(primary solid tumor cohort)
This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 63 peak regions and 8 molecular subtypes across 150 patients, 46 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(1q21.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 3(1q23.3) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 4(3p25.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 7(4q13.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 8(5p15.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 9(6p22.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 12(7p11.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 13(8p11.23) cnvs correlated to 'CN_CNMF'.
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Amp Peak 14(8p11.21) cnvs correlated to 'CN_CNMF'.
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Amp Peak 17(10p15.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 22(17q11.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Amp Peak 24(19q12) cnvs correlated to 'CN_CNMF'.
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Amp Peak 25(19q13.43) cnvs correlated to 'CN_CNMF'.
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Del Peak 4(2q34) 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 'CN_CNMF'.
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Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF', '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 14(6q21) cnvs correlated to 'CN_CNMF'.
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Del Peak 15(6q27) cnvs correlated to 'CN_CNMF'.
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Del Peak 16(8p23.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 17(8p21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 19(9p21.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 22(11p15.5) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 23(11q25) cnvs correlated to 'CN_CNMF'.
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Del Peak 24(13q14.2) cnvs correlated to 'CN_CNMF' and 'RPPA_CNMF'.
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Del Peak 26(14q32.31) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
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Del Peak 27(15q13.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 29(16q23.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 30(17p12) 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 | 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 | |
Amp Peak 3(1q23 3) | 82 (55%) | 68 |
2.59e-05 (0.0127) |
0.0124 (1.00) |
0.925 (1.00) |
0.589 (1.00) |
0.0634 (1.00) |
0.719 (1.00) |
0.000177 (0.0837) |
0.000144 (0.0687) |
Amp Peak 4(3p25 2) | 72 (48%) | 78 |
3.36e-05 (0.0163) |
0.00161 (0.718) |
0.278 (1.00) |
0.0393 (1.00) |
0.000848 (0.386) |
0.000371 (0.173) |
0.00182 (0.8) |
0.000247 (0.116) |
Del Peak 7(3p14 2) | 48 (32%) | 102 |
