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, 117 significant findings detected with Q value < 0.25.
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Amp Peak 2(1q21.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Amp Peak 3(2p16.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Amp Peak 4(2q31.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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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', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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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', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Amp Peak 24(17q25.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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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', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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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', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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'.
-
Del Peak 8(3p12.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 10(4p15.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_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', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 14(5q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 15(5q31.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 16(6p25.3) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 17(6q22.31) cnvs correlated to 'MRNASEQ_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', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 26(10p15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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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 34(14q11.2) cnvs correlated to 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 40(17q11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Del Peak 43(19p13.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_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, 117 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 1(1p36 22) | 0 (0%) | 225 |
1.43e-06 (0.00115) |
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) |
8.67e-14 (7.25e-11) |
9.45e-15 (7.92e-12) |
0.000838 (0.586) |
1.83e-05 (0.0143) |
Del Peak 24(9q21 11) | 0 (0%) | 206 |
0.000177 (0.132) |
4.92e-05 (0.0376) |
5.97e-11 (4.96e-08) |
1.14e-06 (0.000923) |
0.653 (1.00) |
0.239 (1.00) |
4.4e-09 (3.64e-06) |
1.63e-09 (1.35e-06) |
0.000958 (0.664) |
0.000184 (0.137) |
Amp Peak 6(3q26 33) | 0 (0%) | 33 |
0.000427 (0.306) |
1.71e-05 (0.0134) |
7.05e-12 (5.86e-09) |
6.69e-07 (0.000541) |
0.193 (1.00) |
0.0776 (1.00) |
1.26e-06 (0.00101) |
5.04e-05 (0.0384) |
0.148 (1.00) |
3.07e-06 (0.00245) |
Del Peak 5(2q36 2) | 0 (0%) | 265 |
0.000236 (0.174) |
4.76e-05 (0.0364) |
1.7e-12 (1.41e-09) |
2.14e-06 (0.00172) |
0.177 (1.00) |
0.126 (1.00) |
6.61e-07 (0.000535) |
2.98e-08 (2.45e-05) |
0.885 (1.00) |
0.163 (1.00) |
Amp Peak 3(2p16 1) | 0 (0%) | 181 |
0.000305 (0.222) |
0.00165 (1.00) |
3.18e-13 (2.66e-10) |
5.83e-05 (0.0443) |
0.95 (1.00) |
0.643 (1.00) |
1.88e-05 (0.0146) |
7.55e-05 (0.0573) |
0.887 (1.00) |
0.0171 (1.00) |
Del Peak 2(1p13 2) | 0 (0%) | 225 |
0.000237 (0.175) |
0.00055 (0.391) |
1.23e-15 (1.03e-12) |
5.74e-09 (4.73e-06) |
0.119 (1.00) |
0.0712 (1.00) |
5.56e-07 (0.000451) |
1.96e-07 (0.00016) |
0.127 (1.00) |
0.000788 (0.553) |
Del Peak 40(17q11 2) | 0 (0%) | 301 |
1.26e-05 (0.00991) |
6.44e-05 (0.049) |
3.04e-08 (2.5e-05) |
0.0177 (1.00) |
0.495 (1.00) |
0.378 (1.00) |
1.48e-06 (0.00119) |
4.83e-08 (3.95e-05) |
0.143 (1.00) |
0.0373 (1.00) |
Amp Peak 4(2q31 2) | 0 (0%) | 265 |
0.0207 (1.00) |
0.000948 (0.659) |
6.52e-06 (0.00517) |
1.99e-07 (0.000162) |
0.724 (1.00) |
0.887 (1.00) |
0.000194 (0.144) |
0.000248 (0.182) |
0.37 (1.00) |
0.511 (1.00) |
Del Peak 26(10p15 1) | 0 (0%) | 229 |
0.0722 (1.00) |
0.484 (1.00) |
0.000162 (0.121) |
4.03e-06 (0.00321) |
0.469 (1.00) |
0.353 (1.00) |
0.000161 (0.121) |
0.00143 (0.974) |
0.0107 (1.00) |
9.09e-06 (0.00719) |
Del Peak 27(10q23 31) | 0 (0%) | 194 |
0.0392 (1.00) |
0.00386 (1.00) |
2.17e-05 (0.0168) |
2.08e-06 (0.00167) |
0.36 (1.00) |
0.39 (1.00) |
8.54e-06 (0.00677) |
7.23e-07 (0.000584) |
0.219 (1.00) |
0.0644 (1.00) |
Amp Peak 2(1q21 2) | 0 (0%) | 192 |
0.0419 (1.00) |
0.00618 (1.00) |
1.98e-07 (0.000162) |
0.00113 (0.777) |
0.16 (1.00) |
0.0492 (1.00) |
1.87e-05 (0.0146) |
4.11e-05 (0.0316) |
0.0393 (1.00) |
0.00181 (1.00) |
Amp Peak 13(7q21 2) | 0 (0%) | 188 |
0.101 (1.00) |
0.25 (1.00) |
5.34e-10 (4.43e-07) |
1.27e-05 (0.00999) |
0.0573 (1.00) |
0.389 (1.00) |
0.000661 (0.468) |
0.000185 (0.138) |
0.0358 (1.00) |
0.0527 (1.00) |
Amp Peak 23(15q26 3) | 0 (0%) | 258 |
0.151 (1.00) |
0.021 (1.00) |
1.56e-05 (0.0122) |
9.39e-06 (0.00741) |
0.354 (1.00) |
0.0183 (1.00) |
0.000334 (0.242) |
0.00253 (1.00) |
0.0159 (1.00) |
0.00123 (0.838) |
Amp Peak 24(17q25 1) | 0 (0%) | 206 |
0.0177 (1.00) |
0.0608 (1.00) |
6.01e-07 (0.000487) |
2.17e-05 (0.0168) |
0.267 (1.00) |
0.292 (1.00) |
0.0039 (1.00) |
0.000165 (0.123) |
0.796 (1.00) |
0.0783 (1.00) |
Amp Peak 26(18q11 2) | 0 (0%) | 271 |
0.000456 (0.327) |
0.00227 (1.00) |
1.37e-05 (0.0107) |
0.000342 (0.248) |
0.272 (1.00) |
0.74 (1.00) |
0.000841 (0.587) |
5.04e-06 (0.00401) |
0.402 (1.00) |
0.00539 (1.00) |
Del Peak 13(4q35 2) | 0 (0%) | 144 |
0.1 (1.00) |
0.206 (1.00) |
2.84e-06 (0.00227) |
0.000124 (0.0933) |
0.455 (1.00) |
0.47 (1.00) |
0.000143 (0.108) |
0.0105 (1.00) |
0.44 (1.00) |
0.0957 (1.00) |
Del Peak 25(10p15 3) | 0 (0%) | 219 |
0.373 (1.00) |
0.442 (1.00) |
4.8e-05 (0.0368) |
9.6e-05 (0.0727) |
0.329 (1.00) |
0.443 (1.00) |
0.00156 (1.00) |
0.000554 (0.393) |
0.0549 (1.00) |
4.45e-05 (0.0342) |
Amp Peak 25(18p11 32) | 0 (0%) | 260 |
0.0958 (1.00) |
0.00981 (1.00) |
2.48e-05 (0.0192) |
0.000126 (0.0949) |
0.231 (1.00) |
0.451 (1.00) |
0.131 (1.00) |
0.0402 (1.00) |
0.898 (1.00) |
0.0209 (1.00) |
Amp Peak 29(20p12 2) | 0 (0%) | 186 |
0.000987 (0.68) |
0.0043 (1.00) |
8.92e-08 (7.3e-05) |
0.000161 (0.121) |
0.967 (1.00) |
0.221 (1.00) |
0.0408 (1.00) |
0.00273 (1.00) |
0.259 (1.00) |
0.0945 (1.00) |
Del Peak 10(4p15 2) | 0 (0%) | 158 |
0.000807 (0.566) |
0.00171 (1.00) |
6.52e-06 (0.00517) |
