This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 58 focal events and 11 clinical features across 165 patients, 9 significant findings detected with Q value < 0.25.
-
amp_8p11.21 cnv correlated to 'RESIDUAL_TUMOR'.
-
amp_13q12.13 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
amp_13q12.2 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
amp_13q22.1 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
amp_20q11.21 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
amp_20q11.23 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
amp_20q13.33 cnv correlated to 'HISTOLOGICAL_TYPE'.
-
del_10q21.1 cnv correlated to 'RADIATION_THERAPY'.
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del_20p12.1 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 |
RESIDUAL TUMOR |
NUMBER OF LYMPH NODES |
||
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 | |
amp 8p11 21 | 70 (42%) | 95 |
0.196 (0.907) |
0.664 (0.984) |
0.257 (0.959) |
0.444 (0.984) |
0.703 (0.984) |
0.0758 (0.768) |
0.753 (0.984) |
0.461 (0.984) |
0.156 (0.871) |
0.00143 (0.154) |
0.318 (0.961) |
amp 13q12 13 | 126 (76%) | 39 |
0.318 (0.961) |
0.188 (0.907) |
0.0752 (0.768) |
0.0907 (0.788) |
0.0108 (0.33) |
0.798 (0.999) |
0.717 (0.984) |
0.401 (0.984) |
0.00229 (0.182) |
1 (1.00) |
0.00852 (0.32) |
amp 13q12 2 | 125 (76%) | 40 |
0.631 (0.984) |
0.0964 (0.788) |
0.0819 (0.775) |
0.0856 (0.788) |
0.0165 (0.406) |
1 (1.00) |
0.368 (0.967) |
0.28 (0.959) |
0.00279 (0.198) |
1 (1.00) |
0.00852 (0.32) |
amp 13q22 1 | 120 (73%) | 45 |
0.876 (1.00) |
0.663 (0.984) |
0.741 (0.984) |
0.262 (0.959) |
0.139 (0.868) |
1 (1.00) |
0.485 (0.984) |
0.0354 (0.61) |
0.00113 (0.154) |
0.624 (0.984) |
0.0639 (0.763) |
amp 20q11 21 | 146 (88%) | 19 |
0.698 (0.984) |
0.0825 (0.775) |
0.214 (0.946) |
0.603 (0.984) |
0.101 (0.809) |
0.739 (0.984) |
1 (1.00) |
0.723 (0.984) |
0.000663 (0.154) |
0.708 (0.984) |
0.162 (0.871) |
amp 20q11 23 | 147 (89%) | 18 |
0.777 (0.997) |
0.169 (0.882) |
0.193 (0.907) |
0.628 (0.984) |
0.0345 (0.61) |
0.308 (0.96) |
1 (1.00) |
0.71 (0.984) |
0.000447 (0.154) |
0.711 (0.984) |
0.162 (0.871) |
amp 20q13 33 | 146 (88%) | 19 |
0.995 (1.00) |
0.359 (0.967) |
0.259 (0.959) |
0.602 (0.984) |
0.195 (0.907) |
0.739 (0.984) |
0.809 (0.999) |
0.71 (0.984) |
0.000953 (0.154) |
0.712 (0.984) |
0.585 (0.984) |
del 10q21 1 | 41 (25%) | 124 |
0.359 (0.967) |
0.578 (0.984) |
0.822 (1.00) |
0.676 (0.984) |
0.812 (0.999) |
0.129 (0.866) |
0.588 (0.984) |
0.00174 (0.159) |
