This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 55 peak regions and 10 molecular subtypes across 267 patients, 34 significant findings detected with Q value < 0.25.
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Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 3(1q44) cnvs correlated to 'CN_CNMF'.
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Amp Peak 6(5p15.33) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
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Amp Peak 7(5q35.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 8(6p25.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
Amp Peak 10(7p22.3) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 11(7q34) cnvs correlated to 'CN_CNMF'.
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Amp Peak 12(8q11.21) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 13(8q24.21) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 15(11q13.3) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 16(11q13.4) cnvs correlated to 'CN_CNMF'.
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Amp Peak 22(20q13.33) cnvs correlated to 'CN_CNMF'.
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Amp Peak 23(22q13.2) cnvs correlated to 'CN_CNMF'.
-
Del Peak 2(1p22.1) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
-
Del Peak 9(5q31.3) cnvs correlated to 'METHLYATION_CNMF'.
-
Del Peak 10(6q22.31) cnvs correlated to 'CN_CNMF'.
-
Del Peak 11(6q25.3) cnvs correlated to 'CN_CNMF'.
-
Del Peak 12(6q26) cnvs correlated to 'CN_CNMF'.
-
Del Peak 14(9p23) cnvs correlated to 'CN_CNMF'.
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Del Peak 15(9p21.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Del Peak 16(10p15.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Del Peak 17(10q23.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Del Peak 18(10q26.3) cnvs correlated to 'MRNASEQ_CNMF'.
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Del Peak 19(11q23.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 24(14q32.2) cnvs correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 55 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 34 significant findings detected.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
Amp Peak 8(6p25 1) | 0 (0%) | 116 |
3.31e-05 (0.0175) |
0.000379 (0.196) |
0.224 (1.00) |
0.00992 (1.00) |
0.0527 (1.00) |
0.00583 (1.00) |
0.00122 (0.624) |
1.03e-05 (0.00553) |
0.0123 (1.00) |
2.5e-05 (0.0133) |
Amp Peak 6(5p15 33) | 0 (0%) | 182 |
1.27e-09 (6.92e-07) |
0.29 (1.00) |
0.846 (1.00) |
0.421 (1.00) |
0.301 (1.00) |
0.149 (1.00) |
0.000584 (0.301) |
0.0333 (1.00) |
9.59e-05 (0.0502) |
0.0072 (1.00) |
Amp Peak 7(5q35 3) | 0 (0%) | 225 |
2.8e-05 (0.0148) |
0.000302 (0.157) |
0.1 (1.00) |
0.0263 (1.00) |
0.0881 (1.00) |
0.0186 (1.00) |
0.0245 (1.00) |
0.0383 (1.00) |
0.134 (1.00) |
0.101 (1.00) |
Del Peak 2(1p22 1) | 0 (0%) | 199 |
0.0633 (1.00) |
0.000127 (0.0662) |
0.615 (1.00) |
0.0886 (1.00) |
0.000117 (0.0611) |
0.126 (1.00) |
0.497 (1.00) |
0.343 (1.00) |
0.186 (1.00) |
0.289 (1.00) |
Del Peak 15(9p21 3) | 0 (0%) | 61 |
