This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 56 focal events and 15 clinical features across 184 patients, 2 significant findings detected with Q value < 0.25.
-
amp_3p12.2 cnv correlated to 'GENDER'.
-
amp_3q26.2 cnv correlated to 'Time to Death'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
NUMBER PACK YEARS SMOKED |
YEAR OF TOBACCO SMOKING ONSET |
RESIDUAL TUMOR |
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 | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
amp 3p12 2 | 12 (7%) | 172 |
0.275 (0.909) |
0.512 (0.982) |
0.787 (1.00) |
0.849 (1.00) |
0.741 (1.00) |
0.417 (0.962) |
0.000591 (0.248) |
0.189 (0.882) |
1 (1.00) |
1 (1.00) |
0.454 (0.976) |
0.495 (0.982) |
1 (1.00) |
||
amp 3q26 2 | 32 (17%) | 152 |
0.000129 (0.108) |
0.794 (1.00) |
0.644 (0.997) |
0.547 (0.982) |
0.518 (0.982) |
0.237 (0.882) |
0.117 (0.84) |
0.11 (0.821) |
1 (1.00) |
0.943 (1.00) |
0.0638 (0.821) |
0.0653 (0.821) |
0.0286 (0.782) |
0.6 (0.982) |
1 (1.00) |
amp 1p34 2 | 13 (7%) | 171 |
0.48 (0.982) |
0.00524 (0.732) |
0.26 (0.904) |
0.407 (0.962) |
1 (1.00) |
0.0467 (0.798) |
0.389 (0.958) |
0.518 (0.982) |
0.00867 (0.732) |
0.269 (0.909) |
0.2 (0.882) |
1 (1.00) |
0.312 (0.928) |
||
amp 1p12 | 27 (15%) | 157 |
0.521 (0.982) |
0.222 (0.882) |
0.207 (0.882) |
0.461 (0.978) |
1 (1.00) |
0.0311 (0.782) |
1 (1.00) |
0.623 (0.992) |
0.11 (0.821) |
0.222 (0.882) |
0.659 (0.997) |
0.561 (0.982) |
0.526 (0.982) |
0.454 (0.976) |
0.559 (0.982) |
amp 1q21 3 | 62 (34%) | 122 |
0.926 (1.00) |
0.135 (0.846) |
0.215 (0.882) |
0.48 (0.982) |
0.218 (0.882) |
0.335 (0.928) |
0.273 (0.909) |
0.461 (0.978) |
0.395 (0.958) |
0.765 (1.00) |
0.636 (0.997) |
0.729 (1.00) |
0.692 (1.00) |
0.305 (0.928) |
0.166 (0.857) |
amp 2q36 2 | 26 (14%) | 158 |
0.74 (1.00) |
0.442 (0.971) |
0.548 (0.982) |
0.649 (0.997) |
0.472 (0.982) |
1 (1.00) |
0.138 (0.848) |
0.331 (0.928) |
0.782 (1.00) |
0.519 (0.982) |
0.277 (0.909) |
0.188 (0.882) |
0.398 (0.958) |
0.218 (0.882) |
1 (1.00) |
amp 4p16 3 | 15 (8%) | 169 |
0.357 (0.935) |
0.354 (0.933) |
0.606 (0.982) |
0.432 (0.97) |
0.758 (1.00) |
1 (1.00) |
1 (1.00) |
0.76 (1.00) |
0.00966 (0.732) |
0.325 (0.928) |
0.0665 (0.821) |
0.998 (1.00) |
0.0804 (0.821) |