0.000507 (0.233) |
0.56 (1.00) |
0.0759 (1.00) |
0.000294 (0.138) |
0.000425 (0.197) |
0.00753 (1.00) |
0.498 (1.00) |
0.154 (1.00) |
Amp Peak 1(1p34 2) | 45 (30%) | 105 |
0.0002 (0.0943) |
4.09e-05 (0.0199) |
0.894 (1.00) |
0.706 (1.00) |
0.0147 (1.00) |
0.52 (1.00) |
0.0751 (1.00) |
0.616 (1.00) |
Amp Peak 2(1q21 3) | 76 (51%) | 74 |
6.85e-06 (0.00337) |
0.0004 (0.186) |
0.0118 (1.00) |
0.0511 (1.00) |
0.00374 (1.00) |
0.365 (1.00) |
0.0616 (1.00) |
0.155 (1.00) |
Amp Peak 17(10p15 1) | 61 (41%) | 89 |
6.73e-09 (3.38e-06) |
5.25e-06 (0.00259) |
0.893 (1.00) |
0.215 (1.00) |
0.221 (1.00) |
0.0583 (1.00) |
0.336 (1.00) |
0.109 (1.00) |
Amp Peak 22(17q11 2) | 68 (45%) | 82 |
4.62e-08 (2.31e-05) |
0.00122 (0.549) |
0.76 (1.00) |
0.439 (1.00) |
0.000134 (0.064) |
0.00318 (1.00) |
0.0152 (1.00) |
0.0184 (1.00) |
Del Peak 16(8p23 3) | 80 (53%) | 70 |
2.1e-08 (1.06e-05) |
5.24e-05 (0.0253) |
0.145 (1.00) |
0.389 (1.00) |
0.169 (1.00) |
0.969 (1.00) |
0.0059 (1.00) |
0.00931 (1.00) |
Del Peak 17(8p21 1) | 84 (56%) | 66 |
1.53e-09 (7.71e-07) |
5.2e-05 (0.0251) |
0.145 (1.00) |
0.389 (1.00) |
0.713 (1.00) |
0.498 (1.00) |
0.0018 (0.796) |
0.000747 (0.341) |
Del Peak 22(11p15 5) | 73 (49%) | 77 |
5.12e-06 (0.00254) |
0.038 (1.00) |
0.195 (1.00) |
0.673 (1.00) |
0.125 (1.00) |
0.000152 (0.0723) |
0.00164 (0.728) |
0.0164 (1.00) |
Del Peak 24(13q14 2) | 58 (39%) | 92 |
0.000135 (0.0643) |
0.986 (1.00) |
0.000229 (0.108) |
0.00875 (1.00) |
0.0928 (1.00) |
0.235 (1.00) |
0.906 (1.00) |
0.687 (1.00) |
Del Peak 26(14q32 31) | 41 (27%) | 109 |
5.95e-05 (0.0286) |
0.0272 (1.00) |
0.805 (1.00) |
0.843 (1.00) |
0.218 (1.00) |
0.247 (1.00) |
0.000503 (0.231) |
0.00139 (0.622) |
Amp Peak 7(4q13 3) | 23 (15%) | 127 |
8.45e-05 (0.0406) |
0.16 (1.00) |
0.517 (1.00) |
0.867 (1.00) |
0.571 (1.00) |
0.4 (1.00) |
0.288 (1.00) |
0.279 (1.00) |
Amp Peak 8(5p15 1) | 69 (46%) | 81 |
4.5e-05 (0.0218) |
0.202 (1.00) |
0.014 (1.00) |
0.46 (1.00) |
0.094 (1.00) |
0.458 (1.00) |
0.0768 (1.00) |
0.0954 (1.00) |
Amp Peak 9(6p22 3) | 61 (41%) | 89 |
0.000183 (0.0865) |
0.00236 (1.00) |
0.834 (1.00) |
0.872 (1.00) |
0.56 (1.00) |
0.581 (1.00) |
0.0948 (1.00) |
0.449 (1.00) |
Amp Peak 12(7p11 2) | 78 (52%) | 72 |
4.49e-07 (0.000224) |
0.002 (0.875) |
0.481 (1.00) |
0.243 (1.00) |
0.825 (1.00) |
0.678 (1.00) |
0.757 (1.00) |
0.874 (1.00) |
Amp Peak 13(8p11 23) | 48 (32%) | 102 |
0.000492 (0.227) |
0.0488 (1.00) |
0.0732 (1.00) |
0.017 (1.00) |
0.423 (1.00) |
0.271 (1.00) |
0.159 (1.00) |
0.516 (1.00) |
Amp Peak 14(8p11 21) | 48 (32%) | 102 |
1.62e-05 (0.00794) |
0.0146 (1.00) |
0.596 (1.00) |
0.637 (1.00) |
0.268 (1.00) |
0.448 (1.00) |
0.0324 (1.00) |
0.298 (1.00) |
Amp Peak 24(19q12) | 65 (43%) | 85 |
6.35e-06 (0.00313) |
0.00271 (1.00) |
0.37 (1.00) |
0.936 (1.00) |
0.456 (1.00) |
0.438 (1.00) |
0.518 (1.00) |
0.282 (1.00) |