1.09e-09 (5.95e-07) |
0.00226 (1.00) |
0.605 (1.00) |
0.6 (1.00) |
0.000114 (0.0594) |
0.0236 (1.00) |
0.896 (1.00) |
0.698 (1.00) |
0.882 (1.00) |
0.851 (1.00) |
Del Peak 16(10p15 3) | 0 (0%) | 122 |
1.88e-05 (0.01) |
0.0271 (1.00) |
0.685 (1.00) |
0.598 (1.00) |
8.7e-05 (0.0457) |
0.00157 (0.801) |
0.548 (1.00) |
0.506 (1.00) |
0.492 (1.00) |
0.469 (1.00) |
Del Peak 17(10q23 31) | 0 (0%) | 103 |
3.27e-05 (0.0173) |
0.0976 (1.00) |
0.911 (1.00) |
0.076 (1.00) |
8.53e-05 (0.0448) |
0.00778 (1.00) |
0.496 (1.00) |
0.539 (1.00) |
0.772 (1.00) |
0.239 (1.00) |
Amp Peak 2(1q21 3) | 0 (0%) | 132 |
3.14e-10 (1.72e-07) |
0.032 (1.00) |
0.285 (1.00) |
1 (1.00) |
0.027 (1.00) |
0.478 (1.00) |
0.268 (1.00) |
0.0177 (1.00) |
0.49 (1.00) |
0.211 (1.00) |
Amp Peak 3(1q44) | 0 (0%) | 125 |
2.22e-10 (1.22e-07) |
0.00678 (1.00) |
0.109 (1.00) |
0.489 (1.00) |
0.0985 (1.00) |
0.545 (1.00) |
0.135 (1.00) |
0.00209 (1.00) |
0.401 (1.00) |
0.0413 (1.00) |
Amp Peak 10(7p22 3) | 0 (0%) | 124 |
1.15e-05 (0.00616) |
0.492 (1.00) |
0.528 (1.00) |
0.87 (1.00) |
0.0229 (1.00) |
0.404 (1.00) |
0.876 (1.00) |
0.812 (1.00) |
0.695 (1.00) |
0.365 (1.00) |
Amp Peak 11(7q34) | 0 (0%) | 109 |
0.000344 (0.178) |
0.267 (1.00) |
0.331 (1.00) |
0.526 (1.00) |
0.0966 (1.00) |
0.128 (1.00) |
0.0756 (1.00) |
0.189 (1.00) |
0.171 (1.00) |
0.289 (1.00) |
Amp Peak 12(8q11 21) | 0 (0%) | 150 |
1.54e-05 (0.00821) |
0.00353 (1.00) |
0.442 (1.00) |
0.226 (1.00) |
0.026 (1.00) |
0.301 (1.00) |
0.676 (1.00) |
0.966 (1.00) |
0.559 (1.00) |
0.713 (1.00) |
Amp Peak 13(8q24 21) | 0 (0%) | 132 |
3.17e-08 (1.72e-05) |
0.00273 (1.00) |
0.525 (1.00) |
0.532 (1.00) |
0.00933 (1.00) |
0.546 (1.00) |
0.831 (1.00) |
0.585 (1.00) |
0.802 (1.00) |
0.616 (1.00) |
Amp Peak 15(11q13 3) | 0 (0%) | 217 |
7.05e-06 (0.0038) |
0.0868 (1.00) |
0.874 (1.00) |
0.541 (1.00) |
0.44 (1.00) |
1 (1.00) |
0.803 (1.00) |
0.237 (1.00) |
0.492 (1.00) |
0.576 (1.00) |
Amp Peak 16(11q13 4) | 0 (0%) | 221 |
3.58e-06 (0.00193) |
0.017 (1.00) |
0.903 (1.00) |
0.655 (1.00) |
0.121 (1.00) |
0.545 (1.00) |
0.463 (1.00) |
0.124 (1.00) |
0.255 (1.00) |
0.838 (1.00) |
Amp Peak 22(20q13 33) | 0 (0%) | 131 |
0.000106 (0.0553) |
0.0172 (1.00) |
0.737 (1.00) |
0.871 (1.00) |
0.00475 (1.00) |
0.218 (1.00) |
0.573 (1.00) |
0.141 (1.00) |
0.123 (1.00) |
0.0305 (1.00) |
Amp Peak 23(22q13 2) | 0 (0%) | 156 |
3.43e-07 (0.000185) |
0.0422 (1.00) |
0.904 (1.00) |
0.904 (1.00) |
0.532 (1.00) |
0.748 (1.00) |
0.354 (1.00) |
0.726 (1.00) |
0.578 (1.00) |
0.321 (1.00) |
Del Peak 9(5q31 3) | 0 (0%) | 168 |
0.0769 (1.00) |
7.76e-05 (0.0409) |
0.602 (1.00) |
0.978 (1.00) |
0.706 (1.00) |
0.488 (1.00) |
0.786 (1.00) |
0.295 (1.00) |
0.214 (1.00) |
0.125 (1.00) |
Del Peak 10(6q22 31) | 0 (0%) | 108 |
1.4e-14 (7.69e-12) |
0.136 (1.00) |
0.861 (1.00) |
0.14 (1.00) |
0.00412 (1.00) |
0.342 (1.00) |
0.487 (1.00) |
0.562 (1.00) |
0.935 (1.00) |
0.771 (1.00) |
Del Peak 11(6q25 3) | 0 (0%) | 98 |
4.82e-13 (2.64e-10) |
0.237 (1.00) |
0.535 (1.00) |
0.531 (1.00) |
0.00446 (1.00) |
0.457 (1.00) |
0.615 (1.00) |
0.895 (1.00) |
0.973 (1.00) |
0.807 (1.00) |
