This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 68 peak regions and 10 molecular subtypes across 413 patients, 150 significant findings detected with Q value < 0.25.
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Amp Peak 1(2q33.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 2(5p13.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 4(6p21.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 5(8p11.23) cnvs correlated to 'CN_CNMF'.
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Amp Peak 6(8p11.21) cnvs correlated to 'CN_CNMF'.
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Amp Peak 7(8q12.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 8(8q24.21) cnvs correlated to 'CN_CNMF'.
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Amp Peak 9(11p15.5) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
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Amp Peak 11(13q12.13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Amp Peak 12(13q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Amp Peak 13(16p11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
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Amp Peak 14(16q12.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
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Amp Peak 15(17q12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Amp Peak 16(17q24.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Amp Peak 17(19p13.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 19(20p12.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 20(20p11.23) cnvs correlated to 'CN_CNMF'.
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Amp Peak 21(20p11.21) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Amp Peak 22(20q11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Amp Peak 23(20q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Amp Peak 24(20q13.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 1(1p36.11) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 2(1p33) cnvs correlated to 'CN_CNMF'.
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Del Peak 3(1p13.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 4(1q43) cnvs correlated to 'CN_CNMF'.
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Del Peak 6(3p26.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 9(4p16.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 10(4q22.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 11(4q35.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 13(5q21.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 14(5q23.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 15(6p25.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 18(8p23.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 19(8p22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
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Del Peak 20(8p11.22) cnvs correlated to 'CN_CNMF'.
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Del Peak 21(8p11.21) cnvs correlated to 'CN_CNMF'.
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Del Peak 22(9p21.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 23(10p15.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 24(10q21.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 25(10q23.31) cnvs correlated to 'CN_CNMF'.
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Del Peak 26(10q25.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 27(12p13.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 28(13q14.13) cnvs correlated to 'CN_CNMF'.
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Del Peak 29(14q32.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 30(15q11.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 31(15q21.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 32(15q22.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 35(17p12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 37(18p11.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 38(18q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 39(18q21.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 40(18q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 42(20p12.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Del Peak 43(21q11.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 44(22q13.32) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 68 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 150 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 | |
Amp Peak 22(20q11 21) | 0 (0%) | 117 |
1.07e-10 (6.69e-08) |
2.86e-11 (1.8e-08) |
1.54e-43 (1.04e-40) |
2.19e-09 (1.34e-06) |
0.0201 (1.00) |
0.000108 (0.06) |
1.47e-14 (9.62e-12) |
3.85e-12 (2.47e-09) |
0.443 (1.00) |
1 (1.00) |
Amp Peak 23(20q12) | 0 (0%) | 116 |
9.28e-12 (5.91e-09) |
1.82e-11 (1.15e-08) |
6.28e-43 (4.24e-40) |
1.58e-08 (9.58e-06) |
0.00771 (1.00) |
2.18e-05 (0.0125) |
5.48e-14 (3.59e-11) |
1.34e-11 (8.53e-09) |
0.406 (1.00) |
0.948 (1.00) |
Amp Peak 24(20q13 32) | 0 (0%) | 113 |
2.87e-10 (1.79e-07) |
6.27e-12 (4e-09) |
3.18e-43 (2.15e-40) |
1.58e-08 (9.58e-06) |
0.00832 (1.00) |
1.3e-05 (0.00749) |
5.48e-14 (3.59e-11) |
1.34e-11 (8.53e-09) |
0.414 (1.00) |
0.96 (1.00) |
Del Peak 35(17p12) | 0 (0%) | 184 |
6.12e-08 (3.66e-05) |
1.6e-06 (0.000933) |
2.81e-35 (1.89e-32) |
1.8e-09 (1.11e-06) |
0.0465 (1.00) |
7.42e-05 (0.0416) |
1.06e-10 (6.61e-08) |
3.2e-08 (1.92e-05) |
0.363 (1.00) |
0.729 (1.00) |
Del Peak 38(18q12 2) | 0 (0%) | 166 |
8.37e-11 (5.25e-08) |
1.08e-09 (6.69e-07) |
1.87e-45 (1.27e-42) |
8.98e-16 (5.9e-13) |
0.0214 (1.00) |
0.000421 (0.226) |
7.66e-16 (5.04e-13) |
1.07e-08 (6.52e-06) |
0.449 (1.00) |
0.865 (1.00) |
Del Peak 39(18q21 2) | 0 (0%) | 153 |
3.06e-10 (1.91e-07) |
6.85e-10 (4.25e-07) |
1.51e-45 (1.03e-42) |
3.29e-12 (2.11e-09) |
0.0109 (1.00) |
0.000225 (0.122) |
8.74e-13 (5.66e-10) |
7.14e-07 (0.000421) |
0.0517 (1.00) |
0.901 (1.00) |
Del Peak 40(18q22 1) | 0 (0%) | 153 |
6.92e-11 (4.35e-08) |
3.65e-09 (2.23e-06) |
1.58e-47 (1.07e-44) |
2.02e-12 (1.3e-09) |
0.0178 (1.00) |
0.000224 (0.122) |
4.05e-12 (2.59e-09) |
2.76e-07 (0.000164) |
0.0746 (1.00) |
0.912 (1.00) |
Amp Peak 11(13q12 13) | 0 (0%) | 163 |
7.21e-08 (4.31e-05) |
5.27e-06 (0.00307) |
5.04e-36 (3.39e-33) |
0.00027 (0.146) |
0.0709 (1.00) |
0.0124 (1.00) |
1.27e-06 (0.000745) |
0.000196 (0.107) |
0.459 (1.00) |
0.798 (1.00) |
Del Peak 37(18p11 31) | 0 (0%) | 193 |
1.51e-12 (9.71e-10) |
3.65e-09 (2.23e-06) |
1.93e-42 (1.3e-39) |
3.11e-13 (2.02e-10) |
0.0023 (1.00) |
0.00104 (0.527) |
3.11e-17 (2.06e-14) |
8.19e-10 (5.07e-07) |
0.48 (1.00) |
0.841 (1.00) |
Amp Peak 12(13q22 1) | 0 (0%) | 159 |
6.34e-05 (0.0358) |
5.43e-05 (0.0307) |
7.2e-33 (4.83e-30) |
0.00051 (0.27) |
0.152 (1.00) |
0.0444 (1.00) |
1.15e-06 (0.000674) |
7.67e-05 (0.0429) |
0.272 (1.00) |
0.977 (1.00) |
Amp Peak 13(16p11 2) | 0 (0%) | 297 |
0.000447 (0.237) |
0.000375 (0.202) |
8.55e-19 (5.67e-16) |
0.0212 (1.00) |
0.373 (1.00) |
0.033 (1.00) |
0.000429 (0.229) |
0.00838 (1.00) |
0.771 (1.00) |
0.809 (1.00) |
Amp Peak 21(20p11 21) | 0 (0%) | 183 |
0.000692 (0.359) |
4.27e-05 (0.0243) |
4e-23 (2.67e-20) |
0.00113 (0.572) |
0.0624 (1.00) |
0.0394 (1.00) |
2.41e-07 (0.000143) |
1.39e-06 (0.000812) |
0.174 (1.00) |
0.509 (1.00) |
Del Peak 11(4q35 1) | 0 (0%) | 276 |
0.000128 (0.0703) |
0.00928 (1.00) |
1.05e-13 (6.82e-11) |
7.69e-05 (0.043) |
0.173 (1.00) |
0.146 (1.00) |
0.000239 (0.129) |
0.000527 (0.278) |
0.416 (1.00) |
