This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 73 focal events and 13 clinical features across 408 patients, 26 significant findings detected with Q value < 0.25.
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amp_1q21.3 cnv correlated to 'PATHOLOGY_N_STAGE'.
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amp_1q23.3 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGY_N_STAGE'.
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amp_2p25.1 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_3p25.2 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_N_STAGE', and 'GENDER'.
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amp_6p22.3 cnv correlated to 'Time to Death'.
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amp_7p21.1 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', and 'RACE'.
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amp_11p13 cnv correlated to 'PATHOLOGY_N_STAGE'.
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del_3p14.2 cnv correlated to 'PATHOLOGY_N_STAGE' and 'RACE'.
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del_5q12.1 cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.
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del_6q21 cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.
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del_6q27 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.
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del_8p23.3 cnv correlated to 'RACE'.
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del_11p15.5 cnv correlated to 'YEARS_TO_BIRTH'.
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del_12q24.33 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.
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del_14q24.1 cnv correlated to 'PATHOLOGY_N_STAGE'.
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del_16p13.3 cnv correlated to 'RACE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
NUMBER PACK YEARS SMOKED |
NUMBER OF LYMPH NODES |
RACE | ETHNICITY | ||
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 | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
amp 3p25 2 | 190 (47%) | 218 |
0.3 (0.715) |
0.00214 (0.171) |
0.146 (0.56) |
0.0618 (0.434) |
0.00587 (0.223) |
0.757 (0.949) |
0.00469 (0.223) |
0.648 (0.913) |
0.0399 (0.364) |
0.245 (0.671) |
0.00954 (0.279) |
0.0146 (0.317) |
0.514 (0.855) |
amp 7p21 1 | 201 (49%) | 207 |
0.275 (0.695) |
0.0644 (0.434) |
0.00249 (0.171) |
0.13 (0.535) |
0.00297 (0.176) |
1 (1.00) |
0.574 (0.891) |
0.0365 (0.354) |
0.0943 (0.479) |
0.292 (0.712) |
0.0892 (0.479) |
0.00244 (0.171) |
1 (1.00) |
del 6q27 | 190 (47%) | 218 |
0.684 (0.943) |
0.158 (0.576) |
0.00152 (0.171) |
0.244 (0.671) |
0.00038 (0.171) |
0.358 (0.745) |
0.735 (0.949) |
0.363 (0.749) |
0.0375 (0.354) |
0.306 (0.723) |
0.00052 (0.171) |
0.294 (0.712) |
0.312 (0.725) |
amp 1q23 3 | 216 (53%) | 192 |
0.952 (1.00) |
0.00624 (0.228) |
0.0353 (0.354) |
0.576 (0.891) |
0.00255 (0.171) |
0.215 (0.659) |
0.431 (0.811) |
1 (1.00) |
0.0555 (0.418) |
0.354 (0.744) |
0.116 (0.529) |
0.132 (0.537) |
0.743 (0.949) |
del 3p14 2 | 117 (29%) | 291 |
