This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 79 peak regions and 10 molecular subtypes across 358 patients, 87 significant findings detected with Q value < 0.25.
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Amp Peak 1(1p34.2) cnvs correlated to 'CN_CNMF'.
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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 12(7q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 18(12p13.33) cnvs correlated to 'CN_CNMF'.
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Amp Peak 22(15q26.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 23(17q25.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 24(18p11.32) cnvs correlated to 'CN_CNMF'.
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Amp Peak 25(18q11.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 26(19q12) cnvs correlated to 'CN_CNMF'.
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Amp Peak 28(20p12.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 1(1p36.32) 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(3p12.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 9(4p15.31) cnvs correlated to 'CN_CNMF'.
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Del Peak 11(4q32.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 12(4q35.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 13(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 14(5q31.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 20(9p23) cnvs correlated to 'CN_CNMF'.
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Del Peak 21(9p21.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 22(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 24(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 25(11p15.5) cnvs correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
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Del Peak 36(17q11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 39(19p13.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 40(19q13.33) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 41(19q13.43) cnvs correlated to 'CN_CNMF'.
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Del Peak 43(21q22.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 45(Xp22.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 46(Xp21.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 47(Xp11.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 48(Xq22.3) cnvs correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 79 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 87 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 22(9q21 11) | 174 (49%) | 184 |
0.000177 (0.127) |
4.92e-05 (0.0363) |
2.03e-07 (0.000157) |
1.42e-06 (0.00108) |
0.571 (1.00) |
0.24 (1.00) |
4.44e-06 (0.00337) |
2.4e-07 (0.000185) |
0.0445 (1.00) |
3.16e-05 (0.0235) |
Amp Peak 6(3q26 33) | 330 (92%) | 28 |
0.000427 (0.299) |
1.71e-05 (0.0129) |
1.63e-09 (1.27e-06) |
0.000113 (0.0818) |
0.213 (1.00) |
0.0944 (1.00) |
3.81e-05 (0.0283) |
0.000164 (0.118) |
0.205 (1.00) |
9.11e-05 (0.0662) |
Del Peak 1(1p36 32) | 155 (43%) | 203 |
1.28e-06 (0.000976) |
1.29e-08 (1e-05) |
3.34e-28 (2.64e-25) |
4.78e-16 (3.77e-13) |
0.419 (1.00) |
0.00421 (1.00) |
1.02e-10 (8.04e-08) |
6.75e-09 (5.26e-06) |
0.0237 (1.00) |
0.00103 (0.699) |
Del Peak 5(2q36 2) | 116 (32%) | 242 |
0.000236 (0.168) |
4.76e-05 (0.0352) |
5.32e-12 (4.19e-09) |
0.000352 (0.248) |
0.138 (1.00) |
0.113 (1.00) |
8.49e-05 (0.0619) |
6.15e-06 (0.00466) |
0.944 (1.00) |
0.624 (1.00) |
Del Peak 2(1p13 2) | 156 (44%) | 202 |
0.000237 (0.169) |
0.00055 (0.382) |
6.47e-14 (5.1e-11) |
6.52e-09 (5.09e-06) |
0.107 (1.00) |
0.115 (1.00) |
2.35e-05 (0.0175) |
7.07e-05 (0.0517) |
0.196 (1.00) |
0.00967 (1.00) |
Del Peak 36(17q11 2) | 89 (25%) | 269 |
1.26e-05 (0.00949) |
6.44e-05 (0.0473) |
9.35e-09 (7.27e-06) |
0.0579 (1.00) |
0.45 (1.00) |
0.577 (1.00) |
0.000122 (0.0881) |
7.16e-06 (0.00542) |
0.406 (1.00) |
0.0154 (1.00) |
Amp Peak 3(2p16 1) | 194 (54%) | 164 |
0.000305 (0.215) |
0.00165 (1.00) |
2.41e-09 (1.88e-06) |
7e-05 (0.0513) |
0.967 (1.00) |
0.741 (1.00) |
0.000333 (0.235) |
0.00113 (0.764) |
0.879 (1.00) |
0.0312 (1.00) |
Del Peak 24(10q23 31) | 184 (51%) | 174 |
0.0392 (1.00) |
0.00386 (1.00) |
0.00019 (0.136) |
6.42e-05 (0.0472) |
0.283 (1.00) |
0.303 (1.00) |
0.000104 (0.0752) |
2.63e-05 (0.0196) |
0.46 (1.00) |
0.0277 (1.00) |
Amp Peak 22(15q26 3) | 128 (36%) | 230 |
0.151 (1.00) |
0.021 (1.00) |
5.63e-07 (0.000433) |
1.78e-05 (0.0134) |
0.312 (1.00) |
0.0162 (1.00) |
0.000622 (0.429) |
0.00426 (1.00) |
0.0175 (1.00) |
7.14e-05 (0.0521) |
Del Peak 13(5q11 2) | 265 (74%) | 93 |
0.842 (1.00) |
0.303 (1.00) |
5.71e-10 (4.47e-07) |
0.000266 (0.188) |
1 (1.00) |
0.237 (1.00) |
0.248 (1.00) |
0.56 (1.00) |
0.888 (1.00) |
0.000162 (0.116) |
Amp Peak 4(2q31 2) | 121 (34%) | 237 |
0.0207 (1.00) |
0.000948 (0.643) |
6.74e-05 (0.0494) |
4.94e-06 (0.00375) |
0.738 (1.00) |
0.912 (1.00) |
0.000801 (0.548) |
0.000932 (0.633) |
0.465 (1.00) |
0.252 (1.00) |
Amp Peak 12(7q21 2) | 188 (53%) | 170 |
0.101 (1.00) |
0.25 (1.00) |
3.36e-10 (2.64e-07) |
8.35e-06 (0.00631) |
0.0408 (1.00) |
0.215 (1.00) |
0.0165 (1.00) |
0.0221 (1.00) |
0.247 (1.00) |
0.0377 (1.00) |
Amp Peak 23(17q25 1) | 171 (48%) | 187 |
0.0177 (1.00) |
0.0608 (1.00) |
1.87e-06 (0.00143) |
0.000148 (0.107) |
0.297 (1.00) |
0.323 (1.00) |
