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 162 patients, 12 significant findings detected with P value < 0.05 and Q value < 0.25.
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6p gain cnv correlated to 'CN_CNMF'.
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6q gain cnv correlated to 'CN_CNMF'.
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7p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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7q gain cnv correlated to 'CN_CNMF'.
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8q gain cnv correlated to 'CN_CNMF'.
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13q gain cnv correlated to 'CN_CNMF'.
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16q gain cnv correlated to 'CN_CNMF'.
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4p loss cnv correlated to 'CN_CNMF'.
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4q loss cnv correlated to 'CN_CNMF'.
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18p loss cnv correlated to 'CN_CNMF'.
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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 | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | |
7p gain | 100 (62%) | 62 |
0.00239 (1.00) |
0.00528 (1.00) |
7.09e-06 (0.00646) |
0.00274 (1.00) |
0.489 (1.00) |
0.712 (1.00) |
0.00388 (1.00) |
0.000172 (0.155) |
0.0524 (1.00) |
0.02 (1.00) |
0.0369 (1.00) |
0.0705 (1.00) |
6p gain | 40 (25%) | 122 |
0.325 (1.00) |
0.274 (1.00) |
8.59e-05 (0.0775) |
0.00309 (1.00) |
0.767 (1.00) |
0.357 (1.00) |
0.828 (1.00) |
0.465 (1.00) |
0.258 (1.00) |
0.644 (1.00) |
0.41 (1.00) |
0.693 (1.00) |
6q gain | 35 (22%) | 127 |
0.671 (1.00) |
0.163 (1.00) |
2.86e-05 (0.0259) |
0.0252 (1.00) |
0.83 (1.00) |
0.516 (1.00) |
0.606 (1.00) |
0.338 (1.00) |
0.398 (1.00) |
0.437 (1.00) |
0.768 (1.00) |
0.72 (1.00) |
7q gain | 83 (51%) | 79 |
0.044 (1.00) |
0.0439 (1.00) |
7.54e-05 (0.068) |
0.202 (1.00) |
0.595 (1.00) |
0.927 (1.00) |
0.0695 (1.00) |
0.026 (1.00) |
0.495 (1.00) |
0.462 (1.00) |
0.377 (1.00) |
0.502 (1.00) |
8q gain | 88 (54%) | 74 |
0.00684 (1.00) |
0.035 (1.00) |
3.85e-05 (0.0348) |
0.0504 (1.00) |
0.519 (1.00) |
0.841 (1.00) |
0.0771 (1.00) |
0.131 (1.00) |
0.257 (1.00) |
0.122 (1.00) |
0.868 (1.00) |
0.319 (1.00) |
13q gain | 110 (68%) | 52 |
0.293 (1.00) |
0.768 (1.00) |
0.000148 (0.134) |
0.132 (1.00) |
0.821 (1.00) |
0.21 (1.00) |
0.399 (1.00) |
0.000579 (0.519) |
