This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 40 focal events and 10 molecular subtypes across 221 patients, 30 significant findings detected with P value < 0.05 and Q value < 0.25.
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2p cnv correlated to 'CN_CNMF'.
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2q cnv correlated to 'CN_CNMF'.
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3p cnv correlated to 'MIRSEQ_MATURE_CNMF'.
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3q cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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4p cnv correlated to 'CN_CNMF'.
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4q cnv correlated to 'CN_CNMF'.
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5p cnv correlated to 'CN_CNMF'.
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5q cnv correlated to 'CN_CNMF'.
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6q cnv correlated to 'CN_CNMF'.
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7p cnv correlated to 'CN_CNMF'.
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7q cnv correlated to 'CN_CNMF'.
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8p cnv correlated to 'CN_CNMF'.
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10p cnv correlated to 'CN_CNMF'.
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10q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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11p cnv correlated to 'CN_CNMF'.
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11q cnv correlated to 'CN_CNMF'.
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12p cnv correlated to 'CN_CNMF'.
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16p cnv correlated to 'CN_CNMF'.
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16q cnv correlated to 'CN_CNMF'.
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17p cnv correlated to 'CN_CNMF'.
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18p cnv correlated to 'CN_CNMF'.
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18q cnv correlated to 'CN_CNMF'.
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19p cnv correlated to 'CN_CNMF'.
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19q cnv correlated to 'CN_CNMF'.
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20q cnv correlated to 'CN_CNMF'.
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21q cnv correlated to 'CN_CNMF'.
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22q cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Clinical Features |
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 | Chi-square test | Fisher's exact test | Chi-square 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 | |
3q | 109 (49%) | 112 |