0.0274 (1.00) |
0.00807 (1.00) |
0.756 (1.00) |
0.742 (1.00) |
Del Peak 8(3p12 1) | 280 (78%) | 78 |
0.322 (1.00) |
0.0413 (1.00) |
1.46e-07 (0.000113) |
2.79e-05 (0.0207) |
0.688 (1.00) |
0.109 (1.00) |
0.155 (1.00) |
0.00235 (1.00) |
0.174 (1.00) |
0.101 (1.00) |
Del Peak 14(5q31 1) | 277 (77%) | 81 |
0.332 (1.00) |
0.228 (1.00) |
6.21e-07 (0.000477) |
3.25e-05 (0.0241) |
0.352 (1.00) |
0.209 (1.00) |
0.254 (1.00) |
0.401 (1.00) |
0.593 (1.00) |
0.00832 (1.00) |
Del Peak 25(11p15 5) | 173 (48%) | 185 |
0.000689 (0.474) |
0.0528 (1.00) |
6.04e-05 (0.0445) |
0.0117 (1.00) |
0.000449 (0.314) |
2.34e-05 (0.0175) |
0.02 (1.00) |
0.0362 (1.00) |
0.0253 (1.00) |
0.0291 (1.00) |
Del Peak 40(19q13 33) | 96 (27%) | 262 |
0.617 (1.00) |
0.0694 (1.00) |
4.76e-05 (0.0352) |
0.000249 (0.177) |
0.272 (1.00) |
0.635 (1.00) |
0.436 (1.00) |
0.212 (1.00) |
0.34 (1.00) |
0.119 (1.00) |
Del Peak 47(Xp11 3) | 116 (32%) | 242 |
0.062 (1.00) |
0.175 (1.00) |
2.82e-06 (0.00215) |
5.16e-05 (0.038) |
0.0823 (1.00) |
0.0774 (1.00) |
0.0142 (1.00) |
0.0175 (1.00) |
0.133 (1.00) |
0.199 (1.00) |
Amp Peak 1(1p34 2) | 58 (16%) | 300 |
0.028 (1.00) |
0.481 (1.00) |
0.000273 (0.193) |
0.71 (1.00) |
0.419 (1.00) |
0.668 (1.00) |
0.0484 (1.00) |
0.241 (1.00) |
0.299 (1.00) |
0.494 (1.00) |
Amp Peak 2(1q21 2) | 186 (52%) | 172 |
0.0419 (1.00) |
0.00618 (1.00) |
7.32e-07 (0.000561) |
0.00128 (0.865) |
0.155 (1.00) |
0.0576 (1.00) |
0.000685 (0.472) |
0.000488 (0.34) |
0.305 (1.00) |
0.0562 (1.00) |
Amp Peak 8(5p15 33) | 281 (78%) | 77 |
0.853 (1.00) |
0.867 (1.00) |
8.38e-06 (0.00632) |
0.0036 (1.00) |
0.498 (1.00) |
0.422 (1.00) |
0.387 (1.00) |
0.328 (1.00) |
0.841 (1.00) |
0.263 (1.00) |
Amp Peak 9(5p12) | 236 (66%) | 122 |
0.919 (1.00) |
0.514 (1.00) |
1.38e-09 (1.08e-06) |
0.00666 (1.00) |
0.669 (1.00) |
1 (1.00) |
0.0635 (1.00) |
0.586 (1.00) |
0.0413 (1.00) |
0.219 (1.00) |
Amp Peak 18(12p13 33) | 177 (49%) | 181 |
0.0102 (1.00) |
0.0571 (1.00) |
0.000255 (0.18) |
0.0112 (1.00) |
0.353 (1.00) |
0.711 (1.00) |
0.000575 (0.399) |
0.00518 (1.00) |
0.674 (1.00) |
0.429 (1.00) |
Amp Peak 24(18p11 32) | 122 (34%) | 236 |
0.0602 (1.00) |
0.00628 (1.00) |
0.000148 (0.106) |
0.0328 (1.00) |
0.226 (1.00) |
0.844 (1.00) |
0.607 (1.00) |
0.177 (1.00) |
0.526 (1.00) |
0.163 (1.00) |
Amp Peak 25(18q11 2) | 115 (32%) | 243 |
0.000456 (0.318) |
0.00227 (1.00) |
0.000231 (0.164) |
0.00415 (1.00) |
0.252 (1.00) |
0.771 (1.00) |
0.00438 (1.00) |
0.000578 (0.4) |
0.369 (1.00) |
0.00926 (1.00) |
Amp Peak 26(19q12) | 149 (42%) | 209 |
0.455 (1.00) |
0.249 (1.00) |
0.000111 (0.0804) |
0.445 (1.00) |
0.274 (1.00) |
0.0244 (1.00) |
0.193 (1.00) |
0.082 (1.00) |
0.949 (1.00) |
0.686 (1.00) |
Amp Peak 28(20p12 2) | 193 (54%) | 165 |
0.000987 (0.668) |
0.0043 (1.00) |
4.62e-08 (3.58e-05) |
0.00141 (0.949) |
0.95 (1.00) |
0.293 (1.00) |
0.15 (1.00) |
0.0134 (1.00) |
0.488 (1.00) |
0.246 (1.00) |
Del Peak 4(2q22 1) | 96 (27%) | 262 |
0.255 (1.00) |
0.318 (1.00) |
0.000217 (0.155) |
0.0216 (1.00) |
0.653 (1.00) |
0.21 (1.00) |
0.188 (1.00) |
0.231 (1.00) |
0.683 (1.00) |
0.46 (1.00) |
Del Peak 7(3p13) | 310 (87%) | 48 |
0.419 (1.00) |
0.549 (1.00) |
9.68e-05 (0.0703) |
0.00211 (1.00) |
0.91 (1.00) |
0.0127 (1.00) |
0.369 (1.00) |
0.0134 (1.00) |
0.872 (1.00) |
0.00826 (1.00) |
Del Peak 9(4p15 31) | 219 (61%) | 139 |
0.000807 (0.551) |
0.00171 (1.00) |
1.21e-05 (0.00912) |
0.00406 (1.00) |
0.675 (1.00) |
0.0454 (1.00) |
0.0883 (1.00) |
0.0514 (1.00) |
0.403 (1.00) |
1 (1.00) |
Del Peak 11(4q32 3) | 226 (63%) | 132 |
0.00967 (1.00) |
0.0253 (1.00) |
2.97e-07 (0.000229) |
0.0112 (1.00) |
0.102 (1.00) |
0.585 (1.00) |
0.0057 (1.00) |
0.036 (1.00) |
0.438 (1.00) |
0.144 (1.00) |
Del Peak 12(4q35 2) | 229 (64%) | 129 |
0.1 (1.00) |
0.206 (1.00) |
1.07e-06 (0.00082) |
0.00259 (1.00) |
0.455 (1.00) |
0.561 (1.00) |
0.00532 (1.00) |
0.107 (1.00) |
0.671 (1.00) |
0.338 (1.00) |
Del Peak 20(9p23) | 234 (65%) | 124 |
0.00561 (1.00) |
0.00291 (1.00) |
1.21e-07 (9.35e-05) |
0.109 (1.00) |
0.134 (1.00) |
0.185 (1.00) |
0.0261 (1.00) |
0.0876 (1.00) |
1 (1.00) |
0.0901 (1.00) |
Del Peak 21(9p21 3) | 272 (76%) | 86 |
0.372 (1.00) |
0.172 (1.00) |
3.23e-06 (0.00246) |
0.517 (1.00) |
0.679 (1.00) |
0.379 (1.00) |
0.164 (1.00) |
0.846 (1.00) |
0.865 (1.00) |
0.337 (1.00) |
Del Peak 39(19p13 3) | 163 (46%) | 195 |
0.334 (1.00) |
0.0231 (1.00) |
0.000227 (0.162) |
0.14 (1.00) |
0.0928 (1.00) |
0.404 (1.00) |
0.16 (1.00) |
0.0124 (1.00) |
0.0179 (1.00) |
0.0478 (1.00) |
Del Peak 41(19q13 43) | 96 (27%) | 262 |
0.644 (1.00) |
0.207 (1.00) |
9.08e-05 (0.0661) |
0.000797 (0.546) |
0.466 (1.00) |
0.47 (1.00) |
0.465 (1.00) |
0.154 (1.00) |
0.216 (1.00) |
0.308 (1.00) |
Del Peak 43(21q22 3) | 205 (57%) | 153 |
0.957 (1.00) |
0.193 (1.00) |
2.21e-08 (1.72e-05) |
0.00109 (0.737) |
0.478 (1.00) |
0.14 (1.00) |
0.564 (1.00) |
0.302 (1.00) |
0.00871 (1.00) |
0.474 (1.00) |
Del Peak 45(Xp22 2) | 114 (32%) | 244 |
0.599 (1.00) |
0.351 (1.00) |
1.57e-05 (0.0118) |
0.0164 (1.00) |
0.343 (1.00) |
0.664 (1.00) |
0.14 (1.00) |
0.122 (1.00) |
0.195 (1.00) |
0.267 (1.00) |
Del Peak 46(Xp21 1) | 118 (33%) | 240 |
0.354 (1.00) |
0.148 (1.00) |
2e-05 (0.015) |
0.00181 (1.00) |
0.381 (1.00) |
0.57 (1.00) |
0.0779 (1.00) |
0.00716 (1.00) |
0.407 (1.00) |
0.109 (1.00) |
Del Peak 48(Xq22 3) | 91 (25%) | 267 |
0.00853 (1.00) |
0.105 (1.00) |
1.03e-05 (0.00777) |
0.000861 (0.586) |
