This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 84 peak regions and 10 molecular subtypes across 397 patients, 99 significant findings detected with Q value < 0.25.
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Amp Peak 2(1q21.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 3(2p16.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Amp Peak 4(2q31.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 6(3q26.33) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 8(5p15.33) cnvs correlated to 'CN_CNMF'.
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Amp Peak 9(5p12) cnvs correlated to 'CN_CNMF'.
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Amp Peak 13(7q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 19(12p13.33) cnvs correlated to 'CN_CNMF'.
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Amp Peak 23(15q26.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 24(17q25.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 25(18p11.32) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 26(18q11.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF'.
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Amp Peak 28(19q13.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 29(20p12.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 31(22q11.21) cnvs correlated to 'CN_CNMF'.
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Del Peak 1(1p36.22) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 2(1p13.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 4(2q22.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 5(2q36.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 7(3p13) cnvs correlated to 'CN_CNMF'.
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Del Peak 8(3p12.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 10(4p15.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 11(4q22.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 12(4q32.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 13(4q35.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 14(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 15(5q31.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 19(7q11.22) cnvs correlated to 'CN_CNMF'.
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Del Peak 22(9p23) cnvs correlated to 'CN_CNMF'.
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Del Peak 23(9p21.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 24(9q21.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 25(10p15.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 26(10p15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 27(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 28(11p15.5) cnvs correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
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Del Peak 40(17q11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 43(19p13.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 44(19q13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 46(21q22.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 48(22q13.32) cnvs correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.
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Del Peak 49(Xp22.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 50(Xp21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 51(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 52(Xq22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 84 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 99 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 | 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 | |
Del Peak 24(9q21 11) | 191 (48%) | 206 |
0.000177 (0.134) |
4.92e-05 (0.0382) |
5.97e-11 (4.97e-08) |
1.14e-06 (0.000931) |
0.653 (1.00) |
0.239 (1.00) |
4.44e-06 (0.00357) |
2.4e-07 (0.000196) |
0.0643 (1.00) |
0.000283 (0.211) |
Amp Peak 6(3q26 33) | 364 (92%) | 33 |
0.000427 (0.314) |
1.71e-05 (0.0135) |
7.05e-12 (5.88e-09) |
6.69e-07 (0.000545) |
0.193 (1.00) |
0.0776 (1.00) |
3.81e-05 (0.0297) |
0.000164 (0.125) |
0.238 (1.00) |
1.37e-05 (0.0109) |
Del Peak 1(1p36 22) | 172 (43%) | 225 |
1.43e-06 (0.00116) |
1.78e-08 (1.47e-05) |
1.61e-28 (1.36e-25) |
2.1e-14 (1.76e-11) |
0.412 (1.00) |
0.0262 (1.00) |
1.09e-09 (9.05e-07) |
1.35e-08 (1.12e-05) |
0.0227 (1.00) |
0.00387 (1.00) |
Del Peak 5(2q36 2) | 132 (33%) | 265 |
0.000236 (0.178) |
4.76e-05 (0.037) |
1.7e-12 (1.42e-09) |
2.14e-06 (0.00174) |
0.177 (1.00) |
0.126 (1.00) |
8.49e-05 (0.0653) |
6.15e-06 (0.00494) |
0.986 (1.00) |
0.587 (1.00) |
Del Peak 2(1p13 2) | 172 (43%) | 225 |
0.000237 (0.178) |
0.00055 (0.4) |
1.23e-15 (1.03e-12) |
5.74e-09 (4.75e-06) |
0.119 (1.00) |
0.0712 (1.00) |
2.35e-05 (0.0185) |
7.07e-05 (0.0545) |
0.165 (1.00) |
0.0246 (1.00) |
Del Peak 40(17q11 2) | 96 (24%) | 301 |
1.26e-05 (0.01) |
6.44e-05 (0.0497) |
3.04e-08 (2.51e-05) |
0.0177 (1.00) |
0.495 (1.00) |
0.378 (1.00) |
0.000122 (0.0932) |
7.16e-06 (0.00574) |
0.426 (1.00) |
0.0683 (1.00) |
Amp Peak 3(2p16 1) | 216 (54%) | 181 |
0.000305 (0.227) |
0.00165 (1.00) |
3.18e-13 (2.66e-10) |
5.83e-05 (0.045) |
0.95 (1.00) |
0.643 (1.00) |
0.000333 (0.247) |
0.00113 (0.799) |
0.79 (1.00) |
0.043 (1.00) |
Del Peak 27(10q23 31) | 203 (51%) | 194 |
0.0392 (1.00) |
0.00386 (1.00) |
2.17e-05 (0.017) |
2.08e-06 (0.00169) |
0.36 (1.00) |
0.39 (1.00) |
0.000104 (0.0793) |
2.63e-05 (0.0206) |
0.541 (1.00) |
0.0173 (1.00) |
Del Peak 14(5q11 2) | 290 (73%) | 107 |
0.842 (1.00) |
0.303 (1.00) |
2.03e-12 (1.7e-09) |
0.000192 (0.145) |
0.959 (1.00) |
0.244 (1.00) |
0.248 (1.00) |
0.56 (1.00) |
0.953 (1.00) |
8.06e-05 (0.0621) |
Del Peak 26(10p15 1) | 168 (42%) | 229 |
0.0722 (1.00) |
0.484 (1.00) |
0.000162 (0.123) |
4.03e-06 (0.00325) |
0.469 (1.00) |
0.353 (1.00) |
0.000259 (0.194) |
0.0131 (1.00) |
0.0442 (1.00) |
0.00516 (1.00) |
Amp Peak 4(2q31 2) | 132 (33%) | 265 |
0.0207 (1.00) |
0.000948 (0.675) |
6.52e-06 (0.00523) |
1.99e-07 (0.000163) |
0.724 (1.00) |
0.887 (1.00) |
0.000801 (0.575) |
0.000932 (0.665) |
0.426 (1.00) |
0.37 (1.00) |