0.235 (1.00) |
Del Peak 19(8p22) | 0 (0%) | 228 |
0.00115 (0.579) |
0.000958 (0.489) |
2.41e-30 (1.61e-27) |
3.46e-07 (0.000205) |
0.0649 (1.00) |
0.00013 (0.0714) |
2.16e-05 (0.0124) |
0.000656 (0.343) |
0.115 (1.00) |
0.832 (1.00) |
Del Peak 29(14q32 11) | 0 (0%) | 280 |
2.12e-05 (0.0122) |
0.00011 (0.061) |
1.61e-20 (1.07e-17) |
0.000707 (0.366) |
0.00347 (1.00) |
0.0236 (1.00) |
7.3e-05 (0.041) |
0.00084 (0.431) |
0.319 (1.00) |
0.0612 (1.00) |
Del Peak 30(15q11 2) | 0 (0%) | 253 |
0.000422 (0.226) |
0.00683 (1.00) |
1.2e-21 (7.98e-19) |
0.00432 (1.00) |
0.0746 (1.00) |
0.07 (1.00) |
2.09e-06 (0.00122) |
0.000117 (0.0647) |
0.877 (1.00) |
0.893 (1.00) |
Del Peak 32(15q22 33) | 0 (0%) | 268 |
0.000758 (0.391) |
0.00327 (1.00) |
2.48e-21 (1.65e-18) |
0.000435 (0.231) |
0.141 (1.00) |
0.0512 (1.00) |
3.07e-08 (1.84e-05) |
7.55e-06 (0.00437) |
0.949 (1.00) |
0.365 (1.00) |
Amp Peak 9(11p15 5) | 0 (0%) | 327 |
1.38e-05 (0.00795) |
0.000201 (0.11) |
1.54e-09 (9.48e-07) |
0.000612 (0.321) |
0.00156 (0.777) |
0.00358 (1.00) |
0.00193 (0.959) |
0.00845 (1.00) |
0.117 (1.00) |
0.201 (1.00) |
Amp Peak 14(16q12 1) | 0 (0%) | 311 |
3.02e-05 (0.0173) |
0.000126 (0.0696) |
1.67e-20 (1.11e-17) |
0.0511 (1.00) |
0.619 (1.00) |
0.081 (1.00) |
0.000642 (0.336) |
0.00254 (1.00) |
0.902 (1.00) |
0.93 (1.00) |
Del Peak 1(1p36 11) | 0 (0%) | 263 |
6.81e-05 (0.0384) |
0.00576 (1.00) |
6.32e-17 (4.17e-14) |
0.000792 (0.408) |
0.0155 (1.00) |
0.0238 (1.00) |
0.000347 (0.187) |
0.0012 (0.604) |
0.409 (1.00) |
0.0624 (1.00) |
Del Peak 9(4p16 2) | 0 (0%) | 292 |
0.00194 (0.963) |
0.0107 (1.00) |
1.16e-12 (7.47e-10) |
0.011 (1.00) |
0.442 (1.00) |
0.0866 (1.00) |
0.000237 (0.129) |
0.000107 (0.0594) |
0.376 (1.00) |
0.206 (1.00) |
Del Peak 10(4q22 1) | 0 (0%) | 287 |
0.000585 (0.308) |
0.00864 (1.00) |
8.5e-12 (5.42e-09) |
0.00207 (1.00) |
0.516 (1.00) |
0.391 (1.00) |
9.23e-05 (0.0515) |
2.81e-05 (0.0161) |
0.21 (1.00) |
0.518 (1.00) |
Del Peak 31(15q21 1) | 0 (0%) | 262 |
0.013 (1.00) |
0.0411 (1.00) |
8.15e-18 (5.39e-15) |
0.00747 (1.00) |
0.0441 (1.00) |
0.0657 (1.00) |
2.03e-07 (0.000121) |
2.05e-05 (0.0118) |
0.979 (1.00) |
0.621 (1.00) |
Amp Peak 15(17q12) | 0 (0%) | 312 |
0.0989 (1.00) |
0.0852 (1.00) |
7.53e-07 (0.000443) |
0.0164 (1.00) |
0.582 (1.00) |
0.00276 (1.00) |
4.59e-05 (0.026) |
0.0142 (1.00) |
0.0121 (1.00) |
0.986 (1.00) |
Amp Peak 16(17q24 1) | 0 (0%) | 321 |
0.0519 (1.00) |
0.00821 (1.00) |
1.61e-08 (9.69e-06) |
0.0123 (1.00) |
0.304 (1.00) |
0.00527 (1.00) |
6.04e-06 (0.00351) |
0.00312 (1.00) |
0.00254 (1.00) |
0.781 (1.00) |
Del Peak 18(8p23 3) | 0 (0%) | 242 |
0.00276 (1.00) |
0.000603 (0.316) |
6.84e-26 (4.58e-23) |
3.61e-06 (0.00211) |
0.0514 (1.00) |
0.00096 (0.489) |
0.000672 (0.35) |
0.00231 (1.00) |
0.154 (1.00) |
0.848 (1.00) |
Del Peak 42(20p12 1) | 0 (0%) | 334 |
0.0656 (1.00) |
0.173 (1.00) |
1.38e-13 (8.97e-11) |
0.00404 (1.00) |
0.323 (1.00) |
0.278 (1.00) |
0.00015 (0.082) |
0.00674 (1.00) |
0.0931 (1.00) |
0.101 (1.00) |
Del Peak 44(22q13 32) | 0 (0%) | 275 |
0.000428 (0.229) |
0.000747 (0.386) |
9.76e-13 (6.32e-10) |
0.0049 (1.00) |
0.306 (1.00) |
0.218 (1.00) |
0.00222 (1.00) |
0.00106 (0.537) |
0.394 (1.00) |
0.069 (1.00) |
Amp Peak 1(2q33 1) | 0 (0%) | 334 |
0.0734 (1.00) |
0.105 (1.00) |
3.05e-05 (0.0174) |
0.258 (1.00) |
0.245 (1.00) |
0.0652 (1.00) |
0.000516 (0.272) |
0.0137 (1.00) |
0.277 (1.00) |
0.258 (1.00) |
Amp Peak 2(5p13 2) | 0 (0%) | 332 |
0.334 (1.00) |
0.469 (1.00) |
0.000202 (0.11) |
0.15 (1.00) |
0.00999 (1.00) |
0.724 (1.00) |
0.0864 (1.00) |
0.0696 (1.00) |
0.927 (1.00) |
0.581 (1.00) |
Amp Peak 4(6p21 1) | 0 (0%) | 324 |
0.0902 (1.00) |
0.000996 (0.506) |
3.37e-09 (2.06e-06) |
0.17 (1.00) |
0.83 (1.00) |
0.178 (1.00) |
0.00644 (1.00) |
0.033 (1.00) |
0.776 (1.00) |
0.258 (1.00) |
Amp Peak 5(8p11 23) | 0 (0%) | 269 |
0.444 (1.00) |
0.231 (1.00) |
2.99e-13 (1.94e-10) |
0.868 (1.00) |
0.864 (1.00) |
0.733 (1.00) |
0.211 (1.00) |
0.783 (1.00) |
0.179 (1.00) |
0.189 (1.00) |
Amp Peak 6(8p11 21) | 0 (0%) | 240 |
0.355 (1.00) |
0.129 (1.00) |
4.51e-10 (2.8e-07) |
0.886 (1.00) |
0.27 (1.00) |
0.00672 (1.00) |
0.421 (1.00) |
0.606 (1.00) |
0.502 (1.00) |
0.218 (1.00) |
Amp Peak 7(8q12 1) | 0 (0%) | 198 |
0.15 (1.00) |
0.0646 (1.00) |
9.31e-12 (5.92e-09) |
0.0383 (1.00) |
0.0228 (1.00) |
0.00068 (0.354) |
0.0141 (1.00) |
0.228 (1.00) |
0.126 (1.00) |
0.295 (1.00) |
Amp Peak 8(8q24 21) | 0 (0%) | 174 |
0.203 (1.00) |
0.107 (1.00) |
7.86e-14 (5.13e-11) |
0.0102 (1.00) |
0.103 (1.00) |
0.0104 (1.00) |
0.00636 (1.00) |
0.445 (1.00) |
0.404 (1.00) |
0.215 (1.00) |
Amp Peak 17(19p13 2) | 0 (0%) | 348 |
0.0535 (1.00) |
0.0345 (1.00) |
4.82e-05 (0.0273) |
0.283 (1.00) |
0.734 (1.00) |
0.341 (1.00) |
0.501 (1.00) |
0.539 (1.00) |
0.204 (1.00) |
0.385 (1.00) |
Amp Peak 19(20p12 3) | 0 (0%) | 229 |
0.00188 (0.936) |
0.000844 (0.432) |
1.86e-12 (1.2e-09) |
0.434 (1.00) |
0.0113 (1.00) |
0.478 (1.00) |
0.0305 (1.00) |
0.00972 (1.00) |
0.597 (1.00) |
0.195 (1.00) |
Amp Peak 20(20p11 23) | 0 (0%) | 208 |
0.0267 (1.00) |
0.000792 (0.408) |
1.26e-16 (8.32e-14) |
0.105 (1.00) |
0.0479 (1.00) |
0.183 (1.00) |
0.000513 (0.271) |
0.00104 (0.527) |
0.455 (1.00) |
0.212 (1.00) |
Del Peak 2(1p33) | 0 (0%) | 306 |
0.0246 (1.00) |
0.532 (1.00) |
1.09e-11 (6.91e-09) |
0.00668 (1.00) |
0.556 (1.00) |
0.395 (1.00) |
0.0051 (1.00) |
0.0141 (1.00) |
0.893 (1.00) |
0.0519 (1.00) |
Del Peak 3(1p13 1) | 0 (0%) | 310 |
0.115 (1.00) |
0.374 (1.00) |
6.85e-10 (4.25e-07) |
0.185 (1.00) |
0.56 (1.00) |
0.89 (1.00) |
0.0836 (1.00) |
0.00481 (1.00) |
0.868 (1.00) |
0.379 (1.00) |
Del Peak 4(1q43) | 0 (0%) | 369 |
0.0983 (1.00) |
0.458 (1.00) |
6.98e-06 (0.00405) |
0.105 (1.00) |
0.393 (1.00) |
0.664 (1.00) |
0.0312 (1.00) |
0.0114 (1.00) |
0.335 (1.00) |
0.301 (1.00) |
Del Peak 6(3p26 1) | 0 (0%) | 353 |
0.0994 (1.00) |
0.304 (1.00) |
0.00043 (0.229) |
0.268 (1.00) |
0.942 (1.00) |
0.861 (1.00) |
0.539 (1.00) |
0.0883 (1.00) |
0.541 (1.00) |
0.958 (1.00) |
Del Peak 12(5q11 2) | 0 (0%) | 322 |
0.00129 (0.648) |
0.00378 (1.00) |
4.94e-09 (3.01e-06) |
0.0339 (1.00) |
0.048 (1.00) |
0.0118 (1.00) |
0.00142 (0.711) |
0.00781 (1.00) |
0.835 (1.00) |
0.215 (1.00) |
Del Peak 13(5q21 3) | 0 (0%) | 296 |
0.118 (1.00) |
0.0281 (1.00) |
1.14e-09 (7.04e-07) |
0.0359 (1.00) |
0.0651 (1.00) |
0.0971 (1.00) |
0.00438 (1.00) |
0.0104 (1.00) |
0.654 (1.00) |
0.36 (1.00) |
Del Peak 14(5q23 1) | 0 (0%) | 306 |
0.0628 (1.00) |
0.0356 (1.00) |
1.57e-08 (9.52e-06) |
0.087 (1.00) |
0.044 (1.00) |
0.15 (1.00) |
0.0219 (1.00) |
0.0126 (1.00) |
0.622 (1.00) |
0.246 (1.00) |
Del Peak 15(6p25 3) | 0 (0%) | 359 |
0.971 (1.00) |
0.792 (1.00) |
0.000102 (0.0571) |
0.0527 (1.00) |
0.337 (1.00) |
0.828 (1.00) |
0.353 (1.00) |
0.788 (1.00) |
0.406 (1.00) |
0.453 (1.00) |
Del Peak 20(8p11 22) | 0 (0%) | 333 |
0.213 (1.00) |
0.118 (1.00) |
8.88e-09 (5.4e-06) |
0.0614 (1.00) |
0.049 (1.00) |
0.00534 (1.00) |
0.0993 (1.00) |
0.0804 (1.00) |
0.359 (1.00) |
0.831 (1.00) |
Del Peak 21(8p11 21) | 0 (0%) | 370 |
0.0231 (1.00) |
0.351 (1.00) |
5.81e-07 (0.000343) |
0.366 (1.00) |
0.156 (1.00) |
0.024 (1.00) |
0.483 (1.00) |
0.308 (1.00) |
0.0997 (1.00) |
0.549 (1.00) |
Del Peak 22(9p21 3) | 0 (0%) | 357 |
0.251 (1.00) |
0.264 (1.00) |
4.51e-05 (0.0256) |
0.204 (1.00) |
0.768 (1.00) |
0.214 (1.00) |
0.0637 (1.00) |
0.127 (1.00) |
0.904 (1.00) |
0.663 (1.00) |
Del Peak 23(10p15 3) | 0 (0%) | 345 |
0.261 (1.00) |
0.141 (1.00) |
2.25e-08 (1.35e-05) |
0.0291 (1.00) |