0.745 (1.00) |
0.935 (1.00) |
0.0513 (1.00) |
0.485 (1.00) |
0.716 (1.00) |
0.954 (1.00) |
Amp Peak 5(3p11 1) | 73 (20%) | 285 |
0.0748 (1.00) |
0.844 (1.00) |
0.673 (1.00) |
0.826 (1.00) |
0.202 (1.00) |
0.000831 (0.567) |
0.0555 (1.00) |
0.444 (1.00) |
0.41 (1.00) |
0.947 (1.00) |
Amp Peak 7(4q12) | 85 (24%) | 273 |
0.679 (1.00) |
0.759 (1.00) |
0.00548 (1.00) |
0.284 (1.00) |
0.312 (1.00) |
0.0883 (1.00) |
0.555 (1.00) |
0.75 (1.00) |
0.185 (1.00) |
0.577 (1.00) |
Amp Peak 10(6q12) | 107 (30%) | 251 |
1 (1.00) |
0.873 (1.00) |
0.069 (1.00) |
0.26 (1.00) |
0.349 (1.00) |
0.496 (1.00) |
0.395 (1.00) |
0.236 (1.00) |
0.595 (1.00) |
0.155 (1.00) |
Amp Peak 11(7p11 2) | 174 (49%) | 184 |
0.186 (1.00) |
0.0939 (1.00) |
0.00168 (1.00) |
0.00254 (1.00) |
0.642 (1.00) |
0.85 (1.00) |
0.076 (1.00) |
0.0148 (1.00) |
0.7 (1.00) |
0.123 (1.00) |
Amp Peak 13(8p11 23) | 168 (47%) | 190 |
0.00812 (1.00) |
0.168 (1.00) |
0.113 (1.00) |
0.1 (1.00) |
0.217 (1.00) |
0.0871 (1.00) |
0.00631 (1.00) |
0.72 (1.00) |
0.135 (1.00) |
0.62 (1.00) |
Amp Peak 14(8q24 21) | 248 (69%) | 110 |
0.871 (1.00) |
0.644 (1.00) |
0.339 (1.00) |
0.589 (1.00) |
0.958 (1.00) |
0.768 (1.00) |
0.734 (1.00) |
0.428 (1.00) |
0.491 (1.00) |
0.932 (1.00) |
Amp Peak 15(9p24 1) | 67 (19%) | 291 |
0.375 (1.00) |
0.0295 (1.00) |
0.000586 (0.405) |
0.228 (1.00) |
0.00176 (1.00) |
0.00573 (1.00) |
0.0413 (1.00) |
0.00294 (1.00) |
0.561 (1.00) |
0.39 (1.00) |
Amp Peak 16(9p13 3) | 98 (27%) | 260 |
0.17 (1.00) |
0.373 (1.00) |
0.0107 (1.00) |
0.388 (1.00) |
0.0779 (1.00) |
0.00937 (1.00) |
0.022 (1.00) |
0.188 (1.00) |
0.408 (1.00) |
0.889 (1.00) |
Amp Peak 17(11q13 3) | 131 (37%) | 227 |
0.0697 (1.00) |
0.0306 (1.00) |
0.0256 (1.00) |
0.00148 (0.992) |
0.184 (1.00) |
0.0641 (1.00) |
0.0125 (1.00) |
0.139 (1.00) |
0.15 (1.00) |
0.33 (1.00) |
Amp Peak 19(12q15) | 132 (37%) | 226 |
0.312 (1.00) |
0.527 (1.00) |
0.00874 (1.00) |
0.0105 (1.00) |
0.806 (1.00) |
0.409 (1.00) |
0.105 (1.00) |
0.0491 (1.00) |
0.565 (1.00) |
0.926 (1.00) |
Amp Peak 20(13q34) | 64 (18%) | 294 |
0.964 (1.00) |
0.0489 (1.00) |
0.396 (1.00) |
0.166 (1.00) |
0.824 (1.00) |
0.196 (1.00) |
0.803 (1.00) |
0.407 (1.00) |
0.0724 (1.00) |
0.251 (1.00) |
Amp Peak 21(14q13 3) | 110 (31%) | 248 |
0.345 (1.00) |
0.246 (1.00) |
0.528 (1.00) |
0.47 (1.00) |
0.509 (1.00) |
0.0202 (1.00) |
0.617 (1.00) |
0.0847 (1.00) |
0.0167 (1.00) |
0.081 (1.00) |
Amp Peak 27(19q13 2) | 157 (44%) | 201 |
0.473 (1.00) |
0.909 (1.00) |
0.000447 (0.313) |
0.25 (1.00) |
0.318 (1.00) |
0.131 (1.00) |
0.454 (1.00) |
0.0336 (1.00) |
0.975 (1.00) |
0.286 (1.00) |
Amp Peak 29(20q11 21) | 206 (58%) | 152 |
0.991 (1.00) |
0.844 (1.00) |
0.00275 (1.00) |
0.0388 (1.00) |
0.743 (1.00) |
0.697 (1.00) |
0.593 (1.00) |
0.549 (1.00) |
0.937 (1.00) |
0.615 (1.00) |
Amp Peak 30(22q11 21) | 177 (49%) | 181 |
0.111 (1.00) |
0.123 (1.00) |
0.0146 (1.00) |
0.00291 (1.00) |
0.874 (1.00) |
0.339 (1.00) |
0.0671 (1.00) |
0.0677 (1.00) |
0.816 (1.00) |
0.132 (1.00) |
Amp Peak 31(Xq28) | 92 (26%) | 266 |
0.644 (1.00) |
0.515 (1.00) |
0.24 (1.00) |
0.0981 (1.00) |
0.0546 (1.00) |
0.0722 (1.00) |
0.143 (1.00) |
0.225 (1.00) |
0.754 (1.00) |
0.804 (1.00) |
Del Peak 3(2p25 3) | 34 (9%) | 324 |
0.0461 (1.00) |
0.179 (1.00) |
0.0899 (1.00) |
0.367 (1.00) |
0.11 (1.00) |
0.789 (1.00) |
0.32 (1.00) |
0.226 (1.00) |
0.105 (1.00) |
0.0641 (1.00) |
Del Peak 6(3p25 3) | 285 (80%) | 73 |
0.54 (1.00) |
0.176 (1.00) |
0.0292 (1.00) |
0.00407 (1.00) |
0.624 (1.00) |
0.212 (1.00) |
0.327 (1.00) |
0.00876 (1.00) |
0.655 (1.00) |
0.0137 (1.00) |
Del Peak 10(4q22 1) | 199 (56%) | 159 |
0.00685 (1.00) |
0.0579 (1.00) |
0.000473 (0.33) |
0.0405 (1.00) |
0.147 (1.00) |
0.346 (1.00) |
0.0252 (1.00) |
0.00636 (1.00) |
0.37 (1.00) |
0.134 (1.00) |
Del Peak 15(6p25 3) | 90 (25%) | 268 |
0.22 (1.00) |
0.11 (1.00) |
0.0169 (1.00) |
0.000692 (0.475) |
0.542 (1.00) |
0.00967 (1.00) |
0.01 (1.00) |
0.0204 (1.00) |
0.238 (1.00) |
0.179 (1.00) |
Del Peak 16(6q26) | 93 (26%) | 265 |
0.0659 (1.00) |
0.00298 (1.00) |
0.00901 (1.00) |
0.00168 (1.00) |
0.885 (1.00) |
0.866 (1.00) |
0.0687 (1.00) |
0.141 (1.00) |
0.226 (1.00) |
0.108 (1.00) |
Del Peak 17(7q11 22) | 35 (10%) | 323 |
0.908 (1.00) |
0.405 (1.00) |
0.000385 (0.271) |
0.394 (1.00) |
0.958 (1.00) |
0.8 (1.00) |
0.0463 (1.00) |
0.0644 (1.00) |
0.804 (1.00) |
0.526 (1.00) |
Del Peak 18(7q36 1) | 73 (20%) | 285 |
0.393 (1.00) |
0.569 (1.00) |
0.0143 (1.00) |
0.381 (1.00) |
1 (1.00) |
0.286 (1.00) |
0.115 (1.00) |
0.388 (1.00) |
0.361 (1.00) |
0.828 (1.00) |
Del Peak 19(8p23 2) | 243 (68%) | 115 |
0.864 (1.00) |
0.459 (1.00) |
0.00493 (1.00) |
0.295 (1.00) |
0.382 (1.00) |
0.196 (1.00) |
0.157 (1.00) |
0.072 (1.00) |
0.451 (1.00) |
0.167 (1.00) |
Del Peak 23(10p15 3) | 160 (45%) | 198 |
0.373 (1.00) |
0.442 (1.00) |
0.0015 (1.00) |
0.000931 (0.633) |
0.407 (1.00) |
0.391 (1.00) |
0.00383 (1.00) |
0.0165 (1.00) |
0.104 (1.00) |
0.00185 (1.00) |
Del Peak 26(11q22 1) | 108 (30%) | 250 |
0.493 (1.00) |
0.288 (1.00) |
0.00281 (1.00) |
0.0775 (1.00) |
0.0868 (1.00) |
0.975 (1.00) |
0.245 (1.00) |
0.423 (1.00) |
0.278 (1.00) |
0.0526 (1.00) |
Del Peak 27(11q25) | 131 (37%) | 227 |
0.798 (1.00) |
0.429 (1.00) |
0.0229 (1.00) |
0.381 (1.00) |
0.109 (1.00) |
0.867 (1.00) |
0.447 (1.00) |
0.406 (1.00) |
0.185 (1.00) |
0.171 (1.00) |
Del Peak 28(12q24 31) | 57 (16%) | 301 |
0.965 (1.00) |
0.332 (1.00) |
