This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 85 focal events and 10 clinical features across 173 patients, 21 significant findings detected with Q value < 0.25.
-
amp_1q42.3 cnv correlated to 'GENDER'.
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amp_3q26.2 cnv correlated to 'RACE'.
-
amp_5p15.33 cnv correlated to 'PATHOLOGY_T_STAGE'.
-
amp_6q23.3 cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_M_STAGE'.
-
amp_8q24.21 cnv correlated to 'RACE'.
-
amp_9q34.3 cnv correlated to 'YEARS_TO_BIRTH'.
-
amp_12p12.1 cnv correlated to 'GENDER'.
-
amp_14q21.1 cnv correlated to 'PATHOLOGY_T_STAGE', 'GENDER', and 'RACE'.
-
amp_xq28 cnv correlated to 'RACE'.
-
del_3p14.3 cnv correlated to 'RACE'.
-
del_3p14.2 cnv correlated to 'RACE'.
-
del_9p21.3 cnv correlated to 'RACE'.
-
del_10p11.21 cnv correlated to 'RACE'.
-
del_10q21.1 cnv correlated to 'RACE'.
-
del_13q14.2 cnv correlated to 'RACE'.
-
del_xp21.1 cnv correlated to 'NEOPLASM_DISEASESTAGE'.
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del_xp11.3 cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'RACE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
NUMBER PACK YEARS SMOKED |
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 | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
amp 14q21 1 | 55 (32%) | 118 |
0.357 (0.908) |
0.223 (0.773) |
0.967 (1.00) |
0.00368 (0.177) |
0.513 (0.937) |
0.717 (0.993) |
0.000828 (0.103) |
0.64 (0.981) |
0.00438 (0.193) |
0.276 (0.865) |
amp 6q23 3 | 40 (23%) | 133 |
0.694 (0.991) |
0.42 (0.931) |
0.00374 (0.177) |
0.5 (0.936) |
0.206 (0.772) |
0.00093 (0.103) |
1 (1.00) |
0.846 (1.00) |
0.629 (0.977) |
1 (1.00) |
del xp11 3 | 69 (40%) | 104 |
0.815 (1.00) |
0.97 (1.00) |
0.00319 (0.177) |
0.189 (0.763) |
0.0172 (0.354) |
0.08 (0.615) |
0.122 (0.685) |
0.703 (0.993) |
0.00092 (0.103) |
1 (1.00) |
amp 1q42 3 | 87 (50%) | 86 |
0.514 (0.937) |
0.0148 (0.341) |
0.515 (0.937) |
0.331 (0.908) |
0.136 (0.715) |
0.165 (0.732) |
0.00197 (0.12) |
0.975 (1.00) |
0.731 (0.993) |
0.58 (0.961) |
amp 3q26 2 | 118 (68%) | 55 |
0.331 (0.908) |
0.035 (0.474) |
0.324 (0.908) |
0.0572 (0.546) |
0.768 (1.00) |
0.717 (0.993) |
0.155 (0.732) |
0.179 (0.751) |
2e-05 (0.017) |
0.14 (0.721) |
amp 5p15 33 | 89 (51%) | 84 |
0.0954 (0.639) |
0.0452 (0.506) |
0.317 (0.906) |
0.0035 (0.177) |
0.57 (0.958) |
1 (1.00) |
1 (1.00) |
0.612 (0.97) |
0.0262 (0.416) |
0.0815 (0.616) |
amp 8q24 21 | 136 (79%) | 37 |
0.778 (1.00) |
0.145 (0.732) |
0.372 (0.908) |
0.659 (0.987) |
0.155 (0.732) |
0.684 (0.987) |
0.0148 (0.341) |
0.371 (0.908) |
0.00097 (0.103) |
0.474 (0.935) |
amp 9q34 3 | 59 (34%) | 114 |
0.164 (0.732) |
0.00117 (0.11) |
0.636 (0.981) |
0.181 (0.751) |
0.417 (0.928) |
0.161 (0.732) |
0.0192 (0.354) |
