This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 62 peak regions and 8 molecular subtypes across 150 patients, 47 significant findings detected with Q value < 0.25.
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Amp Peak 1(1p34.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 2(1p22.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 3(1q21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 4(1q23.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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Amp Peak 5(3p25.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Amp Peak 9(5p15.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 10(6p22.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 13(7p11.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 14(8p11.23) cnvs correlated to 'CN_CNMF'.
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Amp Peak 16(8q22.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 17(8q24.21) cnvs correlated to 'CN_CNMF'.
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Amp Peak 18(10p15.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 19(11q13.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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Amp Peak 23(17q11.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Amp Peak 24(17q12) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 25(19q12) cnvs correlated to 'CN_CNMF'.
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Amp Peak 26(19q13.43) cnvs correlated to 'CN_CNMF'.
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Amp Peak 27(20q11.21) cnvs correlated to 'CN_CNMF'.
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Del Peak 5(2q37.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 6(3p21.31) cnvs correlated to 'MRNASEQ_CNMF'.
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Del Peak 7(3p14.2) cnvs correlated to 'RPPA_CHIERARCHICAL' and 'MRNASEQ_CNMF'.
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Del Peak 8(3p12.3) cnvs correlated to 'RPPA_CHIERARCHICAL'.
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Del Peak 10(4q34.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 11(5q11.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 12(5q35.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 14(6q21) cnvs correlated to 'CN_CNMF'.
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Del Peak 15(8p23.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 16(9p23) cnvs correlated to 'CN_CNMF'.
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Del Peak 17(9p21.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 19(10q23.31) cnvs correlated to 'CN_CNMF'.
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Del Peak 20(11p15.5) cnvs correlated to 'CN_CNMF'.