0.598 (1.00) |
0.303 (1.00) |
0.359 (1.00) |
0.203 (1.00) |
0.9 (1.00) |
0.689 (1.00) |
0.118 (1.00) |
0.302 (1.00) |
Del Peak 29(13q12 11) | 240 (67%) | 118 |
0.0547 (1.00) |
0.611 (1.00) |
0.0338 (1.00) |
0.156 (1.00) |
1 (1.00) |
0.193 (1.00) |
0.7 (1.00) |
0.214 (1.00) |
0.958 (1.00) |
0.987 (1.00) |
Del Peak 30(13q14 2) | 251 (70%) | 107 |
0.0512 (1.00) |
0.0962 (1.00) |
0.00073 (0.501) |
0.129 (1.00) |
0.85 (1.00) |
0.547 (1.00) |
0.0281 (1.00) |
0.147 (1.00) |
0.654 (1.00) |
0.543 (1.00) |
Del Peak 31(14q11 2) | 130 (36%) | 228 |
0.0546 (1.00) |
0.293 (1.00) |
0.0383 (1.00) |
0.321 (1.00) |
0.243 (1.00) |
0.152 (1.00) |
0.00265 (1.00) |
0.00213 (1.00) |
0.333 (1.00) |
0.172 (1.00) |
Del Peak 32(15q12) | 122 (34%) | 236 |
0.725 (1.00) |
0.228 (1.00) |
0.334 (1.00) |
0.317 (1.00) |
0.0697 (1.00) |
0.00674 (1.00) |
0.132 (1.00) |
0.356 (1.00) |
0.0996 (1.00) |
0.738 (1.00) |
Del Peak 33(16p13 3) | 129 (36%) | 229 |
0.239 (1.00) |
0.245 (1.00) |
0.00318 (1.00) |
0.362 (1.00) |
0.135 (1.00) |
0.496 (1.00) |
0.531 (1.00) |
0.247 (1.00) |
0.643 (1.00) |
0.164 (1.00) |
Del Peak 34(16q23 1) | 144 (40%) | 214 |
0.942 (1.00) |
0.659 (1.00) |
0.0506 (1.00) |
0.312 (1.00) |
0.336 (1.00) |
0.861 (1.00) |
0.205 (1.00) |
0.0264 (1.00) |
0.441 (1.00) |
0.581 (1.00) |
Del Peak 35(17p11 2) | 185 (52%) | 173 |
0.194 (1.00) |
0.401 (1.00) |
0.004 (1.00) |
0.136 (1.00) |
0.135 (1.00) |
0.0101 (1.00) |
0.368 (1.00) |
0.86 (1.00) |
0.0697 (1.00) |
0.022 (1.00) |
Del Peak 37(17q25 3) | 68 (19%) | 290 |
0.00493 (1.00) |
0.022 (1.00) |
0.000468 (0.327) |
0.0796 (1.00) |
0.782 (1.00) |
0.972 (1.00) |
0.0423 (1.00) |
0.000553 (0.384) |
0.581 (1.00) |
0.0108 (1.00) |
Del Peak 38(18q23) | 164 (46%) | 194 |
0.508 (1.00) |
0.788 (1.00) |
0.517 (1.00) |
0.97 (1.00) |
0.858 (1.00) |
0.325 (1.00) |
0.23 (1.00) |
0.115 (1.00) |
0.804 (1.00) |
0.536 (1.00) |
Del Peak 42(21q11 2) | 176 (49%) | 182 |
0.558 (1.00) |
0.223 (1.00) |
0.0058 (1.00) |
0.0647 (1.00) |
0.966 (1.00) |
0.904 (1.00) |
0.908 (1.00) |
0.485 (1.00) |
0.203 (1.00) |
0.233 (1.00) |
Del Peak 44(22q11 21) | 62 (17%) | 296 |
0.0904 (1.00) |
0.0093 (1.00) |
0.172 (1.00) |
0.342 (1.00) |
0.125 (1.00) |
0.114 (1.00) |
0.598 (1.00) |
0.748 (1.00) |
0.149 (1.00) |
0.101 (1.00) |
P value = 0.000273 (Fisher's exact test), Q value = 0.19
Table S1. Gene #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 1(1P34.2) MUTATED | 17 | 9 | 32 |
AMP PEAK 1(1P34.2) WILD-TYPE | 112 | 103 | 85 |
Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 7.32e-07 (Fisher's exact test), Q value = 0.00056
Table S2. Gene #2: 'Amp Peak 2(1q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 2(1Q21.2) MUTATED | 52 | 81 | 53 |
AMP PEAK 2(1Q21.2) WILD-TYPE | 77 | 31 | 64 |
Figure S2. 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 = 0.22
Table S3. 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 S3. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 2.41e-09 (Fisher's exact test), Q value = 1.9e-06
Table S4. Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 3(2P16.1) MUTATED | 48 | 86 | 60 |
AMP PEAK 3(2P16.1) WILD-TYPE | 81 | 26 | 57 |
Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.051
Table S5. Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
AMP PEAK 3(2P16.1) MUTATED | 41 | 56 | 25 |
AMP PEAK 3(2P16.1) WILD-TYPE | 49 | 19 | 34 |
Figure S5. 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 = 0.23
Table S6. 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 S6. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 6.74e-05 (Fisher's exact test), Q value = 0.049
Table S7. Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 4(2Q31.2) MUTATED | 29 | 55 | 37 |
AMP PEAK 4(2Q31.2) WILD-TYPE | 100 | 57 | 80 |
Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 4.94e-06 (Fisher's exact test), Q value = 0.0038
Table S8. Gene #4: 'Amp Peak 4(2q31.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
AMP PEAK 4(2Q31.2) MUTATED | 26 | 42 | 10 |
AMP PEAK 4(2Q31.2) WILD-TYPE | 64 | 33 | 49 |
Figure S8. 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 = 0.013
Table S9. 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 S9. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

P value = 1.63e-09 (Fisher's exact test), Q value = 1.3e-06
Table S10. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 6(3Q26.33) MUTATED | 104 | 112 | 114 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 25 | 0 | 3 |
Figure S10. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.082
Table S11. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
AMP PEAK 6(3Q26.33) MUTATED | 76 | 75 | 57 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 14 | 0 | 2 |
Figure S11. 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 = 0.028
Table S12. 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 S12. 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 S13. 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 S13. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 9.11e-05 (Fisher's exact test), Q value = 0.066
Table S14. Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 173 | 108 |
AMP PEAK 6(3Q26.33) MUTATED | 50 | 150 | 106 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 0 | 23 | 2 |
Figure S14. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

P value = 8.38e-06 (Fisher's exact test), Q value = 0.0063
