This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 67 focal events and 11 clinical features across 425 patients, 28 significant findings detected with Q value < 0.25.
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amp_13q12.13 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_13q22.1 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_16p11.2 cnv correlated to 'PATHOLOGY.N.STAGE'.
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amp_20p11.23 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.M.STAGE'.
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amp_20q11.21 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_20q12 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_20q13.32 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_1p36.11 cnv correlated to 'PATHOLOGY.M.STAGE'.
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del_4p16.2 cnv correlated to 'PATHOLOGY.N.STAGE' and 'PATHOLOGY.M.STAGE'.
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del_5q21.3 cnv correlated to 'PATHOLOGY.N.STAGE'.
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del_8p23.3 cnv correlated to 'PATHOLOGY.N.STAGE'.
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del_8p22 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.N.STAGE'.
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del_13q14.13 cnv correlated to 'PATHOLOGY.M.STAGE'.
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del_17p12 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.N.STAGE', 'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.
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del_18p11.31 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_18q12.2 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_18q21.2 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.
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del_18q22.1 cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.
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del_19p13.3 cnv correlated to 'PATHOLOGY.N.STAGE'.
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 |
||
nCNV (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | |
del 17p12 | 235 (55%) | 190 |
0.423 (1.00) |
0.032 (1.00) |
1.57e-05 (0.0114) |
0.84 (1.00) |
1.45e-05 (0.0105) |
0.00837 (1.00) |
0.243 (1.00) |
2.23e-06 (0.00162) |
0.257 (1.00) |
0.181 (1.00) |
0.000133 (0.0957) |
del 18q21 2 | 268 (63%) | 157 |
0.908 (1.00) |
0.142 (1.00) |
0.000165 (0.118) |
0.794 (1.00) |
7.18e-05 (0.0519) |
0.00488 (1.00) |
0.107 (1.00) |
2.05e-09 (1.5e-06) |
0.3 (1.00) |
0.136 (1.00) |
0.0327 (1.00) |
amp 20p11 23 | 208 (49%) | 217 |
0.549 (1.00) |
0.76 (1.00) |
0.000332 (0.236) |
0.994 (1.00) |
0.0606 (1.00) |
0.000274 (0.195) |
0.331 (1.00) |
0.0134 (1.00) |
0.116 (1.00) |
0.00892 (1.00) |
0.249 (1.00) |
del 4p16 2 | 127 (30%) | 298 |
