This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 74 arm-level results and 11 clinical features across 187 patients, 3 significant findings detected with Q value < 0.25.
-
2p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
2q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
-
8q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | t-test | t-test | Chi-square test | |
2p gain | 0 (0%) | 174 |
0.545 (1.00) |
0.149 (1.00) |
0.769 (1.00) |
0.331 (1.00) |
1 (1.00) |
0.848 (1.00) |
0.344 (1.00) |
0.49 (1.00) |
0.0001 (0.0732) |
0.432 (1.00) |
|
2q gain | 0 (0%) | 172 |
0.247 (1.00) |
0.432 (1.00) |
0.785 (1.00) |
0.322 (1.00) |
1 (1.00) |
1 (1.00) |
0.346 (1.00) |
0.943 (1.00) |
5.92e-06 (0.00434) |
0.381 (1.00) |
|
8q loss | 0 (0%) | 181 |
0.773 (1.00) |
0.828 (1.00) |
1 (1.00) |
0.0887 (1.00) |
1 (1.00) |
0.452 (1.00) |
0.295 (1.00) |
0.563 (1.00) |
0.000203 (0.149) |
0.0169 (1.00) |
|
1p gain | 0 (0%) | 177 |
0.658 (1.00) |
0.995 (1.00) |
0.743 (1.00) |
0.626 (1.00) |
1 (1.00) |
0.163 (1.00) |
0.0203 (1.00) |
0.0685 (1.00) |
0.797 (1.00) |
0.794 (1.00) |
|
1q gain | 0 (0%) | 160 |
0.878 (1.00) |
0.966 (1.00) |
0.394 (1.00) |
0.362 (1.00) |
0.0634 (1.00) |
0.0552 (1.00) |
0.155 (1.00) |
0.773 (1.00) |
0.896 (1.00) |
0.661 (1.00) |
|
3p gain | 0 (0%) | 184 |
0.743 (1.00) |
1 (1.00) |
0.79 (1.00) |
1 (1.00) |
1 (1.00) |
0.956 (1.00) |
0.168 (1.00) |
0.907 (1.00) |
0.967 (1.00) |
||
3q gain | 0 (0%) | 172 |
0.337 (1.00) |
0.0192 (1.00) |
0.0504 (1.00) |
0.496 (1.00) |
1 (1.00) |
0.483 (1.00) |
0.783 (1.00) |
0.607 (1.00) |
0.68 (1.00) |
0.98 (1.00) |
|
4p gain | 0 (0%) | 184 |
0.109 (1.00) |
0.282 (1.00) |
1 (1.00) |
1 (1.00) |
0.956 (1.00) |
0.252 (1.00) |
0.936 (1.00) |
0.00754 (1.00) |
|||
5p gain | 0 (0%) | 159 |
0.971 (1.00) |
0.324 (1.00) |
0.834 (1.00) |
0.361 (1.00) |
1 (1.00) |
0.19 (1.00) |
0.401 (1.00) |
0.259 (1.00) |
0.402 (1.00) |
0.119 (1.00) |
|
5q gain | 0 (0%) | 180 |
0.352 (1.00) |
0.731 (1.00) |
0.707 (1.00) |
0.108 (1.00) |
1 (1.00) |
1 (1.00) |
0.535 (1.00) |
0.838 (1.00) |
0.0621 (1.00) |
0.00163 (1.00) |
|
6p gain | 0 (0%) | 169 |
0.548 (1.00) |
0.718 (1.00) |
1 (1.00) |
0.121 (1.00) |
0.138 (1.00) |
0.238 (1.00) |
0.355 (1.00) |
0.392 (1.00) |
0.105 (1.00) |
0.651 (1.00) |
|
6q gain | 0 (0%) | 172 |
0.258 (1.00) |
0.698 (1.00) |
1 (1.00) |
0.146 (1.00) |