0.312 (0.928) |
|
amp 6p21 31 | 12 (7%) | 172 |
0.313 (0.928) |
0.68 (1.00) |
0.0906 (0.821) |
0.166 (0.857) |
0.0754 (0.821) |
0.0341 (0.782) |
1 (1.00) |
1 (1.00) |
0.269 (0.909) |
0.758 (1.00) |
0.11 (0.821) |
0.345 (0.929) |
0.312 (0.928) |
||
amp 7q22 1 | 56 (30%) | 128 |
0.926 (1.00) |
0.328 (0.928) |
0.154 (0.857) |
0.56 (0.982) |
0.586 (0.982) |
0.129 (0.844) |
0.108 (0.821) |
0.448 (0.975) |
0.399 (0.958) |
0.239 (0.883) |
0.388 (0.958) |
0.0723 (0.821) |
0.387 (0.958) |
0.71 (1.00) |
1 (1.00) |
amp 8p11 22 | 34 (18%) | 150 |
0.468 (0.982) |
0.106 (0.821) |
0.508 (0.982) |
0.472 (0.982) |
0.83 (1.00) |
1 (1.00) |
0.127 (0.844) |
0.183 (0.874) |
0.708 (1.00) |
0.737 (1.00) |
0.653 (0.997) |
0.16 (0.857) |
0.761 (1.00) |
0.467 (0.982) |
1 (1.00) |
amp 8p11 21 | 34 (18%) | 150 |
0.968 (1.00) |
0.427 (0.965) |
0.841 (1.00) |
0.887 (1.00) |
1 (1.00) |
0.581 (0.982) |
0.127 (0.844) |
0.265 (0.909) |
0.205 (0.882) |
0.698 (1.00) |
0.601 (0.982) |
0.403 (0.96) |
0.847 (1.00) |
0.767 (1.00) |
1 (1.00) |
amp 8q24 21 | 74 (40%) | 110 |
0.105 (0.821) |
0.79 (1.00) |
0.897 (1.00) |
0.982 (1.00) |
0.396 (0.958) |
1 (1.00) |
0.227 (0.882) |
0.373 (0.958) |
0.543 (0.982) |
0.258 (0.904) |
0.485 (0.982) |
0.482 (0.982) |
0.367 (0.952) |
0.0754 (0.821) |
0.386 (0.958) |
amp 9p13 3 | 24 (13%) | 160 |
0.672 (0.998) |
0.0345 (0.782) |
0.759 (1.00) |
0.53 (0.982) |
0.805 (1.00) |
0.487 (0.982) |
0.273 (0.909) |
0.599 (0.982) |
0.191 (0.882) |
0.503 (0.982) |
0.696 (1.00) |
0.871 (1.00) |
0.874 (1.00) |
0.5 (0.982) |
0.52 (0.982) |
amp 12p13 33 | 39 (21%) | 145 |
0.845 (1.00) |
0.976 (1.00) |
0.388 (0.958) |
0.315 (0.928) |
0.836 (1.00) |
0.58 (0.982) |
0.0476 (0.798) |
0.142 (0.857) |
0.0168 (0.732) |
0.557 (0.982) |
0.653 (0.997) |
0.0192 (0.732) |
0.0573 (0.805) |
1 (1.00) |
0.584 (0.982) |
amp 12p11 21 | 43 (23%) | 141 |
0.911 (1.00) |
0.992 (1.00) |
0.26 (0.904) |
0.914 (1.00) |
0.689 (1.00) |
0.215 (0.882) |
0.0795 (0.821) |
0.413 (0.962) |
0.12 (0.84) |
0.526 (0.982) |
0.736 (1.00) |
0.0123 (0.732) |
0.23 (0.882) |
1 (1.00) |
0.584 (0.982) |
amp 12q15 | 29 (16%) | 155 |
0.556 (0.982) |
0.268 (0.909) |
0.247 (0.894) |
0.554 (0.982) |
0.811 (1.00) |
1 (1.00) |
0.108 (0.821) |
0.158 (0.857) |
0.108 (0.821) |
