(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 62 peak regions and 10 molecular subtypes across 162 patients, 16 significant findings detected with Q value < 0.25.
-
Amp Peak 4(6p21.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 5(8p11.23) cnvs correlated to 'CN_CNMF'.
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Amp Peak 6(8p11.21) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 7(8q24.21) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 13(13q12.13) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 14(13q12.2) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 15(13q22.1) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 17(16p11.2) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 18(17q12) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 19(17q24.1) cnvs correlated to 'CN_CNMF'.
-
Del Peak 3(1p13.2) cnvs correlated to 'CN_CNMF'.
-
Del Peak 8(4q22.1) cnvs correlated to 'CN_CNMF'.
-
Del Peak 15(8p23.2) cnvs correlated to 'CN_CNMF'.
-
Del Peak 24(15q22.33) cnvs correlated to 'CN_CNMF'.
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Del Peak 30(18q21.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 31(18q22.1) cnvs correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 62 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 16 significant findings detected.
|
Molecular subtypes |
MRNA CNMF |
MRNA CHIERARCHICAL |
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 | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test | |
| Amp Peak 4(6p21 1) | 52 (32%) | 110 |
0.0368 (1.00) |
0.0357 (1.00) |
0.000112 (0.0675) |
0.0397 (1.00) |
0.912 (1.00) |
0.1 (1.00) |
0.738 (1.00) |
0.747 (1.00) |
0.163 (1.00) |
0.413 (1.00) |
| Amp Peak 5(8p11 23) | 52 (32%) | 110 |
0.00181 (1.00) |
0.0377 (1.00) |
2.54e-08 (1.55e-05) |
0.308 (1.00) |
0.376 (1.00) |
0.376 (1.00) |
0.662 (1.00) |
0.823 (1.00) |
0.0568 (1.00) |
0.00668 (1.00) |
| Amp Peak 6(8p11 21) | 69 (43%) | 93 |
0.0103 (1.00) |
0.0203 (1.00) |
2.38e-13 (1.46e-10) |
0.257 (1.00) |
0.371 (1.00) |
0.5 (1.00) |
0.377 (1.00) |
0.935 (1.00) |
0.173 (1.00) |
0.084 (1.00) |
| Amp Peak 7(8q24 21) | 107 (66%) | 55 |
0.0305 (1.00) |
0.0214 (1.00) |
1.7e-09 (1.04e-06) |
0.232 (1.00) |
0.629 (1.00) |
0.59 (1.00) |
0.444 (1.00) |
0.627 (1.00) |
0.566 (1.00) |
0.144 (1.00) |
| Amp Peak 13(13q12 13) | 121 (75%) | 41 |
0.573 (1.00) |
0.575 (1.00) |
3.06e-05 (0.0185) |
0.317 (1.00) |
0.424 (1.00) |
0.427 (1.00) |
0.0118 (1.00) |
0.241 (1.00) |
0.0122 (1.00) |
0.00847 (1.00) |
| Amp Peak 14(13q12 2) | 120 (74%) | 42 |
0.426 (1.00) |
0.421 (1.00) |
4.86e-06 (0.00296) |
0.24 (1.00) |
0.736 (1.00) |
0.548 (1.00) |
0.0325 (1.00) |
0.423 (1.00) |
0.0737 (1.00) |
0.0227 (1.00) |
| Amp Peak 15(13q22 1) | 117 (72%) | 45 |
0.406 (1.00) |