0.0281 (0.418) |
0.0173 (0.354) |
0.549 (0.952) |
amp 12p12 1 | 74 (43%) | 99 |
0.183 (0.752) |
0.148 (0.732) |
0.0209 (0.379) |
0.00712 (0.275) |
0.253 (0.84) |
0.158 (0.732) |
0.00141 (0.11) |
0.33 (0.908) |
0.0133 (0.332) |
0.603 (0.965) |
amp xq28 | 64 (37%) | 109 |
0.481 (0.935) |
0.0452 (0.506) |
0.368 (0.908) |
0.48 (0.935) |
0.107 (0.649) |
0.721 (0.993) |
0.11 (0.649) |
0.239 (0.808) |
0.00453 (0.193) |
0.603 (0.965) |
del 3p14 3 | 116 (67%) | 57 |
0.886 (1.00) |
0.6 (0.965) |
0.412 (0.924) |
0.909 (1.00) |
0.528 (0.946) |
1 (1.00) |
0.485 (0.935) |
0.91 (1.00) |
0.0006 (0.103) |
0.166 (0.732) |
del 3p14 2 | 114 (66%) | 59 |
0.407 (0.922) |
0.371 (0.908) |
0.465 (0.935) |
0.919 (1.00) |
0.486 (0.935) |
0.722 (0.993) |
0.361 (0.908) |
0.81 (1.00) |
0.00185 (0.12) |
0.181 (0.751) |
del 9p21 3 | 131 (76%) | 42 |
0.398 (0.918) |
0.226 (0.777) |
0.177 (0.751) |
0.172 (0.738) |
0.865 (1.00) |
0.207 (0.772) |
0.0182 (0.354) |
0.181 (0.751) |
0.00026 (0.103) |
1 (1.00) |
del 10p11 21 | 45 (26%) | 128 |
0.162 (0.732) |
0.22 (0.772) |
0.572 (0.959) |
0.0525 (0.531) |
0.731 (0.993) |
0.459 (0.935) |
1 (1.00) |
0.158 (0.732) |
0.00149 (0.11) |
0.554 (0.952) |
del 10q21 1 | 40 (23%) | 133 |
0.366 (0.908) |
0.62 (0.975) |
0.504 (0.936) |
0.89 (1.00) |
0.319 (0.908) |
0.691 (0.989) |
0.798 (1.00) |
0.751 (0.993) |
0.00078 (0.103) |
0.554 (0.952) |
del 13q14 2 | 69 (40%) | 104 |
0.423 (0.934) |
0.00834 (0.29) |
0.744 (0.993) |
0.739 (0.993) |
0.475 (0.935) |
0.298 (0.882) |
0.122 (0.685) |
0.362 (0.908) |
0.00156 (0.11) |
1 (1.00) |
del xp21 1 | 65 (38%) | 108 |
0.487 (0.935) |
0.568 (0.958) |
0.0059 (0.239) |
0.531 (0.946) |
0.0664 (0.582) |
0.155 (0.732) |
0.256 (0.841) |
0.73 (0.993) |
0.0293 (0.425) |
0.595 (0.965) |
amp 1p34 2 | 37 (21%) | 136 |
0.925 (1.00) |
0.186 (0.757) |
0.715 (0.993) |
0.748 (0.993) |
0.75 (0.993) |
0.374 (0.908) |
0.789 (1.00) |
0.336 (0.908) |
0.501 (0.936) |
0.497 (0.936) |
amp 1q23 3 | 84 (49%) | 89 |
0.5 (0.936) |
0.164 (0.732) |
0.6 (0.965) |
0.18 (0.751) |
0.67 (0.987) |
0.0918 (0.63) |
0.0153 (0.342) |
0.687 (0.987) |
0.733 (0.993) |
0.595 (0.965) |
amp 2q14 2 | 55 (32%) | 118 |
0.611 (0.97) |
0.0498 (0.531) |
0.797 (1.00) |
0.589 (0.965) |
0.92 (1.00) |
0.446 (0.935) |
1 (1.00) |
0.802 (1.00) |
0.0618 (0.562) |
1 (1.00) |
amp 2q31 1 | 55 (32%) | 118 |
0.966 (1.00) |
0.307 (0.892) |
0.452 (0.935) |
0.794 (1.00) |
0.364 (0.908) |
1 (1.00) |
0.102 (0.648) |
0.672 (0.987) |
0.0608 (0.562) |
1 (1.00) |
amp 4q21 1 | 31 (18%) | 142 |
0.0264 (0.416) |
0.792 (1.00) |
0.351 (0.908) |
0.458 (0.935) |
0.409 (0.922) |
1 (1.00) |
0.774 (1.00) |
0.249 (0.829) |
0.401 (0.921) |
1 (1.00) |
amp 6p21 1 | 65 (38%) | 108 |
0.834 (1.00) |
0.35 (0.908) |
0.378 (0.908) |
0.794 (1.00) |
