This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 80 arm-level events and 8 molecular subtypes across 184 patients, 57 significant findings detected with P value < 0.05 and Q value < 0.25.
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3q gain cnv correlated to 'CN_CNMF'.
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5p gain cnv correlated to 'CN_CNMF'.
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13q gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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22q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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5p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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10q loss cnv correlated to 'CN_CNMF'.
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12p loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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17p loss cnv correlated to 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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18q loss cnv correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
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22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
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 | |
22q gain | 31 (17%) | 153 |
2e-05 (0.0125) |
2e-05 (0.0125) |
0.0002 (0.119) |
0.00016 (0.0957) |
2e-05 (0.0125) |
3e-05 (0.0185) |
1e-05 (0.0064) |
2e-05 (0.0125) |
16q loss | 53 (29%) | 131 |
1e-05 (0.0064) |
2e-05 (0.0125) |
0.00041 (0.239) |
0.00015 (0.0898) |
1e-05 (0.0064) |
3e-05 (0.0185) |
1e-05 (0.0064) |
1e-05 (0.0064) |
13q gain | 43 (23%) | 141 |
0.00248 (1.00) |
1e-05 (0.0064) |
0.00112 (0.637) |
1e-05 (0.0064) |
1e-05 (0.0064) |
5e-05 (0.0305) |
0.00018 (0.107) |
1e-05 (0.0064) |
5p loss | 46 (25%) | 138 |
0.00028 (0.165) |
1e-05 (0.0064) |
0.00513 (1.00) |
0.0357 (1.00) |
8e-05 (0.0483) |
2e-05 (0.0125) |
0.00026 (0.154) |
4e-05 (0.0245) |
16p loss | 54 (29%) | 130 |
0.00048 (0.279) |
0.00014 (0.084) |
0.00204 (1.00) |
0.00032 (0.188) |
0.00024 (0.142) |
0.00016 (0.0957) |
0.00032 (0.188) |
0.00013 (0.0781) |
22q loss | 72 (39%) | 112 |
5e-05 (0.0305) |
1e-05 (0.0064) |
0.0198 (1.00) |
0.0872 (1.00) |
6e-05 (0.0364) |
0.00016 (0.0957) |
3e-05 (0.0185) |
2e-05 (0.0125) |
3p loss | 93 (51%) | 91 |
2e-05 (0.0125) |
7e-05 (0.0424) |
0.00254 (1.00) |
0.00302 (1.00) |
1e-05 (0.0064) |
1e-05 (0.0064) |
0.00117 (0.663) |
1e-05 (0.0064) |
20q gain | 115 (62%) | 69 |
5e-05 (0.0305) |
0.00031 (0.183) |
0.0452 (1.00) |
0.0813 (1.00) |
0.0004 (0.234) |
0.00065 (0.375) |
0.00585 (1.00) |
4e-05 (0.0245) |
17p loss | 71 (39%) | 113 |
0.00237 (1.00) |
0.0001 (0.0603) |
0.00323 (1.00) |
0.00165 (0.931) |
1e-05 (0.0064) |
0.00131 (0.741) |
0.062 (1.00) |
0.00011 (0.0662) |
3q gain | 77 (42%) | 107 |
1e-05 (0.0064) |