0.198 (0.882) |
0.75 (1.00) |
0.0163 (0.732) |
0.0839 (0.821) |
1 (1.00) |
1 (1.00) |
amp 15q26 1 | 22 (12%) | 162 |
0.495 (0.982) |
0.415 (0.962) |
0.22 (0.882) |
0.546 (0.982) |
0.196 (0.882) |
1 (1.00) |
0.654 (0.997) |
0.597 (0.982) |
0.0986 (0.821) |
0.49 (0.982) |
0.755 (1.00) |
0.615 (0.988) |
0.164 (0.857) |
0.15 (0.857) |
0.435 (0.97) |
amp 17p11 2 | 15 (8%) | 169 |
0.012 (0.732) |
0.127 (0.844) |
0.169 (0.857) |
0.133 (0.846) |
0.32 (0.928) |
1 (1.00) |
1 (1.00) |
0.76 (1.00) |
0.0109 (0.732) |
0.649 (0.997) |
0.859 (1.00) |
0.595 (0.982) |
1 (1.00) |
||
amp 17q12 | 31 (17%) | 153 |
0.179 (0.872) |
0.445 (0.975) |
0.259 (0.904) |
0.839 (1.00) |
0.648 (0.997) |
0.417 (0.962) |
0.697 (1.00) |
0.254 (0.902) |
0.126 (0.844) |
0.232 (0.882) |
0.769 (1.00) |
0.326 (0.928) |
0.422 (0.963) |
0.6 (0.982) |
1 (1.00) |
amp 18q11 2 | 56 (30%) | 128 |
0.844 (1.00) |
0.515 (0.982) |
0.0893 (0.821) |
0.25 (0.896) |
0.28 (0.909) |
0.0585 (0.805) |
0.199 (0.882) |
0.849 (1.00) |
0.165 (0.857) |
0.654 (0.997) |
0.926 (1.00) |
0.672 (0.998) |
0.78 (1.00) |
0.0965 (0.821) |
0.329 (0.928) |
amp 19q13 2 | 47 (26%) | 137 |
0.477 (0.982) |
0.0887 (0.821) |
0.949 (1.00) |
0.462 (0.978) |
0.701 (1.00) |
1 (1.00) |
0.0174 (0.732) |
0.843 (1.00) |
0.573 (0.982) |
0.984 (1.00) |
0.222 (0.882) |
0.451 (0.976) |
0.0717 (0.821) |
0.316 (0.928) |
1 (1.00) |
amp 20p11 23 | 38 (21%) | 146 |
0.571 (0.982) |
0.52 (0.982) |
0.79 (1.00) |
0.289 (0.922) |
0.683 (1.00) |
1 (1.00) |
0.146 (0.857) |
0.831 (1.00) |
0.0941 (0.821) |
0.99 (1.00) |
0.659 (0.997) |
0.244 (0.894) |
0.414 (0.962) |
0.211 (0.882) |
0.583 (0.982) |
amp xq28 | 20 (11%) | 164 |
0.108 (0.821) |
0.226 (0.882) |
0.607 (0.982) |
0.331 (0.928) |
0.279 (0.909) |
0.379 (0.958) |
0.476 (0.982) |
1 (1.00) |
0.0344 (0.782) |
0.635 (0.997) |
1 (1.00) |
0.153 (0.857) |
0.687 (1.00) |
0.457 (0.978) |
|
del 1p36 11 | 68 (37%) | 116 |
0.413 (0.962) |
0.265 (0.909) |
0.18 (0.873) |
0.0781 (0.821) |
0.231 (0.882) |
0.656 (0.997) |
0.0216 (0.732) |
0.476 (0.982) |
0.919 (1.00) |
0.212 (0.882) |
0.129 (0.844) |
0.144 (0.857) |
0.485 (0.982) |
0.577 (0.982) |
0.652 (0.997) |
del 2q14 3 | 9 (5%) | 175 |
0.237 (0.882) |
0.344 (0.928) |
0.16 (0.857) |
0.504 (0.982) |