0.472 (0.935) |
0.719 (0.993) |
0.496 (0.936) |
0.967 (1.00) |
0.865 (1.00) |
0.548 (0.952) |
amp 7p11 2 | 117 (68%) | 56 |
0.639 (0.981) |
0.217 (0.772) |
0.834 (1.00) |
0.0804 (0.615) |
0.563 (0.956) |
0.726 (0.993) |
0.348 (0.908) |
0.722 (0.993) |
1 (1.00) |
0.547 (0.952) |
amp 7q21 2 | 107 (62%) | 66 |
0.891 (1.00) |
0.298 (0.882) |
0.875 (1.00) |
0.0172 (0.354) |
0.482 (0.935) |
0.482 (0.935) |
0.498 (0.936) |
0.497 (0.936) |
0.384 (0.908) |
0.284 (0.875) |
amp 8p23 1 | 50 (29%) | 123 |
0.779 (1.00) |
0.107 (0.649) |
0.836 (1.00) |
0.35 (0.908) |
0.463 (0.935) |
0.257 (0.841) |
0.0559 (0.54) |
0.389 (0.908) |
0.14 (0.721) |
0.542 (0.952) |
amp 8p11 21 | 81 (47%) | 92 |
0.688 (0.987) |
0.814 (1.00) |
0.378 (0.908) |
0.749 (0.993) |
0.781 (1.00) |
1 (1.00) |
0.663 (0.987) |
0.519 (0.937) |
0.134 (0.715) |
1 (1.00) |
amp 9p13 3 | 34 (20%) | 139 |
0.522 (0.938) |
0.764 (1.00) |
0.58 (0.961) |
0.2 (0.772) |
0.628 (0.977) |
1 (1.00) |
0.05 (0.531) |
0.17 (0.738) |
1 (1.00) |
1 (1.00) |
amp 11p13 | 49 (28%) | 124 |
0.199 (0.772) |
0.962 (1.00) |
0.481 (0.935) |
0.0533 (0.533) |
0.841 (1.00) |
0.114 (0.667) |
0.225 (0.777) |
0.376 (0.908) |
0.512 (0.937) |
0.558 (0.953) |
amp 11p13 | 46 (27%) | 127 |
0.0997 (0.648) |
0.809 (1.00) |
0.38 (0.908) |
0.297 (0.882) |
0.84 (1.00) |
0.013 (0.332) |
0.322 (0.908) |
0.0719 (0.601) |
0.0404 (0.498) |
0.563 (0.956) |
amp 11q13 3 | 95 (55%) | 78 |
0.505 (0.936) |
0.384 (0.908) |
0.772 (1.00) |
0.415 (0.925) |
0.891 (1.00) |
0.733 (0.993) |
1 (1.00) |
0.194 (0.764) |
0.0859 (0.628) |
0.0628 (0.562) |
amp 12q15 | 49 (28%) | 124 |
0.223 (0.773) |
0.808 (1.00) |
0.0728 (0.601) |
0.148 (0.732) |
0.16 (0.732) |
0.00954 (0.29) |
0.47 (0.935) |
0.762 (1.00) |
0.368 (0.908) |
1 (1.00) |
amp 13q22 1 | 62 (36%) | 111 |
0.713 (0.993) |
0.952 (1.00) |
0.442 (0.935) |
0.214 (0.772) |
0.681 (0.987) |
1 (1.00) |
1 (1.00) |
0.166 (0.732) |
1 (1.00) |
0.0426 (0.504) |
amp 15q26 1 | 54 (31%) | 119 |
0.743 (0.993) |
0.381 (0.908) |
0.481 (0.935) |
0.216 (0.772) |
0.612 (0.97) |
0.247 (0.826) |
1 (1.00) |
0.0188 (0.354) |
0.202 (0.772) |
0.542 (0.952) |
amp 17q12 | 71 (41%) | 102 |
0.869 (1.00) |
0.858 (1.00) |
0.101 (0.648) |
0.289 (0.876) |
0.156 (0.732) |
0.154 (0.732) |
0.117 (0.672) |
0.123 (0.687) |
0.119 (0.676) |
1 (1.00) |
amp 18p11 32 | 64 (37%) | 109 |
0.436 (0.935) |
0.217 (0.772) |
0.193 (0.764) |
0.0332 (0.463) |
0.395 (0.915) |
0.0763 (0.612) |
0.0385 (0.496) |
0.585 (0.965) |
0.0218 (0.386) |
1 (1.00) |
amp 18q11 2 | 56 (32%) | 117 |
0.383 (0.908) |
0.551 (0.952) |
0.461 (0.935) |
0.72 (0.993) |
0.683 (0.987) |
1 (1.00) |
0.817 (1.00) |
0.99 (1.00) |
0.291 (0.88) |
1 (1.00) |
amp 19p13 2 | 30 (17%) | 143 |
0.57 (0.958) |
0.545 (0.952) |
0.317 (0.906) |
0.586 (0.965) |