0.0999 (1.00) |
0.292 (1.00) |
0.494 (1.00) |
0.193 (1.00) |
0.177 (1.00) |
0.936 (1.00) |
|
7p gain | 0 (0%) | 125 |
0.65 (1.00) |
0.191 (1.00) |
0.342 (1.00) |
0.328 (1.00) |
0.687 (1.00) |
0.865 (1.00) |
0.22 (1.00) |
0.625 (1.00) |
0.914 (1.00) |
0.32 (1.00) |
|
7q gain | 0 (0%) | 133 |
0.906 (1.00) |
0.0676 (1.00) |
0.513 (1.00) |
0.32 (1.00) |
1 (1.00) |
0.694 (1.00) |
0.396 (1.00) |
1 (1.00) |
0.765 (1.00) |
0.275 (1.00) |
|
8p gain | 0 (0%) | 130 |
0.887 (1.00) |
0.00737 (1.00) |
0.144 (1.00) |
0.261 (1.00) |
0.203 (1.00) |
0.0406 (1.00) |
0.0575 (1.00) |
0.223 (1.00) |
0.399 (1.00) |
0.86 (1.00) |
|
8q gain | 0 (0%) | 108 |
0.249 (1.00) |
0.013 (1.00) |
0.227 (1.00) |
0.144 (1.00) |
0.135 (1.00) |
0.058 (1.00) |
0.235 (1.00) |
0.119 (1.00) |
0.956 (1.00) |
0.35 (1.00) |
|
9p gain | 0 (0%) | 172 |
0.306 (1.00) |
0.774 (1.00) |
0.586 (1.00) |
0.657 (1.00) |
0.449 (1.00) |
0.65 (1.00) |
0.297 (1.00) |
1 (1.00) |
0.118 (1.00) |
0.169 (1.00) |
|
9q gain | 0 (0%) | 167 |
0.389 (1.00) |
0.951 (1.00) |
1 (1.00) |
0.947 (1.00) |
0.553 (1.00) |
0.632 (1.00) |
0.293 (1.00) |
0.921 (1.00) |
0.334 (1.00) |
0.595 (1.00) |
|
10p gain | 0 (0%) | 156 |
0.926 (1.00) |
0.552 (1.00) |
0.692 (1.00) |
0.316 (1.00) |
0.602 (1.00) |
0.359 (1.00) |
0.879 (1.00) |
0.488 (1.00) |
0.725 (1.00) |
0.159 (1.00) |
|
10q gain | 0 (0%) | 171 |
0.566 (1.00) |
0.829 (1.00) |
0.599 (1.00) |
0.841 (1.00) |
1 (1.00) |
0.369 (1.00) |
0.744 (1.00) |
0.578 (1.00) |
0.983 (1.00) |
0.802 (1.00) |
|
11p gain | 0 (0%) | 180 |
0.648 (1.00) |
0.348 (1.00) |
0.707 (1.00) |
0.634 (1.00) |
0.238 (1.00) |
0.143 (1.00) |
0.832 (1.00) |
0.315 (1.00) |
0.11 (1.00) |
0.642 (1.00) |
|
11q gain | 0 (0%) | 175 |
0.471 (1.00) |
0.633 (1.00) |
1 (1.00) |
0.705 (1.00) |
0.376 (1.00) |
0.234 (1.00) |
0.699 (1.00) |
0.719 (1.00) |
0.005 (1.00) |
0.927 (1.00) |
|
12p gain | 0 (0%) | 167 |
0.442 (1.00) |
0.414 (1.00) |
0.227 (1.00) |
0.895 (1.00) |
1 (1.00) |
0.504 (1.00) |
0.615 (1.00) |
0.523 (1.00) |
0.619 (1.00) |
0.607 (1.00) |
|
12q gain | 0 (0%) | 172 |
0.913 (1.00) |
0.0211 (1.00) |
0.785 (1.00) |
0.318 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.308 (1.00) |
0.693 (1.00) |
0.315 (1.00) |
0.83 (1.00) |
|
13q gain | 0 (0%) | 149 |
0.987 (1.00) |
0.929 (1.00) |
0.578 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.298 (1.00) |
0.809 (1.00) |