0.0673 (1.00) |
0.104 (1.00) |
0.126 (1.00) |
0.034 (1.00) |
0.68 (1.00) |
0.566 (1.00) |
Del Peak 24(10q21 1) | 0 (0%) | 331 |
0.00928 (1.00) |
0.0374 (1.00) |
2.24e-11 (1.41e-08) |
0.194 (1.00) |
0.277 (1.00) |
0.144 (1.00) |
0.191 (1.00) |
0.0431 (1.00) |
0.887 (1.00) |
0.831 (1.00) |
Del Peak 25(10q23 31) | 0 (0%) | 319 |
0.249 (1.00) |
0.0829 (1.00) |
3.46e-07 (0.000205) |
0.0801 (1.00) |
0.123 (1.00) |
0.375 (1.00) |
0.0348 (1.00) |
0.165 (1.00) |
0.885 (1.00) |
0.985 (1.00) |
Del Peak 26(10q25 2) | 0 (0%) | 320 |
0.172 (1.00) |
0.0105 (1.00) |
1.91e-11 (1.21e-08) |
0.0139 (1.00) |
0.03 (1.00) |
0.319 (1.00) |
0.00312 (1.00) |
0.0025 (1.00) |
0.921 (1.00) |
0.593 (1.00) |
Del Peak 27(12p13 2) | 0 (0%) | 369 |
0.0404 (1.00) |
0.00796 (1.00) |
9.87e-08 (5.89e-05) |
0.207 (1.00) |
0.383 (1.00) |
0.87 (1.00) |
0.0262 (1.00) |
0.00369 (1.00) |
0.695 (1.00) |
0.973 (1.00) |
Del Peak 28(13q14 13) | 0 (0%) | 395 |
0.395 (1.00) |
0.876 (1.00) |
0.000128 (0.0703) |
0.153 (1.00) |
0.212 (1.00) |
0.34 (1.00) |
0.228 (1.00) |
0.452 (1.00) |
0.614 (1.00) |
0.834 (1.00) |
Del Peak 43(21q11 2) | 0 (0%) | 288 |
0.00298 (1.00) |
0.0933 (1.00) |
3.37e-09 (2.06e-06) |
0.0302 (1.00) |
0.236 (1.00) |
0.455 (1.00) |
0.000897 (0.458) |
0.0187 (1.00) |
0.923 (1.00) |
0.47 (1.00) |
Amp Peak 3(5q22 3) | 0 (0%) | 373 |
0.78 (1.00) |
0.629 (1.00) |
0.0293 (1.00) |
0.875 (1.00) |
0.394 (1.00) |
0.494 (1.00) |
0.165 (1.00) |
0.112 (1.00) |
0.693 (1.00) |
0.839 (1.00) |
Amp Peak 10(12p13 33) | 0 (0%) | 309 |
0.463 (1.00) |
0.882 (1.00) |
0.0612 (1.00) |
0.247 (1.00) |
0.429 (1.00) |
0.958 (1.00) |
0.334 (1.00) |
0.977 (1.00) |
0.304 (1.00) |
0.173 (1.00) |
Amp Peak 18(19q13 11) | 0 (0%) | 330 |
0.332 (1.00) |
0.0177 (1.00) |
0.002 (0.988) |
0.517 (1.00) |
0.173 (1.00) |
0.688 (1.00) |
0.0736 (1.00) |
0.167 (1.00) |
0.417 (1.00) |
0.491 (1.00) |
Del Peak 5(2q37 2) | 0 (0%) | 392 |
0.928 (1.00) |
0.0598 (1.00) |
0.977 (1.00) |
0.701 (1.00) |
0.23 (1.00) |
0.208 (1.00) |
1 (1.00) |
0.184 (1.00) |
0.447 (1.00) |
0.447 (1.00) |
Del Peak 7(3p14 2) | 0 (0%) | 338 |
0.466 (1.00) |
0.744 (1.00) |
0.205 (1.00) |
0.735 (1.00) |
0.566 (1.00) |
0.29 (1.00) |
0.632 (1.00) |
0.483 (1.00) |
0.203 (1.00) |
0.536 (1.00) |
Del Peak 8(3q26 31) | 0 (0%) | 374 |
0.122 (1.00) |
0.605 (1.00) |
0.00818 (1.00) |
0.497 (1.00) |
0.288 (1.00) |
0.369 (1.00) |
0.458 (1.00) |
0.0223 (1.00) |
0.15 (1.00) |
0.939 (1.00) |
Del Peak 16(6q26) | 0 (0%) | 353 |
0.383 (1.00) |
0.304 (1.00) |
0.157 (1.00) |
0.356 (1.00) |
0.189 (1.00) |
0.355 (1.00) |
0.873 (1.00) |
0.697 (1.00) |
0.797 (1.00) |
0.53 (1.00) |
Del Peak 17(7q31 1) | 0 (0%) | 402 |
1 (1.00) |
0.504 (1.00) |
0.816 (1.00) |
0.795 (1.00) |
0.354 (1.00) |
0.219 (1.00) |
0.49 (1.00) |
1 (1.00) |
1 (1.00) |
0.564 (1.00) |
Del Peak 33(16p13 3) | 0 (0%) | 368 |
0.334 (1.00) |
0.155 (1.00) |
0.208 (1.00) |
0.376 (1.00) |
0.418 (1.00) |
0.913 (1.00) |
0.62 (1.00) |
0.572 (1.00) |
0.842 (1.00) |
0.739 (1.00) |
Del Peak 34(16q23 1) | 0 (0%) | 364 |
0.259 (1.00) |
0.00785 (1.00) |
0.131 (1.00) |
0.337 (1.00) |
0.489 (1.00) |
0.821 (1.00) |
0.0421 (1.00) |
0.0701 (1.00) |
0.977 (1.00) |
0.505 (1.00) |
Del Peak 36(17q24 3) | 0 (0%) | 354 |
0.102 (1.00) |
0.676 (1.00) |
0.00348 (1.00) |
0.0118 (1.00) |
0.874 (1.00) |
0.338 (1.00) |
0.00329 (1.00) |
0.0329 (1.00) |
0.681 (1.00) |
0.979 (1.00) |
Del Peak 41(19p13 3) | 0 (0%) | 356 |
0.268 (1.00) |
0.198 (1.00) |
0.00362 (1.00) |
0.565 (1.00) |
0.88 (1.00) |
0.0676 (1.00) |
0.0512 (1.00) |
0.0244 (1.00) |
0.582 (1.00) |
0.0166 (1.00) |
P value = 3.05e-05 (Fisher's exact test), Q value = 0.017
Table S1. Gene #1: 'Amp Peak 1(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 1(2Q33.1) CNV | 49 | 18 | 8 | 4 |
AMP PEAK 1(2Q33.1) WILD-TYPE | 121 | 169 | 24 | 20 |
Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.11
Table S2. Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 2(5P13.2) CNV | 46 | 20 | 10 | 5 |
AMP PEAK 2(5P13.2) WILD-TYPE | 124 | 167 | 22 | 19 |
Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.1e-06
Table S3. Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 4(6P21.1) CNV | 61 | 16 | 8 | 4 |
AMP PEAK 4(6P21.1) WILD-TYPE | 109 | 171 | 24 | 20 |
Figure S3. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.99e-13 (Fisher's exact test), Q value = 1.9e-10
Table S4. Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 5(8P11.23) CNV | 56 | 47 | 17 | 24 |
AMP PEAK 5(8P11.23) WILD-TYPE | 114 | 140 | 15 | 0 |
Figure S4. Get High-res Image Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.51e-10 (Fisher's exact test), Q value = 2.8e-07
Table S5. Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 6(8P11.21) CNV | 75 | 55 | 21 | 22 |
AMP PEAK 6(8P11.21) WILD-TYPE | 95 | 132 | 11 | 2 |
Figure S5. Get High-res Image Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 9.31e-12 (Fisher's exact test), Q value = 5.9e-09
Table S6. Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 7(8Q12.1) CNV | 106 | 64 | 23 | 22 |
AMP PEAK 7(8Q12.1) WILD-TYPE | 64 | 123 | 9 | 2 |
Figure S6. Get High-res Image Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 7.86e-14 (Fisher's exact test), Q value = 5.1e-11
Table S7. Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 8(8Q24.21) CNV | 119 | 73 | 23 | 24 |
AMP PEAK 8(8Q24.21) WILD-TYPE | 51 | 114 | 9 | 0 |
Figure S7. Get High-res Image Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0079
Table S8. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
AMP PEAK 9(11P15.5) CNV | 1 | 17 | 3 | 13 |
AMP PEAK 9(11P15.5) WILD-TYPE | 30 | 45 | 27 | 10 |
Figure S8. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 0.000201 (Fisher's exact test), Q value = 0.11
Table S9. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
AMP PEAK 9(11P15.5) CNV | 14 | 2 | 18 |
AMP PEAK 9(11P15.5) WILD-TYPE | 42 | 42 | 28 |
Figure S9. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1.54e-09 (Fisher's exact test), Q value = 9.5e-07
Table S10. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 9(11P15.5) CNV | 54 | 17 | 14 | 1 |
AMP PEAK 9(11P15.5) WILD-TYPE | 116 | 170 | 18 | 23 |
Figure S10. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 7.21e-08 (Fisher's exact test), Q value = 4.3e-05
Table S11. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
AMP PEAK 11(13Q12.13) CNV | 14 | 52 | 8 | 18 |
AMP PEAK 11(13Q12.13) WILD-TYPE | 17 | 10 | 22 | 5 |
Figure S11. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 5.27e-06 (Fisher's exact test), Q value = 0.0031
Table S12. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
AMP PEAK 11(13Q12.13) CNV | 39 | 15 | 38 |
AMP PEAK 11(13Q12.13) WILD-TYPE | 17 | 29 | 8 |
Figure S12. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 5.04e-36 (Fisher's exact test), Q value = 3.4e-33
Table S13. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 11(13Q12.13) CNV | 158 | 57 | 18 | 17 |
AMP PEAK 11(13Q12.13) WILD-TYPE | 12 | 130 | 14 | 7 |
Figure S13. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.15
Table S14. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
AMP PEAK 11(13Q12.13) CNV | 79 | 42 | 33 |
AMP PEAK 11(13Q12.13) WILD-TYPE | 26 | 44 | 30 |
Figure S14. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.00075
Table S15. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
AMP PEAK 11(13Q12.13) CNV | 22 | 46 | 26 | 16 |
AMP PEAK 11(13Q12.13) WILD-TYPE | 9 | 13 | 21 | 38 |
Figure S15. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.000196 (Fisher's exact test), Q value = 0.11
