This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 82 peak regions and 10 molecular subtypes across 472 patients, 306 significant findings detected with Q value < 0.25.
-
Amp Peak 1(1p34.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
-
Amp Peak 2(1p22.3) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 3(1q21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 4(3q26.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 5(4q12) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 6(5p15.33) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 7(5p13.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 8(5q35.1) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Amp Peak 9(6p21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
Amp Peak 10(7p21.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
Amp Peak 11(7p11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 12(7q31.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Amp Peak 13(8p11.23) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 14(8p11.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 15(8q11.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 16(8q24.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 17(10p15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 18(11q13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 19(12p12.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 20(12q14.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 21(12q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 23(14q13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 24(17q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 25(17q23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 26(18q11.2) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 28(20p11.21) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 29(20q13.33) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Amp Peak 31(Xq28) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Del Peak 1(1p36.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Del Peak 2(1p13.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
Del Peak 3(1p13.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
Del Peak 5(2q37.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 6(3p21.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
Del Peak 8(3q29) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
-
Del Peak 9(4p16.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 10(4q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 11(4q35.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 13(5q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 15(6q22.31) cnvs correlated to 'METHLYATION_CNMF'.
-
Del Peak 16(6q26) cnvs correlated to 'METHLYATION_CNMF'.
-
Del Peak 17(8p23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
Del Peak 18(8p12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
Del Peak 19(8p11.21) cnvs correlated to 'CN_CNMF'.
-
Del Peak 21(9p23) cnvs correlated to 'CN_CNMF'.
-
Del Peak 22(9p21.3) cnvs correlated to 'CN_CNMF'.
-
Del Peak 23(9q21.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 25(10q26.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
-
Del Peak 26(11p15.5) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 27(11q23.2) cnvs correlated to 'CN_CNMF'.
-
Del Peak 29(12p13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
Del Peak 30(12q12) cnvs correlated to 'CN_CNMF'.
-
Del Peak 31(12q24.33) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
Del Peak 32(13q12.11) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 33(13q12.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 34(13q14.2) cnvs correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 35(13q34) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Del Peak 36(14q32.33) cnvs correlated to 'CN_CNMF'.
-
Del Peak 37(15q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
-
Del Peak 38(16q23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Del Peak 39(16q24.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Del Peak 40(17p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Del Peak 41(18q21.32) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Del Peak 42(18q23) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
Del Peak 43(19p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 44(19p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 45(19p12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 46(19q13.33) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 47(20p13) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