0.0929 (0.788) |
0.746 (0.984) |
0.751 (0.984) |
del 20p12 1 | 49 (30%) | 116 |
0.00145 (0.154) |
0.612 (0.984) |
0.192 (0.907) |
0.923 (1.00) |
0.69 (0.984) |
0.811 (0.999) |
0.495 (0.984) |
0.589 (0.984) |
0.535 (0.984) |
0.688 (0.984) |
0.217 (0.946) |
amp 1q21 3 | 48 (29%) | 117 |
0.521 (0.984) |
0.646 (0.984) |
0.735 (0.984) |
0.0817 (0.775) |
0.482 (0.984) |
0.798 (0.999) |
0.734 (0.984) |
0.593 (0.984) |
1 (1.00) |
0.583 (0.984) |
0.586 (0.984) |
amp 1q32 1 | 49 (30%) | 116 |
0.22 (0.946) |
0.814 (0.999) |
0.489 (0.984) |
0.0231 (0.508) |
0.232 (0.952) |
0.456 (0.984) |
1 (1.00) |
0.599 (0.984) |
1 (1.00) |
0.469 (0.984) |
0.119 (0.816) |
amp 6p21 1 | 54 (33%) | 111 |
0.599 (0.984) |
0.861 (1.00) |
0.0499 (0.692) |
0.495 (0.984) |
0.005 (0.319) |
0.0077 (0.32) |
0.406 (0.984) |
0.304 (0.959) |
0.062 (0.763) |
0.172 (0.882) |
0.0161 (0.406) |
amp 8p11 23 | 53 (32%) | 112 |
0.168 (0.882) |
0.355 (0.967) |
0.334 (0.967) |
0.232 (0.952) |
0.34 (0.967) |
0.148 (0.871) |
0.0941 (0.788) |
0.794 (0.999) |
0.222 (0.946) |
0.00988 (0.33) |
0.135 (0.868) |
amp 8q24 21 | 109 (66%) | 56 |
0.122 (0.831) |
0.343 (0.967) |
0.443 (0.984) |
0.47 (0.984) |
0.624 (0.984) |
0.352 (0.967) |
0.743 (0.984) |
0.805 (0.999) |
0.0328 (0.61) |
0.412 (0.984) |
0.746 (0.984) |
amp 10q22 2 | 11 (7%) | 154 |
0.617 (0.984) |
0.702 (0.984) |
0.812 (0.999) |
0.878 (1.00) |
0.916 (1.00) |
0.664 (0.984) |
0.756 (0.985) |
1 (1.00) |
0.585 (0.984) |
1 (1.00) |
0.632 (0.984) |
amp 11p15 5 | 45 (27%) | 120 |
0.896 (1.00) |
0.913 (1.00) |
0.853 (1.00) |
0.915 (1.00) |
0.231 (0.952) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.114 (0.816) |
1 (1.00) |
0.171 (0.882) |
amp 11q13 3 | 28 (17%) | 137 |
0.315 (0.961) |
0.0462 (0.655) |
0.718 (0.984) |
0.506 (0.984) |
0.449 (0.984) |
0.376 (0.972) |
1 (1.00) |
0.737 (0.984) |
0.468 (0.984) |
0.259 (0.959) |
0.234 (0.953) |
amp 12p13 33 | 41 (25%) | 124 |
0.607 (0.984) |
0.256 (0.959) |
0.803 (0.999) |
0.319 (0.961) |
0.604 (0.984) |
0.597 (0.984) |
0.588 (0.984) |
0.0911 (0.788) |
0.305 (0.959) |
0.504 (0.984) |
0.647 (0.984) |
amp 12p12 1 | 40 (24%) | 125 |
0.806 (0.999) |
0.289 (0.959) |
0.632 (0.984) |
0.269 (0.959) |
0.599 (0.984) |
0.789 (0.999) |
0.716 (0.984) |
0.272 (0.959) |
0.183 (0.897) |
0.321 (0.962) |
0.58 (0.984) |
amp 16p11 2 | 47 (28%) | 118 |
0.747 (0.984) |
0.673 (0.984) |
0.0773 (0.771) |
0.63 (0.984) |
0.054 (0.721) |
0.0438 (0.636) |
0.607 (0.984) |
0.599 (0.984) |
0.0109 (0.33) |
0.0392 (0.61) |