Table S16. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
AMP PEAK 11(13Q12.13) CNV | 16 | 43 | 51 |
AMP PEAK 11(13Q12.13) WILD-TYPE | 33 | 19 | 29 |
Figure S16. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 6.34e-05 (Fisher's exact test), Q value = 0.036
Table S17. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
AMP PEAK 12(13Q22.1) CNV | 15 | 49 | 10 | 17 |
AMP PEAK 12(13Q22.1) WILD-TYPE | 16 | 13 | 20 | 6 |
Figure S17. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 5.43e-05 (Fisher's exact test), Q value = 0.031
Table S18. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
AMP PEAK 12(13Q22.1) CNV | 38 | 16 | 37 |
AMP PEAK 12(13Q22.1) WILD-TYPE | 18 | 28 | 9 |
Figure S18. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 7.2e-33 (Fisher's exact test), Q value = 4.8e-30
Table S19. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 12(13Q22.1) CNV | 158 | 63 | 17 | 16 |
AMP PEAK 12(13Q22.1) WILD-TYPE | 12 | 124 | 15 | 8 |
Figure S19. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00067
Table S20. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
AMP PEAK 12(13Q22.1) CNV | 22 | 49 | 25 | 19 |
AMP PEAK 12(13Q22.1) WILD-TYPE | 9 | 10 | 22 | 35 |
Figure S20. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 7.67e-05 (Fisher's exact test), Q value = 0.043
Table S21. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
AMP PEAK 12(13Q22.1) CNV | 17 | 46 | 52 |
AMP PEAK 12(13Q22.1) WILD-TYPE | 32 | 16 | 28 |
Figure S21. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000447 (Fisher's exact test), Q value = 0.24
Table S22. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
AMP PEAK 13(16P11.2) CNV | 5 | 23 | 3 | 13 |
AMP PEAK 13(16P11.2) WILD-TYPE | 26 | 39 | 27 | 10 |
Figure S22. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 0.000375 (Fisher's exact test), Q value = 0.2
Table S23. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
AMP PEAK 13(16P11.2) CNV | 13 | 7 | 24 |
AMP PEAK 13(16P11.2) WILD-TYPE | 43 | 37 | 22 |
Figure S23. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 8.55e-19 (Fisher's exact test), Q value = 5.7e-16
Table S24. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 13(16P11.2) CNV | 88 | 18 | 8 | 2 |
AMP PEAK 13(16P11.2) WILD-TYPE | 82 | 169 | 24 | 22 |
Figure S24. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000429 (Fisher's exact test), Q value = 0.23
Table S25. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
AMP PEAK 13(16P11.2) CNV | 8 | 24 | 13 | 4 |
AMP PEAK 13(16P11.2) WILD-TYPE | 23 | 35 | 34 | 50 |
Figure S25. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.02e-05 (Fisher's exact test), Q value = 0.017
Table S26. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
AMP PEAK 14(16Q12.1) CNV | 3 | 21 | 2 | 13 |
AMP PEAK 14(16Q12.1) WILD-TYPE | 28 | 41 | 28 | 10 |
Figure S26. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 0.000126 (Fisher's exact test), Q value = 0.07
Table S27. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
AMP PEAK 14(16Q12.1) CNV | 13 | 4 | 22 |
AMP PEAK 14(16Q12.1) WILD-TYPE | 43 | 40 | 24 |
Figure S27. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1.67e-20 (Fisher's exact test), Q value = 1.1e-17
Table S28. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 14(16Q12.1) CNV | 82 | 12 | 7 | 1 |
AMP PEAK 14(16Q12.1) WILD-TYPE | 88 | 175 | 25 | 23 |
Figure S28. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 7.53e-07 (Fisher's exact test), Q value = 0.00044
Table S29. Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 15(17Q12) CNV | 62 | 23 | 8 | 8 |
AMP PEAK 15(17Q12) WILD-TYPE | 108 | 164 | 24 | 16 |
Figure S29. Get High-res Image Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.026
Table S30. Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
AMP PEAK 15(17Q12) CNV | 8 | 26 | 6 | 5 |
AMP PEAK 15(17Q12) WILD-TYPE | 23 | 33 | 41 | 49 |
Figure S30. Get High-res Image Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.61e-08 (Fisher's exact test), Q value = 9.7e-06
Table S31. Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 16(17Q24.1) CNV | 59 | 17 | 8 | 8 |
AMP PEAK 16(17Q24.1) WILD-TYPE | 111 | 170 | 24 | 16 |
Figure S31. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 6.04e-06 (Fisher's exact test), Q value = 0.0035
Table S32. Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
AMP PEAK 16(17Q24.1) CNV | 9 | 26 | 4 | 5 |
AMP PEAK 16(17Q24.1) WILD-TYPE | 22 | 33 | 43 | 49 |
Figure S32. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.027
Table S33. Gene #17: 'Amp Peak 17(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 17(19P13.2) CNV | 39 | 13 | 8 | 5 |
AMP PEAK 17(19P13.2) WILD-TYPE | 131 | 174 | 24 | 19 |
Figure S33. Get High-res Image Gene #17: 'Amp Peak 17(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.86e-12 (Fisher's exact test), Q value = 1.2e-09
Table S34. Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 19(20P12.3) CNV | 83 | 58 | 31 | 12 |
AMP PEAK 19(20P12.3) WILD-TYPE | 87 | 129 | 1 | 12 |
Figure S34. Get High-res Image Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 8.3e-14
Table S35. Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 20(20P11.23) CNV | 102 | 58 | 32 | 13 |
AMP PEAK 20(20P11.23) WILD-TYPE | 68 | 129 | 0 | 11 |
Figure S35. Get High-res Image Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.27e-05 (Fisher's exact test), Q value = 0.024
Table S36. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
AMP PEAK 21(20P11.21) CNV | 38 | 12 | 31 |
AMP PEAK 21(20P11.21) WILD-TYPE | 18 | 32 | 15 |
Figure S36. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 4e-23 (Fisher's exact test), Q value = 2.7e-20
Table S37. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 21(20P11.21) CNV | 126 | 58 | 32 | 14 |
AMP PEAK 21(20P11.21) WILD-TYPE | 44 | 129 | 0 | 10 |
Figure S37. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.41e-07 (Fisher's exact test), Q value = 0.00014
Table S38. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
AMP PEAK 21(20P11.21) CNV | 19 | 44 | 24 | 12 |
AMP PEAK 21(20P11.21) WILD-TYPE | 12 | 15 | 23 | 42 |
Figure S38. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.39e-06 (Fisher's exact test), Q value = 0.00081
Table S39. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
AMP PEAK 21(20P11.21) CNV | 10 | 40 | 49 |
AMP PEAK 21(20P11.21) WILD-TYPE | 39 | 22 | 31 |
Figure S39. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-10 (Fisher's exact test), Q value = 6.7e-08
Table S40. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
AMP PEAK 22(20Q11.21) CNV | 12 | 59 | 14 | 20 |
AMP PEAK 22(20Q11.21) WILD-TYPE | 19 | 3 | 16 | 3 |
Figure S40. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 2.86e-11 (Fisher's exact test), Q value = 1.8e-08
Table S41. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
AMP PEAK 22(20Q11.21) CNV | 50 | 14 | 41 |
AMP PEAK 22(20Q11.21) WILD-TYPE | 6 | 30 | 5 |
Figure S41. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1.54e-43 (Fisher's exact test), Q value = 1e-40
Table S42. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 22(20Q11.21) CNV | 167 | 74 | 32 | 23 |
AMP PEAK 22(20Q11.21) WILD-TYPE | 3 | 113 | 0 | 1 |
Figure S42. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.19e-09 (Fisher's exact test), Q value = 1.3e-06
Table S43. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
AMP PEAK 22(20Q11.21) CNV | 96 | 46 | 40 |
AMP PEAK 22(20Q11.21) WILD-TYPE | 9 | 40 | 23 |