0.0203 (1.00) |
0.286 (1.00) |
0.0301 (1.00) |
0.308 (1.00) |
0.241 (1.00) |
0.167 (1.00) |
0.411 (1.00) |
5p gain | 76 (41%) | 108 |
4e-05 (0.0245) |
0.0273 (1.00) |
0.092 (1.00) |
0.158 (1.00) |
0.0134 (1.00) |
0.0333 (1.00) |
0.0501 (1.00) |
0.0164 (1.00) |
10q loss | 49 (27%) | 135 |
7e-05 (0.0424) |
0.00103 (0.588) |
0.096 (1.00) |
0.0278 (1.00) |
0.00161 (0.91) |
0.0023 (1.00) |
0.0169 (1.00) |
0.00173 (0.974) |
12p loss | 33 (18%) | 151 |
0.0971 (1.00) |
0.00102 (0.583) |
0.0284 (1.00) |
0.0011 (0.627) |
0.00266 (1.00) |
0.00199 (1.00) |
0.0143 (1.00) |
0.00022 (0.13) |
18q loss | 102 (55%) | 82 |
0.0974 (1.00) |
0.0114 (1.00) |
0.118 (1.00) |
0.237 (1.00) |
0.0213 (1.00) |
0.00229 (1.00) |
0.0474 (1.00) |
0.00035 (0.205) |
1p gain | 37 (20%) | 147 |
0.648 (1.00) |
0.224 (1.00) |
0.673 (1.00) |
0.692 (1.00) |
1 (1.00) |
0.884 (1.00) |
0.453 (1.00) |
0.965 (1.00) |
1q gain | 63 (34%) | 121 |
0.0618 (1.00) |
0.207 (1.00) |
0.24 (1.00) |
0.113 (1.00) |
0.383 (1.00) |
0.488 (1.00) |
0.507 (1.00) |
0.628 (1.00) |
2p gain | 61 (33%) | 123 |
0.012 (1.00) |
0.0314 (1.00) |
0.147 (1.00) |
0.416 (1.00) |
0.037 (1.00) |
0.342 (1.00) |
0.00283 (1.00) |
0.507 (1.00) |
2q gain | 46 (25%) | 138 |
0.267 (1.00) |
0.0701 (1.00) |
0.502 (1.00) |
0.178 (1.00) |
0.486 (1.00) |
0.768 (1.00) |
0.256 (1.00) |
0.886 (1.00) |
3p gain | 31 (17%) | 153 |
0.305 (1.00) |
0.447 (1.00) |
0.274 (1.00) |
0.935 (1.00) |
0.779 (1.00) |
0.609 (1.00) |
0.862 (1.00) |
0.616 (1.00) |
4p gain | 19 (10%) | 165 |
0.529 (1.00) |
0.857 (1.00) |
0.113 (1.00) |
1 (1.00) |
1 (1.00) |
0.959 (1.00) |
0.98 (1.00) |
1 (1.00) |
4q gain | 18 (10%) | 166 |
0.0869 (1.00) |
0.327 (1.00) |
0.00261 (1.00) |
0.367 (1.00) |
0.306 (1.00) |
0.545 (1.00) |
0.558 (1.00) |
0.491 (1.00) |
5q gain | 20 (11%) | 164 |
0.409 (1.00) |
0.779 (1.00) |
0.469 (1.00) |
0.604 (1.00) |
0.699 (1.00) |
0.986 (1.00) |
0.752 (1.00) |
0.793 (1.00) |
6p gain | 38 (21%) | 146 |
0.241 (1.00) |
0.369 (1.00) |
0.7 (1.00) |
0.388 (1.00) |
0.251 (1.00) |
0.103 (1.00) |
0.115 (1.00) |
0.0303 (1.00) |
6q gain | 33 (18%) | 151 |
0.235 (1.00) |
0.328 (1.00) |
0.706 (1.00) |
0.247 (1.00) |
0.377 (1.00) |
0.286 (1.00) |
0.149 (1.00) |
0.0829 (1.00) |
7p gain | 110 (60%) | 74 |
0.348 (1.00) |
0.235 (1.00) |
0.115 (1.00) |
0.0273 (1.00) |
0.0748 (1.00) |
0.208 (1.00) |
0.555 (1.00) |
0.11 (1.00) |
7q gain | 89 (48%) | 95 |
0.666 (1.00) |
0.289 (1.00) |
0.697 (1.00) |
0.0231 (1.00) |
0.423 (1.00) |
0.745 (1.00) |
0.836 (1.00) |
0.124 (1.00) |
8p gain | 68 (37%) | 116 |
0.317 (1.00) |
0.537 (1.00) |
0.773 (1.00) |
0.625 (1.00) |
0.373 (1.00) |
0.834 (1.00) |
0.56 (1.00) |
0.737 (1.00) |
8q gain | 101 (55%) | 83 |
0.466 (1.00) |
0.286 (1.00) |
0.406 (1.00) |
0.406 (1.00) |
0.292 (1.00) |
0.726 (1.00) |
0.913 (1.00) |
0.976 (1.00) |
9p gain | 16 (9%) | 168 |
0.799 (1.00) |
0.482 (1.00) |
0.451 (1.00) |
0.795 (1.00) |