0.963 (1.00) |
0.403 (1.00) |
0.691 (1.00) |
|
14q gain | 0 (0%) | 184 |
0.0712 (1.00) |
0.65 (1.00) |
0.058 (1.00) |
0.969 (1.00) |
1 (1.00) |
0.0399 (1.00) |
0.615 (1.00) |
0.0318 (1.00) |
0.639 (1.00) |
0.55 (1.00) |
|
15q gain | 0 (0%) | 179 |
0.119 (1.00) |
0.671 (1.00) |
0.0235 (1.00) |
0.925 (1.00) |
1 (1.00) |
0.411 (1.00) |
0.205 (1.00) |
0.838 (1.00) |
0.863 (1.00) |
0.161 (1.00) |
|
16p gain | 0 (0%) | 174 |
0.456 (1.00) |
0.896 (1.00) |
0.769 (1.00) |
0.694 (1.00) |
0.077 (1.00) |
0.0484 (1.00) |
0.187 (1.00) |
1 (1.00) |
0.34 (1.00) |
0.212 (1.00) |
|
16q gain | 0 (0%) | 177 |
0.478 (1.00) |
0.636 (1.00) |
1 (1.00) |
0.652 (1.00) |
1 (1.00) |
0.0115 (1.00) |
0.673 (1.00) |
0.888 (1.00) |
0.973 (1.00) |
0.332 (1.00) |
|
17p gain | 0 (0%) | 181 |
0.016 (1.00) |
0.572 (1.00) |
0.68 (1.00) |
0.817 (1.00) |
0.207 (1.00) |
0.0215 (1.00) |
0.00437 (1.00) |
0.0108 (1.00) |
0.283 (1.00) |
0.47 (1.00) |
|
17q gain | 0 (0%) | 175 |
0.389 (1.00) |
0.377 (1.00) |
0.768 (1.00) |
0.99 (1.00) |
0.376 (1.00) |
0.00463 (1.00) |
0.16 (1.00) |
0.0607 (1.00) |
0.413 (1.00) |
0.154 (1.00) |
|
18p gain | 0 (0%) | 169 |
0.769 (1.00) |
0.215 (1.00) |
0.621 (1.00) |
0.79 (1.00) |
0.138 (1.00) |
0.69 (1.00) |
0.498 (1.00) |
0.565 (1.00) |
0.701 (1.00) |
0.719 (1.00) |
|
18q gain | 0 (0%) | 177 |
0.705 (1.00) |
0.842 (1.00) |
0.516 (1.00) |
0.508 (1.00) |
0.324 (1.00) |
0.0822 (1.00) |
0.774 (1.00) |
0.166 (1.00) |
0.962 (1.00) |
0.993 (1.00) |
|
19p gain | 0 (0%) | 177 |
0.844 (1.00) |
0.231 (1.00) |
0.0147 (1.00) |
0.698 (1.00) |
1 (1.00) |
0.0208 (1.00) |
0.183 (1.00) |
0.00117 (0.854) |
0.0615 (1.00) |
0.184 (1.00) |
|
19q gain | 0 (0%) | 167 |
0.167 (1.00) |
0.217 (1.00) |
0.148 (1.00) |
0.359 (1.00) |
0.553 (1.00) |
0.16 (1.00) |
0.475 (1.00) |
0.00458 (1.00) |
0.102 (1.00) |
0.113 (1.00) |
|
20p gain | 0 (0%) | 109 |
0.197 (1.00) |
0.207 (1.00) |
0.00602 (1.00) |
0.405 (1.00) |
0.701 (1.00) |
0.0664 (1.00) |
0.4 (1.00) |
0.321 (1.00) |
0.288 (1.00) |
0.352 (1.00) |
|
20q gain | 0 (0%) | 91 |
0.128 (1.00) |
0.163 (1.00) |
0.00259 (1.00) |
0.228 (1.00) |
0.715 (1.00) |
0.0425 (1.00) |
0.56 (1.00) |
0.308 (1.00) |
0.116 (1.00) |
0.274 (1.00) |
|
22q gain | 0 (0%) | 184 |
0.747 (1.00) |
0.383 (1.00) |
1 (1.00) |
0.963 (1.00) |
1 (1.00) |
1 (1.00) |
0.644 (1.00) |
1 (1.00) |
0.82 (1.00) |
||
1p loss | 0 (0%) | 177 |