0.223 (1.00) |
1.02e-07 (6.23e-05) |
0.0513 (1.00) |
0.907 (1.00) |
0.14 (1.00) |
0.372 (1.00) |
0.418 (1.00) |
0.00712 (1.00) |
0.00304 (1.00) |
| Amp Peak 17(16p11 2) | 45 (28%) | 117 |
0.148 (1.00) |
0.0719 (1.00) |
2.96e-05 (0.0179) |
0.14 (1.00) |
0.3 (1.00) |
0.306 (1.00) |
0.388 (1.00) |
0.789 (1.00) |
0.178 (1.00) |
0.816 (1.00) |
| Amp Peak 18(17q12) | 43 (27%) | 119 |
0.00559 (1.00) |
0.146 (1.00) |
0.0002 (0.12) |
0.532 (1.00) |
0.176 (1.00) |
0.895 (1.00) |
0.356 (1.00) |
0.146 (1.00) |
0.171 (1.00) |
0.898 (1.00) |
| Amp Peak 19(17q24 1) | 37 (23%) | 125 |
0.214 (1.00) |
0.943 (1.00) |
0.000331 (0.198) |
0.124 (1.00) |
0.608 (1.00) |
0.63 (1.00) |
0.569 (1.00) |
0.236 (1.00) |
0.599 (1.00) |
0.668 (1.00) |
| Del Peak 3(1p13 2) | 51 (31%) | 111 |
0.74 (1.00) |
0.483 (1.00) |
0.000178 (0.107) |
0.631 (1.00) |
0.544 (1.00) |
0.739 (1.00) |
0.181 (1.00) |
0.5 (1.00) |
0.404 (1.00) |
0.104 (1.00) |
| Del Peak 8(4q22 1) | 72 (44%) | 90 |
0.825 (1.00) |
0.436 (1.00) |
9.65e-05 (0.0582) |
0.297 (1.00) |
0.702 (1.00) |
0.711 (1.00) |
0.0246 (1.00) |
0.0556 (1.00) |
0.917 (1.00) |
0.0816 (1.00) |
| Del Peak 15(8p23 2) | 100 (62%) | 62 |
0.136 (1.00) |
0.0928 (1.00) |
6.4e-06 (0.00388) |
0.273 (1.00) |
1 (1.00) |
0.582 (1.00) |
0.0289 (1.00) |
0.23 (1.00) |
0.643 (1.00) |
0.863 (1.00) |
| Del Peak 24(15q22 33) | 75 (46%) | 87 |
0.624 (1.00) |
0.421 (1.00) |
0.000218 (0.131) |
0.698 (1.00) |
0.194 (1.00) |
0.215 (1.00) |
0.26 (1.00) |
0.51 (1.00) |
0.384 (1.00) |
0.777 (1.00) |
| Del Peak 30(18q21 2) | 143 (88%) | 19 |
0.136 (1.00) |
0.0948 (1.00) |
5.18e-06 (0.00314) |
0.113 (1.00) |
1 (1.00) |
0.573 (1.00) |
0.12 (1.00) |
0.423 (1.00) |
0.433 (1.00) |
0.231 (1.00) |
| Del Peak 31(18q22 1) | 138 (85%) | 24 |
0.0697 (1.00) |
0.049 (1.00) |
2.38e-07 (0.000145) |
0.0309 (1.00) |
0.776 (1.00) |
0.484 (1.00) |
0.00538 (1.00) |
0.475 (1.00) |
0.805 (1.00) |
0.493 (1.00) |
| Amp Peak 1(1q21 3) | 48 (30%) | 114 |
1 (1.00) |
0.882 (1.00) |
0.000676 (0.401) |
0.961 (1.00) |
0.531 (1.00) |
0.18 (1.00) |
0.776 (1.00) |
0.0138 (1.00) |
0.0805 (1.00) |
0.646 (1.00) |
| Amp Peak 2(1q32 2) | 48 (30%) | 114 |
0.686 (1.00) |
1 (1.00) |
0.00918 (1.00) |
0.579 (1.00) |
0.185 (1.00) |
0.0535 (1.00) |
0.912 (1.00) |
0.0667 (1.00) |
0.11 (1.00) |
0.39 (1.00) |
| Amp Peak 3(5q22 3) | 19 (12%) | 143 |
0.0305 (1.00) |
0.446 (1.00) |
0.118 (1.00) |
0.281 (1.00) |
0.159 (1.00) |
0.445 (1.00) |
0.0738 (1.00) |
0.215 (1.00) |
0.485 (1.00) |
0.65 (1.00) |
| Amp Peak 8(10q22 2) | 11 (7%) | 151 |
0.425 (1.00) |
0.872 (1.00) |
0.912 (1.00) |
1 (1.00) |
1 (1.00) |
0.694 (1.00) |
0.387 (1.00) |
0.28 (1.00) |
||
| Amp Peak 9(11p15 5) | 43 (27%) | 119 |
0.418 (1.00) |
0.468 (1.00) |
0.0286 (1.00) |
0.696 (1.00) |
0.697 (1.00) |
0.696 (1.00) |
0.00835 (1.00) |