0.719 (0.949) |
0.283 (0.706) |
0.385 (0.773) |
0.293 (0.712) |
0.0014 (0.171) |
0.143 (0.56) |
0.025 (0.352) |
0.803 (0.972) |
0.0828 (0.47) |
0.802 (0.972) |
0.862 (0.998) |
0.0019 (0.171) |
0.126 (0.529) |
del 5q12 1 | 202 (50%) | 206 |
0.0667 (0.443) |
0.00826 (0.27) |
0.0152 (0.317) |
0.159 (0.577) |
0.00166 (0.171) |
0.122 (0.529) |
1 (1.00) |
0.494 (0.847) |
0.285 (0.708) |
0.728 (0.949) |
0.00442 (0.223) |
0.07 (0.443) |
1 (1.00) |
del 6q21 | 190 (47%) | 218 |
0.984 (1.00) |
0.0909 (0.479) |
0.0102 (0.279) |
0.452 (0.841) |
0.00111 (0.171) |
0.116 (0.529) |
0.368 (0.749) |
0.649 (0.913) |
0.0645 (0.434) |
0.585 (0.891) |
0.00139 (0.171) |
0.293 (0.712) |
0.0881 (0.479) |
amp 1q21 3 | 202 (50%) | 206 |
0.458 (0.846) |
0.123 (0.529) |
0.0367 (0.354) |
0.874 (0.999) |
0.00575 (0.223) |
0.127 (0.529) |
0.91 (1.00) |
0.647 (0.913) |
0.0626 (0.434) |
0.495 (0.847) |
0.0163 (0.317) |
0.233 (0.671) |
1 (1.00) |
amp 2p25 1 | 152 (37%) | 256 |
0.555 (0.881) |
0.00525 (0.223) |
0.0528 (0.407) |
0.979 (1.00) |
0.0307 (0.352) |
0.202 (0.64) |
0.0632 (0.434) |
1 (1.00) |
0.973 (1.00) |
0.32 (0.728) |
0.0135 (0.312) |
0.259 (0.671) |
0.728 (0.949) |
amp 6p22 3 | 171 (42%) | 237 |
0.00271 (0.171) |
0.0364 (0.354) |
0.183 (0.603) |
0.237 (0.671) |
0.341 (0.736) |
1 (1.00) |
0.138 (0.55) |
1 (1.00) |
0.0214 (0.322) |
0.853 (0.993) |
0.85 (0.993) |
0.234 (0.671) |
0.17 (0.598) |
amp 11p13 | 51 (12%) | 357 |
0.369 (0.749) |
0.702 (0.943) |
0.0905 (0.479) |
0.707 (0.945) |
0.00214 (0.171) |
1 (1.00) |
0.865 (0.998) |
0.49 (0.847) |
0.254 (0.671) |
0.771 (0.96) |
0.0305 (0.352) |
0.472 (0.847) |
0.339 (0.733) |
del 8p23 3 | 243 (60%) | 165 |
0.701 (0.943) |
0.0281 (0.352) |
0.0464 (0.39) |
0.699 (0.943) |
0.0286 (0.352) |
0.352 (0.744) |
0.567 (0.885) |
0.246 (0.671) |
0.0831 (0.47) |
0.711 (0.948) |
0.254 (0.671) |
0.00575 (0.223) |
1 (1.00) |
del 11p15 5 | 211 (52%) | 197 |
0.463 (0.847) |
0.00242 (0.171) |
0.0752 (0.456) |
0.626 (0.913) |
0.0233 (0.34) |
0.55 (0.877) |
0.911 (1.00) |
0.819 (0.979) |
0.475 (0.847) |
0.806 (0.972) |
0.0498 (0.401) |
0.253 (0.671) |
0.503 (0.847) |
del 12q24 33 | 88 (22%) | 320 |
0.294 (0.712) |
0.306 (0.723) |
0.0801 (0.466) |
0.681 (0.941) |
0.0755 (0.456) |
0.445 (0.833) |
0.494 (0.847) |
0.404 (0.791) |
0.953 (1.00) |
0.884 (1.00) |
0.0056 (0.223) |
0.272 (0.689) |
0.691 (0.943) |
del 14q24 1 | 137 (34%) | 271 |
0.262 (0.677) |
0.0335 (0.354) |
0.326 (0.732) |
0.956 (1.00) |
0.00535 (0.223) |
1 (1.00) |
0.121 (0.529) |
0.0884 (0.479) |
0.0874 (0.479) |
0.0444 (0.386) |
0.0629 (0.434) |
0.618 (0.912) |
1 (1.00) |
del 16p13 3 | 174 (43%) | 234 |
0.745 (0.949) |
0.097 (0.487) |
0.231 (0.671) |
0.0798 (0.466) |
0.014 (0.317) |
1 (1.00) |
0.495 (0.847) |
0.164 (0.589) |
0.191 (0.616) |
0.698 (0.943) |
0.315 (0.725) |
0.00532 (0.223) |
0.738 (0.949) |
amp 1p34 2 | 101 (25%) | 307 |
0.299 (0.715) |
0.0182 (0.317) |
0.184 (0.603) |
0.921 (1.00) |
0.0194 (0.317) |
1 (1.00) |
0.697 (0.943) |
0.793 (0.968) |
0.878 (1) |
0.271 (0.688) |
0.178 (0.603) |
0.0347 (0.354) |
0.695 (0.943) |
amp 3q26 33 | 218 (53%) | 190 |
0.455 (0.845) |
0.179 (0.603) |
0.591 (0.893) |
0.179 (0.603) |