Figure S43. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.06
Table S44. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 56 | 63 | 180 |
AMP PEAK 22(20Q11.21) CNV | 13 | 29 | 53 | 133 |
AMP PEAK 22(20Q11.21) WILD-TYPE | 13 | 27 | 10 | 47 |
Figure S44. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 1.47e-14 (Fisher's exact test), Q value = 9.6e-12
Table S45. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
AMP PEAK 22(20Q11.21) CNV | 23 | 58 | 34 | 17 |
AMP PEAK 22(20Q11.21) WILD-TYPE | 8 | 1 | 13 | 37 |
Figure S45. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.85e-12 (Fisher's exact test), Q value = 2.5e-09
Table S46. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
AMP PEAK 22(20Q11.21) CNV | 14 | 56 | 62 |
AMP PEAK 22(20Q11.21) WILD-TYPE | 35 | 6 | 18 |
Figure S46. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 9.28e-12 (Fisher's exact test), Q value = 5.9e-09
Table S47. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
AMP PEAK 23(20Q12) CNV | 11 | 59 | 13 | 20 |
AMP PEAK 23(20Q12) WILD-TYPE | 20 | 3 | 17 | 3 |
Figure S47. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 1.82e-11 (Fisher's exact test), Q value = 1.1e-08
Table S48. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
AMP PEAK 23(20Q12) CNV | 49 | 13 | 41 |
AMP PEAK 23(20Q12) WILD-TYPE | 7 | 31 | 5 |
Figure S48. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 6.28e-43 (Fisher's exact test), Q value = 4.2e-40
Table S49. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 23(20Q12) CNV | 167 | 75 | 32 | 23 |
AMP PEAK 23(20Q12) WILD-TYPE | 3 | 112 | 0 | 1 |
Figure S49. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.58e-08 (Fisher's exact test), Q value = 9.6e-06
Table S50. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
AMP PEAK 23(20Q12) CNV | 96 | 48 | 41 |
AMP PEAK 23(20Q12) WILD-TYPE | 9 | 38 | 22 |
Figure S50. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.012
Table S51. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 56 | 63 | 180 |
AMP PEAK 23(20Q12) CNV | 13 | 29 | 55 | 132 |
AMP PEAK 23(20Q12) WILD-TYPE | 13 | 27 | 8 | 48 |
Figure S51. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 5.48e-14 (Fisher's exact test), Q value = 3.6e-11
Table S52. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
AMP PEAK 23(20Q12) CNV | 23 | 58 | 35 | 18 |
AMP PEAK 23(20Q12) WILD-TYPE | 8 | 1 | 12 | 36 |
Figure S52. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.34e-11 (Fisher's exact test), Q value = 8.5e-09
Table S53. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
AMP PEAK 23(20Q12) CNV | 15 | 56 | 63 |
AMP PEAK 23(20Q12) WILD-TYPE | 34 | 6 | 17 |
Figure S53. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.87e-10 (Fisher's exact test), Q value = 1.8e-07
Table S54. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
AMP PEAK 24(20Q13.32) CNV | 12 | 59 | 15 | 20 |
AMP PEAK 24(20Q13.32) WILD-TYPE | 19 | 3 | 15 | 3 |
Figure S54. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 6.27e-12 (Fisher's exact test), Q value = 4e-09
Table S55. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
AMP PEAK 24(20Q13.32) CNV | 51 | 14 | 41 |
AMP PEAK 24(20Q13.32) WILD-TYPE | 5 | 30 | 5 |
Figure S55. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 3.18e-43 (Fisher's exact test), Q value = 2.1e-40
Table S56. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
AMP PEAK 24(20Q13.32) CNV | 168 | 77 | 32 | 23 |
AMP PEAK 24(20Q13.32) WILD-TYPE | 2 | 110 | 0 | 1 |
Figure S56. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.58e-08 (Fisher's exact test), Q value = 9.6e-06
Table S57. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
AMP PEAK 24(20Q13.32) CNV | 96 | 48 | 41 |
AMP PEAK 24(20Q13.32) WILD-TYPE | 9 | 38 | 22 |
Figure S57. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0075
Table S58. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 56 | 63 | 180 |
AMP PEAK 24(20Q13.32) CNV | 13 | 29 | 55 | 135 |
AMP PEAK 24(20Q13.32) WILD-TYPE | 13 | 27 | 8 | 45 |
Figure S58. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 5.48e-14 (Fisher's exact test), Q value = 3.6e-11
Table S59. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
AMP PEAK 24(20Q13.32) CNV | 23 | 58 | 35 | 18 |
AMP PEAK 24(20Q13.32) WILD-TYPE | 8 | 1 | 12 | 36 |
Figure S59. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.34e-11 (Fisher's exact test), Q value = 8.5e-09
Table S60. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
AMP PEAK 24(20Q13.32) CNV | 15 | 56 | 63 |
AMP PEAK 24(20Q13.32) WILD-TYPE | 34 | 6 | 17 |
Figure S60. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 6.81e-05 (Fisher's exact test), Q value = 0.038
Table S61. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
DEL PEAK 1(1P36.11) CNV | 9 | 35 | 3 | 11 |
DEL PEAK 1(1P36.11) WILD-TYPE | 22 | 27 | 27 | 12 |
Figure S61. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 6.32e-17 (Fisher's exact test), Q value = 4.2e-14
Table S62. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 1(1P36.11) CNV | 91 | 28 | 22 | 9 |
DEL PEAK 1(1P36.11) WILD-TYPE | 79 | 159 | 10 | 15 |
Figure S62. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000347 (Fisher's exact test), Q value = 0.19
Table S63. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 1(1P36.11) CNV | 11 | 31 | 17 | 8 |
DEL PEAK 1(1P36.11) WILD-TYPE | 20 | 28 | 30 | 46 |
Figure S63. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.09e-11 (Fisher's exact test), Q value = 6.9e-09
Table S64. Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 2(1P33) CNV | 69 | 20 | 15 | 3 |
DEL PEAK 2(1P33) WILD-TYPE | 101 | 167 | 17 | 21 |
Figure S64. Get High-res Image Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 6.85e-10 (Fisher's exact test), Q value = 4.3e-07
Table S65. Gene #27: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 3(1P13.1) CNV | 66 | 23 | 13 | 1 |
DEL PEAK 3(1P13.1) WILD-TYPE | 104 | 164 | 19 | 23 |
Figure S65. Get High-res Image Gene #27: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.004
Table S66. Gene #28: 'Del Peak 4(1q43)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 4(1Q43) CNV | 32 | 7 | 5 | 0 |
DEL PEAK 4(1Q43) WILD-TYPE | 138 | 180 | 27 | 24 |
Figure S66. Get High-res Image Gene #28: 'Del Peak 4(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.23
Table S67. Gene #30: 'Del Peak 6(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 6(3P26.1) CNV | 36 | 14 | 8 | 2 |
DEL PEAK 6(3P26.1) WILD-TYPE | 134 | 173 | 24 | 22 |
Figure S67. Get High-res Image Gene #30: 'Del Peak 6(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.16e-12 (Fisher's exact test), Q value = 7.5e-10
Table S68. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 9(4P16.2) CNV | 73 | 23 | 19 | 6 |
DEL PEAK 9(4P16.2) WILD-TYPE | 97 | 164 | 13 | 18 |
Figure S68. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.13
Table S69. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 9(4P16.2) CNV | 9 | 24 | 16 | 4 |
DEL PEAK 9(4P16.2) WILD-TYPE | 22 | 35 | 31 | 50 |
Figure S69. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.059
Table S70. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
DEL PEAK 9(4P16.2) CNV | 3 | 23 | 27 |
DEL PEAK 9(4P16.2) WILD-TYPE | 46 | 39 | 53 |
Figure S70. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 8.5e-12 (Fisher's exact test), Q value = 5.4e-09
Table S71. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 10(4Q22.1) CNV | 77 | 28 | 18 | 3 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 93 | 159 | 14 | 21 |
