
0.127 (1.00) |
0.48 (1.00) |
1q gain | 78 (18%) | 361 |
0.514 (1.00) |
0.51 (1.00) |
0.184 (1.00) |
0.461 (1.00) |
0.0938 (1.00) |
0.0171 (1.00) |
0.169 (1.00) |
0.272 (1.00) |
0.445 (1.00) |
0.232 (1.00) |
0.0195 (1.00) |
1 (1.00) |
2p gain | 78 (18%) | 361 |
0.285 (1.00) |
0.883 (1.00) |
0.46 (1.00) |
0.595 (1.00) |
0.239 (1.00) |
0.22 (1.00) |
0.708 (1.00) |
0.0446 (1.00) |
0.445 (1.00) |
0.074 (1.00) |
0.108 (1.00) |
0.841 (1.00) |
2q gain | 74 (17%) | 365 |
0.156 (1.00) |
0.401 (1.00) |
0.238 (1.00) |
0.508 (1.00) |
0.0797 (1.00) |
0.13 (1.00) |
0.899 (1.00) |
0.0639 (1.00) |
0.426 (1.00) |
0.14 (1.00) |
0.0354 (1.00) |
0.598 (1.00) |
3p gain | 45 (10%) | 394 |
0.159 (1.00) |
0.0688 (1.00) |
0.00235 (1.00) |
0.826 (1.00) |
0.191 (1.00) |
0.00074 (0.667) |
0.637 (1.00) |
0.818 (1.00) |
1 (1.00) |
0.946 (1.00) |
0.126 (1.00) |
0.181 (1.00) |
3q gain | 64 (15%) | 375 |
0.168 (1.00) |
0.209 (1.00) |
0.0166 (1.00) |
0.622 (1.00) |
0.0701 (1.00) |
0.00308 (1.00) |
0.499 (1.00) |
0.425 (1.00) |
1 (1.00) |
0.875 (1.00) |
0.123 (1.00) |
0.267 (1.00) |
4p gain | 12 (3%) | 427 |
0.668 (1.00) |
0.254 (1.00) |
0.2 (1.00) |
0.691 (1.00) |
0.027 (1.00) |
0.0918 (1.00) |
0.391 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0153 (1.00) |
0.00144 (1.00) |
4q gain | 17 (4%) | 422 |
0.282 (1.00) |
0.805 (1.00) |
0.422 (1.00) |
0.952 (1.00) |
0.00644 (1.00) |
0.146 (1.00) |
0.458 (1.00) |
0.49 (1.00) |
1 (1.00) |
0.337 (1.00) |
0.00618 (1.00) |
0.0286 (1.00) |
5p gain | 68 (15%) | 371 |
0.559 (1.00) |
0.0598 (1.00) |
0.276 (1.00) |
0.986 (1.00) |
0.0248 (1.00) |
0.377 (1.00) |
0.355 (1.00) |
0.847 (1.00) |
1 (1.00) |
0.294 (1.00) |
0.0162 (1.00) |
0.151 (1.00) |
5q gain | 42 (10%) | 397 |
0.34 (1.00) |
0.906 (1.00) |
0.429 (1.00) |
0.836 (1.00) |
0.307 (1.00) |
0.347 (1.00) |
0.518 (1.00) |
0.634 (1.00) |
1 (1.00) |
0.341 (1.00) |
0.972 (1.00) |
0.173 (1.00) |
6p gain | 82 (19%) | 357 |
0.906 (1.00) |
0.749 (1.00) |
0.131 (1.00) |
0.904 (1.00) |
0.0395 (1.00) |
0.229 (1.00) |
0.271 (1.00) |
0.368 (1.00) |
0.00632 (1.00) |
0.661 (1.00) |
0.0454 (1.00) |
0.294 (1.00) |
6q gain | 74 (17%) | 365 |
0.563 (1.00) |
0.513 (1.00) |
0.0549 (1.00) |
0.911 (1.00) |
0.0497 (1.00) |
0.134 (1.00) |
0.702 (1.00) |
0.35 (1.00) |
0.00463 (1.00) |
0.841 (1.00) |
0.0715 (1.00) |
0.819 (1.00) |
7q gain | 221 (50%) | 218 |
0.824 (1.00) |
0.0564 (1.00) |
0.0191 (1.00) |
0.181 (1.00) |
0.0103 (1.00) |
0.0386 (1.00) |
0.924 (1.00) |
0.0691 (1.00) |
1 (1.00) |
0.462 (1.00) |
0.0108 (1.00) |
0.25 (1.00) |
8p gain | 129 (29%) | 310 |