0.185 (0.604) |
0.542 (0.874) |
0.573 (0.891) |
0.492 (0.847) |
0.0369 (0.354) |
0.431 (0.811) |
0.0898 (0.479) |
0.00734 (0.258) |
1 (1.00) |
amp 4p16 3 | 74 (18%) | 334 |
0.0655 (0.438) |
0.518 (0.857) |
0.0316 (0.352) |
0.0343 (0.354) |
0.109 (0.52) |
0.463 (0.847) |
0.884 (1.00) |
0.228 (0.671) |
0.041 (0.37) |
0.868 (0.998) |
0.0749 (0.456) |
0.0585 (0.431) |
0.66 (0.921) |
amp 4q13 3 | 62 (15%) | 346 |
0.108 (0.52) |
0.845 (0.99) |
0.165 (0.589) |
0.126 (0.529) |
0.677 (0.939) |
0.219 (0.666) |
0.0188 (0.317) |
0.751 (0.949) |
0.838 (0.986) |
0.826 (0.979) |
0.868 (0.998) |
0.915 (1.00) |
0.625 (0.913) |
amp 5p15 33 | 206 (50%) | 202 |
0.473 (0.847) |
0.415 (0.799) |
0.872 (0.998) |
0.856 (0.993) |
0.746 (0.949) |
0.0684 (0.443) |
1 (1.00) |
0.369 (0.749) |
0.0792 (0.466) |
0.908 (1.00) |
0.393 (0.782) |
0.0864 (0.479) |
1 (1.00) |
amp 6q21 | 35 (9%) | 373 |
0.0832 (0.47) |
0.495 (0.847) |
0.201 (0.637) |
0.405 (0.791) |
0.637 (0.913) |
1 (1.00) |
0.841 (0.987) |
0.678 (0.939) |
0.52 (0.857) |
0.316 (0.725) |
0.796 (0.97) |
0.494 (0.847) |
0.565 (0.884) |
amp 6q23 3 | 46 (11%) | 362 |
0.756 (0.949) |
0.157 (0.576) |
0.551 (0.877) |
0.949 (1.00) |
0.156 (0.576) |
0.629 (0.913) |
0.594 (0.893) |
1 (1.00) |
0.816 (0.979) |
0.791 (0.968) |
0.839 (0.986) |
0.209 (0.649) |
1 (1.00) |
amp 7p11 2 | 190 (47%) | 218 |
0.866 (0.998) |
0.0477 (0.39) |
0.231 (0.671) |
0.741 (0.949) |
0.0194 (0.317) |
1 (1.00) |
1 (1.00) |
0.167 (0.591) |
0.335 (0.733) |
0.967 (1.00) |
0.182 (0.603) |
0.0283 (0.352) |
0.738 (0.949) |
amp 8p11 23 | 124 (30%) | 284 |
0.751 (0.949) |
0.405 (0.791) |
0.782 (0.965) |
0.557 (0.881) |
0.125 (0.529) |
0.731 (0.949) |
1 (1.00) |
1 (1.00) |
0.256 (0.671) |
0.247 (0.671) |
0.475 (0.847) |
0.356 (0.744) |
0.132 (0.537) |
amp 8p11 21 | 140 (34%) | 268 |
0.0371 (0.354) |
0.52 (0.857) |
0.871 (0.998) |
0.566 (0.885) |
0.29 (0.712) |
0.00866 (0.274) |
0.408 (0.794) |
0.471 (0.847) |
0.357 (0.745) |
0.316 (0.725) |
0.338 (0.733) |
0.329 (0.732) |
0.486 (0.847) |
amp 8q22 3 | 264 (65%) | 144 |
0.697 (0.943) |
0.0687 (0.443) |
0.857 (0.993) |
0.854 (0.993) |
0.398 (0.786) |
1 (1.00) |
0.638 (0.913) |
1 (1.00) |
0.0774 (0.459) |
0.266 (0.682) |
0.308 (0.725) |
0.252 (0.671) |
0.729 (0.949) |
amp 8q24 21 | 254 (62%) | 154 |
0.7 (0.943) |
0.269 (0.686) |
0.885 (1.00) |
0.774 (0.961) |
0.322 (0.73) |
1 (1.00) |
0.563 (0.883) |
1 (1.00) |
0.336 (0.733) |
0.299 (0.715) |
0.33 (0.732) |
0.373 (0.755) |
0.739 (0.949) |
amp 9p24 1 | 88 (22%) | 320 |
0.355 (0.744) |
0.278 (0.697) |
0.871 (0.998) |
0.689 (0.943) |
0.709 (0.946) |
0.425 (0.811) |
0.494 (0.847) |
0.0898 (0.479) |
0.258 (0.671) |
0.172 (0.601) |
0.93 (1.00) |
0.0494 (0.4) |
0.414 (0.799) |
amp 10p14 | 182 (45%) | 226 |
0.728 (0.949) |
0.0082 (0.27) |
0.626 (0.913) |
0.793 (0.968) |
0.0727 (0.454) |
1 (1.00) |
0.429 (0.811) |
0.252 (0.671) |
0.0691 (0.443) |
0.359 (0.745) |
0.293 (0.712) |
0.62 (0.912) |
1 (1.00) |
amp 11q13 3 | 135 (33%) | 273 |
0.479 (0.847) |
0.0117 (0.299) |
0.231 (0.671) |
0.355 (0.744) |
0.321 (0.728) |
1 (1.00) |
0.283 (0.706) |
0.327 (0.732) |
0.541 (0.874) |
0.667 (0.926) |
0.546 (0.874) |
0.0473 (0.39) |