0.000573 (0.213) |
0.841 (1.00) |
0.582 (1.00) |
0.707 (1.00) |
0.548 (1.00) |
0.622 (1.00) |
0.015 (1.00) |
0.0304 (1.00) |
0.000117 (0.0445) |
0.0105 (1.00) |
10q | 93 (42%) | 128 |
9.94e-06 (0.00388) |
0.000278 (0.104) |
0.41 (1.00) |
0.944 (1.00) |
0.237 (1.00) |
0.145 (1.00) |
0.2 (1.00) |
0.0956 (1.00) |
0.458 (1.00) |
0.19 (1.00) |
22q | 116 (52%) | 105 |
4.24e-10 (1.7e-07) |
0.000263 (0.0986) |
0.825 (1.00) |
0.0768 (1.00) |
0.0509 (1.00) |
0.458 (1.00) |
0.34 (1.00) |
0.0995 (1.00) |
0.254 (1.00) |
0.0272 (1.00) |
2p | 89 (40%) | 132 |
5.84e-08 (2.31e-05) |
0.02 (1.00) |
0.532 (1.00) |
0.888 (1.00) |
0.0279 (1.00) |
0.0433 (1.00) |
0.107 (1.00) |
0.0692 (1.00) |
0.359 (1.00) |
0.0063 (1.00) |
2q | 81 (37%) | 140 |
2.27e-06 (0.000894) |
0.00492 (1.00) |
0.777 (1.00) |
0.824 (1.00) |
0.0413 (1.00) |
0.0585 (1.00) |
0.808 (1.00) |
0.636 (1.00) |
0.851 (1.00) |
0.082 (1.00) |
3p | 104 (47%) | 117 |
0.000836 (0.309) |
0.635 (1.00) |
0.0968 (1.00) |
0.351 (1.00) |
0.6 (1.00) |
0.366 (1.00) |
0.0387 (1.00) |
0.112 (1.00) |
0.000175 (0.0662) |
0.0322 (1.00) |
4p | 100 (45%) | 121 |
4.8e-05 (0.0184) |
0.0886 (1.00) |
0.852 (1.00) |
0.8 (1.00) |
0.364 (1.00) |
0.22 (1.00) |
0.575 (1.00) |
0.377 (1.00) |
0.421 (1.00) |
0.815 (1.00) |
4q | 94 (43%) | 127 |
1.59e-05 (0.00617) |
0.0729 (1.00) |
0.533 (1.00) |
0.631 (1.00) |
0.214 (1.00) |
0.131 (1.00) |
0.236 (1.00) |
0.394 (1.00) |
0.0793 (1.00) |
0.631 (1.00) |
5p | 125 (57%) | 96 |
0.000115 (0.0437) |
0.0819 (1.00) |
0.348 (1.00) |
0.134 (1.00) |
0.149 (1.00) |
0.139 (1.00) |
0.163 (1.00) |
0.245 (1.00) |
0.25 (1.00) |
0.22 (1.00) |
5q | 115 (52%) | 106 |
0.000297 (0.111) |
0.0732 (1.00) |
0.334 (1.00) |
0.751 (1.00) |
0.0243 (1.00) |
0.00391 (1.00) |
0.113 (1.00) |
0.068 (1.00) |
0.0457 (1.00) |
0.137 (1.00) |
6q | 99 (45%) | 122 |
3.25e-06 (0.00127) |
0.00685 (1.00) |
0.87 (1.00) |
0.97 (1.00) |
0.635 (1.00) |
0.59 (1.00) |
0.279 (1.00) |
0.075 (1.00) |
0.214 (1.00) |
0.481 (1.00) |
7p | 102 (46%) | 119 |
5.75e-05 (0.022) |
0.00113 (0.413) |
0.0461 (1.00) |
0.917 (1.00) |
0.391 (1.00) |
0.683 (1.00) |
0.159 (1.00) |
0.183 (1.00) |
0.059 (1.00) |
0.208 (1.00) |
7q | 95 (43%) | 126 |
0.000103 (0.0392) |
0.00724 (1.00) |
0.306 (1.00) |
0.9 (1.00) |
0.532 (1.00) |
0.21 (1.00) |
0.334 (1.00) |
0.258 (1.00) |
0.164 (1.00) |
0.694 (1.00) |
8p | 143 (65%) | 78 |
0.000213 (0.0803) |
0.00577 (1.00) |
0.896 (1.00) |
0.502 (1.00) |
0.00333 (1.00) |
0.291 (1.00) |
0.0809 (1.00) |
0.117 (1.00) |
0.0156 (1.00) |
0.0677 (1.00) |
10p | 105 (48%) | 116 |
2.22e-09 (8.88e-07) |
0.00994 (1.00) |
0.389 (1.00) |
0.72 (1.00) |
0.0442 (1.00) |
0.808 (1.00) |
0.361 (1.00) |
0.417 (1.00) |
0.0718 (1.00) |
0.105 (1.00) |
11p | 110 (50%) | 111 |
2.23e-07 (8.79e-05) |
0.00436 (1.00) |
0.301 (1.00) |
0.554 (1.00) |
0.199 (1.00) |