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Del Peak 22(13q14.2) cnvs correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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Del Peak 24(14q32.31) cnvs correlated to 'MIRSEQ_CNMF'.
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Del Peak 25(15q13.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 26(16p13.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 27(16q23.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 31(22q13.32) cnvs correlated to 'CN_CNMF'.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ 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 | Chi-square test | |
Amp Peak 1(1p34 2) | 0 (0%) | 105 |
7.72e-07 (0.000376) |
4.09e-05 (0.0194) |
0.894 (1.00) |
0.706 (1.00) |
0.0633 (1.00) |
0.0927 (1.00) |
0.259 (1.00) |
0.0481 (1.00) |
Amp Peak 3(1q21 3) | 0 (0%) | 74 |
1.27e-08 (6.29e-06) |
0.0004 (0.182) |
0.0118 (1.00) |
0.0511 (1.00) |
0.0524 (1.00) |
0.176 (1.00) |
0.112 (1.00) |
0.115 (1.00) |
Amp Peak 4(1q23 3) | 0 (0%) | 68 |
7.96e-06 (0.0038) |
0.0124 (1.00) |
0.925 (1.00) |
0.589 (1.00) |
0.177 (1.00) |
0.619 (1.00) |
0.000496 (0.224) |
0.00476 (1.00) |
Amp Peak 5(3p25 2) | 0 (0%) | 80 |
6.76e-06 (0.00324) |
0.00904 (1.00) |
0.278 (1.00) |
0.0393 (1.00) |
0.000333 (0.153) |
0.0311 (1.00) |
0.00155 (0.687) |
0.00323 (1.00) |
Amp Peak 18(10p15 1) | 0 (0%) | 89 |
2.91e-09 (1.44e-06) |
5.25e-06 (0.00252) |
0.893 (1.00) |
0.215 (1.00) |
0.875 (1.00) |
0.467 (1.00) |
0.249 (1.00) |
0.181 (1.00) |
Amp Peak 19(11q13 3) | 0 (0%) | 90 |
8.05e-07 (0.000391) |
0.218 (1.00) |
0.554 (1.00) |
0.597 (1.00) |
0.123 (1.00) |
0.928 (1.00) |
0.000434 (0.197) |
0.035 (1.00) |
Amp Peak 23(17q11 2) | 0 (0%) | 82 |
3.59e-06 (0.00173) |
0.00122 (0.544) |
0.76 (1.00) |
0.439 (1.00) |
9.31e-05 (0.0439) |
0.01 (1.00) |
0.0196 (1.00) |
0.0131 (1.00) |
Amp Peak 24(17q12) | 0 (0%) | 87 |
0.000209 (0.097) |
0.153 (1.00) |
0.939 (1.00) |
0.439 (1.00) |
0.0411 (1.00) |
0.211 (1.00) |
0.0265 (1.00) |
0.000217 (0.1) |
Del Peak 7(3p14 2) | 0 (0%) | 102 |
0.0861 (1.00) |
0.56 (1.00) |
0.0759 (1.00) |
0.000294 (0.135) |
0.000489 (0.222) |
0.00671 (1.00) |
0.326 (1.00) |
0.298 (1.00) |
Del Peak 22(13q14 2) | 0 (0%) | 92 |
0.000254 (0.117) |
0.986 (1.00) |
0.000229 (0.106) |
0.00875 (1.00) |
0.00519 (1.00) |
0.11 (1.00) |
0.844 (1.00) |
0.0599 (1.00) |
Amp Peak 2(1p22 3) | 0 (0%) | 107 |
2.2e-08 (1.08e-05) |
0.341 (1.00) |
0.33 (1.00) |
0.581 (1.00) |
0.464 (1.00) |
0.709 (1.00) |
0.25 (1.00) |
0.0771 (1.00) |
Amp Peak 9(5p15 1) | 0 (0%) | 80 |
2.34e-06 (0.00113) |
0.222 (1.00) |
0.014 (1.00) |
0.46 (1.00) |
0.0265 (1.00) |
0.0886 (1.00) |
0.174 (1.00) |
0.244 (1.00) |
Amp Peak 10(6p22 3) | 0 (0%) | 89 |
8.2e-11 (4.07e-08) |
0.00236 (1.00) |
0.834 (1.00) |
0.872 (1.00) |
0.221 (1.00) |
0.629 (1.00) |
0.058 (1.00) |
0.377 (1.00) |
Amp Peak 13(7p11 2) | 0 (0%) | 70 |
6.99e-08 (3.44e-05) |
0.000984 (0.44) |
0.481 (1.00) |