-
Del Peak 48(21q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 49(21q21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 50(22q13.32) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
-
Del Peak 51(Xp22.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 82 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 306 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 | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
Del Peak 10(4q22 1) | 0 (0%) | 330 |
0.000214 (0.114) |
9.89e-05 (0.0551) |
3.67e-07 (0.00025) |
9.89e-08 (7.07e-05) |
0.151 (1.00) |
0.0286 (1.00) |
3.81e-06 (0.00242) |
9.97e-14 (7.96e-11) |
1.66e-08 (1.22e-05) |
1.54e-06 (0.00101) |
Amp Peak 4(3q26 2) | 0 (0%) | 315 |
0.000264 (0.139) |
0.00332 (1.00) |
5.01e-10 (3.85e-07) |
5.52e-08 (3.98e-05) |
0.000631 (0.32) |
0.00307 (1.00) |
1.62e-09 (1.23e-06) |
5.62e-09 (4.22e-06) |
1.46e-06 (0.000956) |
2.21e-07 (0.000153) |
Amp Peak 11(7p11 2) | 0 (0%) | 220 |
1 (1.00) |
1 (1.00) |
1.27e-18 (1.02e-15) |
2e-05 (0.0118) |
0.00114 (0.554) |
0.000263 (0.139) |
1.06e-08 (7.91e-06) |
1.49e-10 (1.16e-07) |
2.59e-07 (0.000179) |
6.85e-05 (0.0388) |
Amp Peak 24(17q12) | 0 (0%) | 264 |
0.179 (1.00) |
0.049 (1.00) |
6.08e-14 (4.87e-11) |
8.27e-07 (0.000553) |
0.0638 (1.00) |
0.00016 (0.086) |
9.56e-11 (7.47e-08) |
2.02e-06 (0.0013) |
7.33e-07 (0.000491) |
1.1e-06 (0.000724) |
Amp Peak 25(17q23 1) | 0 (0%) | 242 |
0.081 (1.00) |
0.208 (1.00) |
2.25e-14 (1.81e-11) |
2.11e-08 (1.55e-05) |
0.00156 (0.742) |
4.12e-07 (0.000279) |
2.7e-13 (2.15e-10) |
5.99e-10 (4.58e-07) |
1.54e-06 (0.00101) |
5.68e-06 (0.00353) |
Del Peak 11(4q35 1) | 0 (0%) | 300 |
0.00204 (0.938) |
0.00118 (0.573) |
7.48e-10 (5.71e-07) |
1.36e-11 (1.07e-08) |
0.0381 (1.00) |
0.000196 (0.105) |
2.47e-09 (1.87e-06) |
7.36e-18 (5.94e-15) |
1.57e-10 (1.22e-07) |
1e-10 (7.83e-08) |
Amp Peak 14(8p11 21) | 0 (0%) | 310 |
0.253 (1.00) |
0.124 (1.00) |
3.42e-21 (2.78e-18) |
0.000128 (0.0697) |
0.0149 (1.00) |
0.00534 (1.00) |
1.59e-05 (0.00949) |
4.9e-07 (0.000331) |
4.19e-05 (0.0242) |
6.3e-06 (0.0039) |
Amp Peak 15(8q11 1) | 0 (0%) | 258 |
0.00472 (1.00) |
0.0134 (1.00) |
3.04e-22 (2.49e-19) |
1.14e-07 (8.08e-05) |
0.0344 (1.00) |
0.00467 (1.00) |
5.35e-06 (0.00334) |
2.26e-05 (0.0133) |
1.94e-07 (0.000136) |
8.84e-07 (0.000587) |
Amp Peak 16(8q24 21) | 0 (0%) | 174 |
0.0343 (1.00) |
0.0341 (1.00) |
8.4e-20 (6.82e-17) |
3.72e-08 (2.71e-05) |
0.157 (1.00) |
0.00162 (0.763) |
6.65e-05 (0.0378) |
3.27e-06 (0.00209) |
8.41e-07 (0.00056) |
1.26e-05 (0.00762) |
Amp Peak 17(10p15 1) | 0 (0%) | 348 |
0.023 (1.00) |
0.0262 (1.00) |
4.17e-06 (0.00264) |
2.59e-07 (0.000179) |
0.00434 (1.00) |
0.0346 (1.00) |
6.78e-05 (0.0385) |
2.08e-08 (1.54e-05) |
0.000237 (0.125) |
6.08e-05 (0.0346) |
Amp Peak 18(11q13 3) | 0 (0%) | 315 |
0.00118 (0.573) |
0.000736 (0.368) |
5.94e-14 (4.76e-11) |
1.94e-05 (0.0115) |
0.0127 (1.00) |
0.00689 (1.00) |
3.07e-08 (2.25e-05) |
9.49e-07 (0.000629) |
2.08e-10 (1.61e-07) |
2.03e-07 (0.000141) |
Amp Peak 19(12p12 1) | 0 (0%) | 309 |
0.198 (1.00) |
0.033 (1.00) |
5.45e-22 (4.46e-19) |
4.14e-06 (0.00262) |
0.0345 (1.00) |
0.0834 (1.00) |
1.44e-05 (0.00863) |
2.74e-07 (0.000188) |
6.05e-06 (0.00376) |
1.01e-05 (0.00621) |
Amp Peak 20(12q14 1) | 0 (0%) | 324 |
0.406 (1.00) |
0.302 (1.00) |
2.65e-24 (2.17e-21) |
1.45e-07 (0.000103) |
0.0215 (1.00) |
0.00722 (1.00) |
2.93e-07 (0.000201) |
3.88e-10 (2.98e-07) |
6.24e-09 (4.68e-06) |
4.09e-09 (3.09e-06) |
Amp Peak 21(12q15) | 0 (0%) | 321 |
0.221 (1.00) |
0.103 (1.00) |
1.49e-21 (1.22e-18) |
2.35e-08 (1.73e-05) |
0.0146 (1.00) |
0.00471 (1.00) |
7.24e-08 (5.21e-05) |
4.39e-09 (3.31e-06) |
2.17e-09 (1.65e-06) |
1.1e-07 (7.86e-05) |
Amp Peak 23(14q13 3) | 0 (0%) | 261 |
0.562 (1.00) |
0.254 (1.00) |
2.03e-11 (1.6e-08) |
4.73e-06 (0.00297) |
0.00213 (0.972) |
0.0122 (1.00) |
1.28e-09 (9.76e-07) |
3.84e-05 (0.0223) |
8.7e-08 (6.23e-05) |
2.61e-09 (1.98e-06) |
Amp Peak 27(19q12) | 0 (0%) | 346 |
0.0514 (1.00) |
0.0219 (1.00) |
1.29e-08 (9.54e-06) |
0.000304 (0.159) |
0.0685 (1.00) |
0.0791 (1.00) |
0.000438 (0.226) |
4.22e-08 (3.06e-05) |
1.27e-06 (0.000834) |
1.46e-06 (0.000956) |
Del Peak 9(4p16 3) | 0 (0%) | 356 |
0.595 (1.00) |
0.453 (1.00) |
1.56e-05 (0.00931) |
2.31e-05 (0.0136) |
0.0232 (1.00) |
0.0499 (1.00) |
8.4e-07 (0.00056) |
6.36e-11 (4.98e-08) |
2.82e-07 (0.000194) |