0.192 (1.00) |
0.126 (1.00) |
0.308 (1.00) |
0.259 (1.00) |
0.899 (1.00) |
11q | 98 (44%) | 123 |
6.17e-09 (2.45e-06) |
0.0361 (1.00) |
0.0661 (1.00) |
0.22 (1.00) |
0.0681 (1.00) |
0.703 (1.00) |
0.637 (1.00) |
0.892 (1.00) |
0.306 (1.00) |
0.853 (1.00) |
12p | 88 (40%) | 133 |
0.000286 (0.107) |
0.0822 (1.00) |
0.831 (1.00) |
0.669 (1.00) |
0.521 (1.00) |
0.504 (1.00) |
0.567 (1.00) |
0.264 (1.00) |
0.606 (1.00) |
0.142 (1.00) |
16p | 96 (43%) | 125 |
2.14e-05 (0.00829) |
0.0398 (1.00) |
0.298 (1.00) |
0.227 (1.00) |
0.166 (1.00) |
0.463 (1.00) |
0.845 (1.00) |
0.394 (1.00) |
0.332 (1.00) |
0.414 (1.00) |
16q | 100 (45%) | 121 |
2.97e-06 (0.00117) |
0.038 (1.00) |
0.388 (1.00) |
0.418 (1.00) |
0.131 (1.00) |
0.793 (1.00) |
0.397 (1.00) |
0.183 (1.00) |
0.717 (1.00) |
0.233 (1.00) |
17p | 129 (58%) | 92 |
2.75e-05 (0.0106) |
0.199 (1.00) |
0.907 (1.00) |
0.627 (1.00) |
0.0504 (1.00) |
0.808 (1.00) |
0.269 (1.00) |
0.0386 (1.00) |
0.935 (1.00) |
0.66 (1.00) |
18p | 117 (53%) | 104 |
9.03e-09 (3.59e-06) |
0.00557 (1.00) |
0.552 (1.00) |
0.651 (1.00) |
0.0331 (1.00) |
0.716 (1.00) |
1 (1.00) |
0.648 (1.00) |
0.375 (1.00) |
0.573 (1.00) |
18q | 110 (50%) | 111 |
3.67e-05 (0.0141) |
0.0215 (1.00) |
0.281 (1.00) |
0.333 (1.00) |
0.356 (1.00) |
0.854 (1.00) |
0.351 (1.00) |
0.0611 (1.00) |
0.351 (1.00) |
0.753 (1.00) |
19p | 101 (46%) | 120 |
2.94e-05 (0.0114) |
0.0834 (1.00) |
0.92 (1.00) |
0.7 (1.00) |
0.0802 (1.00) |
0.137 (1.00) |
0.147 (1.00) |
0.0205 (1.00) |
0.534 (1.00) |
0.651 (1.00) |
19q | 108 (49%) | 113 |
6.35e-07 (0.00025) |
0.00586 (1.00) |
0.649 (1.00) |
0.87 (1.00) |
0.712 (1.00) |
0.414 (1.00) |
0.236 (1.00) |
0.186 (1.00) |
0.66 (1.00) |
0.354 (1.00) |
20q | 133 (60%) | 88 |
0.000249 (0.0936) |
0.0321 (1.00) |
0.578 (1.00) |
0.379 (1.00) |
0.683 (1.00) |
0.232 (1.00) |
0.294 (1.00) |
0.0458 (1.00) |
0.0376 (1.00) |
0.291 (1.00) |
21q | 102 (46%) | 119 |
3.34e-05 (0.0129) |
0.0373 (1.00) |
0.88 (1.00) |
0.334 (1.00) |
0.323 (1.00) |
0.971 (1.00) |
0.00742 (1.00) |
0.0016 (0.578) |
0.315 (1.00) |
0.0674 (1.00) |
1p | 69 (31%) | 152 |
0.0259 (1.00) |
0.513 (1.00) |
0.375 (1.00) |
0.12 (1.00) |
0.781 (1.00) |
0.523 (1.00) |
0.447 (1.00) |
0.0435 (1.00) |
0.933 (1.00) |
0.611 (1.00) |
1q | 90 (41%) | 131 |
0.286 (1.00) |
0.851 (1.00) |
0.879 (1.00) |
0.754 (1.00) |
0.783 (1.00) |
0.202 (1.00) |
0.698 (1.00) |
0.152 (1.00) |
0.982 (1.00) |
0.697 (1.00) |
6p | 87 (39%) | 134 |
0.000866 (0.32) |
0.016 (1.00) |
0.763 (1.00) |
0.362 (1.00) |
0.789 (1.00) |
0.631 (1.00) |
0.109 (1.00) |
0.149 (1.00) |
0.482 (1.00) |
0.722 (1.00) |
8q | 122 (55%) | 99 |
0.0636 (1.00) |
0.0138 (1.00) |
0.405 (1.00) |
0.19 (1.00) |
0.402 (1.00) |
0.864 (1.00) |
0.478 (1.00) |
0.0905 (1.00) |
0.306 (1.00) |
0.521 (1.00) |
9p | 128 (58%) | 93 |
0.0275 (1.00) |
0.249 (1.00) |