0.00295 (1.00) |
0.0902 (1.00) |
0.47 (1.00) |
| Amp Peak 10(11q13 3) | 26 (16%) | 136 |
0.0312 (1.00) |
0.0536 (1.00) |
0.000568 (0.338) |
0.00789 (1.00) |
0.906 (1.00) |
0.861 (1.00) |
0.105 (1.00) |
0.67 (1.00) |
0.0151 (1.00) |
0.136 (1.00) |
| Amp Peak 11(12p13 33) | 41 (25%) | 121 |
0.475 (1.00) |
0.566 (1.00) |
0.0385 (1.00) |
0.654 (1.00) |
0.113 (1.00) |
0.0558 (1.00) |
0.452 (1.00) |
0.241 (1.00) |
0.593 (1.00) |
0.84 (1.00) |
| Amp Peak 12(12p12 1) | 40 (25%) | 122 |
0.511 (1.00) |
0.786 (1.00) |
0.036 (1.00) |
0.446 (1.00) |
0.0503 (1.00) |
0.0273 (1.00) |
0.605 (1.00) |
0.197 (1.00) |
0.681 (1.00) |
0.42 (1.00) |
| Amp Peak 16(15q26 1) | 15 (9%) | 147 |
0.151 (1.00) |
0.12 (1.00) |
0.314 (1.00) |
0.441 (1.00) |
0.101 (1.00) |
0.244 (1.00) |
0.189 (1.00) |
0.215 (1.00) |
0.503 (1.00) |
0.919 (1.00) |
| Amp Peak 20(19p13 2) | 32 (20%) | 130 |
0.0448 (1.00) |
0.00885 (1.00) |
0.000599 (0.356) |
0.798 (1.00) |
0.389 (1.00) |
0.259 (1.00) |
0.153 (1.00) |
0.531 (1.00) |
0.643 (1.00) |
0.916 (1.00) |
| Amp Peak 21(20q11 21) | 143 (88%) | 19 |
0.0632 (1.00) |
0.0294 (1.00) |
0.00116 (0.683) |
0.0237 (1.00) |
0.194 (1.00) |
0.0766 (1.00) |
0.552 (1.00) |
0.271 (1.00) |
0.0283 (1.00) |
0.0916 (1.00) |
| Amp Peak 22(20q11 23) | 144 (89%) | 18 |
0.0632 (1.00) |
0.0294 (1.00) |
0.00257 (1.00) |
0.0561 (1.00) |
0.194 (1.00) |
0.0766 (1.00) |
0.552 (1.00) |
0.271 (1.00) |
0.0504 (1.00) |
0.0697 (1.00) |
| Amp Peak 23(20q13 31) | 145 (90%) | 17 |
0.0507 (1.00) |
0.0269 (1.00) |
0.00544 (1.00) |
0.0561 (1.00) |
0.194 (1.00) |
0.0766 (1.00) |
0.552 (1.00) |
0.271 (1.00) |
0.0728 (1.00) |
0.109 (1.00) |
| Amp Peak 24(Xp22 2) | 33 (20%) | 129 |
0.0379 (1.00) |
0.109 (1.00) |
0.644 (1.00) |
0.505 (1.00) |
0.795 (1.00) |
0.66 (1.00) |
0.991 (1.00) |
1 (1.00) |
0.775 (1.00) |
0.955 (1.00) |
| Amp Peak 25(Xq27 3) | 38 (23%) | 124 |
0.149 (1.00) |
0.458 (1.00) |
0.0252 (1.00) |
0.0722 (1.00) |
0.586 (1.00) |
0.182 (1.00) |
0.252 (1.00) |
0.702 (1.00) |
0.56 (1.00) |
0.442 (1.00) |
| Del Peak 1(1p36 11) | 71 (44%) | 91 |
0.45 (1.00) |
0.301 (1.00) |
0.429 (1.00) |
0.256 (1.00) |
0.803 (1.00) |
0.801 (1.00) |
0.569 (1.00) |
1 (1.00) |
0.467 (1.00) |
0.755 (1.00) |
| Del Peak 2(1p33) | 49 (30%) | 113 |
0.79 (1.00) |
0.239 (1.00) |
0.00196 (1.00) |
0.217 (1.00) |
0.88 (1.00) |
0.247 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.369 (1.00) |
0.187 (1.00) |
| Del Peak 4(2p12) | 17 (10%) | 145 |
0.295 (1.00) |
0.321 (1.00) |
0.0623 (1.00) |
0.409 (1.00) |
0.344 (1.00) |
0.171 (1.00) |
0.655 (1.00) |
1 (1.00) |
0.37 (1.00) |
0.62 (1.00) |
| Del Peak 5(3p14 2) | 29 (18%) | 133 |
0.591 (1.00) |
0.796 (1.00) |
0.606 (1.00) |
1 (1.00) |
0.217 (1.00) |
0.694 (1.00) |
0.268 (1.00) |
0.319 (1.00) |
0.832 (1.00) |
1 (1.00) |
