This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 78 arm-level events and 12 molecular subtypes across 165 patients, 8 significant findings detected with P value < 0.05 and Q value < 0.25.
-
3q gain cnv correlated to 'CN_CNMF'.
-
7p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
7q gain cnv correlated to 'CN_CNMF'.
-
8q gain cnv correlated to 'CN_CNMF'.
-
13q gain cnv correlated to 'CN_CNMF'.
-
16q gain cnv correlated to 'CN_CNMF'.
-
18q loss cnv correlated to 'CN_CNMF'.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
7p gain | 102 (62%) | 63 |
0.00235 (1.00) |
0.00294 (1.00) |
1e-05 (0.00899) |
0.00335 (1.00) |
0.484 (1.00) |
0.377 (1.00) |
0.0199 (1.00) |
0.00022 (0.196) |
0.0404 (1.00) |
0.0966 (1.00) |
0.597 (1.00) |
0.812 (1.00) |
3q gain | 34 (21%) | 131 |
0.606 (1.00) |
0.614 (1.00) |
0.00018 (0.161) |
0.868 (1.00) |
0.25 (1.00) |
0.42 (1.00) |
0.416 (1.00) |
0.224 (1.00) |
0.219 (1.00) |
0.317 (1.00) |
0.658 (1.00) |
0.896 (1.00) |
7q gain | 85 (52%) | 80 |
0.0473 (1.00) |
0.00761 (1.00) |
2e-05 (0.0179) |
0.136 (1.00) |
0.618 (1.00) |
0.948 (1.00) |
0.0428 (1.00) |
0.00285 (1.00) |
0.499 (1.00) |
0.829 (1.00) |
0.857 (1.00) |
0.854 (1.00) |
8q gain | 89 (54%) | 76 |
0.0365 (1.00) |
0.275 (1.00) |
2e-05 (0.0179) |
0.21 (1.00) |
0.546 (1.00) |
0.789 (1.00) |
0.57 (1.00) |
0.131 (1.00) |
0.243 (1.00) |
0.0655 (1.00) |
0.0206 (1.00) |
0.374 (1.00) |
13q gain | 113 (68%) | 52 |
0.284 (1.00) |
0.381 (1.00) |
1e-05 (0.00899) |
0.071 (1.00) |
0.838 (1.00) |
0.32 (1.00) |
0.0044 (1.00) |
0.0265 (1.00) |
0.00315 (1.00) |
0.0651 (1.00) |
0.713 (1.00) |
0.473 (1.00) |
16q gain | 41 (25%) | 124 |
0.0511 (1.00) |
0.592 (1.00) |
3e-05 (0.0268) |
0.233 (1.00) |
1 (1.00) |
0.667 (1.00) |
0.0302 (1.00) |
0.0438 (1.00) |
0.0211 (1.00) |
0.244 (1.00) |
0.23 (1.00) |
0.917 (1.00) |
18q loss | 138 (84%) | 27 |
0.0204 (1.00) |
0.176 (1.00) |
4e-05 (0.0358) |
0.0124 (1.00) |
0.796 (1.00) |
0.486 (1.00) |
0.888 (1.00) |
0.68 (1.00) |
0.427 (1.00) |
0.0273 (1.00) |
0.514 (1.00) |
0.535 (1.00) |
1p gain | 12 (7%) | 153 |
0.511 (1.00) |
0.941 (1.00) |
0.828 (1.00) |
0.528 (1.00) |
0.0317 (1.00) |
0.0176 (1.00) |
0.219 (1.00) |
0.768 (1.00) |
0.94 (1.00) |
0.46 (1.00) |
0.868 (1.00) |
0.651 (1.00) |