Table S15. Gene #8: 'Amp Peak 8(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 8(5P15.33) MUTATED | 89 | 84 | 108 |
AMP PEAK 8(5P15.33) WILD-TYPE | 40 | 28 | 9 |
Figure S15. Get High-res Image Gene #8: 'Amp Peak 8(5p15.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.38e-09 (Fisher's exact test), Q value = 1.1e-06
Table S16. Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 9(5P12) MUTATED | 63 | 72 | 101 |
AMP PEAK 9(5P12) WILD-TYPE | 66 | 40 | 16 |
Figure S16. Get High-res Image Gene #9: 'Amp Peak 9(5p12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 3.36e-10 (Fisher's exact test), Q value = 2.6e-07
Table S17. Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 12(7Q21.2) MUTATED | 44 | 85 | 59 |
AMP PEAK 12(7Q21.2) WILD-TYPE | 85 | 27 | 58 |
Figure S17. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 8.35e-06 (Fisher's exact test), Q value = 0.0063
Table S18. Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
AMP PEAK 12(7Q21.2) MUTATED | 32 | 54 | 26 |
AMP PEAK 12(7Q21.2) WILD-TYPE | 58 | 21 | 33 |
Figure S18. Get High-res Image Gene #12: 'Amp Peak 12(7q21.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.18
Table S19. Gene #18: 'Amp Peak 18(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 18(12P13.33) MUTATED | 48 | 71 | 58 |
AMP PEAK 18(12P13.33) WILD-TYPE | 81 | 41 | 59 |
Figure S19. Get High-res Image Gene #18: 'Amp Peak 18(12p13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 5.63e-07 (Fisher's exact test), Q value = 0.00043
Table S20. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 22(15Q26.3) MUTATED | 25 | 58 | 45 |
AMP PEAK 22(15Q26.3) WILD-TYPE | 104 | 54 | 72 |
Figure S20. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.78e-05 (Fisher's exact test), Q value = 0.013
Table S21. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
AMP PEAK 22(15Q26.3) MUTATED | 15 | 37 | 24 |
AMP PEAK 22(15Q26.3) WILD-TYPE | 75 | 38 | 35 |
Figure S21. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 7.14e-05 (Fisher's exact test), Q value = 0.052
Table S22. Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 173 | 108 |
AMP PEAK 22(15Q26.3) MUTATED | 28 | 46 | 49 |
AMP PEAK 22(15Q26.3) WILD-TYPE | 22 | 127 | 59 |
Figure S22. Get High-res Image Gene #22: 'Amp Peak 22(15q26.3) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.87e-06 (Fisher's exact test), Q value = 0.0014
Table S23. Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 23(17Q25.1) MUTATED | 40 | 71 | 60 |
AMP PEAK 23(17Q25.1) WILD-TYPE | 89 | 41 | 57 |
Figure S23. Get High-res Image Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.11
Table S24. Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
AMP PEAK 23(17Q25.1) MUTATED | 35 | 49 | 19 |
AMP PEAK 23(17Q25.1) WILD-TYPE | 55 | 26 | 40 |
Figure S24. Get High-res Image Gene #23: 'Amp Peak 23(17q25.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 0.000148 (Fisher's exact test), Q value = 0.11
Table S25. Gene #24: 'Amp Peak 24(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 24(18P11.32) MUTATED | 29 | 54 | 39 |
AMP PEAK 24(18P11.32) WILD-TYPE | 100 | 58 | 78 |
Figure S25. Get High-res Image Gene #24: 'Amp Peak 24(18p11.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000231 (Fisher's exact test), Q value = 0.16
Table S26. Gene #25: 'Amp Peak 25(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 25(18Q11.2) MUTATED | 26 | 50 | 39 |
AMP PEAK 25(18Q11.2) WILD-TYPE | 103 | 62 | 78 |
Figure S26. Get High-res Image Gene #25: 'Amp Peak 25(18q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000111 (Fisher's exact test), Q value = 0.08
Table S27. Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 26(19Q12) MUTATED | 42 | 65 | 42 |
AMP PEAK 26(19Q12) WILD-TYPE | 87 | 47 | 75 |
Figure S27. Get High-res Image Gene #26: 'Amp Peak 26(19q12) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 4.62e-08 (Fisher's exact test), Q value = 3.6e-05
Table S28. Gene #28: 'Amp Peak 28(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
AMP PEAK 28(20P12.2) MUTATED | 48 | 83 | 62 |
AMP PEAK 28(20P12.2) WILD-TYPE | 81 | 29 | 55 |
Figure S28. Get High-res Image Gene #28: 'Amp Peak 28(20p12.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.00098
Table S29. Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 1(1P36.32) MUTATED | 9 | 37 | 12 | 10 |
DEL PEAK 1(1P36.32) WILD-TYPE | 34 | 13 | 18 | 21 |
Figure S29. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 1.29e-08 (Fisher's exact test), Q value = 1e-05
Table S30. Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 1(1P36.32) MUTATED | 10 | 41 | 17 |
DEL PEAK 1(1P36.32) WILD-TYPE | 18 | 13 | 55 |
Figure S30. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

P value = 3.34e-28 (Fisher's exact test), Q value = 2.6e-25
Table S31. Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 1(1P36.32) MUTATED | 33 | 96 | 26 |
DEL PEAK 1(1P36.32) WILD-TYPE | 96 | 16 | 91 |
Figure S31. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 4.78e-16 (Fisher's exact test), Q value = 3.8e-13
Table S32. Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
DEL PEAK 1(1P36.32) MUTATED | 15 | 59 | 19 |
DEL PEAK 1(1P36.32) WILD-TYPE | 75 | 16 | 40 |
Figure S32. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 1.02e-10 (Fisher's exact test), Q value = 8e-08
Table S33. Gene #32: 'Del Peak 1(1p36.32) 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(1P36.32) MUTATED | 16 | 61 | 26 | 11 |
