This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 53 peak regions and 8 molecular subtypes across 139 patients, 20 significant findings detected with Q value < 0.25.
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Amp Peak 2(1q22) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 6(3q26.31) cnvs correlated to 'CN_CNMF'.
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Amp Peak 10(6p21.1) cnvs correlated to 'METHLYATION_CNMF'.
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Amp Peak 12(8q13.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 13(8q24.13) cnvs correlated to 'CN_CNMF'.
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Amp Peak 18(13q32.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 23(19p13.12) cnvs correlated to 'MIRSEQ_MATURE_CNMF'.
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Del Peak 5(3p13) cnvs correlated to 'MRNASEQ_CNMF'.
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Del Peak 7(4q25) cnvs correlated to 'CN_CNMF'.
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Del Peak 8(4q35.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 12(8p23.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 13(8p11.22) cnvs correlated to 'CN_CNMF'.
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Del Peak 16(10q23.31) cnvs correlated to 'MRNASEQ_CNMF'.
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Del Peak 20(13q14.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Del Peak 21(13q22.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Del Peak 22(14q23.3) cnvs correlated to 'MRNASEQ_CNMF'.
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Del Peak 24(17p13.3) cnvs correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 53 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 20 significant findings detected.
|
Molecular subtypes |
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 | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
| Amp Peak 2(1q22) | 0 (0%) | 39 |
9.39e-07 (0.000394) |
7.03e-05 (0.0292) |
0.215 (1.00) |
0.603 (1.00) |
0.13 (1.00) |
0.0591 (1.00) |
0.0908 (1.00) |
0.459 (1.00) |
| Del Peak 20(13q14 2) | 0 (0%) | 76 |
2.03e-06 (0.000847) |
0.23 (1.00) |
9.13e-05 (0.0378) |
0.0169 (1.00) |
0.00181 (0.715) |
0.109 (1.00) |
0.00652 (1.00) |
0.179 (1.00) |
| Del Peak 21(13q22 2) | 0 (0%) | 88 |
0.000431 (0.176) |
0.148 (1.00) |
0.000493 (0.2) |
0.188 (1.00) |
0.0328 (1.00) |
0.486 (1.00) |
0.0595 (1.00) |
0.475 (1.00) |
| Amp Peak 6(3q26 31) | 0 (0%) | 113 |
0.000317 (0.13) |
0.0256 (1.00) |
0.109 (1.00) |
0.079 (1.00) |
0.0385 (1.00) |
0.0212 (1.00) |
0.654 (1.00) |
0.0206 (1.00) |
| Amp Peak 10(6p21 1) | 0 (0%) | 82 |
0.00467 (1.00) |
0.000112 (0.0461) |
0.00375 (1.00) |
0.973 (1.00) |
0.93 (1.00) |
0.653 (1.00) |
0.338 (1.00) |
0.822 (1.00) |
| Amp Peak 12(8q13 1) | 0 (0%) | 70 |
3.51e-09 (1.48e-06) |
0.574 (1.00) |
0.00322 (1.00) |
0.347 (1.00) |
0.229 (1.00) |
0.803 (1.00) |
0.39 (1.00) |
0.882 (1.00) |
| Amp Peak 13(8q24 13) | 0 (0%) | 58 |
1.75e-08 (7.36e-06) |
0.306 (1.00) |
0.00317 (1.00) |
0.409 (1.00) |