0.131 (0.868) |
amp 17q12 | 46 (28%) | 119 |
0.423 (0.984) |
0.33 (0.967) |
0.868 (1.00) |
0.842 (1.00) |
0.262 (0.959) |
0.323 (0.962) |
0.299 (0.959) |
0.588 (0.984) |
0.35 (0.967) |
0.138 (0.868) |
0.878 (1.00) |
amp 17q24 1 | 39 (24%) | 126 |
0.363 (0.967) |
0.25 (0.959) |
0.479 (0.984) |
0.257 (0.959) |
0.252 (0.959) |
0.119 (0.816) |
1 (1.00) |
0.401 (0.984) |
0.0392 (0.61) |
0.2 (0.913) |
0.661 (0.984) |
amp xp22 2 | 32 (19%) | 133 |
0.747 (0.984) |
0.895 (1.00) |
0.0336 (0.61) |
0.818 (1.00) |
0.603 (0.984) |
0.257 (0.959) |
0.238 (0.959) |
1 (1.00) |
0.469 (0.984) |
0.319 (0.961) |
0.752 (0.984) |
amp xq27 3 | 37 (22%) | 128 |
0.888 (1.00) |
0.615 (0.984) |
0.699 (0.984) |
0.267 (0.959) |
0.589 (0.984) |
0.421 (0.984) |
0.575 (0.984) |
1 (1.00) |
0.302 (0.959) |
0.746 (0.984) |
0.721 (0.984) |
del 1p36 11 | 75 (45%) | 90 |
0.735 (0.984) |
0.615 (0.984) |
0.737 (0.984) |
0.104 (0.813) |
0.358 (0.967) |
0.38 (0.972) |
0.877 (1.00) |
0.468 (0.984) |
0.566 (0.984) |
0.711 (0.984) |
0.0674 (0.763) |
del 1p33 | 53 (32%) | 112 |
0.453 (0.984) |
0.51 (0.984) |
0.775 (0.997) |
0.569 (0.984) |
0.425 (0.984) |
1 (1.00) |
0.868 (1.00) |
0.8 (0.999) |
0.0643 (0.763) |
0.856 (1.00) |
0.561 (0.984) |
del 1p13 2 | 54 (33%) | 111 |
0.188 (0.907) |
0.644 (0.984) |
0.381 (0.972) |
0.252 (0.959) |
0.836 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.227 (0.952) |
0.953 (1.00) |
0.293 (0.959) |
del 2p12 | 13 (8%) | 152 |
0.52 (0.984) |
0.0264 (0.561) |
0.733 (0.984) |
1 (1.00) |
0.441 (0.984) |
1 (1.00) |
0.577 (0.984) |
0.371 (0.967) |
1 (1.00) |
1 (1.00) |
0.751 (0.984) |
del 3p14 2 | 31 (19%) | 134 |
0.804 (0.999) |
0.573 (0.984) |
0.312 (0.961) |
0.199 (0.913) |
0.864 (1.00) |
0.149 (0.871) |
0.0158 (0.406) |
0.558 (0.984) |
0.702 (0.984) |
0.118 (0.816) |
0.643 (0.984) |
del 3q26 31 | 18 (11%) | 147 |
0.464 (0.984) |
0.894 (1.00) |
0.0365 (0.61) |
0.724 (0.984) |
0.357 (0.967) |
0.00776 (0.32) |
0.0108 (0.33) |
1 (1.00) |
0.00582 (0.32) |
0.065 (0.763) |
0.14 (0.868) |
del 4p13 | 60 (36%) | 105 |
0.274 (0.959) |
0.704 (0.984) |
0.793 (0.999) |
0.774 (0.997) |
0.306 (0.959) |
0.82 (1.00) |
0.147 (0.871) |
0.458 (0.984) |
0.377 (0.972) |
0.657 (0.984) |
0.273 (0.959) |
del 4q22 1 | 73 (44%) | 92 |
0.155 (0.871) |
0.46 (0.984) |
0.453 (0.984) |
0.51 (0.984) |
0.516 (0.984) |
0.654 (0.984) |
0.16 (0.871) |
0.625 (0.984) |
0.395 (0.983) |
0.493 (0.984) |
0.343 (0.967) |
del 4q35 1 | 72 (44%) | 93 |
0.425 (0.984) |
0.779 (0.997) |
0.398 (0.984) |