Figure S71. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.052
Table S72. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 10(4Q22.1) CNV | 9 | 28 | 15 | 5 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 22 | 31 | 32 | 49 |
Figure S72. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.016
Table S73. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
DEL PEAK 10(4Q22.1) CNV | 3 | 25 | 29 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 46 | 37 | 51 |
Figure S73. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000128 (Fisher's exact test), Q value = 0.07
Table S74. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
DEL PEAK 11(4Q35.1) CNV | 7 | 30 | 3 | 13 |
DEL PEAK 11(4Q35.1) WILD-TYPE | 24 | 32 | 27 | 10 |
Figure S74. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 1.05e-13 (Fisher's exact test), Q value = 6.8e-11
Table S75. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 11(4Q35.1) CNV | 88 | 28 | 16 | 5 |
DEL PEAK 11(4Q35.1) WILD-TYPE | 82 | 159 | 16 | 19 |
Figure S75. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 7.69e-05 (Fisher's exact test), Q value = 0.043
Table S76. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
DEL PEAK 11(4Q35.1) CNV | 46 | 13 | 20 |
DEL PEAK 11(4Q35.1) WILD-TYPE | 59 | 73 | 43 |
Figure S76. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000239 (Fisher's exact test), Q value = 0.13
Table S77. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 11(4Q35.1) CNV | 11 | 30 | 15 | 7 |
DEL PEAK 11(4Q35.1) WILD-TYPE | 20 | 29 | 32 | 47 |
Figure S77. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.94e-09 (Fisher's exact test), Q value = 3e-06
Table S78. Gene #36: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 12(5Q11.2) CNV | 60 | 16 | 9 | 6 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 110 | 171 | 23 | 18 |
Figure S78. Get High-res Image Gene #36: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.14e-09 (Fisher's exact test), Q value = 7e-07
Table S79. Gene #37: 'Del Peak 13(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 13(5Q21.3) CNV | 71 | 24 | 14 | 8 |
DEL PEAK 13(5Q21.3) WILD-TYPE | 99 | 163 | 18 | 16 |
Figure S79. Get High-res Image Gene #37: 'Del Peak 13(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.57e-08 (Fisher's exact test), Q value = 9.5e-06
Table S80. Gene #38: 'Del Peak 14(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 14(5Q23.1) CNV | 64 | 22 | 13 | 8 |
DEL PEAK 14(5Q23.1) WILD-TYPE | 106 | 165 | 19 | 16 |
Figure S80. Get High-res Image Gene #38: 'Del Peak 14(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.057
Table S81. Gene #39: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 15(6P25.3) CNV | 13 | 23 | 9 | 9 |
DEL PEAK 15(6P25.3) WILD-TYPE | 157 | 164 | 23 | 15 |
Figure S81. Get High-res Image Gene #39: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 6.84e-26 (Fisher's exact test), Q value = 4.6e-23
Table S82. Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 18(8P23.3) CNV | 119 | 32 | 6 | 14 |
DEL PEAK 18(8P23.3) WILD-TYPE | 51 | 155 | 26 | 10 |
Figure S82. Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.61e-06 (Fisher's exact test), Q value = 0.0021
Table S83. Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
DEL PEAK 18(8P23.3) CNV | 62 | 21 | 22 |
DEL PEAK 18(8P23.3) WILD-TYPE | 43 | 65 | 41 |
Figure S83. Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 2.41e-30 (Fisher's exact test), Q value = 1.6e-27
Table S84. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 19(8P22) CNV | 129 | 33 | 8 | 15 |
DEL PEAK 19(8P22) WILD-TYPE | 41 | 154 | 24 | 9 |
Figure S84. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00021
Table S85. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
DEL PEAK 19(8P22) CNV | 69 | 24 | 24 |
DEL PEAK 19(8P22) WILD-TYPE | 36 | 62 | 39 |
Figure S85. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.071
Table S86. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 56 | 63 | 180 |
DEL PEAK 19(8P22) CNV | 5 | 15 | 38 | 82 |
DEL PEAK 19(8P22) WILD-TYPE | 21 | 41 | 25 | 98 |
Figure S86. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.012
Table S87. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 19(8P22) CNV | 17 | 38 | 21 | 11 |
DEL PEAK 19(8P22) WILD-TYPE | 14 | 21 | 26 | 43 |
Figure S87. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 8.88e-09 (Fisher's exact test), Q value = 5.4e-06
Table S88. Gene #44: 'Del Peak 20(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 20(8P11.22) CNV | 58 | 18 | 3 | 1 |
DEL PEAK 20(8P11.22) WILD-TYPE | 112 | 169 | 29 | 23 |
Figure S88. Get High-res Image Gene #44: 'Del Peak 20(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 5.81e-07 (Fisher's exact test), Q value = 0.00034
Table S89. Gene #45: 'Del Peak 21(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 21(8P11.21) CNV | 35 | 7 | 1 | 0 |
DEL PEAK 21(8P11.21) WILD-TYPE | 135 | 180 | 31 | 24 |
Figure S89. Get High-res Image Gene #45: 'Del Peak 21(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.51e-05 (Fisher's exact test), Q value = 0.026
Table S90. Gene #46: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 22(9P21.3) CNV | 35 | 10 | 7 | 4 |
DEL PEAK 22(9P21.3) WILD-TYPE | 135 | 177 | 25 | 20 |
Figure S90. Get High-res Image Gene #46: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.25e-08 (Fisher's exact test), Q value = 1.4e-05
Table S91. Gene #47: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 23(10P15.3) CNV | 38 | 12 | 15 | 3 |
DEL PEAK 23(10P15.3) WILD-TYPE | 132 | 175 | 17 | 21 |
Figure S91. Get High-res Image Gene #47: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.24e-11 (Fisher's exact test), Q value = 1.4e-08
Table S92. Gene #48: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 24(10Q21.1) CNV | 48 | 12 | 17 | 5 |
DEL PEAK 24(10Q21.1) WILD-TYPE | 122 | 175 | 15 | 19 |
Figure S92. Get High-res Image Gene #48: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00021
Table S93. Gene #49: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 25(10Q23.31) CNV | 53 | 21 | 15 | 5 |
DEL PEAK 25(10Q23.31) WILD-TYPE | 117 | 166 | 17 | 19 |
Figure S93. Get High-res Image Gene #49: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.91e-11 (Fisher's exact test), Q value = 1.2e-08
Table S94. Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 26(10Q25.2) CNV | 57 | 16 | 17 | 3 |
DEL PEAK 26(10Q25.2) WILD-TYPE | 113 | 171 | 15 | 21 |
Figure S94. Get High-res Image Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 9.87e-08 (Fisher's exact test), Q value = 5.9e-05
Table S95. Gene #51: 'Del Peak 27(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 27(12P13.2) CNV | 34 | 4 | 5 | 1 |
DEL PEAK 27(12P13.2) WILD-TYPE | 136 | 183 | 27 | 23 |
Figure S95. Get High-res Image Gene #51: 'Del Peak 27(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.07
Table S96. Gene #52: 'Del Peak 28(13q14.13)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 28(13Q14.13) CNV | 1 | 9 | 6 | 2 |
DEL PEAK 28(13Q14.13) WILD-TYPE | 169 | 178 | 26 | 22 |
Figure S96. Get High-res Image Gene #52: 'Del Peak 28(13q14.13)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.012
Table S97. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
DEL PEAK 29(14Q32.11) CNV | 7 | 35 | 3 | 11 |
DEL PEAK 29(14Q32.11) WILD-TYPE | 24 | 27 | 27 | 12 |
Figure S97. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.061
Table S98. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