0.0272 (0.418) |
0.622 (0.975) |
0.0819 (0.616) |
0.538 (0.952) |
0.381 (0.908) |
1 (1.00) |
amp 19q12 | 51 (29%) | 122 |
0.167 (0.732) |
0.677 (0.987) |
0.885 (1.00) |
0.989 (1.00) |
0.813 (1.00) |
1 (1.00) |
0.156 (0.732) |
0.508 (0.937) |
0.469 (0.935) |
1 (1.00) |
del 1p36 11 | 70 (40%) | 103 |
0.669 (0.987) |
0.734 (0.993) |
0.131 (0.715) |
0.531 (0.946) |
0.0521 (0.531) |
0.738 (0.993) |
0.825 (1.00) |
0.807 (1.00) |
0.36 (0.908) |
0.549 (0.952) |
del 1p13 2 | 58 (34%) | 115 |
0.107 (0.649) |
0.241 (0.811) |
0.275 (0.865) |
0.936 (1.00) |
0.106 (0.649) |
1 (1.00) |
0.485 (0.935) |
0.304 (0.891) |
0.664 (0.987) |
0.548 (0.952) |
del 1q44 | 17 (10%) | 156 |
0.877 (1.00) |
0.334 (0.908) |
0.212 (0.772) |
0.372 (0.908) |
0.0253 (0.416) |
0.6 (0.965) |
1 (1.00) |
0.813 (1.00) |
0.635 (0.981) |
1 (1.00) |
del 2q22 1 | 52 (30%) | 121 |
0.853 (1.00) |
0.194 (0.764) |
0.653 (0.987) |
0.155 (0.732) |
0.931 (1.00) |
1 (1.00) |
0.472 (0.935) |
0.867 (1.00) |
0.488 (0.935) |
1 (1.00) |
del 2q33 3 | 32 (18%) | 141 |
0.405 (0.921) |
0.568 (0.958) |
0.505 (0.936) |
0.0257 (0.416) |
0.862 (1.00) |
0.206 (0.772) |
1 (1.00) |
0.45 (0.935) |
1 (1.00) |
1 (1.00) |
del 3p26 2 | 101 (58%) | 72 |
0.454 (0.935) |
0.846 (1.00) |
0.673 (0.987) |
0.667 (0.987) |
0.731 (0.993) |
0.482 (0.935) |
0.504 (0.936) |
0.462 (0.935) |
0.0437 (0.504) |
0.273 (0.865) |
del 3q11 1 | 32 (18%) | 141 |
0.662 (0.987) |
0.38 (0.908) |
0.473 (0.935) |
0.354 (0.908) |
0.265 (0.852) |
1 (1.00) |
0.575 (0.959) |
0.617 (0.975) |
0.496 (0.936) |
0.52 (0.937) |
del 3q26 31 | 15 (9%) | 158 |
0.2 (0.772) |
0.533 (0.946) |
0.0438 (0.504) |
0.0384 (0.496) |
0.0839 (0.626) |
0.209 (0.772) |
0.697 (0.993) |
0.338 (0.908) |
0.062 (0.562) |
1 (1.00) |
del 4p15 2 | 100 (58%) | 73 |
0.0313 (0.444) |
0.94 (1.00) |
0.927 (1.00) |
0.152 (0.732) |
0.877 (1.00) |
1 (1.00) |
0.824 (1.00) |
0.218 (0.772) |
0.59 (0.965) |
1 (1.00) |
del 4q22 1 | 100 (58%) | 73 |
0.125 (0.692) |
0.0554 (0.54) |
0.0847 (0.626) |
0.0506 (0.531) |
0.195 (0.764) |
0.0784 (0.615) |
0.266 (0.852) |
0.466 (0.935) |
0.347 (0.908) |
1 (1.00) |
del 4q34 3 | 94 (54%) | 79 |
0.0919 (0.63) |
0.0108 (0.29) |
0.172 (0.738) |
0.625 (0.975) |
0.0611 (0.562) |
0.496 (0.936) |
0.665 (0.987) |
0.994 (1.00) |
0.414 (0.925) |
0.611 (0.97) |
del 5q12 1 | 105 (61%) | 68 |
0.887 (1.00) |
0.381 (0.908) |
0.0295 (0.425) |
0.821 (1.00) |
0.804 (1.00) |
0.153 (0.732) |
0.267 (0.853) |
0.946 (1.00) |
0.792 (1.00) |
1 (1.00) |
del 6p25 3 | 70 (40%) | 103 |
0.211 (0.772) |
0.376 (0.908) |
0.618 (0.975) |
0.682 (0.987) |
0.164 (0.732) |
0.726 (0.993) |
1 (1.00) |
0.899 (1.00) |
0.133 (0.715) |
0.0472 (0.514) |
del 6q16 3 | 51 (29%) | 122 |
0.705 (0.993) |
0.52 (0.937) |
0.991 (1.00) |
0.933 (1.00) |
0.731 (0.993) |