| Del Peak 6(3q26 31) | 17 (10%) | 145 |
1 (1.00) |
0.909 (1.00) |
0.604 (1.00) |
1 (1.00) |
0.746 (1.00) |
0.703 (1.00) |
0.242 (1.00) |
1 (1.00) |
0.0981 (1.00) |
0.933 (1.00) |
| Del Peak 7(4p13) | 58 (36%) | 104 |
0.86 (1.00) |
0.664 (1.00) |
0.000895 (0.53) |
0.0837 (1.00) |
0.787 (1.00) |
0.313 (1.00) |
0.503 (1.00) |
0.293 (1.00) |
0.975 (1.00) |
0.0616 (1.00) |
| Del Peak 9(4q35 1) | 72 (44%) | 90 |
0.428 (1.00) |
0.607 (1.00) |
0.000537 (0.32) |
0.135 (1.00) |
0.506 (1.00) |
0.688 (1.00) |
0.452 (1.00) |
0.038 (1.00) |
0.431 (1.00) |
0.0369 (1.00) |
| Del Peak 10(5q11 2) | 49 (30%) | 113 |
0.205 (1.00) |
0.0825 (1.00) |
0.102 (1.00) |
0.00214 (1.00) |
0.94 (1.00) |
0.24 (1.00) |
0.117 (1.00) |
0.93 (1.00) |
0.458 (1.00) |
0.0378 (1.00) |
| Del Peak 11(5q22 2) | 55 (34%) | 107 |
0.37 (1.00) |
0.165 (1.00) |
0.0844 (1.00) |
0.308 (1.00) |
0.684 (1.00) |
0.987 (1.00) |
0.468 (1.00) |
0.675 (1.00) |
0.66 (1.00) |
0.191 (1.00) |
| Del Peak 12(6p25 3) | 24 (15%) | 138 |
1 (1.00) |
1 (1.00) |
0.648 (1.00) |
0.0222 (1.00) |
0.654 (1.00) |
0.988 (1.00) |
0.68 (1.00) |
0.554 (1.00) |
0.69 (1.00) |
0.568 (1.00) |
| Del Peak 13(6q26) | 30 (19%) | 132 |
0.199 (1.00) |
0.0584 (1.00) |
0.159 (1.00) |
0.679 (1.00) |
0.0993 (1.00) |
0.343 (1.00) |
0.89 (1.00) |
0.648 (1.00) |
0.0771 (1.00) |
0.0645 (1.00) |
| Del Peak 14(7q31 1) | 4 (2%) | 158 |
0.311 (1.00) |
1 (1.00) |
0.459 (1.00) |
0.749 (1.00) |
1 (1.00) |
|||||
| Del Peak 16(8p11 21) | 24 (15%) | 138 |
0.175 (1.00) |
0.422 (1.00) |
0.14 (1.00) |
0.204 (1.00) |
0.112 (1.00) |
0.56 (1.00) |
0.408 (1.00) |
0.423 (1.00) |
0.0753 (1.00) |
0.117 (1.00) |
| Del Peak 17(10q21 1) | 37 (23%) | 125 |
0.167 (1.00) |
0.272 (1.00) |
0.0716 (1.00) |
0.432 (1.00) |
0.0595 (1.00) |
0.0237 (1.00) |
0.183 (1.00) |
0.62 (1.00) |
0.747 (1.00) |
0.892 (1.00) |
| Del Peak 18(10q25 2) | 47 (29%) | 115 |
0.508 (1.00) |
0.843 (1.00) |
0.806 (1.00) |
0.596 (1.00) |
0.455 (1.00) |
0.203 (1.00) |
0.129 (1.00) |
0.928 (1.00) |
0.703 (1.00) |
0.742 (1.00) |
| Del Peak 19(11q22 3) | 37 (23%) | 125 |
0.00143 (0.844) |
0.0103 (1.00) |
0.0015 (0.882) |
0.0392 (1.00) |
0.826 (1.00) |
0.0557 (1.00) |
0.0198 (1.00) |
0.000489 (0.292) |
0.444 (1.00) |
0.617 (1.00) |
| Del Peak 20(12p13 1) | 33 (20%) | 129 |
1 (1.00) |
0.655 (1.00) |
0.657 (1.00) |
0.285 (1.00) |
0.535 (1.00) |
0.311 (1.00) |
0.391 (1.00) |
0.00666 (1.00) |
0.287 (1.00) |
0.224 (1.00) |
| Del Peak 21(12q21 33) | 28 (17%) | 134 |
0.724 (1.00) |
0.923 (1.00) |
0.0206 (1.00) |
0.694 (1.00) |
0.606 (1.00) |
0.775 (1.00) |
0.383 (1.00) |
0.0422 (1.00) |
0.467 (1.00) |
0.247 (1.00) |
| Del Peak 22(14q11 2) | 67 (41%) | 95 |
0.907 (1.00) |
0.335 (1.00) |
0.00346 (1.00) |
0.931 (1.00) |
0.803 (1.00) |
0.888 (1.00) |
0.395 (1.00) |
0.39 (1.00) |
0.0858 (1.00) |