Del Peak 12(6q26) | 0 (0%) | 101 |
8.58e-15 (4.72e-12) |
0.146 (1.00) |
0.61 (1.00) |
0.549 (1.00) |
0.0047 (1.00) |
0.417 (1.00) |
0.344 (1.00) |
0.642 (1.00) |
0.79 (1.00) |
0.932 (1.00) |
Del Peak 14(9p23) | 0 (0%) | 85 |
1.2e-05 (0.0064) |
0.0535 (1.00) |
0.409 (1.00) |
0.782 (1.00) |
0.0027 (1.00) |
0.0658 (1.00) |
0.708 (1.00) |
0.247 (1.00) |
0.293 (1.00) |
0.303 (1.00) |
Del Peak 18(10q26 3) | 0 (0%) | 100 |
0.00114 (0.585) |
0.274 (1.00) |
0.677 (1.00) |
0.443 (1.00) |
1.91e-05 (0.0101) |
0.000579 (0.299) |
0.764 (1.00) |
0.946 (1.00) |
0.543 (1.00) |
0.808 (1.00) |
Del Peak 19(11q23 3) | 0 (0%) | 122 |
1.43e-07 (7.76e-05) |
0.12 (1.00) |
0.989 (1.00) |
0.299 (1.00) |
0.242 (1.00) |
0.657 (1.00) |
0.198 (1.00) |
0.0827 (1.00) |
0.0942 (1.00) |
0.216 (1.00) |
Del Peak 24(14q32 2) | 0 (0%) | 176 |
7.99e-06 (0.0043) |
0.799 (1.00) |
0.311 (1.00) |
0.24 (1.00) |
0.00356 (1.00) |
0.64 (1.00) |
0.699 (1.00) |
0.69 (1.00) |
0.664 (1.00) |
0.478 (1.00) |
Amp Peak 1(1p12) | 0 (0%) | 186 |
0.00179 (0.91) |
0.357 (1.00) |
0.488 (1.00) |
1 (1.00) |
0.118 (1.00) |
0.491 (1.00) |
0.49 (1.00) |
0.56 (1.00) |
0.452 (1.00) |
0.961 (1.00) |
Amp Peak 4(3p13) | 0 (0%) | 198 |
0.444 (1.00) |
0.696 (1.00) |
0.0978 (1.00) |
0.0104 (1.00) |
0.907 (1.00) |
0.681 (1.00) |
0.827 (1.00) |
0.148 (1.00) |
1 (1.00) |
0.177 (1.00) |
Amp Peak 5(4q12) | 0 (0%) | 217 |
0.0263 (1.00) |
0.386 (1.00) |
0.0894 (1.00) |
0.0641 (1.00) |
0.469 (1.00) |
0.299 (1.00) |
0.021 (1.00) |
0.013 (1.00) |
0.0185 (1.00) |
0.00611 (1.00) |
Amp Peak 9(6q12) | 0 (0%) | 207 |
0.618 (1.00) |
0.521 (1.00) |
0.839 (1.00) |
0.00495 (1.00) |
0.0939 (1.00) |
0.0757 (1.00) |
0.211 (1.00) |
0.278 (1.00) |
0.817 (1.00) |
0.527 (1.00) |
Amp Peak 14(9p24 1) | 0 (0%) | 244 |
1 (1.00) |
0.511 (1.00) |
0.72 (1.00) |
0.786 (1.00) |
0.491 (1.00) |
0.491 (1.00) |
0.219 (1.00) |
0.531 (1.00) |
0.0989 (1.00) |
0.462 (1.00) |
Amp Peak 17(12q14 1) | 0 (0%) | 221 |
0.00121 (0.618) |
0.564 (1.00) |
0.71 (1.00) |
0.296 (1.00) |
0.121 (1.00) |
0.159 (1.00) |
0.712 (1.00) |
0.397 (1.00) |
0.857 (1.00) |
0.819 (1.00) |
Amp Peak 18(12q15) | 0 (0%) | 223 |
0.0152 (1.00) |
0.647 (1.00) |
0.497 (1.00) |
0.391 (1.00) |
0.557 (1.00) |
0.617 (1.00) |
0.89 (1.00) |
0.422 (1.00) |
0.833 (1.00) |
0.943 (1.00) |
Amp Peak 19(15q26 2) | 0 (0%) | 178 |
0.0441 (1.00) |
0.712 (1.00) |
0.93 (1.00) |
0.534 (1.00) |
0.629 (1.00) |
0.343 (1.00) |
0.753 (1.00) |
0.557 (1.00) |
0.803 (1.00) |
0.673 (1.00) |
Amp Peak 20(17q25 3) | 0 (0%) | 175 |
0.00327 (1.00) |
0.00229 (1.00) |
0.0165 (1.00) |
0.0318 (1.00) |
0.2 (1.00) |
0.365 (1.00) |
0.302 (1.00) |
0.0109 (1.00) |
0.0159 (1.00) |
0.0451 (1.00) |
Amp Peak 21(19p13 2) | 0 (0%) | 214 |
0.0554 (1.00) |
0.119 (1.00) |
0.301 (1.00) |
0.702 (1.00) |
0.0105 (1.00) |
0.00394 (1.00) |
0.715 (1.00) |
0.0475 (1.00) |
0.114 (1.00) |
0.0135 (1.00) |
Del Peak 1(1p36 31) | 0 (0%) | 203 |
0.21 (1.00) |
0.000694 (0.357) |
0.677 (1.00) |
0.135 (1.00) |
0.0717 (1.00) |
0.0208 (1.00) |
0.491 (1.00) |
0.468 (1.00) |
0.868 (1.00) |
0.54 (1.00) |
Del Peak 3(2q37 3) | 0 (0%) | 200 |
0.49 (1.00) |
0.0252 (1.00) |