DEL PEAK 1(1P36.32) WILD-TYPE | 44 | 19 | 53 | 27 |
Figure S33. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 6.75e-09 (Fisher's exact test), Q value = 5.3e-06
Table S34. Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 86 | 55 |
DEL PEAK 1(1P36.32) MUTATED | 37 | 61 | 16 |
DEL PEAK 1(1P36.32) WILD-TYPE | 79 | 25 | 39 |
Figure S34. Get High-res Image Gene #32: 'Del Peak 1(1p36.32) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000237 (Fisher's exact test), Q value = 0.17
Table S35. Gene #33: '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 S35. Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 6.47e-14 (Fisher's exact test), Q value = 5.1e-11
Table S36. Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 2(1P13.2) MUTATED | 34 | 82 | 40 |
DEL PEAK 2(1P13.2) WILD-TYPE | 95 | 30 | 77 |
Figure S36. Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 6.52e-09 (Fisher's exact test), Q value = 5.1e-06
Table S37. Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
DEL PEAK 2(1P13.2) MUTATED | 19 | 51 | 24 |
DEL PEAK 2(1P13.2) WILD-TYPE | 71 | 24 | 35 |
Figure S37. Get High-res Image Gene #33: '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 S38. Gene #33: '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 S38. Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 7.07e-05 (Fisher's exact test), Q value = 0.052
Table S39. Gene #33: '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 S39. Get High-res Image Gene #33: 'Del Peak 2(1p13.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000217 (Fisher's exact test), Q value = 0.15
Table S40. Gene #35: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 4(2Q22.1) MUTATED | 19 | 41 | 36 |
DEL PEAK 4(2Q22.1) WILD-TYPE | 110 | 71 | 81 |
Figure S40. Get High-res Image Gene #35: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.17
Table S41. Gene #36: '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 S41. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.035
Table S42. Gene #36: '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 S42. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

P value = 5.32e-12 (Fisher's exact test), Q value = 4.2e-09
Table S43. Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 5(2Q36.2) MUTATED | 20 | 65 | 31 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 109 | 47 | 86 |
Figure S43. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.25
Table S44. Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
DEL PEAK 5(2Q36.2) MUTATED | 19 | 38 | 19 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 71 | 37 | 40 |
Figure S44. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 8.49e-05 (Fisher's exact test), Q value = 0.062
Table S45. Gene #36: '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 S45. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 6.15e-06 (Fisher's exact test), Q value = 0.0047
Table S46. Gene #36: '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 S46. Get High-res Image Gene #36: 'Del Peak 5(2q36.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 9.68e-05 (Fisher's exact test), Q value = 0.07
Table S47. Gene #38: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 7(3P13) MUTATED | 98 | 104 | 108 |
DEL PEAK 7(3P13) WILD-TYPE | 31 | 8 | 9 |
Figure S47. Get High-res Image Gene #38: 'Del Peak 7(3p13) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.46e-07 (Fisher's exact test), Q value = 0.00011
Table S48. Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 8(3P12.1) MUTATED | 80 | 101 | 99 |
DEL PEAK 8(3P12.1) WILD-TYPE | 49 | 11 | 18 |
Figure S48. Get High-res Image Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.021
Table S49. Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
DEL PEAK 8(3P12.1) MUTATED | 59 | 66 | 55 |
DEL PEAK 8(3P12.1) WILD-TYPE | 31 | 9 | 4 |
Figure S49. Get High-res Image Gene #39: 'Del Peak 8(3p12.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.0091
Table S50. Gene #40: 'Del Peak 9(4p15.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 9(4P15.31) MUTATED | 65 | 88 | 66 |
DEL PEAK 9(4P15.31) WILD-TYPE | 64 | 24 | 51 |
Figure S50. Get High-res Image Gene #40: 'Del Peak 9(4p15.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2.97e-07 (Fisher's exact test), Q value = 0.00023
Table S51. Gene #42: 'Del Peak 11(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 11(4Q32.3) MUTATED | 67 | 93 | 66 |
DEL PEAK 11(4Q32.3) WILD-TYPE | 62 | 19 | 51 |
Figure S51. Get High-res Image Gene #42: 'Del Peak 11(4q32.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00082
Table S52. Gene #43: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 12(4Q35.2) MUTATED | 70 | 93 | 66 |
DEL PEAK 12(4Q35.2) WILD-TYPE | 59 | 19 | 51 |
Figure S52. Get High-res Image Gene #43: 'Del Peak 12(4q35.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 5.71e-10 (Fisher's exact test), Q value = 4.5e-07
Table S53. Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 13(5Q11.2) MUTATED | 69 | 96 | 100 |
DEL PEAK 13(5Q11.2) WILD-TYPE | 60 | 16 | 17 |
Figure S53. Get High-res Image Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000266 (Fisher's exact test), Q value = 0.19
Table S54. Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
DEL PEAK 13(5Q11.2) MUTATED | 54 | 62 | 51 |
DEL PEAK 13(5Q11.2) WILD-TYPE | 36 | 13 | 8 |
Figure S54. Get High-res Image Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 0.000162 (Fisher's exact test), Q value = 0.12