0.336 (1.00) |
0.773 (1.00) |
0.571 (1.00) |
0.826 (1.00) |
| Amp Peak 18(13q32 3) | 0 (0%) | 113 |
0.000372 (0.152) |
0.0405 (1.00) |
0.0714 (1.00) |
0.0373 (1.00) |
0.19 (1.00) |
0.346 (1.00) |
0.846 (1.00) |
0.451 (1.00) |
| Amp Peak 23(19p13 12) | 0 (0%) | 104 |
0.0418 (1.00) |
0.00125 (0.495) |
0.000869 (0.347) |
0.00566 (1.00) |
0.0126 (1.00) |
0.0865 (1.00) |
0.000159 (0.0655) |
0.23 (1.00) |
| Del Peak 5(3p13) | 0 (0%) | 117 |
0.0258 (1.00) |
0.127 (1.00) |
3.88e-05 (0.0161) |
0.00117 (0.464) |
0.0961 (1.00) |
0.329 (1.00) |
0.064 (1.00) |
0.0387 (1.00) |
| Del Peak 7(4q25) | 0 (0%) | 75 |
6.25e-07 (0.000263) |
0.00812 (1.00) |
0.00584 (1.00) |
0.147 (1.00) |
0.767 (1.00) |
0.91 (1.00) |
0.506 (1.00) |
0.827 (1.00) |
| Del Peak 8(4q35 1) | 0 (0%) | 80 |
0.000487 (0.198) |
0.00279 (1.00) |
0.0074 (1.00) |
0.263 (1.00) |
0.923 (1.00) |
0.682 (1.00) |
1 (1.00) |
0.548 (1.00) |
| Del Peak 12(8p23 2) | 0 (0%) | 55 |
1.28e-15 (5.43e-13) |
0.0693 (1.00) |
0.584 (1.00) |
0.617 (1.00) |
0.568 (1.00) |
0.504 (1.00) |
1 (1.00) |
0.456 (1.00) |
| Del Peak 13(8p11 22) | 0 (0%) | 72 |
7.27e-15 (3.07e-12) |
0.367 (1.00) |
0.816 (1.00) |
0.507 (1.00) |
0.754 (1.00) |
0.338 (1.00) |
0.626 (1.00) |
0.17 (1.00) |
| Del Peak 16(10q23 31) | 0 (0%) | 92 |
0.00192 (0.755) |
0.622 (1.00) |
0.000277 (0.114) |
0.0419 (1.00) |
0.0407 (1.00) |
0.131 (1.00) |
0.0549 (1.00) |
0.381 (1.00) |
| Del Peak 22(14q23 3) | 0 (0%) | 90 |
0.134 (1.00) |
0.0609 (1.00) |
0.000548 (0.222) |
0.00495 (1.00) |
0.247 (1.00) |
0.101 (1.00) |
0.196 (1.00) |
0.0615 (1.00) |
| Del Peak 24(17p13 3) | 0 (0%) | 62 |
3.32e-06 (0.00138) |
0.216 (1.00) |
0.00553 (1.00) |
0.0665 (1.00) |
0.00315 (1.00) |
0.00225 (0.877) |
0.0313 (1.00) |
0.00203 (0.792) |
| Amp Peak 1(1p22 3) | 0 (0%) | 102 |
0.00189 (0.744) |
0.0813 (1.00) |
0.0213 (1.00) |
0.0347 (1.00) |
0.529 (1.00) |
0.669 (1.00) |
0.534 (1.00) |
0.727 (1.00) |
| Amp Peak 3(1q42 3) | 0 (0%) | 44 |
0.00324 (1.00) |
0.00801 (1.00) |
0.885 (1.00) |
0.284 (1.00) |
0.733 (1.00) |
0.27 (1.00) |
0.405 (1.00) |
0.302 (1.00) |
| Amp Peak 4(2p24 1) | 0 (0%) | 110 |
0.000838 (0.336) |
0.814 (1.00) |
0.0376 (1.00) |
0.0394 (1.00) |
0.316 (1.00) |
0.511 (1.00) |
0.73 (1.00) |
0.366 (1.00) |
| Amp Peak 5(2q31 2) | 0 (0%) | 110 |
0.00924 (1.00) |
0.583 (1.00) |
0.399 (1.00) |
0.48 (1.00) |
0.419 (1.00) |
1 (1.00) |
0.73 (1.00) |
0.721 (1.00) |
| Amp Peak 7(5p15 33) | 0 (0%) | 71 |
0.00296 (1.00) |
0.241 (1.00) |
0.525 (1.00) |
0.947 (1.00) |
0.239 (1.00) |
0.0901 (1.00) |
0.52 (1.00) |
0.234 (1.00) |
| Amp Peak 8(5q35 3) | 0 (0%) | 92 |
0.02 (1.00) |
0.653 (1.00) |
0.859 (1.00) |
0.377 (1.00) |
0.254 (1.00) |
0.473 (1.00) |
0.314 (1.00) |
0.198 (1.00) |
| Amp Peak 9(6p25 2) | 0 (0%) | 81 |
0.00262 (1.00) |
0.00335 (1.00) |
0.0282 (1.00) |
0.194 (1.00) |
0.941 (1.00) |
0.936 (1.00) |
0.454 (1.00) |
0.968 (1.00) |
| Amp Peak 11(7q21 2) | 0 (0%) | 89 |
0.18 (1.00) |
0.153 (1.00) |
0.192 (1.00) |
0.342 (1.00) |
0.151 (1.00) |
0.0914 (1.00) |
0.842 (1.00) |
0.231 (1.00) |
| Amp Peak 14(9q34 2) | 0 (0%) | 121 |