0.0432 (1.00) |
0.688 (1.00) |
0.000802 (0.56) |
0.577 (1.00) |
0.000203 (0.145) |
0.0002 (0.142) |
0.671 (1.00) |
0.0182 (1.00) |
0.0262 (1.00) |
0.0364 (1.00) |
0.0112 (1.00) |
del 8p22 | 189 (44%) | 236 |
0.208 (1.00) |
0.111 (1.00) |
9.38e-05 (0.0675) |
0.185 (1.00) |
1.42e-06 (0.00104) |
0.000666 (0.47) |
0.117 (1.00) |
0.0193 (1.00) |
0.587 (1.00) |
0.0545 (1.00) |
0.00104 (0.725) |
del 18q22 1 | 268 (63%) | 157 |
0.997 (1.00) |
0.238 (1.00) |
0.000463 (0.327) |
0.794 (1.00) |
0.000147 (0.105) |
0.00488 (1.00) |
0.107 (1.00) |
2.21e-10 (1.62e-07) |
0.3 (1.00) |
0.23 (1.00) |
0.0415 (1.00) |
amp 13q12 13 | 259 (61%) | 166 |
0.546 (1.00) |
0.523 (1.00) |
0.00162 (1.00) |
0.953 (1.00) |
0.00097 (0.675) |
0.00201 (1.00) |
0.842 (1.00) |
4.37e-07 (0.00032) |
0.284 (1.00) |
0.0341 (1.00) |
0.083 (1.00) |
amp 13q22 1 | 262 (62%) | 163 |
0.407 (1.00) |
0.475 (1.00) |
0.00343 (1.00) |
0.981 (1.00) |
0.00077 (0.539) |
0.00598 (1.00) |
0.272 (1.00) |
4.66e-06 (0.00339) |
0.289 (1.00) |
0.0715 (1.00) |
0.117 (1.00) |
amp 16p11 2 | 119 (28%) | 306 |
0.344 (1.00) |
0.162 (1.00) |
0.00139 (0.957) |
0.563 (1.00) |
0.000294 (0.209) |
0.606 (1.00) |
0.665 (1.00) |
0.00601 (1.00) |
1 (1.00) |
0.693 (1.00) |
0.00853 (1.00) |
amp 20q11 21 | 304 (72%) | 121 |
0.932 (1.00) |
0.625 (1.00) |
0.0029 (1.00) |
0.359 (1.00) |
0.0166 (1.00) |
0.00905 (1.00) |
0.282 (1.00) |
3.92e-06 (0.00285) |
0.561 (1.00) |
0.131 (1.00) |
0.12 (1.00) |
amp 20q12 | 305 (72%) | 120 |
0.945 (1.00) |
0.665 (1.00) |
0.00116 (0.806) |
0.502 (1.00) |
0.0215 (1.00) |
0.00416 (1.00) |
0.235 (1.00) |
6.64e-07 (0.000486) |
0.562 (1.00) |
0.129 (1.00) |
0.155 (1.00) |
amp 20q13 32 | 308 (72%) | 117 |
0.978 (1.00) |
0.699 (1.00) |
0.00175 (1.00) |
0.43 (1.00) |
0.0138 (1.00) |
0.00583 (1.00) |
0.277 (1.00) |
1.43e-06 (0.00104) |
0.565 (1.00) |
0.123 (1.00) |
0.0512 (1.00) |
del 1p36 11 | 159 (37%) | 266 |
0.0594 (1.00) |
0.142 (1.00) |
0.0035 (1.00) |
0.847 (1.00) |
0.013 (1.00) |
9.09e-05 (0.0655) |
0.315 (1.00) |
0.00153 (1.00) |
1 (1.00) |
0.0795 (1.00) |
0.0103 (1.00) |
del 5q21 3 | 121 (28%) | 304 |
0.251 (1.00) |
0.146 (1.00) |
0.00121 (0.836) |
0.932 (1.00) |
8.5e-05 (0.0613) |
0.0212 (1.00) |
0.591 (1.00) |
0.151 (1.00) |
0.0227 (1.00) |
0.26 (1.00) |
0.00868 (1.00) |
del 8p23 3 | 175 (41%) | 250 |
0.901 (1.00) |
0.26 (1.00) |
0.00607 (1.00) |
0.136 (1.00) |
0.000119 (0.0855) |
0.0131 (1.00) |
0.0605 (1.00) |
0.0568 (1.00) |
0.571 (1.00) |
0.107 (1.00) |
0.0051 (1.00) |
del 13q14 13 | 18 (4%) | 407 |
0.643 (1.00) |
0.289 (1.00) |
0.000701 (0.492) |
0.669 (1.00) |
0.0639 (1.00) |
3.22e-05 (0.0233) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.867 (1.00) |
0.225 (1.00) |
del 18p11 31 | 229 (54%) | 196 |
0.623 (1.00) |
0.0358 (1.00) |
0.00437 (1.00) |
0.919 (1.00) |
0.0308 (1.00) |
0.000694 (0.488) |
0.846 (1.00) |