0.00472 (1.00) |
0.0373 (1.00) |
0.194 (1.00) |
0.401 (1.00) |
16q gain | 39 (24%) | 123 |
0.0523 (1.00) |
0.621 (1.00) |
3.96e-05 (0.0358) |
0.639 (1.00) |
1 (1.00) |
0.95 (1.00) |
0.0669 (1.00) |
0.455 (1.00) |
0.025 (1.00) |
0.109 (1.00) |
0.0258 (1.00) |
0.358 (1.00) |
4p loss | 58 (36%) | 104 |
0.618 (1.00) |
0.154 (1.00) |
2.3e-05 (0.0209) |
0.0118 (1.00) |
0.956 (1.00) |
0.368 (1.00) |
0.921 (1.00) |
0.902 (1.00) |
0.973 (1.00) |
0.0154 (1.00) |
0.534 (1.00) |
0.212 (1.00) |
4q loss | 65 (40%) | 97 |
0.786 (1.00) |
0.217 (1.00) |
1.47e-05 (0.0134) |
0.00589 (1.00) |
0.798 (1.00) |
0.579 (1.00) |
0.903 (1.00) |
0.777 (1.00) |
0.808 (1.00) |
0.0829 (1.00) |
0.909 (1.00) |
0.659 (1.00) |
18p loss | 125 (77%) | 37 |
0.0505 (1.00) |
0.249 (1.00) |
5.26e-06 (0.0048) |
0.0551 (1.00) |
0.558 (1.00) |
0.33 (1.00) |
0.304 (1.00) |
0.236 (1.00) |
0.172 (1.00) |
0.12 (1.00) |
0.177 (1.00) |
0.963 (1.00) |
18q loss | 135 (83%) | 27 |
0.0206 (1.00) |
0.0506 (1.00) |
1.21e-05 (0.011) |
0.0233 (1.00) |
0.799 (1.00) |
0.662 (1.00) |
0.54 (1.00) |
0.441 (1.00) |
0.384 (1.00) |
0.157 (1.00) |
0.0233 (1.00) |
0.559 (1.00) |
1p gain | 12 (7%) | 150 |
0.511 (1.00) |
0.716 (1.00) |
0.323 (1.00) |
0.467 (1.00) |
0.0321 (1.00) |
0.0154 (1.00) |
0.847 (1.00) |
1 (1.00) |
0.977 (1.00) |
1 (1.00) |
0.932 (1.00) |
0.854 (1.00) |
1q gain | 32 (20%) | 130 |
0.671 (1.00) |
1 (1.00) |
0.0191 (1.00) |
0.699 (1.00) |
0.0351 (1.00) |
0.257 (1.00) |
0.87 (1.00) |
0.923 (1.00) |
0.614 (1.00) |
0.664 (1.00) |
0.149 (1.00) |
0.324 (1.00) |
2p gain | 39 (24%) | 123 |
0.506 (1.00) |
0.54 (1.00) |
0.0556 (1.00) |
0.113 (1.00) |
0.648 (1.00) |
0.909 (1.00) |
0.0478 (1.00) |
0.091 (1.00) |
0.259 (1.00) |
0.0249 (1.00) |
0.898 (1.00) |
0.0332 (1.00) |
2q gain | 41 (25%) | 121 |
0.0874 (1.00) |
0.124 (1.00) |
0.0297 (1.00) |
0.0895 (1.00) |
0.693 (1.00) |
0.945 (1.00) |
0.0228 (1.00) |
0.0563 (1.00) |
0.257 (1.00) |
0.14 (1.00) |
0.533 (1.00) |
0.00853 (1.00) |
3p gain | 27 (17%) | 135 |
1 (1.00) |
0.8 (1.00) |
0.216 (1.00) |
0.588 (1.00) |
0.0894 (1.00) |
0.249 (1.00) |
0.484 (1.00) |
0.56 (1.00) |
0.42 (1.00) |
0.0919 (1.00) |
0.634 (1.00) |
0.594 (1.00) |
3q gain | 34 (21%) | 128 |
0.605 (1.00) |
1 (1.00) |
0.0914 (1.00) |
0.934 (1.00) |
0.251 (1.00) |
0.0905 (1.00) |
0.481 (1.00) |
0.346 (1.00) |
0.244 (1.00) |
0.187 (1.00) |
0.934 (1.00) |
0.841 (1.00) |
4p gain | 9 (6%) | 153 |
1 (1.00) |
0.171 (1.00) |
0.963 (1.00) |
1 (1.00) |
0.0881 (1.00) |