0.688 (1.00) |
1 (1.00) |
0.516 (0.982) |
0.698 (1.00) |
0.0494 (0.798) |
0.285 (0.919) |
0.772 (1.00) |
0.621 (0.992) |
1 (1.00) |
||
del 3p21 31 | 51 (28%) | 133 |
0.421 (0.963) |
0.9 (1.00) |
0.836 (1.00) |
0.881 (1.00) |
1 (1.00) |
0.583 (0.982) |
0.0493 (0.798) |
0.337 (0.928) |
0.76 (1.00) |
0.813 (1.00) |
0.565 (0.982) |
0.936 (1.00) |
0.425 (0.963) |
0.913 (1.00) |
1 (1.00) |
del 4q22 1 | 27 (15%) | 157 |
0.403 (0.96) |
0.75 (1.00) |
0.847 (1.00) |
0.822 (1.00) |
0.35 (0.929) |
1 (1.00) |
0.0364 (0.782) |
1 (1.00) |
0.0512 (0.803) |
0.535 (0.982) |
0.146 (0.857) |
0.959 (1.00) |
0.41 (0.962) |
0.484 (0.982) |
0.134 (0.846) |
del 4q34 3 | 35 (19%) | 149 |
0.628 (0.997) |
0.52 (0.982) |
0.513 (0.982) |
0.839 (1.00) |
1 (1.00) |
0.579 (0.982) |
0.0894 (0.821) |
0.657 (0.997) |
0.607 (0.982) |
0.247 (0.894) |
0.689 (1.00) |
0.865 (1.00) |
0.875 (1.00) |
0.204 (0.882) |
0.229 (0.882) |
del 5q14 2 | 35 (19%) | 149 |
0.28 (0.909) |
0.399 (0.958) |
0.714 (1.00) |
0.634 (0.997) |
0.836 (1.00) |
0.581 (0.982) |
0.708 (1.00) |
0.376 (0.958) |
0.0919 (0.821) |
0.0591 (0.805) |
0.497 (0.982) |
0.774 (1.00) |
0.596 (0.982) |
0.323 (0.928) |
0.0484 (0.798) |
del 6p25 2 | 74 (40%) | 110 |
0.599 (0.982) |
0.156 (0.857) |
0.29 (0.922) |
0.835 (1.00) |
0.313 (0.928) |
0.0752 (0.821) |
0.131 (0.846) |
0.375 (0.958) |
0.105 (0.821) |
0.1 (0.821) |
0.393 (0.958) |
0.639 (0.997) |
0.232 (0.882) |
0.798 (1.00) |
1 (1.00) |
del 6p22 2 | 70 (38%) | 114 |
0.594 (0.982) |
0.149 (0.857) |
0.493 (0.982) |
0.671 (0.998) |
0.391 (0.958) |
0.152 (0.857) |
0.173 (0.857) |
0.858 (1.00) |
0.127 (0.844) |
0.088 (0.821) |
0.711 (1.00) |
0.794 (1.00) |
0.137 (0.846) |
0.927 (1.00) |
1 (1.00) |
del 6q25 3 | 91 (49%) | 93 |
0.12 (0.84) |
0.815 (1.00) |
0.397 (0.958) |
0.237 (0.882) |
1 (1.00) |
1 (1.00) |
0.0395 (0.782) |
1 (1.00) |
0.526 (0.982) |
0.423 (0.963) |
0.982 (1.00) |
0.895 (1.00) |
0.47 (0.982) |
0.413 (0.962) |
0.668 (0.998) |
del 7q31 1 | 15 (8%) | 169 |
0.833 (1.00) |
0.534 (0.982) |
0.761 (1.00) |
0.792 (1.00) |
0.764 (1.00) |
0.339 (0.928) |
0.592 (0.982) |
0.744 (1.00) |
0.109 (0.821) |
0.781 (1.00) |
0.809 (1.00) |
0.422 (0.963) |
0.338 (0.928) |
||
del 7q36 1 | 15 (8%) | 169 |
0.745 (1.00) |
0.319 (0.928) |