1.93e-11 (1.42e-08) |
0.253 (1.00) |
0.0289 (1.00) |
0.466 (1.00) |
del 18q12 2 | 255 (60%) | 170 |
0.805 (1.00) |
0.0783 (1.00) |
0.0016 (1.00) |
0.727 (1.00) |
0.00121 (0.834) |
0.011 (1.00) |
0.321 (1.00) |
1.5e-10 (1.1e-07) |
0.278 (1.00) |
0.147 (1.00) |
0.121 (1.00) |
del 19p13 3 | 59 (14%) | 366 |
0.678 (1.00) |
0.178 (1.00) |
0.000433 (0.306) |
0.966 (1.00) |
7.75e-05 (0.0559) |
0.0186 (1.00) |
0.485 (1.00) |
0.205 (1.00) |
0.362 (1.00) |
0.0734 (1.00) |
0.00195 (1.00) |
amp 2q33 1 | 83 (20%) | 342 |
0.0219 (1.00) |
0.316 (1.00) |
0.232 (1.00) |
0.782 (1.00) |
0.0269 (1.00) |
0.169 (1.00) |
0.391 (1.00) |
0.366 (1.00) |
0.48 (1.00) |
0.084 (1.00) |
0.0845 (1.00) |
amp 5p13 2 | 81 (19%) | 344 |
0.81 (1.00) |
0.172 (1.00) |
0.156 (1.00) |
0.538 (1.00) |
0.0421 (1.00) |
0.695 (1.00) |
0.325 (1.00) |
0.855 (1.00) |
1 (1.00) |
0.168 (1.00) |
0.048 (1.00) |
amp 5q22 3 | 41 (10%) | 384 |
0.477 (1.00) |
0.687 (1.00) |
0.435 (1.00) |
0.812 (1.00) |
0.308 (1.00) |
0.0109 (1.00) |
0.87 (1.00) |
0.333 (1.00) |
0.263 (1.00) |
0.0927 (1.00) |
0.306 (1.00) |
amp 6p21 1 | 91 (21%) | 334 |
0.986 (1.00) |
0.537 (1.00) |
0.095 (1.00) |
0.451 (1.00) |
0.00742 (1.00) |
0.552 (1.00) |
0.288 (1.00) |
0.0511 (1.00) |
0.00956 (1.00) |
0.674 (1.00) |
0.0199 (1.00) |
amp 8p11 23 | 149 (35%) | 276 |
0.924 (1.00) |
0.398 (1.00) |
0.459 (1.00) |
0.751 (1.00) |
0.701 (1.00) |
0.5 (1.00) |
0.839 (1.00) |
0.13 (1.00) |
0.282 (1.00) |
0.821 (1.00) |
0.663 (1.00) |
amp 8p11 21 | 179 (42%) | 246 |
0.85 (1.00) |
0.547 (1.00) |
0.618 (1.00) |
0.677 (1.00) |
0.618 (1.00) |
0.443 (1.00) |
0.201 (1.00) |
0.144 (1.00) |
0.575 (1.00) |
0.317 (1.00) |
0.959 (1.00) |
amp 8q12 1 | 221 (52%) | 204 |
0.707 (1.00) |
0.215 (1.00) |
0.808 (1.00) |
0.713 (1.00) |
0.65 (1.00) |
0.198 (1.00) |
0.697 (1.00) |
0.0136 (1.00) |
0.249 (1.00) |
0.484 (1.00) |
0.115 (1.00) |
amp 8q24 21 | 245 (58%) | 180 |
0.522 (1.00) |
0.135 (1.00) |
0.343 (1.00) |
0.409 (1.00) |
0.38 (1.00) |
0.121 (1.00) |
0.377 (1.00) |
0.0573 (1.00) |
0.266 (1.00) |
0.395 (1.00) |
0.0885 (1.00) |
amp 11p15 5 | 88 (21%) | 337 |
0.939 (1.00) |
0.0328 (1.00) |
0.621 (1.00) |
0.286 (1.00) |
0.0789 (1.00) |
0.267 (1.00) |
0.549 (1.00) |
0.00197 (1.00) |
0.11 (1.00) |
0.461 (1.00) |
0.272 (1.00) |
amp 12p13 33 | 105 (25%) | 320 |
0.139 (1.00) |
0.138 (1.00) |
0.193 (1.00) |
0.102 (1.00) |
0.429 (1.00) |
0.305 (1.00) |
0.91 (1.00) |
0.738 (1.00) |
1 (1.00) |
0.463 (1.00) |
0.742 (1.00) |
amp 16q12 1 | 105 (25%) | 320 |
0.0803 (1.00) |
0.0501 (1.00) |
0.000422 (0.299) |
0.945 (1.00) |
0.000691 (0.486) |
0.433 (1.00) |
0.573 (1.00) |
0.0112 (1.00) |
0.574 (1.00) |
0.701 (1.00) |
0.0236 (1.00) |
amp 17q12 | 105 (25%) | 320 |
0.322 (1.00) |
0.561 (1.00) |
0.131 (1.00) |
0.163 (1.00) |
0.17 (1.00) |
0.00793 (1.00) |
0.177 (1.00) |
0.313 (1.00) |
0.574 (1.00) |
0.128 (1.00) |