0.0931 (1.00) |
0.69 (1.00) |
0.154 (1.00) |
0.115 (1.00) |
0.309 (1.00) |
0.601 (1.00) |
0.0404 (1.00) |
4q gain | 5 (3%) | 157 |
0.297 (1.00) |
0.449 (1.00) |
0.986 (1.00) |
0.219 (1.00) |
0.587 (1.00) |
1 (1.00) |
1 (1.00) |
0.843 (1.00) |
0.843 (1.00) |
|||
5p gain | 34 (21%) | 128 |
0.181 (1.00) |
0.485 (1.00) |
0.0433 (1.00) |
0.124 (1.00) |
0.198 (1.00) |
0.473 (1.00) |
0.0338 (1.00) |
0.0448 (1.00) |
0.176 (1.00) |
0.725 (1.00) |
0.202 (1.00) |
0.504 (1.00) |
5q gain | 22 (14%) | 140 |
0.243 (1.00) |
0.421 (1.00) |
0.407 (1.00) |
0.0319 (1.00) |
0.0801 (1.00) |
0.689 (1.00) |
0.103 (1.00) |
0.0874 (1.00) |
0.374 (1.00) |
0.728 (1.00) |
0.253 (1.00) |
0.176 (1.00) |
8p gain | 39 (24%) | 123 |
0.586 (1.00) |
0.357 (1.00) |
0.0151 (1.00) |
0.617 (1.00) |
0.299 (1.00) |
0.305 (1.00) |
0.0283 (1.00) |
0.0934 (1.00) |
0.819 (1.00) |
0.169 (1.00) |
0.189 (1.00) |
0.827 (1.00) |
9p gain | 42 (26%) | 120 |
0.0158 (1.00) |
0.138 (1.00) |
0.629 (1.00) |
0.219 (1.00) |
0.667 (1.00) |
0.318 (1.00) |
0.778 (1.00) |
0.551 (1.00) |
0.286 (1.00) |
0.799 (1.00) |
0.13 (1.00) |
0.475 (1.00) |
9q gain | 33 (20%) | 129 |
0.0155 (1.00) |
0.141 (1.00) |
0.322 (1.00) |
0.515 (1.00) |
0.597 (1.00) |
0.309 (1.00) |
1 (1.00) |
0.715 (1.00) |
0.727 (1.00) |
0.708 (1.00) |
0.303 (1.00) |
0.574 (1.00) |
10p gain | 12 (7%) | 150 |
1 (1.00) |
0.753 (1.00) |
0.367 (1.00) |
0.321 (1.00) |
0.667 (1.00) |
0.736 (1.00) |
0.325 (1.00) |
0.261 (1.00) |
0.545 (1.00) |
1 (1.00) |
0.387 (1.00) |
0.0895 (1.00) |
10q gain | 6 (4%) | 156 |
0.517 (1.00) |
0.787 (1.00) |
0.297 (1.00) |
0.784 (1.00) |
1 (1.00) |
0.842 (1.00) |
0.534 (1.00) |
0.0952 (1.00) |
0.544 (1.00) |
1 (1.00) |
||
11p gain | 30 (19%) | 132 |
0.135 (1.00) |
0.187 (1.00) |
0.0209 (1.00) |
0.243 (1.00) |
0.83 (1.00) |
0.583 (1.00) |
0.235 (1.00) |
0.36 (1.00) |
0.0344 (1.00) |
0.182 (1.00) |
0.128 (1.00) |
0.49 (1.00) |
11q gain | 25 (15%) | 137 |
0.239 (1.00) |
0.223 (1.00) |
0.000797 (0.714) |
0.018 (1.00) |
0.563 (1.00) |
0.431 (1.00) |
0.0866 (1.00) |
0.346 (1.00) |
0.0233 (1.00) |
0.48 (1.00) |
0.231 (1.00) |
0.98 (1.00) |
12p gain | 33 (20%) | 129 |
0.649 (1.00) |
1 (1.00) |
0.00105 (0.935) |
0.717 (1.00) |
0.18 (1.00) |
0.0805 (1.00) |
0.489 (1.00) |
0.284 (1.00) |
0.352 (1.00) |
0.39 (1.00) |
0.38 (1.00) |
0.507 (1.00) |
12q gain | 23 (14%) | 139 |
0.912 (1.00) |
0.421 (1.00) |
0.047 (1.00) |
0.335 (1.00) |
0.356 (1.00) |
0.0857 (1.00) |
0.84 (1.00) |
0.251 (1.00) |