0.581 (0.982) |
0.43 (0.969) |
1 (1.00) |
0.298 (0.928) |
0.79 (1.00) |
1 (1.00) |
0.805 (1.00) |
0.584 (0.982) |
0.204 (0.882) |
0.78 (1.00) |
0.749 (1.00) |
1 (1.00) |
0.363 (0.945) |
del 8p21 3 | 62 (34%) | 122 |
0.878 (1.00) |
0.0526 (0.803) |
0.882 (1.00) |
0.308 (0.928) |
0.599 (0.982) |
0.656 (0.997) |
0.273 (0.909) |
0.58 (0.982) |
0.526 (0.982) |
0.118 (0.84) |
0.793 (1.00) |
0.537 (0.982) |
0.313 (0.928) |
0.217 (0.882) |
0.665 (0.997) |
del 9p21 3 | 116 (63%) | 68 |
0.0155 (0.732) |
0.782 (1.00) |
0.226 (0.882) |
0.646 (0.997) |
0.493 (0.982) |
1 (1.00) |
0.22 (0.882) |
0.592 (0.982) |
0.0363 (0.782) |
0.561 (0.982) |
0.606 (0.982) |
0.709 (1.00) |
0.54 (0.982) |
0.235 (0.882) |
0.648 (0.997) |
del 10p15 3 | 41 (22%) | 143 |
0.385 (0.958) |
0.487 (0.982) |
0.215 (0.882) |
0.56 (0.982) |
0.314 (0.928) |
0.307 (0.928) |
1 (1.00) |
0.683 (1.00) |
0.288 (0.922) |
0.331 (0.928) |
0.339 (0.928) |
0.537 (0.982) |
0.182 (0.874) |
0.0831 (0.821) |
1 (1.00) |
del 10q23 33 | 35 (19%) | 149 |
0.841 (1.00) |
0.775 (1.00) |
0.171 (0.857) |
1 (1.00) |
0.202 (0.882) |
0.331 (0.928) |
0.573 (0.982) |
0.659 (0.997) |
0.169 (0.857) |
0.534 (0.982) |
0.352 (0.93) |
0.604 (0.982) |
0.438 (0.97) |
0.62 (0.992) |
0.229 (0.882) |
del 11p15 4 | 29 (16%) | 155 |
0.35 (0.929) |
0.392 (0.958) |
0.182 (0.874) |
1 (1.00) |
0.037 (0.782) |
0.585 (0.982) |
0.424 (0.963) |
0.48 (0.982) |
1 (1.00) |
0.441 (0.971) |
0.23 (0.882) |
0.49 (0.982) |
0.0596 (0.805) |
0.497 (0.982) |
0.173 (0.857) |
del 12p13 1 | 29 (16%) | 155 |
0.981 (1.00) |
0.549 (0.982) |
0.856 (1.00) |
0.567 (0.982) |
0.821 (1.00) |
1 (1.00) |
0.424 (0.963) |
0.0884 (0.821) |
0.277 (0.909) |
0.0423 (0.782) |
0.938 (1.00) |
0.0426 (0.782) |
0.7 (1.00) |
0.072 (0.821) |
1 (1.00) |
del 12q24 33 | 43 (23%) | 141 |
0.956 (1.00) |
0.788 (1.00) |
0.894 (1.00) |
0.343 (0.928) |
0.56 (0.982) |
1 (1.00) |
0.294 (0.928) |
0.681 (1.00) |
1 (1.00) |
0.153 (0.857) |
0.915 (1.00) |
0.393 (0.958) |
0.784 (1.00) |
0.00351 (0.732) |
0.591 (0.982) |
del 14q11 2 | 20 (11%) | 164 |
0.692 (1.00) |
0.779 (1.00) |
0.355 (0.933) |
0.864 (1.00) |
0.177 (0.868) |
0.417 (0.962) |
0.813 (1.00) |
1 (1.00) |
0.439 (0.971) |
0.201 (0.882) |
0.613 (0.988) |
0.671 (0.998) |