1q gain | 34 (21%) | 131 |
0.586 (1.00) |
0.654 (1.00) |
0.138 (1.00) |
0.314 (1.00) |
0.0704 (1.00) |
0.211 (1.00) |
0.541 (1.00) |
0.946 (1.00) |
0.542 (1.00) |
0.881 (1.00) |
0.871 (1.00) |
0.368 (1.00) |
2p gain | 41 (25%) | 124 |
0.509 (1.00) |
0.0194 (1.00) |
0.259 (1.00) |
0.0255 (1.00) |
0.667 (1.00) |
0.642 (1.00) |
0.046 (1.00) |
0.0394 (1.00) |
0.188 (1.00) |
0.0773 (1.00) |
0.724 (1.00) |
0.503 (1.00) |
2q gain | 43 (26%) | 122 |
0.092 (1.00) |
0.057 (1.00) |
0.122 (1.00) |
0.0599 (1.00) |
0.72 (1.00) |
0.828 (1.00) |
0.0823 (1.00) |
0.00933 (1.00) |
0.215 (1.00) |
0.304 (1.00) |
0.162 (1.00) |
0.192 (1.00) |
3p gain | 27 (16%) | 138 |
1 (1.00) |
0.902 (1.00) |
0.00048 (0.428) |
0.654 (1.00) |
0.0874 (1.00) |
0.454 (1.00) |
0.426 (1.00) |
0.621 (1.00) |
0.378 (1.00) |
0.361 (1.00) |
0.656 (1.00) |
0.825 (1.00) |
4p gain | 9 (5%) | 156 |
1 (1.00) |
0.791 (1.00) |
0.965 (1.00) |
0.766 (1.00) |
0.0866 (1.00) |
0.171 (1.00) |
0.355 (1.00) |
0.437 (1.00) |
0.221 (1.00) |
0.376 (1.00) |
0.742 (1.00) |
0.95 (1.00) |
4q gain | 5 (3%) | 160 |
0.297 (1.00) |
0.649 (1.00) |
0.677 (1.00) |
0.218 (1.00) |
0.486 (1.00) |
0.554 (1.00) |
1 (1.00) |
0.89 (1.00) |
1 (1.00) |
|||
5p gain | 36 (22%) | 129 |
0.201 (1.00) |
0.099 (1.00) |
0.00164 (1.00) |
0.0992 (1.00) |
0.216 (1.00) |
0.686 (1.00) |
0.045 (1.00) |
0.00377 (1.00) |
0.192 (1.00) |
0.924 (1.00) |
0.493 (1.00) |
0.629 (1.00) |
5q gain | 24 (15%) | 141 |
0.243 (1.00) |
0.0869 (1.00) |
0.00675 (1.00) |
0.0742 (1.00) |
0.185 (1.00) |
0.961 (1.00) |
0.51 (1.00) |
0.164 (1.00) |
0.246 (1.00) |
0.522 (1.00) |
1 (1.00) |
0.654 (1.00) |
6p gain | 41 (25%) | 124 |
0.336 (1.00) |
0.563 (1.00) |
0.0089 (1.00) |
0.00351 (1.00) |
0.774 (1.00) |
0.254 (1.00) |
0.616 (1.00) |
0.594 (1.00) |
0.24 (1.00) |
0.3 (1.00) |
0.279 (1.00) |
0.811 (1.00) |
6q gain | 36 (22%) | 129 |
0.671 (1.00) |
0.229 (1.00) |
0.0166 (1.00) |
0.00655 (1.00) |
0.844 (1.00) |
0.472 (1.00) |
0.663 (1.00) |
0.33 (1.00) |
0.341 (1.00) |
0.581 (1.00) |
0.202 (1.00) |
0.563 (1.00) |
8p gain | 42 (25%) | 123 |
0.419 (1.00) |
0.235 (1.00) |
0.00179 (1.00) |
0.516 (1.00) |
0.454 (1.00) |
0.0912 (1.00) |
0.154 (1.00) |
0.333 (1.00) |
0.812 (1.00) |
0.287 (1.00) |
0.916 (1.00) |
0.142 (1.00) |