Amp Peak 25(19q13 43) | 63 (42%) | 87 |
9.08e-05 (0.0435) |
0.0258 (1.00) |
0.778 (1.00) |
0.767 (1.00) |
0.0812 (1.00) |
0.819 (1.00) |
0.202 (1.00) |
0.0537 (1.00) |
Del Peak 4(2q34) | 60 (40%) | 90 |
3.53e-06 (0.00175) |
0.137 (1.00) |
0.309 (1.00) |
0.472 (1.00) |
0.152 (1.00) |
0.111 (1.00) |
0.117 (1.00) |
0.137 (1.00) |
Del Peak 5(2q37 1) | 73 (49%) | 77 |
3.3e-05 (0.0161) |
0.0128 (1.00) |
0.908 (1.00) |
0.875 (1.00) |
0.0659 (1.00) |
0.0184 (1.00) |
0.0665 (1.00) |
0.0164 (1.00) |
Del Peak 6(3p21 31) | 47 (31%) | 103 |
0.000394 (0.184) |
0.12 (1.00) |
0.00649 (1.00) |
0.0023 (1.00) |
0.000558 (0.255) |
0.0203 (1.00) |
0.0827 (1.00) |
0.0512 (1.00) |
Del Peak 8(3p12 3) | 41 (27%) | 109 |
0.0127 (1.00) |
0.455 (1.00) |
0.0189 (1.00) |
0.000495 (0.228) |
0.00164 (0.728) |
0.0523 (1.00) |
0.508 (1.00) |
0.184 (1.00) |
Del Peak 14(6q21) | 63 (42%) | 87 |
7.29e-07 (0.000363) |
0.0129 (1.00) |
0.0799 (1.00) |
0.272 (1.00) |
0.314 (1.00) |
0.0153 (1.00) |
0.479 (1.00) |
0.101 (1.00) |
Del Peak 15(6q27) | 62 (41%) | 88 |
2.04e-06 (0.00102) |
0.00235 (1.00) |
0.156 (1.00) |
0.346 (1.00) |
0.221 (1.00) |
0.00625 (1.00) |
0.183 (1.00) |
0.292 (1.00) |
Del Peak 19(9p21 3) | 86 (57%) | 64 |
0.000482 (0.223) |
0.566 (1.00) |
0.0718 (1.00) |
0.93 (1.00) |
0.251 (1.00) |
0.128 (1.00) |
0.752 (1.00) |
0.525 (1.00) |
Del Peak 23(11q25) | 47 (31%) | 103 |
4.26e-05 (0.0207) |
0.337 (1.00) |
0.378 (1.00) |
1 (1.00) |
0.2 (1.00) |
0.549 (1.00) |
0.112 (1.00) |
0.0588 (1.00) |
Del Peak 27(15q13 1) | 54 (36%) | 96 |
0.000301 (0.141) |
0.00312 (1.00) |
0.0829 (1.00) |
0.46 (1.00) |
0.58 (1.00) |
0.78 (1.00) |
0.0842 (1.00) |
0.0283 (1.00) |
Del Peak 29(16q23 1) | 38 (25%) | 112 |
1.99e-05 (0.00975) |
0.0434 (1.00) |
0.232 (1.00) |
0.753 (1.00) |
0.611 (1.00) |
0.96 (1.00) |
0.0773 (1.00) |
0.0801 (1.00) |
Del Peak 30(17p12) | 77 (51%) | 73 |
2.91e-08 (1.46e-05) |
0.0175 (1.00) |
0.556 (1.00) |
0.405 (1.00) |
0.0218 (1.00) |
0.0245 (1.00) |
0.225 (1.00) |
0.528 (1.00) |
Amp Peak 5(3q26 32) | 84 (56%) | 66 |
0.0044 (1.00) |
0.664 (1.00) |
0.161 (1.00) |
0.812 (1.00) |
0.601 (1.00) |
0.875 (1.00) |
0.624 (1.00) |
0.27 (1.00) |
Amp Peak 6(4p16 3) | 31 (21%) | 119 |
0.0176 (1.00) |
0.172 (1.00) |
0.162 (1.00) |
0.189 (1.00) |
0.103 (1.00) |
0.118 (1.00) |
0.0379 (1.00) |
0.286 (1.00) |
Amp Peak 10(6q12) | 25 (17%) | 125 |
0.00601 (1.00) |
0.627 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.667 (1.00) |
0.179 (1.00) |
0.00507 (1.00) |
Amp Peak 11(6q21) | 18 (12%) | 132 |
0.245 (1.00) |
0.0512 (1.00) |
0.621 (1.00) |
0.584 (1.00) |
0.198 (1.00) |
0.155 (1.00) |
0.898 (1.00) |
1 (1.00) |
Amp Peak 15(8q22 3) | 92 (61%) | 58 |
0.00409 (1.00) |
0.00206 (0.897) |
0.168 (1.00) |
0.208 (1.00) |
0.108 (1.00) |
0.437 (1.00) |
0.0146 (1.00) |
0.192 (1.00) |
Amp Peak 16(8q24 21) | 88 (59%) | 62 |
0.00138 (0.616) |