0.329 (1.00) |
0.223 (1.00) |
0.637 (1.00) |
0.776 (1.00) |
0.551 (1.00) |
0.937 (1.00) |
0.917 (1.00) |
0.358 (1.00) |
0.208 (1.00) |
0.47 (1.00) |
0.359 (1.00) |
0.979 (1.00) |
8q gain | 222 (51%) | 217 |
0.891 (1.00) |
0.0202 (1.00) |
0.583 (1.00) |
0.236 (1.00) |
0.6 (1.00) |
0.32 (1.00) |
0.504 (1.00) |
0.0353 (1.00) |
0.248 (1.00) |
0.557 (1.00) |
0.494 (1.00) |
0.886 (1.00) |
9p gain | 78 (18%) | 361 |
0.0118 (1.00) |
0.287 (1.00) |
0.0175 (1.00) |
0.358 (1.00) |
0.141 (1.00) |
0.0374 (1.00) |
0.803 (1.00) |
0.00992 (1.00) |
1 (1.00) |
0.904 (1.00) |
0.143 (1.00) |
0.0308 (1.00) |
9q gain | 69 (16%) | 370 |
0.0121 (1.00) |
0.398 (1.00) |
0.139 (1.00) |
0.309 (1.00) |
0.451 (1.00) |
0.172 (1.00) |
0.896 (1.00) |
0.0195 (1.00) |
1 (1.00) |
0.943 (1.00) |
0.39 (1.00) |
0.0831 (1.00) |
10p gain | 34 (8%) | 405 |
0.0206 (1.00) |
0.266 (1.00) |
0.365 (1.00) |
0.236 (1.00) |
0.037 (1.00) |
0.302 (1.00) |
0.725 (1.00) |
1 (1.00) |
1 (1.00) |
0.315 (1.00) |
0.0341 (1.00) |
0.165 (1.00) |
10q gain | 20 (5%) | 419 |
0.607 (1.00) |
0.0119 (1.00) |
0.389 (1.00) |
0.833 (1.00) |
0.0527 (1.00) |
0.281 (1.00) |
0.648 (1.00) |
0.329 (1.00) |
1 (1.00) |
0.68 (1.00) |
0.0133 (1.00) |
0.0465 (1.00) |
11p gain | 52 (12%) | 387 |
0.862 (1.00) |
0.0133 (1.00) |
0.0129 (1.00) |
0.096 (1.00) |
0.0228 (1.00) |
0.0563 (1.00) |
1 (1.00) |
0.00749 (1.00) |
0.0382 (1.00) |
0.217 (1.00) |
0.0199 (1.00) |
0.486 (1.00) |
11q gain | 49 (11%) | 390 |
0.749 (1.00) |
0.00035 (0.319) |
0.00789 (1.00) |
0.328 (1.00) |
0.0111 (1.00) |
0.154 (1.00) |
1 (1.00) |
0.000703 (0.634) |
0.0341 (1.00) |
0.373 (1.00) |
0.0177 (1.00) |
0.686 (1.00) |
12p gain | 92 (21%) | 347 |
0.429 (1.00) |
0.316 (1.00) |
0.0833 (1.00) |
0.375 (1.00) |
0.242 (1.00) |
0.0493 (1.00) |
0.907 (1.00) |
0.607 (1.00) |
1 (1.00) |
0.502 (1.00) |
0.117 (1.00) |
0.925 (1.00) |
12q gain | 85 (19%) | 354 |
0.814 (1.00) |
0.154 (1.00) |
0.00796 (1.00) |
0.455 (1.00) |
0.0727 (1.00) |
0.0077 (1.00) |
0.904 (1.00) |
0.218 (1.00) |
1 (1.00) |
0.34 (1.00) |
0.0282 (1.00) |
0.61 (1.00) |
14q gain | 34 (8%) | 405 |
0.697 (1.00) |
0.923 (1.00) |
0.618 (1.00) |
0.799 (1.00) |
0.663 (1.00) |
0.0161 (1.00) |
0.481 (1.00) |
0.111 (1.00) |
1 (1.00) |
0.717 (1.00) |
0.461 (1.00) |
0.0146 (1.00) |
15q gain | 12 (3%) | 427 |
0.62 (1.00) |
0.289 (1.00) |
0.758 (1.00) |
0.506 (1.00) |
0.722 (1.00) |
0.121 (1.00) |
0.0757 (1.00) |
1 (1.00) |
1 (1.00) |
0.0504 (1.00) |
0.32 (1.00) |
0.293 (1.00) |
16p gain | 105 (24%) | 334 |
0.352 (1.00) |
0.104 (1.00) |
0.00371 (1.00) |
0.933 (1.00) |