1.11e-07 (7.86e-05) |
Del Peak 12(5q11 2) | 0 (0%) | 306 |
0.26 (1.00) |
0.254 (1.00) |
1.9e-12 (1.5e-09) |
2.02e-07 (0.000141) |
0.00426 (1.00) |
0.0113 (1.00) |
1.35e-06 (0.000888) |
2.57e-09 (1.95e-06) |
4.53e-08 (3.28e-05) |
2.11e-06 (0.00136) |
Del Peak 13(5q22 1) | 0 (0%) | 283 |
0.0447 (1.00) |
0.0515 (1.00) |
1.08e-12 (8.57e-10) |
2.56e-08 (1.88e-05) |
0.0017 (0.795) |
0.00377 (1.00) |
1.55e-08 (1.14e-05) |
3.56e-10 (2.74e-07) |
5.97e-10 (4.58e-07) |
8.43e-09 (6.29e-06) |
Del Peak 17(8p23 2) | 0 (0%) | 243 |
0.00526 (1.00) |
0.00382 (1.00) |
7.67e-17 (6.18e-14) |
9.17e-05 (0.0514) |
0.018 (1.00) |
0.000354 (0.183) |
8.22e-09 (6.14e-06) |
2.29e-07 (0.000159) |
3.58e-06 (0.00228) |
0.00312 (1.00) |
Del Peak 33(13q12 13) | 0 (0%) | 206 |
0.00862 (1.00) |
0.0218 (1.00) |
1.05e-19 (8.48e-17) |
0.000107 (0.0596) |
0.000524 (0.27) |
6.68e-07 (0.00045) |
1.2e-07 (8.53e-05) |
8.17e-08 (5.86e-05) |
0.00386 (1.00) |
0.000138 (0.0749) |
Del Peak 34(13q14 2) | 0 (0%) | 216 |
0.00862 (1.00) |
0.0218 (1.00) |
7.61e-22 (6.22e-19) |
0.000783 (0.39) |
0.000647 (0.327) |
1.04e-05 (0.00636) |
4.15e-09 (3.13e-06) |
1.54e-07 (0.000109) |
0.000206 (0.11) |
4.69e-05 (0.027) |
Del Peak 37(15q11 2) | 0 (0%) | 233 |
0.168 (1.00) |
0.157 (1.00) |
1.81e-10 (1.41e-07) |
0.000193 (0.103) |
0.0928 (1.00) |
0.000161 (0.0866) |
1.91e-13 (1.53e-10) |
1.4e-05 (0.00841) |
2.82e-05 (0.0165) |
0.000803 (0.396) |
Del Peak 43(19p13 3) | 0 (0%) | 220 |
0.572 (1.00) |
0.665 (1.00) |
2.6e-12 (2.05e-09) |
2.35e-07 (0.000163) |
0.564 (1.00) |
0.306 (1.00) |
3.43e-10 (2.64e-07) |
3.14e-07 (0.000215) |
3.65e-06 (0.00232) |
1.63e-07 (0.000115) |
Del Peak 44(19p13 2) | 0 (0%) | 226 |
0.694 (1.00) |
1 (1.00) |
1.25e-11 (9.88e-09) |
2.22e-08 (1.63e-05) |
0.378 (1.00) |
0.187 (1.00) |
3.34e-10 (2.58e-07) |
4.01e-07 (0.000272) |
2.46e-06 (0.00158) |
2.87e-07 (0.000197) |
Del Peak 48(21q11 2) | 0 (0%) | 315 |
0.0604 (1.00) |
0.0501 (1.00) |
3.1e-11 (2.44e-08) |
0.000131 (0.0713) |
0.00624 (1.00) |
0.00469 (1.00) |
3.59e-08 (2.61e-05) |
3.78e-07 (0.000257) |
2.25e-05 (0.0132) |
3.55e-08 (2.59e-05) |
Del Peak 49(21q21 3) | 0 (0%) | 319 |
0.0288 (1.00) |
0.033 (1.00) |
9.45e-11 (7.39e-08) |
1.28e-05 (0.00773) |
0.000525 (0.27) |
0.00065 (0.328) |
3.24e-10 (2.51e-07) |
5.51e-10 (4.23e-07) |
1.04e-05 (0.00633) |
1.28e-07 (9.06e-05) |
Del Peak 50(22q13 32) | 0 (0%) | 248 |
0.0692 (1.00) |
0.0871 (1.00) |
6.18e-13 (4.91e-10) |
4.57e-08 (3.3e-05) |
0.00863 (1.00) |
0.0171 (1.00) |
1.51e-10 (1.17e-07) |
6.29e-11 (4.93e-08) |
1.66e-07 (0.000117) |
2.72e-08 (1.99e-05) |
Amp Peak 10(7p21 1) | 0 (0%) | 211 |
0.743 (1.00) |
1 (1.00) |
6.95e-20 (5.65e-17) |
4.93e-06 (0.00309) |
0.00184 (0.858) |
0.00104 (0.508) |
7.66e-09 (5.73e-06) |
7.98e-08 (5.73e-05) |
8.38e-06 (0.00515) |
0.00203 (0.938) |
Del Peak 6(3p21 31) | 0 (0%) | 245 |
0.132 (1.00) |
0.478 (1.00) |
7.53e-06 (0.00465) |
3.21e-06 (0.00206) |
0.0411 (1.00) |
0.00737 (1.00) |
3.35e-05 (0.0195) |
6.23e-09 (4.67e-06) |
1.18e-05 (0.00715) |
0.000743 (0.371) |
Del Peak 18(8p12) | 0 (0%) | 267 |
0.106 (1.00) |
0.12 (1.00) |
1.83e-15 (1.47e-12) |
1.95e-05 (0.0116) |
0.0424 (1.00) |
0.0222 (1.00) |
4.61e-05 (0.0267) |
5.37e-06 (0.00335) |
5.26e-05 (0.0301) |
0.00432 (1.00) |
Del Peak 23(9q21 11) | 0 (0%) | 241 |
0.0335 (1.00) |
0.597 (1.00) |
1.49e-07 (0.000105) |
5.08e-05 (0.0292) |
0.0726 (1.00) |
0.0112 (1.00) |
0.000116 (0.0644) |
1.67e-07 (0.000117) |
0.00333 (1.00) |
0.000126 (0.0689) |
Del Peak 32(13q12 11) | 0 (0%) | 207 |
0.00113 (0.553) |
0.0134 (1.00) |
1.38e-19 (1.12e-16) |
0.000608 (0.311) |
0.00188 (0.873) |
1.49e-06 (0.000971) |
2.73e-07 (0.000188) |
4.07e-08 (2.95e-05) |
0.00248 (1.00) |
8.51e-05 (0.0479) |
Del Peak 45(19p12) | 0 (0%) | 273 |
0.519 (1.00) |
0.658 (1.00) |
9.72e-13 (7.71e-10) |
1.71e-05 (0.0102) |
0.603 (1.00) |
0.266 (1.00) |
0.00153 (0.726) |
0.00012 (0.0662) |
2.79e-05 (0.0164) |
1.27e-05 (0.00765) |
Amp Peak 3(1q21 3) | 0 (0%) | 136 |
0.362 (1.00) |
0.465 (1.00) |
5.64e-06 (0.00351) |
8.32e-07 (0.000556) |
0.458 (1.00) |
0.357 (1.00) |
4.43e-06 (0.00279) |
0.473 (1.00) |
0.000695 (0.35) |
0.000211 (0.112) |
Amp Peak 6(5p15 33) | 0 (0%) | 168 |
0.878 (1.00) |
0.901 (1.00) |
2.75e-21 (2.24e-18) |
0.0397 (1.00) |
0.0565 (1.00) |
0.000798 (0.396) |
1.77e-07 (0.000124) |
0.00166 (0.777) |
0.000225 (0.119) |
0.000304 (0.159) |
Amp Peak 7(5p13 1) | 0 (0%) | 192 |
0.263 (1.00) |
0.897 (1.00) |
5.67e-18 (4.58e-15) |
0.0135 (1.00) |
0.443 (1.00) |