1 (1.00) |
0.0554 (0.54) |
0.0869 (0.628) |
0.106 (0.649) |
1 (1.00) |
del 6q26 | 48 (28%) | 125 |
0.532 (0.946) |
0.728 (0.993) |
0.256 (0.841) |
0.35 (0.908) |
0.587 (0.965) |
0.446 (0.935) |
0.228 (0.78) |
0.22 (0.772) |
0.158 (0.732) |
1 (1.00) |
del 7q31 1 | 55 (32%) | 118 |
0.00855 (0.29) |
0.0351 (0.474) |
0.0717 (0.601) |
0.621 (0.975) |
0.619 (0.975) |
1 (1.00) |
0.102 (0.648) |
0.216 (0.772) |
0.642 (0.981) |
1 (1.00) |
del 7q36 3 | 66 (38%) | 107 |
0.389 (0.908) |
0.47 (0.935) |
0.141 (0.724) |
0.721 (0.993) |
0.31 (0.901) |
0.314 (0.906) |
1 (1.00) |
0.864 (1.00) |
0.736 (0.993) |
1 (1.00) |
del 8p23 2 | 81 (47%) | 92 |
0.852 (1.00) |
0.0439 (0.504) |
0.279 (0.868) |
0.654 (0.987) |
0.216 (0.772) |
1 (1.00) |
0.188 (0.763) |
0.066 (0.582) |
0.133 (0.715) |
1 (1.00) |
del 8p12 | 68 (39%) | 105 |
0.56 (0.955) |
0.83 (1.00) |
0.074 (0.605) |
1 (1.00) |
0.0899 (0.63) |
0.51 (0.937) |
0.369 (0.908) |
0.152 (0.732) |
0.578 (0.961) |
1 (1.00) |
del 9p23 | 102 (59%) | 71 |
0.934 (1.00) |
0.733 (0.993) |
0.102 (0.648) |
0.136 (0.715) |
0.134 (0.715) |
1 (1.00) |
0.00744 (0.275) |
0.596 (0.965) |
0.0187 (0.354) |
0.284 (0.875) |
del 10p15 3 | 48 (28%) | 125 |
0.136 (0.715) |
0.636 (0.981) |
0.844 (1.00) |
0.0775 (0.615) |
0.259 (0.843) |
0.724 (0.993) |
1 (1.00) |
0.745 (0.993) |
0.0256 (0.416) |
1 (1.00) |
del 10q23 31 | 59 (34%) | 114 |
0.876 (1.00) |
0.439 (0.935) |
0.914 (1.00) |
0.364 (0.908) |
0.625 (0.975) |
1 (1.00) |
0.487 (0.935) |
0.429 (0.934) |
0.0105 (0.29) |
0.293 (0.88) |
del 11p15 4 | 74 (43%) | 99 |
0.95 (1.00) |
0.355 (0.908) |
0.81 (1.00) |
0.368 (0.908) |
0.885 (1.00) |
1 (1.00) |
0.0752 (0.609) |
0.441 (0.935) |
0.0106 (0.29) |
1 (1.00) |
del 11q25 | 73 (42%) | 100 |
0.0944 (0.637) |
0.0718 (0.601) |
0.391 (0.909) |
0.662 (0.987) |
0.601 (0.965) |
0.489 (0.935) |
0.381 (0.908) |
0.612 (0.97) |
0.219 (0.772) |
1 (1.00) |
del 12q23 1 | 47 (27%) | 126 |
0.14 (0.721) |
0.427 (0.934) |
0.598 (0.965) |
0.481 (0.935) |
0.886 (1.00) |
0.7 (0.993) |
0.135 (0.715) |
0.357 (0.908) |
0.101 (0.648) |
1 (1.00) |
del 13q12 11 | 71 (41%) | 102 |
0.596 (0.965) |
0.0886 (0.628) |
0.739 (0.993) |
0.287 (0.876) |
0.82 (1.00) |
1 (1.00) |
0.265 (0.852) |
0.365 (0.908) |
0.0181 (0.354) |
1 (1.00) |
del 13q21 31 | 64 (37%) | 109 |
0.672 (0.987) |
0.279 (0.868) |
0.934 (1.00) |
0.679 (0.987) |
0.681 (0.987) |
0.482 (0.935) |
0.11 (0.649) |
0.673 (0.987) |
0.0108 (0.29) |
0.568 (0.958) |
del 14q23 3 | 49 (28%) | 124 |
0.553 (0.952) |
0.69 (0.988) |
0.577 (0.961) |
0.285 (0.875) |
0.387 (0.908) |
0.257 (0.841) |
1 (1.00) |
0.641 (0.981) |
0.388 (0.908) |
0.52 (0.937) |
del 15q11 2 | 59 (34%) | 114 |
0.987 (1.00) |
0.337 (0.908) |
0.699 (0.993) |
0.452 (0.935) |
0.655 (0.987) |
0.276 (0.865) |