0.243 (1.00) |
0.319 (1.00) |
0.888 (1.00) |
0.414 (1.00) |
0.48 (1.00) |
Amp Peak 14(8p11 23) | 0 (0%) | 101 |
0.000144 (0.067) |
0.0745 (1.00) |
0.0732 (1.00) |
0.017 (1.00) |
0.814 (1.00) |
0.409 (1.00) |
0.211 (1.00) |
0.751 (1.00) |
Amp Peak 16(8q22 3) | 0 (0%) | 57 |
2.25e-07 (0.000111) |
0.00267 (1.00) |
0.168 (1.00) |
0.208 (1.00) |
0.321 (1.00) |
0.523 (1.00) |
0.013 (1.00) |
0.279 (1.00) |
Amp Peak 17(8q24 21) | 0 (0%) | 61 |
0.000129 (0.0604) |
0.0256 (1.00) |
0.226 (1.00) |
0.354 (1.00) |
0.115 (1.00) |
0.675 (1.00) |
0.0281 (1.00) |
0.597 (1.00) |
Amp Peak 25(19q12) | 0 (0%) | 85 |
4.82e-05 (0.0229) |
0.00271 (1.00) |
0.37 (1.00) |
0.936 (1.00) |
0.645 (1.00) |
0.463 (1.00) |
0.372 (1.00) |
0.318 (1.00) |
Amp Peak 26(19q13 43) | 0 (0%) | 87 |
0.000105 (0.0491) |
0.0258 (1.00) |
0.778 (1.00) |
0.767 (1.00) |
0.14 (1.00) |
0.461 (1.00) |
0.152 (1.00) |
0.0946 (1.00) |
Amp Peak 27(20q11 21) | 0 (0%) | 46 |
2.07e-06 (0.001) |
0.428 (1.00) |
0.342 (1.00) |
0.865 (1.00) |
0.579 (1.00) |
0.659 (1.00) |
0.311 (1.00) |
0.32 (1.00) |
Del Peak 5(2q37 1) | 0 (0%) | 77 |
0.000526 (0.237) |
0.0128 (1.00) |
0.908 (1.00) |
0.875 (1.00) |
0.165 (1.00) |
0.172 (1.00) |
0.0434 (1.00) |
0.109 (1.00) |
Del Peak 6(3p21 31) | 0 (0%) | 103 |
0.179 (1.00) |
0.12 (1.00) |
0.00649 (1.00) |
0.0023 (1.00) |
0.000115 (0.0538) |
0.0108 (1.00) |
0.105 (1.00) |
0.204 (1.00) |
Del Peak 8(3p12 3) | 0 (0%) | 109 |
0.0107 (1.00) |
0.455 (1.00) |
0.0189 (1.00) |
0.000495 (0.224) |
0.00132 (0.587) |
0.0877 (1.00) |
0.418 (1.00) |
0.633 (1.00) |
Del Peak 10(4q34 2) | 0 (0%) | 85 |
7.79e-05 (0.0368) |
0.374 (1.00) |
0.422 (1.00) |
0.875 (1.00) |
0.387 (1.00) |
0.452 (1.00) |
0.121 (1.00) |
0.0135 (1.00) |
Del Peak 11(5q11 2) | 0 (0%) | 75 |
3.24e-07 (0.000159) |
0.0336 (1.00) |
0.814 (1.00) |
0.474 (1.00) |
0.271 (1.00) |
0.668 (1.00) |
0.167 (1.00) |
0.151 (1.00) |
Del Peak 12(5q35 1) | 0 (0%) | 78 |
0.000355 (0.162) |
0.00394 (1.00) |
0.567 (1.00) |
0.568 (1.00) |
0.501 (1.00) |
0.282 (1.00) |
0.0563 (1.00) |
0.141 (1.00) |
Del Peak 14(6q21) | 0 (0%) | 87 |
0.000367 (0.168) |
0.0129 (1.00) |
0.0799 (1.00) |
0.272 (1.00) |
0.569 (1.00) |
0.0603 (1.00) |
0.344 (1.00) |
0.686 (1.00) |
Del Peak 15(8p23 1) | 0 (0%) | 67 |
8.84e-06 (0.00422) |
0.000649 (0.291) |
0.169 (1.00) |
0.446 (1.00) |
0.438 (1.00) |
0.846 (1.00) |
0.0123 (1.00) |
0.00835 (1.00) |
Del Peak 16(9p23) | 0 (0%) | 84 |
0.000501 (0.226) |
0.752 (1.00) |
0.274 (1.00) |
0.717 (1.00) |
0.73 (1.00) |
0.162 (1.00) |
0.45 (1.00) |
0.954 (1.00) |
Del Peak 17(9p21 3) | 0 (0%) | 63 |
4.52e-07 (0.00022) |
0.406 (1.00) |
0.0718 (1.00) |
0.93 (1.00) |
0.379 (1.00) |
0.0983 (1.00) |
0.637 (1.00) |
0.591 (1.00) |
Del Peak 19(10q23 31) | 0 (0%) | 90 |
0.000115 (0.054) |
0.0025 (1.00) |
0.228 (1.00) |
0.929 (1.00) |
0.562 (1.00) |
0.195 (1.00) |
0.322 (1.00) |
0.409 (1.00) |
