This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 68 focal events and 12 clinical features across 439 patients, 42 significant findings detected with Q value < 0.25.
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amp_7p21.2 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.N.STAGE', and 'NUMBER.OF.LYMPH.NODES'.
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amp_13q12.13 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'HISTOLOGICAL.TYPE'.
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amp_13q22.1 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'HISTOLOGICAL.TYPE'.
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amp_16p11.2 cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.
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amp_16q12.1 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.N.STAGE', and 'NUMBER.OF.LYMPH.NODES'.
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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_20q13.12 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.M.STAGE' and 'NUMBER.OF.LYMPH.NODES'.
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del_4q22.1 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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del_5q21.1 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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del_8p23.3 cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.
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del_8p22 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.
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del_14q31.1 cnv correlated to 'HISTOLOGICAL.TYPE'.
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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_17q24.3 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
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del_18p11.31 cnv correlated to 'PATHOLOGY.M.STAGE' and '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', 'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.
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del_19p13.3 cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.
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del_22q13.32 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 | |
del 8p22 | 196 (45%) | 243 |
0.2 (1.00) |
0.0263 (1.00) |
1e-05 (0.00803) |
0.0416 (1.00) |
1e-05 (0.00803) |
0.00014 (0.11) |
0.0543 (1.00) |
0.0108 (1.00) |
0.588 (1.00) |
0.041 (1.00) |
2.68e-07 (0.000217) |
0.395 (1.00) |
del 17p12 | 245 (56%) | 194 |
0.306 (1.00) |
0.0138 (1.00) |
1e-05 (0.00803) |
0.9 (1.00) |
1e-05 (0.00803) |
0.00419 (1.00) |
0.213 (1.00) |
2.35e-06 (0.00189) |
0.258 (1.00) |
0.132 (1.00) |
1.18e-06 (0.000953) |
0.851 (1.00) |
del 18q21 2 | 280 (64%) | 159 |
0.99 (1.00) |
0.0207 (1.00) |
5e-05 (0.0397) |
0.808 (1.00) |
2e-05 (0.016) |
0.00077 (0.586) |
0.0745 (1.00) |
7.32e-09 (5.96e-06) |
0.557 (1.00) |
0.0815 (1.00) |
2.57e-05 (0.0205) |
0.794 (1.00) |
amp 7p21 2 | 249 (57%) | 190 |
0.921 (1.00) |
0.0608 (1.00) |
0.00013 (0.102) |
0.386 (1.00) |
5e-05 (0.0397) |
0.0502 (1.00) |
1 (1.00) |
0.0472 (1.00) |
0.262 (1.00) |
0.264 (1.00) |
0.000153 (0.119) |
0.5 (1.00) |
amp 16q12 1 | 108 (25%) | 331 |
0.146 (1.00) |
0.0546 (1.00) |
0.0002 (0.156) |
0.933 (1.00) |
0.00021 (0.163) |
0.474 (1.00) |
0.507 (1.00) |
0.0144 (1.00) |