0.564 (1.00) |
0.184 (1.00) |
0.587 (1.00) |
0.468 (1.00) |
9q gain | 33 (18%) | 151 |
0.394 (1.00) |
0.257 (1.00) |
0.335 (1.00) |
0.942 (1.00) |
0.384 (1.00) |
0.029 (1.00) |
0.673 (1.00) |
0.0798 (1.00) |
10p gain | 40 (22%) | 144 |
0.0363 (1.00) |
0.0274 (1.00) |
0.201 (1.00) |
0.31 (1.00) |
0.119 (1.00) |
0.218 (1.00) |
0.0556 (1.00) |
0.0753 (1.00) |
10q gain | 30 (16%) | 154 |
0.015 (1.00) |
0.0342 (1.00) |
0.15 (1.00) |
0.232 (1.00) |
0.0804 (1.00) |
0.0701 (1.00) |
0.0518 (1.00) |
0.0224 (1.00) |
11p gain | 39 (21%) | 145 |
0.646 (1.00) |
0.917 (1.00) |
0.149 (1.00) |
0.677 (1.00) |
0.345 (1.00) |
0.318 (1.00) |
0.875 (1.00) |
0.481 (1.00) |
11q gain | 29 (16%) | 155 |
0.288 (1.00) |
0.316 (1.00) |
0.105 (1.00) |
0.0228 (1.00) |
0.0477 (1.00) |
0.174 (1.00) |
0.0816 (1.00) |
0.0772 (1.00) |
12p gain | 58 (32%) | 126 |
0.0226 (1.00) |
0.00385 (1.00) |
0.00857 (1.00) |
0.00555 (1.00) |
0.00592 (1.00) |
0.00283 (1.00) |
0.0033 (1.00) |
0.00938 (1.00) |
12q gain | 38 (21%) | 146 |
0.174 (1.00) |
0.321 (1.00) |
0.427 (1.00) |
0.28 (1.00) |
0.393 (1.00) |
0.45 (1.00) |
0.268 (1.00) |
0.258 (1.00) |
14q gain | 48 (26%) | 136 |
0.0351 (1.00) |
0.084 (1.00) |
0.139 (1.00) |
0.0577 (1.00) |
0.0385 (1.00) |
0.035 (1.00) |
0.138 (1.00) |
0.0526 (1.00) |
15q gain | 30 (16%) | 154 |
0.389 (1.00) |
0.28 (1.00) |
0.35 (1.00) |
0.034 (1.00) |
0.454 (1.00) |
0.375 (1.00) |
0.319 (1.00) |
0.365 (1.00) |
16p gain | 41 (22%) | 143 |
0.00378 (1.00) |
0.0981 (1.00) |
0.0195 (1.00) |
0.00451 (1.00) |
0.0257 (1.00) |
0.0345 (1.00) |
0.0829 (1.00) |
0.0566 (1.00) |
16q gain | 38 (21%) | 146 |
0.00082 (0.471) |
0.0272 (1.00) |
0.00905 (1.00) |
0.0032 (1.00) |
0.0123 (1.00) |
0.00619 (1.00) |
0.00289 (1.00) |
0.00677 (1.00) |
17p gain | 33 (18%) | 151 |
0.0507 (1.00) |
0.0314 (1.00) |
0.302 (1.00) |
0.243 (1.00) |
0.366 (1.00) |
0.451 (1.00) |
0.543 (1.00) |
0.552 (1.00) |
17q gain | 45 (24%) | 139 |
0.14 (1.00) |
0.206 (1.00) |
0.37 (1.00) |
0.411 (1.00) |
0.854 (1.00) |
0.938 (1.00) |
0.992 (1.00) |
0.637 (1.00) |
18p gain | 50 (27%) | 134 |
0.0617 (1.00) |
0.377 (1.00) |
0.644 (1.00) |
0.333 (1.00) |
0.0228 (1.00) |
0.873 (1.00) |
0.937 (1.00) |
0.812 (1.00) |
18q gain | 26 (14%) | 158 |
0.738 (1.00) |
0.815 (1.00) |
0.972 (1.00) |
0.772 (1.00) |
0.398 (1.00) |
0.303 (1.00) |
0.382 (1.00) |
0.227 (1.00) |
19p gain | 28 (15%) | 156 |
0.43 (1.00) |
0.282 (1.00) |
0.263 (1.00) |
0.62 (1.00) |
0.381 (1.00) |
0.906 (1.00) |
0.537 (1.00) |
0.497 (1.00) |
19q gain | 38 (21%) | 146 |
0.101 (1.00) |
0.14 (1.00) |
0.178 (1.00) |
0.101 (1.00) |
0.0442 (1.00) |
0.353 (1.00) |
0.398 (1.00) |
0.111 (1.00) |
20p gain | 108 (59%) | 76 |
0.00464 (1.00) |
0.0582 (1.00) |
0.182 (1.00) |
0.532 (1.00) |
0.0991 (1.00) |
0.263 (1.00) |
0.385 (1.00) |
0.0577 (1.00) |
21q gain | 18 (10%) | 166 |
1 (1.00) |
0.564 (1.00) |
0.0291 (1.00) |
0.297 (1.00) |
0.213 (1.00) |