0.022 (1.00) |
0.226 (1.00) |
0.354 (1.00) |
0.125 (1.00) |
0.196 (1.00) |
0.0311 (1.00) |
0.375 (1.00) |
Amp Peak 18(11q13 3) | 59 (39%) | 91 |
0.00169 (0.748) |
0.237 (1.00) |
0.554 (1.00) |
0.597 (1.00) |
0.222 (1.00) |
0.319 (1.00) |
0.00136 (0.611) |
0.124 (1.00) |
Amp Peak 19(12q15) | 48 (32%) | 102 |
0.0509 (1.00) |
0.107 (1.00) |
0.76 (1.00) |
0.439 (1.00) |
0.0082 (1.00) |
0.00219 (0.955) |
0.202 (1.00) |
0.281 (1.00) |
Amp Peak 20(13q22 1) | 49 (33%) | 101 |
0.58 (1.00) |
0.659 (1.00) |
0.641 (1.00) |
0.0971 (1.00) |
0.886 (1.00) |
0.898 (1.00) |
0.455 (1.00) |
0.521 (1.00) |
Amp Peak 21(16p12 1) | 39 (26%) | 111 |
0.0104 (1.00) |
0.112 (1.00) |
0.0783 (1.00) |
0.453 (1.00) |
0.9 (1.00) |
0.846 (1.00) |
0.526 (1.00) |
0.79 (1.00) |
Amp Peak 23(17q12) | 63 (42%) | 87 |
0.0019 (0.834) |
0.153 (1.00) |
0.939 (1.00) |
0.439 (1.00) |
0.0505 (1.00) |
0.26 (1.00) |
0.0112 (1.00) |
0.069 (1.00) |
Amp Peak 26(20q11 21) | 104 (69%) | 46 |
0.0007 (0.32) |
0.428 (1.00) |
0.342 (1.00) |
0.865 (1.00) |
0.204 (1.00) |
0.226 (1.00) |
0.271 (1.00) |
0.218 (1.00) |
Amp Peak 27(22q11 23) | 35 (23%) | 115 |
0.00131 (0.587) |
0.383 (1.00) |
0.837 (1.00) |
0.0916 (1.00) |
0.146 (1.00) |
0.232 (1.00) |
0.275 (1.00) |
0.601 (1.00) |
Del Peak 1(1p36 11) | 27 (18%) | 123 |
0.967 (1.00) |
0.00499 (1.00) |
0.0699 (1.00) |
0.0114 (1.00) |
0.216 (1.00) |
0.181 (1.00) |
0.764 (1.00) |
0.0323 (1.00) |
Del Peak 2(1q32 1) | 28 (19%) | 122 |
0.0723 (1.00) |
0.115 (1.00) |
0.738 (1.00) |
0.38 (1.00) |
0.282 (1.00) |
0.111 (1.00) |
0.928 (1.00) |
0.687 (1.00) |
Del Peak 3(2q22 1) | 43 (29%) | 107 |
0.00317 (1.00) |
0.295 (1.00) |
0.315 (1.00) |
0.278 (1.00) |
0.577 (1.00) |
0.102 (1.00) |
0.177 (1.00) |
0.76 (1.00) |
Del Peak 9(4q22 1) | 59 (39%) | 91 |
0.539 (1.00) |
0.628 (1.00) |
0.358 (1.00) |
1 (1.00) |
0.296 (1.00) |
0.149 (1.00) |
0.953 (1.00) |
0.489 (1.00) |
Del Peak 10(4q34 2) | 65 (43%) | 85 |
0.0654 (1.00) |
0.374 (1.00) |
0.422 (1.00) |
0.875 (1.00) |
0.527 (1.00) |
0.0333 (1.00) |
0.0732 (1.00) |
0.00832 (1.00) |
Del Peak 11(5q11 2) | 75 (50%) | 75 |
0.00105 (0.475) |
0.0511 (1.00) |
0.814 (1.00) |
0.474 (1.00) |
0.739 (1.00) |
0.0906 (1.00) |
0.248 (1.00) |
0.0289 (1.00) |
Del Peak 12(5q35 1) | 72 (48%) | 78 |
0.0228 (1.00) |
0.0061 (1.00) |
0.567 (1.00) |
0.568 (1.00) |
0.61 (1.00) |
0.214 (1.00) |
0.101 (1.00) |
0.0826 (1.00) |
Del Peak 13(6p25 3) | 40 (27%) | 110 |
0.0207 (1.00) |
0.269 (1.00) |
0.135 (1.00) |
0.66 (1.00) |
0.512 (1.00) |
0.824 (1.00) |
0.389 (1.00) |
0.756 (1.00) |
Del Peak 18(9p23) | 65 (43%) | 85 |
0.00199 (0.871) |
0.874 (1.00) |
0.274 (1.00) |
0.717 (1.00) |
0.46 (1.00) |
0.0633 (1.00) |
0.417 (1.00) |
0.915 (1.00) |
Del Peak 20(10p12 1) | 29 (19%) | 121 |
0.91 (1.00) |
0.769 (1.00) |
0.455 (1.00) |
0.906 (1.00) |
0.0686 (1.00) |
0.0293 (1.00) |
0.233 (1.00) |
0.0451 (1.00) |