Amp Peak 13(7q21 2) | 209 (53%) | 188 |
0.101 (1.00) |
0.25 (1.00) |
5.34e-10 (4.44e-07) |
1.27e-05 (0.0101) |
0.0573 (1.00) |
0.389 (1.00) |
0.0165 (1.00) |
0.0221 (1.00) |
0.122 (1.00) |
0.0892 (1.00) |
Amp Peak 23(15q26 3) | 139 (35%) | 258 |
0.151 (1.00) |
0.021 (1.00) |
1.56e-05 (0.0123) |
9.39e-06 (0.0075) |
0.354 (1.00) |
0.0183 (1.00) |
0.000622 (0.45) |
0.00426 (1.00) |
0.0241 (1.00) |
0.000437 (0.321) |
Amp Peak 24(17q25 1) | 191 (48%) | 206 |
0.0177 (1.00) |
0.0608 (1.00) |
6.01e-07 (0.00049) |
2.17e-05 (0.017) |
0.267 (1.00) |
0.292 (1.00) |
0.0274 (1.00) |
0.00807 (1.00) |
0.611 (1.00) |
0.893 (1.00) |
Amp Peak 25(18p11 32) | 137 (35%) | 260 |
0.0958 (1.00) |
0.00981 (1.00) |
2.48e-05 (0.0195) |
0.000126 (0.096) |
0.231 (1.00) |
0.451 (1.00) |
0.41 (1.00) |
0.121 (1.00) |
0.66 (1.00) |
0.135 (1.00) |
Amp Peak 29(20p12 2) | 211 (53%) | 186 |
0.000987 (0.698) |
0.0043 (1.00) |
8.92e-08 (7.34e-05) |
0.000161 (0.123) |
0.967 (1.00) |
0.221 (1.00) |
0.15 (1.00) |
0.0134 (1.00) |
0.611 (1.00) |
0.279 (1.00) |
Del Peak 13(4q35 2) | 253 (64%) | 144 |
0.1 (1.00) |
0.206 (1.00) |
2.84e-06 (0.0023) |
0.000124 (0.0944) |
0.455 (1.00) |
0.47 (1.00) |
0.00532 (1.00) |
0.107 (1.00) |
0.63 (1.00) |
0.309 (1.00) |
Del Peak 15(5q31 1) | 308 (78%) | 89 |
0.332 (1.00) |
0.228 (1.00) |
5.7e-09 (4.72e-06) |
3e-05 (0.0235) |
0.272 (1.00) |
0.166 (1.00) |
0.294 (1.00) |
0.445 (1.00) |
0.709 (1.00) |
0.000462 (0.339) |
Del Peak 25(10p15 3) | 178 (45%) | 219 |
0.373 (1.00) |
0.442 (1.00) |
4.8e-05 (0.0373) |
9.6e-05 (0.0736) |
0.329 (1.00) |
0.443 (1.00) |
0.00383 (1.00) |
0.0165 (1.00) |
0.122 (1.00) |
0.00273 (1.00) |
Del Peak 28(11p15 5) | 183 (46%) | 214 |
0.000689 (0.497) |
0.0528 (1.00) |
1.28e-06 (0.00104) |
0.0352 (1.00) |
0.000764 (0.549) |
2.02e-05 (0.0159) |
0.02 (1.00) |
0.0362 (1.00) |
0.0436 (1.00) |
0.0754 (1.00) |
Del Peak 44(19q13 33) | 106 (27%) | 291 |
0.617 (1.00) |
0.0694 (1.00) |
0.000167 (0.126) |
0.000187 (0.141) |
0.244 (1.00) |
0.719 (1.00) |
0.436 (1.00) |
0.212 (1.00) |
0.438 (1.00) |
0.126 (1.00) |
Del Peak 48(22q13 32) | 95 (24%) | 302 |
0.000281 (0.21) |
8.68e-05 (0.0667) |
0.0172 (1.00) |
0.351 (1.00) |
0.543 (1.00) |
0.0759 (1.00) |
0.0575 (1.00) |
0.162 (1.00) |
0.0961 (1.00) |
0.0162 (1.00) |
Del Peak 50(Xp21 1) | 127 (32%) | 270 |
0.354 (1.00) |
0.148 (1.00) |
5.39e-05 (0.0417) |
0.00024 (0.18) |
0.344 (1.00) |
0.681 (1.00) |
0.0779 (1.00) |
0.00716 (1.00) |
0.321 (1.00) |
0.0974 (1.00) |
Del Peak 51(Xp11 3) | 125 (31%) | 272 |
0.062 (1.00) |
0.175 (1.00) |
9.19e-06 (0.00735) |
4.09e-05 (0.0319) |
0.0923 (1.00) |
0.124 (1.00) |
0.0142 (1.00) |
0.0175 (1.00) |
0.0635 (1.00) |
0.193 (1.00) |
Del Peak 52(Xq22 3) | 95 (24%) | 302 |
0.00853 (1.00) |
0.105 (1.00) |
1.91e-05 (0.015) |
0.000249 (0.187) |
0.663 (1.00) |
0.92 (1.00) |
0.0513 (1.00) |
0.485 (1.00) |
0.535 (1.00) |
0.942 (1.00) |
Amp Peak 2(1q21 2) | 205 (52%) | 192 |
0.0419 (1.00) |
0.00618 (1.00) |
1.98e-07 (0.000163) |
0.00113 (0.798) |
0.16 (1.00) |
0.0492 (1.00) |
0.000685 (0.495) |
0.000488 (0.357) |
0.178 (1.00) |
0.0377 (1.00) |
Amp Peak 8(5p15 33) | 314 (79%) | 83 |
0.853 (1.00) |
0.867 (1.00) |
1.07e-05 (0.00852) |
0.0129 (1.00) |
0.405 (1.00) |
0.502 (1.00) |
0.387 (1.00) |
0.328 (1.00) |
0.71 (1.00) |
0.18 (1.00) |
Amp Peak 9(5p12) | 261 (66%) | 136 |
0.919 (1.00) |
0.514 (1.00) |
7.58e-10 (6.29e-07) |
0.00874 (1.00) |
0.563 (1.00) |
1 (1.00) |
0.0635 (1.00) |
0.586 (1.00) |
0.0397 (1.00) |
0.116 (1.00) |
Amp Peak 19(12p13 33) | 198 (50%) | 199 |
0.0102 (1.00) |
0.0571 (1.00) |
1.23e-05 (0.00977) |
0.000492 (0.359) |
0.313 (1.00) |
0.729 (1.00) |
0.000575 (0.418) |
0.00518 (1.00) |
0.583 (1.00) |
0.539 (1.00) |
Amp Peak 26(18q11 2) | 126 (32%) | 271 |
0.000456 (0.334) |
0.00227 (1.00) |
1.37e-05 (0.0108) |
0.000342 (0.253) |
0.272 (1.00) |
0.74 (1.00) |
0.00438 (1.00) |
0.000578 (0.419) |
0.32 (1.00) |
0.012 (1.00) |
Amp Peak 27(19q12) | 167 (42%) | 230 |
0.455 (1.00) |
0.249 (1.00) |
4.07e-06 (0.00328) |
0.182 (1.00) |
0.231 (1.00) |
0.0287 (1.00) |
0.193 (1.00) |
0.082 (1.00) |
0.951 (1.00) |
0.609 (1.00) |
Amp Peak 28(19q13 2) | 170 (43%) | 227 |
0.715 (1.00) |
1 (1.00) |
0.000195 (0.147) |
0.0708 (1.00) |
0.356 (1.00) |
0.117 (1.00) |
0.626 (1.00) |
0.053 (1.00) |
0.872 (1.00) |
0.454 (1.00) |
Amp Peak 31(22q11 21) | 199 (50%) | 198 |
0.111 (1.00) |
0.123 (1.00) |
0.000296 (0.22) |
0.000477 (0.349) |
0.888 (1.00) |
0.349 (1.00) |
0.0671 (1.00) |
0.0677 (1.00) |
0.727 (1.00) |
0.103 (1.00) |
Del Peak 4(2q22 1) | 105 (26%) | 292 |
0.255 (1.00) |
0.318 (1.00) |
0.000271 (0.203) |
0.0198 (1.00) |
0.667 (1.00) |
0.0777 (1.00) |
0.188 (1.00) |
0.231 (1.00) |
0.648 (1.00) |
0.551 (1.00) |
Del Peak 7(3p13) | 340 (86%) | 57 |
0.419 (1.00) |
0.549 (1.00) |
2.67e-06 (0.00216) |
0.000858 (0.613) |
0.882 (1.00) |
0.0379 (1.00) |
0.369 (1.00) |
0.0134 (1.00) |
0.926 (1.00) |
0.0046 (1.00) |
Del Peak 8(3p12 3) | 332 (84%) | 65 |
0.258 (1.00) |
0.342 (1.00) |
3.03e-05 (0.0236) |
0.00259 (1.00) |
1 (1.00) |
0.092 (1.00) |
0.24 (1.00) |
0.0162 (1.00) |
0.894 (1.00) |
0.00899 (1.00) |
Del Peak 10(4p15 2) | 239 (60%) | 158 |
0.000807 (0.579) |
0.00171 (1.00) |
6.52e-06 (0.00523) |
0.000341 (0.252) |
0.662 (1.00) |
0.0343 (1.00) |
0.0883 (1.00) |
0.0514 (1.00) |
0.325 (1.00) |
0.921 (1.00) |
Del Peak 11(4q22 1) | 217 (55%) | 180 |
0.00685 (1.00) |
0.0579 (1.00) |
0.000102 (0.0782) |
0.00829 (1.00) |
0.123 (1.00) |
0.381 (1.00) |
0.0252 (1.00) |
0.00636 (1.00) |
0.219 (1.00) |
0.242 (1.00) |
Del Peak 12(4q32 3) | 248 (62%) | 149 |
0.00967 (1.00) |
0.0253 (1.00) |
3.5e-07 (0.000286) |
0.000596 (0.432) |
0.101 (1.00) |
0.523 (1.00) |
0.0057 (1.00) |
0.036 (1.00) |
0.344 (1.00) |
0.0974 (1.00) |
Del Peak 19(7q11 22) | 37 (9%) | 360 |
0.908 (1.00) |
0.405 (1.00) |
4.4e-05 (0.0342) |
0.829 (1.00) |
0.958 (1.00) |
0.75 (1.00) |
0.0463 (1.00) |
0.0644 (1.00) |
0.837 (1.00) |
0.524 (1.00) |
Del Peak 22(9p23) | 258 (65%) | 139 |
0.00561 (1.00) |
0.00291 (1.00) |
1.97e-10 (1.64e-07) |
0.104 (1.00) |
0.146 (1.00) |
0.208 (1.00) |
0.0261 (1.00) |
0.0876 (1.00) |
0.986 (1.00) |
0.0652 (1.00) |