0.0187 (1.00) |
0.000119 (0.0661) |
0.00342 (1.00) |
0.000122 (0.0671) |
0.000274 (0.144) |
Amp Peak 12(7q31 2) | 0 (0%) | 272 |
0.482 (1.00) |
0.429 (1.00) |
2.86e-09 (2.16e-06) |
5.48e-05 (0.0313) |
0.206 (1.00) |
0.052 (1.00) |
2.97e-06 (0.0019) |
1.37e-08 (1.01e-05) |
0.00637 (1.00) |
0.00978 (1.00) |
Amp Peak 13(8p11 23) | 0 (0%) | 346 |
0.294 (1.00) |
0.107 (1.00) |
2.17e-16 (1.75e-13) |
8.25e-06 (0.00507) |
0.0844 (1.00) |
0.0267 (1.00) |
0.00309 (1.00) |
7.16e-06 (0.00443) |
0.0131 (1.00) |
0.000479 (0.247) |
Amp Peak 26(18q11 2) | 0 (0%) | 378 |
0.195 (1.00) |
0.0151 (1.00) |
0.000918 (0.451) |
1.07e-08 (7.93e-06) |
0.0431 (1.00) |
0.000816 (0.402) |
0.000799 (0.396) |
9.61e-05 (0.0538) |
1.06e-05 (0.00643) |
6.73e-07 (0.000452) |
Amp Peak 28(20p11 21) | 0 (0%) | 293 |
0.0611 (1.00) |
0.0953 (1.00) |
1.1e-05 (0.00669) |
0.00708 (1.00) |
0.338 (1.00) |
0.0379 (1.00) |
0.000221 (0.117) |
0.00159 (0.749) |
0.000145 (0.0785) |
7.51e-05 (0.0424) |
Amp Peak 29(20q13 33) | 0 (0%) | 247 |
0.00559 (1.00) |
0.0301 (1.00) |
1.03e-07 (7.35e-05) |
0.00296 (1.00) |
0.00426 (1.00) |
0.00335 (1.00) |
1.37e-05 (0.00821) |
0.0184 (1.00) |
2.53e-06 (0.00163) |
4.24e-07 (0.000287) |
Del Peak 1(1p36 13) | 0 (0%) | 364 |
0.795 (1.00) |
0.441 (1.00) |
1.59e-06 (0.00104) |
2.18e-05 (0.0129) |
0.437 (1.00) |
0.363 (1.00) |
8.06e-06 (0.00497) |
8.99e-06 (0.00551) |
0.0253 (1.00) |
0.00486 (1.00) |
Del Peak 38(16q23 1) | 0 (0%) | 312 |
0.0587 (1.00) |
0.312 (1.00) |
2.59e-07 (0.000179) |
0.00046 (0.237) |
0.000698 (0.35) |
0.0174 (1.00) |
1.73e-06 (0.00112) |
3.21e-07 (0.000219) |
0.013 (1.00) |
0.0559 (1.00) |
Del Peak 40(17p13 3) | 0 (0%) | 220 |
0.386 (1.00) |
0.609 (1.00) |
2.78e-13 (2.21e-10) |
7.56e-08 (5.44e-05) |
0.0334 (1.00) |
0.00158 (0.747) |
5.6e-08 (4.04e-05) |
9.79e-07 (0.000648) |
0.0102 (1.00) |
0.00603 (1.00) |
Amp Peak 8(5q35 1) | 0 (0%) | 362 |
0.0862 (1.00) |
0.453 (1.00) |
0.00391 (1.00) |
8.8e-07 (0.000585) |
0.0909 (1.00) |
0.2 (1.00) |
4.73e-05 (0.0272) |
0.000159 (0.0858) |
0.0134 (1.00) |
0.00294 (1.00) |
Amp Peak 31(Xq28) | 0 (0%) | 321 |
0.301 (1.00) |
0.123 (1.00) |
3.01e-10 (2.33e-07) |
5.94e-05 (0.0338) |
0.0244 (1.00) |
0.0308 (1.00) |
0.00146 (0.696) |
9.71e-05 (0.0543) |
0.0059 (1.00) |
0.033 (1.00) |
Del Peak 25(10q26 3) | 0 (0%) | 342 |
0.748 (1.00) |
0.283 (1.00) |
4.78e-06 (0.003) |
0.000256 (0.135) |
0.00268 (1.00) |
0.0237 (1.00) |
5.65e-05 (0.0323) |
0.00205 (0.938) |
0.0532 (1.00) |
0.00789 (1.00) |
Del Peak 26(11p15 5) | 0 (0%) | 346 |
0.268 (1.00) |
0.0576 (1.00) |
4.04e-06 (0.00256) |
0.012 (1.00) |
0.00767 (1.00) |
0.00204 (0.938) |
0.00111 (0.54) |
4.36e-06 (0.00275) |
0.00453 (1.00) |
0.000108 (0.0598) |
Del Peak 35(13q34) | 0 (0%) | 255 |
0.0356 (1.00) |
0.0445 (1.00) |
2.2e-15 (1.77e-12) |
0.0508 (1.00) |
0.00359 (1.00) |
0.00079 (0.392) |
3.71e-06 (0.00236) |
3.09e-05 (0.018) |
0.0215 (1.00) |
0.00462 (1.00) |
Del Peak 39(16q24 3) | 0 (0%) | 294 |
0.16 (1.00) |
0.631 (1.00) |
1.66e-06 (0.00108) |
0.00282 (1.00) |
0.0186 (1.00) |
0.08 (1.00) |
2.9e-05 (0.0169) |
4.88e-05 (0.028) |
0.0216 (1.00) |
0.0345 (1.00) |
Del Peak 41(18q21 32) | 0 (0%) | 239 |
0.115 (1.00) |
0.227 (1.00) |
8.58e-10 (6.55e-07) |
0.0508 (1.00) |
0.00133 (0.638) |
0.0023 (1.00) |
9.08e-09 (6.76e-06) |
0.00012 (0.0662) |
0.00925 (1.00) |
0.105 (1.00) |
Del Peak 42(18q23) | 0 (0%) | 244 |
0.029 (1.00) |
0.0968 (1.00) |
9.31e-13 (7.39e-10) |
0.0205 (1.00) |
0.00395 (1.00) |
0.00135 (0.65) |
1.04e-08 (7.74e-06) |
1.28e-05 (0.00773) |
0.00388 (1.00) |
0.0798 (1.00) |
Del Peak 46(19q13 33) | 0 (0%) | 298 |
0.272 (1.00) |
0.383 (1.00) |
2.02e-07 (0.000141) |
0.00292 (1.00) |
0.0819 (1.00) |
0.208 (1.00) |
0.0184 (1.00) |
0.00194 (0.9) |
2.52e-05 (0.0147) |
1.41e-05 (0.00844) |
Amp Peak 1(1p34 3) | 0 (0%) | 347 |
0.553 (1.00) |
0.384 (1.00) |
5.41e-07 (0.000365) |
0.00816 (1.00) |
0.169 (1.00) |
0.243 (1.00) |
4.96e-06 (0.00311) |
0.149 (1.00) |
0.184 (1.00) |
0.147 (1.00) |
Amp Peak 9(6p21 1) | 0 (0%) | 299 |
0.675 (1.00) |
0.206 (1.00) |
0.000168 (0.0903) |
1.05e-07 (7.46e-05) |
0.081 (1.00) |
0.609 (1.00) |
0.00918 (1.00) |
0.727 (1.00) |
0.012 (1.00) |
0.0168 (1.00) |
Del Peak 2(1p13 3) | 0 (0%) | 333 |
0.844 (1.00) |
0.896 (1.00) |
9.97e-07 (0.000659) |
9.81e-05 (0.0547) |
0.626 (1.00) |
0.717 (1.00) |
0.00705 (1.00) |
0.0574 (1.00) |
0.0693 (1.00) |
0.00638 (1.00) |
Del Peak 3(1p13 1) | 0 (0%) | 335 |
0.703 (1.00) |
0.707 (1.00) |
1.93e-06 (0.00125) |
2.2e-05 (0.013) |