0.00177 (1.00) |
0.384 (1.00) |
0.911 (1.00) |
0.00795 (1.00) |
0.561 (1.00) |
0.862 (1.00) |
0.00166 (1.00) |
0.425 (1.00) |
16q gain | 103 (23%) | 336 |
0.313 (1.00) |
0.0737 (1.00) |
0.00107 (0.961) |
0.949 (1.00) |
0.00111 (0.993) |
0.496 (1.00) |
0.822 (1.00) |
0.00812 (1.00) |
0.553 (1.00) |
0.713 (1.00) |
0.0016 (1.00) |
0.441 (1.00) |
17p gain | 26 (6%) | 413 |
0.121 (1.00) |
0.704 (1.00) |
0.665 (1.00) |
0.769 (1.00) |
0.347 (1.00) |
0.113 (1.00) |
0.546 (1.00) |
0.767 (1.00) |
1 (1.00) |
0.901 (1.00) |
0.666 (1.00) |
0.0892 (1.00) |
17q gain | 79 (18%) | 360 |
0.216 (1.00) |
0.295 (1.00) |
0.155 (1.00) |
0.378 (1.00) |
0.156 (1.00) |
0.024 (1.00) |
1 (1.00) |
0.272 (1.00) |
0.449 (1.00) |
0.293 (1.00) |
0.859 (1.00) |
0.707 (1.00) |
18p gain | 22 (5%) | 417 |
0.471 (1.00) |
0.51 (1.00) |
0.0908 (1.00) |
0.967 (1.00) |
0.0296 (1.00) |
0.27 (1.00) |
0.382 (1.00) |
0.0189 (1.00) |
1 (1.00) |
0.53 (1.00) |
0.0538 (1.00) |
0.878 (1.00) |
18q gain | 13 (3%) | 426 |
0.754 (1.00) |
0.0874 (1.00) |
0.451 (1.00) |
0.718 (1.00) |
0.298 (1.00) |
1 (1.00) |
0.584 (1.00) |
0.0207 (1.00) |
1 (1.00) |
1 (1.00) |
0.881 (1.00) |
0.479 (1.00) |
19p gain | 71 (16%) | 368 |
0.662 (1.00) |
0.964 (1.00) |
0.541 (1.00) |
0.643 (1.00) |
0.119 (1.00) |
0.0279 (1.00) |
0.0686 (1.00) |
0.253 (1.00) |
0.412 (1.00) |
0.293 (1.00) |
0.747 (1.00) |
1 (1.00) |
19q gain | 79 (18%) | 360 |
0.626 (1.00) |
0.783 (1.00) |
0.89 (1.00) |
0.908 (1.00) |
0.29 (1.00) |
0.0355 (1.00) |
0.214 (1.00) |
1 (1.00) |
0.449 (1.00) |
0.339 (1.00) |
0.951 (1.00) |
0.967 (1.00) |
21q gain | 22 (5%) | 417 |
0.482 (1.00) |
0.000765 (0.688) |
0.503 (1.00) |
0.145 (1.00) |
0.328 (1.00) |
0.5 (1.00) |
0.829 (1.00) |
0.507 (1.00) |
1 (1.00) |
0.469 (1.00) |
0.18 (1.00) |
0.799 (1.00) |
22q gain | 12 (3%) | 427 |
0.827 (1.00) |
0.535 (1.00) |
0.508 (1.00) |
0.272 (1.00) |
1 (1.00) |
0.512 (1.00) |
0.776 (1.00) |
0.383 (1.00) |
1 (1.00) |
0.306 (1.00) |
0.826 (1.00) |
1 (1.00) |
xq gain | 73 (17%) | 366 |
0.439 (1.00) |
0.691 (1.00) |
0.156 (1.00) |
0.0143 (1.00) |
0.706 (1.00) |
0.528 (1.00) |
0.523 (1.00) |
0.576 (1.00) |
0.421 (1.00) |
0.895 (1.00) |
0.609 (1.00) |
0.641 (1.00) |
1p loss | 94 (21%) | 345 |
0.0568 (1.00) |
0.961 (1.00) |
0.0416 (1.00) |
0.627 (1.00) |
0.00197 (1.00) |
0.0109 (1.00) |
0.352 (1.00) |
0.237 (1.00) |
1 (1.00) |
0.47 (1.00) |
0.000877 (0.788) |
0.447 (1.00) |
1q loss | 54 (12%) | 385 |
0.134 (1.00) |
0.581 (1.00) |
0.173 (1.00) |
0.881 (1.00) |
0.0638 (1.00) |
0.193 (1.00) |
0.244 (1.00) |
0.676 (1.00) |
1 (1.00) |