Del Peak 23(9p21 3) | 302 (76%) | 95 |
0.372 (1.00) |
0.172 (1.00) |
4.99e-07 (0.000408) |
0.409 (1.00) |
0.695 (1.00) |
0.388 (1.00) |
0.164 (1.00) |
0.846 (1.00) |
0.852 (1.00) |
0.296 (1.00) |
Del Peak 43(19p13 3) | 173 (44%) | 224 |
0.334 (1.00) |
0.0231 (1.00) |
1.38e-05 (0.0109) |
0.145 (1.00) |
0.0588 (1.00) |
0.251 (1.00) |
0.16 (1.00) |
0.0124 (1.00) |
0.0229 (1.00) |
0.0692 (1.00) |
Del Peak 46(21q22 3) | 224 (56%) | 173 |
0.957 (1.00) |
0.193 (1.00) |
2.13e-08 (1.75e-05) |
0.00206 (1.00) |
0.396 (1.00) |
0.0991 (1.00) |
0.564 (1.00) |
0.302 (1.00) |
0.00395 (1.00) |
0.347 (1.00) |
Del Peak 49(Xp22 2) | 126 (32%) | 271 |
0.599 (1.00) |
0.351 (1.00) |
0.000249 (0.187) |
0.0101 (1.00) |
0.277 (1.00) |
0.783 (1.00) |
0.14 (1.00) |
0.122 (1.00) |
0.122 (1.00) |
0.244 (1.00) |
Amp Peak 1(1p34 2) | 63 (16%) | 334 |
0.028 (1.00) |
0.481 (1.00) |
0.000892 (0.637) |
0.644 (1.00) |
0.363 (1.00) |
0.619 (1.00) |
0.0484 (1.00) |
0.241 (1.00) |
0.222 (1.00) |
0.654 (1.00) |
Amp Peak 5(3p11 1) | 80 (20%) | 317 |
0.0748 (1.00) |
0.844 (1.00) |
0.744 (1.00) |
0.957 (1.00) |
0.214 (1.00) |
0.0013 (0.913) |
0.0555 (1.00) |
0.444 (1.00) |
0.382 (1.00) |
0.772 (1.00) |
Amp Peak 7(4q12) | 93 (23%) | 304 |
0.679 (1.00) |
0.759 (1.00) |
0.000353 (0.261) |
0.124 (1.00) |
0.356 (1.00) |
0.131 (1.00) |
0.555 (1.00) |
0.75 (1.00) |
0.163 (1.00) |
0.439 (1.00) |
Amp Peak 10(6p12 1) | 130 (33%) | 267 |
0.557 (1.00) |
0.383 (1.00) |
0.0018 (1.00) |
0.168 (1.00) |
0.962 (1.00) |
0.3 (1.00) |
0.178 (1.00) |
0.841 (1.00) |
0.933 (1.00) |
0.464 (1.00) |
Amp Peak 11(6q12) | 117 (29%) | 280 |
1 (1.00) |
0.873 (1.00) |
0.00114 (0.802) |
0.0454 (1.00) |
0.348 (1.00) |
0.408 (1.00) |
0.395 (1.00) |
0.236 (1.00) |
0.595 (1.00) |
0.214 (1.00) |
Amp Peak 12(7p11 2) | 193 (49%) | 204 |
0.186 (1.00) |
0.0939 (1.00) |
0.00097 (0.687) |
0.00366 (1.00) |
0.687 (1.00) |
0.801 (1.00) |
0.076 (1.00) |
0.0148 (1.00) |
0.46 (1.00) |
0.157 (1.00) |
Amp Peak 14(8p11 23) | 184 (46%) | 213 |
0.00812 (1.00) |
0.168 (1.00) |
0.0254 (1.00) |
0.0352 (1.00) |
0.192 (1.00) |
0.0988 (1.00) |
0.00631 (1.00) |
0.72 (1.00) |
0.131 (1.00) |
0.771 (1.00) |
Amp Peak 15(8q24 21) | 280 (71%) | 117 |
0.871 (1.00) |
0.644 (1.00) |
0.554 (1.00) |
0.969 (1.00) |
0.917 (1.00) |
0.708 (1.00) |
0.734 (1.00) |
0.428 (1.00) |
0.392 (1.00) |
0.935 (1.00) |
Amp Peak 16(9p24 1) | 73 (18%) | 324 |
0.375 (1.00) |
0.0295 (1.00) |
0.000354 (0.261) |
0.177 (1.00) |
0.0017 (1.00) |
0.00501 (1.00) |
0.0413 (1.00) |
0.00294 (1.00) |
0.461 (1.00) |
0.236 (1.00) |
Amp Peak 17(9p13 3) | 109 (27%) | 288 |
0.17 (1.00) |
0.373 (1.00) |
0.043 (1.00) |
0.0387 (1.00) |
0.0708 (1.00) |
0.00898 (1.00) |
0.022 (1.00) |
0.188 (1.00) |
0.411 (1.00) |
0.973 (1.00) |
Amp Peak 18(11q13 3) | 143 (36%) | 254 |
0.0697 (1.00) |
0.0306 (1.00) |
0.00486 (1.00) |
0.000518 (0.377) |
0.19 (1.00) |
0.0358 (1.00) |
0.0125 (1.00) |
0.139 (1.00) |
0.142 (1.00) |
0.214 (1.00) |
Amp Peak 20(12q15) | 144 (36%) | 253 |
0.312 (1.00) |
0.527 (1.00) |
0.00531 (1.00) |
0.00136 (0.956) |
0.764 (1.00) |
0.524 (1.00) |
0.105 (1.00) |
0.0491 (1.00) |
0.509 (1.00) |
0.93 (1.00) |
Amp Peak 21(13q34) | 71 (18%) | 326 |
0.964 (1.00) |
0.0489 (1.00) |
0.0384 (1.00) |
0.182 (1.00) |
0.87 (1.00) |
0.0834 (1.00) |
0.803 (1.00) |
0.407 (1.00) |
0.0664 (1.00) |
0.216 (1.00) |
Amp Peak 22(14q13 3) | 121 (30%) | 276 |
0.345 (1.00) |
0.246 (1.00) |
0.127 (1.00) |
0.0969 (1.00) |
0.57 (1.00) |
0.00826 (1.00) |
0.617 (1.00) |
0.0847 (1.00) |
0.0275 (1.00) |
0.0972 (1.00) |
Amp Peak 30(20q11 21) | 229 (58%) | 168 |
0.991 (1.00) |
0.844 (1.00) |
0.00052 (0.379) |
0.0132 (1.00) |
0.669 (1.00) |
0.588 (1.00) |
0.593 (1.00) |
0.549 (1.00) |
0.904 (1.00) |
0.519 (1.00) |
Amp Peak 32(Xq28) | 106 (27%) | 291 |
0.633 (1.00) |
0.636 (1.00) |
0.039 (1.00) |
0.0815 (1.00) |
0.0701 (1.00) |
0.069 (1.00) |
0.136 (1.00) |
0.165 (1.00) |
0.502 (1.00) |
0.734 (1.00) |
Del Peak 3(2p25 3) | 37 (9%) | 360 |
0.0461 (1.00) |
0.179 (1.00) |
0.0773 (1.00) |
0.37 (1.00) |
0.11 (1.00) |
0.838 (1.00) |
0.32 (1.00) |
0.226 (1.00) |
0.096 (1.00) |
0.0676 (1.00) |
Del Peak 6(3p25 3) | 313 (79%) | 84 |
0.54 (1.00) |
0.176 (1.00) |
0.0278 (1.00) |
0.00221 (1.00) |
0.637 (1.00) |
0.18 (1.00) |
0.327 (1.00) |
0.00876 (1.00) |
0.759 (1.00) |
0.00743 (1.00) |
Del Peak 9(3q11 1) | 59 (15%) | 338 |
0.759 (1.00) |
0.478 (1.00) |
0.117 (1.00) |
0.0538 (1.00) |
0.765 (1.00) |
0.282 (1.00) |
0.925 (1.00) |
0.674 (1.00) |
0.74 (1.00) |
0.891 (1.00) |
Del Peak 16(6p25 3) | 100 (25%) | 297 |
0.22 (1.00) |
0.11 (1.00) |
0.00878 (1.00) |
0.00143 (1.00) |
0.393 (1.00) |
0.013 (1.00) |
0.01 (1.00) |
0.0204 (1.00) |
0.159 (1.00) |
0.181 (1.00) |
Del Peak 17(6q22 31) | 95 (24%) | 302 |
0.0192 (1.00) |
0.00224 (1.00) |
0.00513 (1.00) |
0.000818 (0.586) |
0.629 (1.00) |
0.354 (1.00) |
0.0217 (1.00) |
0.0133 (1.00) |
0.194 (1.00) |
0.243 (1.00) |
Del Peak 18(6q26) | 103 (26%) | 294 |
0.0659 (1.00) |
0.00298 (1.00) |
0.00234 (1.00) |
0.000727 (0.523) |
0.921 (1.00) |
0.69 (1.00) |
0.0687 (1.00) |
0.141 (1.00) |
0.149 (1.00) |
0.0889 (1.00) |
Del Peak 20(7q36 3) | 81 (20%) | 316 |
0.187 (1.00) |
0.112 (1.00) |
0.00095 (0.675) |
0.274 (1.00) |
1 (1.00) |
0.315 (1.00) |
0.0928 (1.00) |
0.0698 (1.00) |
0.138 (1.00) |
0.163 (1.00) |
Del Peak 21(8p23 2) | 267 (67%) | 130 |
0.864 (1.00) |
0.459 (1.00) |
0.000961 (0.682) |
0.173 (1.00) |
0.345 (1.00) |
0.141 (1.00) |
0.157 (1.00) |
0.072 (1.00) |
0.345 (1.00) |
0.285 (1.00) |
Del Peak 29(11q22 1) | 118 (30%) | 279 |
0.493 (1.00) |
0.288 (1.00) |
0.0053 (1.00) |
0.0314 (1.00) |
0.103 (1.00) |
0.995 (1.00) |
0.259 (1.00) |
0.426 (1.00) |
0.219 (1.00) |
0.0584 (1.00) |
Del Peak 30(11q25) | 143 (36%) | 254 |
0.798 (1.00) |
0.429 (1.00) |
0.0746 (1.00) |
0.333 (1.00) |
0.113 (1.00) |
0.908 (1.00) |
0.447 (1.00) |
0.406 (1.00) |
0.14 (1.00) |
0.189 (1.00) |
Del Peak 31(12q24 31) | 63 (16%) | 334 |
0.965 (1.00) |
0.332 (1.00) |
0.426 (1.00) |
0.435 (1.00) |
0.323 (1.00) |
0.207 (1.00) |
0.9 (1.00) |
0.689 (1.00) |
0.282 (1.00) |
0.322 (1.00) |
Del Peak 32(13q12 11) | 260 (65%) | 137 |