9p gain | 42 (25%) | 123 |
0.0167 (1.00) |
0.199 (1.00) |
0.441 (1.00) |
0.166 (1.00) |
0.651 (1.00) |
0.229 (1.00) |
0.0223 (1.00) |
0.994 (1.00) |
0.274 (1.00) |
0.328 (1.00) |
0.865 (1.00) |
0.868 (1.00) |
9q gain | 33 (20%) | 132 |
0.0153 (1.00) |
0.21 (1.00) |
0.282 (1.00) |
0.468 (1.00) |
0.564 (1.00) |
0.0987 (1.00) |
0.242 (1.00) |
0.162 (1.00) |
0.786 (1.00) |
0.622 (1.00) |
0.831 (1.00) |
0.931 (1.00) |
10p gain | 13 (8%) | 152 |
1 (1.00) |
0.919 (1.00) |
0.339 (1.00) |
0.712 (1.00) |
0.666 (1.00) |
0.751 (1.00) |
0.088 (1.00) |
0.0416 (1.00) |
0.654 (1.00) |
0.918 (1.00) |
0.613 (1.00) |
0.789 (1.00) |
10q gain | 7 (4%) | 158 |
0.519 (1.00) |
0.0815 (1.00) |
0.256 (1.00) |
1 (1.00) |
1 (1.00) |
0.871 (1.00) |
0.411 (1.00) |
0.0833 (1.00) |
0.77 (1.00) |
0.862 (1.00) |
||
11p gain | 32 (19%) | 133 |
0.135 (1.00) |
0.39 (1.00) |
0.00896 (1.00) |
0.42 (1.00) |
0.721 (1.00) |
0.361 (1.00) |
0.241 (1.00) |
0.0406 (1.00) |
0.0204 (1.00) |
0.206 (1.00) |
0.653 (1.00) |
0.538 (1.00) |
11q gain | 26 (16%) | 139 |
0.238 (1.00) |
0.431 (1.00) |
0.00209 (1.00) |
0.019 (1.00) |
0.571 (1.00) |
0.302 (1.00) |
0.05 (1.00) |
0.00115 (1.00) |
0.0258 (1.00) |
0.591 (1.00) |
0.12 (1.00) |
0.157 (1.00) |
12p gain | 33 (20%) | 132 |
0.691 (1.00) |
0.481 (1.00) |
0.237 (1.00) |
0.728 (1.00) |
0.18 (1.00) |
0.123 (1.00) |
0.232 (1.00) |
0.325 (1.00) |
0.372 (1.00) |
0.552 (1.00) |
0.283 (1.00) |
0.872 (1.00) |
12q gain | 24 (15%) | 141 |
0.775 (1.00) |
0.523 (1.00) |
0.743 (1.00) |
0.307 (1.00) |
0.263 (1.00) |
0.213 (1.00) |
0.196 (1.00) |
0.815 (1.00) |
0.224 (1.00) |
0.739 (1.00) |
0.0541 (1.00) |
0.949 (1.00) |
14q gain | 8 (5%) | 157 |
0.833 (1.00) |
0.914 (1.00) |
0.112 (1.00) |
0.226 (1.00) |
0.52 (1.00) |
0.547 (1.00) |
0.412 (1.00) |
0.403 (1.00) |
0.13 (1.00) |
0.862 (1.00) |
||
15q gain | 3 (2%) | 162 |
0.418 (1.00) |
0.484 (1.00) |
0.35 (1.00) |
0.695 (1.00) |
||||||||
16p gain | 41 (25%) | 124 |
0.148 (1.00) |
0.853 (1.00) |
0.00124 (1.00) |
0.272 (1.00) |
0.924 (1.00) |
1 (1.00) |
0.251 (1.00) |
0.321 (1.00) |
0.152 (1.00) |
0.678 (1.00) |
0.338 (1.00) |
0.981 (1.00) |
17p gain | 8 (5%) | 157 |
0.11 (1.00) |
0.378 (1.00) |
0.233 (1.00) |
0.466 (1.00) |
1 (1.00) |
0.873 (1.00) |
0.146 (1.00) |