0.203 (1.00) |
0.28 (1.00) |
0.192 (1.00) |
0.548 (1.00) |
1 (1.00) |
0.0208 (1.00) |
0.453 (1.00) |
0.00852 (1.00) |
0.497 (1.00) |
0.0832 (1.00) |
|
2p loss | 0 (0%) | 184 |
0.562 (1.00) |
0.109 (1.00) |
1 (1.00) |
0.365 (1.00) |
0.252 (1.00) |
0.595 (1.00) |
0.55 (1.00) |
||||
3p loss | 0 (0%) | 171 |
0.914 (1.00) |
0.397 (1.00) |
0.599 (1.00) |
0.947 (1.00) |
1 (1.00) |
1 (1.00) |
0.165 (1.00) |
0.268 (1.00) |
0.102 (1.00) |
0.417 (1.00) |
|
3q loss | 0 (0%) | 177 |
0.763 (1.00) |
0.763 (1.00) |
0.32 (1.00) |
0.93 (1.00) |
1 (1.00) |
0.667 (1.00) |
0.639 (1.00) |
0.531 (1.00) |
0.159 (1.00) |
0.315 (1.00) |
|
4p loss | 0 (0%) | 156 |
0.259 (1.00) |
0.315 (1.00) |
0.692 (1.00) |
0.341 (1.00) |
0.0907 (1.00) |
0.795 (1.00) |
0.623 (1.00) |
0.305 (1.00) |
0.844 (1.00) |
0.0902 (1.00) |
|
4q loss | 0 (0%) | 158 |
0.691 (1.00) |
0.921 (1.00) |
0.537 (1.00) |
0.266 (1.00) |
0.0764 (1.00) |
0.923 (1.00) |
0.776 (1.00) |
0.313 (1.00) |
0.407 (1.00) |
0.173 (1.00) |
|
5p loss | 0 (0%) | 176 |
0.863 (1.00) |
0.303 (1.00) |
0.533 (1.00) |
0.325 (1.00) |
1 (1.00) |
0.681 (1.00) |
0.15 (1.00) |
1 (1.00) |
0.516 (1.00) |
0.0604 (1.00) |
|
5q loss | 0 (0%) | 166 |
0.255 (1.00) |
0.913 (1.00) |
0.158 (1.00) |
0.0793 (1.00) |
0.179 (1.00) |
0.3 (1.00) |
0.637 (1.00) |
0.199 (1.00) |
0.205 (1.00) |
0.179 (1.00) |
|
6p loss | 0 (0%) | 178 |
0.763 (1.00) |
0.327 (1.00) |
0.738 (1.00) |
0.0381 (1.00) |
1 (1.00) |
0.476 (1.00) |
0.0178 (1.00) |
0.888 (1.00) |
0.617 (1.00) |
0.669 (1.00) |
|
6q loss | 0 (0%) | 172 |
0.649 (1.00) |
0.549 (1.00) |
0.412 (1.00) |
0.258 (1.00) |
1 (1.00) |
0.153 (1.00) |
0.244 (1.00) |
0.637 (1.00) |
0.708 (1.00) |
0.427 (1.00) |
|
7p loss | 0 (0%) | 184 |
0.184 (1.00) |
0.253 (1.00) |
0.282 (1.00) |
0.645 (1.00) |
1 (1.00) |
1 (1.00) |
0.286 (1.00) |
1 (1.00) |
0.569 (1.00) |
0.155 (1.00) |
|
7q loss | 0 (0%) | 181 |
0.178 (1.00) |
0.3 (1.00) |
0.0831 (1.00) |
0.278 (1.00) |
1 (1.00) |
0.452 (1.00) |
0.335 (1.00) |
0.811 (1.00) |
0.573 (1.00) |
0.312 (1.00) |
|
8p loss | 0 (0%) | 168 |
0.918 (1.00) |
0.247 (1.00) |
0.622 (1.00) |
0.221 (1.00) |
1 (1.00) |
0.224 (1.00) |
0.395 (1.00) |
0.736 (1.00) |
0.00107 (0.778) |
0.337 (1.00) |
|
9p loss | 0 (0%) | 154 |
0.0454 (1.00) |
0.936 (1.00) |
0.557 (1.00) |
0.135 (1.00) |
0.609 (1.00) |
0.745 (1.00) |
0.477 (1.00) |
0.726 (1.00) |