0.0547 (1.00) |
0.611 (1.00) |
0.0344 (1.00) |
0.164 (1.00) |
0.907 (1.00) |
0.268 (1.00) |
0.7 (1.00) |
0.214 (1.00) |
0.973 (1.00) |
1 (1.00) |
Del Peak 33(13q14 2) | 271 (68%) | 126 |
0.0512 (1.00) |
0.0962 (1.00) |
0.00096 (0.682) |
0.053 (1.00) |
0.707 (1.00) |
0.682 (1.00) |
0.0281 (1.00) |
0.147 (1.00) |
0.905 (1.00) |
0.561 (1.00) |
Del Peak 34(14q11 2) | 140 (35%) | 257 |
0.0546 (1.00) |
0.293 (1.00) |
0.163 (1.00) |
0.437 (1.00) |
0.206 (1.00) |
0.159 (1.00) |
0.00265 (1.00) |
0.00213 (1.00) |
0.252 (1.00) |
0.274 (1.00) |
Del Peak 35(15q12) | 131 (33%) | 266 |
0.725 (1.00) |
0.228 (1.00) |
0.45 (1.00) |
0.347 (1.00) |
0.0717 (1.00) |
0.00798 (1.00) |
0.132 (1.00) |
0.356 (1.00) |
0.0723 (1.00) |
0.636 (1.00) |
Del Peak 36(15q21 1) | 124 (31%) | 273 |
0.643 (1.00) |
0.242 (1.00) |
0.298 (1.00) |
0.969 (1.00) |
0.138 (1.00) |
0.00763 (1.00) |
0.156 (1.00) |
0.354 (1.00) |
0.228 (1.00) |
0.318 (1.00) |
Del Peak 37(16p13 3) | 148 (37%) | 249 |
0.239 (1.00) |
0.245 (1.00) |
0.00525 (1.00) |
0.197 (1.00) |
0.149 (1.00) |
0.606 (1.00) |
0.531 (1.00) |
0.247 (1.00) |
0.618 (1.00) |
0.0677 (1.00) |
Del Peak 38(16q23 1) | 166 (42%) | 231 |
0.942 (1.00) |
0.659 (1.00) |
0.0863 (1.00) |
0.271 (1.00) |
0.354 (1.00) |
0.761 (1.00) |
0.205 (1.00) |
0.0264 (1.00) |
0.535 (1.00) |
0.337 (1.00) |
Del Peak 39(17p11 2) | 202 (51%) | 195 |
0.194 (1.00) |
0.401 (1.00) |
0.00185 (1.00) |
0.161 (1.00) |
0.15 (1.00) |
0.0182 (1.00) |
0.368 (1.00) |
0.86 (1.00) |
0.0666 (1.00) |
0.0313 (1.00) |
Del Peak 41(17q25 3) | 76 (19%) | 321 |
0.00515 (1.00) |
0.0421 (1.00) |
0.000405 (0.299) |
0.0446 (1.00) |
0.622 (1.00) |
0.994 (1.00) |
0.13 (1.00) |
0.0021 (1.00) |
0.946 (1.00) |
0.111 (1.00) |
Del Peak 42(18q23) | 179 (45%) | 218 |
0.508 (1.00) |
0.788 (1.00) |
0.502 (1.00) |
0.898 (1.00) |
0.801 (1.00) |
0.397 (1.00) |
0.23 (1.00) |
0.115 (1.00) |
0.773 (1.00) |
0.502 (1.00) |
Del Peak 45(21q21 1) | 189 (48%) | 208 |
0.481 (1.00) |
0.135 (1.00) |
0.0117 (1.00) |
0.0293 (1.00) |
0.585 (1.00) |
0.89 (1.00) |
0.996 (1.00) |
0.815 (1.00) |
0.0562 (1.00) |
0.0687 (1.00) |
Del Peak 47(22q11 21) | 68 (17%) | 329 |
0.0904 (1.00) |
0.0093 (1.00) |
0.0672 (1.00) |
0.0841 (1.00) |
0.145 (1.00) |
0.129 (1.00) |
0.598 (1.00) |
0.748 (1.00) |
0.172 (1.00) |
0.126 (1.00) |
P value = 1.98e-07 (Fisher's exact test), Q value = 0.00016
Table S1. Gene #2: 'Amp Peak 2(1q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 2(1Q21.2) MUTATED | 57 | 92 | 56 |
AMP PEAK 2(1Q21.2) WILD-TYPE | 86 | 37 | 69 |
Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(1q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000305 (Fisher's exact test), Q value = 0.23
Table S2. Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
AMP PEAK 3(2P16.1) MUTATED | 19 | 40 | 12 | 15 |
AMP PEAK 3(2P16.1) WILD-TYPE | 24 | 10 | 18 | 16 |
Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 3.18e-13 (Fisher's exact test), Q value = 2.7e-10
Table S3. Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 3(2P16.1) MUTATED | 49 | 102 | 65 |
AMP PEAK 3(2P16.1) WILD-TYPE | 94 | 27 | 60 |
Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 5.83e-05 (Fisher's exact test), Q value = 0.045
Table S4. Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 3(2P16.1) MUTATED | 43 | 61 | 31 |
AMP PEAK 3(2P16.1) WILD-TYPE | 55 | 22 | 38 |
Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 0.000333 (Fisher's exact test), Q value = 0.25
Table S5. Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 60 | 80 | 79 | 38 |
AMP PEAK 3(2P16.1) MUTATED | 23 | 58 | 44 | 17 |
AMP PEAK 3(2P16.1) WILD-TYPE | 37 | 22 | 35 | 21 |
Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 6.52e-06 (Fisher's exact test), Q value = 0.0052
Table S6. Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 4(2Q31.2) MUTATED | 30 | 63 | 39 |
AMP PEAK 4(2Q31.2) WILD-TYPE | 113 | 66 | 86 |
Figure S6. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.99e-07 (Fisher's exact test), Q value = 0.00016
Table S7. Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 4(2Q31.2) MUTATED | 23 | 48 | 14 |
AMP PEAK 4(2Q31.2) WILD-TYPE | 75 | 35 | 55 |
Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.014
Table S8. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
AMP PEAK 6(3Q26.33) MUTATED | 19 | 54 | 67 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 9 | 0 | 5 |
Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

P value = 7.05e-12 (Fisher's exact test), Q value = 5.9e-09
Table S9. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 6(3Q26.33) MUTATED | 113 | 129 | 122 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 30 | 0 | 3 |
Figure S9. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 6.69e-07 (Fisher's exact test), Q value = 0.00055
Table S10. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 6(3Q26.33) MUTATED | 79 | 83 | 67 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 19 | 0 | 2 |
Figure S10. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 3.81e-05 (Fisher's exact test), Q value = 0.03
Table S11. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 60 | 80 | 79 | 38 |
AMP PEAK 6(3Q26.33) MUTATED | 57 | 80 | 66 | 31 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 3 | 0 | 13 | 7 |
Figure S11. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 0.000164 (Fisher's exact test), Q value = 0.12
Table S12. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 86 | 55 |
AMP PEAK 6(3Q26.33) MUTATED | 100 | 86 | 48 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 16 | 0 | 7 |
Figure S12. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.011
Table S13. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 176 | 118 |
AMP PEAK 6(3Q26.33) MUTATED | 53 | 151 | 116 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 0 | 25 | 2 |
Figure S13. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.0085
Table S14. Gene #8: 'Amp Peak 8(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 8(5P15.33) MUTATED | 99 | 100 | 115 |
AMP PEAK 8(5P15.33) WILD-TYPE | 44 | 29 | 10 |