0.558 (1.00) |
0.49 (1.00) |
0.44 (1.00) |
||
17q gain | 32 (19%) | 133 |
0.198 (1.00) |
0.943 (1.00) |
0.0065 (1.00) |
0.419 (1.00) |
0.88 (1.00) |
0.941 (1.00) |
0.418 (1.00) |
0.372 (1.00) |
0.0552 (1.00) |
0.463 (1.00) |
0.12 (1.00) |
0.637 (1.00) |
18p gain | 8 (5%) | 157 |
0.515 (1.00) |
0.39 (1.00) |
0.218 (1.00) |
0.73 (1.00) |
0.806 (1.00) |
0.736 (1.00) |
0.885 (1.00) |
0.925 (1.00) |
0.507 (1.00) |
0.559 (1.00) |
1 (1.00) |
0.891 (1.00) |
18q gain | 6 (4%) | 159 |
0.791 (1.00) |
0.382 (1.00) |
0.492 (1.00) |
0.892 (1.00) |
0.458 (1.00) |
0.891 (1.00) |
0.655 (1.00) |
0.63 (1.00) |
1 (1.00) |
0.891 (1.00) |
||
19p gain | 33 (20%) | 132 |
0.0661 (1.00) |
0.418 (1.00) |
0.105 (1.00) |
0.766 (1.00) |
0.544 (1.00) |
0.461 (1.00) |
0.572 (1.00) |
0.637 (1.00) |
0.14 (1.00) |
0.957 (1.00) |
1 (1.00) |
0.974 (1.00) |
19q gain | 32 (19%) | 133 |
0.0824 (1.00) |
0.532 (1.00) |
0.073 (1.00) |
0.53 (1.00) |
0.958 (1.00) |
0.595 (1.00) |
0.0784 (1.00) |
0.353 (1.00) |
0.356 (1.00) |
0.579 (1.00) |
1 (1.00) |
0.973 (1.00) |
20p gain | 109 (66%) | 56 |
0.0959 (1.00) |
0.726 (1.00) |
0.139 (1.00) |
0.254 (1.00) |
0.133 (1.00) |
0.833 (1.00) |
0.208 (1.00) |
0.13 (1.00) |
0.0972 (1.00) |
0.047 (1.00) |
0.307 (1.00) |
0.0757 (1.00) |
20q gain | 145 (88%) | 20 |
0.00785 (1.00) |
0.162 (1.00) |
0.00058 (0.516) |
0.234 (1.00) |
0.161 (1.00) |
0.339 (1.00) |
0.123 (1.00) |
0.0199 (1.00) |
0.0443 (1.00) |
0.364 (1.00) |
0.361 (1.00) |
1 (1.00) |
21q gain | 10 (6%) | 155 |
0.537 (1.00) |
0.656 (1.00) |
0.635 (1.00) |
1 (1.00) |
0.619 (1.00) |
0.792 (1.00) |
0.886 (1.00) |
0.737 (1.00) |
0.291 (1.00) |
0.725 (1.00) |
||
22q gain | 9 (5%) | 156 |
0.73 (1.00) |
0.0614 (1.00) |
0.0729 (1.00) |
1 (1.00) |
0.426 (1.00) |
0.234 (1.00) |
0.48 (1.00) |
0.0828 (1.00) |
1 (1.00) |
1 (1.00) |
||
xq gain | 34 (21%) | 131 |
0.156 (1.00) |
0.382 (1.00) |
0.0456 (1.00) |
0.293 (1.00) |
0.819 (1.00) |
0.302 (1.00) |
0.16 (1.00) |
0.548 (1.00) |
0.98 (1.00) |
1 (1.00) |
0.459 (1.00) |
0.21 (1.00) |
1p loss | 46 (28%) | 119 |
0.69 (1.00) |
0.0263 (1.00) |
0.052 (1.00) |
0.185 (1.00) |
0.935 (1.00) |
0.206 (1.00) |
0.805 (1.00) |
0.071 (1.00) |
0.444 (1.00) |
0.609 (1.00) |
0.559 (1.00) |
0.568 (1.00) |
1q loss | 26 (16%) | 139 |