0.49 (1.00) |
0.0567 (1.00) |
0.222 (1.00) |
2p loss | 6 (1%) | 433 |
0.75 (1.00) |
0.684 (1.00) |
0.229 (1.00) |
0.843 (1.00) |
0.851 (1.00) |
1 (1.00) |
0.22 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.519 (1.00) |
|
2q loss | 7 (2%) | 432 |
0.997 (1.00) |
0.657 (1.00) |
0.286 (1.00) |
1 (1.00) |
1 (1.00) |
0.593 (1.00) |
0.126 (1.00) |
0.601 (1.00) |
1 (1.00) |
1 (1.00) |
0.801 (1.00) |
|
3p loss | 52 (12%) | 387 |
0.493 (1.00) |
0.412 (1.00) |
0.26 (1.00) |
0.142 (1.00) |
0.0805 (1.00) |
0.127 (1.00) |
0.884 (1.00) |
0.278 (1.00) |
1 (1.00) |
0.823 (1.00) |
0.0971 (1.00) |
0.779 (1.00) |
3q loss | 32 (7%) | 407 |
0.494 (1.00) |
0.615 (1.00) |
0.692 (1.00) |
0.501 (1.00) |
0.846 (1.00) |
0.28 (1.00) |
0.468 (1.00) |
0.6 (1.00) |
1 (1.00) |
0.865 (1.00) |
0.844 (1.00) |
0.475 (1.00) |
4q loss | 117 (27%) | 322 |
0.0529 (1.00) |
0.768 (1.00) |
0.0274 (1.00) |
0.297 (1.00) |
0.00313 (1.00) |
0.0368 (1.00) |
0.746 (1.00) |
0.0817 (1.00) |
0.0186 (1.00) |
0.551 (1.00) |
0.00108 (0.965) |
0.829 (1.00) |
5p loss | 53 (12%) | 386 |
0.13 (1.00) |
0.292 (1.00) |
0.00442 (1.00) |
0.329 (1.00) |
0.0107 (1.00) |
0.0455 (1.00) |
0.883 (1.00) |
0.519 (1.00) |
0.0397 (1.00) |
0.386 (1.00) |
0.012 (1.00) |
0.545 (1.00) |
6p loss | 33 (8%) | 406 |
0.00562 (1.00) |
0.192 (1.00) |
0.75 (1.00) |
0.116 (1.00) |
0.72 (1.00) |
0.305 (1.00) |
0.371 (1.00) |
0.79 (1.00) |
1 (1.00) |
0.114 (1.00) |
0.947 (1.00) |
0.048 (1.00) |
6q loss | 45 (10%) | 394 |
0.0112 (1.00) |
0.81 (1.00) |
0.674 (1.00) |
0.228 (1.00) |
0.112 (1.00) |
0.068 (1.00) |
0.531 (1.00) |
0.647 (1.00) |
1 (1.00) |
0.174 (1.00) |
0.00686 (1.00) |
0.0192 (1.00) |
8p loss | 137 (31%) | 302 |
0.781 (1.00) |
0.423 (1.00) |
0.0135 (1.00) |
0.214 (1.00) |
0.00107 (0.961) |
0.00376 (1.00) |
0.258 (1.00) |
0.0689 (1.00) |
1 (1.00) |
0.0581 (1.00) |
0.000436 (0.395) |
0.348 (1.00) |
8q loss | 23 (5%) | 416 |
0.963 (1.00) |
0.957 (1.00) |
0.0168 (1.00) |
0.0586 (1.00) |
0.0167 (1.00) |
0.0325 (1.00) |
0.522 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.788 (1.00) |
0.608 (1.00) |
0.0367 (1.00) |
9p loss | 51 (12%) | 388 |
0.831 (1.00) |
0.229 (1.00) |
0.945 (1.00) |
0.077 (1.00) |
0.262 (1.00) |
0.508 (1.00) |
0.237 (1.00) |
0.0295 (1.00) |
1 (1.00) |
0.493 (1.00) |
0.0954 (1.00) |
0.75 (1.00) |
9q loss | 51 (12%) | 388 |
0.855 (1.00) |
0.0398 (1.00) |
0.642 (1.00) |
0.13 (1.00) |
0.103 (1.00) |
0.176 (1.00) |
0.768 (1.00) |
0.0449 (1.00) |
1 (1.00) |
0.495 (1.00) |
0.0729 (1.00) |
0.718 (1.00) |
10p loss | 67 (15%) | 372 |
0.974 (1.00) |
0.191 (1.00) |