Figure S14. Get High-res Image Gene #8: 'Amp Peak 8(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 7.58e-10 (Fisher's exact test), Q value = 6.3e-07
Table S15. Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 9(5P12) MUTATED | 70 | 84 | 107 |
AMP PEAK 9(5P12) WILD-TYPE | 73 | 45 | 18 |
Figure S15. Get High-res Image Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 5.34e-10 (Fisher's exact test), Q value = 4.4e-07
Table S16. Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 13(7Q21.2) MUTATED | 51 | 96 | 62 |
AMP PEAK 13(7Q21.2) WILD-TYPE | 92 | 33 | 63 |
Figure S16. Get High-res Image Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.01
Table S17. Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 13(7Q21.2) MUTATED | 35 | 58 | 30 |
AMP PEAK 13(7Q21.2) WILD-TYPE | 63 | 25 | 39 |
Figure S17. Get High-res Image Gene #13: 'Amp Peak 13(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0098
Table S18. Gene #19: 'Amp Peak 19(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 19(12P13.33) MUTATED | 51 | 83 | 64 |
AMP PEAK 19(12P13.33) WILD-TYPE | 92 | 46 | 61 |
Figure S18. Get High-res Image Gene #19: 'Amp Peak 19(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.012
Table S19. Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 23(15Q26.3) MUTATED | 30 | 61 | 48 |
AMP PEAK 23(15Q26.3) WILD-TYPE | 113 | 68 | 77 |
Figure S19. Get High-res Image Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 9.39e-06 (Fisher's exact test), Q value = 0.0075
Table S20. Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 23(15Q26.3) MUTATED | 16 | 40 | 27 |
AMP PEAK 23(15Q26.3) WILD-TYPE | 82 | 43 | 42 |
Figure S20. Get High-res Image Gene #23: 'Amp Peak 23(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 6.01e-07 (Fisher's exact test), Q value = 0.00049
Table S21. Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 24(17Q25.1) MUTATED | 46 | 83 | 62 |
AMP PEAK 24(17Q25.1) WILD-TYPE | 97 | 46 | 63 |
Figure S21. Get High-res Image Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.017
Table S22. Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 24(17Q25.1) MUTATED | 34 | 55 | 25 |
AMP PEAK 24(17Q25.1) WILD-TYPE | 64 | 28 | 44 |
Figure S22. Get High-res Image Gene #24: 'Amp Peak 24(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.019
Table S23. Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 25(18P11.32) MUTATED | 32 | 63 | 42 |
AMP PEAK 25(18P11.32) WILD-TYPE | 111 | 66 | 83 |
Figure S23. Get High-res Image Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.096
Table S24. Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 25(18P11.32) MUTATED | 18 | 38 | 28 |
AMP PEAK 25(18P11.32) WILD-TYPE | 80 | 45 | 41 |
Figure S24. Get High-res Image Gene #25: 'Amp Peak 25(18p11.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.011
Table S25. Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 26(18Q11.2) MUTATED | 26 | 57 | 43 |
AMP PEAK 26(18Q11.2) WILD-TYPE | 117 | 72 | 82 |
Figure S25. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 4.07e-06 (Fisher's exact test), Q value = 0.0033
Table S26. Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 27(19Q12) MUTATED | 45 | 77 | 45 |
AMP PEAK 27(19Q12) WILD-TYPE | 98 | 52 | 80 |
Figure S26. Get High-res Image Gene #27: 'Amp Peak 27(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.15
Table S27. Gene #28: 'Amp Peak 28(19q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 28(19Q13.2) MUTATED | 48 | 74 | 48 |
AMP PEAK 28(19Q13.2) WILD-TYPE | 95 | 55 | 77 |
Figure S27. Get High-res Image Gene #28: 'Amp Peak 28(19q13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 8.92e-08 (Fisher's exact test), Q value = 7.3e-05
Table S28. Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 29(20P12.2) MUTATED | 53 | 92 | 66 |
AMP PEAK 29(20P12.2) WILD-TYPE | 90 | 37 | 59 |
Figure S28. Get High-res Image Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.12
Table S29. Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 29(20P12.2) MUTATED | 42 | 60 | 33 |
AMP PEAK 29(20P12.2) WILD-TYPE | 56 | 23 | 36 |
Figure S29. Get High-res Image Gene #29: 'Amp Peak 29(20p12.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.22
Table S30. Gene #31: 'Amp Peak 31(22q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 31(22Q11.21) MUTATED | 54 | 80 | 65 |
AMP PEAK 31(22Q11.21) WILD-TYPE | 89 | 49 | 60 |
Figure S30. Get High-res Image Gene #31: 'Amp Peak 31(22q11.21) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0012
Table S31. Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 1(1P36.22) MUTATED | 9 | 37 | 13 | 10 |
DEL PEAK 1(1P36.22) WILD-TYPE | 34 | 13 | 17 | 21 |
Figure S31. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 1.78e-08 (Fisher's exact test), Q value = 1.5e-05
Table S32. Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 1(1P36.22) MUTATED | 11 | 41 | 17 |
DEL PEAK 1(1P36.22) WILD-TYPE | 17 | 13 | 55 |
Figure S32. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

P value = 1.61e-28 (Fisher's exact test), Q value = 1.4e-25
Table S33. Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 1(1P36.22) MUTATED | 34 | 107 | 31 |
DEL PEAK 1(1P36.22) WILD-TYPE | 109 | 22 | 94 |
Figure S33. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2.1e-14 (Fisher's exact test), Q value = 1.8e-11
Table S34. Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 1(1P36.22) MUTATED | 17 | 61 | 22 |
DEL PEAK 1(1P36.22) WILD-TYPE | 81 | 22 | 47 |
Figure S34. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 1.09e-09 (Fisher's exact test), Q value = 9e-07
Table S35. Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 60 | 80 | 79 | 38 |
DEL PEAK 1(1P36.22) MUTATED | 16 | 60 | 27 | 12 |
DEL PEAK 1(1P36.22) WILD-TYPE | 44 | 20 | 52 | 26 |
Figure S35. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 1.35e-08 (Fisher's exact test), Q value = 1.1e-05
Table S36. Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 86 | 55 |
DEL PEAK 1(1P36.22) MUTATED | 36 | 61 | 18 |
DEL PEAK 1(1P36.22) WILD-TYPE | 80 | 25 | 37 |
Figure S36. Get High-res Image Gene #33: 'Del Peak 1(1p36.22) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000237 (Fisher's exact test), Q value = 0.18