0.912 (1.00) |
0.0563 (1.00) |
0.262 (1.00) |
0.0284 (1.00) |
0.844 (1.00) |
0.528 (1.00) |
0.892 (1.00) |
0.651 (1.00) |
0.563 (1.00) |
0.228 (1.00) |
0.502 (1.00) |
0.274 (1.00) |
2p loss | 11 (7%) | 154 |
0.64 (1.00) |
0.751 (1.00) |
0.00387 (1.00) |
0.484 (1.00) |
0.907 (1.00) |
0.542 (1.00) |
0.123 (1.00) |
0.241 (1.00) |
0.433 (1.00) |
0.604 (1.00) |
||
2q loss | 6 (4%) | 159 |
1 (1.00) |
0.569 (1.00) |
0.0519 (1.00) |
0.102 (1.00) |
0.307 (1.00) |
0.201 (1.00) |
0.225 (1.00) |
0.206 (1.00) |
0.468 (1.00) |
|||
3p loss | 15 (9%) | 150 |
1 (1.00) |
0.366 (1.00) |
0.206 (1.00) |
0.775 (1.00) |
0.259 (1.00) |
0.896 (1.00) |
0.159 (1.00) |
0.537 (1.00) |
0.454 (1.00) |
0.137 (1.00) |
0.0969 (1.00) |
0.0429 (1.00) |
3q loss | 10 (6%) | 155 |
0.516 (1.00) |
0.793 (1.00) |
0.196 (1.00) |
0.412 (1.00) |
0.325 (1.00) |
0.659 (1.00) |
0.038 (1.00) |
0.287 (1.00) |
0.493 (1.00) |
0.00956 (1.00) |
0.42 (1.00) |
0.368 (1.00) |
4p loss | 59 (36%) | 106 |
0.668 (1.00) |
0.373 (1.00) |
0.00193 (1.00) |
0.0275 (1.00) |
0.97 (1.00) |
0.513 (1.00) |
0.525 (1.00) |
0.647 (1.00) |
0.975 (1.00) |
0.0986 (1.00) |
0.225 (1.00) |
0.207 (1.00) |
4q loss | 66 (40%) | 99 |
0.781 (1.00) |
0.269 (1.00) |
0.00111 (0.986) |
0.0396 (1.00) |
0.818 (1.00) |
0.518 (1.00) |
0.702 (1.00) |
0.266 (1.00) |
0.812 (1.00) |
0.217 (1.00) |
0.566 (1.00) |
0.919 (1.00) |
5p loss | 26 (16%) | 139 |
0.238 (1.00) |
0.816 (1.00) |
0.137 (1.00) |
0.178 (1.00) |
0.527 (1.00) |
0.0647 (1.00) |
0.695 (1.00) |
0.228 (1.00) |
0.723 (1.00) |
0.58 (1.00) |
0.168 (1.00) |
0.246 (1.00) |
5q loss | 40 (24%) | 125 |
0.0901 (1.00) |
0.0113 (1.00) |
0.217 (1.00) |
0.167 (1.00) |
1 (1.00) |
0.544 (1.00) |
0.993 (1.00) |
0.206 (1.00) |
0.912 (1.00) |
0.211 (1.00) |
0.112 (1.00) |
0.228 (1.00) |
6p loss | 13 (8%) | 152 |
0.543 (1.00) |
0.929 (1.00) |
0.699 (1.00) |
0.123 (1.00) |
0.312 (1.00) |
0.36 (1.00) |
0.725 (1.00) |
0.241 (1.00) |
0.561 (1.00) |
0.253 (1.00) |
||
6q loss | 22 (13%) | 143 |
0.169 (1.00) |
0.644 (1.00) |
0.153 (1.00) |
0.418 (1.00) |
0.451 (1.00) |
0.605 (1.00) |
0.134 (1.00) |
0.0374 (1.00) |
0.263 (1.00) |
0.41 (1.00) |
0.0122 (1.00) |
0.556 (1.00) |
7q loss | 3 (2%) | 162 |
0.357 (1.00) |
0.787 (1.00) |
0.773 (1.00) |
0.599 (1.00) |