0.352 (1.00) |
0.467 (1.00) |
0.0692 (1.00) |
0.0991 (1.00) |
14q gain | 8 (5%) | 154 |
0.832 (1.00) |
0.82 (1.00) |
0.293 (1.00) |
0.678 (1.00) |
0.52 (1.00) |
0.505 (1.00) |
0.222 (1.00) |
0.63 (1.00) |
0.0388 (1.00) |
1 (1.00) |
||
15q gain | 3 (2%) | 159 |
0.547 (1.00) |
0.475 (1.00) |
0.602 (1.00) |
0.649 (1.00) |
||||||||
16p gain | 39 (24%) | 123 |
0.159 (1.00) |
0.72 (1.00) |
0.00352 (1.00) |
0.493 (1.00) |
0.925 (1.00) |
0.994 (1.00) |
0.368 (1.00) |
0.859 (1.00) |
0.148 (1.00) |
0.446 (1.00) |
0.0617 (1.00) |
0.467 (1.00) |
17p gain | 8 (5%) | 154 |
0.11 (1.00) |
0.208 (1.00) |
0.0573 (1.00) |
0.288 (1.00) |
1 (1.00) |
0.759 (1.00) |
0.529 (1.00) |
0.922 (1.00) |
0.52 (1.00) |
0.87 (1.00) |
0.228 (1.00) |
0.579 (1.00) |
17q gain | 30 (19%) | 132 |
0.194 (1.00) |
0.491 (1.00) |
0.000484 (0.435) |
0.451 (1.00) |
0.853 (1.00) |
0.897 (1.00) |
1 (1.00) |
0.816 (1.00) |
0.0745 (1.00) |
0.9 (1.00) |
0.414 (1.00) |
0.433 (1.00) |
18p gain | 8 (5%) | 154 |
0.517 (1.00) |
1 (1.00) |
0.00178 (1.00) |
0.851 (1.00) |
0.807 (1.00) |
0.652 (1.00) |
0.717 (1.00) |
0.869 (1.00) |
0.594 (1.00) |
0.884 (1.00) |
0.622 (1.00) |
0.601 (1.00) |
18q gain | 6 (4%) | 156 |
0.0441 (1.00) |
0.457 (1.00) |
0.492 (1.00) |
0.665 (1.00) |
0.748 (1.00) |
0.819 (1.00) |
0.512 (1.00) |
0.509 (1.00) |
0.622 (1.00) |
0.601 (1.00) |
||
19p gain | 31 (19%) | 131 |
0.068 (1.00) |
0.0974 (1.00) |
0.00772 (1.00) |
0.922 (1.00) |
0.556 (1.00) |
0.387 (1.00) |
0.7 (1.00) |
0.912 (1.00) |
0.108 (1.00) |
0.725 (1.00) |
0.665 (1.00) |
0.574 (1.00) |
19q gain | 30 (19%) | 132 |
0.078 (1.00) |
0.104 (1.00) |
0.0119 (1.00) |
0.776 (1.00) |
0.937 (1.00) |
0.349 (1.00) |
0.547 (1.00) |
0.694 (1.00) |
0.341 (1.00) |
0.635 (1.00) |
0.255 (1.00) |
0.119 (1.00) |
20p gain | 104 (64%) | 58 |
0.0946 (1.00) |
0.248 (1.00) |
0.378 (1.00) |
0.679 (1.00) |
0.0615 (1.00) |
0.724 (1.00) |
0.0705 (1.00) |
0.165 (1.00) |
0.442 (1.00) |
0.0412 (1.00) |
0.557 (1.00) |
0.0352 (1.00) |
20q gain | 142 (88%) | 20 |
0.00777 (1.00) |
0.376 (1.00) |
0.000973 (0.87) |
0.359 (1.00) |
0.165 (1.00) |
0.116 (1.00) |
0.551 (1.00) |
0.00138 (1.00) |
0.0928 (1.00) |
0.2 (1.00) |
0.338 (1.00) |
0.369 (1.00) |
21q gain | 10 (6%) | 152 |
0.538 (1.00) |
0.0487 (1.00) |
0.203 (1.00) |
0.875 (1.00) |
0.621 (1.00) |
0.515 (1.00) |
0.641 (1.00) |
0.947 (1.00) |
0.253 (1.00) |
0.716 (1.00) |
0.695 (1.00) |
0.491 (1.00) |
22q gain | 9 (6%) | 153 |
0.729 (1.00) |
0.28 (1.00) |
0.341 (1.00) |