0.738 (1.00) |
0.839 (1.00) |
|
9q loss | 0 (0%) | 172 |
0.561 (1.00) |
0.244 (1.00) |
0.168 (1.00) |
0.527 (1.00) |
0.0999 (1.00) |
0.0202 (1.00) |
0.319 (1.00) |
0.259 (1.00) |
0.64 (1.00) |
0.345 (1.00) |
|
10p loss | 0 (0%) | 173 |
0.252 (1.00) |
0.814 (1.00) |
0.571 (1.00) |
0.0771 (1.00) |
0.0882 (1.00) |
0.311 (1.00) |
0.481 (1.00) |
0.784 (1.00) |
0.737 (1.00) |
0.162 (1.00) |
|
10q loss | 0 (0%) | 175 |
0.337 (1.00) |
0.354 (1.00) |
1 (1.00) |
0.00511 (1.00) |
0.0664 (1.00) |
0.234 (1.00) |
0.9 (1.00) |
1 (1.00) |
0.48 (1.00) |
0.694 (1.00) |
|
11p loss | 0 (0%) | 174 |
0.527 (1.00) |
0.0801 (1.00) |
1 (1.00) |
0.374 (1.00) |
1 (1.00) |
0.136 (1.00) |
0.658 (1.00) |
0.0276 (1.00) |
0.785 (1.00) |
0.935 (1.00) |
|
11q loss | 0 (0%) | 175 |
0.126 (1.00) |
0.571 (1.00) |
0.131 (1.00) |
0.655 (1.00) |
1 (1.00) |
0.393 (1.00) |
0.661 (1.00) |
0.1 (1.00) |
0.583 (1.00) |
0.7 (1.00) |
|
12p loss | 0 (0%) | 173 |
0.174 (1.00) |
0.325 (1.00) |
1 (1.00) |
0.322 (1.00) |
0.425 (1.00) |
0.634 (1.00) |
0.00356 (1.00) |
0.81 (1.00) |
0.0989 (1.00) |
0.00245 (1.00) |
|
12q loss | 0 (0%) | 177 |
0.41 (1.00) |
0.639 (1.00) |
0.32 (1.00) |
0.597 (1.00) |
1 (1.00) |
0.522 (1.00) |
0.293 (1.00) |
0.713 (1.00) |
0.413 (1.00) |
0.193 (1.00) |
|
13q loss | 0 (0%) | 181 |
0.679 (1.00) |
0.868 (1.00) |
1 (1.00) |
0.575 (1.00) |
0.207 (1.00) |
0.273 (1.00) |
0.467 (1.00) |
0.0156 (1.00) |
0.522 (1.00) |
0.44 (1.00) |
|
14q loss | 0 (0%) | 170 |
0.547 (1.00) |
0.0438 (1.00) |
0.446 (1.00) |
0.964 (1.00) |
1 (1.00) |
0.337 (1.00) |
0.446 (1.00) |
0.76 (1.00) |
0.251 (1.00) |
0.616 (1.00) |
|
15q loss | 0 (0%) | 170 |
0.62 (1.00) |
0.197 (1.00) |
1 (1.00) |
0.0774 (1.00) |
0.00142 (1.00) |
0.528 (1.00) |
0.657 (1.00) |
0.831 (1.00) |
0.937 (1.00) |
0.849 (1.00) |
|
16p loss | 0 (0%) | 171 |
0.48 (1.00) |
0.65 (1.00) |
0.599 (1.00) |
0.291 (1.00) |
0.112 (1.00) |
0.757 (1.00) |
0.562 (1.00) |
0.449 (1.00) |
0.879 (1.00) |
0.667 (1.00) |
|
16q loss | 0 (0%) | 168 |
0.481 (1.00) |
0.904 (1.00) |
0.622 (1.00) |
0.447 (1.00) |
0.0242 (1.00) |
0.49 (1.00) |
0.367 (1.00) |
0.548 (1.00) |
0.62 (1.00) |
0.923 (1.00) |
|
17p loss | 0 (0%) | 148 |
0.883 (1.00) |
0.283 (1.00) |
0.142 (1.00) |
0.0046 (1.00) |
0.0355 (1.00) |
0.456 (1.00) |
0.403 (1.00) |
0.116 (1.00) |
0.679 (1.00) |
0.869 (1.00) |
|
17q loss | 0 (0%) | 176 |
0.198 (1.00) |