1 (1.00) |
0.858 (1.00) |
1 (1.00) |
|||||
8p loss | 73 (44%) | 92 |
0.122 (1.00) |
0.245 (1.00) |
0.134 (1.00) |
0.965 (1.00) |
0.786 (1.00) |
0.252 (1.00) |
0.368 (1.00) |
0.293 (1.00) |
0.893 (1.00) |
0.973 (1.00) |
0.734 (1.00) |
0.229 (1.00) |
8q loss | 11 (7%) | 154 |
0.688 (1.00) |
0.715 (1.00) |
0.409 (1.00) |
0.465 (1.00) |
0.795 (1.00) |
0.279 (1.00) |
0.185 (1.00) |
0.237 (1.00) |
0.866 (1.00) |
0.302 (1.00) |
0.167 (1.00) |
0.407 (1.00) |
9p loss | 23 (14%) | 142 |
0.636 (1.00) |
0.617 (1.00) |
0.321 (1.00) |
0.14 (1.00) |
0.749 (1.00) |
0.567 (1.00) |
0.82 (1.00) |
0.955 (1.00) |
0.311 (1.00) |
0.0462 (1.00) |
0.708 (1.00) |
0.0384 (1.00) |
9q loss | 23 (14%) | 142 |
0.209 (1.00) |
0.447 (1.00) |
0.28 (1.00) |
0.138 (1.00) |
0.943 (1.00) |
0.904 (1.00) |
0.988 (1.00) |
0.382 (1.00) |
0.0697 (1.00) |
0.00165 (1.00) |
0.465 (1.00) |
0.0142 (1.00) |
10p loss | 33 (20%) | 132 |
0.144 (1.00) |
0.173 (1.00) |
0.139 (1.00) |
0.0658 (1.00) |
0.145 (1.00) |
0.239 (1.00) |
0.876 (1.00) |
0.509 (1.00) |
0.838 (1.00) |
0.115 (1.00) |
0.817 (1.00) |
0.747 (1.00) |
10q loss | 38 (23%) | 127 |
0.177 (1.00) |
0.157 (1.00) |
0.0584 (1.00) |
0.0919 (1.00) |
0.129 (1.00) |
0.0314 (1.00) |
0.495 (1.00) |
0.162 (1.00) |
0.683 (1.00) |
0.0875 (1.00) |
0.899 (1.00) |
0.537 (1.00) |
11p loss | 23 (14%) | 142 |
0.241 (1.00) |
0.375 (1.00) |
0.00622 (1.00) |
0.206 (1.00) |
0.226 (1.00) |
0.175 (1.00) |
0.465 (1.00) |
0.0906 (1.00) |
0.977 (1.00) |
0.742 (1.00) |
0.601 (1.00) |
0.29 (1.00) |
11q loss | 30 (18%) | 135 |
0.0546 (1.00) |
0.205 (1.00) |
0.00694 (1.00) |
0.0255 (1.00) |
0.605 (1.00) |
0.383 (1.00) |
0.11 (1.00) |
0.00759 (1.00) |
0.205 (1.00) |
0.375 (1.00) |
0.414 (1.00) |
0.665 (1.00) |
12p loss | 22 (13%) | 143 |
0.424 (1.00) |
0.285 (1.00) |
0.658 (1.00) |
0.401 (1.00) |
0.694 (1.00) |
0.077 (1.00) |
0.922 (1.00) |
0.217 (1.00) |
0.451 (1.00) |
0.778 (1.00) |
0.0671 (1.00) |
0.509 (1.00) |
12q loss | 19 (12%) | 146 |
0.503 (1.00) |
0.769 (1.00) |
0.237 (1.00) |
0.932 (1.00) |
0.557 (1.00) |
0.26 (1.00) |
0.822 (1.00) |
0.112 (1.00) |
0.379 (1.00) |
0.319 (1.00) |
0.272 (1.00) |
0.867 (1.00) |
13q loss | 8 (5%) | 157 |
0.516 (1.00) |
1 (1.00) |
0.654 (1.00) |
0.105 (1.00) |
0.0551 (1.00) |