0.572 (1.00) |
0.604 (1.00) |
0.000209 (0.162) |
0.203 (1.00) |
amp 13q12 13 | 267 (61%) | 172 |
0.658 (1.00) |
0.603 (1.00) |
8e-05 (0.0633) |
0.885 (1.00) |
0.00078 (0.593) |
0.0009 (0.681) |
0.769 (1.00) |
1.05e-07 (8.55e-05) |
0.283 (1.00) |
0.0226 (1.00) |
0.00317 (1.00) |
0.131 (1.00) |
amp 13q22 1 | 271 (62%) | 168 |
0.474 (1.00) |
0.664 (1.00) |
0.00014 (0.11) |
0.882 (1.00) |
0.00039 (0.301) |
0.00286 (1.00) |
0.28 (1.00) |
1.05e-06 (0.000844) |
0.29 (1.00) |
0.0479 (1.00) |
0.00377 (1.00) |
0.103 (1.00) |
amp 16p11 2 | 122 (28%) | 317 |
0.541 (1.00) |
0.157 (1.00) |
0.0004 (0.309) |
0.567 (1.00) |
0.00015 (0.117) |
0.562 (1.00) |
0.67 (1.00) |
0.00781 (1.00) |
1 (1.00) |
0.641 (1.00) |
7.29e-05 (0.0578) |
0.457 (1.00) |
del 4p16 2 | 130 (30%) | 309 |
0.00719 (1.00) |
0.954 (1.00) |
0.00074 (0.564) |
0.458 (1.00) |
0.00056 (0.429) |
0.00012 (0.0944) |
0.53 (1.00) |
0.0218 (1.00) |
0.0255 (1.00) |
0.0317 (1.00) |
0.000114 (0.0899) |
0.443 (1.00) |
del 8p23 3 | 183 (42%) | 256 |
0.831 (1.00) |
0.0948 (1.00) |
0.00091 (0.688) |
0.132 (1.00) |
8e-05 (0.0633) |
0.00536 (1.00) |
0.0199 (1.00) |
0.0336 (1.00) |
0.573 (1.00) |
0.0896 (1.00) |
2.63e-05 (0.021) |
0.384 (1.00) |
del 18p11 31 | 239 (54%) | 200 |
0.897 (1.00) |
0.00353 (1.00) |
0.00113 (0.847) |
0.902 (1.00) |
0.0293 (1.00) |
0.00014 (0.11) |
0.774 (1.00) |
3.4e-10 (2.78e-07) |
0.254 (1.00) |
0.0264 (1.00) |
0.0197 (1.00) |
0.909 (1.00) |
del 19p13 3 | 61 (14%) | 378 |
0.575 (1.00) |
0.119 (1.00) |
0.00479 (1.00) |
0.923 (1.00) |
0.00012 (0.0944) |
0.0306 (1.00) |
0.335 (1.00) |
0.307 (1.00) |
0.362 (1.00) |
0.078 (1.00) |
2.52e-06 (0.00203) |
1 (1.00) |
amp 20q11 21 | 313 (71%) | 126 |
0.755 (1.00) |
0.442 (1.00) |
0.00266 (1.00) |
0.282 (1.00) |
0.00775 (1.00) |
0.0173 (1.00) |
0.247 (1.00) |
7.13e-07 (0.000577) |
0.561 (1.00) |
0.0931 (1.00) |
0.0126 (1.00) |
0.709 (1.00) |
amp 20q12 | 314 (72%) | 125 |
0.891 (1.00) |
0.442 (1.00) |
0.00114 (0.854) |
0.39 (1.00) |
0.0103 (1.00) |
0.00643 (1.00) |
0.205 (1.00) |
1.11e-07 (9.01e-05) |
0.561 (1.00) |
0.0905 (1.00) |
0.0131 (1.00) |
0.652 (1.00) |
amp 20q13 12 | 317 (72%) | 122 |
0.636 (1.00) |
0.463 (1.00) |
0.00047 (0.361) |
0.495 (1.00) |
0.00664 (1.00) |
0.00215 (1.00) |
0.286 (1.00) |
2.39e-07 (0.000194) |
0.564 (1.00) |
0.0905 (1.00) |
0.00515 (1.00) |
0.606 (1.00) |
del 1p36 11 | 163 (37%) | 276 |
0.0377 (1.00) |
0.0662 (1.00) |
0.00049 (0.376) |
0.789 (1.00) |
0.0151 (1.00) |
3e-05 (0.0239) |
0.198 (1.00) |
0.00136 (1.00) |
1 (1.00) |
0.0922 (1.00) |
0.00244 (1.00) |
0.0885 (1.00) |
del 4q22 1 | 142 (32%) | 297 |
0.0407 (1.00) |
0.318 (1.00) |
0.00364 (1.00) |
0.162 (1.00) |
0.00043 (0.331) |
0.121 (1.00) |
0.358 (1.00) |
0.00674 (1.00) |
0.0334 (1.00) |
0.914 (1.00) |
0.000104 (0.0817) |
0.844 (1.00) |
del 5q21 1 | 121 (28%) | 318 |
0.0962 (1.00) |
0.122 (1.00) |
0.00036 (0.279) |
0.981 (1.00) |
0.00058 (0.444) |
0.00259 (1.00) |
0.201 (1.00) |
0.35 (1.00) |
0.0206 (1.00) |
0.445 (1.00) |
0.000235 (0.182) |
0.326 (1.00) |
del 14q31 1 | 144 (33%) | 295 |
0.465 (1.00) |
0.195 (1.00) |
0.227 (1.00) |
0.304 (1.00) |
0.0388 (1.00) |
0.0232 (1.00) |
0.611 (1.00) |
8.69e-06 (0.00699) |
0.554 (1.00) |
0.312 (1.00) |
0.0124 (1.00) |
0.956 (1.00) |
del 17q24 3 | 68 (15%) | 371 |
0.0751 (1.00) |
0.211 (1.00) |
0.00542 (1.00) |
0.232 (1.00) |
0.00266 (1.00) |
0.00101 (0.762) |
0.294 (1.00) |
0.703 (1.00) |