1 (1.00) |
0.424 (1.00) |
0.543 (1.00) |
0.325 (1.00) |
0.938 (1.00) |
0.975 (1.00) |
1 (1.00) |
0.688 (1.00) |
0.528 (1.00) |
xq gain | 32 (20%) | 130 |
0.0991 (1.00) |
0.124 (1.00) |
0.0749 (1.00) |
0.299 (1.00) |
0.793 (1.00) |
0.59 (1.00) |
0.248 (1.00) |
0.853 (1.00) |
0.962 (1.00) |
0.838 (1.00) |
0.714 (1.00) |
0.696 (1.00) |
1p loss | 44 (27%) | 118 |
0.649 (1.00) |
0.00424 (1.00) |
0.000717 (0.642) |
0.0592 (1.00) |
0.906 (1.00) |
0.263 (1.00) |
0.699 (1.00) |
0.949 (1.00) |
0.429 (1.00) |
0.293 (1.00) |
0.905 (1.00) |
0.844 (1.00) |
1q loss | 25 (15%) | 137 |
0.912 (1.00) |
0.0771 (1.00) |
0.0264 (1.00) |
0.0274 (1.00) |
0.674 (1.00) |
0.358 (1.00) |
0.87 (1.00) |
1 (1.00) |
0.606 (1.00) |
0.118 (1.00) |
0.804 (1.00) |
0.117 (1.00) |
2p loss | 11 (7%) | 151 |
0.638 (1.00) |
0.566 (1.00) |
0.0172 (1.00) |
0.784 (1.00) |
0.907 (1.00) |
0.708 (1.00) |
0.301 (1.00) |
0.342 (1.00) |
0.56 (1.00) |
0.735 (1.00) |
1 (1.00) |
0.754 (1.00) |
2q loss | 6 (4%) | 156 |
1 (1.00) |
1 (1.00) |
0.175 (1.00) |
0.102 (1.00) |
0.455 (1.00) |
0.573 (1.00) |
0.146 (1.00) |
0.309 (1.00) |
0.549 (1.00) |
|||
3p loss | 15 (9%) | 147 |
1 (1.00) |
0.229 (1.00) |
0.137 (1.00) |
0.836 (1.00) |
0.255 (1.00) |
0.458 (1.00) |
0.28 (1.00) |
0.0183 (1.00) |
0.485 (1.00) |
0.262 (1.00) |
0.115 (1.00) |
0.274 (1.00) |
3q loss | 10 (6%) | 152 |
0.517 (1.00) |
0.449 (1.00) |
0.0508 (1.00) |
0.413 (1.00) |
0.325 (1.00) |
0.512 (1.00) |
0.151 (1.00) |
0.0501 (1.00) |
0.687 (1.00) |
0.222 (1.00) |
0.29 (1.00) |
0.307 (1.00) |
5p loss | 26 (16%) | 136 |
0.239 (1.00) |
0.277 (1.00) |
0.249 (1.00) |
0.47 (1.00) |
0.483 (1.00) |
0.236 (1.00) |
0.744 (1.00) |
0.522 (1.00) |
0.625 (1.00) |
0.154 (1.00) |
0.315 (1.00) |
0.416 (1.00) |
5q loss | 40 (25%) | 122 |
0.0929 (1.00) |
0.0278 (1.00) |
0.00981 (1.00) |
0.453 (1.00) |
1 (1.00) |
0.913 (1.00) |
1 (1.00) |
0.939 (1.00) |
0.946 (1.00) |
0.0776 (1.00) |
0.636 (1.00) |
0.704 (1.00) |
6p loss | 13 (8%) | 149 |
0.544 (1.00) |
0.681 (1.00) |
0.76 (1.00) |
0.166 (1.00) |
0.31 (1.00) |
0.415 (1.00) |
1 (1.00) |
0.536 (1.00) |
0.444 (1.00) |
0.35 (1.00) |
0.387 (1.00) |
0.371 (1.00) |
6q loss | 22 (14%) | 140 |
0.158 (1.00) |
0.132 (1.00) |
0.0731 (1.00) |
0.549 (1.00) |
0.414 (1.00) |
0.932 (1.00) |
0.146 (1.00) |
0.289 (1.00) |
0.276 (1.00) |
0.206 (1.00) |
0.172 (1.00) |
0.627 (1.00) |
7q loss | 3 (2%) | 159 |
0.238 (1.00) |
0.785 (1.00) |
0.237 (1.00) |
0.798 (1.00) |
0.82 (1.00) |
0.669 (1.00) |