Table S55. Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 173 | 108 |
DEL PEAK 13(5Q11.2) MUTATED | 39 | 115 | 95 |
DEL PEAK 13(5Q11.2) WILD-TYPE | 11 | 58 | 13 |
Figure S55. Get High-res Image Gene #44: 'Del Peak 13(5q11.2) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

P value = 6.21e-07 (Fisher's exact test), Q value = 0.00048
Table S56. Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 14(5Q31.1) MUTATED | 79 | 97 | 101 |
DEL PEAK 14(5Q31.1) WILD-TYPE | 50 | 15 | 16 |
Figure S56. Get High-res Image Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 3.25e-05 (Fisher's exact test), Q value = 0.024
Table S57. Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
DEL PEAK 14(5Q31.1) MUTATED | 58 | 64 | 55 |
DEL PEAK 14(5Q31.1) WILD-TYPE | 32 | 11 | 4 |
Figure S57. Get High-res Image Gene #45: 'Del Peak 14(5q31.1) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 1.21e-07 (Fisher's exact test), Q value = 9.4e-05
Table S58. Gene #51: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 20(9P23) MUTATED | 68 | 67 | 99 |
DEL PEAK 20(9P23) WILD-TYPE | 61 | 45 | 18 |
Figure S58. Get High-res Image Gene #51: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 3.23e-06 (Fisher's exact test), Q value = 0.0025
Table S59. Gene #52: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 21(9P21.3) MUTATED | 81 | 86 | 105 |
DEL PEAK 21(9P21.3) WILD-TYPE | 48 | 26 | 12 |
Figure S59. Get High-res Image Gene #52: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.13
Table S60. Gene #53: 'Del Peak 22(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 22(9Q21.11) MUTATED | 28 | 12 | 19 | 15 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 15 | 38 | 11 | 16 |
Figure S60. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 4.92e-05 (Fisher's exact test), Q value = 0.036
Table S61. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 22(9Q21.11) MUTATED | 16 | 13 | 45 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 12 | 41 | 27 |
Figure S61. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

P value = 2.03e-07 (Fisher's exact test), Q value = 0.00016
Table S62. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 22(9Q21.11) MUTATED | 62 | 34 | 78 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 67 | 78 | 39 |
Figure S62. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.42e-06 (Fisher's exact test), Q value = 0.0011
Table S63. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
DEL PEAK 22(9Q21.11) MUTATED | 49 | 19 | 40 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 41 | 56 | 19 |
Figure S63. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 4.44e-06 (Fisher's exact test), Q value = 0.0034
Table S64. Gene #53: 'Del Peak 22(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 22(9Q21.11) MUTATED | 33 | 19 | 48 | 22 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 27 | 61 | 31 | 16 |
Figure S64. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 2.4e-07 (Fisher's exact test), Q value = 0.00018
Table S65. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 86 | 55 |
DEL PEAK 22(9Q21.11) MUTATED | 64 | 21 | 37 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 52 | 65 | 18 |
Figure S65. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 3.16e-05 (Fisher's exact test), Q value = 0.023
Table S66. Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 173 | 108 |
DEL PEAK 22(9Q21.11) MUTATED | 10 | 90 | 61 |
DEL PEAK 22(9Q21.11) WILD-TYPE | 40 | 83 | 47 |
Figure S66. Get High-res Image Gene #53: 'Del Peak 22(9q21.11) mutation analysis' versus Clinical Feature #10: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.14
Table S67. Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 24(10Q23.31) MUTATED | 53 | 75 | 56 |
DEL PEAK 24(10Q23.31) WILD-TYPE | 76 | 37 | 61 |
Figure S67. Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 6.42e-05 (Fisher's exact test), Q value = 0.047
Table S68. Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
DEL PEAK 24(10Q23.31) MUTATED | 33 | 53 | 30 |
DEL PEAK 24(10Q23.31) WILD-TYPE | 57 | 22 | 29 |
Figure S68. Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.075
Table S69. Gene #55: 'Del Peak 24(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 24(10Q23.31) MUTATED | 22 | 57 | 35 | 16 |
DEL PEAK 24(10Q23.31) WILD-TYPE | 38 | 23 | 44 | 22 |
Figure S69. Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.02
Table S70. Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 86 | 55 |
DEL PEAK 24(10Q23.31) MUTATED | 42 | 59 | 29 |
DEL PEAK 24(10Q23.31) WILD-TYPE | 74 | 27 | 26 |
Figure S70. Get High-res Image Gene #55: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 6.04e-05 (Fisher's exact test), Q value = 0.044
Table S71. Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 25(11P15.5) MUTATED | 47 | 51 | 75 |
DEL PEAK 25(11P15.5) WILD-TYPE | 82 | 61 | 42 |
Figure S71. Get High-res Image Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2.34e-05 (Fisher's exact test), Q value = 0.017
Table S72. Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 47 | 48 | 58 | 41 |
DEL PEAK 25(11P15.5) MUTATED | 35 | 17 | 29 | 11 |
DEL PEAK 25(11P15.5) WILD-TYPE | 12 | 31 | 29 | 30 |
Figure S72. Get High-res Image Gene #56: 'Del Peak 25(11p15.5) mutation analysis' versus Clinical Feature #6: 'RPPA_CHIERARCHICAL'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0095