0.141 (1.00) |
| Del Peak 23(14q31 1) | 69 (43%) | 93 |
0.907 (1.00) |
0.373 (1.00) |
0.0115 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.316 (1.00) |
0.261 (1.00) |
0.442 (1.00) |
0.161 (1.00) |
0.2 (1.00) |
| Del Peak 25(16p13 3) | 13 (8%) | 149 |
0.781 (1.00) |
0.609 (1.00) |
0.535 (1.00) |
0.0203 (1.00) |
0.725 (1.00) |
0.667 (1.00) |
0.747 (1.00) |
1 (1.00) |
0.237 (1.00) |
0.317 (1.00) |
| Del Peak 26(16q23 1) | 23 (14%) | 139 |
0.106 (1.00) |
0.102 (1.00) |
0.0873 (1.00) |
0.135 (1.00) |
0.589 (1.00) |
0.711 (1.00) |
0.44 (1.00) |
1 (1.00) |
0.619 (1.00) |
0.103 (1.00) |
| Del Peak 27(17p12) | 110 (68%) | 52 |
0.119 (1.00) |
0.356 (1.00) |
0.0299 (1.00) |
0.329 (1.00) |
0.521 (1.00) |
0.756 (1.00) |
0.206 (1.00) |
0.0314 (1.00) |
0.87 (1.00) |
0.446 (1.00) |
| Del Peak 28(17p11 2) | 102 (63%) | 60 |
0.237 (1.00) |
0.56 (1.00) |
0.0494 (1.00) |
0.593 (1.00) |
0.919 (1.00) |
0.379 (1.00) |
0.0582 (1.00) |
0.0696 (1.00) |
0.999 (1.00) |
0.915 (1.00) |
| Del Peak 29(17q25 3) | 24 (15%) | 138 |
0.607 (1.00) |
0.536 (1.00) |
0.192 (1.00) |
0.00558 (1.00) |
0.457 (1.00) |
0.171 (1.00) |
0.0483 (1.00) |
0.015 (1.00) |
0.352 (1.00) |
0.155 (1.00) |
| Del Peak 32(19p13 3) | 38 (23%) | 124 |
0.212 (1.00) |
0.637 (1.00) |
0.0671 (1.00) |
0.047 (1.00) |
0.893 (1.00) |
0.958 (1.00) |
0.409 (1.00) |
0.0191 (1.00) |
0.492 (1.00) |
0.0125 (1.00) |
| Del Peak 33(20p12 1) | 60 (37%) | 102 |
0.591 (1.00) |
0.909 (1.00) |
0.0361 (1.00) |
0.787 (1.00) |
0.54 (1.00) |
0.28 (1.00) |
0.233 (1.00) |
0.93 (1.00) |
0.0474 (1.00) |
0.234 (1.00) |
| Del Peak 34(20p12 1) | 60 (37%) | 102 |
0.591 (1.00) |
0.909 (1.00) |
0.0361 (1.00) |
0.787 (1.00) |
0.54 (1.00) |
0.28 (1.00) |
0.233 (1.00) |
0.93 (1.00) |
0.0474 (1.00) |
0.234 (1.00) |
| Del Peak 35(21q11 2) | 70 (43%) | 92 |
0.414 (1.00) |
0.302 (1.00) |
0.304 (1.00) |
0.837 (1.00) |
0.924 (1.00) |
0.41 (1.00) |
0.55 (1.00) |
0.937 (1.00) |
0.052 (1.00) |
0.465 (1.00) |
| Del Peak 36(22q13 31) | 66 (41%) | 96 |
1 (1.00) |
0.862 (1.00) |
0.222 (1.00) |
0.835 (1.00) |
0.532 (1.00) |
0.462 (1.00) |
0.264 (1.00) |
0.194 (1.00) |
0.00619 (1.00) |
0.337 (1.00) |
| Del Peak 37(Xp22 33) | 33 (20%) | 129 |
0.938 (1.00) |
0.828 (1.00) |
0.266 (1.00) |
0.00275 (1.00) |
0.724 (1.00) |
0.801 (1.00) |
0.91 (1.00) |
1 (1.00) |
0.643 (1.00) |
0.819 (1.00) |
P value = 0.000112 (Chi-square test), Q value = 0.068
Table S1. Gene #4: 'Amp Peak 4(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| AMP PEAK 4(6P21.1) MUTATED | 4 | 16 | 11 | 8 | 13 |
| AMP PEAK 4(6P21.1) WILD-TYPE | 3 | 16 | 35 | 47 | 9 |
Figure S1. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 2.54e-08 (Chi-square test), Q value = 1.5e-05
Table S2. Gene #5: 'Amp Peak 5(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| AMP PEAK 5(8P11.23) MUTATED | 2 | 12 | 29 | 2 | 7 |