Del Peak 20(11p15 5) | 0 (0%) | 77 |
7.69e-05 (0.0364) |
0.038 (1.00) |
0.195 (1.00) |
0.673 (1.00) |
0.0596 (1.00) |
0.0178 (1.00) |
0.00472 (1.00) |
0.0411 (1.00) |
Del Peak 24(14q32 31) | 0 (0%) | 109 |
0.128 (1.00) |
0.0272 (1.00) |
0.805 (1.00) |
0.843 (1.00) |
0.407 (1.00) |
0.862 (1.00) |
0.00025 (0.115) |
0.0843 (1.00) |
Del Peak 25(15q13 1) | 0 (0%) | 95 |
4.32e-06 (0.00208) |
0.00534 (1.00) |
0.0829 (1.00) |
0.46 (1.00) |
0.0723 (1.00) |
0.137 (1.00) |
0.0942 (1.00) |
0.116 (1.00) |
Del Peak 26(16p13 3) | 0 (0%) | 96 |
3.5e-06 (0.00169) |
0.00652 (1.00) |
0.191 (1.00) |
0.23 (1.00) |
0.665 (1.00) |
0.975 (1.00) |
0.497 (1.00) |
0.642 (1.00) |
Del Peak 27(16q23 1) | 0 (0%) | 112 |
1.76e-05 (0.00837) |
0.0434 (1.00) |
0.232 (1.00) |
0.753 (1.00) |
0.118 (1.00) |
0.358 (1.00) |
0.0492 (1.00) |
0.215 (1.00) |
Del Peak 31(22q13 32) | 0 (0%) | 90 |
2.97e-07 (0.000145) |
0.26 (1.00) |
0.128 (1.00) |
0.0675 (1.00) |
0.0283 (1.00) |
0.15 (1.00) |
0.576 (1.00) |
0.115 (1.00) |
Amp Peak 6(3q26 32) | 0 (0%) | 66 |
0.00494 (1.00) |
0.664 (1.00) |
0.161 (1.00) |
0.812 (1.00) |
0.0558 (1.00) |
0.953 (1.00) |
0.495 (1.00) |
0.62 (1.00) |
Amp Peak 7(4p16 3) | 0 (0%) | 120 |
0.585 (1.00) |
0.15 (1.00) |
0.162 (1.00) |
0.189 (1.00) |
0.0903 (1.00) |
0.135 (1.00) |
0.117 (1.00) |
0.324 (1.00) |
Amp Peak 8(4q13 3) | 0 (0%) | 127 |
0.00397 (1.00) |
0.16 (1.00) |
0.517 (1.00) |
0.867 (1.00) |
0.922 (1.00) |
0.643 (1.00) |
0.23 (1.00) |
0.169 (1.00) |
Amp Peak 11(6q12) | 0 (0%) | 125 |
0.0102 (1.00) |
0.627 (1.00) |
1 (1.00) |
1 (1.00) |
0.255 (1.00) |
0.606 (1.00) |
0.172 (1.00) |
0.00284 (1.00) |
Amp Peak 12(6q21) | 0 (0%) | 132 |
0.0363 (1.00) |
0.0512 (1.00) |
0.621 (1.00) |
0.584 (1.00) |
0.0546 (1.00) |
0.849 (1.00) |
0.853 (1.00) |
0.62 (1.00) |
Amp Peak 15(8p11 21) | 0 (0%) | 100 |
0.00229 (1.00) |
0.0126 (1.00) |
0.596 (1.00) |
0.637 (1.00) |
0.275 (1.00) |
0.618 (1.00) |
0.0852 (1.00) |
0.683 (1.00) |
Amp Peak 20(12q15) | 0 (0%) | 102 |
0.00662 (1.00) |
0.107 (1.00) |
0.76 (1.00) |
0.439 (1.00) |
0.0608 (1.00) |
0.157 (1.00) |
0.232 (1.00) |
0.0388 (1.00) |
Amp Peak 21(13q34) | 0 (0%) | 95 |
0.0588 (1.00) |
0.933 (1.00) |
0.0164 (1.00) |
0.0318 (1.00) |
0.0221 (1.00) |
0.501 (1.00) |
0.212 (1.00) |
0.641 (1.00) |
Amp Peak 22(16p12 1) | 0 (0%) | 111 |
0.00842 (1.00) |
0.112 (1.00) |
0.0783 (1.00) |
0.453 (1.00) |
0.728 (1.00) |
0.266 (1.00) |
0.396 (1.00) |
0.376 (1.00) |
Amp Peak 28(22q11 23) | 0 (0%) | 115 |
0.126 (1.00) |
0.383 (1.00) |
0.837 (1.00) |
0.0916 (1.00) |
0.344 (1.00) |
0.822 (1.00) |
0.217 (1.00) |
0.265 (1.00) |
Del Peak 1(1p36 11) | 0 (0%) | 123 |
0.226 (1.00) |
0.00499 (1.00) |
0.0699 (1.00) |
0.0114 (1.00) |
0.684 (1.00) |
0.099 (1.00) |
0.763 (1.00) |
0.276 (1.00) |
Del Peak 2(1q32 1) | 0 (0%) | 122 |
0.0686 (1.00) |
0.115 (1.00) |
0.738 (1.00) |
0.38 (1.00) |
0.98 (1.00) |
0.329 (1.00) |
0.963 (1.00) |