Table S37. Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 2(1P13.2) MUTATED | 17 | 35 | 8 | 10 |
DEL PEAK 2(1P13.2) WILD-TYPE | 26 | 15 | 22 | 21 |
Figure S37. Get High-res Image Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 1.23e-15 (Fisher's exact test), Q value = 1e-12
Table S38. Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 2(1P13.2) MUTATED | 35 | 93 | 44 |
DEL PEAK 2(1P13.2) WILD-TYPE | 108 | 36 | 81 |
Figure S38. Get High-res Image Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 5.74e-09 (Fisher's exact test), Q value = 4.8e-06
Table S39. Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 2(1P13.2) MUTATED | 20 | 54 | 28 |
DEL PEAK 2(1P13.2) WILD-TYPE | 78 | 29 | 41 |
Figure S39. Get High-res Image Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 2.35e-05 (Fisher's exact test), Q value = 0.018
Table S40. Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 60 | 80 | 79 | 38 |
DEL PEAK 2(1P13.2) MUTATED | 23 | 53 | 25 | 12 |
DEL PEAK 2(1P13.2) WILD-TYPE | 37 | 27 | 54 | 26 |
Figure S40. Get High-res Image Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 7.07e-05 (Fisher's exact test), Q value = 0.055
Table S41. Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 86 | 55 |
DEL PEAK 2(1P13.2) MUTATED | 38 | 54 | 21 |
DEL PEAK 2(1P13.2) WILD-TYPE | 78 | 32 | 34 |
Figure S41. Get High-res Image Gene #34: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000271 (Fisher's exact test), Q value = 0.2
Table S42. Gene #36: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 4(2Q22.1) MUTATED | 22 | 47 | 36 |
DEL PEAK 4(2Q22.1) WILD-TYPE | 121 | 82 | 89 |
Figure S42. Get High-res Image Gene #36: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.18
Table S43. Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 5(2Q36.2) MUTATED | 9 | 26 | 3 | 12 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 34 | 24 | 27 | 19 |
Figure S43. Get High-res Image Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.037
Table S44. Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 5(2Q36.2) MUTATED | 5 | 30 | 15 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 23 | 24 | 57 |
Figure S44. Get High-res Image Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

P value = 1.7e-12 (Fisher's exact test), Q value = 1.4e-09
Table S45. Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 5(2Q36.2) MUTATED | 23 | 74 | 35 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 120 | 55 | 90 |
Figure S45. Get High-res Image Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2.14e-06 (Fisher's exact test), Q value = 0.0017
Table S46. Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 5(2Q36.2) MUTATED | 17 | 44 | 25 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 81 | 39 | 44 |
Figure S46. Get High-res Image Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 8.49e-05 (Fisher's exact test), Q value = 0.065
Table S47. Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 60 | 80 | 79 | 38 |
DEL PEAK 5(2Q36.2) MUTATED | 17 | 40 | 18 | 5 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 43 | 40 | 61 | 33 |
Figure S47. Get High-res Image Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 6.15e-06 (Fisher's exact test), Q value = 0.0049
Table S48. Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 86 | 55 |
DEL PEAK 5(2Q36.2) MUTATED | 23 | 44 | 13 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 93 | 42 | 42 |
Figure S48. Get High-res Image Gene #37: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.67e-06 (Fisher's exact test), Q value = 0.0022
Table S49. Gene #39: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 7(3P13) MUTATED | 105 | 119 | 116 |
DEL PEAK 7(3P13) WILD-TYPE | 38 | 10 | 9 |
Figure S49. Get High-res Image Gene #39: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.024
Table S50. Gene #40: 'Del Peak 8(3p12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 8(3P12.3) MUTATED | 103 | 116 | 113 |
DEL PEAK 8(3P12.3) WILD-TYPE | 40 | 13 | 12 |
Figure S50. Get High-res Image Gene #40: 'Del Peak 8(3p12.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 6.52e-06 (Fisher's exact test), Q value = 0.0052
Table S51. Gene #42: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 10(4P15.2) MUTATED | 70 | 99 | 70 |
DEL PEAK 10(4P15.2) WILD-TYPE | 73 | 30 | 55 |
Figure S51. Get High-res Image Gene #42: 'Del Peak 10(4p15.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.078
Table S52. Gene #43: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 11(4Q22.1) MUTATED | 65 | 90 | 62 |
DEL PEAK 11(4Q22.1) WILD-TYPE | 78 | 39 | 63 |
Figure S52. Get High-res Image Gene #43: 'Del Peak 11(4q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 3.5e-07 (Fisher's exact test), Q value = 0.00029
Table S53. Gene #44: 'Del Peak 12(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 12(4Q32.3) MUTATED | 72 | 104 | 72 |
DEL PEAK 12(4Q32.3) WILD-TYPE | 71 | 25 | 53 |
Figure S53. Get High-res Image Gene #44: 'Del Peak 12(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0023
Table S54. Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 13(4Q35.2) MUTATED | 76 | 104 | 73 |
DEL PEAK 13(4Q35.2) WILD-TYPE | 67 | 25 | 52 |
Figure S54. Get High-res Image Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000124 (Fisher's exact test), Q value = 0.094
Table S55. Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 13(4Q35.2) MUTATED | 47 | 65 | 42 |
DEL PEAK 13(4Q35.2) WILD-TYPE | 51 | 18 | 27 |
Figure S55. Get High-res Image Gene #45: 'Del Peak 13(4q35.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 2.03e-12 (Fisher's exact test), Q value = 1.7e-09
Table S56. Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 14(5Q11.2) MUTATED | 73 | 108 | 109 |
DEL PEAK 14(5Q11.2) WILD-TYPE | 70 | 21 | 16 |
Figure S56. Get High-res Image Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.15
Table S57. Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 14(5Q11.2) MUTATED | 57 | 69 | 56 |
DEL PEAK 14(5Q11.2) WILD-TYPE | 41 | 14 | 13 |