0.000341 (0.247) |
0.662 (1.00) |
0.0343 (1.00) |
0.0138 (1.00) |
0.00689 (1.00) |
0.302 (1.00) |
0.864 (1.00) |
Del Peak 14(5q11 2) | 0 (0%) | 107 |
0.842 (1.00) |
0.303 (1.00) |
2.03e-12 (1.69e-09) |
0.000192 (0.143) |
0.959 (1.00) |
0.244 (1.00) |
0.0104 (1.00) |
0.0858 (1.00) |
0.987 (1.00) |
0.00113 (0.777) |
Del Peak 15(5q31 1) | 0 (0%) | 89 |
0.332 (1.00) |
0.228 (1.00) |
5.7e-09 (4.71e-06) |
3e-05 (0.0232) |
0.272 (1.00) |
0.166 (1.00) |
0.0582 (1.00) |
0.0639 (1.00) |
0.684 (1.00) |
0.00713 (1.00) |
Del Peak 28(11p15 5) | 0 (0%) | 214 |
0.000689 (0.486) |
0.0528 (1.00) |
1.28e-06 (0.00103) |
0.0352 (1.00) |
0.000764 (0.538) |
2.02e-05 (0.0157) |
0.00293 (1.00) |
0.031 (1.00) |
0.00193 (1.00) |
0.0459 (1.00) |
Del Peak 43(19p13 3) | 0 (0%) | 224 |
0.334 (1.00) |
0.0231 (1.00) |
1.38e-05 (0.0108) |
0.145 (1.00) |
0.0588 (1.00) |
0.251 (1.00) |
0.284 (1.00) |
0.0283 (1.00) |
0.000224 (0.166) |
0.00297 (1.00) |
Del Peak 44(19q13 33) | 0 (0%) | 291 |
0.617 (1.00) |
0.0694 (1.00) |
0.000167 (0.125) |
0.000187 (0.139) |
0.244 (1.00) |
0.719 (1.00) |
0.0819 (1.00) |
0.0398 (1.00) |
0.0341 (1.00) |
0.334 (1.00) |
Del Peak 48(22q13 32) | 0 (0%) | 302 |
0.000281 (0.205) |
8.68e-05 (0.0658) |
0.0172 (1.00) |
0.351 (1.00) |
0.543 (1.00) |
0.0759 (1.00) |
0.119 (1.00) |
0.1 (1.00) |
0.0185 (1.00) |
0.0144 (1.00) |
Del Peak 50(Xp21 1) | 0 (0%) | 270 |
0.354 (1.00) |
0.148 (1.00) |
5.39e-05 (0.0411) |
0.00024 (0.177) |
0.344 (1.00) |
0.681 (1.00) |
0.137 (1.00) |
0.00706 (1.00) |
0.538 (1.00) |
0.163 (1.00) |
Del Peak 51(Xp11 3) | 0 (0%) | 272 |
0.062 (1.00) |
0.175 (1.00) |
9.19e-06 (0.00726) |
4.09e-05 (0.0315) |
0.0923 (1.00) |
0.124 (1.00) |
0.0631 (1.00) |
0.00391 (1.00) |
0.131 (1.00) |
0.138 (1.00) |
Del Peak 52(Xq22 3) | 0 (0%) | 302 |
0.00853 (1.00) |
0.105 (1.00) |
1.91e-05 (0.0148) |
0.000249 (0.183) |
0.663 (1.00) |
0.92 (1.00) |
0.0422 (1.00) |
0.438 (1.00) |
0.276 (1.00) |
0.797 (1.00) |
Amp Peak 8(5p15 33) | 0 (0%) | 83 |
0.853 (1.00) |
0.867 (1.00) |
1.07e-05 (0.00841) |
0.0129 (1.00) |
0.405 (1.00) |
0.502 (1.00) |
0.262 (1.00) |
0.487 (1.00) |
0.45 (1.00) |
0.735 (1.00) |
Amp Peak 9(5p12) | 0 (0%) | 136 |
0.919 (1.00) |
0.514 (1.00) |
7.58e-10 (6.28e-07) |
0.00874 (1.00) |
0.563 (1.00) |
1 (1.00) |
0.225 (1.00) |
0.21 (1.00) |
0.792 (1.00) |
0.236 (1.00) |
Amp Peak 19(12p13 33) | 0 (0%) | 199 |
0.0102 (1.00) |
0.0571 (1.00) |
1.23e-05 (0.00965) |
0.000492 (0.352) |
0.313 (1.00) |
0.729 (1.00) |
0.000418 (0.301) |
0.0103 (1.00) |
0.837 (1.00) |
0.218 (1.00) |
Amp Peak 27(19q12) | 0 (0%) | 230 |
0.455 (1.00) |
0.249 (1.00) |
4.07e-06 (0.00324) |
0.182 (1.00) |
0.231 (1.00) |
0.0287 (1.00) |
0.00823 (1.00) |
0.13 (1.00) |
0.913 (1.00) |
0.37 (1.00) |
Amp Peak 28(19q13 2) | 0 (0%) | 227 |
0.715 (1.00) |
1 (1.00) |
0.000195 (0.144) |
0.0708 (1.00) |
0.356 (1.00) |
0.117 (1.00) |
0.106 (1.00) |
0.085 (1.00) |
0.77 (1.00) |
0.246 (1.00) |
Amp Peak 31(22q11 21) | 0 (0%) | 198 |
0.111 (1.00) |
0.123 (1.00) |
0.000296 (0.216) |
0.000477 (0.342) |
0.888 (1.00) |
0.349 (1.00) |
0.0122 (1.00) |
0.0463 (1.00) |
0.751 (1.00) |
0.027 (1.00) |
Del Peak 4(2q22 1) | 0 (0%) | 292 |
0.255 (1.00) |
0.318 (1.00) |
0.000271 (0.198) |
0.0198 (1.00) |
0.667 (1.00) |
0.0777 (1.00) |
0.0219 (1.00) |
0.0165 (1.00) |
0.512 (1.00) |
0.226 (1.00) |
Del Peak 7(3p13) | 0 (0%) | 57 |
0.419 (1.00) |
0.549 (1.00) |
2.67e-06 (0.00214) |
0.000858 (0.598) |
0.882 (1.00) |
0.0379 (1.00) |
0.0756 (1.00) |
0.0171 (1.00) |
0.432 (1.00) |
0.00134 (0.915) |
Del Peak 8(3p12 3) | 0 (0%) | 65 |
0.258 (1.00) |
0.342 (1.00) |
3.03e-05 (0.0233) |
0.00259 (1.00) |
1 (1.00) |
0.092 (1.00) |
0.12 (1.00) |
0.0235 (1.00) |
0.701 (1.00) |
0.00577 (1.00) |
Del Peak 11(4q22 1) | 0 (0%) | 180 |
0.00685 (1.00) |
0.0579 (1.00) |
0.000102 (0.0771) |
0.00829 (1.00) |
0.123 (1.00) |
0.381 (1.00) |
0.00473 (1.00) |
0.00722 (1.00) |
0.35 (1.00) |
0.168 (1.00) |
Del Peak 12(4q32 3) | 0 (0%) | 149 |
0.00967 (1.00) |
0.0253 (1.00) |
3.5e-07 (0.000285) |
0.000596 (0.422) |
0.101 (1.00) |
0.523 (1.00) |
0.0012 (0.819) |
0.00455 (1.00) |
0.663 (1.00) |
0.242 (1.00) |
Del Peak 16(6p25 3) | 0 (0%) | 297 |
0.22 (1.00) |
0.11 (1.00) |
0.00878 (1.00) |
0.00143 (0.971) |
0.393 (1.00) |
0.013 (1.00) |
0.00219 (1.00) |
0.000305 (0.222) |
0.179 (1.00) |
0.0797 (1.00) |
Del Peak 17(6q22 31) | 0 (0%) | 302 |
0.0192 (1.00) |
0.00224 (1.00) |
0.00513 (1.00) |
0.000818 (0.573) |
0.629 (1.00) |
0.354 (1.00) |
0.000249 (0.183) |
0.000587 (0.416) |
0.374 (1.00) |
0.218 (1.00) |
Del Peak 19(7q11 22) | 0 (0%) | 360 |
0.908 (1.00) |
0.405 (1.00) |
4.4e-05 (0.0338) |
0.829 (1.00) |
0.958 (1.00) |
0.75 (1.00) |
0.0465 (1.00) |
0.0493 (1.00) |
0.61 (1.00) |
0.358 (1.00) |
Del Peak 22(9p23) | 0 (0%) | 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) |
0.00281 (1.00) |
0.0746 (1.00) |
0.0991 (1.00) |
0.0328 (1.00) |
Del Peak 23(9p21 3) | 0 (0%) | 95 |
0.372 (1.00) |
0.172 (1.00) |
4.99e-07 (0.000406) |
0.409 (1.00) |
0.695 (1.00) |
0.388 (1.00) |
0.0535 (1.00) |
0.472 (1.00) |
0.351 (1.00) |
0.421 (1.00) |
Del Peak 34(14q11 2) | 0 (0%) | 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) |
0.000386 (0.278) |
9.8e-05 (0.0741) |
0.183 (1.00) |
0.493 (1.00) |
Del Peak 46(21q22 3) | 0 (0%) | 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) |
0.13 (1.00) |
0.0131 (1.00) |
0.0589 (1.00) |
0.161 (1.00) |
Del Peak 49(Xp22 2) | 0 (0%) | 271 |
0.599 (1.00) |
0.351 (1.00) |
0.000249 (0.183) |
0.0101 (1.00) |
0.277 (1.00) |
0.783 (1.00) |
0.236 (1.00) |
0.103 (1.00) |
0.179 (1.00) |
0.235 (1.00) |
Amp Peak 1(1p34 2) | 0 (0%) | 334 |
0.028 (1.00) |
0.481 (1.00) |
0.000892 (0.621) |
0.644 (1.00) |
0.363 (1.00) |
0.619 (1.00) |
0.0242 (1.00) |
0.0572 (1.00) |
0.088 (1.00) |
0.669 (1.00) |
Amp Peak 5(3p11 1) | 0 (0%) | 317 |
0.0748 (1.00) |
0.844 (1.00) |
0.744 (1.00) |
0.957 (1.00) |
0.214 (1.00) |
0.0013 (0.887) |
0.239 (1.00) |
0.541 (1.00) |
0.845 (1.00) |
0.602 (1.00) |
Amp Peak 7(4q12) | 0 (0%) | 304 |
0.679 (1.00) |
0.759 (1.00) |
0.000353 (0.255) |
0.124 (1.00) |
0.356 (1.00) |
0.131 (1.00) |
0.221 (1.00) |
0.106 (1.00) |
0.178 (1.00) |
0.393 (1.00) |
Amp Peak 10(6p12 1) | 0 (0%) | 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) |
0.106 (1.00) |
0.522 (1.00) |
0.27 (1.00) |
0.267 (1.00) |
Amp Peak 11(6q12) | 0 (0%) | 280 |
1 (1.00) |
0.873 (1.00) |
0.00114 (0.781) |
0.0454 (1.00) |
0.348 (1.00) |