0.295 (1.00) |
Del Peak 3(2q22 1) | 0 (0%) | 107 |
0.178 (1.00) |
0.295 (1.00) |
0.315 (1.00) |
0.278 (1.00) |
0.12 (1.00) |
0.67 (1.00) |
0.229 (1.00) |
0.16 (1.00) |
Del Peak 4(2q34) | 0 (0%) | 90 |
0.00149 (0.661) |
0.137 (1.00) |
0.309 (1.00) |
0.472 (1.00) |
0.511 (1.00) |
0.468 (1.00) |
0.0785 (1.00) |
0.278 (1.00) |
Del Peak 9(4q22 1) | 0 (0%) | 91 |
0.121 (1.00) |
0.628 (1.00) |
0.358 (1.00) |
1 (1.00) |
0.408 (1.00) |
0.0884 (1.00) |
0.886 (1.00) |
0.508 (1.00) |
Del Peak 13(6p25 3) | 0 (0%) | 111 |
0.122 (1.00) |
0.271 (1.00) |
0.135 (1.00) |
0.66 (1.00) |
0.232 (1.00) |
0.426 (1.00) |
0.658 (1.00) |
0.927 (1.00) |
Del Peak 18(10p12 1) | 0 (0%) | 121 |
0.101 (1.00) |
0.769 (1.00) |
0.455 (1.00) |
0.906 (1.00) |
0.18 (1.00) |
0.119 (1.00) |
0.283 (1.00) |
0.2 (1.00) |
Del Peak 21(11q25) | 0 (0%) | 103 |
0.00973 (1.00) |
0.337 (1.00) |
0.378 (1.00) |
1 (1.00) |
0.00528 (1.00) |
0.213 (1.00) |
0.0704 (1.00) |
0.0599 (1.00) |
Del Peak 23(14q12) | 0 (0%) | 107 |
0.00133 (0.592) |
0.000941 (0.422) |
0.805 (1.00) |
0.598 (1.00) |
0.194 (1.00) |
0.261 (1.00) |
0.0884 (1.00) |
0.527 (1.00) |
Del Peak 28(17p12) | 0 (0%) | 73 |
0.00217 (0.956) |
0.0175 (1.00) |
0.556 (1.00) |
0.405 (1.00) |
0.0394 (1.00) |
0.377 (1.00) |
0.192 (1.00) |
0.777 (1.00) |
Del Peak 29(18q23) | 0 (0%) | 87 |
0.0616 (1.00) |
0.485 (1.00) |
0.979 (1.00) |
0.763 (1.00) |
0.903 (1.00) |
0.281 (1.00) |
0.0308 (1.00) |
0.0197 (1.00) |
Del Peak 30(19p13 3) | 0 (0%) | 91 |
0.00274 (1.00) |
0.0503 (1.00) |
1 (1.00) |
0.757 (1.00) |
0.598 (1.00) |
0.82 (1.00) |
0.345 (1.00) |
0.111 (1.00) |
Del Peak 32(Xp11 3) | 0 (0%) | 110 |
0.15 (1.00) |
0.0054 (1.00) |
0.775 (1.00) |
0.922 (1.00) |
0.628 (1.00) |
0.236 (1.00) |
0.554 (1.00) |
0.336 (1.00) |
Del Peak 33(Xq21 33) | 0 (0%) | 115 |
0.211 (1.00) |
0.0789 (1.00) |
0.173 (1.00) |
0.173 (1.00) |
0.0242 (1.00) |
0.0868 (1.00) |
0.153 (1.00) |
0.315 (1.00) |
Del Peak 34(Xq23) | 0 (0%) | 117 |
0.297 (1.00) |
0.0273 (1.00) |
0.173 (1.00) |
0.173 (1.00) |
0.0109 (1.00) |
0.0775 (1.00) |
0.165 (1.00) |
0.0924 (1.00) |
P value = 7.72e-07 (Fisher's exact test), Q value = 0.00038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 1(1P34.2) CNV | 15 | 8 | 22 |
AMP PEAK 1(1P34.2) WILD-TYPE | 30 | 61 | 14 |
P value = 4.09e-05 (Fisher's exact test), Q value = 0.019
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 50 | 39 | 25 |
AMP PEAK 1(1P34.2) CNV | 20 | 17 | 3 | 5 |
AMP PEAK 1(1P34.2) WILD-TYPE | 16 | 33 | 36 | 20 |
P value = 2.2e-08 (Fisher's exact test), Q value = 1.1e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 2(1P22.3) CNV | 17 | 5 | 21 |
AMP PEAK 2(1P22.3) WILD-TYPE | 28 | 64 | 15 |
P value = 1.27e-08 (Fisher's exact test), Q value = 6.3e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 3(1Q21.3) CNV | 31 | 17 | 28 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 14 | 52 | 8 |