0.0641 (1.00) |
0.277 (1.00) |
0.558 (1.00) |
0.118 (1.00) |
0.789 (1.00) |
0.396 (1.00) |
0.88 (1.00) |
0.936 (1.00) |
9q | 116 (52%) | 105 |
0.0729 (1.00) |
0.354 (1.00) |
0.173 (1.00) |
0.546 (1.00) |
0.437 (1.00) |
0.0344 (1.00) |
0.767 (1.00) |
0.709 (1.00) |
0.648 (1.00) |
0.551 (1.00) |
12q | 77 (35%) | 144 |
0.00155 (0.561) |
0.0905 (1.00) |
0.645 (1.00) |
0.245 (1.00) |
0.753 (1.00) |
0.512 (1.00) |
0.154 (1.00) |
0.0506 (1.00) |
0.427 (1.00) |
0.185 (1.00) |
13q | 104 (47%) | 117 |
0.00725 (1.00) |
0.337 (1.00) |
0.0223 (1.00) |
0.0364 (1.00) |
0.0818 (1.00) |
0.852 (1.00) |
0.853 (1.00) |
0.36 (1.00) |
0.627 (1.00) |
0.388 (1.00) |
14q | 99 (45%) | 122 |
0.000999 (0.367) |
0.0178 (1.00) |
0.458 (1.00) |
0.224 (1.00) |
0.0381 (1.00) |
0.76 (1.00) |
0.0508 (1.00) |
0.227 (1.00) |
0.298 (1.00) |
0.759 (1.00) |
15q | 96 (43%) | 125 |
0.0314 (1.00) |
0.0922 (1.00) |
0.2 (1.00) |
0.705 (1.00) |
0.0768 (1.00) |
0.384 (1.00) |
0.189 (1.00) |
0.258 (1.00) |
0.201 (1.00) |
0.26 (1.00) |
17q | 103 (47%) | 118 |
0.000917 (0.337) |
0.065 (1.00) |
0.148 (1.00) |
0.451 (1.00) |
0.0417 (1.00) |
0.0957 (1.00) |
0.0293 (1.00) |
0.00593 (1.00) |
0.0429 (1.00) |
0.0384 (1.00) |
20p | 128 (58%) | 93 |
0.00111 (0.406) |
0.093 (1.00) |
0.844 (1.00) |
0.208 (1.00) |
0.895 (1.00) |
0.0737 (1.00) |
0.257 (1.00) |
0.00934 (1.00) |
0.0214 (1.00) |
0.0505 (1.00) |
xq | 71 (32%) | 150 |
0.00113 (0.413) |
0.00729 (1.00) |
0.84 (1.00) |
0.847 (1.00) |
0.0186 (1.00) |
0.414 (1.00) |
0.0755 (1.00) |
0.548 (1.00) |
0.352 (1.00) |
0.409 (1.00) |
P value = 5.84e-08 (Chi-square test), Q value = 2.3e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
2P MUTATED | 8 | 11 | 8 | 9 | 23 | 13 | 12 | 5 |
2P WILD-TYPE | 10 | 68 | 15 | 5 | 15 | 12 | 2 | 5 |
P value = 2.27e-06 (Chi-square test), Q value = 0.00089
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
2Q MUTATED | 9 | 10 | 9 | 6 | 23 | 9 | 10 | 5 |
2Q WILD-TYPE | 9 | 69 | 14 | 8 | 15 | 16 | 4 | 5 |
P value = 0.000175 (Fisher's exact test), Q value = 0.066
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 60 | 67 | 49 |
3P MUTATED | 23 | 35 | 20 | 18 |
3P WILD-TYPE | 10 | 25 | 47 | 31 |
P value = 0.000573 (Chi-square test), Q value = 0.21
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
3Q MUTATED | 11 | 28 | 6 | 9 | 19 | 19 | 11 | 6 |
3Q WILD-TYPE | 7 | 51 | 17 | 5 | 19 | 6 | 3 | 4 |
P value = 0.000117 (Fisher's exact test), Q value = 0.045
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 33 | 60 | 67 | 49 |
3Q MUTATED | 26 | 33 | 23 | 19 |
3Q WILD-TYPE | 7 | 27 | 44 | 30 |
P value = 4.8e-05 (Chi-square test), Q value = 0.018
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
4P MUTATED | 10 | 18 | 9 | 11 | 24 | 15 | 7 | 6 |
4P WILD-TYPE | 8 | 61 | 14 | 3 | 14 | 10 | 7 | 4 |