0.426 (1.00) |
0.387 (1.00) |
0.229 (1.00) |
xq gain | 36 (20%) | 148 |
0.0631 (1.00) |
0.0375 (1.00) |
0.221 (1.00) |
0.0658 (1.00) |
0.0118 (1.00) |
0.0194 (1.00) |
0.0641 (1.00) |
0.0763 (1.00) |
1p loss | 38 (21%) | 146 |
0.00904 (1.00) |
0.0232 (1.00) |
0.00273 (1.00) |
0.234 (1.00) |
0.0205 (1.00) |
0.032 (1.00) |
0.00961 (1.00) |
0.044 (1.00) |
1q loss | 22 (12%) | 162 |
0.0386 (1.00) |
0.231 (1.00) |
0.114 (1.00) |
0.175 (1.00) |
0.0745 (1.00) |
0.12 (1.00) |
0.0235 (1.00) |
0.127 (1.00) |
2p loss | 11 (6%) | 173 |
0.855 (1.00) |
0.134 (1.00) |
0.0885 (1.00) |
0.819 (1.00) |
0.381 (1.00) |
0.00178 (1.00) |
0.833 (1.00) |
0.373 (1.00) |
2q loss | 18 (10%) | 166 |
0.356 (1.00) |
0.0319 (1.00) |
0.272 (1.00) |
0.322 (1.00) |
0.0643 (1.00) |
0.00705 (1.00) |
0.282 (1.00) |
0.0878 (1.00) |
3q loss | 33 (18%) | 151 |
0.857 (1.00) |
0.67 (1.00) |
0.312 (1.00) |
0.51 (1.00) |
0.653 (1.00) |
0.913 (1.00) |
0.663 (1.00) |
0.891 (1.00) |
4p loss | 105 (57%) | 79 |
0.0006 (0.347) |
0.0762 (1.00) |
0.0194 (1.00) |
0.153 (1.00) |
0.0177 (1.00) |
0.285 (1.00) |
0.184 (1.00) |
0.41 (1.00) |
4q loss | 87 (47%) | 97 |
0.00043 (0.251) |
0.0461 (1.00) |
0.00372 (1.00) |
0.418 (1.00) |
0.0391 (1.00) |
0.221 (1.00) |
0.122 (1.00) |
0.0857 (1.00) |
5q loss | 86 (47%) | 98 |
0.0194 (1.00) |
0.00897 (1.00) |
0.0921 (1.00) |
0.681 (1.00) |
0.0201 (1.00) |
0.113 (1.00) |
0.211 (1.00) |
0.0925 (1.00) |
6p loss | 39 (21%) | 145 |
0.339 (1.00) |
0.621 (1.00) |
0.0761 (1.00) |
0.667 (1.00) |
0.369 (1.00) |
0.366 (1.00) |
0.861 (1.00) |
0.462 (1.00) |
6q loss | 39 (21%) | 145 |
0.334 (1.00) |
0.662 (1.00) |
0.273 (1.00) |
0.456 (1.00) |
0.488 (1.00) |
0.68 (1.00) |
0.831 (1.00) |
0.275 (1.00) |
7p loss | 13 (7%) | 171 |
0.817 (1.00) |
0.555 (1.00) |
0.00843 (1.00) |
0.221 (1.00) |
0.578 (1.00) |
0.586 (1.00) |
0.301 (1.00) |
0.649 (1.00) |
7q loss | 22 (12%) | 162 |
0.173 (1.00) |
0.337 (1.00) |
0.0485 (1.00) |
0.885 (1.00) |
0.585 (1.00) |
0.858 (1.00) |
0.227 (1.00) |
0.804 (1.00) |
8p loss | 63 (34%) | 121 |
0.00468 (1.00) |
0.463 (1.00) |
0.889 (1.00) |
0.71 (1.00) |
0.309 (1.00) |
0.594 (1.00) |
0.387 (1.00) |
0.306 (1.00) |
8q loss | 23 (12%) | 161 |
0.781 (1.00) |
1 (1.00) |
0.981 (1.00) |
0.457 (1.00) |
0.824 (1.00) |
0.258 (1.00) |
0.713 (1.00) |
1 (1.00) |
9p loss | 101 (55%) | 83 |
0.089 (1.00) |
0.113 (1.00) |
0.0519 (1.00) |
0.176 (1.00) |
0.529 (1.00) |
0.569 (1.00) |
0.785 (1.00) |
0.543 (1.00) |
9q loss | 65 (35%) | 119 |
0.0633 (1.00) |
0.178 (1.00) |
0.838 (1.00) |
0.446 (1.00) |
0.648 (1.00) |
0.23 (1.00) |
0.0686 (1.00) |
0.795 (1.00) |
10p loss | 50 (27%) | 134 |
0.00193 (1.00) |
0.00446 (1.00) |
0.0599 (1.00) |
0.112 (1.00) |
0.00211 (1.00) |
0.00811 (1.00) |
0.0125 (1.00) |
0.00239 (1.00) |
11p loss | 52 (28%) | 132 |
0.1 (1.00) |
0.228 (1.00) |
0.76 (1.00) |
0.405 (1.00) |
0.901 (1.00) |
0.651 (1.00) |
0.822 (1.00) |