| AMP PEAK 5(8P11.23) WILD-TYPE | 5 | 20 | 17 | 53 | 15 |
Figure S2. Get High-res Image Gene #5: 'Amp Peak 5(8p11.23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 2.38e-13 (Chi-square test), Q value = 1.5e-10
Table S3. Gene #6: 'Amp Peak 6(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| AMP PEAK 6(8P11.21) MUTATED | 3 | 13 | 40 | 4 | 9 |
| AMP PEAK 6(8P11.21) WILD-TYPE | 4 | 19 | 6 | 51 | 13 |
Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(8p11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 1.7e-09 (Chi-square test), Q value = 1e-06
Table S4. Gene #7: 'Amp Peak 7(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| AMP PEAK 7(8Q24.21) MUTATED | 4 | 25 | 46 | 22 | 10 |
| AMP PEAK 7(8Q24.21) WILD-TYPE | 3 | 7 | 0 | 33 | 12 |
Figure S4. Get High-res Image Gene #7: 'Amp Peak 7(8q24.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 3.06e-05 (Chi-square test), Q value = 0.018
Table S5. Gene #13: 'Amp Peak 13(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| AMP PEAK 13(13Q12.13) MUTATED | 6 | 30 | 33 | 30 | 22 |
| AMP PEAK 13(13Q12.13) WILD-TYPE | 1 | 2 | 13 | 25 | 0 |
Figure S5. Get High-res Image Gene #13: 'Amp Peak 13(13q12.13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 4.86e-06 (Chi-square test), Q value = 0.003
Table S6. Gene #14: 'Amp Peak 14(13q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| AMP PEAK 14(13Q12.2) MUTATED | 6 | 30 | 34 | 28 | 22 |
| AMP PEAK 14(13Q12.2) WILD-TYPE | 1 | 2 | 12 | 27 | 0 |
Figure S6. Get High-res Image Gene #14: 'Amp Peak 14(13q12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 1.02e-07 (Chi-square test), Q value = 6.2e-05
Table S7. Gene #15: 'Amp Peak 15(13q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| AMP PEAK 15(13Q22.1) MUTATED | 7 | 30 | 33 | 25 | 22 |
| AMP PEAK 15(13Q22.1) WILD-TYPE | 0 | 2 | 13 | 30 | 0 |
Figure S7. Get High-res Image Gene #15: 'Amp Peak 15(13q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 2.96e-05 (Chi-square test), Q value = 0.018
Table S8. Gene #17: 'Amp Peak 17(16p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| AMP PEAK 17(16P11.2) MUTATED | 2 | 16 | 10 | 5 | 12 |
| AMP PEAK 17(16P11.2) WILD-TYPE | 5 | 16 | 36 | 50 | 10 |
Figure S8. Get High-res Image Gene #17: 'Amp Peak 17(16p11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 2e-04 (Chi-square test), Q value = 0.12
Table S9. Gene #18: 'Amp Peak 18(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| AMP PEAK 18(17Q12) MUTATED | 2 | 17 | 15 | 8 | 1 |
| AMP PEAK 18(17Q12) WILD-TYPE | 5 | 15 | 31 | 47 | 21 |
Figure S9. Get High-res Image Gene #18: 'Amp Peak 18(17q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 0.000331 (Chi-square test), Q value = 0.2