0.0371 (1.00) |
0.00703 (1.00) |
0.00713 (1.00) |
0.0241 (1.00) |
0.0309 (1.00) |
0.0447 (1.00) |
0.112 (1.00) |
0.0629 (1.00) |
Del Peak 4(3p21 2) | 0 (0%) | 217 |
0.8 (1.00) |
0.902 (1.00) |
0.721 (1.00) |
0.756 (1.00) |
0.406 (1.00) |
0.311 (1.00) |
0.554 (1.00) |
0.67 (1.00) |
0.46 (1.00) |
0.759 (1.00) |
Del Peak 5(3q23) | 0 (0%) | 226 |
0.275 (1.00) |
0.0183 (1.00) |
0.276 (1.00) |
0.404 (1.00) |
0.316 (1.00) |
0.599 (1.00) |
1 (1.00) |
0.649 (1.00) |
0.928 (1.00) |
0.6 (1.00) |
Del Peak 6(4q34 3) | 0 (0%) | 197 |
0.419 (1.00) |
0.091 (1.00) |
0.943 (1.00) |
0.468 (1.00) |
0.0568 (1.00) |
0.00942 (1.00) |
0.00905 (1.00) |
0.00244 (1.00) |
0.00213 (1.00) |
0.0041 (1.00) |
Del Peak 7(5p15 31) | 0 (0%) | 212 |
0.268 (1.00) |
0.296 (1.00) |
0.446 (1.00) |
0.449 (1.00) |
0.252 (1.00) |
0.799 (1.00) |
0.601 (1.00) |
0.27 (1.00) |
0.355 (1.00) |
0.465 (1.00) |
Del Peak 8(5q11 2) | 0 (0%) | 194 |
0.00554 (1.00) |
0.109 (1.00) |
0.306 (1.00) |
0.417 (1.00) |
0.719 (1.00) |
0.555 (1.00) |
0.951 (1.00) |
0.406 (1.00) |
0.205 (1.00) |
0.477 (1.00) |
Del Peak 13(8p23 3) | 0 (0%) | 202 |
0.518 (1.00) |
0.0762 (1.00) |
0.192 (1.00) |
0.058 (1.00) |
0.101 (1.00) |
0.749 (1.00) |
0.257 (1.00) |
0.386 (1.00) |
0.238 (1.00) |
0.558 (1.00) |
Del Peak 20(12p13 31) | 0 (0%) | 224 |
0.759 (1.00) |
0.252 (1.00) |
0.471 (1.00) |
0.0454 (1.00) |
0.0546 (1.00) |
0.527 (1.00) |
0.975 (1.00) |
0.967 (1.00) |
0.952 (1.00) |
1 (1.00) |
Del Peak 21(12q23 3) | 0 (0%) | 203 |
0.0781 (1.00) |
0.013 (1.00) |
0.791 (1.00) |
0.441 (1.00) |
0.423 (1.00) |
0.547 (1.00) |
0.713 (1.00) |
0.306 (1.00) |
0.534 (1.00) |
0.478 (1.00) |
Del Peak 22(13q12 11) | 0 (0%) | 206 |
0.004 (1.00) |
0.266 (1.00) |
0.167 (1.00) |
0.664 (1.00) |
1 (1.00) |
0.981 (1.00) |
0.166 (1.00) |
0.107 (1.00) |
0.219 (1.00) |
0.543 (1.00) |
Del Peak 23(13q34) | 0 (0%) | 205 |
0.246 (1.00) |
0.00347 (1.00) |
0.0674 (1.00) |
0.357 (1.00) |
0.916 (1.00) |
0.279 (1.00) |
0.91 (1.00) |
0.298 (1.00) |
0.801 (1.00) |
0.435 (1.00) |
Del Peak 25(15q13 3) | 0 (0%) | 204 |
0.0473 (1.00) |
0.0774 (1.00) |
0.133 (1.00) |
0.39 (1.00) |
0.435 (1.00) |
0.183 (1.00) |
0.525 (1.00) |
0.734 (1.00) |
0.504 (1.00) |
0.89 (1.00) |
Del Peak 26(15q15 1) | 0 (0%) | 200 |
0.0459 (1.00) |
0.0295 (1.00) |
0.383 (1.00) |
0.0595 (1.00) |
0.661 (1.00) |
0.396 (1.00) |
0.839 (1.00) |
0.693 (1.00) |
0.966 (1.00) |
1 (1.00) |
Del Peak 27(16p13 3) | 0 (0%) | 218 |
0.4 (1.00) |
0.176 (1.00) |
0.00834 (1.00) |
0.103 (1.00) |
0.165 (1.00) |
0.267 (1.00) |
0.14 (1.00) |
0.308 (1.00) |
0.211 (1.00) |
0.529 (1.00) |
Del Peak 28(16q12 1) | 0 (0%) | 182 |
0.286 (1.00) |
0.685 (1.00) |
0.0151 (1.00) |
0.37 (1.00) |
0.101 (1.00) |
0.206 (1.00) |
0.194 (1.00) |
0.132 (1.00) |
0.238 (1.00) |
0.0445 (1.00) |
Del Peak 29(16q24 3) | 0 (0%) | 174 |
0.00563 (1.00) |
0.566 (1.00) |
0.0934 (1.00) |
0.61 (1.00) |
0.0139 (1.00) |
0.0551 (1.00) |
0.0935 (1.00) |
0.0519 (1.00) |
0.0889 (1.00) |
0.0329 (1.00) |
Del Peak 30(17q21 31) | 0 (0%) | 209 |
0.913 (1.00) |
0.744 (1.00) |
0.325 (1.00) |
0.773 (1.00) |
0.479 (1.00) |
0.612 (1.00) |
0.804 (1.00) |
0.355 (1.00) |