0.124 (1.00) |
0.535 (1.00) |
0.00221 (1.00) |
0.0349 (1.00) |
0.0702 (1.00) |
0.0131 (1.00) |
Del Peak 5(2q37 3) | 0 (0%) | 409 |
0.703 (1.00) |
0.206 (1.00) |
0.00033 (0.171) |
0.0016 (0.756) |
0.22 (1.00) |
0.151 (1.00) |
0.178 (1.00) |
0.00905 (1.00) |
0.00691 (1.00) |
0.000153 (0.0827) |
Del Peak 8(3q29) | 0 (0%) | 343 |
0.71 (1.00) |
0.602 (1.00) |
0.145 (1.00) |
8.11e-05 (0.0457) |
0.00515 (1.00) |
0.0168 (1.00) |
3.27e-08 (2.39e-05) |
0.0171 (1.00) |
0.666 (1.00) |
0.684 (1.00) |
Del Peak 29(12p13 2) | 0 (0%) | 346 |
0.255 (1.00) |
0.719 (1.00) |
0.000172 (0.0921) |
7.21e-07 (0.000484) |
0.0774 (1.00) |
0.021 (1.00) |
0.00802 (1.00) |
0.111 (1.00) |
0.824 (1.00) |
1 (1.00) |
Del Peak 31(12q24 33) | 0 (0%) | 357 |
0.063 (1.00) |
0.0396 (1.00) |
6.54e-06 (0.00405) |
0.00195 (0.901) |
0.0223 (1.00) |
0.00328 (1.00) |
0.000614 (0.313) |
0.000306 (0.159) |
0.0538 (1.00) |
0.0151 (1.00) |
Del Peak 47(20p13) | 0 (0%) | 351 |
0.105 (1.00) |
0.268 (1.00) |
2.4e-06 (0.00155) |
0.000655 (0.33) |
0.00552 (1.00) |
0.00106 (0.52) |
0.000127 (0.0693) |
0.0117 (1.00) |
0.742 (1.00) |
0.772 (1.00) |
Del Peak 51(Xp22 2) | 0 (0%) | 335 |
0.691 (1.00) |
0.896 (1.00) |
1.99e-07 (0.000139) |
0.00131 (0.631) |
0.0885 (1.00) |
0.0284 (1.00) |
0.0141 (1.00) |
0.000322 (0.167) |
0.499 (1.00) |
0.244 (1.00) |
Amp Peak 2(1p22 3) | 0 (0%) | 348 |
0.876 (1.00) |
1 (1.00) |
4.8e-07 (0.000324) |
0.00253 (1.00) |
0.183 (1.00) |
0.399 (1.00) |
0.00168 (0.788) |
0.0091 (1.00) |
0.136 (1.00) |
0.131 (1.00) |
Amp Peak 5(4q12) | 0 (0%) | 384 |
0.703 (1.00) |
0.206 (1.00) |
6.06e-09 (4.55e-06) |
0.0314 (1.00) |
0.0221 (1.00) |
0.0265 (1.00) |
0.155 (1.00) |
0.0258 (1.00) |
0.00241 (1.00) |
0.00429 (1.00) |
Del Peak 15(6q22 31) | 0 (0%) | 238 |
0.54 (1.00) |
0.187 (1.00) |
0.022 (1.00) |
1.29e-06 (0.000849) |
0.308 (1.00) |
0.0544 (1.00) |
0.0184 (1.00) |
0.709 (1.00) |
0.9 (1.00) |
0.571 (1.00) |
Del Peak 16(6q26) | 0 (0%) | 234 |
0.368 (1.00) |
0.276 (1.00) |
0.0119 (1.00) |
8.64e-05 (0.0486) |
0.168 (1.00) |
0.00944 (1.00) |
0.141 (1.00) |
0.807 (1.00) |
0.81 (1.00) |
0.41 (1.00) |
Del Peak 19(8p11 21) | 0 (0%) | 365 |
0.795 (1.00) |
0.504 (1.00) |
2.79e-11 (2.2e-08) |
0.018 (1.00) |
0.721 (1.00) |
0.318 (1.00) |
0.000627 (0.318) |
0.185 (1.00) |
0.0376 (1.00) |
0.512 (1.00) |
Del Peak 21(9p23) | 0 (0%) | 214 |
0.521 (1.00) |
0.901 (1.00) |
3.22e-07 (0.000219) |
0.582 (1.00) |
0.62 (1.00) |
0.598 (1.00) |
0.0154 (1.00) |
0.0119 (1.00) |
0.639 (1.00) |
0.286 (1.00) |
Del Peak 22(9p21 3) | 0 (0%) | 208 |
0.521 (1.00) |
0.901 (1.00) |
1.79e-06 (0.00116) |
0.521 (1.00) |
0.328 (1.00) |
0.288 (1.00) |
0.022 (1.00) |
0.00284 (1.00) |
0.934 (1.00) |
0.464 (1.00) |
Del Peak 27(11q23 2) | 0 (0%) | 363 |
0.433 (1.00) |
0.453 (1.00) |
0.000122 (0.0669) |
0.0184 (1.00) |
0.009 (1.00) |
0.00266 (1.00) |
0.00156 (0.742) |
0.00172 (0.803) |
0.00296 (1.00) |
0.00545 (1.00) |
Del Peak 30(12q12) | 0 (0%) | 382 |
0.597 (1.00) |
0.644 (1.00) |
1.19e-05 (0.00722) |
0.021 (1.00) |
0.107 (1.00) |
0.0158 (1.00) |
0.00415 (1.00) |
0.0474 (1.00) |
0.204 (1.00) |
0.052 (1.00) |
Del Peak 36(14q32 33) | 0 (0%) | 332 |
0.703 (1.00) |
0.302 (1.00) |
0.000135 (0.0734) |
0.521 (1.00) |
0.16 (1.00) |
0.0627 (1.00) |
0.131 (1.00) |
0.0451 (1.00) |
0.0909 (1.00) |
0.0117 (1.00) |
Amp Peak 22(13q33 3) | 0 (0%) | 400 |
0.172 (1.00) |
0.105 (1.00) |
0.433 (1.00) |
0.00285 (1.00) |
0.663 (1.00) |
0.298 (1.00) |
0.0293 (1.00) |
0.229 (1.00) |
0.129 (1.00) |
0.0824 (1.00) |
Amp Peak 30(22q11 22) | 0 (0%) | 391 |
0.268 (1.00) |
0.162 (1.00) |
0.0014 (0.671) |
0.601 (1.00) |
0.0232 (1.00) |
0.119 (1.00) |
0.44 (1.00) |
0.0532 (1.00) |
0.0402 (1.00) |
0.125 (1.00) |
Del Peak 4(2q22 1) | 0 (0%) | 425 |
0.869 (1.00) |
0.78 (1.00) |
0.00238 (1.00) |
0.0379 (1.00) |
0.0306 (1.00) |
0.471 (1.00) |
0.151 (1.00) |
0.0213 (1.00) |
0.0739 (1.00) |
0.008 (1.00) |
Del Peak 7(3q11 1) | 0 (0%) | 339 |
0.609 (1.00) |
0.602 (1.00) |
0.0414 (1.00) |
0.0274 (1.00) |
0.366 (1.00) |
0.298 (1.00) |
0.0472 (1.00) |
0.0162 (1.00) |
0.183 (1.00) |
0.936 (1.00) |
Del Peak 14(6q12) | 0 (0%) | 314 |
0.532 (1.00) |
1 (1.00) |
0.0598 (1.00) |
0.0244 (1.00) |
0.243 (1.00) |
0.159 (1.00) |
0.575 (1.00) |
0.891 (1.00) |
0.0536 (1.00) |
0.476 (1.00) |
Del Peak 20(8q11 21) | 0 (0%) | 413 |
1 (1.00) |
1 (1.00) |
0.796 (1.00) |
0.0628 (1.00) |
0.537 (1.00) |
0.676 (1.00) |
0.000831 (0.409) |
0.604 (1.00) |
0.151 (1.00) |
0.464 (1.00) |
Del Peak 24(10p15 3) | 0 (0%) | 359 |
1 (1.00) |