Figure S57. Get High-res Image Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 8.06e-05 (Fisher's exact test), Q value = 0.062
Table S58. Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 176 | 118 |
DEL PEAK 14(5Q11.2) MUTATED | 41 | 115 | 103 |
DEL PEAK 14(5Q11.2) WILD-TYPE | 12 | 61 | 15 |
Figure S58. Get High-res Image Gene #46: 'Del Peak 14(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

P value = 5.7e-09 (Fisher's exact test), Q value = 4.7e-06
Table S59. Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 15(5Q31.1) MUTATED | 86 | 111 | 111 |
DEL PEAK 15(5Q31.1) WILD-TYPE | 57 | 18 | 14 |
Figure S59. Get High-res Image Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.023
Table S60. Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 15(5Q31.1) MUTATED | 63 | 71 | 63 |
DEL PEAK 15(5Q31.1) WILD-TYPE | 35 | 12 | 6 |
Figure S60. Get High-res Image Gene #47: 'Del Peak 15(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 4.4e-05 (Fisher's exact test), Q value = 0.034
Table S61. Gene #51: 'Del Peak 19(7q11.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 19(7Q11.22) MUTATED | 11 | 3 | 23 |
DEL PEAK 19(7Q11.22) WILD-TYPE | 132 | 126 | 102 |
Figure S61. Get High-res Image Gene #51: 'Del Peak 19(7q11.22) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.97e-10 (Fisher's exact test), Q value = 1.6e-07
Table S62. Gene #54: 'Del Peak 22(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 22(9P23) MUTATED | 74 | 75 | 109 |
DEL PEAK 22(9P23) WILD-TYPE | 69 | 54 | 16 |
Figure S62. Get High-res Image Gene #54: 'Del Peak 22(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 4.99e-07 (Fisher's exact test), Q value = 0.00041
Table S63. Gene #55: 'Del Peak 23(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 23(9P21.3) MUTATED | 92 | 96 | 114 |
DEL PEAK 23(9P21.3) WILD-TYPE | 51 | 33 | 11 |
Figure S63. Get High-res Image Gene #55: 'Del Peak 23(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.13
Table S64. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 24(9Q21.11) MUTATED | 28 | 12 | 19 | 15 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 15 | 38 | 11 | 16 |
Figure S64. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 4.92e-05 (Fisher's exact test), Q value = 0.038
Table S65. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 24(9Q21.11) MUTATED | 16 | 13 | 45 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 12 | 41 | 27 |
Figure S65. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

P value = 5.97e-11 (Fisher's exact test), Q value = 5e-08
Table S66. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 24(9Q21.11) MUTATED | 69 | 35 | 87 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 74 | 94 | 38 |
Figure S66. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00093
Table S67. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 24(9Q21.11) MUTATED | 54 | 22 | 46 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 44 | 61 | 23 |
Figure S67. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 4.44e-06 (Fisher's exact test), Q value = 0.0036
Table S68. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 60 | 80 | 79 | 38 |
DEL PEAK 24(9Q21.11) MUTATED | 33 | 19 | 48 | 22 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 27 | 61 | 31 | 16 |
Figure S68. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 2.4e-07 (Fisher's exact test), Q value = 2e-04
Table S69. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 86 | 55 |
DEL PEAK 24(9Q21.11) MUTATED | 64 | 21 | 37 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 52 | 65 | 18 |
Figure S69. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000283 (Fisher's exact test), Q value = 0.21
Table S70. Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 176 | 118 |
DEL PEAK 24(9Q21.11) MUTATED | 13 | 90 | 67 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 40 | 86 | 51 |
Figure S70. Get High-res Image Gene #56: 'Del Peak 24(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

P value = 4.8e-05 (Fisher's exact test), Q value = 0.037
Table S71. Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 25(10P15.3) MUTATED | 45 | 75 | 58 |
DEL PEAK 25(10P15.3) WILD-TYPE | 98 | 54 | 67 |
Figure S71. Get High-res Image Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 9.6e-05 (Fisher's exact test), Q value = 0.074
Table S72. Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 25(10P15.3) MUTATED | 34 | 54 | 27 |
DEL PEAK 25(10P15.3) WILD-TYPE | 64 | 29 | 42 |
Figure S72. Get High-res Image Gene #57: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.12
Table S73. Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 26(10P15.1) MUTATED | 43 | 71 | 54 |
DEL PEAK 26(10P15.1) WILD-TYPE | 100 | 58 | 71 |
Figure S73. Get High-res Image Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 4.03e-06 (Fisher's exact test), Q value = 0.0033
Table S74. Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 26(10P15.1) MUTATED | 32 | 55 | 23 |
DEL PEAK 26(10P15.1) WILD-TYPE | 66 | 28 | 46 |
Figure S74. Get High-res Image Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 0.000259 (Fisher's exact test), Q value = 0.19
Table S75. Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 60 | 80 | 79 | 38 |
DEL PEAK 26(10P15.1) MUTATED | 17 | 48 | 32 | 10 |
DEL PEAK 26(10P15.1) WILD-TYPE | 43 | 32 | 47 | 28 |
Figure S75. Get High-res Image Gene #58: 'Del Peak 26(10p15.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.017
Table S76. Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 27(10Q23.31) MUTATED | 58 | 87 | 58 |
DEL PEAK 27(10Q23.31) WILD-TYPE | 85 | 42 | 67 |
Figure S76. Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.0017
Table S77. Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 27(10Q23.31) MUTATED | 34 | 60 | 33 |
DEL PEAK 27(10Q23.31) WILD-TYPE | 64 | 23 | 36 |
Figure S77. Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.079
Table S78. Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 60 | 80 | 79 | 38 |
DEL PEAK 27(10Q23.31) MUTATED | 22 | 57 | 35 | 16 |
DEL PEAK 27(10Q23.31) WILD-TYPE | 38 | 23 | 44 | 22 |