0.408 (1.00) |
0.19 (1.00) |
0.42 (1.00) |
0.198 (1.00) |
0.0784 (1.00) |
Amp Peak 12(7p11 2) | 0 (0%) | 204 |
0.186 (1.00) |
0.0939 (1.00) |
0.00097 (0.669) |
0.00366 (1.00) |
0.687 (1.00) |
0.801 (1.00) |
0.0273 (1.00) |
0.000542 (0.386) |
0.634 (1.00) |
0.0644 (1.00) |
Amp Peak 14(8p11 23) | 0 (0%) | 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) |
0.363 (1.00) |
0.537 (1.00) |
0.135 (1.00) |
0.371 (1.00) |
Amp Peak 15(8q24 21) | 0 (0%) | 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) |
0.995 (1.00) |
0.509 (1.00) |
0.866 (1.00) |
0.497 (1.00) |
Amp Peak 16(9p24 1) | 0 (0%) | 324 |
0.375 (1.00) |
0.0295 (1.00) |
0.000354 (0.255) |
0.177 (1.00) |
0.0017 (1.00) |
0.00501 (1.00) |
0.00699 (1.00) |
0.000767 (0.539) |
0.117 (1.00) |
0.0167 (1.00) |
Amp Peak 17(9p13 3) | 0 (0%) | 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) |
0.0114 (1.00) |
0.00149 (1.00) |
0.823 (1.00) |
0.555 (1.00) |
Amp Peak 18(11q13 3) | 0 (0%) | 254 |
0.0697 (1.00) |
0.0306 (1.00) |
0.00486 (1.00) |
0.000518 (0.37) |
0.19 (1.00) |
0.0358 (1.00) |
0.0123 (1.00) |
0.124 (1.00) |
0.0454 (1.00) |
0.00669 (1.00) |
Amp Peak 20(12q15) | 0 (0%) | 253 |
0.312 (1.00) |
0.527 (1.00) |
0.00531 (1.00) |
0.00136 (0.927) |
0.764 (1.00) |
0.524 (1.00) |
0.0588 (1.00) |
0.0807 (1.00) |
1 (1.00) |
0.437 (1.00) |
Amp Peak 21(13q34) | 0 (0%) | 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) |
0.578 (1.00) |
0.809 (1.00) |
0.155 (1.00) |
0.381 (1.00) |
Amp Peak 22(14q13 3) | 0 (0%) | 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) |
0.0675 (1.00) |
0.0164 (1.00) |
0.0032 (1.00) |
0.532 (1.00) |
Amp Peak 30(20q11 21) | 0 (0%) | 168 |
0.991 (1.00) |
0.844 (1.00) |
0.00052 (0.371) |
0.0132 (1.00) |
0.669 (1.00) |
0.588 (1.00) |
0.585 (1.00) |
0.757 (1.00) |
0.941 (1.00) |
0.373 (1.00) |
Amp Peak 32(Xq28) | 0 (0%) | 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) |
0.109 (1.00) |
0.0781 (1.00) |
0.518 (1.00) |
0.303 (1.00) |
Del Peak 3(2p25 3) | 0 (0%) | 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) |
0.319 (1.00) |
0.128 (1.00) |
0.0533 (1.00) |
0.0247 (1.00) |
Del Peak 6(3p25 3) | 0 (0%) | 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) |
0.078 (1.00) |
0.0433 (1.00) |
0.602 (1.00) |
0.0597 (1.00) |
Del Peak 9(3q11 1) | 0 (0%) | 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) |
0.885 (1.00) |
0.803 (1.00) |
0.289 (1.00) |
0.887 (1.00) |
Del Peak 18(6q26) | 0 (0%) | 294 |
0.0659 (1.00) |
0.00298 (1.00) |
0.00234 (1.00) |
0.000727 (0.512) |
0.921 (1.00) |
0.69 (1.00) |
0.00204 (1.00) |
0.00223 (1.00) |
0.184 (1.00) |
0.085 (1.00) |
Del Peak 20(7q36 3) | 0 (0%) | 316 |
0.187 (1.00) |
0.112 (1.00) |
0.00095 (0.659) |
0.274 (1.00) |
1 (1.00) |
0.315 (1.00) |
0.00254 (1.00) |
0.0054 (1.00) |
0.028 (1.00) |
0.166 (1.00) |
Del Peak 21(8p23 2) | 0 (0%) | 130 |
0.864 (1.00) |
0.459 (1.00) |
0.000961 (0.665) |
0.173 (1.00) |
0.345 (1.00) |
0.141 (1.00) |
0.494 (1.00) |
0.0421 (1.00) |
0.68 (1.00) |
0.0705 (1.00) |
Del Peak 29(11q22 1) | 0 (0%) | 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) |
0.13 (1.00) |
0.263 (1.00) |
0.382 (1.00) |
0.849 (1.00) |
Del Peak 30(11q25) | 0 (0%) | 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) |
0.134 (1.00) |
0.104 (1.00) |
0.49 (1.00) |
1 (1.00) |
Del Peak 31(12q24 31) | 0 (0%) | 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) |
0.849 (1.00) |
0.808 (1.00) |
0.0766 (1.00) |
0.362 (1.00) |
Del Peak 32(13q12 11) | 0 (0%) | 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) |
0.73 (1.00) |
0.286 (1.00) |
0.812 (1.00) |
0.681 (1.00) |
Del Peak 33(13q14 2) | 0 (0%) | 126 |
0.0512 (1.00) |
0.0962 (1.00) |
0.00096 (0.665) |
0.053 (1.00) |
0.707 (1.00) |
0.682 (1.00) |
0.108 (1.00) |
0.121 (1.00) |
0.893 (1.00) |
0.672 (1.00) |
Del Peak 35(15q12) | 0 (0%) | 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) |
0.215 (1.00) |
0.149 (1.00) |
0.024 (1.00) |
0.189 (1.00) |
Del Peak 36(15q21 1) | 0 (0%) | 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) |
0.299 (1.00) |
0.104 (1.00) |
0.0265 (1.00) |
0.199 (1.00) |
Del Peak 37(16p13 3) | 0 (0%) | 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) |
0.371 (1.00) |
0.268 (1.00) |
0.427 (1.00) |
0.401 (1.00) |
Del Peak 38(16q23 1) | 0 (0%) | 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) |
0.198 (1.00) |
0.203 (1.00) |
0.931 (1.00) |
0.56 (1.00) |
Del Peak 39(17p11 2) | 0 (0%) | 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) |
0.0446 (1.00) |
0.0798 (1.00) |
0.183 (1.00) |
0.165 (1.00) |
Del Peak 41(17q25 3) | 0 (0%) | 321 |
0.00515 (1.00) |
0.0421 (1.00) |
0.000405 (0.292) |
0.0446 (1.00) |
0.622 (1.00) |
0.994 (1.00) |
0.146 (1.00) |
0.00187 (1.00) |
0.529 (1.00) |
0.223 (1.00) |
Del Peak 42(18q23) | 0 (0%) | 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) |
0.524 (1.00) |
0.0228 (1.00) |
0.942 (1.00) |
0.444 (1.00) |
Del Peak 45(21q21 1) | 0 (0%) | 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) |
0.373 (1.00) |
0.533 (1.00) |
0.0379 (1.00) |
0.0275 (1.00) |
Del Peak 47(22q11 21) | 0 (0%) | 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) |
0.645 (1.00) |
0.329 (1.00) |
0.0583 (1.00) |
0.0974 (1.00) |
P value = 1.98e-07 (Fisher's exact test), Q value = 0.00016
Table S1. Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 2(1Q21.2) CNV | 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)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.87e-05 (Fisher's exact test), Q value = 0.015
Table S2. Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
AMP PEAK 2(1Q21.2) CNV | 27 | 72 | 55 | 25 |
AMP PEAK 2(1Q21.2) WILD-TYPE | 50 | 30 | 56 | 30 |
Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.11e-05 (Fisher's exact test), Q value = 0.032
Table S3. Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
AMP PEAK 2(1Q21.2) CNV | 74 | 35 | 70 |
AMP PEAK 2(1Q21.2) WILD-TYPE | 33 | 35 | 98 |
Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000305 (Fisher's exact test), Q value = 0.22
Table S4. Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
AMP PEAK 3(2P16.1) CNV | 19 | 40 | 12 | 15 |
AMP PEAK 3(2P16.1) WILD-TYPE | 24 | 10 | 18 | 16 |
Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 3.18e-13 (Fisher's exact test), Q value = 2.7e-10
Table S5. Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 3(2P16.1) CNV | 49 | 102 | 65 |
AMP PEAK 3(2P16.1) WILD-TYPE | 94 | 27 | 60 |
Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 5.83e-05 (Fisher's exact test), Q value = 0.044
Table S6. Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 3(2P16.1) CNV | 43 | 61 | 31 |
AMP PEAK 3(2P16.1) WILD-TYPE | 55 | 22 | 38 |
Figure S6. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.015
Table S7. Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
AMP PEAK 3(2P16.1) CNV | 29 | 71 | 64 | 21 |
AMP PEAK 3(2P16.1) WILD-TYPE | 48 | 31 | 47 | 34 |
Figure S7. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 7.55e-05 (Fisher's exact test), Q value = 0.057
Table S8. Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
AMP PEAK 3(2P16.1) CNV | 75 | 37 | 73 |
AMP PEAK 3(2P16.1) WILD-TYPE | 32 | 33 | 95 |
Figure S8. Get High-res Image Gene #3: 'Amp Peak 3(2p16.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 6.52e-06 (Fisher's exact test), Q value = 0.0052
Table S9. Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 4(2Q31.2) CNV | 30 | 63 | 39 |
AMP PEAK 4(2Q31.2) WILD-TYPE | 113 | 66 | 86 |
Figure S9. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.99e-07 (Fisher's exact test), Q value = 0.00016
Table S10. Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 4(2Q31.2) CNV | 23 | 48 | 14 |
AMP PEAK 4(2Q31.2) WILD-TYPE | 75 | 35 | 55 |
Figure S10. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000194 (Fisher's exact test), Q value = 0.14
Table S11. Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
AMP PEAK 4(2Q31.2) CNV | 20 | 53 | 31 | 14 |
AMP PEAK 4(2Q31.2) WILD-TYPE | 57 | 49 | 80 | 41 |
Figure S11. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.000248 (Fisher's exact test), Q value = 0.18
Table S12. Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
AMP PEAK 4(2Q31.2) CNV | 53 | 22 | 43 |
AMP PEAK 4(2Q31.2) WILD-TYPE | 54 | 48 | 125 |
Figure S12. Get High-res Image Gene #4: 'Amp Peak 4(2q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.71e-05 (Fisher's exact test), Q value = 0.013
Table S13. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
AMP PEAK 6(3Q26.33) CNV | 19 | 54 | 67 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 9 | 0 | 5 |
Figure S13. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 7.05e-12 (Fisher's exact test), Q value = 5.9e-09
Table S14. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 6(3Q26.33) CNV | 113 | 129 | 122 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 30 | 0 | 3 |
Figure S14. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 6.69e-07 (Fisher's exact test), Q value = 0.00054
Table S15. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 6(3Q26.33) CNV | 79 | 83 | 67 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 19 | 0 | 2 |
Figure S15. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.26e-06 (Fisher's exact test), Q value = 0.001
Table S16. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
AMP PEAK 6(3Q26.33) CNV | 73 | 102 | 100 | 42 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 4 | 0 | 11 | 13 |
Figure S16. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 5.04e-05 (Fisher's exact test), Q value = 0.038
Table S17. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
AMP PEAK 6(3Q26.33) CNV | 107 | 63 | 147 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 0 | 7 | 21 |
Figure S17. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 3.07e-06 (Fisher's exact test), Q value = 0.0024
Table S18. Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 181 | 73 |
AMP PEAK 6(3Q26.33) CNV | 111 | 155 | 73 |
AMP PEAK 6(3Q26.33) WILD-TYPE | 2 | 26 | 0 |
Figure S18. Get High-res Image Gene #6: 'Amp Peak 6(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.0084
Table S19. Gene #8: 'Amp Peak 8(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 8(5P15.33) CNV | 99 | 100 | 115 |
AMP PEAK 8(5P15.33) WILD-TYPE | 44 | 29 | 10 |
Figure S19. Get High-res Image Gene #8: 'Amp Peak 8(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 7.58e-10 (Fisher's exact test), Q value = 6.3e-07
Table S20. Gene #9: 'Amp Peak 9(5p12)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 9(5P12) CNV | 70 | 84 | 107 |
AMP PEAK 9(5P12) WILD-TYPE | 73 | 45 | 18 |
Figure S20. Get High-res Image Gene #9: 'Amp Peak 9(5p12)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 5.34e-10 (Fisher's exact test), Q value = 4.4e-07
Table S21. Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 13(7Q21.2) CNV | 51 | 96 | 62 |
AMP PEAK 13(7Q21.2) WILD-TYPE | 92 | 33 | 63 |
Figure S21. Get High-res Image Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.01
Table S22. Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 13(7Q21.2) CNV | 35 | 58 | 30 |
AMP PEAK 13(7Q21.2) WILD-TYPE | 63 | 25 | 39 |
Figure S22. Get High-res Image Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000185 (Fisher's exact test), Q value = 0.14
Table S23. Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
AMP PEAK 13(7Q21.2) CNV | 74 | 33 | 75 |
AMP PEAK 13(7Q21.2) WILD-TYPE | 33 | 37 | 93 |
Figure S23. Get High-res Image Gene #13: 'Amp Peak 13(7q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0097
Table S24. Gene #19: 'Amp Peak 19(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 19(12P13.33) CNV | 51 | 83 | 64 |
AMP PEAK 19(12P13.33) WILD-TYPE | 92 | 46 | 61 |
Figure S24. Get High-res Image Gene #19: 'Amp Peak 19(12p13.33)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.012
Table S25. Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 23(15Q26.3) CNV | 30 | 61 | 48 |
AMP PEAK 23(15Q26.3) WILD-TYPE | 113 | 68 | 77 |
Figure S25. Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 9.39e-06 (Fisher's exact test), Q value = 0.0074
Table S26. Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 23(15Q26.3) CNV | 16 | 40 | 27 |
AMP PEAK 23(15Q26.3) WILD-TYPE | 82 | 43 | 42 |
Figure S26. Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000334 (Fisher's exact test), Q value = 0.24
Table S27. Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
AMP PEAK 23(15Q26.3) CNV | 17 | 52 | 33 | 17 |
AMP PEAK 23(15Q26.3) WILD-TYPE | 60 | 50 | 78 | 38 |
Figure S27. Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 6.01e-07 (Fisher's exact test), Q value = 0.00049
Table S28. Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 24(17Q25.1) CNV | 46 | 83 | 62 |
AMP PEAK 24(17Q25.1) WILD-TYPE | 97 | 46 | 63 |
Figure S28. Get High-res Image Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.017