1 (1.00) |
0.379 (0.908) |
1 (1.00) |
1 (1.00) |
del 16p13 3 | 63 (36%) | 110 |
0.11 (0.649) |
0.652 (0.987) |
0.543 (0.952) |
0.483 (0.935) |
0.0399 (0.498) |
1 (1.00) |
0.499 (0.936) |
0.674 (0.987) |
0.231 (0.788) |
0.0383 (0.496) |
del 16q23 1 | 80 (46%) | 93 |
0.676 (0.987) |
0.751 (0.993) |
0.305 (0.891) |
0.211 (0.772) |
0.203 (0.772) |
1 (1.00) |
0.386 (0.908) |
0.925 (1.00) |
0.103 (0.648) |
0.0628 (0.562) |
del 17p12 | 81 (47%) | 92 |
0.951 (1.00) |
0.0404 (0.498) |
0.3 (0.885) |
0.452 (0.935) |
0.452 (0.935) |
1 (1.00) |
0.382 (0.908) |
0.881 (1.00) |
0.0109 (0.29) |
0.558 (0.953) |
del 17q25 3 | 40 (23%) | 133 |
0.0521 (0.531) |
0.272 (0.865) |
0.41 (0.922) |
0.392 (0.909) |
0.362 (0.908) |
1 (1.00) |
0.798 (1.00) |
0.155 (0.732) |
0.182 (0.751) |
1 (1.00) |
del 18p11 23 | 56 (32%) | 117 |
0.656 (0.987) |
0.0883 (0.628) |
0.43 (0.934) |
0.0684 (0.594) |
0.381 (0.908) |
1 (1.00) |
0.348 (0.908) |
0.0418 (0.504) |
0.292 (0.88) |
1 (1.00) |
del 18q12 2 | 103 (60%) | 70 |
0.193 (0.764) |
0.212 (0.772) |
0.784 (1.00) |
0.47 (0.935) |
0.487 (0.935) |
0.741 (0.993) |
1 (1.00) |
0.109 (0.649) |
0.586 (0.965) |
1 (1.00) |
del 18q21 2 | 110 (64%) | 63 |
0.456 (0.935) |
0.383 (0.908) |
0.801 (1.00) |
0.861 (1.00) |
0.726 (0.993) |
1 (1.00) |
0.649 (0.987) |
0.155 (0.732) |
0.116 (0.669) |
0.262 (0.85) |
del 18q22 3 | 103 (60%) | 70 |
0.83 (1.00) |
0.315 (0.906) |
0.661 (0.987) |
0.215 (0.772) |
0.333 (0.908) |
1 (1.00) |
0.825 (1.00) |
0.171 (0.738) |
0.0989 (0.648) |
0.241 (0.811) |
del 19p13 3 | 88 (51%) | 85 |
0.739 (0.993) |
0.463 (0.935) |
0.638 (0.981) |
0.324 (0.908) |
0.472 (0.935) |
1 (1.00) |
0.0793 (0.615) |
0.0878 (0.628) |
0.28 (0.868) |
1 (1.00) |
del 19q11 | 46 (27%) | 127 |
0.947 (1.00) |
0.234 (0.794) |
0.849 (1.00) |
0.425 (0.934) |
0.218 (0.772) |
0.7 (0.993) |
0.322 (0.908) |
0.0728 (0.601) |
0.303 (0.891) |
1 (1.00) |
del 20p12 1 | 32 (18%) | 141 |
0.0279 (0.418) |
0.53 (0.946) |
0.833 (1.00) |
0.425 (0.934) |
0.518 (0.937) |
1 (1.00) |
0.575 (0.959) |
0.63 (0.977) |
1 (1.00) |
0.426 (0.934) |
del 21q11 2 | 99 (57%) | 74 |
0.708 (0.993) |
0.468 (0.935) |
0.404 (0.921) |
0.885 (1.00) |
0.791 (1.00) |
0.507 (0.936) |
1 (1.00) |
0.404 (0.921) |
0.175 (0.749) |
1 (1.00) |
del 21q21 1 | 101 (58%) | 72 |
0.398 (0.918) |
0.516 (0.937) |
0.745 (0.993) |
0.852 (1.00) |
0.906 (1.00) |
1 (1.00) |
0.662 (0.987) |
0.296 (0.882) |
0.593 (0.965) |
1 (1.00) |
del 21q22 12 | 101 (58%) | 72 |
0.336 (0.908) |
0.437 (0.935) |
0.685 (0.987) |
0.897 (1.00) |
0.749 (0.993) |
1 (1.00) |
0.504 (0.936) |
0.0908 (0.63) |
0.428 (0.934) |
1 (1.00) |
del 22q11 1 | 76 (44%) | 97 |
0.0464 (0.512) |
0.409 (0.922) |
0.115 (0.669) |
0.0103 (0.29) |
0.0141 (0.341) |
0.185 (0.757) |
1 (1.00) |
0.625 (0.975) |