0.165 (1.00) |
0.0488 (1.00) |
0.285 (1.00) |
0.0679 (1.00) |
0.373 (1.00) |
0.193 (1.00) |
0.64 (1.00) |
0.0109 (1.00) |
| Amp Peak 15(10p15 1) | 0 (0%) | 109 |
0.517 (1.00) |
0.15 (1.00) |
0.294 (1.00) |
0.329 (1.00) |
0.815 (1.00) |
0.835 (1.00) |
0.162 (1.00) |
0.915 (1.00) |
| Amp Peak 16(11q13 3) | 0 (0%) | 114 |
0.0611 (1.00) |
1 (1.00) |
0.0497 (1.00) |
0.623 (1.00) |
0.0576 (1.00) |
0.255 (1.00) |
0.0333 (1.00) |
0.395 (1.00) |
| Amp Peak 17(12q23 1) | 0 (0%) | 113 |
0.0232 (1.00) |
0.391 (1.00) |
0.237 (1.00) |
0.0626 (1.00) |
0.839 (1.00) |
0.819 (1.00) |
0.883 (1.00) |
0.951 (1.00) |
| Amp Peak 19(15q26 3) | 0 (0%) | 117 |
0.0245 (1.00) |
0.819 (1.00) |
0.433 (1.00) |
0.197 (1.00) |
0.458 (1.00) |
0.436 (1.00) |
0.908 (1.00) |
0.384 (1.00) |
| Amp Peak 20(17p11 2) | 0 (0%) | 120 |
0.61 (1.00) |
0.938 (1.00) |
0.132 (1.00) |
0.0768 (1.00) |
0.872 (1.00) |
0.938 (1.00) |
1 (1.00) |
0.939 (1.00) |
| Amp Peak 21(17q23 1) | 0 (0%) | 82 |
0.00811 (1.00) |
0.195 (1.00) |
0.129 (1.00) |
0.281 (1.00) |
0.509 (1.00) |
0.635 (1.00) |
0.707 (1.00) |
0.431 (1.00) |
| Amp Peak 22(17q25 3) | 0 (0%) | 79 |
0.000934 (0.373) |
0.0398 (1.00) |
0.13 (1.00) |
0.801 (1.00) |
0.339 (1.00) |
0.492 (1.00) |
0.364 (1.00) |
0.325 (1.00) |
| Amp Peak 24(19q13 11) | 0 (0%) | 96 |
0.0717 (1.00) |
0.155 (1.00) |
0.0151 (1.00) |
0.183 (1.00) |
0.255 (1.00) |
0.162 (1.00) |
0.0666 (1.00) |
0.318 (1.00) |
| Amp Peak 25(20q13 33) | 0 (0%) | 87 |
0.00196 (0.767) |
0.0464 (1.00) |
0.0202 (1.00) |
0.0603 (1.00) |
0.585 (1.00) |
0.906 (1.00) |
0.319 (1.00) |
0.821 (1.00) |
| Del Peak 1(1p36 32) | 0 (0%) | 78 |
0.0165 (1.00) |
0.0105 (1.00) |
0.041 (1.00) |
0.263 (1.00) |
0.819 (1.00) |
0.774 (1.00) |
0.948 (1.00) |
0.619 (1.00) |
| Del Peak 2(1p35 2) | 0 (0%) | 90 |
0.0324 (1.00) |
0.00625 (1.00) |
0.0599 (1.00) |
0.0319 (1.00) |
0.424 (1.00) |
0.165 (1.00) |
0.649 (1.00) |
0.0969 (1.00) |
| Del Peak 3(2q22 1) | 0 (0%) | 123 |
0.119 (1.00) |
0.0872 (1.00) |
0.0442 (1.00) |
0.643 (1.00) |
0.0316 (1.00) |
0.00855 (1.00) |
0.526 (1.00) |
0.0181 (1.00) |
| Del Peak 4(2q37 3) | 0 (0%) | 112 |
0.00333 (1.00) |
0.804 (1.00) |
0.000708 (0.285) |
0.251 (1.00) |
0.0704 (1.00) |
0.0421 (1.00) |
0.437 (1.00) |
0.114 (1.00) |
| Del Peak 6(4p16 1) | 0 (0%) | 111 |
0.308 (1.00) |
0.0298 (1.00) |
0.316 (1.00) |
0.391 (1.00) |
0.64 (1.00) |
0.582 (1.00) |
0.157 (1.00) |
0.217 (1.00) |
| Del Peak 9(5q23 1) | 0 (0%) | 120 |
0.284 (1.00) |
0.149 (1.00) |
0.91 (1.00) |
0.211 (1.00) |
0.336 (1.00) |
0.643 (1.00) |
0.621 (1.00) |
0.461 (1.00) |
| Del Peak 10(6q16 3) | 0 (0%) | 91 |
0.00903 (1.00) |
0.525 (1.00) |
0.00239 (0.924) |
0.134 (1.00) |
0.137 (1.00) |
0.41 (1.00) |
0.701 (1.00) |
0.33 (1.00) |
| Del Peak 11(6q26) | 0 (0%) | 86 |
0.00211 (0.824) |
0.165 (1.00) |
0.00894 (1.00) |
0.0504 (1.00) |
0.00496 (1.00) |
0.111 (1.00) |
0.481 (1.00) |
0.0643 (1.00) |
| Del Peak 14(9p21 3) | 0 (0%) | 89 |
0.00656 (1.00) |
0.766 (1.00) |
0.0777 (1.00) |
0.239 (1.00) |
0.679 (1.00) |
0.581 (1.00) |
1 (1.00) |
0.359 (1.00) |
| Del Peak 15(9q34 3) | 0 (0%) | 91 |