Table S29. Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 24(17Q25.1) CNV | 34 | 55 | 25 |
AMP PEAK 24(17Q25.1) WILD-TYPE | 64 | 28 | 44 |
Figure S29. Get High-res Image Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000165 (Fisher's exact test), Q value = 0.12
Table S30. Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
AMP PEAK 24(17Q25.1) CNV | 67 | 32 | 62 |
AMP PEAK 24(17Q25.1) WILD-TYPE | 40 | 38 | 106 |
Figure S30. Get High-res Image Gene #24: 'Amp Peak 24(17q25.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.48e-05 (Fisher's exact test), Q value = 0.019
Table S31. Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 25(18P11.32) CNV | 32 | 63 | 42 |
AMP PEAK 25(18P11.32) WILD-TYPE | 111 | 66 | 83 |
Figure S31. Get High-res Image Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.095
Table S32. Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 25(18P11.32) CNV | 18 | 38 | 28 |
AMP PEAK 25(18P11.32) WILD-TYPE | 80 | 45 | 41 |
Figure S32. Get High-res Image Gene #25: 'Amp Peak 25(18p11.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.011
Table S33. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 26(18Q11.2) CNV | 26 | 57 | 43 |
AMP PEAK 26(18Q11.2) WILD-TYPE | 117 | 72 | 82 |
Figure S33. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000342 (Fisher's exact test), Q value = 0.25
Table S34. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 26(18Q11.2) CNV | 17 | 37 | 21 |
AMP PEAK 26(18Q11.2) WILD-TYPE | 81 | 46 | 48 |
Figure S34. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 5.04e-06 (Fisher's exact test), Q value = 0.004
Table S35. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
AMP PEAK 26(18Q11.2) CNV | 46 | 31 | 32 |
AMP PEAK 26(18Q11.2) WILD-TYPE | 61 | 39 | 136 |
Figure S35. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 4.07e-06 (Fisher's exact test), Q value = 0.0032
Table S36. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 27(19Q12) CNV | 45 | 77 | 45 |
AMP PEAK 27(19Q12) WILD-TYPE | 98 | 52 | 80 |
Figure S36. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.14
Table S37. Gene #28: 'Amp Peak 28(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 28(19Q13.2) CNV | 48 | 74 | 48 |
AMP PEAK 28(19Q13.2) WILD-TYPE | 95 | 55 | 77 |
Figure S37. Get High-res Image Gene #28: 'Amp Peak 28(19q13.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 8.92e-08 (Fisher's exact test), Q value = 7.3e-05
Table S38. Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 29(20P12.2) CNV | 53 | 92 | 66 |
AMP PEAK 29(20P12.2) WILD-TYPE | 90 | 37 | 59 |
Figure S38. Get High-res Image Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.12
Table S39. Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
AMP PEAK 29(20P12.2) CNV | 42 | 60 | 33 |
AMP PEAK 29(20P12.2) WILD-TYPE | 56 | 23 | 36 |
Figure S39. Get High-res Image Gene #29: 'Amp Peak 29(20p12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000296 (Fisher's exact test), Q value = 0.22
Table S40. Gene #31: 'Amp Peak 31(22q11.21)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
AMP PEAK 31(22Q11.21) CNV | 54 | 80 | 65 |
AMP PEAK 31(22Q11.21) WILD-TYPE | 89 | 49 | 60 |
Figure S40. Get High-res Image Gene #31: 'Amp Peak 31(22q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.43e-06 (Fisher's exact test), Q value = 0.0011
Table S41. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 1(1P36.22) CNV | 9 | 37 | 13 | 10 |
DEL PEAK 1(1P36.22) WILD-TYPE | 34 | 13 | 17 | 21 |
Figure S41. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 1.78e-08 (Fisher's exact test), Q value = 1.5e-05
Table S42. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 1(1P36.22) CNV | 11 | 41 | 17 |
DEL PEAK 1(1P36.22) WILD-TYPE | 17 | 13 | 55 |
Figure S42. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1.61e-28 (Fisher's exact test), Q value = 1.4e-25
Table S43. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 1(1P36.22) CNV | 34 | 107 | 31 |
DEL PEAK 1(1P36.22) WILD-TYPE | 109 | 22 | 94 |
Figure S43. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.1e-14 (Fisher's exact test), Q value = 1.8e-11
Table S44. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 1(1P36.22) CNV | 17 | 61 | 22 |
DEL PEAK 1(1P36.22) WILD-TYPE | 81 | 22 | 47 |
Figure S44. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 8.67e-14 (Fisher's exact test), Q value = 7.2e-11
Table S45. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
DEL PEAK 1(1P36.22) CNV | 19 | 77 | 35 | 18 |
DEL PEAK 1(1P36.22) WILD-TYPE | 58 | 25 | 76 | 37 |
Figure S45. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 9.45e-15 (Fisher's exact test), Q value = 7.9e-12
Table S46. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
DEL PEAK 1(1P36.22) CNV | 80 | 18 | 51 |
DEL PEAK 1(1P36.22) WILD-TYPE | 27 | 52 | 117 |
Figure S46. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.014
Table S47. Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 181 | 73 |
DEL PEAK 1(1P36.22) CNV | 42 | 66 | 49 |
DEL PEAK 1(1P36.22) WILD-TYPE | 71 | 115 | 24 |
Figure S47. Get High-res Image Gene #33: 'Del Peak 1(1p36.22)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 0.000237 (Fisher's exact test), Q value = 0.17
Table S48. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 2(1P13.2) CNV | 17 | 35 | 8 | 10 |
DEL PEAK 2(1P13.2) WILD-TYPE | 26 | 15 | 22 | 21 |
Figure S48. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 1.23e-15 (Fisher's exact test), Q value = 1e-12
Table S49. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 2(1P13.2) CNV | 35 | 93 | 44 |
DEL PEAK 2(1P13.2) WILD-TYPE | 108 | 36 | 81 |
Figure S49. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 5.74e-09 (Fisher's exact test), Q value = 4.7e-06
Table S50. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 2(1P13.2) CNV | 20 | 54 | 28 |
DEL PEAK 2(1P13.2) WILD-TYPE | 78 | 29 | 41 |
Figure S50. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 5.56e-07 (Fisher's exact test), Q value = 0.00045
Table S51. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
DEL PEAK 2(1P13.2) CNV | 27 | 68 | 38 | 17 |
DEL PEAK 2(1P13.2) WILD-TYPE | 50 | 34 | 73 | 38 |
Figure S51. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.96e-07 (Fisher's exact test), Q value = 0.00016
Table S52. Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
DEL PEAK 2(1P13.2) CNV | 70 | 26 | 54 |