P value = 1.59e-05 (Chi-square test), Q value = 0.0062
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
4Q MUTATED | 11 | 14 | 11 | 9 | 24 | 13 | 8 | 4 |
4Q WILD-TYPE | 7 | 65 | 12 | 5 | 14 | 12 | 6 | 6 |
P value = 0.000115 (Chi-square test), Q value = 0.044
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
5P MUTATED | 14 | 28 | 14 | 10 | 24 | 19 | 12 | 4 |
5P WILD-TYPE | 4 | 51 | 9 | 4 | 14 | 6 | 2 | 6 |
P value = 0.000297 (Chi-square test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
5Q MUTATED | 14 | 24 | 15 | 10 | 24 | 15 | 9 | 4 |
5Q WILD-TYPE | 4 | 55 | 8 | 4 | 14 | 10 | 5 | 6 |
P value = 3.25e-06 (Chi-square test), Q value = 0.0013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
6Q MUTATED | 12 | 16 | 11 | 8 | 25 | 10 | 9 | 8 |
6Q WILD-TYPE | 6 | 63 | 12 | 6 | 13 | 15 | 5 | 2 |
P value = 5.75e-05 (Chi-square test), Q value = 0.022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
7P MUTATED | 10 | 19 | 8 | 9 | 25 | 15 | 9 | 7 |
7P WILD-TYPE | 8 | 60 | 15 | 5 | 13 | 10 | 5 | 3 |
P value = 0.000103 (Chi-square test), Q value = 0.039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
7Q MUTATED | 9 | 18 | 8 | 5 | 25 | 14 | 9 | 7 |
7Q WILD-TYPE | 9 | 61 | 15 | 9 | 13 | 11 | 5 | 3 |
P value = 0.000213 (Chi-square test), Q value = 0.08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
8P MUTATED | 15 | 34 | 17 | 12 | 28 | 21 | 9 | 7 |
8P WILD-TYPE | 3 | 45 | 6 | 2 | 10 | 4 | 5 | 3 |
P value = 2.22e-09 (Chi-square test), Q value = 8.9e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
10P MUTATED | 11 | 12 | 12 | 9 | 26 | 18 | 10 | 7 |
10P WILD-TYPE | 7 | 67 | 11 | 5 | 12 | 7 | 4 | 3 |
P value = 9.94e-06 (Chi-square test), Q value = 0.0039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
10Q MUTATED | 9 | 13 | 11 | 9 | 23 | 14 | 9 | 5 |
10Q WILD-TYPE | 9 | 66 | 12 | 5 | 15 | 11 | 5 | 5 |
P value = 0.000278 (Fisher's exact test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 81 | 88 | 52 |
10Q MUTATED | 48 | 31 | 14 |
10Q WILD-TYPE | 33 | 57 | 38 |
P value = 2.23e-07 (Chi-square test), Q value = 8.8e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
11P MUTATED | 15 | 20 | 9 | 8 | 28 | 14 | 7 | 9 |
11P WILD-TYPE | 3 | 59 | 14 | 6 | 10 | 11 | 7 | 1 |
P value = 6.17e-09 (Chi-square test), Q value = 2.5e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
11Q MUTATED | 14 | 13 | 8 | 8 | 25 | 13 | 8 | 9 |
11Q WILD-TYPE | 4 | 66 | 15 | 6 | 13 | 12 | 6 | 1 |
P value = 0.000286 (Chi-square test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
12P MUTATED | 11 | 16 | 9 | 9 | 20 | 12 | 4 | 7 |
12P WILD-TYPE | 7 | 63 | 14 | 5 | 18 | 13 | 10 | 3 |
P value = 2.14e-05 (Chi-square test), Q value = 0.0083
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
16P MUTATED | 11 | 15 | 16 | 8 | 19 | 13 | 7 | 7 |
16P WILD-TYPE | 7 | 64 | 7 | 6 | 19 | 12 | 7 | 3 |