1 (1.00) |
0.403 (1.00) |
4.67e-05 (0.0372) |
0.292 (1.00) |
del 18q12 2 | 266 (61%) | 173 |
0.884 (1.00) |
0.0102 (1.00) |
0.00064 (0.489) |
0.766 (1.00) |
0.00096 (0.725) |
0.00438 (1.00) |
0.24 (1.00) |
5.78e-09 (4.71e-06) |
0.282 (1.00) |
0.1 (1.00) |
0.00108 (0.813) |
0.891 (1.00) |
del 22q13 32 | 153 (35%) | 286 |
0.118 (1.00) |
0.289 (1.00) |
0.00593 (1.00) |
0.609 (1.00) |
0.00068 (0.519) |
0.0181 (1.00) |
0.689 (1.00) |
0.00184 (1.00) |
1 (1.00) |
0.54 (1.00) |
0.000153 (0.119) |
0.491 (1.00) |
amp 2q33 1 | 88 (20%) | 351 |
0.0321 (1.00) |
0.48 (1.00) |
0.299 (1.00) |
0.83 (1.00) |
0.0219 (1.00) |
0.104 (1.00) |
0.474 (1.00) |
0.384 (1.00) |
0.49 (1.00) |
0.113 (1.00) |
0.0086 (1.00) |
0.388 (1.00) |
amp 5p13 2 | 86 (20%) | 353 |
0.684 (1.00) |
0.0918 (1.00) |
0.237 (1.00) |
0.514 (1.00) |
0.0288 (1.00) |
0.324 (1.00) |
0.47 (1.00) |
0.861 (1.00) |
1 (1.00) |
0.152 (1.00) |
0.0182 (1.00) |
0.268 (1.00) |
amp 5q22 3 | 43 (10%) | 396 |
0.576 (1.00) |
0.697 (1.00) |
0.568 (1.00) |
0.939 (1.00) |
0.305 (1.00) |
0.055 (1.00) |
0.631 (1.00) |
0.243 (1.00) |
0.267 (1.00) |
0.0888 (1.00) |
0.18 (1.00) |
0.594 (1.00) |
amp 6p21 1 | 94 (21%) | 345 |
0.941 (1.00) |
0.749 (1.00) |
0.0367 (1.00) |
0.628 (1.00) |
0.00956 (1.00) |
0.167 (1.00) |
0.244 (1.00) |
0.128 (1.00) |
0.00957 (1.00) |
0.631 (1.00) |
0.00904 (1.00) |
0.155 (1.00) |
amp 8p11 23 | 155 (35%) | 284 |
0.758 (1.00) |
0.367 (1.00) |
0.488 (1.00) |
0.725 (1.00) |
0.714 (1.00) |
0.324 (1.00) |
0.764 (1.00) |
0.188 (1.00) |
0.285 (1.00) |
0.669 (1.00) |
0.561 (1.00) |
0.748 (1.00) |
amp 8p11 21 | 184 (42%) | 255 |
0.985 (1.00) |
0.291 (1.00) |
0.464 (1.00) |
0.607 (1.00) |
0.576 (1.00) |
0.252 (1.00) |
0.208 (1.00) |
0.322 (1.00) |
0.575 (1.00) |
0.26 (1.00) |
0.496 (1.00) |
0.412 (1.00) |
amp 8q12 1 | 230 (52%) | 209 |
0.769 (1.00) |
0.0556 (1.00) |
0.646 (1.00) |
0.683 (1.00) |
0.512 (1.00) |
0.072 (1.00) |
0.566 (1.00) |
0.0255 (1.00) |
0.25 (1.00) |
0.464 (1.00) |
0.401 (1.00) |
0.647 (1.00) |
amp 8q24 21 | 254 (58%) | 185 |
0.641 (1.00) |
0.0606 (1.00) |
0.0964 (1.00) |
0.37 (1.00) |
0.277 (1.00) |
0.0339 (1.00) |
0.287 (1.00) |
0.0897 (1.00) |
0.267 (1.00) |
0.369 (1.00) |
0.28 (1.00) |
0.69 (1.00) |
amp 11p15 5 | 90 (21%) | 349 |
0.992 (1.00) |
0.0199 (1.00) |
0.424 (1.00) |
0.183 (1.00) |
0.0483 (1.00) |
0.215 (1.00) |
0.724 (1.00) |
0.00084 (0.637) |
0.108 (1.00) |
0.437 (1.00) |
0.0451 (1.00) |
0.226 (1.00) |
amp 12p13 33 | 110 (25%) | 329 |
0.211 (1.00) |
0.372 (1.00) |
0.107 (1.00) |
0.128 (1.00) |
0.309 (1.00) |
0.173 (1.00) |
0.826 (1.00) |
0.873 (1.00) |
0.576 (1.00) |
0.443 (1.00) |
0.465 (1.00) |
0.596 (1.00) |
amp 17p11 2 | 43 (10%) | 396 |
0.538 (1.00) |
0.599 (1.00) |
0.675 (1.00) |
0.644 (1.00) |
0.77 (1.00) |
0.51 (1.00) |
0.749 (1.00) |
1 (1.00) |
1 (1.00) |
0.799 (1.00) |
0.693 (1.00) |
0.17 (1.00) |
amp 17q12 | 111 (25%) | 328 |
0.143 (1.00) |
0.313 (1.00) |
0.204 (1.00) |
0.165 (1.00) |
0.145 (1.00) |
0.00986 (1.00) |
0.272 (1.00) |
0.26 (1.00) |
1 (1.00) |
0.142 (1.00) |
0.16 (1.00) |
0.356 (1.00) |
amp 17q24 1 | 102 (23%) | 337 |
0.0379 (1.00) |
0.518 (1.00) |
0.65 (1.00) |
0.241 (1.00) |
0.497 (1.00) |
0.0551 (1.00) |
0.572 (1.00) |
0.0681 (1.00) |
0.549 (1.00) |
0.28 (1.00) |
0.676 (1.00) |
0.942 (1.00) |
amp 19p13 2 | 73 (17%) | 366 |
0.995 (1.00) |
0.885 (1.00) |
0.723 (1.00) |
0.633 (1.00) |
0.0326 (1.00) |
0.0275 (1.00) |