0.724 (0.949) |
amp 11q22 2 | 71 (17%) | 337 |
0.591 (0.893) |
0.0618 (0.434) |
0.11 (0.523) |
0.753 (0.949) |
0.0743 (0.456) |
1 (1.00) |
0.883 (1.00) |
0.22 (0.666) |
0.876 (1) |
0.227 (0.671) |
0.295 (0.712) |
0.128 (0.529) |
1 (1.00) |
amp 12p12 1 | 132 (32%) | 276 |
0.611 (0.907) |
0.0203 (0.321) |
0.168 (0.592) |
0.415 (0.799) |
0.546 (0.874) |
1 (1.00) |
1 (1.00) |
0.476 (0.847) |
0.83 (0.983) |
0.531 (0.873) |
0.584 (0.891) |
0.836 (0.986) |
0.725 (0.949) |
amp 12q15 | 118 (29%) | 290 |
0.734 (0.949) |
0.0155 (0.317) |
0.735 (0.949) |
0.699 (0.943) |
0.951 (1.00) |
0.754 (0.949) |
0.458 (0.846) |
1 (1.00) |
0.551 (0.877) |
0.52 (0.857) |
0.877 (1) |
0.256 (0.671) |
1 (1.00) |
amp 13q22 1 | 128 (31%) | 280 |
0.389 (0.777) |
0.0503 (0.401) |
0.583 (0.891) |
0.563 (0.883) |
0.7 (0.943) |
0.751 (0.949) |
0.0699 (0.443) |
0.629 (0.913) |
0.0319 (0.352) |
0.8 (0.972) |
0.546 (0.874) |
0.0249 (0.352) |
1 (1.00) |
amp 16p13 2 | 87 (21%) | 321 |
0.0866 (0.479) |
0.356 (0.744) |
0.178 (0.603) |
0.0106 (0.279) |
0.115 (0.529) |
0.238 (0.671) |
1 (1.00) |
0.586 (0.891) |
0.213 (0.656) |
0.414 (0.799) |
0.176 (0.603) |
0.245 (0.671) |
0.691 (0.943) |
amp 16p11 2 | 98 (24%) | 310 |
0.429 (0.811) |
0.382 (0.768) |
0.0453 (0.39) |
0.0378 (0.354) |
0.0415 (0.372) |
0.139 (0.55) |
1 (1.00) |
0.792 (0.968) |
0.0575 (0.426) |
0.831 (0.983) |
0.0428 (0.378) |
0.0194 (0.317) |
0.694 (0.943) |
amp 16q22 1 | 108 (26%) | 300 |
0.356 (0.744) |
0.124 (0.529) |
0.109 (0.52) |
0.043 (0.378) |
0.351 (0.744) |
0.135 (0.544) |
0.0561 (0.419) |
0.793 (0.968) |
0.984 (1.00) |
0.978 (1.00) |
0.925 (1.00) |
0.131 (0.537) |
1 (1.00) |
amp 17p11 2 | 88 (22%) | 320 |
0.167 (0.591) |
0.496 (0.847) |
0.339 (0.733) |
0.635 (0.913) |
0.113 (0.527) |
0.456 (0.845) |
0.587 (0.891) |
1 (1.00) |
0.0308 (0.352) |
0.432 (0.811) |
0.148 (0.562) |
0.539 (0.874) |
1 (1.00) |
amp 17q11 2 | 174 (43%) | 234 |
0.537 (0.874) |
0.0326 (0.354) |
0.147 (0.56) |
0.89 (1.00) |
0.0359 (0.354) |
0.536 (0.874) |
0.734 (0.949) |
0.253 (0.671) |
0.214 (0.656) |
0.988 (1.00) |
0.103 (0.513) |
0.241 (0.671) |
0.501 (0.847) |
amp 17q12 | 165 (40%) | 243 |
0.219 (0.666) |
0.064 (0.434) |
0.32 (0.728) |
0.2 (0.637) |
0.105 (0.519) |
1 (1.00) |
0.819 (0.979) |
0.163 (0.589) |
0.0961 (0.485) |
0.229 (0.671) |
0.27 (0.686) |
0.587 (0.891) |
0.164 (0.589) |
amp 17q23 3 | 194 (48%) | 214 |
0.235 (0.671) |
0.0507 (0.401) |
0.0261 (0.352) |
0.315 (0.725) |
0.0233 (0.34) |
1 (1.00) |
0.369 (0.749) |
1 (1.00) |
0.121 (0.529) |
0.503 (0.847) |
0.0302 (0.352) |
0.399 (0.786) |
0.316 (0.725) |
amp 19q12 | 164 (40%) | 244 |
0.205 (0.643) |
0.231 (0.671) |
0.0933 (0.479) |
0.14 (0.55) |
0.108 (0.52) |
0.759 (0.951) |
0.422 (0.81) |
0.241 (0.671) |
0.632 (0.913) |
0.0526 (0.407) |
0.0172 (0.317) |
0.704 (0.944) |
1 (1.00) |
amp 19q13 43 | 155 (38%) | 253 |
0.365 (0.749) |
0.459 (0.847) |
0.0932 (0.479) |
0.0392 (0.361) |
0.0524 (0.407) |
0.539 (0.874) |
0.643 (0.913) |
0.153 (0.572) |
0.636 (0.913) |
0.615 (0.911) |
0.0129 (0.312) |
0.592 (0.893) |
1 (1.00) |
amp 20q11 21 | 263 (64%) | 145 |
0.987 (1.00) |
0.15 (0.566) |
0.31 (0.725) |
0.843 (0.989) |