DEL PEAK 2(1P13.2) WILD-TYPE | 37 | 44 | 114 |
Figure S52. Get High-res Image Gene #34: 'Del Peak 2(1p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000271 (Fisher's exact test), Q value = 0.2
Table S53. Gene #36: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 4(2Q22.1) CNV | 22 | 47 | 36 |
DEL PEAK 4(2Q22.1) WILD-TYPE | 121 | 82 | 89 |
Figure S53. Get High-res Image Gene #36: 'Del Peak 4(2q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.17
Table S54. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 5(2Q36.2) CNV | 9 | 26 | 3 | 12 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 34 | 24 | 27 | 19 |
Figure S54. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.036
Table S55. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 5(2Q36.2) CNV | 5 | 30 | 15 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 23 | 24 | 57 |
Figure S55. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1.7e-12 (Fisher's exact test), Q value = 1.4e-09
Table S56. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 5(2Q36.2) CNV | 23 | 74 | 35 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 120 | 55 | 90 |
Figure S56. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.14e-06 (Fisher's exact test), Q value = 0.0017
Table S57. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 5(2Q36.2) CNV | 17 | 44 | 25 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 81 | 39 | 44 |
Figure S57. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 6.61e-07 (Fisher's exact test), Q value = 0.00054
Table S58. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
DEL PEAK 5(2Q36.2) CNV | 27 | 53 | 30 | 6 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 50 | 49 | 81 | 49 |
Figure S58. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.98e-08 (Fisher's exact test), Q value = 2.5e-05
Table S59. Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
DEL PEAK 5(2Q36.2) CNV | 60 | 19 | 37 |
DEL PEAK 5(2Q36.2) WILD-TYPE | 47 | 51 | 131 |
Figure S59. Get High-res Image Gene #37: 'Del Peak 5(2q36.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.67e-06 (Fisher's exact test), Q value = 0.0021
Table S60. Gene #39: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 7(3P13) CNV | 105 | 119 | 116 |
DEL PEAK 7(3P13) WILD-TYPE | 38 | 10 | 9 |
Figure S60. Get High-res Image Gene #39: 'Del Peak 7(3p13)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.03e-05 (Fisher's exact test), Q value = 0.023
Table S61. Gene #40: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 8(3P12.3) CNV | 103 | 116 | 113 |
DEL PEAK 8(3P12.3) WILD-TYPE | 40 | 13 | 12 |
Figure S61. Get High-res Image Gene #40: 'Del Peak 8(3p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 6.52e-06 (Fisher's exact test), Q value = 0.0052
Table S62. Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 10(4P15.2) CNV | 70 | 99 | 70 |
DEL PEAK 10(4P15.2) WILD-TYPE | 73 | 30 | 55 |
Figure S62. Get High-res Image Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000341 (Fisher's exact test), Q value = 0.25
Table S63. Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 10(4P15.2) CNV | 44 | 61 | 44 |
DEL PEAK 10(4P15.2) WILD-TYPE | 54 | 22 | 25 |
Figure S63. Get High-res Image Gene #42: 'Del Peak 10(4p15.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.077
Table S64. Gene #43: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 11(4Q22.1) CNV | 65 | 90 | 62 |
DEL PEAK 11(4Q22.1) WILD-TYPE | 78 | 39 | 63 |
Figure S64. Get High-res Image Gene #43: 'Del Peak 11(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.5e-07 (Fisher's exact test), Q value = 0.00028
Table S65. Gene #44: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 12(4Q32.3) CNV | 72 | 104 | 72 |
DEL PEAK 12(4Q32.3) WILD-TYPE | 71 | 25 | 53 |
Figure S65. Get High-res Image Gene #44: 'Del Peak 12(4q32.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0023
Table S66. Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 13(4Q35.2) CNV | 76 | 104 | 73 |
DEL PEAK 13(4Q35.2) WILD-TYPE | 67 | 25 | 52 |
Figure S66. Get High-res Image Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000124 (Fisher's exact test), Q value = 0.093
Table S67. Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 13(4Q35.2) CNV | 47 | 65 | 42 |
DEL PEAK 13(4Q35.2) WILD-TYPE | 51 | 18 | 27 |
Figure S67. Get High-res Image Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000143 (Fisher's exact test), Q value = 0.11
Table S68. Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
DEL PEAK 13(4Q35.2) CNV | 40 | 82 | 67 | 30 |
DEL PEAK 13(4Q35.2) WILD-TYPE | 37 | 20 | 44 | 25 |
Figure S68. Get High-res Image Gene #45: 'Del Peak 13(4q35.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.03e-12 (Fisher's exact test), Q value = 1.7e-09
Table S69. Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 14(5Q11.2) CNV | 73 | 108 | 109 |
DEL PEAK 14(5Q11.2) WILD-TYPE | 70 | 21 | 16 |
Figure S69. Get High-res Image Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.14
Table S70. Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 14(5Q11.2) CNV | 57 | 69 | 56 |
DEL PEAK 14(5Q11.2) WILD-TYPE | 41 | 14 | 13 |
Figure S70. Get High-res Image Gene #46: 'Del Peak 14(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 5.7e-09 (Fisher's exact test), Q value = 4.7e-06
Table S71. Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 15(5Q31.1) CNV | 86 | 111 | 111 |
DEL PEAK 15(5Q31.1) WILD-TYPE | 57 | 18 | 14 |
Figure S71. Get High-res Image Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.023
Table S72. Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 15(5Q31.1) CNV | 63 | 71 | 63 |
DEL PEAK 15(5Q31.1) WILD-TYPE | 35 | 12 | 6 |
Figure S72. Get High-res Image Gene #47: 'Del Peak 15(5q31.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000305 (Fisher's exact test), Q value = 0.22
Table S73. Gene #48: 'Del Peak 16(6p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
DEL PEAK 16(6P25.3) CNV | 43 | 11 | 36 |
DEL PEAK 16(6P25.3) WILD-TYPE | 64 | 59 | 132 |
Figure S73. Get High-res Image Gene #48: 'Del Peak 16(6p25.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000249 (Fisher's exact test), Q value = 0.18
Table S74. Gene #49: 'Del Peak 17(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
DEL PEAK 17(6Q22.31) CNV | 9 | 38 | 19 | 14 |
DEL PEAK 17(6Q22.31) WILD-TYPE | 68 | 64 | 92 | 41 |