Del Peak 21(10q23 31) | 60 (40%) | 90 |
0.0105 (1.00) |
0.0025 (1.00) |
0.228 (1.00) |
0.929 (1.00) |
0.277 (1.00) |
0.0457 (1.00) |
0.453 (1.00) |
0.109 (1.00) |
Del Peak 25(14q12) | 43 (29%) | 107 |
0.000894 (0.406) |
0.000941 (0.426) |
0.805 (1.00) |
0.598 (1.00) |
0.142 (1.00) |
0.0342 (1.00) |
0.125 (1.00) |
0.0979 (1.00) |
Del Peak 28(16p13 3) | 54 (36%) | 96 |
0.00332 (1.00) |
0.00652 (1.00) |
0.191 (1.00) |
0.23 (1.00) |
1 (1.00) |
0.499 (1.00) |
0.591 (1.00) |
0.377 (1.00) |
Del Peak 31(18q23) | 63 (42%) | 87 |
0.00377 (1.00) |
0.485 (1.00) |
0.979 (1.00) |
0.763 (1.00) |
0.846 (1.00) |
0.37 (1.00) |
0.0194 (1.00) |
0.00278 (1.00) |
Del Peak 32(19p13 3) | 60 (40%) | 90 |
0.0227 (1.00) |
0.0266 (1.00) |
1 (1.00) |
0.757 (1.00) |
0.944 (1.00) |
0.0831 (1.00) |
0.428 (1.00) |
0.215 (1.00) |
Del Peak 33(22q13 32) | 60 (40%) | 90 |
0.00112 (0.503) |
0.26 (1.00) |
0.128 (1.00) |
0.0675 (1.00) |
0.106 (1.00) |
0.115 (1.00) |
0.679 (1.00) |
0.215 (1.00) |
Del Peak 34(Xp11 3) | 39 (26%) | 111 |
0.2 (1.00) |
0.00294 (1.00) |
0.775 (1.00) |
0.922 (1.00) |
0.0767 (1.00) |
0.236 (1.00) |
0.407 (1.00) |
0.943 (1.00) |
Del Peak 35(Xq21 33) | 35 (23%) | 115 |
0.334 (1.00) |
0.0789 (1.00) |
0.173 (1.00) |
0.173 (1.00) |
0.00919 (1.00) |
0.735 (1.00) |
0.197 (1.00) |
0.249 (1.00) |
Del Peak 36(Xq22 3) | 32 (21%) | 118 |
0.136 (1.00) |
0.0173 (1.00) |
0.149 (1.00) |
0.52 (1.00) |
0.0174 (1.00) |
0.796 (1.00) |
0.0914 (1.00) |
0.277 (1.00) |
P value = 2e-04 (Chi-square test), Q value = 0.094
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 1(1P34.2) MUTATED | 2 | 11 | 14 | 3 | 6 | 9 |
AMP PEAK 1(1P34.2) WILD-TYPE | 12 | 42 | 10 | 26 | 7 | 8 |
P value = 4.09e-05 (Fisher's exact test), Q value = 0.02
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 50 | 39 | 25 |
AMP PEAK 1(1P34.2) MUTATED | 20 | 17 | 3 | 5 |
AMP PEAK 1(1P34.2) WILD-TYPE | 16 | 33 | 36 | 20 |
P value = 6.85e-06 (Chi-square test), Q value = 0.0034
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 2(1Q21.3) MUTATED | 9 | 18 | 20 | 7 | 9 | 13 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 5 | 35 | 4 | 22 | 4 | 4 |
P value = 4e-04 (Fisher's exact test), Q value = 0.19
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 50 | 39 | 25 |
AMP PEAK 2(1Q21.3) MUTATED | 29 | 20 | 15 | 12 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 7 | 30 | 24 | 13 |
P value = 2.59e-05 (Chi-square test), Q value = 0.013
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 3(1Q23.3) MUTATED | 9 | 22 | 21 | 8 | 8 | 14 |
AMP PEAK 3(1Q23.3) WILD-TYPE | 5 | 31 | 3 | 21 | 5 | 3 |
P value = 0.000177 (Fisher's exact test), Q value = 0.084
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 68 | 46 |
AMP PEAK 3(1Q23.3) MUTATED | 29 | 28 | 24 |
AMP PEAK 3(1Q23.3) WILD-TYPE | 6 | 40 | 22 |
P value = 0.000144 (Fisher's exact test), Q value = 0.069