0.748 (1.00) |
|||||
8p loss | 75 (46%) | 87 |
0.168 (1.00) |
0.773 (1.00) |
0.0208 (1.00) |
0.611 (1.00) |
0.67 (1.00) |
0.437 (1.00) |
0.207 (1.00) |
0.233 (1.00) |
0.831 (1.00) |
0.56 (1.00) |
0.0187 (1.00) |
0.303 (1.00) |
8q loss | 11 (7%) | 151 |
0.178 (1.00) |
0.236 (1.00) |
0.332 (1.00) |
1 (1.00) |
0.795 (1.00) |
0.648 (1.00) |
0.526 (1.00) |
0.265 (1.00) |
0.896 (1.00) |
0.436 (1.00) |
0.743 (1.00) |
0.688 (1.00) |
9p loss | 22 (14%) | 140 |
0.634 (1.00) |
0.624 (1.00) |
0.294 (1.00) |
0.308 (1.00) |
0.774 (1.00) |
0.332 (1.00) |
0.94 (1.00) |
0.68 (1.00) |
0.297 (1.00) |
0.0844 (1.00) |
0.155 (1.00) |
0.0191 (1.00) |
9q loss | 22 (14%) | 140 |
0.208 (1.00) |
0.54 (1.00) |
0.384 (1.00) |
0.169 (1.00) |
0.897 (1.00) |
0.572 (1.00) |
0.906 (1.00) |
0.609 (1.00) |
0.0442 (1.00) |
0.015 (1.00) |
0.162 (1.00) |
0.00724 (1.00) |
10p loss | 32 (20%) | 130 |
0.143 (1.00) |
0.133 (1.00) |
0.674 (1.00) |
0.0487 (1.00) |
0.136 (1.00) |
0.156 (1.00) |
0.442 (1.00) |
0.324 (1.00) |
0.884 (1.00) |
0.391 (1.00) |
0.86 (1.00) |
0.203 (1.00) |
10q loss | 37 (23%) | 125 |
0.163 (1.00) |
0.581 (1.00) |
0.135 (1.00) |
0.0703 (1.00) |
0.13 (1.00) |
0.0233 (1.00) |
0.128 (1.00) |
0.119 (1.00) |
0.682 (1.00) |
0.554 (1.00) |
0.818 (1.00) |
0.217 (1.00) |
11p loss | 24 (15%) | 138 |
0.243 (1.00) |
0.376 (1.00) |
0.00944 (1.00) |
0.117 (1.00) |
0.2 (1.00) |
0.178 (1.00) |
0.602 (1.00) |
0.861 (1.00) |
0.979 (1.00) |
0.428 (1.00) |
0.491 (1.00) |
0.186 (1.00) |
11q loss | 30 (19%) | 132 |
0.0517 (1.00) |
0.0823 (1.00) |
0.00192 (1.00) |
0.0253 (1.00) |
0.576 (1.00) |
0.284 (1.00) |
0.104 (1.00) |
0.109 (1.00) |
0.175 (1.00) |
0.161 (1.00) |
0.31 (1.00) |
0.168 (1.00) |
12p loss | 22 (14%) | 140 |
0.425 (1.00) |
0.526 (1.00) |
0.153 (1.00) |
0.347 (1.00) |
0.64 (1.00) |
0.135 (1.00) |
1 (1.00) |
0.651 (1.00) |
0.374 (1.00) |
0.422 (1.00) |
0.236 (1.00) |
0.677 (1.00) |
12q loss | 20 (12%) | 142 |
0.28 (1.00) |
0.778 (1.00) |
0.0909 (1.00) |
0.601 (1.00) |
0.612 (1.00) |
0.534 (1.00) |
0.809 (1.00) |
0.595 (1.00) |
0.48 (1.00) |
0.0801 (1.00) |
0.267 (1.00) |
0.712 (1.00) |
13q loss | 8 (5%) | 154 |
0.517 (1.00) |
0.104 (1.00) |
0.316 (1.00) |
0.1 (1.00) |
0.0558 (1.00) |
0.373 (1.00) |
1 (1.00) |
1 (1.00) |
0.101 (1.00) |
1 (1.00) |
0.743 (1.00) |
0.594 (1.00) |
14q loss | 65 (40%) | 97 |
0.471 (1.00) |
0.444 (1.00) |
0.0129 (1.00) |
0.752 (1.00) |
0.776 (1.00) |
0.341 (1.00) |
0.61 (1.00) |
0.852 (1.00) |
0.327 (1.00) |
0.229 (1.00) |