0.0933 (0.634) |
1 (1.00) |
del xq11 2 | 40 (23%) | 133 |
0.55 (0.952) |
0.372 (0.908) |
0.387 (0.908) |
0.685 (0.987) |
0.403 (0.921) |
0.683 (0.987) |
0.442 (0.935) |
0.704 (0.993) |
0.44 (0.935) |
0.542 (0.952) |
del xq21 33 | 39 (23%) | 134 |
0.807 (1.00) |
0.558 (0.953) |
0.0229 (0.397) |
0.759 (1.00) |
0.221 (0.772) |
0.687 (0.987) |
0.191 (0.764) |
0.288 (0.876) |
0.347 (0.908) |
1 (1.00) |
P value = 0.00197 (Fisher's exact test), Q value = 0.12
nPatients | FEMALE | MALE |
---|---|---|
ALL | 24 | 149 |
AMP PEAK 3(1Q42.3) MUTATED | 5 | 82 |
AMP PEAK 3(1Q42.3) WILD-TYPE | 19 | 67 |
P value = 2e-05 (Fisher's exact test), Q value = 0.017
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 41 | 2 | 111 |
AMP PEAK 6(3Q26.2) MUTATED | 38 | 1 | 66 |
AMP PEAK 6(3Q26.2) WILD-TYPE | 3 | 1 | 45 |
P value = 0.0035 (Fisher's exact test), Q value = 0.18
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 31 | 36 | 85 | 5 |
AMP PEAK 8(5P15.33) MUTATED | 9 | 19 | 54 | 1 |
AMP PEAK 8(5P15.33) WILD-TYPE | 22 | 17 | 31 | 4 |
P value = 0.00374 (Fisher's exact test), Q value = 0.18
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 5 | 7 | 1 | 39 | 29 | 25 | 12 | 10 | 7 | 5 | 4 |
AMP PEAK 10(6Q23.3) MUTATED | 5 | 0 | 1 | 0 | 7 | 7 | 4 | 1 | 1 | 3 | 4 | 3 |
AMP PEAK 10(6Q23.3) WILD-TYPE | 3 | 5 | 6 | 1 | 32 | 22 | 21 | 11 | 9 | 4 | 1 | 1 |
P value = 0.00093 (Fisher's exact test), Q value = 0.1
nPatients | 0 | 1 |
---|---|---|
ALL | 126 | 9 |
AMP PEAK 10(6Q23.3) MUTATED | 27 | 7 |
AMP PEAK 10(6Q23.3) WILD-TYPE | 99 | 2 |
P value = 0.00097 (Fisher's exact test), Q value = 0.1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 41 | 2 | 111 |
AMP PEAK 15(8Q24.21) MUTATED | 39 | 1 | 79 |
AMP PEAK 15(8Q24.21) WILD-TYPE | 2 | 1 | 32 |
P value = 0.00117 (Wilcoxon-test), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 173 | 62.6 (12.1) |
AMP PEAK 17(9Q34.3) MUTATED | 59 | 58.5 (12.7) |
AMP PEAK 17(9Q34.3) WILD-TYPE | 114 | 64.7 (11.3) |
P value = 0.00141 (Fisher's exact test), Q value = 0.11
nPatients | FEMALE | MALE |
---|---|---|
ALL | 24 | 149 |
AMP PEAK 21(12P12.1) MUTATED | 3 | 71 |
AMP PEAK 21(12P12.1) WILD-TYPE | 21 | 78 |
P value = 0.00368 (Fisher's exact test), Q value = 0.18
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 31 | 36 | 85 | 5 |
AMP PEAK 24(14Q21.1) MUTATED | 4 | 16 | 26 | 4 |
AMP PEAK 24(14Q21.1) WILD-TYPE | 27 | 20 | 59 | 1 |
P value = 0.000828 (Fisher's exact test), Q value = 0.1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 24 | 149 |
AMP PEAK 24(14Q21.1) MUTATED | 1 | 54 |
AMP PEAK 24(14Q21.1) WILD-TYPE | 23 | 95 |
P value = 0.00438 (Fisher's exact test), Q value = 0.19
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 41 | 2 | 111 |
AMP PEAK 24(14Q21.1) MUTATED | 21 | 0 | 28 |