P value = 4e-04 (Fisher's exact test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 50 | 39 | 25 |
AMP PEAK 3(1Q21.3) CNV | 29 | 20 | 15 | 12 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 7 | 30 | 24 | 13 |
P value = 7.96e-06 (Fisher's exact test), Q value = 0.0038
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 4(1Q23.3) CNV | 33 | 23 | 26 |
AMP PEAK 4(1Q23.3) WILD-TYPE | 12 | 46 | 10 |
P value = 0.000496 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 68 | 48 |
AMP PEAK 4(1Q23.3) CNV | 28 | 29 | 25 |
AMP PEAK 4(1Q23.3) WILD-TYPE | 6 | 39 | 23 |
P value = 6.76e-06 (Fisher's exact test), Q value = 0.0032
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 5(3P25.2) CNV | 33 | 19 | 18 |
AMP PEAK 5(3P25.2) WILD-TYPE | 12 | 50 | 18 |
P value = 0.000333 (Fisher's exact test), Q value = 0.15
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 55 | 23 | 45 | 25 |
AMP PEAK 5(3P25.2) CNV | 31 | 16 | 10 | 13 |
AMP PEAK 5(3P25.2) WILD-TYPE | 24 | 7 | 35 | 12 |
P value = 2.34e-06 (Fisher's exact test), Q value = 0.0011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 9(5P15.1) CNV | 31 | 17 | 22 |
AMP PEAK 9(5P15.1) WILD-TYPE | 14 | 52 | 14 |
P value = 8.2e-11 (Fisher's exact test), Q value = 4.1e-08
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 10(6P22.3) CNV | 25 | 9 | 27 |
AMP PEAK 10(6P22.3) WILD-TYPE | 20 | 60 | 9 |
P value = 6.99e-08 (Fisher's exact test), Q value = 3.4e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 13(7P11.2) CNV | 36 | 20 | 24 |
AMP PEAK 13(7P11.2) WILD-TYPE | 9 | 49 | 12 |
P value = 0.000144 (Fisher's exact test), Q value = 0.067
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 14(8P11.23) CNV | 26 | 16 | 7 |
AMP PEAK 14(8P11.23) WILD-TYPE | 19 | 53 | 29 |
P value = 2.25e-07 (Fisher's exact test), Q value = 0.00011
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 16(8Q22.3) CNV | 42 | 34 | 17 |
AMP PEAK 16(8Q22.3) WILD-TYPE | 3 | 35 | 19 |
P value = 0.000129 (Fisher's exact test), Q value = 0.06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 17(8Q24.21) CNV | 38 | 34 | 17 |
AMP PEAK 17(8Q24.21) WILD-TYPE | 7 | 35 | 19 |
P value = 2.91e-09 (Fisher's exact test), Q value = 1.4e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 18(10P15.1) CNV | 30 | 10 | 21 |
AMP PEAK 18(10P15.1) WILD-TYPE | 15 | 59 | 15 |
P value = 5.25e-06 (Fisher's exact test), Q value = 0.0025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 50 | 39 | 25 |
AMP PEAK 18(10P15.1) CNV | 28 | 15 | 12 | 6 |
AMP PEAK 18(10P15.1) WILD-TYPE | 8 | 35 | 27 | 19 |
P value = 8.05e-07 (Fisher's exact test), Q value = 0.00039
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 19(11Q13.3) CNV | 32 | 15 | 13 |
AMP PEAK 19(11Q13.3) WILD-TYPE | 13 | 54 | 23 |
P value = 0.000434 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 68 | 48 |