0.788 (1.00) |
0.0539 (0.805) |
1 (1.00) |
del 15q15 1 | 36 (20%) | 148 |
0.697 (1.00) |
0.1 (0.821) |
0.478 (0.982) |
0.606 (0.982) |
0.529 (0.982) |
1 (1.00) |
0.136 (0.846) |
0.663 (0.997) |
0.077 (0.821) |
0.813 (1.00) |
0.772 (1.00) |
0.659 (0.997) |
0.685 (1.00) |
0.276 (0.909) |
0.201 (0.882) |
del 16q23 1 | 19 (10%) | 165 |
0.335 (0.928) |
0.922 (1.00) |
0.159 (0.857) |
0.435 (0.97) |
0.783 (1.00) |
0.417 (0.962) |
0.0933 (0.821) |
1 (1.00) |
0.0156 (0.732) |
0.32 (0.928) |
0.722 (1.00) |
0.15 (0.857) |
0.553 (0.982) |
0.151 (0.857) |
0.363 (0.945) |
del 17p12 | 89 (48%) | 95 |
0.0288 (0.782) |
0.678 (1.00) |
0.248 (0.894) |
0.401 (0.96) |
0.621 (0.992) |
0.656 (0.997) |
0.768 (1.00) |
0.729 (1.00) |
0.048 (0.798) |
0.0875 (0.821) |
0.53 (0.982) |
0.103 (0.821) |
0.926 (1.00) |
1 (1.00) |
1 (1.00) |
del 17q22 | 49 (27%) | 135 |
0.0218 (0.732) |
0.973 (1.00) |
0.75 (1.00) |
0.901 (1.00) |
1 (1.00) |
0.615 (0.988) |
0.867 (1.00) |
0.69 (1.00) |
0.0613 (0.805) |
0.0284 (0.782) |
0.542 (0.982) |
0.0203 (0.732) |
0.956 (1.00) |
0.573 (0.982) |
1 (1.00) |
del 18p11 31 | 54 (29%) | 130 |
0.976 (1.00) |
0.0217 (0.732) |
0.813 (1.00) |
0.951 (1.00) |
0.856 (1.00) |
0.343 (0.928) |
0.516 (0.982) |
0.7 (1.00) |
0.448 (0.975) |
0.817 (1.00) |
0.895 (1.00) |
0.978 (1.00) |
0.856 (1.00) |
0.434 (0.97) |
0.13 (0.844) |
del 18q21 2 | 126 (68%) | 58 |
0.0183 (0.732) |
0.0321 (0.782) |
0.0266 (0.782) |
0.126 (0.844) |
0.59 (0.982) |
0.323 (0.928) |
0.038 (0.782) |
0.46 (0.978) |
0.0169 (0.732) |
0.754 (1.00) |
0.608 (0.982) |
0.0839 (0.821) |
0.975 (1.00) |
0.23 (0.882) |
0.654 (0.997) |
del 19p13 3 | 36 (20%) | 148 |
0.564 (0.982) |
0.38 (0.958) |
0.35 (0.929) |
0.371 (0.957) |
0.298 (0.928) |
0.307 (0.928) |
0.458 (0.978) |
1 (1.00) |
0.193 (0.882) |
0.384 (0.958) |
0.78 (1.00) |
0.698 (1.00) |
0.0586 (0.805) |
0.716 (1.00) |
0.258 (0.904) |
del 19p13 2 | 28 (15%) | 156 |
0.891 (1.00) |
0.56 (0.982) |
0.84 (1.00) |
0.234 (0.882) |
0.254 (0.902) |
1 (1.00) |
0.309 (0.928) |
1 (1.00) |
0.11 (0.821) |
0.584 (0.982) |
0.878 (1.00) |
0.889 (1.00) |
0.0699 (0.821) |
1 (1.00) |
0.173 (0.857) |
del 19q13 33 | 22 (12%) | 162 |
0.553 (0.982) |
0.0422 (0.782) |
0.669 (0.998) |
0.512 (0.982) |
0.196 (0.882) |