0.0197 (0.317) |
0.75 (0.949) |
0.29 (0.712) |
0.475 (0.847) |
0.767 (0.958) |
0.945 (1.00) |
0.212 (0.655) |
0.00966 (0.279) |
0.296 (0.714) |
amp 22q12 2 | 87 (21%) | 321 |
0.105 (0.519) |
0.503 (0.847) |
0.144 (0.56) |
0.647 (0.913) |
0.241 (0.671) |
1 (1.00) |
0.891 (1.00) |
1 (1.00) |
0.0833 (0.47) |
0.856 (0.993) |
0.0101 (0.279) |
0.232 (0.671) |
0.399 (0.786) |
del 1p36 11 | 91 (22%) | 317 |
0.863 (0.998) |
0.536 (0.874) |
0.979 (1.00) |
0.337 (0.733) |
0.0318 (0.352) |
0.25 (0.671) |
0.893 (1.00) |
0.585 (0.891) |
0.78 (0.965) |
0.949 (1.00) |
0.606 (0.904) |
0.112 (0.527) |
0.422 (0.81) |
del 1q32 1 | 72 (18%) | 336 |
0.545 (0.874) |
0.978 (1.00) |
0.181 (0.603) |
0.894 (1.00) |
0.0936 (0.479) |
0.686 (0.943) |
0.184 (0.603) |
0.221 (0.667) |
0.931 (1.00) |
0.184 (0.603) |
0.125 (0.529) |
0.478 (0.847) |
0.208 (0.648) |
del 2q22 1 | 134 (33%) | 274 |
0.294 (0.712) |
0.824 (0.979) |
0.93 (1.00) |
0.662 (0.923) |
0.556 (0.881) |
0.186 (0.605) |
0.187 (0.605) |
0.806 (0.972) |
0.784 (0.965) |
0.107 (0.52) |
0.286 (0.71) |
0.631 (0.913) |
0.486 (0.847) |
del 2q34 | 174 (43%) | 234 |
0.618 (0.912) |
0.929 (1.00) |
0.409 (0.794) |
0.467 (0.847) |
0.0609 (0.434) |
0.757 (0.949) |
0.428 (0.811) |
0.644 (0.913) |
0.612 (0.907) |
0.682 (0.942) |
0.0922 (0.479) |
0.199 (0.637) |
0.503 (0.847) |
del 2q37 1 | 207 (51%) | 201 |
0.621 (0.912) |
0.762 (0.953) |
0.125 (0.529) |
0.779 (0.965) |
0.0214 (0.322) |
1 (1.00) |
0.0717 (0.451) |
0.366 (0.749) |
0.719 (0.949) |
0.465 (0.847) |
0.0461 (0.39) |
0.311 (0.725) |
0.175 (0.603) |
del 4q22 1 | 161 (39%) | 247 |
0.302 (0.719) |
0.029 (0.352) |
0.249 (0.671) |
0.312 (0.725) |
0.0596 (0.434) |
0.334 (0.733) |
0.73 (0.949) |
0.488 (0.847) |
0.0938 (0.479) |
0.792 (0.968) |
0.278 (0.697) |
0.0609 (0.434) |
0.493 (0.847) |
del 4q34 2 | 177 (43%) | 231 |
0.888 (1.00) |
0.0684 (0.443) |
0.0933 (0.479) |
0.118 (0.529) |
0.0157 (0.317) |
1 (1.00) |
0.91 (1.00) |
0.821 (0.979) |
0.402 (0.79) |
0.208 (0.648) |
0.224 (0.671) |
0.0805 (0.466) |
0.184 (0.603) |
del 6p25 3 | 106 (26%) | 302 |
0.631 (0.913) |
0.124 (0.529) |
0.586 (0.891) |
0.0733 (0.455) |
0.0768 (0.458) |
1 (1.00) |
0.305 (0.723) |
0.117 (0.529) |
0.0606 (0.434) |
0.846 (0.99) |
0.154 (0.572) |
0.0103 (0.279) |
0.249 (0.671) |
del 7q36 3 | 60 (15%) | 348 |
0.164 (0.589) |
0.752 (0.949) |
0.737 (0.949) |
0.513 (0.855) |
0.361 (0.749) |
1 (1.00) |
0.43 (0.811) |
0.332 (0.733) |
0.519 (0.857) |
0.621 (0.912) |
0.612 (0.907) |
0.636 (0.913) |
0.146 (0.56) |
del 8p21 3 | 252 (62%) | 156 |
0.392 (0.781) |
0.0313 (0.352) |
0.03 (0.352) |
0.151 (0.567) |
0.0555 (0.418) |
0.128 (0.529) |
0.356 (0.744) |
0.349 (0.744) |
0.193 (0.619) |
0.586 (0.891) |
0.259 (0.671) |
0.0381 (0.354) |
1 (1.00) |
del 9p23 | 177 (43%) | 231 |
0.881 (1.00) |
0.321 (0.728) |
0.739 (0.949) |
0.968 (1.00) |
0.803 (0.972) |
1 (1.00) |
0.734 (0.949) |
0.647 (0.913) |
0.276 (0.696) |
0.326 (0.732) |
0.777 (0.964) |
0.955 (1.00) |
1 (1.00) |
del 9p21 3 | 239 (59%) | 169 |
0.433 (0.813) |
0.0546 (0.418) |
0.815 (0.979) |
0.87 (0.998) |
0.819 (0.979) |
0.757 (0.949) |
0.494 (0.847) |
0.648 (0.913) |
0.136 (0.546) |
0.554 (0.881) |
0.587 (0.891) |