1 (1.00) |
0.000735 (0.368) |
0.000614 (0.313) |
0.504 (1.00) |
0.56 (1.00) |
0.000546 (0.28) |
0.366 (1.00) |
0.0266 (1.00) |
0.0103 (1.00) |
Del Peak 28(11q25) | 0 (0%) | 367 |
0.108 (1.00) |
0.0799 (1.00) |
0.00149 (0.711) |
0.0454 (1.00) |
0.0012 (0.581) |
0.00644 (1.00) |
0.0264 (1.00) |
0.00517 (1.00) |
0.141 (1.00) |
0.0854 (1.00) |
P value = 5.41e-07 (Fisher's exact test), Q value = 0.00036
Table S1. Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 1(1P34.3) CNV | 64 | 33 | 21 | 7 |
AMP PEAK 1(1P34.3) WILD-TYPE | 84 | 155 | 66 | 42 |
Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.96e-06 (Chi-square test), Q value = 0.0031
Table S2. Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 1(1P34.3) CNV | 22 | 33 | 15 | 6 | 5 | 13 | 8 | 3 | 4 |
AMP PEAK 1(1P34.3) WILD-TYPE | 53 | 22 | 41 | 36 | 24 | 35 | 31 | 21 | 19 |
Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1p34.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.8e-07 (Fisher's exact test), Q value = 0.00032
Table S3. Gene #2: 'Amp Peak 2(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 2(1P22.3) CNV | 64 | 31 | 20 | 9 |
AMP PEAK 2(1P22.3) WILD-TYPE | 84 | 157 | 67 | 40 |
Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1p22.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 5.64e-06 (Fisher's exact test), Q value = 0.0035
Table S4. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 3(1Q21.3) CNV | 118 | 110 | 65 | 43 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 30 | 78 | 22 | 6 |
Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 8.32e-07 (Chi-square test), Q value = 0.00056
Table S5. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 3(1Q21.3) CNV | 63 | 82 | 70 | 52 | 22 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 27 | 12 | 25 | 48 | 3 |
Figure S5. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 4.43e-06 (Chi-square test), Q value = 0.0028
Table S6. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 3(1Q21.3) CNV | 58 | 39 | 35 | 40 | 18 | 42 | 18 | 15 | 12 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 17 | 16 | 21 | 2 | 11 | 6 | 21 | 9 | 11 |
Figure S6. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.000211 (Fisher's exact test), Q value = 0.11
Table S7. Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 3(1Q21.3) CNV | 105 | 193 | 34 |
AMP PEAK 3(1Q21.3) WILD-TYPE | 59 | 51 | 25 |
Figure S7. Get High-res Image Gene #3: 'Amp Peak 3(1q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 0.000264 (Fisher's exact test), Q value = 0.14
Table S8. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 5 | 9 | 12 | 6 |
AMP PEAK 4(3Q26.2) CNV | 0 | 6 | 0 | 4 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 5 | 3 | 12 | 2 |
Figure S8. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 5.01e-10 (Fisher's exact test), Q value = 3.8e-07
Table S9. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 4(3Q26.2) CNV | 52 | 35 | 52 | 18 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 96 | 153 | 35 | 31 |
Figure S9. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 5.52e-08 (Chi-square test), Q value = 4e-05
Table S10. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 4(3Q26.2) CNV | 7 | 43 | 31 | 36 | 14 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 83 | 51 | 64 | 64 | 11 |
Figure S10. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.62e-09 (Chi-square test), Q value = 1.2e-06
Table S11. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 4(3Q26.2) CNV | 28 | 10 | 39 | 4 | 13 | 19 | 14 | 10 | 2 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 47 | 45 | 17 | 38 | 16 | 29 | 25 | 14 | 21 |
Figure S11. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 5.62e-09 (Fisher's exact test), Q value = 4.2e-06
Table S12. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 4(3Q26.2) CNV | 29 | 44 | 66 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 129 | 61 | 62 |
Figure S12. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.00096
Table S13. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 4(3Q26.2) CNV | 36 | 91 | 28 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 135 | 107 | 70 |
Figure S13. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 2.21e-07 (Fisher's exact test), Q value = 0.00015
Table S14. Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 4(3Q26.2) CNV | 34 | 109 | 12 |
AMP PEAK 4(3Q26.2) WILD-TYPE | 130 | 135 | 47 |