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 8 | 32 | 109 |
AMP PEAK 3(1Q23.3) MUTATED | 5 | 27 | 49 |
AMP PEAK 3(1Q23.3) WILD-TYPE | 3 | 5 | 60 |
P value = 3.36e-05 (Chi-square test), Q value = 0.016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 4(3P25.2) MUTATED | 11 | 15 | 15 | 11 | 5 | 15 |
AMP PEAK 4(3P25.2) WILD-TYPE | 3 | 38 | 9 | 18 | 8 | 2 |
P value = 0.000371 (Fisher's exact test), Q value = 0.17
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 39 | 18 | 64 |
AMP PEAK 4(3P25.2) MUTATED | 10 | 9 | 42 |
AMP PEAK 4(3P25.2) WILD-TYPE | 29 | 9 | 22 |
P value = 0.000247 (Fisher's exact test), Q value = 0.12
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 8 | 32 | 109 |
AMP PEAK 4(3P25.2) MUTATED | 2 | 25 | 45 |
AMP PEAK 4(3P25.2) WILD-TYPE | 6 | 7 | 64 |
P value = 8.45e-05 (Chi-square test), Q value = 0.041
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 7(4Q13.3) MUTATED | 0 | 2 | 11 | 4 | 2 | 4 |
AMP PEAK 7(4Q13.3) WILD-TYPE | 14 | 51 | 13 | 25 | 11 | 13 |
P value = 4.5e-05 (Chi-square test), Q value = 0.022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 8(5P15.1) MUTATED | 10 | 13 | 18 | 11 | 10 | 7 |
AMP PEAK 8(5P15.1) WILD-TYPE | 4 | 40 | 6 | 18 | 3 | 10 |
P value = 0.000183 (Chi-square test), Q value = 0.087
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 9(6P22.3) MUTATED | 8 | 13 | 16 | 7 | 10 | 7 |
AMP PEAK 9(6P22.3) WILD-TYPE | 6 | 40 | 8 | 22 | 3 | 10 |
P value = 4.49e-07 (Chi-square test), Q value = 0.00022
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 12(7P11.2) MUTATED | 10 | 12 | 19 | 13 | 10 | 14 |
AMP PEAK 12(7P11.2) WILD-TYPE | 4 | 41 | 5 | 16 | 3 | 3 |
P value = 0.000492 (Chi-square test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 13(8P11.23) MUTATED | 4 | 5 | 12 | 15 | 5 | 7 |
AMP PEAK 13(8P11.23) WILD-TYPE | 10 | 48 | 12 | 14 | 8 | 10 |
P value = 1.62e-05 (Chi-square test), Q value = 0.0079
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 14(8P11.21) MUTATED | 9 | 4 | 7 | 16 | 6 | 6 |
AMP PEAK 14(8P11.21) WILD-TYPE | 5 | 49 | 17 | 13 | 7 | 11 |
P value = 6.73e-09 (Chi-square test), Q value = 3.4e-06
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 17(10P15.1) MUTATED | 9 | 6 | 14 | 8 | 10 | 14 |
AMP PEAK 17(10P15.1) WILD-TYPE | 5 | 47 | 10 | 21 | 3 | 3 |
P value = 5.25e-06 (Fisher's exact test), Q value = 0.0026
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 50 | 39 | 25 |
AMP PEAK 17(10P15.1) MUTATED | 28 | 15 | 12 | 6 |
AMP PEAK 17(10P15.1) WILD-TYPE | 8 | 35 | 27 | 19 |
P value = 4.62e-08 (Chi-square test), Q value = 2.3e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 22(17Q11.2) MUTATED | 13 | 7 | 13 | 20 | 6 | 9 |
AMP PEAK 22(17Q11.2) WILD-TYPE | 1 | 46 | 11 | 9 | 7 | 8 |
P value = 0.000134 (Fisher's exact test), Q value = 0.064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 33 | 38 |