0.0358 (1.00) |
0.947 (1.00) |
0.0717 (1.00) |
0.0611 (1.00) |
0.791 (1.00) |
0.33 (1.00) |
0.0622 (1.00) |
0.553 (1.00) |
0.0311 (1.00) |
0.582 (1.00) |
10q loss | 71 (16%) | 368 |
0.698 (1.00) |
0.127 (1.00) |
0.146 (1.00) |
0.908 (1.00) |
0.187 (1.00) |
0.15 (1.00) |
0.699 (1.00) |
0.253 (1.00) |
0.0694 (1.00) |
0.249 (1.00) |
0.122 (1.00) |
0.693 (1.00) |
11p loss | 50 (11%) | 389 |
0.294 (1.00) |
0.471 (1.00) |
0.419 (1.00) |
0.776 (1.00) |
0.0656 (1.00) |
0.0444 (1.00) |
0.882 (1.00) |
0.829 (1.00) |
1 (1.00) |
0.448 (1.00) |
0.00936 (1.00) |
0.586 (1.00) |
11q loss | 61 (14%) | 378 |
0.242 (1.00) |
0.489 (1.00) |
0.224 (1.00) |
0.184 (1.00) |
0.0608 (1.00) |
0.0336 (1.00) |
0.582 (1.00) |
1 (1.00) |
1 (1.00) |
0.417 (1.00) |
0.0311 (1.00) |
0.404 (1.00) |
12p loss | 46 (10%) | 393 |
0.232 (1.00) |
0.329 (1.00) |
0.395 (1.00) |
0.454 (1.00) |
0.0837 (1.00) |
0.261 (1.00) |
1 (1.00) |
0.0117 (1.00) |
0.283 (1.00) |
0.904 (1.00) |
0.0382 (1.00) |
0.938 (1.00) |
12q loss | 48 (11%) | 391 |
0.381 (1.00) |
0.453 (1.00) |
0.152 (1.00) |
0.486 (1.00) |
0.034 (1.00) |
0.281 (1.00) |
0.76 (1.00) |
0.0442 (1.00) |
1 (1.00) |
0.87 (1.00) |
0.0134 (1.00) |
0.5 (1.00) |
13q loss | 12 (3%) | 427 |
0.269 (1.00) |
0.995 (1.00) |
0.776 (1.00) |
0.478 (1.00) |
0.0902 (1.00) |
0.279 (1.00) |
0.776 (1.00) |
0.175 (1.00) |
1 (1.00) |
0.82 (1.00) |
0.0131 (1.00) |
0.0185 (1.00) |
15q loss | 150 (34%) | 289 |
0.384 (1.00) |
0.406 (1.00) |
0.0314 (1.00) |
0.616 (1.00) |
0.0335 (1.00) |
0.00453 (1.00) |
0.763 (1.00) |
0.0181 (1.00) |
0.0394 (1.00) |
0.382 (1.00) |
0.024 (1.00) |
0.0528 (1.00) |
16p loss | 30 (7%) | 409 |
0.0968 (1.00) |
0.0743 (1.00) |
0.392 (1.00) |
0.54 (1.00) |
0.543 (1.00) |
0.163 (1.00) |
0.571 (1.00) |
0.271 (1.00) |
1 (1.00) |
0.181 (1.00) |
0.44 (1.00) |
0.251 (1.00) |
16q loss | 27 (6%) | 412 |
0.175 (1.00) |
0.0232 (1.00) |
0.563 (1.00) |
0.751 (1.00) |
0.702 (1.00) |
0.11 (1.00) |
0.692 (1.00) |
0.39 (1.00) |
1 (1.00) |
0.266 (1.00) |
0.613 (1.00) |
0.23 (1.00) |
17q loss | 65 (15%) | 374 |
0.083 (1.00) |
0.823 (1.00) |
0.149 (1.00) |
0.374 (1.00) |
0.0213 (1.00) |
0.0215 (1.00) |
0.894 (1.00) |
1 (1.00) |
1 (1.00) |
0.726 (1.00) |
0.000527 (0.477) |
0.135 (1.00) |
19q loss | 36 (8%) | 403 |
0.0836 (1.00) |
0.492 (1.00) |
0.045 (1.00) |
1 (1.00) |
0.00677 (1.00) |
0.00435 (1.00) |
0.731 (1.00) |
0.449 (1.00) |
0.227 (1.00) |
0.269 (1.00) |
0.000396 (0.36) |
0.0892 (1.00) |
20p loss | 43 (10%) | 396 |
0.665 (1.00) |
0.59 (1.00) |
0.553 (1.00) |
0.928 (1.00) |
0.449 (1.00) |
0.762 (1.00) |