Table S73. Gene #67: 'Del Peak 36(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 36(17Q11.2) MUTATED | 21 | 3 | 11 | 7 |
DEL PEAK 36(17Q11.2) WILD-TYPE | 22 | 47 | 19 | 24 |
Figure S73. Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #1: 'MRNA_CNMF'

P value = 6.44e-05 (Fisher's exact test), Q value = 0.047
Table S74. Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 36(17Q11.2) MUTATED | 9 | 4 | 29 |
DEL PEAK 36(17Q11.2) WILD-TYPE | 19 | 50 | 43 |
Figure S74. Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #2: 'MRNA_CHIERARCHICAL'

P value = 9.35e-09 (Fisher's exact test), Q value = 7.3e-06
Table S75. Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 36(17Q11.2) MUTATED | 34 | 8 | 47 |
DEL PEAK 36(17Q11.2) WILD-TYPE | 95 | 104 | 70 |
Figure S75. Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.088
Table S76. Gene #67: 'Del Peak 36(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 36(17Q11.2) MUTATED | 20 | 6 | 23 | 13 |
DEL PEAK 36(17Q11.2) WILD-TYPE | 40 | 74 | 56 | 25 |
Figure S76. Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #7: 'MRNASEQ_CNMF'

P value = 7.16e-06 (Fisher's exact test), Q value = 0.0054
Table S77. Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 86 | 55 |
DEL PEAK 36(17Q11.2) MUTATED | 39 | 6 | 17 |
DEL PEAK 36(17Q11.2) WILD-TYPE | 77 | 80 | 38 |
Figure S77. Get High-res Image Gene #67: 'Del Peak 36(17q11.2) mutation analysis' versus Clinical Feature #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000227 (Fisher's exact test), Q value = 0.16
Table S78. Gene #70: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 39(19P13.3) MUTATED | 46 | 46 | 71 |
DEL PEAK 39(19P13.3) WILD-TYPE | 83 | 66 | 46 |
Figure S78. Get High-res Image Gene #70: 'Del Peak 39(19p13.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.035
Table S79. Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 40(19Q13.33) MUTATED | 20 | 46 | 30 |
DEL PEAK 40(19Q13.33) WILD-TYPE | 109 | 66 | 87 |
Figure S79. Get High-res Image Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.18
Table S80. Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
DEL PEAK 40(19Q13.33) MUTATED | 11 | 27 | 21 |
DEL PEAK 40(19Q13.33) WILD-TYPE | 79 | 48 | 38 |
Figure S80. Get High-res Image Gene #71: 'Del Peak 40(19q13.33) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 9.08e-05 (Fisher's exact test), Q value = 0.066
Table S81. Gene #72: 'Del Peak 41(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 41(19Q13.43) MUTATED | 20 | 45 | 31 |
DEL PEAK 41(19Q13.43) WILD-TYPE | 109 | 67 | 86 |
Figure S81. Get High-res Image Gene #72: 'Del Peak 41(19q13.43) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2.21e-08 (Fisher's exact test), Q value = 1.7e-05
Table S82. Gene #74: 'Del Peak 43(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 43(21Q22.3) MUTATED | 48 | 82 | 75 |
DEL PEAK 43(21Q22.3) WILD-TYPE | 81 | 30 | 42 |
Figure S82. Get High-res Image Gene #74: 'Del Peak 43(21q22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 1.57e-05 (Fisher's exact test), Q value = 0.012
Table S83. Gene #76: 'Del Peak 45(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 45(XP22.2) MUTATED | 22 | 48 | 44 |
DEL PEAK 45(XP22.2) WILD-TYPE | 107 | 64 | 73 |
Figure S83. Get High-res Image Gene #76: 'Del Peak 45(Xp22.2) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.015
Table S84. Gene #77: 'Del Peak 46(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 46(XP21.1) MUTATED | 24 | 51 | 43 |
DEL PEAK 46(XP21.1) WILD-TYPE | 105 | 61 | 74 |
Figure S84. Get High-res Image Gene #77: 'Del Peak 46(Xp21.1) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 2.82e-06 (Fisher's exact test), Q value = 0.0021
Table S85. Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 47(XP11.3) MUTATED | 22 | 52 | 42 |
DEL PEAK 47(XP11.3) WILD-TYPE | 107 | 60 | 75 |
Figure S85. Get High-res Image Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

P value = 5.16e-05 (Fisher's exact test), Q value = 0.038
Table S86. Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 90 | 75 | 59 |
DEL PEAK 47(XP11.3) MUTATED | 15 | 36 | 22 |
DEL PEAK 47(XP11.3) WILD-TYPE | 75 | 39 | 37 |
Figure S86. Get High-res Image Gene #78: 'Del Peak 47(Xp11.3) mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

P value = 1.03e-05 (Fisher's exact test), Q value = 0.0078
Table S87. Gene #79: 'Del Peak 48(Xq22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 129 | 112 | 117 |
DEL PEAK 48(XQ22.3) MUTATED | 16 | 30 | 45 |
DEL PEAK 48(XQ22.3) WILD-TYPE | 113 | 82 | 72 |
Figure S87. Get High-res Image Gene #79: 'Del Peak 48(Xq22.3) mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

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Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
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Molecular subtype file = LUSC-TP.transferedmergedcluster.txt
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Number of patients = 358
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Number of copy number variation regions = 79
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Number of molecular subtypes = 10
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Exclude regions that fewer than K tumors have alterations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For 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.