0.831 (0.983) |
0.497 (0.847) |
del 9q22 33 | 178 (44%) | 230 |
0.587 (0.891) |
0.25 (0.671) |
0.633 (0.913) |
0.502 (0.847) |
0.707 (0.945) |
0.542 (0.874) |
0.821 (0.979) |
0.648 (0.913) |
0.546 (0.874) |
0.0889 (0.479) |
0.69 (0.943) |
0.43 (0.811) |
0.738 (0.949) |
del 10p11 21 | 74 (18%) | 334 |
0.147 (0.56) |
0.154 (0.572) |
0.983 (1.00) |
0.638 (0.913) |
0.116 (0.529) |
0.407 (0.793) |
0.884 (1.00) |
0.773 (0.961) |
0.466 (0.847) |
0.644 (0.913) |
0.664 (0.924) |
0.0344 (0.354) |
1 (1.00) |
del 10q23 31 | 168 (41%) | 240 |
0.117 (0.529) |
0.0174 (0.317) |
0.601 (0.9) |
0.907 (1.00) |
0.139 (0.55) |
0.339 (0.733) |
1 (1.00) |
0.816 (0.979) |
0.265 (0.68) |
0.802 (0.972) |
0.121 (0.529) |
0.0467 (0.39) |
0.743 (0.949) |
del 11q23 3 | 153 (38%) | 255 |
0.449 (0.838) |
0.241 (0.671) |
0.898 (1.00) |
0.103 (0.513) |
0.467 (0.847) |
0.75 (0.949) |
0.561 (0.883) |
0.242 (0.671) |
0.602 (0.9) |
0.837 (0.986) |
0.352 (0.744) |
0.338 (0.733) |
0.728 (0.949) |
del 11q25 | 144 (35%) | 264 |
0.856 (0.993) |
0.449 (0.838) |
0.783 (0.965) |
0.14 (0.55) |
0.948 (1.00) |
1 (1.00) |
0.48 (0.847) |
0.343 (0.738) |
0.561 (0.883) |
0.378 (0.761) |
0.242 (0.671) |
0.179 (0.603) |
0.504 (0.847) |
del 12p13 1 | 68 (17%) | 340 |
0.478 (0.847) |
0.397 (0.786) |
0.375 (0.757) |
0.134 (0.54) |
0.511 (0.855) |
0.651 (0.914) |
0.228 (0.671) |
1 (1.00) |
0.224 (0.671) |
0.719 (0.949) |
0.258 (0.671) |
0.924 (1.00) |
0.656 (0.92) |
del 13q14 2 | 156 (38%) | 252 |
0.769 (0.959) |
0.204 (0.641) |
0.367 (0.749) |
0.244 (0.671) |
0.176 (0.603) |
0.335 (0.733) |
0.729 (0.949) |
1 (1.00) |
0.66 (0.921) |
0.597 (0.896) |
0.257 (0.671) |
0.0134 (0.312) |
0.298 (0.715) |
del 15q13 1 | 160 (39%) | 248 |
0.633 (0.913) |
0.508 (0.851) |
0.481 (0.847) |
0.355 (0.744) |
0.157 (0.576) |
0.737 (0.949) |
0.646 (0.913) |
0.241 (0.671) |
0.126 (0.529) |
0.182 (0.603) |
0.246 (0.671) |
0.0209 (0.322) |
0.325 (0.732) |
del 16q23 1 | 119 (29%) | 289 |
0.542 (0.874) |
0.264 (0.68) |
0.559 (0.882) |
0.823 (0.979) |
0.203 (0.64) |
0.482 (0.847) |
0.0476 (0.39) |
0.804 (0.972) |
0.0336 (0.354) |
0.328 (0.732) |
0.226 (0.671) |
0.122 (0.529) |
0.128 (0.529) |
del 17p12 | 208 (51%) | 200 |
0.52 (0.857) |
0.0135 (0.312) |
0.593 (0.893) |
0.263 (0.678) |
0.329 (0.732) |
0.538 (0.874) |
0.368 (0.749) |
0.172 (0.601) |
0.794 (0.968) |
0.578 (0.891) |
0.477 (0.847) |
0.545 (0.874) |
0.336 (0.733) |
del 18q23 | 179 (44%) | 229 |
0.118 (0.529) |
0.396 (0.786) |
0.627 (0.913) |
0.595 (0.894) |
0.823 (0.979) |
0.0264 (0.352) |
0.498 (0.847) |
0.252 (0.671) |
0.966 (1.00) |
0.227 (0.671) |
0.856 (0.993) |
0.696 (0.943) |
0.512 (0.855) |
del 19p13 3 | 145 (36%) | 263 |
0.314 (0.725) |
0.495 (0.847) |
0.0148 (0.317) |
0.0167 (0.317) |
0.0267 (0.352) |
0.0171 (0.317) |
0.64 (0.913) |
0.154 (0.572) |
0.0181 (0.317) |
0.576 (0.891) |
0.18 (0.603) |
0.183 (0.603) |
0.0759 (0.456) |
del 22q13 32 | 188 (46%) | 220 |
0.427 (0.811) |
0.106 (0.52) |
0.147 (0.56) |
0.363 (0.749) |
0.0279 (0.352) |
1 (1.00) |
0.822 (0.979) |
0.0692 (0.443) |
0.0269 (0.352) |
0.723 (0.949) |
0.241 (0.671) |
0.0306 (0.352) |
0.313 (0.725) |
del xp11 3 | 91 (22%) | 317 |