0.631 (1.00) |
0.818 (1.00) |
1 (1.00) |
1 (1.00) |
0.709 (1.00) |
0.802 (1.00) |
20q loss | 4 (1%) | 435 |
0.243 (1.00) |
0.247 (1.00) |
0.464 (1.00) |
0.776 (1.00) |
0.127 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.16 (1.00) |
|
21q loss | 120 (27%) | 319 |
0.826 (1.00) |
0.966 (1.00) |
0.544 (1.00) |
0.488 (1.00) |
0.0305 (1.00) |
0.147 (1.00) |
0.83 (1.00) |
0.0114 (1.00) |
1 (1.00) |
0.784 (1.00) |
0.0195 (1.00) |
0.404 (1.00) |
xq loss | 50 (11%) | 389 |
0.536 (1.00) |
0.739 (1.00) |
0.156 (1.00) |
0.258 (1.00) |
0.0228 (1.00) |
0.0392 (1.00) |
0.456 (1.00) |
1 (1.00) |
1 (1.00) |
0.467 (1.00) |
0.00375 (1.00) |
0.816 (1.00) |
P value = 6e-05 (Fisher's exact test), Q value = 0.056
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 72 | 1 | 28 | 131 | 8 | 1 | 21 | 12 | 55 | 38 | 43 | 18 | 2 |
7P GAIN MUTATED | 39 | 1 | 14 | 52 | 2 | 0 | 12 | 12 | 36 | 25 | 29 | 13 | 1 |
7P GAIN WILD-TYPE | 33 | 0 | 14 | 79 | 6 | 1 | 9 | 0 | 19 | 13 | 14 | 5 | 1 |
P value = 9e-05 (Fisher's exact test), Q value = 0.083
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 256 | 103 | 79 |
7P GAIN MUTATED | 119 | 70 | 52 |
7P GAIN WILD-TYPE | 137 | 33 | 27 |
P value = 8.48e-07 (Fisher's exact test), Q value = 0.00079
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
13Q GAIN MUTATED | 233 | 16 |
13Q GAIN WILD-TYPE | 145 | 43 |
P value = 1e-04 (Fisher's exact test), Q value = 0.092
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 72 | 1 | 28 | 131 | 8 | 1 | 21 | 12 | 55 | 38 | 43 | 18 | 2 |
20P GAIN MUTATED | 40 | 1 | 13 | 60 | 3 | 0 | 9 | 12 | 24 | 20 | 33 | 14 | 1 |
20P GAIN WILD-TYPE | 32 | 0 | 15 | 71 | 5 | 1 | 12 | 0 | 31 | 18 | 10 | 4 | 1 |
P value = 0.000215 (Fisher's exact test), Q value = 0.2
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
20P GAIN MUTATED | 216 | 18 |
20P GAIN WILD-TYPE | 162 | 41 |
P value = 9.99e-07 (Fisher's exact test), Q value = 0.00093
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
20Q GAIN MUTATED | 284 | 25 |
20Q GAIN WILD-TYPE | 94 | 34 |
P value = 0.00026 (Fisher's exact test), Q value = 0.24
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 320 | 52 | 8 | 2 | 50 |
4P LOSS MUTATED | 78 | 28 | 4 | 1 | 14 |
4P LOSS WILD-TYPE | 242 | 24 | 4 | 1 | 36 |
P value = 6.4e-05 (Wilcoxon-test), Q value = 0.059
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
5Q LOSS MUTATED | 70 | 3.8 (5.8) |
5Q LOSS WILD-TYPE | 345 | 1.7 (4.1) |
P value = 6.05e-06 (Fisher's exact test), Q value = 0.0056
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