0.498 (0.984) |
0.333 (0.967) |
1 (1.00) |
0.348 (0.967) |
0.625 (0.984) |
0.156 (0.871) |
0.366 (0.967) |
0.288 (0.959) |
del 5q12 1 | 53 (32%) | 112 |
0.91 (1.00) |
0.555 (0.984) |
0.698 (0.984) |
0.928 (1.00) |
1 (1.00) |
0.337 (0.967) |
0.407 (0.984) |
0.605 (0.984) |
0.224 (0.946) |
0.902 (1.00) |
0.923 (1.00) |
del 5q22 2 | 59 (36%) | 106 |
0.54 (0.984) |
0.366 (0.967) |
0.775 (0.997) |
0.473 (0.984) |
0.598 (0.984) |
1 (1.00) |
0.416 (0.984) |
0.623 (0.984) |
0.135 (0.868) |
0.878 (1.00) |
0.63 (0.984) |
del 6p25 3 | 24 (15%) | 141 |
0.563 (0.984) |
0.346 (0.967) |
0.287 (0.959) |
0.256 (0.959) |
0.39 (0.98) |
0.533 (0.984) |
0.665 (0.984) |
0.315 (0.961) |
0.383 (0.972) |
0.689 (0.984) |
0.22 (0.946) |
del 6q26 | 30 (18%) | 135 |
0.551 (0.984) |
0.963 (1.00) |
0.614 (0.984) |
0.431 (0.984) |
0.0975 (0.788) |
1 (1.00) |
0.157 (0.871) |
0.0727 (0.768) |
0.0125 (0.363) |
0.617 (0.984) |
0.537 (0.984) |
del 7q31 1 | 4 (2%) | 161 |
0.523 (0.984) |
0.215 (0.946) |
0.852 (1.00) |
1 (1.00) |
0.531 (0.984) |
1 (1.00) |
1 (1.00) |
0.109 (0.816) |
0.291 (0.959) |
1 (1.00) |
0.701 (0.984) |
del 8p23 2 | 100 (61%) | 65 |
0.0884 (0.788) |
0.26 (0.959) |
0.405 (0.984) |
0.191 (0.907) |
0.483 (0.984) |
0.503 (0.984) |
1 (1.00) |
0.811 (0.999) |
0.769 (0.997) |
0.298 (0.959) |
0.252 (0.959) |
del 8q11 1 | 17 (10%) | 148 |
0.103 (0.813) |
0.83 (1.00) |
0.679 (0.984) |
0.601 (0.984) |
0.114 (0.816) |
0.14 (0.868) |
0.0706 (0.764) |
0.69 (0.984) |
1 (1.00) |
0.827 (1.00) |
0.173 (0.882) |
del 10q25 2 | 48 (29%) | 117 |
0.183 (0.897) |
0.455 (0.984) |
0.756 (0.985) |
0.152 (0.871) |
0.699 (0.984) |
0.151 (0.871) |
0.864 (1.00) |
0.284 (0.959) |
0.0542 (0.721) |
0.288 (0.959) |
0.929 (1.00) |
del 11q22 3 | 38 (23%) | 127 |
0.865 (1.00) |
0.862 (1.00) |
0.284 (0.959) |
0.386 (0.974) |
0.938 (1.00) |
0.0277 (0.571) |
0.584 (0.984) |
0.159 (0.871) |
0.0341 (0.61) |
0.181 (0.897) |
0.948 (1.00) |
del 12q13 2 | 20 (12%) | 145 |
0.997 (1.00) |
0.71 (0.984) |
0.369 (0.967) |
0.94 (1.00) |
0.95 (1.00) |
0.739 (0.984) |
0.637 (0.984) |
0.265 (0.959) |
1 (1.00) |
0.615 (0.984) |
0.773 (0.997) |
del 14q11 2 | 70 (42%) | 95 |
0.42 (0.984) |
0.541 (0.984) |
0.802 (0.999) |
0.699 (0.984) |
0.37 (0.967) |
0.498 (0.984) |
0.753 (0.984) |
0.223 (0.946) |
0.0431 (0.636) |
0.0911 (0.788) |
0.673 (0.984) |
del 14q31 1 | 72 (44%) | 93 |
0.501 (0.984) |
0.962 (1.00) |
0.629 (0.984) |
0.233 (0.952) |
0.0826 (0.775) |
0.826 (1.00) |
0.531 (0.984) |
0.472 (0.984) |
0.00712 (0.32) |