0.00082 (0.33) |
0.0839 (1.00) |
0.0348 (1.00) |
0.235 (1.00) |
0.94 (1.00) |
0.297 (1.00) |
0.792 (1.00) |
0.152 (1.00) |
| Del Peak 17(11q23 3) | 0 (0%) | 109 |
0.219 (1.00) |
0.445 (1.00) |
0.155 (1.00) |
0.165 (1.00) |
0.777 (1.00) |
0.659 (1.00) |
0.0172 (1.00) |
0.55 (1.00) |
| Del Peak 18(12p12 1) | 0 (0%) | 107 |
0.0145 (1.00) |
0.382 (1.00) |
0.00276 (1.00) |
0.329 (1.00) |
0.312 (1.00) |
0.214 (1.00) |
0.268 (1.00) |
0.323 (1.00) |
| Del Peak 19(12q24 33) | 0 (0%) | 115 |
0.00496 (1.00) |
0.204 (1.00) |
0.0968 (1.00) |
0.322 (1.00) |
0.891 (1.00) |
0.724 (1.00) |
0.768 (1.00) |
0.621 (1.00) |
| Del Peak 23(16q23 1) | 0 (0%) | 81 |
0.0139 (1.00) |
0.00936 (1.00) |
0.00233 (0.905) |
0.0198 (1.00) |
0.283 (1.00) |
0.0998 (1.00) |
0.746 (1.00) |
0.105 (1.00) |
| Del Peak 25(17p11 2) | 0 (0%) | 62 |
0.0013 (0.515) |
0.298 (1.00) |
0.0641 (1.00) |
0.0252 (1.00) |
0.000628 (0.254) |
0.00349 (1.00) |
0.177 (1.00) |
0.0025 (0.964) |
| Del Peak 26(18q21 2) | 0 (0%) | 111 |
0.0163 (1.00) |
0.0151 (1.00) |
0.0777 (1.00) |
0.695 (1.00) |
0.321 (1.00) |
0.582 (1.00) |
0.641 (1.00) |
0.459 (1.00) |
| Del Peak 27(19p13 3) | 0 (0%) | 107 |
0.0789 (1.00) |
0.0169 (1.00) |
0.00841 (1.00) |
0.41 (1.00) |
0.157 (1.00) |
0.191 (1.00) |
0.6 (1.00) |
0.105 (1.00) |
| Del Peak 28(22q13 32) | 0 (0%) | 100 |
0.0549 (1.00) |
0.55 (1.00) |
0.0844 (1.00) |
0.629 (1.00) |
0.879 (1.00) |
0.265 (1.00) |
0.968 (1.00) |
0.763 (1.00) |
P value = 9.39e-07 (Fisher's exact test), Q value = 0.00039
Table S1. Gene #2: 'Amp Peak 2(1q22)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| AMP PEAK 2(1Q22) CNV | 33 | 21 | 46 |
| AMP PEAK 2(1Q22) WILD-TYPE | 6 | 27 | 6 |
Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(1q22)' versus Molecular Subtype #1: 'CN_CNMF'
P value = 7.03e-05 (Fisher's exact test), Q value = 0.029
Table S2. Gene #2: 'Amp Peak 2(1q22)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 32 | 35 | 56 |
| AMP PEAK 2(1Q22) CNV | 14 | 29 | 48 |
| AMP PEAK 2(1Q22) WILD-TYPE | 18 | 6 | 8 |
Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q22)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 0.000317 (Fisher's exact test), Q value = 0.13
Table S3. Gene #6: 'Amp Peak 6(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| AMP PEAK 6(3Q26.31) CNV | 3 | 4 | 19 |
| AMP PEAK 6(3Q26.31) WILD-TYPE | 36 | 44 | 33 |
Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.000112 (Fisher's exact test), Q value = 0.046
Table S4. Gene #10: 'Amp Peak 10(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 32 | 35 | 56 |
| AMP PEAK 10(6P21.1) CNV | 4 | 16 | 32 |
| AMP PEAK 10(6P21.1) WILD-TYPE | 28 | 19 | 24 |
Figure S4. Get High-res Image Gene #10: 'Amp Peak 10(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
P value = 3.51e-09 (Fisher's exact test), Q value = 1.5e-06
Table S5. Gene #12: 'Amp Peak 12(8q13.1)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| AMP PEAK 12(8Q13.1) CNV | 35 | 14 | 20 |
| AMP PEAK 12(8Q13.1) WILD-TYPE | 4 | 34 | 32 |