0.498 (1.00) |
0.386 (1.00) |
Del Peak 31(19p13 3) | 0 (0%) | 190 |
0.0212 (1.00) |
0.621 (1.00) |
0.00261 (1.00) |
0.0275 (1.00) |
0.00838 (1.00) |
0.091 (1.00) |
0.726 (1.00) |
0.272 (1.00) |
0.606 (1.00) |
0.223 (1.00) |
Del Peak 32(22q13 1) | 0 (0%) | 240 |
0.371 (1.00) |
0.343 (1.00) |
0.848 (1.00) |
0.904 (1.00) |
0.874 (1.00) |
0.56 (1.00) |
0.135 (1.00) |
0.821 (1.00) |
0.667 (1.00) |
0.869 (1.00) |
P value = 3.14e-10 (Fisher's exact test), Q value = 1.7e-07
Table S1. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 2(1Q21.3) CNV | 67 | 41 | 27 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 17 | 65 | 50 |
Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D2V1.png)
P value = 2.22e-10 (Fisher's exact test), Q value = 1.2e-07
Table S2. Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 3(1Q44) CNV | 69 | 45 | 28 |
AMP PEAK 3(1Q44) WILD-TYPE | 15 | 61 | 49 |
Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(1q44)' versus Molecular Subtype #1: 'CN_CNMF'
![](D3V1.png)
P value = 1.27e-09 (Fisher's exact test), Q value = 6.9e-07
Table S3. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 6(5P15.33) CNV | 39 | 11 | 35 |
AMP PEAK 6(5P15.33) WILD-TYPE | 45 | 95 | 42 |
Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'
![](D6V1.png)
P value = 9.59e-05 (Fisher's exact test), Q value = 0.05
Table S4. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 82 | 109 | 69 |
AMP PEAK 6(5P15.33) CNV | 32 | 41 | 8 |
AMP PEAK 6(5P15.33) WILD-TYPE | 50 | 68 | 61 |
Figure S4. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D6V9.png)
P value = 2.8e-05 (Fisher's exact test), Q value = 0.015
Table S5. Gene #7: 'Amp Peak 7(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 7(5Q35.3) CNV | 15 | 5 | 22 |
AMP PEAK 7(5Q35.3) WILD-TYPE | 69 | 101 | 55 |
Figure S5. Get High-res Image Gene #7: 'Amp Peak 7(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D7V1.png)
P value = 0.000302 (Fisher's exact test), Q value = 0.16
Table S6. Gene #7: 'Amp Peak 7(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 98 | 102 |
AMP PEAK 7(5Q35.3) CNV | 21 | 13 | 8 |
AMP PEAK 7(5Q35.3) WILD-TYPE | 46 | 85 | 94 |
Figure S6. Get High-res Image Gene #7: 'Amp Peak 7(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D7V2.png)
P value = 3.31e-05 (Fisher's exact test), Q value = 0.017
Table S7. Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 8(6P25.1) CNV | 58 | 42 | 51 |
AMP PEAK 8(6P25.1) WILD-TYPE | 26 | 64 | 26 |
Figure S7. Get High-res Image Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D8V1.png)
P value = 0.000379 (Fisher's exact test), Q value = 0.2
Table S8. Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 98 | 102 |
AMP PEAK 8(6P25.1) CNV | 48 | 60 | 43 |
AMP PEAK 8(6P25.1) WILD-TYPE | 19 | 38 | 59 |
Figure S8. Get High-res Image Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D8V2.png)
P value = 1.03e-05 (Fisher's exact test), Q value = 0.0055
Table S9. Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 83 | 149 |
AMP PEAK 8(6P25.1) CNV | 15 | 30 | 102 |
AMP PEAK 8(6P25.1) WILD-TYPE | 13 | 53 | 47 |