0.0718 (1.00) |
0.35 (1.00) |
0.421 (1.00) |
0.109 (1.00) |
0.728 (1.00) |
0.929 (1.00) |
amp 19q13 11 | 92 (21%) | 347 |
0.491 (1.00) |
0.913 (1.00) |
0.788 (1.00) |
0.679 (1.00) |
0.118 (1.00) |
0.0897 (1.00) |
0.0999 (1.00) |
0.494 (1.00) |
0.507 (1.00) |
0.767 (1.00) |
0.765 (1.00) |
1 (1.00) |
amp 20p12 1 | 203 (46%) | 236 |
0.0536 (1.00) |
0.749 (1.00) |
0.00081 (0.615) |
0.698 (1.00) |
0.396 (1.00) |
0.00607 (1.00) |
0.213 (1.00) |
0.0247 (1.00) |
0.0981 (1.00) |
0.0208 (1.00) |
0.304 (1.00) |
0.319 (1.00) |
amp 20p11 21 | 244 (56%) | 195 |
0.232 (1.00) |
0.552 (1.00) |
0.00143 (1.00) |
0.769 (1.00) |
0.197 (1.00) |
0.00365 (1.00) |
0.25 (1.00) |
0.00116 (0.867) |
0.258 (1.00) |
0.0184 (1.00) |
0.316 (1.00) |
0.482 (1.00) |
del 1p33 | 119 (27%) | 320 |
0.00859 (1.00) |
0.905 (1.00) |
0.0174 (1.00) |
0.4 (1.00) |
0.0141 (1.00) |
0.00983 (1.00) |
0.52 (1.00) |
0.0601 (1.00) |
0.566 (1.00) |
0.249 (1.00) |
0.00486 (1.00) |
0.367 (1.00) |
del 1p13 1 | 114 (26%) | 325 |
0.141 (1.00) |
0.459 (1.00) |
0.00697 (1.00) |
0.582 (1.00) |
0.00354 (1.00) |
0.00292 (1.00) |
0.327 (1.00) |
0.11 (1.00) |
1 (1.00) |
0.13 (1.00) |
0.000533 (0.409) |
0.299 (1.00) |
del 1q43 | 52 (12%) | 387 |
0.636 (1.00) |
0.259 (1.00) |
0.0725 (1.00) |
0.112 (1.00) |
0.476 (1.00) |
0.255 (1.00) |
0.768 (1.00) |
0.829 (1.00) |
0.316 (1.00) |
0.436 (1.00) |
0.284 (1.00) |
0.184 (1.00) |
del 2p21 | 16 (4%) | 423 |
0.713 (1.00) |
0.359 (1.00) |
0.156 (1.00) |
0.516 (1.00) |
0.288 (1.00) |
0.218 (1.00) |
0.611 (1.00) |
0.708 (1.00) |
1 (1.00) |
0.634 (1.00) |
0.339 (1.00) |
0.758 (1.00) |
del 2q22 1 | 24 (5%) | 415 |
0.585 (1.00) |
0.738 (1.00) |
0.241 (1.00) |
0.279 (1.00) |
0.0695 (1.00) |
0.627 (1.00) |
0.676 (1.00) |
1 (1.00) |
1 (1.00) |
0.726 (1.00) |
0.00903 (1.00) |
0.00726 (1.00) |
del 3p26 2 | 69 (16%) | 370 |
0.305 (1.00) |
0.436 (1.00) |
0.0582 (1.00) |
0.151 (1.00) |
0.00825 (1.00) |
0.0204 (1.00) |
0.896 (1.00) |
0.0528 (1.00) |
1 (1.00) |
0.339 (1.00) |
0.00605 (1.00) |
0.906 (1.00) |
del 3p14 2 | 85 (19%) | 354 |
0.62 (1.00) |
0.299 (1.00) |
0.223 (1.00) |
0.12 (1.00) |
0.037 (1.00) |
0.141 (1.00) |
0.545 (1.00) |
0.48 (1.00) |
1 (1.00) |
0.635 (1.00) |
0.0195 (1.00) |
0.719 (1.00) |
del 3q26 31 | 44 (10%) | 395 |
0.643 (1.00) |
0.397 (1.00) |
0.214 (1.00) |
0.19 (1.00) |
0.236 (1.00) |
0.442 (1.00) |
0.751 (1.00) |
0.244 (1.00) |
1 (1.00) |
0.775 (1.00) |
0.422 (1.00) |
0.816 (1.00) |
del 4q35 1 | 150 (34%) | 289 |
0.523 (1.00) |
0.0698 (1.00) |
0.0537 (1.00) |
0.329 (1.00) |
0.00295 (1.00) |
0.056 (1.00) |
0.314 (1.00) |
0.0774 (1.00) |
0.0394 (1.00) |
0.371 (1.00) |
0.000404 (0.312) |
0.357 (1.00) |
del 5q12 1 | 100 (23%) | 339 |
0.0627 (1.00) |
0.0469 (1.00) |
0.00533 (1.00) |
0.9 (1.00) |
0.00244 (1.00) |
0.0117 (1.00) |
0.173 (1.00) |
0.0688 (1.00) |
0.0115 (1.00) |
0.728 (1.00) |
0.00112 (0.842) |
0.477 (1.00) |
del 5q22 2 | 125 (28%) | 314 |
0.0819 (1.00) |
0.163 (1.00) |
0.0179 (1.00) |
0.977 (1.00) |
0.0125 (1.00) |
0.00326 (1.00) |
0.112 (1.00) |
0.163 (1.00) |
0.0227 (1.00) |
0.123 (1.00) |
0.00646 (1.00) |
0.264 (1.00) |
del 6p25 3 | 54 (12%) | 385 |
0.0716 (1.00) |
0.0767 (1.00) |
0.692 (1.00) |
0.416 (1.00) |
0.88 (1.00) |
0.278 (1.00) |
0.08 (1.00) |
0.4 (1.00) |
1 (1.00) |
0.387 (1.00) |
0.859 (1.00) |
0.0239 (1.00) |
del 6q26 | 61 (14%) | 378 |
0.0148 (1.00) |
0.888 (1.00) |
0.113 (1.00) |
0.452 (1.00) |