AMP PEAK 19(11Q13.3) CNV | 14 | 37 | 9 |
AMP PEAK 19(11Q13.3) WILD-TYPE | 20 | 31 | 39 |
P value = 3.59e-06 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 23(17Q11.2) CNV | 34 | 20 | 14 |
AMP PEAK 23(17Q11.2) WILD-TYPE | 11 | 49 | 22 |
P value = 9.31e-05 (Fisher's exact test), Q value = 0.044
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 55 | 23 | 45 | 25 |
AMP PEAK 23(17Q11.2) CNV | 33 | 16 | 10 | 9 |
AMP PEAK 23(17Q11.2) WILD-TYPE | 22 | 7 | 35 | 16 |
P value = 0.000209 (Fisher's exact test), Q value = 0.097
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 24(17Q12) CNV | 30 | 24 | 9 |
AMP PEAK 24(17Q12) WILD-TYPE | 15 | 45 | 27 |
P value = 0.000217 (Chi-square test), Q value = 0.1
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 75 | 7 | 37 | 10 |
AMP PEAK 24(17Q12) CNV | 17 | 31 | 0 | 10 | 5 |
AMP PEAK 24(17Q12) WILD-TYPE | 4 | 44 | 7 | 27 | 5 |
P value = 4.82e-05 (Fisher's exact test), Q value = 0.023
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 25(19Q12) CNV | 29 | 17 | 19 |
AMP PEAK 25(19Q12) WILD-TYPE | 16 | 52 | 17 |
P value = 0.000105 (Fisher's exact test), Q value = 0.049
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 26(19Q13.43) CNV | 29 | 17 | 17 |
AMP PEAK 26(19Q13.43) WILD-TYPE | 16 | 52 | 19 |
P value = 2.07e-06 (Fisher's exact test), Q value = 0.001
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
AMP PEAK 27(20Q11.21) CNV | 41 | 34 | 29 |
AMP PEAK 27(20Q11.21) WILD-TYPE | 4 | 35 | 7 |
P value = 0.000526 (Fisher's exact test), Q value = 0.24
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 5(2Q37.1) CNV | 30 | 22 | 21 |
DEL PEAK 5(2Q37.1) WILD-TYPE | 15 | 47 | 15 |
P value = 0.000115 (Fisher's exact test), Q value = 0.054
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 55 | 23 | 45 | 25 |
DEL PEAK 6(3P21.31) CNV | 13 | 9 | 23 | 1 |
DEL PEAK 6(3P21.31) WILD-TYPE | 42 | 14 | 22 | 24 |
P value = 0.000294 (Fisher's exact test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 13 | 14 | 24 |
DEL PEAK 7(3P14.2) CNV | 7 | 9 | 2 |
DEL PEAK 7(3P14.2) WILD-TYPE | 6 | 5 | 22 |
P value = 0.000489 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 55 | 23 | 45 | 25 |
DEL PEAK 7(3P14.2) CNV | 14 | 6 | 24 | 2 |
DEL PEAK 7(3P14.2) WILD-TYPE | 41 | 17 | 21 | 23 |
P value = 0.000495 (Fisher's exact test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 13 | 14 | 24 |
DEL PEAK 8(3P12.3) CNV | 6 | 9 | 2 |
DEL PEAK 8(3P12.3) WILD-TYPE | 7 | 5 | 22 |
P value = 7.79e-05 (Fisher's exact test), Q value = 0.037
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 10(4Q34.2) CNV | 28 | 17 | 20 |
DEL PEAK 10(4Q34.2) WILD-TYPE | 17 | 52 | 16 |
P value = 3.24e-07 (Fisher's exact test), Q value = 0.00016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 11(5Q11.2) CNV | 32 | 18 | 25 |
DEL PEAK 11(5Q11.2) WILD-TYPE | 13 | 51 | 11 |