Table S10. Gene #19: 'Amp Peak 19(17q24.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| AMP PEAK 19(17Q24.1) MUTATED | 1 | 16 | 10 | 10 | 0 |
| AMP PEAK 19(17Q24.1) WILD-TYPE | 6 | 16 | 36 | 45 | 22 |
Figure S10. Get High-res Image Gene #19: 'Amp Peak 19(17q24.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 0.000178 (Chi-square test), Q value = 0.11
Table S11. Gene #28: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| DEL PEAK 3(1P13.2) MUTATED | 6 | 15 | 16 | 7 | 7 |
| DEL PEAK 3(1P13.2) WILD-TYPE | 1 | 17 | 30 | 48 | 15 |
Figure S11. Get High-res Image Gene #28: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 9.65e-05 (Chi-square test), Q value = 0.058
Table S12. Gene #33: 'Del Peak 8(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| DEL PEAK 8(4Q22.1) MUTATED | 6 | 18 | 19 | 13 | 16 |
| DEL PEAK 8(4Q22.1) WILD-TYPE | 1 | 14 | 27 | 42 | 6 |
Figure S12. Get High-res Image Gene #33: 'Del Peak 8(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 6.4e-06 (Chi-square test), Q value = 0.0039
Table S13. Gene #40: 'Del Peak 15(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| DEL PEAK 15(8P23.2) MUTATED | 6 | 25 | 37 | 19 | 13 |
| DEL PEAK 15(8P23.2) WILD-TYPE | 1 | 7 | 9 | 36 | 9 |
Figure S13. Get High-res Image Gene #40: 'Del Peak 15(8p23.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 0.000218 (Chi-square test), Q value = 0.13
Table S14. Gene #49: 'Del Peak 24(15q22.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| DEL PEAK 24(15Q22.33) MUTATED | 6 | 20 | 22 | 13 | 14 |
| DEL PEAK 24(15Q22.33) WILD-TYPE | 1 | 12 | 24 | 42 | 8 |
Figure S14. Get High-res Image Gene #49: 'Del Peak 24(15q22.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 5.18e-06 (Chi-square test), Q value = 0.0031
Table S15. Gene #55: 'Del Peak 30(18q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| DEL PEAK 30(18Q21.2) MUTATED | 7 | 32 | 45 | 38 | 21 |
| DEL PEAK 30(18Q21.2) WILD-TYPE | 0 | 0 | 1 | 17 | 1 |
Figure S15. Get High-res Image Gene #55: 'Del Peak 30(18q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
P value = 2.38e-07 (Chi-square test), Q value = 0.00015
Table S16. Gene #56: 'Del Peak 31(18q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
|---|---|---|---|---|---|
| ALL | 7 | 32 | 46 | 55 | 22 |
| DEL PEAK 31(18Q22.1) MUTATED | 7 | 32 | 44 | 34 | 21 |
| DEL PEAK 31(18Q22.1) WILD-TYPE | 0 | 0 | 2 | 21 | 1 |
Figure S16. Get High-res Image Gene #56: 'Del Peak 31(18q22.1) mutation analysis' versus Clinical Feature #3: '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.
-
Molecular subtype file = READ-TP.transferedmergedcluster.txt
-
Number of patients = 162
-
Number of copy number variation regions = 62
-
Number of molecular subtypes = 10
-
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.