14Q LOSS MUTATED | 127 | 4 |
14Q LOSS WILD-TYPE | 251 | 55 |
P value = 7e-05 (Fisher's exact test), Q value = 0.065
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 72 | 1 | 28 | 131 | 8 | 1 | 21 | 12 | 55 | 38 | 43 | 18 | 2 |
17P LOSS MUTATED | 31 | 0 | 13 | 54 | 1 | 1 | 11 | 10 | 30 | 27 | 32 | 12 | 2 |
17P LOSS WILD-TYPE | 41 | 1 | 15 | 77 | 7 | 0 | 10 | 2 | 25 | 11 | 11 | 6 | 0 |
P value = 1e-04 (Fisher's exact test), Q value = 0.092
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 256 | 103 | 79 |
17P LOSS MUTATED | 112 | 63 | 54 |
17P LOSS WILD-TYPE | 144 | 40 | 25 |
P value = 9.99e-06 (Fisher's exact test), Q value = 0.0093
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
17P LOSS MUTATED | 213 | 15 |
17P LOSS WILD-TYPE | 165 | 44 |
P value = 8.56e-06 (Wilcoxon-test), Q value = 0.0079
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
17P LOSS MUTATED | 218 | 2.8 (5.5) |
17P LOSS WILD-TYPE | 197 | 1.2 (2.6) |
P value = 2.29e-09 (Fisher's exact test), Q value = 2.1e-06
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
18P LOSS MUTATED | 233 | 12 |
18P LOSS WILD-TYPE | 145 | 47 |
P value = 7e-05 (Fisher's exact test), Q value = 0.065
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 72 | 1 | 28 | 131 | 8 | 1 | 21 | 12 | 55 | 38 | 43 | 18 | 2 |
18Q LOSS MUTATED | 36 | 0 | 14 | 68 | 2 | 1 | 10 | 11 | 36 | 29 | 35 | 15 | 1 |
18Q LOSS WILD-TYPE | 36 | 1 | 14 | 63 | 6 | 0 | 11 | 1 | 19 | 9 | 8 | 3 | 1 |
P value = 0.00013 (Fisher's exact test), Q value = 0.12
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 256 | 103 | 79 |
18Q LOSS MUTATED | 133 | 72 | 58 |
18Q LOSS WILD-TYPE | 123 | 31 | 21 |
P value = 7.48e-09 (Fisher's exact test), Q value = 7e-06
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
18Q LOSS MUTATED | 248 | 15 |
18Q LOSS WILD-TYPE | 130 | 44 |
P value = 0.000114 (Wilcoxon-test), Q value = 0.1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
18Q LOSS MUTATED | 251 | 2.4 (4.7) |
18Q LOSS WILD-TYPE | 164 | 1.6 (4.1) |
P value = 7.31e-05 (Wilcoxon-test), Q value = 0.067
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
19P LOSS MUTATED | 37 | 4.5 (5.3) |
19P LOSS WILD-TYPE | 378 | 1.8 (4.3) |
P value = 0.000191 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
22Q LOSS MUTATED | 132 | 2.9 (5.0) |
22Q LOSS WILD-TYPE | 283 | 1.7 (4.1) |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = COAD-TP.merged_data.txt
-
Number of patients = 439
-
Number of significantly arm-level cnvs = 78
-
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.