AMP PEAK 24(14Q21.1) WILD-TYPE | 20 | 2 | 83 |
P value = 0.00453 (Fisher's exact test), Q value = 0.19
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 41 | 2 | 111 |
AMP PEAK 31(XQ28) MUTATED | 24 | 1 | 35 |
AMP PEAK 31(XQ28) WILD-TYPE | 17 | 1 | 76 |
P value = 6e-04 (Fisher's exact test), Q value = 0.1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 41 | 2 | 111 |
DEL PEAK 7(3P14.3) MUTATED | 36 | 1 | 65 |
DEL PEAK 7(3P14.3) WILD-TYPE | 5 | 1 | 46 |
P value = 0.00185 (Fisher's exact test), Q value = 0.12
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 41 | 2 | 111 |
DEL PEAK 8(3P14.2) MUTATED | 35 | 1 | 64 |
DEL PEAK 8(3P14.2) WILD-TYPE | 6 | 1 | 47 |
P value = 0.00026 (Fisher's exact test), Q value = 0.1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 41 | 2 | 111 |
DEL PEAK 23(9P21.3) MUTATED | 39 | 1 | 75 |
DEL PEAK 23(9P21.3) WILD-TYPE | 2 | 1 | 36 |
P value = 0.00149 (Fisher's exact test), Q value = 0.11
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 41 | 2 | 111 |
DEL PEAK 25(10P11.21) MUTATED | 19 | 1 | 21 |
DEL PEAK 25(10P11.21) WILD-TYPE | 22 | 1 | 90 |
P value = 0.00078 (Fisher's exact test), Q value = 0.1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 41 | 2 | 111 |
DEL PEAK 26(10Q21.1) MUTATED | 18 | 1 | 18 |
DEL PEAK 26(10Q21.1) WILD-TYPE | 23 | 1 | 93 |
P value = 0.00156 (Fisher's exact test), Q value = 0.11
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 41 | 2 | 111 |
DEL PEAK 32(13Q14.2) MUTATED | 26 | 0 | 38 |
DEL PEAK 32(13Q14.2) WILD-TYPE | 15 | 2 | 73 |
P value = 0.0059 (Fisher's exact test), Q value = 0.24
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 5 | 7 | 1 | 39 | 29 | 25 | 12 | 10 | 7 | 5 | 4 |
DEL PEAK 51(XP21.1) MUTATED | 1 | 2 | 0 | 0 | 16 | 14 | 6 | 7 | 8 | 1 | 1 | 0 |
DEL PEAK 51(XP21.1) WILD-TYPE | 7 | 3 | 7 | 1 | 23 | 15 | 19 | 5 | 2 | 6 | 4 | 4 |
P value = 0.00319 (Fisher's exact test), Q value = 0.18
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 8 | 5 | 7 | 1 | 39 | 29 | 25 | 12 | 10 | 7 | 5 | 4 |
DEL PEAK 52(XP11.3) MUTATED | 1 | 2 | 1 | 0 | 18 | 13 | 10 | 7 | 9 | 0 | 1 | 0 |
DEL PEAK 52(XP11.3) WILD-TYPE | 7 | 3 | 6 | 1 | 21 | 16 | 15 | 5 | 1 | 7 | 4 | 4 |
P value = 0.00092 (Fisher's exact test), Q value = 0.1
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 41 | 2 | 111 |
DEL PEAK 52(XP11.3) MUTATED | 26 | 0 | 36 |
DEL PEAK 52(XP11.3) WILD-TYPE | 15 | 2 | 75 |
-
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/ESCA-TP/15084414/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/15078602/ESCA-TP.merged_data.txt
-
Number of patients = 173
-
Number of significantly focal cnvs = 85
-
Number of selected clinical features = 10
-
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.