0.18 (1.00) |
amp 17q24 1 | 97 (23%) | 328 |
0.0622 (1.00) |
0.6 (1.00) |
0.445 (1.00) |
0.365 (1.00) |
0.349 (1.00) |
0.0323 (1.00) |
0.73 (1.00) |
0.0595 (1.00) |
0.541 (1.00) |
0.326 (1.00) |
0.992 (1.00) |
amp 19p13 2 | 69 (16%) | 356 |
0.985 (1.00) |
0.761 (1.00) |
0.779 (1.00) |
0.521 (1.00) |
0.0164 (1.00) |
0.0184 (1.00) |
0.0346 (1.00) |
0.328 (1.00) |
0.413 (1.00) |
0.0942 (1.00) |
0.369 (1.00) |
amp 19q13 11 | 87 (20%) | 338 |
0.359 (1.00) |
0.708 (1.00) |
0.751 (1.00) |
0.768 (1.00) |
0.0617 (1.00) |
0.0425 (1.00) |
0.0406 (1.00) |
0.478 (1.00) |
0.498 (1.00) |
0.757 (1.00) |
0.894 (1.00) |
del 1p33 | 115 (27%) | 310 |
0.0055 (1.00) |
0.912 (1.00) |
0.04 (1.00) |
0.485 (1.00) |
0.0138 (1.00) |
0.00617 (1.00) |
0.743 (1.00) |
0.0726 (1.00) |
0.566 (1.00) |
0.226 (1.00) |
0.0232 (1.00) |
del 1p13 1 | 110 (26%) | 315 |
0.151 (1.00) |
0.678 (1.00) |
0.0103 (1.00) |
0.556 (1.00) |
0.00361 (1.00) |
0.0011 (0.761) |
0.506 (1.00) |
0.0989 (1.00) |
1 (1.00) |
0.117 (1.00) |
0.0194 (1.00) |
del 1q43 | 51 (12%) | 374 |
0.94 (1.00) |
0.338 (1.00) |
0.0441 (1.00) |
0.132 (1.00) |
0.378 (1.00) |
0.0895 (1.00) |
0.881 (1.00) |
0.657 (1.00) |
0.319 (1.00) |
0.453 (1.00) |
0.475 (1.00) |
del 2p21 | 16 (4%) | 409 |
0.812 (1.00) |
0.328 (1.00) |
0.311 (1.00) |
0.517 (1.00) |
0.264 (1.00) |
0.264 (1.00) |
0.457 (1.00) |
0.706 (1.00) |
1 (1.00) |
0.643 (1.00) |
0.778 (1.00) |
del 2q22 1 | 20 (5%) | 405 |
0.92 (1.00) |
0.285 (1.00) |
0.349 (1.00) |
0.402 (1.00) |
0.186 (1.00) |
0.831 (1.00) |
1 (1.00) |
0.734 (1.00) |
1 (1.00) |
1 (1.00) |
0.332 (1.00) |
del 2q37 2 | 21 (5%) | 404 |
0.191 (1.00) |
0.412 (1.00) |
0.823 (1.00) |
0.434 (1.00) |
0.819 (1.00) |
0.323 (1.00) |
0.375 (1.00) |
0.745 (1.00) |
1 (1.00) |
0.212 (1.00) |
0.164 (1.00) |
del 3p26 1 | 65 (15%) | 360 |
0.0804 (1.00) |
0.488 (1.00) |
0.0885 (1.00) |
0.193 (1.00) |
0.0185 (1.00) |
0.00596 (1.00) |
0.893 (1.00) |
0.106 (1.00) |
1 (1.00) |
0.286 (1.00) |
0.128 (1.00) |
del 3p14 2 | 80 (19%) | 345 |
0.279 (1.00) |
0.424 (1.00) |
0.169 (1.00) |
0.197 (1.00) |
0.0657 (1.00) |
0.0813 (1.00) |
0.387 (1.00) |
0.268 (1.00) |
1 (1.00) |
0.487 (1.00) |
0.0433 (1.00) |
del 3q26 31 | 44 (10%) | 381 |
0.714 (1.00) |
0.91 (1.00) |
0.142 (1.00) |
0.129 (1.00) |
0.926 (1.00) |
0.626 (1.00) |
0.875 (1.00) |
0.0963 (1.00) |
1 (1.00) |
0.952 (1.00) |
0.12 (1.00) |
del 4q22 1 | 136 (32%) | 289 |
0.155 (1.00) |
0.659 (1.00) |
0.00275 (1.00) |
0.254 (1.00) |
0.000781 (0.546) |
0.168 (1.00) |
0.603 (1.00) |
0.00802 (1.00) |
0.0323 (1.00) |
0.946 (1.00) |
0.0237 (1.00) |
del 4q35 1 | 144 (34%) | 281 |
0.584 (1.00) |
0.192 (1.00) |
0.0892 (1.00) |
0.527 (1.00) |
0.00471 (1.00) |
0.124 (1.00) |
0.183 (1.00) |
0.0474 (1.00) |
0.0384 (1.00) |
0.375 (1.00) |
0.07 (1.00) |
del 5q11 2 | 96 (23%) | 329 |
0.204 (1.00) |
0.102 (1.00) |
0.0153 (1.00) |