0.623 (1.00) |
0.753 (1.00) |
0.0633 (1.00) |
0.351 (1.00) |
0.341 (1.00) |
0.814 (1.00) |
0.392 (1.00) |
0.749 (1.00) |
0.748 (1.00) |
|
18p loss | 0 (0%) | 172 |
0.484 (1.00) |
0.79 (1.00) |
0.785 (1.00) |
0.625 (1.00) |
1 (1.00) |
0.194 (1.00) |
0.186 (1.00) |
0.329 (1.00) |
0.293 (1.00) |
0.481 (1.00) |
|
18q loss | 0 (0%) | 158 |
0.385 (1.00) |
0.891 (1.00) |
1 (1.00) |
0.826 (1.00) |
1 (1.00) |
0.283 (1.00) |
0.102 (1.00) |
0.0306 (1.00) |
0.081 (1.00) |
0.527 (1.00) |
|
19p loss | 0 (0%) | 167 |
0.868 (1.00) |
0.617 (1.00) |
0.471 (1.00) |
0.372 (1.00) |
1 (1.00) |
1 (1.00) |
0.504 (1.00) |
0.404 (1.00) |
0.567 (1.00) |
0.297 (1.00) |
|
19q loss | 0 (0%) | 173 |
0.771 (1.00) |
0.0602 (1.00) |
0.571 (1.00) |
0.286 (1.00) |
1 (1.00) |
0.738 (1.00) |
0.349 (1.00) |
0.483 (1.00) |
0.763 (1.00) |
0.519 (1.00) |
|
20p loss | 0 (0%) | 182 |
0.337 (1.00) |
0.763 (1.00) |
0.077 (1.00) |
0.758 (1.00) |
0.175 (1.00) |
0.118 (1.00) |
0.113 (1.00) |
0.00908 (1.00) |
0.554 (1.00) |
0.442 (1.00) |
|
21q loss | 0 (0%) | 151 |
0.76 (1.00) |
0.309 (1.00) |
0.849 (1.00) |
0.633 (1.00) |
0.132 (1.00) |
0.812 (1.00) |
0.602 (1.00) |
0.546 (1.00) |
0.492 (1.00) |
0.421 (1.00) |
|
22q loss | 0 (0%) | 162 |
0.416 (1.00) |
0.951 (1.00) |
1 (1.00) |
0.169 (1.00) |
0.0516 (1.00) |
0.831 (1.00) |
0.446 (1.00) |
0.459 (1.00) |
0.512 (1.00) |
0.621 (1.00) |
|
Xq loss | 0 (0%) | 179 |
0.204 (1.00) |
0.0916 (1.00) |
1 (1.00) |
0.941 (1.00) |
0.267 (1.00) |
1 (1.00) |
0.436 (1.00) |
0.0547 (1.00) |
0.434 (1.00) |
0.359 (1.00) |
P value = 1e-04 (t-test), Q value = 0.073
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 166 | 4.6 (6.5) |
2P GAIN CNV | 11 | 1.5 (1.9) |
2P GAIN WILD-TYPE | 155 | 4.9 (6.7) |
P value = 5.92e-06 (t-test), Q value = 0.0043
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 166 | 4.6 (6.5) |
2Q GAIN CNV | 13 | 1.2 (1.8) |
2Q GAIN WILD-TYPE | 153 | 4.9 (6.7) |
P value = 0.000203 (t-test), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 166 | 4.6 (6.5) |
8Q LOSS CNV | 5 | 0.6 (1.3) |
8Q LOSS WILD-TYPE | 161 | 4.8 (6.6) |
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = STAD-TP.clin.merged.picked.txt
-
Number of patients = 187
-
Number of significantly arm-level cnvs = 74
-
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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.