1 (1.00) |
0.038 (0.782) |
0.599 (0.982) |
0.168 (0.857) |
0.454 (0.976) |
0.0116 (0.732) |
0.944 (1.00) |
0.0844 (0.821) |
0.599 (0.982) |
1 (1.00) |
del 21q11 2 | 62 (34%) | 122 |
0.34 (0.928) |
0.223 (0.882) |
0.135 (0.846) |
0.0103 (0.732) |
0.0137 (0.732) |
0.398 (0.958) |
0.638 (0.997) |
0.71 (1.00) |
0.222 (0.882) |
0.333 (0.928) |
0.311 (0.928) |
0.193 (0.882) |
0.0073 (0.732) |
0.923 (1.00) |
0.333 (0.928) |
del 22q13 31 | 60 (33%) | 124 |
0.437 (0.97) |
0.0697 (0.821) |
0.039 (0.782) |
0.285 (0.919) |
0.724 (1.00) |
0.343 (0.928) |
0.117 (0.84) |
0.852 (1.00) |
1 (1.00) |
0.112 (0.825) |
0.279 (0.909) |
0.369 (0.953) |
0.892 (1.00) |
0.664 (0.997) |
1 (1.00) |
del 22q13 32 | 61 (33%) | 123 |
0.387 (0.958) |
0.0295 (0.782) |
0.0856 (0.821) |
0.24 (0.883) |
1 (1.00) |
0.343 (0.928) |
0.161 (0.857) |
0.851 (1.00) |
1 (1.00) |
0.052 (0.803) |
0.454 (0.976) |
0.152 (0.857) |
0.653 (0.997) |
0.664 (0.997) |
0.661 (0.997) |
del xp21 1 | 28 (15%) | 156 |
0.221 (0.882) |
0.648 (0.997) |
0.162 (0.857) |
0.544 (0.982) |
0.254 (0.902) |
1 (1.00) |
0.309 (0.928) |
0.347 (0.929) |
0.327 (0.928) |
0.476 (0.982) |
0.173 (0.857) |
0.0994 (0.821) |
0.118 (0.84) |
0.753 (1.00) |
0.578 (0.982) |
del xq11 2 | 23 (12%) | 161 |
0.245 (0.894) |
0.731 (1.00) |
0.214 (0.882) |
0.831 (1.00) |
0.446 (0.975) |
1 (1.00) |
0.0718 (0.821) |
0.603 (0.982) |
0.0428 (0.782) |
0.0587 (0.805) |
0.0604 (0.805) |
0.269 (0.909) |
0.154 (0.857) |
0.348 (0.929) |
1 (1.00) |
P value = 0.000591 (Fisher's exact test), Q value = 0.25
nPatients | FEMALE | MALE |
---|---|---|
ALL | 83 | 101 |
AMP PEAK 5(3P12.2) MUTATED | 0 | 12 |
AMP PEAK 5(3P12.2) WILD-TYPE | 83 | 89 |
P value = 0.000129 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 183 | 100 | 0.1 - 90.1 (15.3) |
AMP PEAK 6(3Q26.2) MUTATED | 32 | 24 | 0.1 - 31.9 (9.6) |
AMP PEAK 6(3Q26.2) WILD-TYPE | 151 | 76 | 0.2 - 90.1 (15.8) |
-
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/PAAD-TP/22533736/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PAAD-TP/22507097/PAAD-TP.merged_data.txt
-
Number of patients = 184
-
Number of significantly focal cnvs = 56
-
Number of selected clinical features = 15
-
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.