0.967 (1.00) |
0.00319 (1.00) |
0.0462 (1.00) |
0.296 (1.00) |
0.0248 (1.00) |
0.0112 (1.00) |
0.754 (1.00) |
0.0246 (1.00) |
del 5q23 1 | 112 (26%) | 313 |
0.306 (1.00) |
0.327 (1.00) |
0.0292 (1.00) |
0.964 (1.00) |
0.00582 (1.00) |
0.00939 (1.00) |
0.27 (1.00) |
0.0729 (1.00) |
0.0179 (1.00) |
0.319 (1.00) |
0.0434 (1.00) |
del 6p25 3 | 54 (13%) | 371 |
0.1 (1.00) |
0.138 (1.00) |
0.637 (1.00) |
0.342 (1.00) |
0.843 (1.00) |
0.145 (1.00) |
0.0797 (1.00) |
0.516 (1.00) |
1 (1.00) |
0.361 (1.00) |
0.745 (1.00) |
del 6q26 | 59 (14%) | 366 |
0.021 (1.00) |
0.923 (1.00) |
0.0669 (1.00) |
0.517 (1.00) |
0.0174 (1.00) |
0.0232 (1.00) |
0.889 (1.00) |
0.837 (1.00) |
1 (1.00) |
0.138 (1.00) |
0.0164 (1.00) |
del 7q31 1 | 12 (3%) | 413 |
0.862 (1.00) |
0.838 (1.00) |
0.945 (1.00) |
0.646 (1.00) |
1 (1.00) |
0.17 (1.00) |
0.56 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.588 (1.00) |
del 8p11 21 | 44 (10%) | 381 |
0.535 (1.00) |
0.439 (1.00) |
0.00323 (1.00) |
0.131 (1.00) |
0.000903 (0.629) |
0.00925 (1.00) |
1 (1.00) |
0.634 (1.00) |
0.28 (1.00) |
0.109 (1.00) |
0.0207 (1.00) |
del 9p21 3 | 57 (13%) | 368 |
0.816 (1.00) |
0.0524 (1.00) |
0.535 (1.00) |
0.351 (1.00) |
0.286 (1.00) |
0.0983 (1.00) |
0.201 (1.00) |
0.0872 (1.00) |
1 (1.00) |
0.636 (1.00) |
0.423 (1.00) |
del 10p15 3 | 75 (18%) | 350 |
0.842 (1.00) |
0.346 (1.00) |
0.00308 (1.00) |
0.94 (1.00) |
0.0109 (1.00) |
0.00264 (1.00) |
0.8 (1.00) |
0.349 (1.00) |
0.0818 (1.00) |
0.666 (1.00) |
0.113 (1.00) |
del 10q21 1 | 90 (21%) | 335 |
0.466 (1.00) |
0.0677 (1.00) |
0.00367 (1.00) |
0.995 (1.00) |
0.0131 (1.00) |
0.0947 (1.00) |
0.905 (1.00) |
0.0511 (1.00) |
0.115 (1.00) |
0.0569 (1.00) |
0.114 (1.00) |
del 10q23 31 | 101 (24%) | 324 |
0.86 (1.00) |
0.00849 (1.00) |
0.00425 (1.00) |
0.939 (1.00) |
0.0268 (1.00) |
0.0219 (1.00) |
0.733 (1.00) |
0.0418 (1.00) |
0.142 (1.00) |
0.169 (1.00) |
0.281 (1.00) |
del 10q25 2 | 101 (24%) | 324 |
0.0317 (1.00) |
0.109 (1.00) |
0.0248 (1.00) |
0.34 (1.00) |
0.00282 (1.00) |
0.0422 (1.00) |
0.82 (1.00) |
0.0911 (1.00) |
0.142 (1.00) |
0.064 (1.00) |
0.121 (1.00) |
del 12p13 2 | 54 (13%) | 371 |
0.0577 (1.00) |
0.291 (1.00) |
0.105 (1.00) |
0.808 (1.00) |
0.0335 (1.00) |
0.213 (1.00) |
0.663 (1.00) |
0.00464 (1.00) |
1 (1.00) |
0.399 (1.00) |
0.514 (1.00) |
del 14q32 11 | 140 (33%) | 285 |
0.442 (1.00) |
0.405 (1.00) |
0.131 (1.00) |
0.325 (1.00) |
0.0601 (1.00) |
0.0337 (1.00) |
0.757 (1.00) |
0.000577 (0.408) |
0.554 (1.00) |
0.317 (1.00) |
0.145 (1.00) |
del 15q11 2 | 165 (39%) | 260 |
0.684 (1.00) |
0.869 (1.00) |
0.0444 (1.00) |
0.973 (1.00) |
0.0103 (1.00) |
0.0485 (1.00) |
0.842 (1.00) |
0.0171 (1.00) |
0.0579 (1.00) |
0.485 (1.00) |
0.268 (1.00) |
del 15q21 1 | 157 (37%) | 268 |
0.219 (1.00) |
0.851 (1.00) |
0.16 (1.00) |
0.99 (1.00) |
0.045 (1.00) |
0.0141 (1.00) |
0.616 (1.00) |