Figure S5. Get High-res Image Gene #12: 'Amp Peak 12(8q13.1)' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1.75e-08 (Fisher's exact test), Q value = 7.4e-06
Table S6. Gene #13: 'Amp Peak 13(8q24.13)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| AMP PEAK 13(8Q24.13) CNV | 37 | 19 | 25 |
| AMP PEAK 13(8Q24.13) WILD-TYPE | 2 | 29 | 27 |
Figure S6. Get High-res Image Gene #13: 'Amp Peak 13(8q24.13)' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.000372 (Fisher's exact test), Q value = 0.15
Table S7. Gene #18: 'Amp Peak 18(13q32.3)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| AMP PEAK 18(13Q32.3) CNV | 6 | 2 | 18 |
| AMP PEAK 18(13Q32.3) WILD-TYPE | 33 | 46 | 34 |
Figure S7. Get High-res Image Gene #18: 'Amp Peak 18(13q32.3)' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.000159 (Fisher's exact test), Q value = 0.065
Table S8. Gene #23: 'Amp Peak 23(19p13.12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 29 | 62 | 43 |
| AMP PEAK 23(19P13.12) CNV | 4 | 9 | 21 |
| AMP PEAK 23(19P13.12) WILD-TYPE | 25 | 53 | 22 |
Figure S8. Get High-res Image Gene #23: 'Amp Peak 23(19p13.12)' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
P value = 3.88e-05 (Chi-square test), Q value = 0.016
Table S9. Gene #30: 'Del Peak 5(3p13)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 32 | 18 | 27 | 25 | 31 |
| DEL PEAK 5(3P13) CNV | 14 | 2 | 1 | 1 | 3 |
| DEL PEAK 5(3P13) WILD-TYPE | 18 | 16 | 26 | 24 | 28 |
Figure S9. Get High-res Image Gene #30: 'Del Peak 5(3p13)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 6.25e-07 (Fisher's exact test), Q value = 0.00026
Table S10. Gene #32: 'Del Peak 7(4q25)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| DEL PEAK 7(4Q25) CNV | 12 | 13 | 39 |
| DEL PEAK 7(4Q25) WILD-TYPE | 27 | 35 | 13 |
Figure S10. Get High-res Image Gene #32: 'Del Peak 7(4q25)' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.000487 (Fisher's exact test), Q value = 0.2
Table S11. Gene #33: 'Del Peak 8(4q35.1)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| DEL PEAK 8(4Q35.1) CNV | 13 | 13 | 33 |
| DEL PEAK 8(4Q35.1) WILD-TYPE | 26 | 35 | 19 |
Figure S11. Get High-res Image Gene #33: 'Del Peak 8(4q35.1)' versus Molecular Subtype #1: 'CN_CNMF'
P value = 1.28e-15 (Fisher's exact test), Q value = 5.4e-13
Table S12. Gene #37: 'Del Peak 12(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| DEL PEAK 12(8P23.2) CNV | 39 | 10 | 35 |
| DEL PEAK 12(8P23.2) WILD-TYPE | 0 | 38 | 17 |
Figure S12. Get High-res Image Gene #37: 'Del Peak 12(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'
P value = 7.27e-15 (Fisher's exact test), Q value = 3.1e-12
Table S13. Gene #38: 'Del Peak 13(8p11.22)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| DEL PEAK 13(8P11.22) CNV | 33 | 3 | 31 |
| DEL PEAK 13(8P11.22) WILD-TYPE | 6 | 45 | 21 |
Figure S13. Get High-res Image Gene #38: 'Del Peak 13(8p11.22)' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.000277 (Chi-square test), Q value = 0.11
Table S14. Gene #41: 'Del Peak 16(10q23.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 32 | 18 | 27 | 25 | 31 |
| DEL PEAK 16(10Q23.31) CNV | 11 | 12 | 4 | 3 | 15 |