Figure S9. Get High-res Image Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
![](D8V8.png)
P value = 2.5e-05 (Fisher's exact test), Q value = 0.013
Table S10. Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 77 | 151 | 32 |
AMP PEAK 8(6P25.1) CNV | 27 | 101 | 19 |
AMP PEAK 8(6P25.1) WILD-TYPE | 50 | 50 | 13 |
Figure S10. Get High-res Image Gene #8: 'Amp Peak 8(6p25.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D8V10.png)
P value = 1.15e-05 (Fisher's exact test), Q value = 0.0062
Table S11. Gene #10: 'Amp Peak 10(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 10(7P22.3) CNV | 57 | 38 | 48 |
AMP PEAK 10(7P22.3) WILD-TYPE | 27 | 68 | 29 |
Figure S11. Get High-res Image Gene #10: 'Amp Peak 10(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D10V1.png)
P value = 0.000344 (Fisher's exact test), Q value = 0.18
Table S12. Gene #11: 'Amp Peak 11(7q34)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 11(7Q34) CNV | 51 | 49 | 58 |
AMP PEAK 11(7Q34) WILD-TYPE | 33 | 57 | 19 |
Figure S12. Get High-res Image Gene #11: 'Amp Peak 11(7q34)' versus Molecular Subtype #1: 'CN_CNMF'
![](D11V1.png)
P value = 1.54e-05 (Fisher's exact test), Q value = 0.0082
Table S13. Gene #12: 'Amp Peak 12(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 12(8Q11.21) CNV | 46 | 28 | 43 |
AMP PEAK 12(8Q11.21) WILD-TYPE | 38 | 78 | 34 |
Figure S13. Get High-res Image Gene #12: 'Amp Peak 12(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'
![](D12V1.png)
P value = 3.17e-08 (Fisher's exact test), Q value = 1.7e-05
Table S14. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 13(8Q24.21) CNV | 50 | 31 | 54 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 34 | 75 | 23 |
Figure S14. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'
![](D13V1.png)
P value = 7.05e-06 (Fisher's exact test), Q value = 0.0038
Table S15. Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 15(11Q13.3) CNV | 8 | 13 | 29 |
AMP PEAK 15(11Q13.3) WILD-TYPE | 76 | 93 | 48 |
Figure S15. Get High-res Image Gene #15: 'Amp Peak 15(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D15V1.png)
P value = 3.58e-06 (Fisher's exact test), Q value = 0.0019
Table S16. Gene #16: 'Amp Peak 16(11q13.4)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 16(11Q13.4) CNV | 8 | 10 | 28 |
AMP PEAK 16(11Q13.4) WILD-TYPE | 76 | 96 | 49 |
Figure S16. Get High-res Image Gene #16: 'Amp Peak 16(11q13.4)' versus Molecular Subtype #1: 'CN_CNMF'
![](D16V1.png)
P value = 0.000106 (Fisher's exact test), Q value = 0.055
Table S17. Gene #22: 'Amp Peak 22(20q13.33)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 22(20Q13.33) CNV | 53 | 37 | 46 |
AMP PEAK 22(20Q13.33) WILD-TYPE | 31 | 69 | 31 |
Figure S17. Get High-res Image Gene #22: 'Amp Peak 22(20q13.33)' versus Molecular Subtype #1: 'CN_CNMF'
![](D22V1.png)
P value = 3.43e-07 (Fisher's exact test), Q value = 0.00019
Table S18. Gene #23: 'Amp Peak 23(22q13.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
AMP PEAK 23(22Q13.2) CNV | 55 | 29 | 27 |
AMP PEAK 23(22Q13.2) WILD-TYPE | 29 | 77 | 50 |