0.0159 (1.00) |
0.0498 (1.00) |
0.215 (1.00) |
0.489 (1.00) |
del 15q22 33 | 151 (36%) | 274 |
0.293 (1.00) |
0.586 (1.00) |
0.0245 (1.00) |
0.542 (1.00) |
0.0153 (1.00) |
0.00517 (1.00) |
0.612 (1.00) |
0.00398 (1.00) |
0.0443 (1.00) |
0.628 (1.00) |
0.349 (1.00) |
del 16p13 3 | 51 (12%) | 374 |
0.0211 (1.00) |
0.816 (1.00) |
0.0693 (1.00) |
0.0457 (1.00) |
0.0844 (1.00) |
0.473 (1.00) |
0.881 (1.00) |
1 (1.00) |
1 (1.00) |
0.353 (1.00) |
0.13 (1.00) |
del 16q23 1 | 55 (13%) | 370 |
0.0144 (1.00) |
0.552 (1.00) |
0.942 (1.00) |
0.591 (1.00) |
0.683 (1.00) |
0.678 (1.00) |
0.248 (1.00) |
0.396 (1.00) |
1 (1.00) |
0.779 (1.00) |
0.358 (1.00) |
del 17q24 3 | 62 (15%) | 363 |
0.191 (1.00) |
0.79 (1.00) |
0.0212 (1.00) |
0.652 (1.00) |
0.00568 (1.00) |
0.0514 (1.00) |
0.275 (1.00) |
1 (1.00) |
1 (1.00) |
0.283 (1.00) |
0.0559 (1.00) |
del 20p12 1 | 80 (19%) | 345 |
0.608 (1.00) |
0.541 (1.00) |
0.492 (1.00) |
0.624 (1.00) |
0.444 (1.00) |
0.967 (1.00) |
0.537 (1.00) |
0.138 (1.00) |
1 (1.00) |
0.699 (1.00) |
0.569 (1.00) |
del 21q11 2 | 133 (31%) | 292 |
0.366 (1.00) |
0.717 (1.00) |
0.188 (1.00) |
0.375 (1.00) |
0.0203 (1.00) |
0.114 (1.00) |
0.834 (1.00) |
0.00454 (1.00) |
0.232 (1.00) |
0.64 (1.00) |
0.0121 (1.00) |
del 22q13 32 | 148 (35%) | 277 |
0.148 (1.00) |
0.743 (1.00) |
0.00516 (1.00) |
0.696 (1.00) |
0.000728 (0.511) |
0.0155 (1.00) |
0.839 (1.00) |
0.00143 (0.983) |
1 (1.00) |
0.45 (1.00) |
0.0128 (1.00) |
P value = 4.37e-07 (Fisher's exact test), Q value = 0.00032
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 368 | 55 |
AMP PEAK 11(13Q12.13) MUTATED | 242 | 16 |
AMP PEAK 11(13Q12.13) WILD-TYPE | 126 | 39 |
P value = 4.66e-06 (Fisher's exact test), Q value = 0.0034
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 368 | 55 |
AMP PEAK 12(13Q22.1) MUTATED | 243 | 18 |
AMP PEAK 12(13Q22.1) WILD-TYPE | 125 | 37 |
P value = 0.000294 (Fisher's exact test), Q value = 0.21
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 249 | 101 | 74 |
AMP PEAK 13(16P11.2) MUTATED | 52 | 36 | 31 |
AMP PEAK 13(16P11.2) WILD-TYPE | 197 | 65 | 43 |
P value = 0.000332 (Chi-square test), Q value = 0.24
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 | 71 | 1 | 33 | 120 | 8 | 1 | 22 | 13 | 52 | 36 | 42 | 16 | 1 |
AMP PEAK 19(20P11.23) MUTATED | 33 | 1 | 14 | 50 | 3 | 0 | 10 | 12 | 19 | 16 | 33 | 10 | 0 |
AMP PEAK 19(20P11.23) WILD-TYPE | 38 | 0 | 19 | 70 | 5 | 1 | 12 | 1 | 33 | 20 | 9 | 6 | 1 |
P value = 0.000274 (Chi-square test), Q value = 0.2
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 318 | 50 | 7 | 1 | 42 |
AMP PEAK 19(20P11.23) MUTATED | 140 | 35 | 7 | 0 | 24 |
AMP PEAK 19(20P11.23) WILD-TYPE | 178 | 15 | 0 | 1 | 18 |
P value = 3.92e-06 (Fisher's exact test), Q value = 0.0029
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 368 | 55 |