0.77 (1.00) |
11q loss | 58 (32%) | 126 |
0.00053 (0.308) |
0.0427 (1.00) |
0.362 (1.00) |
0.0591 (1.00) |
0.0143 (1.00) |
0.133 (1.00) |
0.0771 (1.00) |
0.0682 (1.00) |
12q loss | 31 (17%) | 153 |
0.165 (1.00) |
0.0027 (1.00) |
0.0747 (1.00) |
0.0135 (1.00) |
0.0246 (1.00) |
0.0124 (1.00) |
0.00905 (1.00) |
0.00709 (1.00) |
13q loss | 67 (36%) | 117 |
0.0163 (1.00) |
0.0664 (1.00) |
0.249 (1.00) |
0.0481 (1.00) |
0.0431 (1.00) |
0.148 (1.00) |
0.0584 (1.00) |
0.105 (1.00) |
14q loss | 45 (24%) | 139 |
0.00054 (0.313) |
0.00497 (1.00) |
0.00216 (1.00) |
0.00254 (1.00) |
0.0294 (1.00) |
0.00305 (1.00) |
0.0371 (1.00) |
0.001 (0.573) |
15q loss | 57 (31%) | 127 |
0.285 (1.00) |
0.03 (1.00) |
0.259 (1.00) |
0.509 (1.00) |
0.0969 (1.00) |
0.00556 (1.00) |
0.323 (1.00) |
0.00081 (0.467) |
17q loss | 25 (14%) | 159 |
0.792 (1.00) |
0.605 (1.00) |
0.871 (1.00) |
0.92 (1.00) |
0.516 (1.00) |
0.888 (1.00) |
0.363 (1.00) |
0.868 (1.00) |
18p loss | 71 (39%) | 113 |
0.0121 (1.00) |
0.00091 (0.522) |
0.222 (1.00) |
0.0417 (1.00) |
0.00115 (0.653) |
0.0233 (1.00) |
0.025 (1.00) |
0.00581 (1.00) |
19p loss | 65 (35%) | 119 |
0.0491 (1.00) |
0.393 (1.00) |
0.219 (1.00) |
0.236 (1.00) |
0.0623 (1.00) |
0.121 (1.00) |
0.0957 (1.00) |
0.00943 (1.00) |
19q loss | 52 (28%) | 132 |
0.00451 (1.00) |
0.111 (1.00) |
0.307 (1.00) |
0.0602 (1.00) |
0.0594 (1.00) |
0.0935 (1.00) |
0.0188 (1.00) |
0.00909 (1.00) |
20p loss | 19 (10%) | 165 |
0.582 (1.00) |
0.858 (1.00) |
0.555 (1.00) |
0.19 (1.00) |
0.598 (1.00) |
0.419 (1.00) |
0.687 (1.00) |
0.48 (1.00) |
20q loss | 8 (4%) | 176 |
0.899 (1.00) |
0.704 (1.00) |
0.265 (1.00) |
0.317 (1.00) |
1 (1.00) |
0.674 (1.00) |
0.747 (1.00) |
0.445 (1.00) |
21q loss | 106 (58%) | 78 |
0.0313 (1.00) |
0.006 (1.00) |
0.0588 (1.00) |
0.258 (1.00) |
0.0206 (1.00) |
0.147 (1.00) |
0.0425 (1.00) |
0.0851 (1.00) |
xq loss | 43 (23%) | 141 |
0.0152 (1.00) |
0.0314 (1.00) |
0.272 (1.00) |
0.123 (1.00) |
0.167 (1.00) |
0.00062 (0.358) |
0.0352 (1.00) |
0.0146 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 44 | 75 |
3Q GAIN MUTATED | 29 | 5 | 43 |
3Q GAIN WILD-TYPE | 36 | 39 | 32 |
P value = 4e-05 (Fisher's exact test), Q value = 0.025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 44 | 75 |
5P GAIN MUTATED | 22 | 9 | 45 |
5P GAIN WILD-TYPE | 43 | 35 | 30 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 76 | 32 | 76 |
13Q GAIN MUTATED | 31 | 5 | 7 |
13Q GAIN WILD-TYPE | 45 | 27 | 69 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 39 | 74 | 12 |
13Q GAIN MUTATED | 12 | 6 | 8 |
13Q GAIN WILD-TYPE | 27 | 68 | 4 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 87 | 12 |
13Q GAIN MUTATED | 34 | 9 | 0 |
13Q GAIN WILD-TYPE | 50 | 78 | 12 |
P value = 5e-05 (Fisher's exact test), Q value = 0.03
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 62 | 26 | 62 | 33 |
13Q GAIN MUTATED | 25 | 9 | 5 | 4 |