P value = 0.000355 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 12(5Q35.1) CNV | 29 | 21 | 22 |
DEL PEAK 12(5Q35.1) WILD-TYPE | 16 | 48 | 14 |
P value = 0.000367 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 14(6Q21) CNV | 30 | 21 | 12 |
DEL PEAK 14(6Q21) WILD-TYPE | 15 | 48 | 24 |
P value = 8.84e-06 (Fisher's exact test), Q value = 0.0042
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 15(8P23.1) CNV | 28 | 25 | 30 |
DEL PEAK 15(8P23.1) WILD-TYPE | 17 | 44 | 6 |
P value = 0.000501 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 16(9P23) CNV | 23 | 37 | 6 |
DEL PEAK 16(9P23) WILD-TYPE | 22 | 32 | 30 |
P value = 4.52e-07 (Fisher's exact test), Q value = 0.00022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 17(9P21.3) CNV | 31 | 49 | 7 |
DEL PEAK 17(9P21.3) WILD-TYPE | 14 | 20 | 29 |
P value = 0.000115 (Fisher's exact test), Q value = 0.054
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 19(10Q23.31) CNV | 25 | 15 | 20 |
DEL PEAK 19(10Q23.31) WILD-TYPE | 20 | 54 | 16 |
P value = 7.69e-05 (Fisher's exact test), Q value = 0.036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 20(11P15.5) CNV | 34 | 25 | 14 |
DEL PEAK 20(11P15.5) WILD-TYPE | 11 | 44 | 22 |
P value = 0.000254 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 22(13Q14.2) CNV | 22 | 15 | 21 |
DEL PEAK 22(13Q14.2) WILD-TYPE | 23 | 54 | 15 |
P value = 0.000229 (Fisher's exact test), Q value = 0.11
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 11 | 10 | 14 | 16 |
DEL PEAK 22(13Q14.2) CNV | 2 | 6 | 1 | 12 |
DEL PEAK 22(13Q14.2) WILD-TYPE | 9 | 4 | 13 | 4 |
P value = 0.00025 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 68 | 48 |
DEL PEAK 24(14Q32.31) CNV | 19 | 13 | 9 |
DEL PEAK 24(14Q32.31) WILD-TYPE | 15 | 55 | 39 |
P value = 4.32e-06 (Fisher's exact test), Q value = 0.0021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 25(15Q13.1) CNV | 24 | 11 | 20 |
DEL PEAK 25(15Q13.1) WILD-TYPE | 21 | 58 | 16 |
P value = 3.5e-06 (Fisher's exact test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 26(16P13.3) CNV | 21 | 11 | 22 |
DEL PEAK 26(16P13.3) WILD-TYPE | 24 | 58 | 14 |
P value = 1.76e-05 (Fisher's exact test), Q value = 0.0084
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 27(16Q23.1) CNV | 15 | 6 | 17 |
DEL PEAK 27(16Q23.1) WILD-TYPE | 30 | 63 | 19 |
P value = 2.97e-07 (Fisher's exact test), Q value = 0.00015
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 45 | 69 | 36 |
DEL PEAK 31(22Q13.32) CNV | 16 | 16 | 28 |
DEL PEAK 31(22Q13.32) WILD-TYPE | 29 | 53 | 8 |
-
Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
-
Molecular subtype file = BLCA-TP.transferedmergedcluster.txt
-
Number of patients = 150
-
Number of copy number variation regions = 62
-
Number of molecular subtypes = 8
-
Exclude regions that fewer than K tumors have alterations, 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.