AMP PEAK 20(20Q11.21) MUTATED | 278 | 24 |
AMP PEAK 20(20Q11.21) WILD-TYPE | 90 | 31 |
P value = 6.64e-07 (Fisher's exact test), Q value = 0.00049
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 368 | 55 |
AMP PEAK 21(20Q12) MUTATED | 280 | 23 |
AMP PEAK 21(20Q12) WILD-TYPE | 88 | 32 |
P value = 1.43e-06 (Fisher's exact test), Q value = 0.001
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 368 | 55 |
AMP PEAK 22(20Q13.32) MUTATED | 282 | 24 |
AMP PEAK 22(20Q13.32) WILD-TYPE | 86 | 31 |
P value = 9.09e-05 (Chi-square test), Q value = 0.065
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 318 | 50 | 7 | 1 | 42 |
DEL PEAK 1(1P36.11) MUTATED | 104 | 34 | 3 | 0 | 17 |
DEL PEAK 1(1P36.11) WILD-TYPE | 214 | 16 | 4 | 1 | 25 |
P value = 0.000203 (Fisher's exact test), Q value = 0.15
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 249 | 101 | 74 |
DEL PEAK 11(4P16.2) MUTATED | 56 | 38 | 33 |
DEL PEAK 11(4P16.2) WILD-TYPE | 193 | 63 | 41 |
P value = 2e-04 (Chi-square test), Q value = 0.14
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 318 | 50 | 7 | 1 | 42 |
DEL PEAK 11(4P16.2) MUTATED | 78 | 28 | 3 | 0 | 14 |
DEL PEAK 11(4P16.2) WILD-TYPE | 240 | 22 | 4 | 1 | 28 |
P value = 8.5e-05 (Fisher's exact test), Q value = 0.061
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 249 | 101 | 74 |
DEL PEAK 15(5Q21.3) MUTATED | 52 | 36 | 33 |
DEL PEAK 15(5Q21.3) WILD-TYPE | 197 | 65 | 41 |
P value = 0.000119 (Fisher's exact test), Q value = 0.086
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 249 | 101 | 74 |
DEL PEAK 20(8P23.3) MUTATED | 82 | 49 | 43 |
DEL PEAK 20(8P23.3) WILD-TYPE | 167 | 52 | 31 |
P value = 9.38e-05 (Chi-square test), Q value = 0.067
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 | 71 | 1 | 33 | 120 | 8 | 1 | 22 | 13 | 52 | 36 | 42 | 16 | 1 |
DEL PEAK 21(8P22) MUTATED | 24 | 0 | 9 | 41 | 2 | 0 | 11 | 8 | 27 | 23 | 28 | 12 | 1 |
DEL PEAK 21(8P22) WILD-TYPE | 47 | 1 | 24 | 79 | 6 | 1 | 11 | 5 | 25 | 13 | 14 | 4 | 0 |
P value = 1.42e-06 (Fisher's exact test), Q value = 0.001
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 249 | 101 | 74 |
DEL PEAK 21(8P22) MUTATED | 86 | 53 | 49 |
DEL PEAK 21(8P22) WILD-TYPE | 163 | 48 | 25 |
P value = 3.22e-05 (Chi-square test), Q value = 0.023
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 318 | 50 | 7 | 1 | 42 |
DEL PEAK 29(13Q14.13) MUTATED | 12 | 1 | 0 | 1 | 2 |
DEL PEAK 29(13Q14.13) WILD-TYPE | 306 | 49 | 7 | 0 | 40 |
P value = 1.57e-05 (Chi-square test), Q value = 0.011
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 | 71 | 1 | 33 | 120 | 8 | 1 | 22 | 13 | 52 | 36 | 42 | 16 | 1 |
DEL PEAK 36(17P12) MUTATED | 34 | 0 | 15 | 50 | 1 | 1 | 13 | 12 | 31 | 27 | 32 | 12 | 1 |
DEL PEAK 36(17P12) WILD-TYPE | 37 | 1 | 18 | 70 | 7 | 0 | 9 | 1 | 21 | 9 | 10 | 4 | 0 |
P value = 1.45e-05 (Fisher's exact test), Q value = 0.01