0.768 (1.00) |
0.973 (1.00) |
15q loss | 72 (44%) | 90 |
0.422 (1.00) |
0.0221 (1.00) |
0.00173 (1.00) |
0.93 (1.00) |
0.0834 (1.00) |
0.139 (1.00) |
0.72 (1.00) |
0.625 (1.00) |
0.802 (1.00) |
1 (1.00) |
0.955 (1.00) |
0.907 (1.00) |
16p loss | 9 (6%) | 153 |
0.378 (1.00) |
0.0762 (1.00) |
0.108 (1.00) |
0.0789 (1.00) |
0.651 (1.00) |
0.678 (1.00) |
1 (1.00) |
0.578 (1.00) |
0.409 (1.00) |
0.775 (1.00) |
0.675 (1.00) |
0.649 (1.00) |
16q loss | 14 (9%) | 148 |
0.28 (1.00) |
0.314 (1.00) |
0.000444 (0.399) |
0.217 (1.00) |
0.643 (1.00) |
0.603 (1.00) |
0.376 (1.00) |
0.588 (1.00) |
0.413 (1.00) |
0.384 (1.00) |
0.79 (1.00) |
0.535 (1.00) |
17p loss | 104 (64%) | 58 |
0.194 (1.00) |
0.49 (1.00) |
0.0478 (1.00) |
0.291 (1.00) |
0.954 (1.00) |
0.397 (1.00) |
0.675 (1.00) |
0.734 (1.00) |
0.972 (1.00) |
0.29 (1.00) |
0.524 (1.00) |
0.613 (1.00) |
17q loss | 25 (15%) | 137 |
0.904 (1.00) |
0.47 (1.00) |
0.00346 (1.00) |
0.269 (1.00) |
0.71 (1.00) |
0.924 (1.00) |
0.549 (1.00) |
0.651 (1.00) |
0.903 (1.00) |
0.66 (1.00) |
0.393 (1.00) |
0.5 (1.00) |
19p loss | 22 (14%) | 140 |
0.729 (1.00) |
0.84 (1.00) |
0.103 (1.00) |
0.077 (1.00) |
0.713 (1.00) |
0.997 (1.00) |
0.299 (1.00) |
0.211 (1.00) |
0.285 (1.00) |
0.0052 (1.00) |
0.675 (1.00) |
0.364 (1.00) |
19q loss | 21 (13%) | 141 |
0.832 (1.00) |
0.208 (1.00) |
0.47 (1.00) |
0.077 (1.00) |
0.884 (1.00) |
0.918 (1.00) |
0.23 (1.00) |
0.112 (1.00) |
0.0787 (1.00) |
0.00202 (1.00) |
0.759 (1.00) |
0.203 (1.00) |
20p loss | 25 (15%) | 137 |
1 (1.00) |
1 (1.00) |
0.0957 (1.00) |
0.332 (1.00) |
0.215 (1.00) |
0.759 (1.00) |
0.194 (1.00) |
0.398 (1.00) |
0.157 (1.00) |
0.168 (1.00) |
0.0297 (1.00) |
0.158 (1.00) |
21q loss | 66 (41%) | 96 |
0.264 (1.00) |
0.204 (1.00) |
0.0267 (1.00) |
1 (1.00) |
0.954 (1.00) |
0.613 (1.00) |
0.92 (1.00) |
0.934 (1.00) |
0.0196 (1.00) |
0.4 (1.00) |
0.424 (1.00) |
0.481 (1.00) |
22q loss | 57 (35%) | 105 |
0.794 (1.00) |
0.252 (1.00) |
0.0676 (1.00) |
0.634 (1.00) |
0.739 (1.00) |
0.569 (1.00) |
0.0508 (1.00) |
0.352 (1.00) |
0.0074 (1.00) |
0.467 (1.00) |
0.371 (1.00) |
0.194 (1.00) |
xq loss | 25 (15%) | 137 |
1 (1.00) |
0.917 (1.00) |
0.08 (1.00) |
0.468 (1.00) |
0.562 (1.00) |
0.975 (1.00) |
0.759 (1.00) |
0.734 (1.00) |
0.95 (1.00) |
0.819 (1.00) |
0.972 (1.00) |
0.727 (1.00) |
P value = 8.59e-05 (Chi-square test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
6P GAIN MUTATED | 5 | 11 | 4 | 6 | 13 | 1 |