Figure S78. Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.021
Table S79. Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 86 | 55 |
DEL PEAK 27(10Q23.31) MUTATED | 42 | 59 | 29 |
DEL PEAK 27(10Q23.31) WILD-TYPE | 74 | 27 | 26 |
Figure S79. Get High-res Image Gene #59: 'Del Peak 27(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.001
Table S80. Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 28(11P15.5) MUTATED | 49 | 53 | 81 |
DEL PEAK 28(11P15.5) WILD-TYPE | 94 | 76 | 44 |
Figure S80. Get High-res Image Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.016
Table S81. Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 47 | 49 | 40 |
DEL PEAK 28(11P15.5) MUTATED | 29 | 17 | 36 | 10 |
DEL PEAK 28(11P15.5) WILD-TYPE | 29 | 30 | 13 | 30 |
Figure S81. Get High-res Image Gene #60: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.01
Table S82. Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 40(17Q11.2) MUTATED | 21 | 3 | 11 | 7 |
DEL PEAK 40(17Q11.2) WILD-TYPE | 22 | 47 | 19 | 24 |
Figure S82. Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 6.44e-05 (Fisher's exact test), Q value = 0.05
Table S83. Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 40(17Q11.2) MUTATED | 9 | 4 | 29 |
DEL PEAK 40(17Q11.2) WILD-TYPE | 19 | 50 | 43 |
Figure S83. Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

P value = 3.04e-08 (Fisher's exact test), Q value = 2.5e-05
Table S84. Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 40(17Q11.2) MUTATED | 40 | 10 | 46 |
DEL PEAK 40(17Q11.2) WILD-TYPE | 103 | 119 | 79 |
Figure S84. Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.093
Table S85. Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 60 | 80 | 79 | 38 |
DEL PEAK 40(17Q11.2) MUTATED | 20 | 6 | 23 | 13 |
DEL PEAK 40(17Q11.2) WILD-TYPE | 40 | 74 | 56 | 25 |
Figure S85. Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 7.16e-06 (Fisher's exact test), Q value = 0.0057
Table S86. Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 86 | 55 |
DEL PEAK 40(17Q11.2) MUTATED | 39 | 6 | 17 |
DEL PEAK 40(17Q11.2) WILD-TYPE | 77 | 80 | 38 |
Figure S86. Get High-res Image Gene #72: 'Del Peak 40(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.011
Table S87. Gene #75: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 43(19P13.3) MUTATED | 48 | 49 | 76 |
DEL PEAK 43(19P13.3) WILD-TYPE | 95 | 80 | 49 |
Figure S87. Get High-res Image Gene #75: 'Del Peak 43(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.13
Table S88. Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 44(19Q13.33) MUTATED | 22 | 48 | 36 |
DEL PEAK 44(19Q13.33) WILD-TYPE | 121 | 81 | 89 |
Figure S88. Get High-res Image Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.14
Table S89. Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 44(19Q13.33) MUTATED | 12 | 30 | 23 |
DEL PEAK 44(19Q13.33) WILD-TYPE | 86 | 53 | 46 |
Figure S89. Get High-res Image Gene #76: 'Del Peak 44(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 2.13e-08 (Fisher's exact test), Q value = 1.8e-05
Table S90. Gene #78: 'Del Peak 46(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 46(21Q22.3) MUTATED | 53 | 91 | 80 |
DEL PEAK 46(21Q22.3) WILD-TYPE | 90 | 38 | 45 |
Figure S90. Get High-res Image Gene #78: 'Del Peak 46(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.21
Table S91. Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 48(22Q13.32) MUTATED | 9 | 7 | 7 | 18 |
DEL PEAK 48(22Q13.32) WILD-TYPE | 34 | 43 | 23 | 13 |
Figure S91. Get High-res Image Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 8.68e-05 (Fisher's exact test), Q value = 0.067
Table S92. Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 48(22Q13.32) MUTATED | 17 | 9 | 15 |
DEL PEAK 48(22Q13.32) WILD-TYPE | 11 | 45 | 57 |
Figure S92. Get High-res Image Gene #80: 'Del Peak 48(22q13.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

P value = 0.000249 (Fisher's exact test), Q value = 0.19
Table S93. Gene #81: 'Del Peak 49(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 49(XP22.2) MUTATED | 28 | 53 | 45 |
DEL PEAK 49(XP22.2) WILD-TYPE | 115 | 76 | 80 |
Figure S93. Get High-res Image Gene #81: 'Del Peak 49(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 5.39e-05 (Fisher's exact test), Q value = 0.042
Table S94. Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 50(XP21.1) MUTATED | 27 | 55 | 45 |
DEL PEAK 50(XP21.1) WILD-TYPE | 116 | 74 | 80 |
Figure S94. Get High-res Image Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.18
Table S95. Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 50(XP21.1) MUTATED | 18 | 36 | 29 |
DEL PEAK 50(XP21.1) WILD-TYPE | 80 | 47 | 40 |
Figure S95. Get High-res Image Gene #82: 'Del Peak 50(Xp21.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 9.19e-06 (Fisher's exact test), Q value = 0.0073
Table S96. Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 51(XP11.3) MUTATED | 26 | 58 | 41 |
DEL PEAK 51(XP11.3) WILD-TYPE | 117 | 71 | 84 |
Figure S96. Get High-res Image Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 4.09e-05 (Fisher's exact test), Q value = 0.032
Table S97. Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 51(XP11.3) MUTATED | 16 | 38 | 26 |
DEL PEAK 51(XP11.3) WILD-TYPE | 82 | 45 | 43 |
Figure S97. Get High-res Image Gene #83: 'Del Peak 51(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.015
Table S98. Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 52(XQ22.3) MUTATED | 18 | 31 | 46 |
DEL PEAK 52(XQ22.3) WILD-TYPE | 125 | 98 | 79 |
Figure S98. Get High-res Image Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.19
Table S99. Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 52(XQ22.3) MUTATED | 10 | 20 | 25 |
DEL PEAK 52(XQ22.3) WILD-TYPE | 88 | 63 | 44 |
Figure S99. Get High-res Image Gene #84: 'Del Peak 52(Xq22.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

-
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 = LUSC-TP.transferedmergedcluster.txt
-
Number of patients = 397
-
Number of copy number variation regions = 84
-
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.