Figure S14. Get High-res Image Gene #4: 'Amp Peak 4(3q26.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 6.06e-09 (Fisher's exact test), Q value = 4.6e-06
Table S15. Gene #5: 'Amp Peak 5(4q12)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 5(4Q12) CNV | 45 | 13 | 25 | 5 |
AMP PEAK 5(4Q12) WILD-TYPE | 103 | 175 | 62 | 44 |
Figure S15. Get High-res Image Gene #5: 'Amp Peak 5(4q12)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.75e-21 (Fisher's exact test), Q value = 2.2e-18
Table S16. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 6(5P15.33) CNV | 136 | 83 | 48 | 37 |
AMP PEAK 6(5P15.33) WILD-TYPE | 12 | 105 | 39 | 12 |
Figure S16. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.77e-07 (Chi-square test), Q value = 0.00012
Table S17. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 6(5P15.33) CNV | 59 | 44 | 44 | 21 | 8 | 31 | 18 | 15 | 11 |
AMP PEAK 6(5P15.33) WILD-TYPE | 16 | 11 | 12 | 21 | 21 | 17 | 21 | 9 | 12 |
Figure S17. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.000225 (Fisher's exact test), Q value = 0.12
Table S18. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 6(5P15.33) CNV | 92 | 147 | 64 |
AMP PEAK 6(5P15.33) WILD-TYPE | 79 | 51 | 34 |
Figure S18. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 0.000304 (Fisher's exact test), Q value = 0.16
Table S19. Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 6(5P15.33) CNV | 87 | 177 | 39 |
AMP PEAK 6(5P15.33) WILD-TYPE | 77 | 67 | 20 |
Figure S19. Get High-res Image Gene #6: 'Amp Peak 6(5p15.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 5.67e-18 (Fisher's exact test), Q value = 4.6e-15
Table S20. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 7(5P13.1) CNV | 124 | 75 | 42 | 39 |
AMP PEAK 7(5P13.1) WILD-TYPE | 24 | 113 | 45 | 10 |
Figure S20. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000119 (Chi-square test), Q value = 0.066
Table S21. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 7(5P13.1) CNV | 48 | 38 | 41 | 19 | 7 | 32 | 18 | 14 | 10 |
AMP PEAK 7(5P13.1) WILD-TYPE | 27 | 17 | 15 | 23 | 22 | 16 | 21 | 10 | 13 |
Figure S21. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.000122 (Fisher's exact test), Q value = 0.067
Table S22. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 7(5P13.1) CNV | 82 | 138 | 59 |
AMP PEAK 7(5P13.1) WILD-TYPE | 89 | 60 | 39 |
Figure S22. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 0.000274 (Fisher's exact test), Q value = 0.14
Table S23. Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 7(5P13.1) CNV | 78 | 165 | 36 |
AMP PEAK 7(5P13.1) WILD-TYPE | 86 | 79 | 23 |
Figure S23. Get High-res Image Gene #7: 'Amp Peak 7(5p13.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 8.8e-07 (Chi-square test), Q value = 0.00058
Table S24. Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 8(5Q35.1) CNV | 41 | 14 | 16 | 17 | 8 |
AMP PEAK 8(5Q35.1) WILD-TYPE | 49 | 80 | 79 | 83 | 17 |
Figure S24. Get High-res Image Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 4.73e-05 (Chi-square test), Q value = 0.027
Table S25. Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 8(5Q35.1) CNV | 17 | 27 | 5 | 9 | 2 | 10 | 9 | 6 | 3 |
AMP PEAK 8(5Q35.1) WILD-TYPE | 58 | 28 | 51 | 33 | 27 | 38 | 30 | 18 | 20 |
Figure S25. Get High-res Image Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.000159 (Fisher's exact test), Q value = 0.086
Table S26. Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 8(5Q35.1) CNV | 49 | 25 | 14 |
AMP PEAK 8(5Q35.1) WILD-TYPE | 109 | 80 | 114 |
Figure S26. Get High-res Image Gene #8: 'Amp Peak 8(5q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000168 (Fisher's exact test), Q value = 0.09
Table S27. Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 9(6P21.1) CNV | 62 | 49 | 34 | 28 |
AMP PEAK 9(6P21.1) WILD-TYPE | 86 | 139 | 53 | 21 |
Figure S27. Get High-res Image Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.05e-07 (Chi-square test), Q value = 7.5e-05
Table S28. Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 9(6P21.1) CNV | 31 | 54 | 34 | 17 | 14 |
AMP PEAK 9(6P21.1) WILD-TYPE | 59 | 40 | 61 | 83 | 11 |
Figure S28. Get High-res Image Gene #9: 'Amp Peak 9(6p21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 6.95e-20 (Fisher's exact test), Q value = 5.6e-17
Table S29. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 10(7P21.1) CNV | 125 | 70 | 50 | 16 |
AMP PEAK 10(7P21.1) WILD-TYPE | 23 | 118 | 37 | 33 |
Figure S29. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.93e-06 (Chi-square test), Q value = 0.0031