13Q GAIN WILD-TYPE | 37 | 17 | 57 | 29 |
P value = 0.00018 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 66 | 35 | 11 |
13Q GAIN MUTATED | 28 | 8 | 4 | 3 |
13Q GAIN WILD-TYPE | 38 | 58 | 31 | 8 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 22 | 94 |
13Q GAIN MUTATED | 26 | 8 | 9 |
13Q GAIN WILD-TYPE | 36 | 14 | 85 |
P value = 5e-05 (Fisher's exact test), Q value = 0.03
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 44 | 75 |
20Q GAIN MUTATED | 54 | 21 | 40 |
20Q GAIN WILD-TYPE | 11 | 23 | 35 |
P value = 0.00031 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 76 | 32 | 76 |
20Q GAIN MUTATED | 60 | 18 | 37 |
20Q GAIN WILD-TYPE | 16 | 14 | 39 |
P value = 4e-04 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 87 | 12 |
20Q GAIN MUTATED | 65 | 44 | 5 |
20Q GAIN WILD-TYPE | 19 | 43 | 7 |
P value = 4e-05 (Fisher's exact test), Q value = 0.025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 22 | 94 |
20Q GAIN MUTATED | 52 | 15 | 46 |
20Q GAIN WILD-TYPE | 10 | 7 | 48 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 44 | 75 |
22Q GAIN MUTATED | 3 | 3 | 25 |
22Q GAIN WILD-TYPE | 62 | 41 | 50 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 76 | 32 | 76 |
22Q GAIN MUTATED | 3 | 3 | 25 |
22Q GAIN WILD-TYPE | 73 | 29 | 51 |
P value = 2e-04 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 11 | 26 | 31 | 11 |
22Q GAIN MUTATED | 1 | 1 | 10 | 10 | 1 |
22Q GAIN WILD-TYPE | 45 | 10 | 16 | 21 | 10 |
P value = 0.00016 (Fisher's exact test), Q value = 0.096
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 39 | 74 | 12 |
22Q GAIN MUTATED | 1 | 22 | 0 |
22Q GAIN WILD-TYPE | 38 | 52 | 12 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 87 | 12 |
22Q GAIN MUTATED | 3 | 26 | 2 |
22Q GAIN WILD-TYPE | 81 | 61 | 10 |
P value = 3e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 62 | 26 | 62 | 33 |
22Q GAIN MUTATED | 2 | 1 | 22 | 6 |
22Q GAIN WILD-TYPE | 60 | 25 | 40 | 27 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 66 | 35 | 11 |
22Q GAIN MUTATED | 2 | 25 | 3 | 1 |
22Q GAIN WILD-TYPE | 64 | 41 | 32 | 10 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 22 | 94 |
22Q GAIN MUTATED | 2 | 1 | 28 |
22Q GAIN WILD-TYPE | 60 | 21 | 66 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 44 | 75 |
3P LOSS MUTATED | 24 | 15 | 54 |
3P LOSS WILD-TYPE | 41 | 29 | 21 |
P value = 7e-05 (Fisher's exact test), Q value = 0.042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 76 | 32 | 76 |
3P LOSS MUTATED | 24 | 18 | 51 |
3P LOSS WILD-TYPE | 52 | 14 | 25 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 87 | 12 |
3P LOSS MUTATED | 27 | 60 | 6 |
3P LOSS WILD-TYPE | 57 | 27 | 6 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 62 | 26 | 62 | 33 |
3P LOSS MUTATED | 20 | 8 | 42 | 23 |
3P LOSS WILD-TYPE | 42 | 18 | 20 | 10 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 22 | 94 |