0.432 (0.984) |
0.779 (0.997) |
del 15q21 1 | 79 (48%) | 86 |
0.862 (1.00) |
0.876 (1.00) |
0.592 (0.984) |
0.436 (0.984) |
0.554 (0.984) |
0.827 (1.00) |
0.211 (0.942) |
0.628 (0.984) |
1 (1.00) |
0.818 (1.00) |
0.136 (0.868) |
del 15q22 33 | 77 (47%) | 88 |
0.848 (1.00) |
0.941 (1.00) |
0.154 (0.871) |
0.0372 (0.61) |
0.293 (0.959) |
1 (1.00) |
0.531 (0.984) |
0.811 (0.999) |
1 (1.00) |
0.602 (0.984) |
0.0559 (0.728) |
del 16p13 3 | 14 (8%) | 151 |
0.788 (0.999) |
0.527 (0.984) |
0.596 (0.984) |
0.653 (0.984) |
0.497 (0.984) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.288 (0.959) |
1 (1.00) |
0.736 (0.984) |
del 16q23 1 | 23 (14%) | 142 |
0.922 (1.00) |
0.498 (0.984) |
0.0632 (0.763) |
0.518 (0.984) |
0.0197 (0.457) |
0.749 (0.984) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.297 (0.959) |
del 17p11 2 | 113 (68%) | 52 |
0.798 (0.999) |
0.0672 (0.763) |
0.901 (1.00) |
0.0148 (0.406) |
0.855 (1.00) |
1 (1.00) |
0.614 (0.984) |
0.611 (0.984) |
0.118 (0.816) |
0.909 (1.00) |
0.854 (1.00) |
del 18p11 31 | 125 (76%) | 40 |
0.326 (0.967) |
0.654 (0.984) |
0.255 (0.959) |
0.169 (0.882) |
0.371 (0.967) |
0.108 (0.816) |
0.857 (1.00) |
0.272 (0.959) |
0.0755 (0.768) |
0.603 (0.984) |
0.303 (0.959) |
del 18q21 2 | 145 (88%) | 20 |
0.467 (0.984) |
0.418 (0.984) |
0.177 (0.89) |
0.02 (0.457) |
0.106 (0.816) |
0.0438 (0.636) |
1 (1.00) |
0.464 (0.984) |
0.656 (0.984) |
0.559 (0.984) |
0.0392 (0.61) |
del 18q22 1 | 141 (85%) | 24 |
0.623 (0.984) |
0.361 (0.967) |
0.42 (0.984) |
0.0691 (0.763) |
0.354 (0.967) |
0.204 (0.916) |
0.665 (0.984) |
1 (1.00) |
0.393 (0.983) |
0.776 (0.997) |
0.096 (0.788) |
del 18q23 | 141 (85%) | 24 |
0.678 (0.984) |
0.677 (0.984) |
0.597 (0.984) |
0.0694 (0.763) |
0.514 (0.984) |
0.204 (0.916) |
0.665 (0.984) |
0.307 (0.959) |
1 (1.00) |
0.884 (1.00) |
0.117 (0.816) |
del 19p13 3 | 36 (22%) | 129 |
0.364 (0.967) |
0.839 (1.00) |
0.526 (0.984) |
0.405 (0.984) |
0.462 (0.984) |
0.191 (0.907) |
0.852 (1.00) |
0.362 (0.967) |
0.302 (0.959) |
0.848 (1.00) |
0.341 (0.967) |
del 21q11 2 | 73 (44%) | 92 |
0.657 (0.984) |
0.59 (0.984) |
0.455 (0.984) |
0.113 (0.816) |
0.384 (0.973) |
0.508 (0.984) |
0.64 (0.984) |
0.809 (0.999) |
0.152 (0.871) |
0.291 (0.959) |
0.491 (0.984) |
del 22q13 31 | 68 (41%) | 97 |
0.162 (0.871) |
0.096 (0.788) |
0.379 (0.972) |
0.274 (0.959) |
0.00821 (0.32) |
0.265 (0.959) |
0.527 (0.984) |
0.461 (0.984) |
0.562 (0.984) |
0.518 (0.984) |
0.174 (0.882) |
del xp22 33 | 34 (21%) | 131 |