0.748 (0.949) |
0.187 (0.605) |
0.921 (1.00) |
0.386 (0.773) |
0.499 (0.847) |
1 (1.00) |
1 (1.00) |
0.784 (0.965) |
0.608 (0.905) |
0.736 (0.949) |
0.918 (1.00) |
0.468 (0.847) |
0.69 (0.943) |
del xq21 33 | 84 (21%) | 324 |
0.111 (0.523) |
0.346 (0.743) |
0.499 (0.847) |
0.659 (0.921) |
0.982 (1.00) |
0.128 (0.529) |
0.58 (0.891) |
0.577 (0.891) |
0.461 (0.847) |
0.7 (0.943) |
0.49 (0.847) |
0.255 (0.671) |
0.0917 (0.479) |
P value = 0.00575 (Fisher's exact test), Q value = 0.22
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
AMP PEAK 2(1Q21.3) MUTATED | 101 | 29 | 41 | 7 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 135 | 18 | 34 | 1 |
P value = 0.00624 (Wilcoxon-test), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 68.1 (10.6) |
AMP PEAK 3(1Q23.3) MUTATED | 215 | 69.6 (9.9) |
AMP PEAK 3(1Q23.3) WILD-TYPE | 192 | 66.4 (11.1) |
P value = 0.00255 (Fisher's exact test), Q value = 0.17
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
AMP PEAK 3(1Q23.3) MUTATED | 111 | 30 | 43 | 8 |
AMP PEAK 3(1Q23.3) WILD-TYPE | 125 | 17 | 32 | 0 |
P value = 0.00525 (Wilcoxon-test), Q value = 0.22
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 68.1 (10.6) |
AMP PEAK 4(2P25.1) MUTATED | 151 | 70.1 (9.7) |
AMP PEAK 4(2P25.1) WILD-TYPE | 256 | 66.9 (11.0) |
P value = 0.00214 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 68.1 (10.6) |
AMP PEAK 5(3P25.2) MUTATED | 189 | 69.8 (10.6) |
AMP PEAK 5(3P25.2) WILD-TYPE | 218 | 66.6 (10.5) |
P value = 0.00587 (Fisher's exact test), Q value = 0.22
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
AMP PEAK 5(3P25.2) MUTATED | 94 | 22 | 45 | 6 |
AMP PEAK 5(3P25.2) WILD-TYPE | 142 | 25 | 30 | 2 |
P value = 0.00469 (Fisher's exact test), Q value = 0.22
nPatients | FEMALE | MALE |
---|---|---|
ALL | 107 | 301 |
AMP PEAK 5(3P25.2) MUTATED | 37 | 153 |
AMP PEAK 5(3P25.2) WILD-TYPE | 70 | 148 |
P value = 0.00271 (logrank test), Q value = 0.17
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 405 | 178 | 0.5 - 166.0 (17.6) |
AMP PEAK 10(6P22.3) MUTATED | 171 | 61 | 0.5 - 166.0 (19.1) |
AMP PEAK 10(6P22.3) WILD-TYPE | 234 | 117 | 0.7 - 163.3 (16.7) |
P value = 0.00249 (Fisher's exact test), Q value = 0.17
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 2 | 129 | 140 | 135 |
AMP PEAK 13(7P21.1) MUTATED | 1 | 50 | 68 | 82 |
AMP PEAK 13(7P21.1) WILD-TYPE | 1 | 79 | 72 | 53 |
P value = 0.00297 (Fisher's exact test), Q value = 0.18
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
AMP PEAK 13(7P21.1) MUTATED | 102 | 29 | 44 | 7 |
AMP PEAK 13(7P21.1) WILD-TYPE | 134 | 18 | 31 | 1 |
P value = 0.00244 (Fisher's exact test), Q value = 0.17
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 43 | 22 | 327 |
AMP PEAK 13(7P21.1) MUTATED | 11 | 13 | 171 |
AMP PEAK 13(7P21.1) WILD-TYPE | 32 | 9 | 156 |
P value = 0.00214 (Fisher's exact test), Q value = 0.17
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
AMP PEAK 21(11P13) MUTATED | 21 | 6 | 15 | 4 |
AMP PEAK 21(11P13) WILD-TYPE | 215 | 41 | 60 | 4 |
P value = 0.0014 (Fisher's exact test), Q value = 0.17
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
DEL PEAK 6(3P14.2) MUTATED | 64 | 21 | 16 | 6 |