0.00616 (1.00) |
0.0688 (1.00) |
0.679 (1.00) |
1 (1.00) |
1 (1.00) |
0.152 (1.00) |
0.00102 (0.767) |
0.0619 (1.00) |
del 7q31 1 | 12 (3%) | 427 |
0.917 (1.00) |
0.972 (1.00) |
0.712 (1.00) |
0.603 (1.00) |
1 (1.00) |
0.164 (1.00) |
0.561 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.86 (1.00) |
0.48 (1.00) |
del 8q11 1 | 30 (7%) | 409 |
0.801 (1.00) |
0.401 (1.00) |
0.128 (1.00) |
0.618 (1.00) |
0.125 (1.00) |
0.169 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.451 (1.00) |
0.0996 (1.00) |
0.0418 (1.00) |
del 9p21 3 | 59 (13%) | 380 |
0.714 (1.00) |
0.0339 (1.00) |
0.838 (1.00) |
0.329 (1.00) |
0.296 (1.00) |
0.398 (1.00) |
0.208 (1.00) |
0.041 (1.00) |
1 (1.00) |
0.666 (1.00) |
0.0991 (1.00) |
0.429 (1.00) |
del 10p15 3 | 77 (18%) | 362 |
0.81 (1.00) |
0.429 (1.00) |
0.0017 (1.00) |
0.926 (1.00) |
0.00685 (1.00) |
0.00349 (1.00) |
0.802 (1.00) |
0.464 (1.00) |
0.0809 (1.00) |
0.672 (1.00) |
0.00251 (1.00) |
0.553 (1.00) |
del 10q21 1 | 94 (21%) | 345 |
0.571 (1.00) |
0.04 (1.00) |
0.00534 (1.00) |
0.979 (1.00) |
0.008 (1.00) |
0.0419 (1.00) |
0.908 (1.00) |
0.0605 (1.00) |
0.117 (1.00) |
0.0728 (1.00) |
0.00385 (1.00) |
0.628 (1.00) |
del 10q23 31 | 105 (24%) | 334 |
0.954 (1.00) |
0.00483 (1.00) |
0.00374 (1.00) |
0.918 (1.00) |
0.0319 (1.00) |
0.0141 (1.00) |
0.578 (1.00) |
0.0492 (1.00) |
0.144 (1.00) |
0.186 (1.00) |
0.00903 (1.00) |
0.782 (1.00) |
del 10q25 2 | 106 (24%) | 333 |
0.0754 (1.00) |
0.0629 (1.00) |
0.0338 (1.00) |
0.424 (1.00) |
0.00505 (1.00) |
0.0583 (1.00) |
1 (1.00) |
0.102 (1.00) |
0.146 (1.00) |
0.0801 (1.00) |
0.00369 (1.00) |
0.972 (1.00) |
del 12p13 2 | 57 (13%) | 382 |
0.021 (1.00) |
0.154 (1.00) |
0.127 (1.00) |
0.813 (1.00) |
0.0533 (1.00) |
0.094 (1.00) |
0.777 (1.00) |
0.02 (1.00) |
1 (1.00) |
0.432 (1.00) |
0.0485 (1.00) |
0.867 (1.00) |
del 15q11 2 | 170 (39%) | 269 |
0.916 (1.00) |
0.446 (1.00) |
0.0127 (1.00) |
0.969 (1.00) |
0.00877 (1.00) |
0.00964 (1.00) |
0.695 (1.00) |
0.0307 (1.00) |
0.0574 (1.00) |
0.432 (1.00) |
0.00614 (1.00) |
0.165 (1.00) |
del 15q15 2 | 164 (37%) | 275 |
0.712 (1.00) |
0.172 (1.00) |
0.0176 (1.00) |
0.964 (1.00) |
0.00624 (1.00) |
0.00159 (1.00) |
0.693 (1.00) |
0.029 (1.00) |
0.0515 (1.00) |
0.273 (1.00) |
0.00897 (1.00) |
0.161 (1.00) |
del 15q21 1 | 162 (37%) | 277 |
0.362 (1.00) |
0.422 (1.00) |
0.0757 (1.00) |
0.978 (1.00) |
0.0369 (1.00) |
0.00334 (1.00) |
0.552 (1.00) |
0.0291 (1.00) |
0.0497 (1.00) |
0.176 (1.00) |
0.0421 (1.00) |
0.0669 (1.00) |
del 15q22 33 | 154 (35%) | 285 |
0.929 (1.00) |
0.277 (1.00) |
0.00841 (1.00) |
0.566 (1.00) |
0.00808 (1.00) |
0.00298 (1.00) |
0.618 (1.00) |
0.0278 (1.00) |
0.0426 (1.00) |
0.413 (1.00) |
0.00765 (1.00) |
0.101 (1.00) |
del 16p13 3 | 54 (12%) | 385 |
0.00267 (1.00) |
0.503 (1.00) |
0.0318 (1.00) |
0.0354 (1.00) |
0.118 (1.00) |
0.172 (1.00) |
0.771 (1.00) |
1 (1.00) |
1 (1.00) |
0.329 (1.00) |
0.0727 (1.00) |
0.304 (1.00) |
del 16q23 1 | 58 (13%) | 381 |
0.0127 (1.00) |
0.862 (1.00) |
0.849 (1.00) |
0.539 (1.00) |
0.699 (1.00) |
0.294 (1.00) |
0.325 (1.00) |
0.408 (1.00) |
1 (1.00) |
0.795 (1.00) |
0.49 (1.00) |
0.108 (1.00) |
del 20p12 1 | 83 (19%) | 356 |
0.308 (1.00) |
0.646 (1.00) |
0.487 (1.00) |
0.59 (1.00) |
0.243 (1.00) |
0.979 (1.00) |
0.903 (1.00) |
0.0739 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.18 (1.00) |
0.369 (1.00) |
del 21q11 2 | 136 (31%) | 303 |