Figure S74. Get High-res Image Gene #49: 'Del Peak 17(6q22.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.4e-05 (Fisher's exact test), Q value = 0.034
Table S75. Gene #51: 'Del Peak 19(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 19(7Q11.22) CNV | 11 | 3 | 23 |
DEL PEAK 19(7Q11.22) WILD-TYPE | 132 | 126 | 102 |
Figure S75. Get High-res Image Gene #51: 'Del Peak 19(7q11.22)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.97e-10 (Fisher's exact test), Q value = 1.6e-07
Table S76. Gene #54: 'Del Peak 22(9p23)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 22(9P23) CNV | 74 | 75 | 109 |
DEL PEAK 22(9P23) WILD-TYPE | 69 | 54 | 16 |
Figure S76. Get High-res Image Gene #54: 'Del Peak 22(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.99e-07 (Fisher's exact test), Q value = 0.00041
Table S77. Gene #55: 'Del Peak 23(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 23(9P21.3) CNV | 92 | 96 | 114 |
DEL PEAK 23(9P21.3) WILD-TYPE | 51 | 33 | 11 |
Figure S77. Get High-res Image Gene #55: 'Del Peak 23(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000177 (Fisher's exact test), Q value = 0.13
Table S78. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 24(9Q21.11) CNV | 28 | 12 | 19 | 15 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 15 | 38 | 11 | 16 |
Figure S78. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 4.92e-05 (Fisher's exact test), Q value = 0.038
Table S79. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 24(9Q21.11) CNV | 16 | 13 | 45 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 12 | 41 | 27 |
Figure S79. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 5.97e-11 (Fisher's exact test), Q value = 5e-08
Table S80. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 24(9Q21.11) CNV | 69 | 35 | 87 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 74 | 94 | 38 |
Figure S80. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00092
Table S81. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 24(9Q21.11) CNV | 54 | 22 | 46 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 44 | 61 | 23 |
Figure S81. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 4.4e-09 (Fisher's exact test), Q value = 3.6e-06
Table S82. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
DEL PEAK 24(9Q21.11) CNV | 43 | 23 | 71 | 29 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 34 | 79 | 40 | 26 |
Figure S82. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.63e-09 (Fisher's exact test), Q value = 1.3e-06
Table S83. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
DEL PEAK 24(9Q21.11) CNV | 25 | 45 | 96 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 82 | 25 | 72 |
Figure S83. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000184 (Fisher's exact test), Q value = 0.14
Table S84. Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 181 | 73 |
DEL PEAK 24(9Q21.11) CNV | 65 | 91 | 20 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 48 | 90 | 53 |
Figure S84. Get High-res Image Gene #56: 'Del Peak 24(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 4.8e-05 (Fisher's exact test), Q value = 0.037
Table S85. Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 25(10P15.3) CNV | 45 | 75 | 58 |
DEL PEAK 25(10P15.3) WILD-TYPE | 98 | 54 | 67 |
Figure S85. Get High-res Image Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 9.6e-05 (Fisher's exact test), Q value = 0.073
Table S86. Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 25(10P15.3) CNV | 34 | 54 | 27 |
DEL PEAK 25(10P15.3) WILD-TYPE | 64 | 29 | 42 |
Figure S86. Get High-res Image Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 4.45e-05 (Fisher's exact test), Q value = 0.034
Table S87. Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 181 | 73 |
DEL PEAK 25(10P15.3) CNV | 60 | 63 | 46 |
DEL PEAK 25(10P15.3) WILD-TYPE | 53 | 118 | 27 |
Figure S87. Get High-res Image Gene #57: 'Del Peak 25(10p15.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 0.000162 (Fisher's exact test), Q value = 0.12
Table S88. Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 26(10P15.1) CNV | 43 | 71 | 54 |
DEL PEAK 26(10P15.1) WILD-TYPE | 100 | 58 | 71 |
Figure S88. Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.03e-06 (Fisher's exact test), Q value = 0.0032
Table S89. Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 26(10P15.1) CNV | 32 | 55 | 23 |
DEL PEAK 26(10P15.1) WILD-TYPE | 66 | 28 | 46 |
Figure S89. Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.12
Table S90. Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
DEL PEAK 26(10P15.1) CNV | 26 | 60 | 47 | 14 |
DEL PEAK 26(10P15.1) WILD-TYPE | 51 | 42 | 64 | 41 |
Figure S90. Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 9.09e-06 (Fisher's exact test), Q value = 0.0072
Table S91. Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 181 | 73 |
DEL PEAK 26(10P15.1) CNV | 53 | 58 | 47 |
DEL PEAK 26(10P15.1) WILD-TYPE | 60 | 123 | 26 |
Figure S91. Get High-res Image Gene #58: 'Del Peak 26(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.017
Table S92. Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 27(10Q23.31) CNV | 58 | 87 | 58 |
DEL PEAK 27(10Q23.31) WILD-TYPE | 85 | 42 | 67 |
Figure S92. Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.0017
Table S93. Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 27(10Q23.31) CNV | 34 | 60 | 33 |
DEL PEAK 27(10Q23.31) WILD-TYPE | 64 | 23 | 36 |
Figure S93. Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 8.54e-06 (Fisher's exact test), Q value = 0.0068
Table S94. Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
DEL PEAK 27(10Q23.31) CNV | 27 | 72 | 51 | 24 |
DEL PEAK 27(10Q23.31) WILD-TYPE | 50 | 30 | 60 | 31 |
Figure S94. Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 7.23e-07 (Fisher's exact test), Q value = 0.00058
Table S95. Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
DEL PEAK 27(10Q23.31) CNV | 75 | 36 | 63 |
DEL PEAK 27(10Q23.31) WILD-TYPE | 32 | 34 | 105 |
Figure S95. Get High-res Image Gene #59: 'Del Peak 27(10q23.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.001
Table S96. Gene #60: 'Del Peak 28(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 28(11P15.5) CNV | 49 | 53 | 81 |
DEL PEAK 28(11P15.5) WILD-TYPE | 94 | 76 | 44 |
Figure S96. Get High-res Image Gene #60: 'Del Peak 28(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.016