DEL PEAK 29(14Q32.11) CNV | 22 | 7 | 27 |
DEL PEAK 29(14Q32.11) WILD-TYPE | 34 | 37 | 19 |
Figure S98. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1.61e-20 (Fisher's exact test), Q value = 1.1e-17
Table S99. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 29(14Q32.11) CNV | 98 | 22 | 10 | 3 |
DEL PEAK 29(14Q32.11) WILD-TYPE | 72 | 165 | 22 | 21 |
Figure S99. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 7.3e-05 (Fisher's exact test), Q value = 0.041
Table S100. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 29(14Q32.11) CNV | 11 | 28 | 13 | 5 |
DEL PEAK 29(14Q32.11) WILD-TYPE | 20 | 31 | 34 | 49 |
Figure S100. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.000422 (Fisher's exact test), Q value = 0.23
Table S101. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
DEL PEAK 30(15Q11.2) CNV | 8 | 35 | 5 | 12 |
DEL PEAK 30(15Q11.2) WILD-TYPE | 23 | 27 | 25 | 11 |
Figure S101. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 1.2e-21 (Fisher's exact test), Q value = 8e-19
Table S102. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 30(15Q11.2) CNV | 104 | 29 | 22 | 5 |
DEL PEAK 30(15Q11.2) WILD-TYPE | 66 | 158 | 10 | 19 |
Figure S102. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.09e-06 (Fisher's exact test), Q value = 0.0012
Table S103. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 30(15Q11.2) CNV | 13 | 32 | 19 | 5 |
DEL PEAK 30(15Q11.2) WILD-TYPE | 18 | 27 | 28 | 49 |
Figure S103. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.000117 (Fisher's exact test), Q value = 0.065
Table S104. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
DEL PEAK 30(15Q11.2) CNV | 6 | 29 | 34 |
DEL PEAK 30(15Q11.2) WILD-TYPE | 43 | 33 | 46 |
Figure S104. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 8.15e-18 (Fisher's exact test), Q value = 5.4e-15
Table S105. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 31(15Q21.1) CNV | 97 | 30 | 20 | 4 |
DEL PEAK 31(15Q21.1) WILD-TYPE | 73 | 157 | 12 | 20 |
Figure S105. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.03e-07 (Fisher's exact test), Q value = 0.00012
Table S106. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 31(15Q21.1) CNV | 12 | 31 | 17 | 3 |
DEL PEAK 31(15Q21.1) WILD-TYPE | 19 | 28 | 30 | 51 |
Figure S106. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.012
Table S107. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
DEL PEAK 31(15Q21.1) CNV | 4 | 28 | 31 |
DEL PEAK 31(15Q21.1) WILD-TYPE | 45 | 34 | 49 |
Figure S107. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.48e-21 (Fisher's exact test), Q value = 1.7e-18
Table S108. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 32(15Q22.33) CNV | 96 | 23 | 21 | 5 |
DEL PEAK 32(15Q22.33) WILD-TYPE | 74 | 164 | 11 | 19 |
Figure S108. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000435 (Fisher's exact test), Q value = 0.23
Table S109. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
DEL PEAK 32(15Q22.33) CNV | 49 | 17 | 22 |
DEL PEAK 32(15Q22.33) WILD-TYPE | 56 | 69 | 41 |
Figure S109. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3.07e-08 (Fisher's exact test), Q value = 1.8e-05
Table S110. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 32(15Q22.33) CNV | 13 | 33 | 17 | 3 |
DEL PEAK 32(15Q22.33) WILD-TYPE | 18 | 26 | 30 | 51 |
Figure S110. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 7.55e-06 (Fisher's exact test), Q value = 0.0044
Table S111. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
DEL PEAK 32(15Q22.33) CNV | 4 | 29 | 33 |
DEL PEAK 32(15Q22.33) WILD-TYPE | 45 | 33 | 47 |
Figure S111. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 6.12e-08 (Fisher's exact test), Q value = 3.7e-05
Table S112. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
DEL PEAK 35(17P12) CNV | 10 | 49 | 7 | 16 |
DEL PEAK 35(17P12) WILD-TYPE | 21 | 13 | 23 | 7 |
Figure S112. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 1.6e-06 (Fisher's exact test), Q value = 0.00093
Table S113. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
DEL PEAK 35(17P12) CNV | 36 | 11 | 35 |
DEL PEAK 35(17P12) WILD-TYPE | 20 | 33 | 11 |
Figure S113. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 2.81e-35 (Fisher's exact test), Q value = 1.9e-32
Table S114. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 35(17P12) CNV | 146 | 43 | 24 | 16 |
DEL PEAK 35(17P12) WILD-TYPE | 24 | 144 | 8 | 8 |
Figure S114. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.8e-09 (Fisher's exact test), Q value = 1.1e-06
Table S115. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
DEL PEAK 35(17P12) CNV | 82 | 30 | 29 |
DEL PEAK 35(17P12) WILD-TYPE | 23 | 56 | 34 |
Figure S115. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 7.42e-05 (Fisher's exact test), Q value = 0.042
Table S116. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 56 | 63 | 180 |
DEL PEAK 35(17P12) CNV | 8 | 19 | 43 | 106 |
DEL PEAK 35(17P12) WILD-TYPE | 18 | 37 | 20 | 74 |
Figure S116. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 1.06e-10 (Fisher's exact test), Q value = 6.6e-08
Table S117. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 35(17P12) CNV | 20 | 49 | 23 | 11 |
DEL PEAK 35(17P12) WILD-TYPE | 11 | 10 | 24 | 43 |
Figure S117. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.2e-08 (Fisher's exact test), Q value = 1.9e-05
Table S118. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
DEL PEAK 35(17P12) CNV | 11 | 48 | 44 |
DEL PEAK 35(17P12) WILD-TYPE | 38 | 14 | 36 |
Figure S118. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.51e-12 (Fisher's exact test), Q value = 9.7e-10
Table S119. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
DEL PEAK 37(18P11.31) CNV | 6 | 51 | 5 | 16 |
DEL PEAK 37(18P11.31) WILD-TYPE | 25 | 11 | 25 | 7 |
Figure S119. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 3.65e-09 (Fisher's exact test), Q value = 2.2e-06
Table S120. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
DEL PEAK 37(18P11.31) CNV | 36 | 7 | 35 |
DEL PEAK 37(18P11.31) WILD-TYPE | 20 | 37 | 11 |
Figure S120. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1.93e-42 (Fisher's exact test), Q value = 1.3e-39
Table S121. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 37(18P11.31) CNV | 145 | 34 | 28 | 13 |
DEL PEAK 37(18P11.31) WILD-TYPE | 25 | 153 | 4 | 11 |
Figure S121. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.11e-13 (Fisher's exact test), Q value = 2e-10
Table S122. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
DEL PEAK 37(18P11.31) CNV | 83 | 22 | 31 |
DEL PEAK 37(18P11.31) WILD-TYPE | 22 | 64 | 32 |
Figure S122. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3.11e-17 (Fisher's exact test), Q value = 2.1e-14
Table S123. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 37(18P11.31) CNV | 17 | 52 | 24 | 5 |
DEL PEAK 37(18P11.31) WILD-TYPE | 14 | 7 | 23 | 49 |
Figure S123. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 8.19e-10 (Fisher's exact test), Q value = 5.1e-07
Table S124. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
DEL PEAK 37(18P11.31) CNV | 7 | 45 | 46 |
DEL PEAK 37(18P11.31) WILD-TYPE | 42 | 17 | 34 |
Figure S124. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 8.37e-11 (Fisher's exact test), Q value = 5.2e-08
Table S125. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
DEL PEAK 38(18Q12.2) CNV | 8 | 53 | 8 | 17 |
DEL PEAK 38(18Q12.2) WILD-TYPE | 23 | 9 | 22 | 6 |
Figure S125. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 1.08e-09 (Fisher's exact test), Q value = 6.7e-07