0.361 (1.00) |
0.779 (1.00) |
0.262 (1.00) |
0.37 (1.00) |
0.0357 (1.00) |
0.188 (1.00) |
0.837 (1.00) |
0.00213 (1.00) |
0.228 (1.00) |
0.625 (1.00) |
0.0238 (1.00) |
0.506 (1.00) |
P value = 0.00013 (Fisher's exact test), Q value = 0.1
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 |
AMP PEAK 5(7P21.2) MUTATED | 39 | 1 | 15 | 54 | 2 | 0 | 13 | 11 | 37 | 26 | 30 | 14 | 1 |
AMP PEAK 5(7P21.2) WILD-TYPE | 33 | 0 | 13 | 77 | 6 | 1 | 8 | 1 | 18 | 12 | 13 | 4 | 1 |
P value = 5e-05 (Fisher's exact test), Q value = 0.04
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 256 | 103 | 79 |
AMP PEAK 5(7P21.2) MUTATED | 122 | 70 | 56 |
AMP PEAK 5(7P21.2) WILD-TYPE | 134 | 33 | 23 |
P value = 0.000153 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
AMP PEAK 5(7P21.2) MUTATED | 241 | 2.5 (4.8) |
AMP PEAK 5(7P21.2) WILD-TYPE | 174 | 1.5 (3.9) |
P value = 8e-05 (Fisher's exact test), Q value = 0.063
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 |
AMP PEAK 12(13Q12.13) MUTATED | 42 | 0 | 14 | 68 | 2 | 1 | 11 | 11 | 38 | 24 | 36 | 15 | 0 |
AMP PEAK 12(13Q12.13) WILD-TYPE | 30 | 1 | 14 | 63 | 6 | 0 | 10 | 1 | 17 | 14 | 7 | 3 | 2 |
P value = 1.05e-07 (Fisher's exact test), Q value = 8.6e-05
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
AMP PEAK 12(13Q12.13) MUTATED | 249 | 17 |
AMP PEAK 12(13Q12.13) WILD-TYPE | 129 | 42 |
P value = 0.00014 (Fisher's exact test), Q value = 0.11
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 |
AMP PEAK 13(13Q22.1) MUTATED | 44 | 0 | 15 | 66 | 2 | 1 | 12 | 11 | 38 | 26 | 35 | 15 | 0 |
AMP PEAK 13(13Q22.1) WILD-TYPE | 28 | 1 | 13 | 65 | 6 | 0 | 9 | 1 | 17 | 12 | 8 | 3 | 2 |
P value = 1.05e-06 (Fisher's exact test), Q value = 0.00084
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
AMP PEAK 13(13Q22.1) MUTATED | 251 | 19 |
AMP PEAK 13(13Q22.1) WILD-TYPE | 127 | 40 |
P value = 0.00015 (Fisher's exact test), Q value = 0.12
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 256 | 103 | 79 |
AMP PEAK 14(16P11.2) MUTATED | 52 | 37 | 33 |
AMP PEAK 14(16P11.2) WILD-TYPE | 204 | 66 | 46 |
P value = 7.29e-05 (Wilcoxon-test), Q value = 0.058
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
AMP PEAK 14(16P11.2) MUTATED | 117 | 3.3 (6.2) |
AMP PEAK 14(16P11.2) WILD-TYPE | 298 | 1.6 (3.4) |
P value = 2e-04 (Fisher's exact test), Q value = 0.16
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 |
AMP PEAK 15(16Q12.1) MUTATED | 13 | 1 | 3 | 22 | 1 | 0 | 5 | 9 | 20 | 14 | 11 | 4 | 1 |
AMP PEAK 15(16Q12.1) WILD-TYPE | 59 | 0 | 25 | 109 | 7 | 1 | 16 | 3 | 35 | 24 | 32 | 14 | 1 |
P value = 0.00021 (Fisher's exact test), Q value = 0.16
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 256 | 103 | 79 |
AMP PEAK 15(16Q12.1) MUTATED | 45 | 35 | 28 |
AMP PEAK 15(16Q12.1) WILD-TYPE | 211 | 68 | 51 |
P value = 0.000209 (Wilcoxon-test), Q value = 0.16
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
AMP PEAK 15(16Q12.1) MUTATED | 104 | 3.2 (6.2) |
AMP PEAK 15(16Q12.1) WILD-TYPE | 311 | 1.7 (3.6) |
P value = 7.13e-07 (Fisher's exact test), Q value = 0.00058
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
AMP PEAK 23(20Q11.21) MUTATED | 286 | 25 |
AMP PEAK 23(20Q11.21) WILD-TYPE | 92 | 34 |
P value = 1.11e-07 (Fisher's exact test), Q value = 9e-05
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
AMP PEAK 24(20Q12) MUTATED | 288 | 24 |
AMP PEAK 24(20Q12) WILD-TYPE | 90 | 35 |