Figure S18. Get High-res Image Gene #23: 'Amp Peak 23(22q13.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D23V1.png)
P value = 0.000127 (Fisher's exact test), Q value = 0.066
Table S19. Gene #25: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 98 | 102 |
DEL PEAK 2(1P22.1) CNV | 30 | 15 | 23 |
DEL PEAK 2(1P22.1) WILD-TYPE | 37 | 83 | 79 |
Figure S19. Get High-res Image Gene #25: 'Del Peak 2(1p22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D25V2.png)
P value = 0.000117 (Fisher's exact test), Q value = 0.061
Table S20. Gene #25: 'Del Peak 2(1p22.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 91 | 72 | 103 |
DEL PEAK 2(1P22.1) CNV | 37 | 9 | 22 |
DEL PEAK 2(1P22.1) WILD-TYPE | 54 | 63 | 81 |
Figure S20. Get High-res Image Gene #25: 'Del Peak 2(1p22.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D25V5.png)
P value = 7.76e-05 (Fisher's exact test), Q value = 0.041
Table S21. Gene #32: 'Del Peak 9(5q31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 98 | 102 |
DEL PEAK 9(5Q31.3) CNV | 13 | 51 | 35 |
DEL PEAK 9(5Q31.3) WILD-TYPE | 54 | 47 | 67 |
Figure S21. Get High-res Image Gene #32: 'Del Peak 9(5q31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D32V2.png)
P value = 1.4e-14 (Fisher's exact test), Q value = 7.7e-12
Table S22. Gene #33: 'Del Peak 10(6q22.31)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
DEL PEAK 10(6Q22.31) CNV | 52 | 37 | 70 |
DEL PEAK 10(6Q22.31) WILD-TYPE | 32 | 69 | 7 |
Figure S22. Get High-res Image Gene #33: 'Del Peak 10(6q22.31)' versus Molecular Subtype #1: 'CN_CNMF'
![](D33V1.png)
P value = 4.82e-13 (Fisher's exact test), Q value = 2.6e-10
Table S23. Gene #34: 'Del Peak 11(6q25.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
DEL PEAK 11(6Q25.3) CNV | 55 | 43 | 71 |
DEL PEAK 11(6Q25.3) WILD-TYPE | 29 | 63 | 6 |
Figure S23. Get High-res Image Gene #34: 'Del Peak 11(6q25.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D34V1.png)
P value = 8.58e-15 (Fisher's exact test), Q value = 4.7e-12
Table S24. Gene #35: 'Del Peak 12(6q26)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
DEL PEAK 12(6Q26) CNV | 56 | 39 | 71 |
DEL PEAK 12(6Q26) WILD-TYPE | 28 | 67 | 6 |
Figure S24. Get High-res Image Gene #35: 'Del Peak 12(6q26)' versus Molecular Subtype #1: 'CN_CNMF'
![](D35V1.png)
P value = 1.2e-05 (Fisher's exact test), Q value = 0.0064
Table S25. Gene #37: 'Del Peak 14(9p23)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
DEL PEAK 14(9P23) CNV | 63 | 55 | 64 |
DEL PEAK 14(9P23) WILD-TYPE | 21 | 51 | 13 |
Figure S25. Get High-res Image Gene #37: 'Del Peak 14(9p23)' versus Molecular Subtype #1: 'CN_CNMF'
![](D37V1.png)
P value = 1.09e-09 (Fisher's exact test), Q value = 5.9e-07
Table S26. Gene #38: 'Del Peak 15(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
DEL PEAK 15(9P21.3) CNV | 70 | 62 | 74 |
DEL PEAK 15(9P21.3) WILD-TYPE | 14 | 44 | 3 |
Figure S26. Get High-res Image Gene #38: 'Del Peak 15(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D38V1.png)
P value = 0.000114 (Fisher's exact test), Q value = 0.059
Table S27. Gene #38: 'Del Peak 15(9p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 91 | 72 | 103 |