0.431 (1.00) |
1 (1.00) |
0.89 (1.00) |
0.177 (1.00) |
1 (1.00) |
||
14q loss | 67 (41%) | 98 |
0.502 (1.00) |
0.246 (1.00) |
0.0198 (1.00) |
0.572 (1.00) |
0.805 (1.00) |
0.494 (1.00) |
0.107 (1.00) |
0.166 (1.00) |
0.332 (1.00) |
0.201 (1.00) |
0.752 (1.00) |
0.782 (1.00) |
15q loss | 73 (44%) | 92 |
0.447 (1.00) |
0.112 (1.00) |
0.00069 (0.613) |
1 (1.00) |
0.0898 (1.00) |
0.249 (1.00) |
0.866 (1.00) |
0.501 (1.00) |
0.818 (1.00) |
0.633 (1.00) |
0.907 (1.00) |
0.745 (1.00) |
16p loss | 9 (5%) | 156 |
0.377 (1.00) |
0.759 (1.00) |
0.0981 (1.00) |
0.0619 (1.00) |
0.653 (1.00) |
0.633 (1.00) |
0.965 (1.00) |
0.964 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.25 (1.00) |
0.489 (1.00) |
16q loss | 15 (9%) | 150 |
0.279 (1.00) |
0.677 (1.00) |
0.0485 (1.00) |
0.334 (1.00) |
0.726 (1.00) |
0.899 (1.00) |
0.824 (1.00) |
0.9 (1.00) |
0.869 (1.00) |
1 (1.00) |
0.939 (1.00) |
0.963 (1.00) |
17p loss | 107 (65%) | 58 |
0.207 (1.00) |
0.374 (1.00) |
0.0941 (1.00) |
0.197 (1.00) |
0.971 (1.00) |
0.321 (1.00) |
0.8 (1.00) |
0.962 (1.00) |
0.981 (1.00) |
0.396 (1.00) |
0.29 (1.00) |
0.665 (1.00) |
17q loss | 26 (16%) | 139 |
0.904 (1.00) |
0.737 (1.00) |
0.0284 (1.00) |
0.0898 (1.00) |
0.749 (1.00) |
0.975 (1.00) |
0.315 (1.00) |
0.627 (1.00) |
0.87 (1.00) |
0.947 (1.00) |
0.424 (1.00) |
0.477 (1.00) |
18p loss | 128 (78%) | 37 |
0.0586 (1.00) |
0.71 (1.00) |
0.00135 (1.00) |
0.0259 (1.00) |
0.601 (1.00) |
0.152 (1.00) |
0.657 (1.00) |
0.233 (1.00) |
0.17 (1.00) |
0.163 (1.00) |
0.615 (1.00) |
0.594 (1.00) |
19p loss | 21 (13%) | 144 |
0.728 (1.00) |
0.835 (1.00) |
0.134 (1.00) |
0.0305 (1.00) |
0.646 (1.00) |
0.806 (1.00) |
0.382 (1.00) |
0.33 (1.00) |
0.378 (1.00) |
0.0188 (1.00) |
0.964 (1.00) |
0.74 (1.00) |
19q loss | 20 (12%) | 145 |
0.833 (1.00) |
0.503 (1.00) |
0.0692 (1.00) |
0.0826 (1.00) |
0.822 (1.00) |
0.777 (1.00) |
0.436 (1.00) |
0.366 (1.00) |
0.0679 (1.00) |
0.00862 (1.00) |
1 (1.00) |
0.745 (1.00) |
20p loss | 23 (14%) | 142 |
1 (1.00) |
0.951 (1.00) |
0.0508 (1.00) |
0.283 (1.00) |
0.378 (1.00) |
0.985 (1.00) |
0.485 (1.00) |
0.3 (1.00) |
0.0321 (1.00) |
0.0212 (1.00) |
0.306 (1.00) |
0.0142 (1.00) |
21q loss | 68 (41%) | 97 |
0.288 (1.00) |
0.249 (1.00) |