P value = 2.97e-06 (Chi-square test), Q value = 0.0012
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
16Q MUTATED | 12 | 15 | 14 | 8 | 23 | 14 | 6 | 8 |
16Q WILD-TYPE | 6 | 64 | 9 | 6 | 15 | 11 | 8 | 2 |
P value = 2.75e-05 (Chi-square test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
17P MUTATED | 16 | 29 | 12 | 7 | 27 | 19 | 11 | 8 |
17P WILD-TYPE | 2 | 50 | 11 | 7 | 11 | 6 | 3 | 2 |
P value = 9.03e-09 (Chi-square test), Q value = 3.6e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
18P MUTATED | 10 | 17 | 17 | 11 | 28 | 17 | 10 | 7 |
18P WILD-TYPE | 8 | 62 | 6 | 3 | 10 | 8 | 4 | 3 |
P value = 3.67e-05 (Chi-square test), Q value = 0.014
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
18Q MUTATED | 11 | 21 | 16 | 12 | 24 | 12 | 8 | 6 |
18Q WILD-TYPE | 7 | 58 | 7 | 2 | 14 | 13 | 6 | 4 |
P value = 2.94e-05 (Chi-square test), Q value = 0.011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
19P MUTATED | 5 | 20 | 10 | 9 | 24 | 15 | 11 | 7 |
19P WILD-TYPE | 13 | 59 | 13 | 5 | 14 | 10 | 3 | 3 |
P value = 6.35e-07 (Chi-square test), Q value = 0.00025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
19Q MUTATED | 7 | 19 | 10 | 9 | 28 | 17 | 11 | 7 |
19Q WILD-TYPE | 11 | 60 | 13 | 5 | 10 | 8 | 3 | 3 |
P value = 0.000249 (Chi-square test), Q value = 0.094
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
20Q MUTATED | 14 | 30 | 15 | 10 | 26 | 19 | 10 | 9 |
20Q WILD-TYPE | 4 | 49 | 8 | 4 | 12 | 6 | 4 | 1 |
P value = 3.34e-05 (Chi-square test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
21Q MUTATED | 10 | 17 | 14 | 10 | 21 | 17 | 7 | 6 |
21Q WILD-TYPE | 8 | 62 | 9 | 4 | 17 | 8 | 7 | 4 |
P value = 4.24e-10 (Chi-square test), Q value = 1.7e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 18 | 79 | 23 | 14 | 38 | 25 | 14 | 10 |
22Q MUTATED | 12 | 16 | 18 | 8 | 26 | 20 | 7 | 9 |
22Q WILD-TYPE | 6 | 63 | 5 | 6 | 12 | 5 | 7 | 1 |
P value = 0.000263 (Fisher's exact test), Q value = 0.099
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 81 | 88 | 52 |
22Q MUTATED | 54 | 46 | 16 |
22Q WILD-TYPE | 27 | 42 | 36 |
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Copy number data file = transformed.cor.cli.txt
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Molecular subtype file = BLCA-TP.transferedmergedcluster.txt
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Number of patients = 221
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Number of significantly focal cnvs = 40
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Number of molecular subtypes = 10
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Exclude genes that fewer than K tumors have alterations, K = 3
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 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.