AMP PEAK 22(17Q11.2) MUTATED | 33 | 11 | 9 |
AMP PEAK 22(17Q11.2) WILD-TYPE | 17 | 22 | 29 |
P value = 6.35e-06 (Chi-square test), Q value = 0.0031
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 24(19Q12) MUTATED | 9 | 9 | 19 | 13 | 5 | 10 |
AMP PEAK 24(19Q12) WILD-TYPE | 5 | 44 | 5 | 16 | 8 | 7 |
P value = 9.08e-05 (Chi-square test), Q value = 0.043
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
AMP PEAK 25(19Q13.43) MUTATED | 10 | 9 | 16 | 14 | 5 | 9 |
AMP PEAK 25(19Q13.43) WILD-TYPE | 4 | 44 | 8 | 15 | 8 | 8 |
P value = 3.53e-06 (Chi-square test), Q value = 0.0017
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 4(2Q34) MUTATED | 5 | 9 | 19 | 9 | 8 | 10 |
DEL PEAK 4(2Q34) WILD-TYPE | 9 | 44 | 5 | 20 | 5 | 7 |
P value = 3.3e-05 (Chi-square test), Q value = 0.016
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 5(2Q37.1) MUTATED | 7 | 13 | 20 | 13 | 8 | 12 |
DEL PEAK 5(2Q37.1) WILD-TYPE | 7 | 40 | 4 | 16 | 5 | 5 |
P value = 0.000394 (Chi-square test), Q value = 0.18
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 6(3P21.31) MUTATED | 4 | 10 | 13 | 14 | 6 | 0 |
DEL PEAK 6(3P21.31) WILD-TYPE | 10 | 43 | 11 | 15 | 7 | 17 |
P value = 0.000507 (Chi-square test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 7(3P14.2) MUTATED | 7 | 10 | 13 | 12 | 6 | 0 |
DEL PEAK 7(3P14.2) WILD-TYPE | 7 | 43 | 11 | 17 | 7 | 17 |
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) MUTATED | 7 | 9 | 2 |
DEL PEAK 7(3P14.2) WILD-TYPE | 6 | 5 | 22 |
P value = 0.000425 (Fisher's exact test), Q value = 0.2
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 33 | 38 |
DEL PEAK 7(3P14.2) MUTATED | 14 | 4 | 21 |
DEL PEAK 7(3P14.2) WILD-TYPE | 36 | 29 | 17 |
P value = 0.000495 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 13 | 14 | 24 |
DEL PEAK 8(3P12.3) MUTATED | 6 | 9 | 2 |
DEL PEAK 8(3P12.3) WILD-TYPE | 7 | 5 | 22 |
P value = 7.29e-07 (Chi-square test), Q value = 0.00036
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 14(6Q21) MUTATED | 6 | 7 | 13 | 16 | 6 | 15 |
DEL PEAK 14(6Q21) WILD-TYPE | 8 | 46 | 11 | 13 | 7 | 2 |
P value = 2.04e-06 (Chi-square test), Q value = 0.001
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 15(6Q27) MUTATED | 9 | 8 | 11 | 14 | 5 | 15 |
DEL PEAK 15(6Q27) WILD-TYPE | 5 | 45 | 13 | 15 | 8 | 2 |
P value = 2.1e-08 (Chi-square test), Q value = 1.1e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 16(8P23.3) MUTATED | 12 | 23 | 20 | 3 | 11 | 11 |
DEL PEAK 16(8P23.3) WILD-TYPE | 2 | 30 | 4 | 26 | 2 | 6 |
P value = 5.24e-05 (Fisher's exact test), Q value = 0.025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 50 | 39 | 25 |
DEL PEAK 16(8P23.3) MUTATED | 28 | 30 | 10 | 12 |
DEL PEAK 16(8P23.3) WILD-TYPE | 8 | 20 | 29 | 13 |
P value = 1.53e-09 (Chi-square test), Q value = 7.7e-07
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 17(8P21.1) MUTATED | 11 | 22 | 21 | 4 | 12 | 14 |