3P LOSS MUTATED | 19 | 8 | 64 |
3P LOSS WILD-TYPE | 43 | 14 | 30 |
P value = 0.00028 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 44 | 75 |
5P LOSS MUTATED | 27 | 10 | 9 |
5P LOSS WILD-TYPE | 38 | 34 | 66 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 76 | 32 | 76 |
5P LOSS MUTATED | 32 | 2 | 12 |
5P LOSS WILD-TYPE | 44 | 30 | 64 |
P value = 8e-05 (Fisher's exact test), Q value = 0.048
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 87 | 12 |
5P LOSS MUTATED | 33 | 12 | 0 |
5P LOSS WILD-TYPE | 51 | 75 | 12 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 62 | 26 | 62 | 33 |
5P LOSS MUTATED | 29 | 5 | 7 | 4 |
5P LOSS WILD-TYPE | 33 | 21 | 55 | 29 |
P value = 0.00026 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 66 | 35 | 11 |
5P LOSS MUTATED | 28 | 11 | 3 | 1 |
5P LOSS WILD-TYPE | 38 | 55 | 32 | 10 |
P value = 4e-05 (Fisher's exact test), Q value = 0.025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 22 | 94 |
5P LOSS MUTATED | 28 | 4 | 11 |
5P LOSS WILD-TYPE | 34 | 18 | 83 |
P value = 7e-05 (Fisher's exact test), Q value = 0.042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 44 | 75 |
10Q LOSS MUTATED | 9 | 7 | 33 |
10Q LOSS WILD-TYPE | 56 | 37 | 42 |
P value = 0.00022 (Fisher's exact test), Q value = 0.13
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 22 | 94 |
12P LOSS MUTATED | 16 | 9 | 8 |
12P LOSS WILD-TYPE | 46 | 13 | 86 |
P value = 0.00014 (Fisher's exact test), Q value = 0.084
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 76 | 32 | 76 |
16P LOSS MUTATED | 35 | 7 | 12 |
16P LOSS WILD-TYPE | 41 | 25 | 64 |
P value = 0.00032 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 39 | 74 | 12 |
16P LOSS MUTATED | 15 | 10 | 7 |
16P LOSS WILD-TYPE | 24 | 64 | 5 |
P value = 0.00024 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 87 | 12 |
16P LOSS MUTATED | 37 | 14 | 2 |
16P LOSS WILD-TYPE | 47 | 73 | 10 |
P value = 0.00016 (Fisher's exact test), Q value = 0.096
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 62 | 26 | 62 | 33 |
16P LOSS MUTATED | 30 | 8 | 10 | 5 |
16P LOSS WILD-TYPE | 32 | 18 | 52 | 28 |
P value = 0.00032 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 66 | 35 | 11 |
16P LOSS MUTATED | 31 | 10 | 7 | 3 |
16P LOSS WILD-TYPE | 35 | 56 | 28 | 8 |
P value = 0.00013 (Fisher's exact test), Q value = 0.078
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 22 | 94 |
16P LOSS MUTATED | 28 | 8 | 15 |
16P LOSS WILD-TYPE | 34 | 14 | 79 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 44 | 75 |
16Q LOSS MUTATED | 33 | 12 | 8 |
16Q LOSS WILD-TYPE | 32 | 32 | 67 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 76 | 32 | 76 |
16Q LOSS MUTATED | 35 | 8 | 10 |
16Q LOSS WILD-TYPE | 41 | 24 | 66 |
P value = 0.00041 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 46 | 11 | 26 | 31 | 11 |
16Q LOSS MUTATED | 23 | 3 | 3 | 3 | 2 |