P value = 2.39e-07 (Fisher's exact test), Q value = 0.00019
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
AMP PEAK 25(20Q13.12) MUTATED | 290 | 25 |
AMP PEAK 25(20Q13.12) WILD-TYPE | 88 | 34 |
P value = 3e-05 (Fisher's exact test), Q value = 0.024
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 320 | 52 | 8 | 2 | 50 |
DEL PEAK 1(1P36.11) MUTATED | 105 | 35 | 4 | 0 | 18 |
DEL PEAK 1(1P36.11) WILD-TYPE | 215 | 17 | 4 | 2 | 32 |
P value = 0.00012 (Fisher's exact test), Q value = 0.094
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 320 | 52 | 8 | 2 | 50 |
DEL PEAK 10(4P16.2) MUTATED | 79 | 29 | 4 | 0 | 14 |
DEL PEAK 10(4P16.2) WILD-TYPE | 241 | 23 | 4 | 2 | 36 |
P value = 0.000114 (Wilcoxon-test), Q value = 0.09
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
DEL PEAK 10(4P16.2) MUTATED | 126 | 3.0 (4.7) |
DEL PEAK 10(4P16.2) WILD-TYPE | 289 | 1.7 (4.3) |
P value = 0.000104 (Wilcoxon-test), Q value = 0.082
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
DEL PEAK 11(4Q22.1) MUTATED | 136 | 2.9 (4.5) |
DEL PEAK 11(4Q22.1) WILD-TYPE | 279 | 1.7 (4.4) |
P value = 0.000235 (Wilcoxon-test), Q value = 0.18
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
DEL PEAK 14(5Q21.1) MUTATED | 116 | 3.0 (4.9) |
DEL PEAK 14(5Q21.1) WILD-TYPE | 299 | 1.7 (4.2) |
P value = 8e-05 (Fisher's exact test), Q value = 0.063
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 256 | 103 | 79 |
DEL PEAK 19(8P23.3) MUTATED | 84 | 50 | 48 |
DEL PEAK 19(8P23.3) WILD-TYPE | 172 | 53 | 31 |
P value = 2.63e-05 (Wilcoxon-test), Q value = 0.021
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
DEL PEAK 19(8P23.3) MUTATED | 177 | 2.9 (5.5) |
DEL PEAK 19(8P23.3) WILD-TYPE | 238 | 1.4 (3.3) |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
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 |
DEL PEAK 20(8P22) MUTATED | 23 | 0 | 9 | 42 | 2 | 0 | 10 | 8 | 30 | 25 | 29 | 14 | 1 |
DEL PEAK 20(8P22) WILD-TYPE | 49 | 1 | 19 | 89 | 6 | 1 | 11 | 4 | 25 | 13 | 14 | 4 | 1 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 256 | 103 | 79 |
DEL PEAK 20(8P22) MUTATED | 87 | 54 | 54 |
DEL PEAK 20(8P22) WILD-TYPE | 169 | 49 | 25 |
P value = 0.00014 (Fisher's exact test), Q value = 0.11
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 320 | 52 | 8 | 2 | 50 |
DEL PEAK 20(8P22) MUTATED | 130 | 38 | 5 | 1 | 20 |
DEL PEAK 20(8P22) WILD-TYPE | 190 | 14 | 3 | 1 | 30 |
P value = 2.68e-07 (Wilcoxon-test), Q value = 0.00022
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
DEL PEAK 20(8P22) MUTATED | 190 | 3.0 (5.4) |
DEL PEAK 20(8P22) WILD-TYPE | 225 | 1.3 (3.3) |
P value = 8.69e-06 (Fisher's exact test), Q value = 0.007
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
DEL PEAK 28(14Q31.1) MUTATED | 137 | 5 |
DEL PEAK 28(14Q31.1) WILD-TYPE | 241 | 54 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
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 |
DEL PEAK 35(17P12) MUTATED | 35 | 0 | 13 | 55 | 1 | 1 | 12 | 11 | 34 | 29 | 33 | 13 | 2 |
DEL PEAK 35(17P12) WILD-TYPE | 37 | 1 | 15 | 76 | 7 | 0 | 9 | 1 | 21 | 9 | 10 | 5 | 0 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 256 | 103 | 79 |
DEL PEAK 35(17P12) MUTATED | 118 | 69 | 57 |
DEL PEAK 35(17P12) WILD-TYPE | 138 | 34 | 22 |
P value = 2.35e-06 (Fisher's exact test), Q value = 0.0019
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