DEL PEAK 15(9P21.3) CNV | 83 | 47 | 76 |
DEL PEAK 15(9P21.3) WILD-TYPE | 8 | 25 | 27 |
Figure S27. Get High-res Image Gene #38: 'Del Peak 15(9p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D38V5.png)
P value = 1.88e-05 (Fisher's exact test), Q value = 0.01
Table S28. Gene #39: 'Del Peak 16(10p15.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
DEL PEAK 16(10P15.3) CNV | 56 | 39 | 50 |
DEL PEAK 16(10P15.3) WILD-TYPE | 28 | 67 | 27 |
Figure S28. Get High-res Image Gene #39: 'Del Peak 16(10p15.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D39V1.png)
P value = 8.7e-05 (Fisher's exact test), Q value = 0.046
Table S29. Gene #39: 'Del Peak 16(10p15.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 91 | 72 | 103 |
DEL PEAK 16(10P15.3) CNV | 66 | 34 | 45 |
DEL PEAK 16(10P15.3) WILD-TYPE | 25 | 38 | 58 |
Figure S29. Get High-res Image Gene #39: 'Del Peak 16(10p15.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D39V5.png)
P value = 3.27e-05 (Fisher's exact test), Q value = 0.017
Table S30. Gene #40: 'Del Peak 17(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
DEL PEAK 17(10Q23.31) CNV | 64 | 48 | 52 |
DEL PEAK 17(10Q23.31) WILD-TYPE | 20 | 58 | 25 |
Figure S30. Get High-res Image Gene #40: 'Del Peak 17(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'
![](D40V1.png)
P value = 8.53e-05 (Fisher's exact test), Q value = 0.045
Table S31. Gene #40: 'Del Peak 17(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 91 | 72 | 103 |
DEL PEAK 17(10Q23.31) CNV | 72 | 39 | 53 |
DEL PEAK 17(10Q23.31) WILD-TYPE | 19 | 33 | 50 |
Figure S31. Get High-res Image Gene #40: 'Del Peak 17(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D40V5.png)
P value = 1.91e-05 (Fisher's exact test), Q value = 0.01
Table S32. Gene #41: 'Del Peak 18(10q26.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 91 | 72 | 103 |
DEL PEAK 18(10Q26.3) CNV | 74 | 40 | 53 |
DEL PEAK 18(10Q26.3) WILD-TYPE | 17 | 32 | 50 |
Figure S32. Get High-res Image Gene #41: 'Del Peak 18(10q26.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D41V5.png)
P value = 1.43e-07 (Fisher's exact test), Q value = 7.8e-05
Table S33. Gene #42: 'Del Peak 19(11q23.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
DEL PEAK 19(11Q23.3) CNV | 66 | 42 | 37 |
DEL PEAK 19(11Q23.3) WILD-TYPE | 18 | 64 | 40 |
Figure S33. Get High-res Image Gene #42: 'Del Peak 19(11q23.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D42V1.png)
P value = 7.99e-06 (Fisher's exact test), Q value = 0.0043
Table S34. Gene #47: 'Del Peak 24(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 84 | 106 | 77 |
DEL PEAK 24(14Q32.2) CNV | 33 | 19 | 39 |
DEL PEAK 24(14Q32.2) WILD-TYPE | 51 | 87 | 38 |
Figure S34. Get High-res Image Gene #47: 'Del Peak 24(14q32.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D47V1.png)
-
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 = SKCM-TM.transferedmergedcluster.txt
-
Number of patients = 267
-
Number of copy number variation regions = 55
-
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 multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.