| DEL PEAK 16(10Q23.31) WILD-TYPE | 21 | 6 | 23 | 22 | 16 |
Figure S14. Get High-res Image Gene #41: 'Del Peak 16(10q23.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 2.03e-06 (Fisher's exact test), Q value = 0.00085
Table S15. Gene #45: 'Del Peak 20(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| DEL PEAK 20(13Q14.2) CNV | 12 | 13 | 38 |
| DEL PEAK 20(13Q14.2) WILD-TYPE | 27 | 35 | 14 |
Figure S15. Get High-res Image Gene #45: 'Del Peak 20(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'
P value = 9.13e-05 (Chi-square test), Q value = 0.038
Table S16. Gene #45: 'Del Peak 20(13q14.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 32 | 18 | 27 | 25 | 31 |
| DEL PEAK 20(13Q14.2) CNV | 23 | 10 | 7 | 4 | 17 |
| DEL PEAK 20(13Q14.2) WILD-TYPE | 9 | 8 | 20 | 21 | 14 |
Figure S16. Get High-res Image Gene #45: 'Del Peak 20(13q14.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 0.000431 (Fisher's exact test), Q value = 0.18
Table S17. Gene #46: 'Del Peak 21(13q22.2)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| DEL PEAK 21(13Q22.2) CNV | 9 | 12 | 30 |
| DEL PEAK 21(13Q22.2) WILD-TYPE | 30 | 36 | 22 |
Figure S17. Get High-res Image Gene #46: 'Del Peak 21(13q22.2)' versus Molecular Subtype #1: 'CN_CNMF'
P value = 0.000493 (Chi-square test), Q value = 0.2
Table S18. Gene #46: 'Del Peak 21(13q22.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 32 | 18 | 27 | 25 | 31 |
| DEL PEAK 21(13Q22.2) CNV | 20 | 5 | 5 | 4 | 15 |
| DEL PEAK 21(13Q22.2) WILD-TYPE | 12 | 13 | 22 | 21 | 16 |
Figure S18. Get High-res Image Gene #46: 'Del Peak 21(13q22.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 0.000548 (Chi-square test), Q value = 0.22
Table S19. Gene #47: 'Del Peak 22(14q23.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 32 | 18 | 27 | 25 | 31 |
| DEL PEAK 22(14Q23.3) CNV | 15 | 13 | 5 | 4 | 11 |
| DEL PEAK 22(14Q23.3) WILD-TYPE | 17 | 5 | 22 | 21 | 20 |
Figure S19. Get High-res Image Gene #47: 'Del Peak 22(14q23.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
P value = 3.32e-06 (Fisher's exact test), Q value = 0.0014
Table S20. Gene #49: 'Del Peak 24(17p13.3)' versus Molecular Subtype #1: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
|---|---|---|---|
| ALL | 39 | 48 | 52 |
| DEL PEAK 24(17P13.3) CNV | 12 | 23 | 42 |
| DEL PEAK 24(17P13.3) WILD-TYPE | 27 | 25 | 10 |
Figure S20. Get High-res Image Gene #49: 'Del Peak 24(17p13.3)' versus Molecular Subtype #1: 'CN_CNMF'
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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.
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Molecular subtype file = LIHC-TP.transferedmergedcluster.txt
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Number of patients = 139
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Number of copy number variation regions = 53
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Number of molecular subtypes = 8
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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.