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 249 | 101 | 74 |
DEL PEAK 36(17P12) MUTATED | 114 | 67 | 53 |
DEL PEAK 36(17P12) WILD-TYPE | 135 | 34 | 21 |
P value = 2.23e-06 (Fisher's exact test), Q value = 0.0016
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 368 | 55 |
DEL PEAK 36(17P12) MUTATED | 219 | 14 |
DEL PEAK 36(17P12) WILD-TYPE | 149 | 41 |
P value = 0.000133 (t-test), Q value = 0.096
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 401 | 2.0 (4.5) |
DEL PEAK 36(17P12) MUTATED | 222 | 2.7 (5.4) |
DEL PEAK 36(17P12) WILD-TYPE | 179 | 1.2 (2.6) |
P value = 1.93e-11 (Fisher's exact test), Q value = 1.4e-08
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 368 | 55 |
DEL PEAK 38(18P11.31) MUTATED | 220 | 7 |
DEL PEAK 38(18P11.31) WILD-TYPE | 148 | 48 |
P value = 1.5e-10 (Fisher's exact test), Q value = 1.1e-07
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 368 | 55 |
DEL PEAK 39(18Q12.2) MUTATED | 243 | 11 |
DEL PEAK 39(18Q12.2) WILD-TYPE | 125 | 44 |
P value = 0.000165 (Chi-square test), Q value = 0.12
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 | 71 | 1 | 33 | 120 | 8 | 1 | 22 | 13 | 52 | 36 | 42 | 16 | 1 |
DEL PEAK 40(18Q21.2) MUTATED | 38 | 0 | 18 | 65 | 2 | 1 | 12 | 12 | 35 | 29 | 36 | 13 | 1 |
DEL PEAK 40(18Q21.2) WILD-TYPE | 33 | 1 | 15 | 55 | 6 | 0 | 10 | 1 | 17 | 7 | 6 | 3 | 0 |
P value = 7.18e-05 (Fisher's exact test), Q value = 0.052
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 249 | 101 | 74 |
DEL PEAK 40(18Q21.2) MUTATED | 136 | 73 | 58 |
DEL PEAK 40(18Q21.2) WILD-TYPE | 113 | 28 | 16 |
P value = 2.05e-09 (Fisher's exact test), Q value = 1.5e-06
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 368 | 55 |
DEL PEAK 40(18Q21.2) MUTATED | 253 | 14 |
DEL PEAK 40(18Q21.2) WILD-TYPE | 115 | 41 |
P value = 0.000147 (Fisher's exact test), Q value = 0.11
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 249 | 101 | 74 |
DEL PEAK 41(18Q22.1) MUTATED | 137 | 72 | 58 |
DEL PEAK 41(18Q22.1) WILD-TYPE | 112 | 29 | 16 |
P value = 2.21e-10 (Fisher's exact test), Q value = 1.6e-07
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 368 | 55 |
DEL PEAK 41(18Q22.1) MUTATED | 254 | 13 |
DEL PEAK 41(18Q22.1) WILD-TYPE | 114 | 42 |
P value = 7.75e-05 (Fisher's exact test), Q value = 0.056
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 249 | 101 | 74 |
DEL PEAK 42(19P13.3) MUTATED | 22 | 15 | 22 |
DEL PEAK 42(19P13.3) WILD-TYPE | 227 | 86 | 52 |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = COAD-TP.merged_data.txt
-
Number of patients = 425
-
Number of significantly focal cnvs = 67
-
Number of selected clinical features = 11
-
Exclude genes 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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' 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.