6P GAIN WILD-TYPE | 5 | 23 | 38 | 24 | 11 | 21 |
P value = 2.86e-05 (Chi-square test), Q value = 0.026
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
6Q GAIN MUTATED | 4 | 12 | 3 | 3 | 12 | 1 |
6Q GAIN WILD-TYPE | 6 | 22 | 39 | 27 | 12 | 21 |
P value = 7.09e-06 (Chi-square test), Q value = 0.0065
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
7P GAIN MUTATED | 7 | 31 | 16 | 12 | 18 | 16 |
7P GAIN WILD-TYPE | 3 | 3 | 26 | 18 | 6 | 6 |
P value = 0.000172 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 7 | 50 | 31 |
7P GAIN MUTATED | 37 | 1 | 42 | 17 |
7P GAIN WILD-TYPE | 29 | 6 | 8 | 14 |
P value = 7.54e-05 (Chi-square test), Q value = 0.068
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
7Q GAIN MUTATED | 4 | 25 | 13 | 9 | 18 | 14 |
7Q GAIN WILD-TYPE | 6 | 9 | 29 | 21 | 6 | 8 |
P value = 3.85e-05 (Chi-square test), Q value = 0.035
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
8Q GAIN MUTATED | 6 | 21 | 12 | 17 | 11 | 21 |
8Q GAIN WILD-TYPE | 4 | 13 | 30 | 13 | 13 | 1 |
P value = 0.000148 (Chi-square test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
13Q GAIN MUTATED | 8 | 28 | 18 | 17 | 22 | 17 |
13Q GAIN WILD-TYPE | 2 | 6 | 24 | 13 | 2 | 5 |
P value = 3.96e-05 (Chi-square test), Q value = 0.036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
16Q GAIN MUTATED | 5 | 13 | 1 | 3 | 11 | 6 |
16Q GAIN WILD-TYPE | 5 | 21 | 41 | 27 | 13 | 16 |
P value = 2.3e-05 (Chi-square test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
4P LOSS MUTATED | 4 | 13 | 5 | 15 | 17 | 4 |
4P LOSS WILD-TYPE | 6 | 21 | 37 | 15 | 7 | 18 |
P value = 1.47e-05 (Chi-square test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
4Q LOSS MUTATED | 5 | 16 | 6 | 17 | 17 | 4 |
4Q LOSS WILD-TYPE | 5 | 18 | 36 | 13 | 7 | 18 |
P value = 5.26e-06 (Chi-square test), Q value = 0.0048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
18P LOSS MUTATED | 10 | 33 | 23 | 18 | 20 | 21 |
18P LOSS WILD-TYPE | 0 | 1 | 19 | 12 | 4 | 1 |
P value = 1.21e-05 (Chi-square test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 10 | 34 | 42 | 30 | 24 | 22 |
18Q LOSS MUTATED | 10 | 34 | 25 | 23 | 22 | 21 |
18Q LOSS WILD-TYPE | 0 | 0 | 17 | 7 | 2 | 1 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtypes file = READ-TP.transferedmergedcluster.txt
-
Number of patients = 162
-
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 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.
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.