0.35 (0.967) |
0.609 (0.984) |
0.983 (1.00) |
0.657 (0.984) |
0.903 (1.00) |
0.579 (0.984) |
0.7 (0.984) |
0.545 (0.984) |
0.719 (0.984) |
0.847 (1.00) |
0.506 (0.984) |
P value = 0.00143 (Fisher's exact test), Q value = 0.15
nPatients | R0 | R1 | R2 | RX |
---|---|---|---|---|
ALL | 123 | 2 | 12 | 4 |
AMP PEAK 5(8P11.21) MUTATED | 41 | 2 | 9 | 3 |
AMP PEAK 5(8P11.21) WILD-TYPE | 82 | 0 | 3 | 1 |
P value = 0.00229 (Fisher's exact test), Q value = 0.18
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 146 | 13 |
AMP PEAK 12(13Q12.13) MUTATED | 117 | 5 |
AMP PEAK 12(13Q12.13) WILD-TYPE | 29 | 8 |
P value = 0.00279 (Fisher's exact test), Q value = 0.2
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 146 | 13 |
AMP PEAK 13(13Q12.2) MUTATED | 116 | 5 |
AMP PEAK 13(13Q12.2) WILD-TYPE | 30 | 8 |
P value = 0.00113 (Fisher's exact test), Q value = 0.15
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 146 | 13 |
AMP PEAK 14(13Q22.1) MUTATED | 112 | 4 |
AMP PEAK 14(13Q22.1) WILD-TYPE | 34 | 9 |
P value = 0.000663 (Fisher's exact test), Q value = 0.15
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 146 | 13 |
AMP PEAK 18(20Q11.21) MUTATED | 135 | 7 |
AMP PEAK 18(20Q11.21) WILD-TYPE | 11 | 6 |
P value = 0.000447 (Fisher's exact test), Q value = 0.15
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 146 | 13 |
AMP PEAK 19(20Q11.23) MUTATED | 136 | 7 |
AMP PEAK 19(20Q11.23) WILD-TYPE | 10 | 6 |
P value = 0.000953 (Fisher's exact test), Q value = 0.15
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 146 | 13 |
AMP PEAK 20(20Q13.33) MUTATED | 134 | 7 |
AMP PEAK 20(20Q13.33) WILD-TYPE | 12 | 6 |
P value = 0.00174 (Fisher's exact test), Q value = 0.16
nPatients | NO | YES |
---|---|---|
ALL | 112 | 20 |
DEL PEAK 17(10Q21.1) MUTATED | 22 | 11 |
DEL PEAK 17(10Q21.1) WILD-TYPE | 90 | 9 |
P value = 0.00145 (logrank test), Q value = 0.15
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 158 | 27 | 0.4 - 129.3 (21.0) |
DEL PEAK 33(20P12.1) MUTATED | 44 | 15 | 1.0 - 86.6 (22.0) |
DEL PEAK 33(20P12.1) WILD-TYPE | 114 | 12 | 0.4 - 129.3 (21.0) |
-
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/READ-TP/22532761/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/READ-TP/22507018/READ-TP.merged_data.txt
-
Number of patients = 165
-
Number of significantly focal cnvs = 58
-
Number of selected clinical features = 11
-
Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For 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.