Table S97. Gene #60: 'Del Peak 28(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 47 | 49 | 40 |
DEL PEAK 28(11P15.5) CNV | 29 | 17 | 36 | 10 |
DEL PEAK 28(11P15.5) WILD-TYPE | 29 | 30 | 13 | 30 |
Figure S97. Get High-res Image Gene #60: 'Del Peak 28(11p15.5)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 9.8e-05 (Fisher's exact test), Q value = 0.074
Table S98. Gene #66: 'Del Peak 34(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
DEL PEAK 34(14Q11.2) CNV | 38 | 39 | 44 |
DEL PEAK 34(14Q11.2) WILD-TYPE | 69 | 31 | 124 |
Figure S98. Get High-res Image Gene #66: 'Del Peak 34(14q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0099
Table S99. Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 40(17Q11.2) CNV | 21 | 3 | 11 | 7 |
DEL PEAK 40(17Q11.2) WILD-TYPE | 22 | 47 | 19 | 24 |
Figure S99. Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 6.44e-05 (Fisher's exact test), Q value = 0.049
Table S100. Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 40(17Q11.2) CNV | 9 | 4 | 29 |
DEL PEAK 40(17Q11.2) WILD-TYPE | 19 | 50 | 43 |
Figure S100. Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 3.04e-08 (Fisher's exact test), Q value = 2.5e-05
Table S101. Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 40(17Q11.2) CNV | 40 | 10 | 46 |
DEL PEAK 40(17Q11.2) WILD-TYPE | 103 | 119 | 79 |
Figure S101. Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.48e-06 (Fisher's exact test), Q value = 0.0012
Table S102. Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 77 | 102 | 111 | 55 |
DEL PEAK 40(17Q11.2) CNV | 24 | 7 | 36 | 19 |
DEL PEAK 40(17Q11.2) WILD-TYPE | 53 | 95 | 75 | 36 |
Figure S102. Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.83e-08 (Fisher's exact test), Q value = 4e-05
Table S103. Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 70 | 168 |
DEL PEAK 40(17Q11.2) CNV | 7 | 20 | 59 |
DEL PEAK 40(17Q11.2) WILD-TYPE | 100 | 50 | 109 |
Figure S103. Get High-res Image Gene #72: 'Del Peak 40(17q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.011
Table S104. Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 43(19P13.3) CNV | 48 | 49 | 76 |
DEL PEAK 43(19P13.3) WILD-TYPE | 95 | 80 | 49 |
Figure S104. Get High-res Image Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.17
Table S105. Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 133 | 166 | 68 |
DEL PEAK 43(19P13.3) CNV | 71 | 72 | 16 |
DEL PEAK 43(19P13.3) WILD-TYPE | 62 | 94 | 52 |
Figure S105. Get High-res Image Gene #75: 'Del Peak 43(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 0.000167 (Fisher's exact test), Q value = 0.12
Table S106. Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 44(19Q13.33) CNV | 22 | 48 | 36 |
DEL PEAK 44(19Q13.33) WILD-TYPE | 121 | 81 | 89 |
Figure S106. Get High-res Image Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.14
Table S107. Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 44(19Q13.33) CNV | 12 | 30 | 23 |
DEL PEAK 44(19Q13.33) WILD-TYPE | 86 | 53 | 46 |
Figure S107. Get High-res Image Gene #76: 'Del Peak 44(19q13.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 2.13e-08 (Fisher's exact test), Q value = 1.8e-05
Table S108. Gene #78: 'Del Peak 46(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 46(21Q22.3) CNV | 53 | 91 | 80 |
DEL PEAK 46(21Q22.3) WILD-TYPE | 90 | 38 | 45 |
Figure S108. Get High-res Image Gene #78: 'Del Peak 46(21q22.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000281 (Fisher's exact test), Q value = 0.21
Table S109. Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 43 | 50 | 30 | 31 |
DEL PEAK 48(22Q13.32) CNV | 9 | 7 | 7 | 18 |
DEL PEAK 48(22Q13.32) WILD-TYPE | 34 | 43 | 23 | 13 |
Figure S109. Get High-res Image Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 8.68e-05 (Fisher's exact test), Q value = 0.066
Table S110. Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 28 | 54 | 72 |
DEL PEAK 48(22Q13.32) CNV | 17 | 9 | 15 |
DEL PEAK 48(22Q13.32) WILD-TYPE | 11 | 45 | 57 |
Figure S110. Get High-res Image Gene #80: 'Del Peak 48(22q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.000249 (Fisher's exact test), Q value = 0.18
Table S111. Gene #81: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 49(XP22.2) CNV | 28 | 53 | 45 |
DEL PEAK 49(XP22.2) WILD-TYPE | 115 | 76 | 80 |
Figure S111. Get High-res Image Gene #81: 'Del Peak 49(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 5.39e-05 (Fisher's exact test), Q value = 0.041
Table S112. Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 50(XP21.1) CNV | 27 | 55 | 45 |
DEL PEAK 50(XP21.1) WILD-TYPE | 116 | 74 | 80 |
Figure S112. Get High-res Image Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.18
Table S113. Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 50(XP21.1) CNV | 18 | 36 | 29 |
DEL PEAK 50(XP21.1) WILD-TYPE | 80 | 47 | 40 |
Figure S113. Get High-res Image Gene #82: 'Del Peak 50(Xp21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 9.19e-06 (Fisher's exact test), Q value = 0.0073
Table S114. Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 51(XP11.3) CNV | 26 | 58 | 41 |
DEL PEAK 51(XP11.3) WILD-TYPE | 117 | 71 | 84 |
Figure S114. Get High-res Image Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.09e-05 (Fisher's exact test), Q value = 0.032
Table S115. Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 51(XP11.3) CNV | 16 | 38 | 26 |
DEL PEAK 51(XP11.3) WILD-TYPE | 82 | 45 | 43 |
Figure S115. Get High-res Image Gene #83: 'Del Peak 51(Xp11.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.91e-05 (Fisher's exact test), Q value = 0.015
Table S116. Gene #84: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 143 | 129 | 125 |
DEL PEAK 52(XQ22.3) CNV | 18 | 31 | 46 |
DEL PEAK 52(XQ22.3) WILD-TYPE | 125 | 98 | 79 |
Figure S116. Get High-res Image Gene #84: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.18
Table S117. Gene #84: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 98 | 83 | 69 |
DEL PEAK 52(XQ22.3) CNV | 10 | 20 | 25 |
DEL PEAK 52(XQ22.3) WILD-TYPE | 88 | 63 | 44 |
Figure S117. Get High-res Image Gene #84: 'Del Peak 52(Xq22.3)' versus Molecular Subtype #4: 'METHLYATION_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 = 397
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Number of copy number variation regions = 84
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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.