DEL PEAK 6(3P14.2) WILD-TYPE | 172 | 26 | 59 | 2 |
P value = 0.0019 (Fisher's exact test), Q value = 0.17
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 43 | 22 | 327 |
DEL PEAK 6(3P14.2) MUTATED | 3 | 7 | 101 |
DEL PEAK 6(3P14.2) WILD-TYPE | 40 | 15 | 226 |
P value = 0.00166 (Fisher's exact test), Q value = 0.17
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
DEL PEAK 9(5Q12.1) MUTATED | 97 | 28 | 46 | 6 |
DEL PEAK 9(5Q12.1) WILD-TYPE | 139 | 19 | 29 | 2 |
P value = 0.00442 (Wilcoxon-test), Q value = 0.22
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 297 | 2.1 (7.0) |
DEL PEAK 9(5Q12.1) MUTATED | 151 | 2.9 (9.2) |
DEL PEAK 9(5Q12.1) WILD-TYPE | 146 | 1.2 (3.4) |
P value = 0.00111 (Fisher's exact test), Q value = 0.17
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
DEL PEAK 11(6Q21) MUTATED | 92 | 24 | 48 | 4 |
DEL PEAK 11(6Q21) WILD-TYPE | 144 | 23 | 27 | 4 |
P value = 0.00139 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 297 | 2.1 (7.0) |
DEL PEAK 11(6Q21) MUTATED | 146 | 3.0 (9.3) |
DEL PEAK 11(6Q21) WILD-TYPE | 151 | 1.2 (3.3) |
P value = 0.00152 (Fisher's exact test), Q value = 0.17
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 2 | 129 | 140 | 135 |
DEL PEAK 12(6Q27) MUTATED | 0 | 51 | 58 | 80 |
DEL PEAK 12(6Q27) WILD-TYPE | 2 | 78 | 82 | 55 |
P value = 0.00038 (Fisher's exact test), Q value = 0.17
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
DEL PEAK 12(6Q27) MUTATED | 93 | 23 | 50 | 5 |
DEL PEAK 12(6Q27) WILD-TYPE | 143 | 24 | 25 | 3 |
P value = 0.00052 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 297 | 2.1 (7.0) |
DEL PEAK 12(6Q27) MUTATED | 147 | 3.2 (9.6) |
DEL PEAK 12(6Q27) WILD-TYPE | 150 | 1.0 (2.4) |
P value = 0.00575 (Fisher's exact test), Q value = 0.22
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 43 | 22 | 327 |
DEL PEAK 14(8P23.3) MUTATED | 18 | 18 | 198 |
DEL PEAK 14(8P23.3) WILD-TYPE | 25 | 4 | 129 |
P value = 0.00242 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 68.1 (10.6) |
DEL PEAK 21(11P15.5) MUTATED | 210 | 69.5 (10.5) |
DEL PEAK 21(11P15.5) WILD-TYPE | 197 | 66.6 (10.6) |
P value = 0.0056 (Wilcoxon-test), Q value = 0.22
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 297 | 2.1 (7.0) |
DEL PEAK 25(12Q24.33) MUTATED | 64 | 3.1 (6.0) |
DEL PEAK 25(12Q24.33) WILD-TYPE | 233 | 1.8 (7.2) |
P value = 0.00535 (Fisher's exact test), Q value = 0.22
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
DEL PEAK 27(14Q24.1) MUTATED | 71 | 12 | 38 | 2 |
DEL PEAK 27(14Q24.1) WILD-TYPE | 165 | 35 | 37 | 6 |
P value = 0.00532 (Fisher's exact test), Q value = 0.22
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 43 | 22 | 327 |
DEL PEAK 29(16P13.3) MUTATED | 10 | 6 | 150 |
DEL PEAK 29(16P13.3) WILD-TYPE | 33 | 16 | 177 |
-
Copy number data file = all_lesions.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/22507728/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/22506467/BLCA-TP.merged_data.txt
-
Number of patients = 408
-
Number of significantly focal cnvs = 73
-
Number of selected clinical features = 13
-
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.