DEL PEAK 17(8P21.1) WILD-TYPE | 3 | 31 | 3 | 25 | 1 | 3 |
P value = 5.2e-05 (Fisher's exact test), Q value = 0.025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 36 | 50 | 39 | 25 |
DEL PEAK 17(8P21.1) MUTATED | 31 | 28 | 14 | 11 |
DEL PEAK 17(8P21.1) WILD-TYPE | 5 | 22 | 25 | 14 |
P value = 0.000482 (Chi-square test), Q value = 0.22
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 19(9P21.3) MUTATED | 8 | 28 | 16 | 24 | 1 | 9 |
DEL PEAK 19(9P21.3) WILD-TYPE | 6 | 25 | 8 | 5 | 12 | 8 |
P value = 5.12e-06 (Chi-square test), Q value = 0.0025
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 22(11P15.5) MUTATED | 9 | 14 | 19 | 16 | 2 | 13 |
DEL PEAK 22(11P15.5) WILD-TYPE | 5 | 39 | 5 | 13 | 11 | 4 |
P value = 0.000152 (Fisher's exact test), Q value = 0.072
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 39 | 18 | 64 |
DEL PEAK 22(11P15.5) MUTATED | 14 | 3 | 42 |
DEL PEAK 22(11P15.5) WILD-TYPE | 25 | 15 | 22 |
P value = 4.26e-05 (Chi-square test), Q value = 0.021
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 23(11Q25) MUTATED | 7 | 5 | 14 | 14 | 2 | 5 |
DEL PEAK 23(11Q25) WILD-TYPE | 7 | 48 | 10 | 15 | 11 | 12 |
P value = 0.000135 (Chi-square test), Q value = 0.064
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 24(13Q14.2) MUTATED | 3 | 12 | 15 | 10 | 11 | 7 |
DEL PEAK 24(13Q14.2) WILD-TYPE | 11 | 41 | 9 | 19 | 2 | 10 |
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 24(13Q14.2) MUTATED | 2 | 6 | 1 | 12 |
DEL PEAK 24(13Q14.2) WILD-TYPE | 9 | 4 | 13 | 4 |
P value = 5.95e-05 (Chi-square test), Q value = 0.029
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 26(14Q32.31) MUTATED | 10 | 5 | 5 | 8 | 5 | 8 |
DEL PEAK 26(14Q32.31) WILD-TYPE | 4 | 48 | 19 | 21 | 8 | 9 |
P value = 0.000503 (Fisher's exact test), Q value = 0.23
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 35 | 68 | 46 |
DEL PEAK 26(14Q32.31) MUTATED | 19 | 13 | 9 |
DEL PEAK 26(14Q32.31) WILD-TYPE | 16 | 55 | 37 |
P value = 0.000301 (Chi-square test), Q value = 0.14
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 27(15Q13.1) MUTATED | 10 | 14 | 14 | 4 | 7 | 5 |
DEL PEAK 27(15Q13.1) WILD-TYPE | 4 | 39 | 10 | 25 | 6 | 12 |
P value = 1.99e-05 (Chi-square test), Q value = 0.0097
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 29(16Q23.1) MUTATED | 8 | 7 | 2 | 5 | 6 | 10 |
DEL PEAK 29(16Q23.1) WILD-TYPE | 6 | 46 | 22 | 24 | 7 | 7 |
P value = 2.91e-08 (Chi-square test), Q value = 1.5e-05
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 14 | 53 | 24 | 29 | 13 | 17 |
DEL PEAK 30(17P12) MUTATED | 11 | 11 | 17 | 21 | 3 | 14 |
DEL PEAK 30(17P12) WILD-TYPE | 3 | 42 | 7 | 8 | 10 | 3 |
-
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 = 63
-
Number of molecular subtypes = 8
-
Exclude regions 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.