0.417 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.53 (1.00) |
0.581 (1.00) |
0.833 (1.00) |
0.0161 (1.00) |
0.183 (1.00) |
0.224 (1.00) |
0.0686 (1.00) |
22q loss | 58 (35%) | 107 |
0.851 (1.00) |
0.309 (1.00) |
0.0644 (1.00) |
0.776 (1.00) |
0.75 (1.00) |
0.297 (1.00) |
0.0677 (1.00) |
0.0935 (1.00) |
0.00633 (1.00) |
0.181 (1.00) |
0.125 (1.00) |
0.0194 (1.00) |
xq loss | 25 (15%) | 140 |
0.911 (1.00) |
0.582 (1.00) |
0.867 (1.00) |
0.313 (1.00) |
0.548 (1.00) |
0.87 (1.00) |
0.807 (1.00) |
0.978 (1.00) |
0.917 (1.00) |
0.493 (1.00) |
0.474 (1.00) |
0.802 (1.00) |
P value = 0.00018 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
3Q GAIN MUTATED | 4 | 12 | 11 | 7 |
3Q GAIN WILD-TYPE | 62 | 20 | 20 | 29 |
P value = 1e-05 (Fisher's exact test), Q value = 0.009
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
7P GAIN MUTATED | 24 | 26 | 28 | 24 |
7P GAIN WILD-TYPE | 42 | 6 | 3 | 12 |
P value = 0.00022 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 55 | 35 | 41 | 30 |
7P GAIN MUTATED | 45 | 17 | 17 | 20 |
7P GAIN WILD-TYPE | 10 | 18 | 24 | 10 |
P value = 2e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
7Q GAIN MUTATED | 18 | 23 | 22 | 22 |
7Q GAIN WILD-TYPE | 48 | 9 | 9 | 14 |
P value = 2e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
8Q GAIN MUTATED | 29 | 13 | 15 | 32 |
8Q GAIN WILD-TYPE | 37 | 19 | 16 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.009
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
13Q GAIN MUTATED | 32 | 30 | 26 | 25 |
13Q GAIN WILD-TYPE | 34 | 2 | 5 | 11 |
P value = 3e-05 (Fisher's exact test), Q value = 0.027
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
16Q GAIN MUTATED | 5 | 15 | 13 | 8 |
16Q GAIN WILD-TYPE | 61 | 17 | 18 | 28 |
P value = 4e-05 (Fisher's exact test), Q value = 0.036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 32 | 31 | 36 |
18Q LOSS MUTATED | 45 | 28 | 31 | 34 |
18Q LOSS WILD-TYPE | 21 | 4 | 0 | 2 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtypes file = READ-TP.transferedmergedcluster.txt
-
Number of patients = 165
-
Number of significantly arm-level cnvs = 78
-
Number of molecular subtypes = 12
-
Exclude genes that fewer than K tumors have mutations, K = 3
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.