DEL PEAK 35(17P12) MUTATED | 227 | 16 |
DEL PEAK 35(17P12) WILD-TYPE | 151 | 43 |
P value = 1.18e-06 (Wilcoxon-test), Q value = 0.00095
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
DEL PEAK 35(17P12) MUTATED | 232 | 2.8 (5.4) |
DEL PEAK 35(17P12) WILD-TYPE | 183 | 1.2 (2.6) |
P value = 4.67e-05 (Wilcoxon-test), Q value = 0.037
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
DEL PEAK 36(17Q24.3) MUTATED | 64 | 3.0 (3.9) |
DEL PEAK 36(17Q24.3) WILD-TYPE | 351 | 1.9 (4.5) |
P value = 0.00014 (Fisher's exact test), Q value = 0.11
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 320 | 52 | 8 | 2 | 50 |
DEL PEAK 37(18P11.31) MUTATED | 160 | 40 | 8 | 1 | 27 |
DEL PEAK 37(18P11.31) WILD-TYPE | 160 | 12 | 0 | 1 | 23 |
P value = 3.4e-10 (Fisher's exact test), Q value = 2.8e-07
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
DEL PEAK 37(18P11.31) MUTATED | 227 | 10 |
DEL PEAK 37(18P11.31) WILD-TYPE | 151 | 49 |
P value = 5.78e-09 (Fisher's exact test), Q value = 4.7e-06
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
DEL PEAK 38(18Q12.2) MUTATED | 250 | 15 |
DEL PEAK 38(18Q12.2) WILD-TYPE | 128 | 44 |
P value = 5e-05 (Fisher's exact test), Q value = 0.04
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 |
DEL PEAK 39(18Q21.2) MUTATED | 39 | 0 | 16 | 71 | 2 | 1 | 11 | 11 | 39 | 30 | 37 | 15 | 2 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 33 | 1 | 12 | 60 | 6 | 0 | 10 | 1 | 16 | 8 | 6 | 3 | 0 |
P value = 2e-05 (Fisher's exact test), Q value = 0.016
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 256 | 103 | 79 |
DEL PEAK 39(18Q21.2) MUTATED | 141 | 76 | 62 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 115 | 27 | 17 |
P value = 7.32e-09 (Fisher's exact test), Q value = 6e-06
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 378 | 59 |
DEL PEAK 39(18Q21.2) MUTATED | 262 | 17 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 116 | 42 |
P value = 2.57e-05 (Wilcoxon-test), Q value = 0.02
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
DEL PEAK 39(18Q21.2) MUTATED | 267 | 2.4 (4.6) |
DEL PEAK 39(18Q21.2) WILD-TYPE | 148 | 1.5 (4.1) |
P value = 0.00012 (Fisher's exact test), Q value = 0.094
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 256 | 103 | 79 |
DEL PEAK 40(19P13.3) MUTATED | 23 | 15 | 23 |
DEL PEAK 40(19P13.3) WILD-TYPE | 233 | 88 | 56 |
P value = 2.52e-06 (Wilcoxon-test), Q value = 0.002
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
DEL PEAK 40(19P13.3) MUTATED | 59 | 4.3 (6.0) |
DEL PEAK 40(19P13.3) WILD-TYPE | 356 | 1.7 (4.0) |
P value = 0.000153 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 415 | 2.1 (4.4) |
DEL PEAK 43(22Q13.32) MUTATED | 145 | 2.8 (4.9) |
DEL PEAK 43(22Q13.32) WILD-TYPE | 270 | 1.7 (4.2) |
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Copy number data file = transformed.cor.cli.txt
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Clinical data file = COAD-TP.merged_data.txt
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Number of patients = 439
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Number of significantly focal cnvs = 68
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Number of selected clinical features = 12
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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 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.