Table S126. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
DEL PEAK 38(18Q12.2) CNV | 39 | 9 | 38 |
DEL PEAK 38(18Q12.2) WILD-TYPE | 17 | 35 | 8 |
Figure S126. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1.87e-45 (Fisher's exact test), Q value = 1.3e-42
Table S127. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 38(18Q12.2) CNV | 157 | 44 | 27 | 19 |
DEL PEAK 38(18Q12.2) WILD-TYPE | 13 | 143 | 5 | 5 |
Figure S127. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 8.98e-16 (Fisher's exact test), Q value = 5.9e-13
Table S128. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
DEL PEAK 38(18Q12.2) CNV | 93 | 29 | 31 |
DEL PEAK 38(18Q12.2) WILD-TYPE | 12 | 57 | 32 |
Figure S128. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000421 (Fisher's exact test), Q value = 0.23
Table S129. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 56 | 63 | 180 |
DEL PEAK 38(18Q12.2) CNV | 9 | 22 | 43 | 113 |
DEL PEAK 38(18Q12.2) WILD-TYPE | 17 | 34 | 20 | 67 |
Figure S129. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 7.66e-16 (Fisher's exact test), Q value = 5e-13
Table S130. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 38(18Q12.2) CNV | 21 | 53 | 28 | 8 |
DEL PEAK 38(18Q12.2) WILD-TYPE | 10 | 6 | 19 | 46 |
Figure S130. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.07e-08 (Fisher's exact test), Q value = 6.5e-06
Table S131. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
DEL PEAK 38(18Q12.2) CNV | 11 | 48 | 51 |
DEL PEAK 38(18Q12.2) WILD-TYPE | 38 | 14 | 29 |
Figure S131. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 3.06e-10 (Fisher's exact test), Q value = 1.9e-07
Table S132. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
DEL PEAK 39(18Q21.2) CNV | 8 | 53 | 9 | 17 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 23 | 9 | 21 | 6 |
Figure S132. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 6.85e-10 (Fisher's exact test), Q value = 4.3e-07
Table S133. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
DEL PEAK 39(18Q21.2) CNV | 40 | 9 | 38 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 16 | 35 | 8 |
Figure S133. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1.51e-45 (Fisher's exact test), Q value = 1e-42
Table S134. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 39(18Q21.2) CNV | 161 | 51 | 28 | 20 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 9 | 136 | 4 | 4 |
Figure S134. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.29e-12 (Fisher's exact test), Q value = 2.1e-09
Table S135. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
DEL PEAK 39(18Q21.2) CNV | 94 | 38 | 33 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 11 | 48 | 30 |
Figure S135. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000225 (Fisher's exact test), Q value = 0.12
Table S136. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 56 | 63 | 180 |
DEL PEAK 39(18Q21.2) CNV | 10 | 24 | 46 | 120 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 16 | 32 | 17 | 60 |
Figure S136. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 8.74e-13 (Fisher's exact test), Q value = 5.7e-10
Table S137. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 39(18Q21.2) CNV | 21 | 54 | 29 | 13 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 10 | 5 | 18 | 41 |
Figure S137. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 7.14e-07 (Fisher's exact test), Q value = 0.00042
Table S138. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
DEL PEAK 39(18Q21.2) CNV | 15 | 49 | 53 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 34 | 13 | 27 |
Figure S138. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 6.92e-11 (Fisher's exact test), Q value = 4.3e-08
Table S139. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
DEL PEAK 40(18Q22.1) CNV | 8 | 54 | 9 | 17 |
DEL PEAK 40(18Q22.1) WILD-TYPE | 23 | 8 | 21 | 6 |
Figure S139. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 3.65e-09 (Fisher's exact test), Q value = 2.2e-06
Table S140. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 44 | 46 |
DEL PEAK 40(18Q22.1) CNV | 40 | 10 | 38 |
DEL PEAK 40(18Q22.1) WILD-TYPE | 16 | 34 | 8 |
Figure S140. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 1.58e-47 (Fisher's exact test), Q value = 1.1e-44
Table S141. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 40(18Q22.1) CNV | 162 | 50 | 29 | 19 |
DEL PEAK 40(18Q22.1) WILD-TYPE | 8 | 137 | 3 | 5 |
Figure S141. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.02e-12 (Fisher's exact test), Q value = 1.3e-09
Table S142. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 86 | 63 |
DEL PEAK 40(18Q22.1) CNV | 94 | 38 | 32 |
DEL PEAK 40(18Q22.1) WILD-TYPE | 11 | 48 | 31 |
Figure S142. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.12
Table S143. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 26 | 56 | 63 | 180 |
DEL PEAK 40(18Q22.1) CNV | 10 | 24 | 45 | 122 |
DEL PEAK 40(18Q22.1) WILD-TYPE | 16 | 32 | 18 | 58 |
Figure S143. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 4.05e-12 (Fisher's exact test), Q value = 2.6e-09
Table S144. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 40(18Q22.1) CNV | 21 | 54 | 29 | 14 |
DEL PEAK 40(18Q22.1) WILD-TYPE | 10 | 5 | 18 | 40 |
Figure S144. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.76e-07 (Fisher's exact test), Q value = 0.00016
Table S145. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 49 | 62 | 80 |
DEL PEAK 40(18Q22.1) CNV | 15 | 50 | 53 |
DEL PEAK 40(18Q22.1) WILD-TYPE | 34 | 12 | 27 |
Figure S145. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-13 (Fisher's exact test), Q value = 9e-11
Table S146. Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 42(20P12.1) CNV | 61 | 12 | 0 | 6 |
DEL PEAK 42(20P12.1) WILD-TYPE | 109 | 175 | 32 | 18 |
Figure S146. Get High-res Image Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.082
Table S147. Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 59 | 47 | 54 |
DEL PEAK 42(20P12.1) CNV | 8 | 24 | 7 | 4 |
DEL PEAK 42(20P12.1) WILD-TYPE | 23 | 35 | 40 | 50 |
Figure S147. Get High-res Image Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.1e-06
Table S148. Gene #67: 'Del Peak 43(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 43(21Q11.2) CNV | 72 | 30 | 18 | 5 |
DEL PEAK 43(21Q11.2) WILD-TYPE | 98 | 157 | 14 | 19 |
Figure S148. Get High-res Image Gene #67: 'Del Peak 43(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000428 (Fisher's exact test), Q value = 0.23
Table S149. Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 31 | 62 | 30 | 23 |
DEL PEAK 44(22Q13.32) CNV | 8 | 34 | 4 | 10 |
DEL PEAK 44(22Q13.32) WILD-TYPE | 23 | 28 | 26 | 13 |
Figure S149. Get High-res Image Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 9.76e-13 (Fisher's exact test), Q value = 6.3e-10
Table S150. Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 170 | 187 | 32 | 24 |
DEL PEAK 44(22Q13.32) CNV | 85 | 28 | 17 | 8 |
DEL PEAK 44(22Q13.32) WILD-TYPE | 85 | 159 | 15 | 16 |
Figure S150. Get High-res Image Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #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 = COAD-TP.transferedmergedcluster.txt
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Number of patients = 413
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Number of copy number variation regions = 68
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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.