16Q LOSS WILD-TYPE | 23 | 8 | 23 | 28 | 9 |
P value = 0.00015 (Fisher's exact test), Q value = 0.09
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 39 | 74 | 12 |
16Q LOSS MUTATED | 17 | 10 | 7 |
16Q LOSS WILD-TYPE | 22 | 64 | 5 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 87 | 12 |
16Q LOSS MUTATED | 40 | 12 | 0 |
16Q LOSS WILD-TYPE | 44 | 75 | 12 |
P value = 3e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 62 | 26 | 62 | 33 |
16Q LOSS MUTATED | 31 | 9 | 8 | 4 |
16Q LOSS WILD-TYPE | 31 | 17 | 54 | 29 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 66 | 35 | 11 |
16Q LOSS MUTATED | 35 | 10 | 4 | 1 |
16Q LOSS WILD-TYPE | 31 | 56 | 31 | 10 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 22 | 94 |
16Q LOSS MUTATED | 31 | 7 | 12 |
16Q LOSS WILD-TYPE | 31 | 15 | 82 |
P value = 1e-04 (Fisher's exact test), Q value = 0.06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 76 | 32 | 76 |
17P LOSS MUTATED | 43 | 10 | 18 |
17P LOSS WILD-TYPE | 33 | 22 | 58 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 87 | 12 |
17P LOSS MUTATED | 46 | 25 | 0 |
17P LOSS WILD-TYPE | 38 | 62 | 12 |
P value = 0.00011 (Fisher's exact test), Q value = 0.066
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 22 | 94 |
17P LOSS MUTATED | 33 | 13 | 23 |
17P LOSS WILD-TYPE | 29 | 9 | 71 |
P value = 0.00035 (Fisher's exact test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 22 | 94 |
18Q LOSS MUTATED | 36 | 20 | 44 |
18Q LOSS WILD-TYPE | 26 | 2 | 50 |
P value = 5e-05 (Fisher's exact test), Q value = 0.03
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 44 | 75 |
22Q LOSS MUTATED | 40 | 13 | 19 |
22Q LOSS WILD-TYPE | 25 | 31 | 56 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 76 | 32 | 76 |
22Q LOSS MUTATED | 45 | 10 | 17 |
22Q LOSS WILD-TYPE | 31 | 22 | 59 |
P value = 6e-05 (Fisher's exact test), Q value = 0.036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 87 | 12 |
22Q LOSS MUTATED | 47 | 24 | 1 |
22Q LOSS WILD-TYPE | 37 | 63 | 11 |
P value = 0.00016 (Fisher's exact test), Q value = 0.096
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 62 | 26 | 62 | 33 |
22Q LOSS MUTATED | 37 | 11 | 14 | 10 |
22Q LOSS WILD-TYPE | 25 | 15 | 48 | 23 |
P value = 3e-05 (Fisher's exact test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 66 | 35 | 11 |
22Q LOSS MUTATED | 43 | 18 | 7 | 3 |
22Q LOSS WILD-TYPE | 23 | 48 | 28 | 8 |
P value = 2e-05 (Fisher's exact test), Q value = 0.012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 62 | 22 | 94 |
22Q LOSS MUTATED | 39 | 9 | 23 |
22Q LOSS WILD-TYPE | 23 | 13 | 71 |
-
Copy number data file = transformed.cor.cli.txt
-
Molecular subtypes file = ESCA-TP.transferedmergedcluster.txt
-
Number of patients = 184
-
Number of significantly arm-level cnvs = 80
-
Number of molecular subtypes = 8
-
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.