Table S30. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 10(7P21.1) CNV | 37 | 45 | 62 | 55 | 24 |
AMP PEAK 10(7P21.1) WILD-TYPE | 53 | 49 | 33 | 45 | 1 |
Figure S30. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 7.66e-09 (Chi-square test), Q value = 5.7e-06
Table S31. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 10(7P21.1) CNV | 59 | 40 | 28 | 12 | 11 | 21 | 25 | 13 | 5 |
AMP PEAK 10(7P21.1) WILD-TYPE | 16 | 15 | 28 | 30 | 18 | 27 | 14 | 11 | 18 |
Figure S31. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 7.98e-08 (Fisher's exact test), Q value = 5.7e-05
Table S32. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 10(7P21.1) CNV | 67 | 81 | 66 |
AMP PEAK 10(7P21.1) WILD-TYPE | 91 | 24 | 62 |
Figure S32. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 8.38e-06 (Fisher's exact test), Q value = 0.0051
Table S33. Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 10(7P21.1) CNV | 72 | 116 | 70 |
AMP PEAK 10(7P21.1) WILD-TYPE | 99 | 82 | 28 |
Figure S33. Get High-res Image Gene #10: 'Amp Peak 10(7p21.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.27e-18 (Fisher's exact test), Q value = 1e-15
Table S34. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 11(7P11.2) CNV | 120 | 66 | 51 | 15 |
AMP PEAK 11(7P11.2) WILD-TYPE | 28 | 122 | 36 | 34 |
Figure S34. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2e-05 (Chi-square test), Q value = 0.012
Table S35. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 11(7P11.2) CNV | 35 | 44 | 58 | 57 | 23 |
AMP PEAK 11(7P11.2) WILD-TYPE | 55 | 50 | 37 | 43 | 2 |
Figure S35. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000263 (Fisher's exact test), Q value = 0.14
Table S36. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 89 | 65 | 58 |
AMP PEAK 11(7P11.2) CNV | 7 | 62 | 37 | 23 |
AMP PEAK 11(7P11.2) WILD-TYPE | 16 | 27 | 28 | 35 |
Figure S36. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 1.06e-08 (Chi-square test), Q value = 7.9e-06
Table S37. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 11(7P11.2) CNV | 58 | 37 | 28 | 11 | 10 | 19 | 25 | 12 | 5 |
AMP PEAK 11(7P11.2) WILD-TYPE | 17 | 18 | 28 | 31 | 19 | 29 | 14 | 12 | 18 |
Figure S37. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.49e-10 (Fisher's exact test), Q value = 1.2e-07
Table S38. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 11(7P11.2) CNV | 58 | 82 | 65 |
AMP PEAK 11(7P11.2) WILD-TYPE | 100 | 23 | 63 |
Figure S38. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.59e-07 (Fisher's exact test), Q value = 0.00018
Table S39. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 11(7P11.2) CNV | 64 | 117 | 68 |
AMP PEAK 11(7P11.2) WILD-TYPE | 107 | 81 | 30 |
Figure S39. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 6.85e-05 (Fisher's exact test), Q value = 0.039
Table S40. Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 11(7P11.2) CNV | 65 | 147 | 37 |
AMP PEAK 11(7P11.2) WILD-TYPE | 99 | 97 | 22 |
Figure S40. Get High-res Image Gene #11: 'Amp Peak 11(7p11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2.86e-09 (Fisher's exact test), Q value = 2.2e-06
Table S41. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 12(7Q31.2) CNV | 94 | 54 | 34 | 18 |
AMP PEAK 12(7Q31.2) WILD-TYPE | 54 | 134 | 53 | 31 |
Figure S41. Get High-res Image Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 5.48e-05 (Chi-square test), Q value = 0.031
Table S42. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 12(7Q31.2) CNV | 26 | 29 | 51 | 48 | 17 |
AMP PEAK 12(7Q31.2) WILD-TYPE | 64 | 65 | 44 | 52 | 8 |
Figure S42. Get High-res Image Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 2.97e-06 (Chi-square test), Q value = 0.0019
Table S43. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 12(7Q31.2) CNV | 48 | 29 | 24 | 9 | 7 | 13 | 20 | 11 | 4 |
AMP PEAK 12(7Q31.2) WILD-TYPE | 27 | 26 | 32 | 33 | 22 | 35 | 19 | 13 | 19 |
Figure S43. Get High-res Image Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.37e-08 (Fisher's exact test), Q value = 1e-05
Table S44. Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 12(7Q31.2) CNV | 48 | 70 | 47 |
AMP PEAK 12(7Q31.2) WILD-TYPE | 110 | 35 | 81 |
Figure S44. Get High-res Image Gene #12: 'Amp Peak 12(7q31.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.17e-16 (Fisher's exact test), Q value = 1.7e-13
Table S45. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 13(8P11.23) CNV | 34 | 26 | 28 | 38 |
AMP PEAK 13(8P11.23) WILD-TYPE | 114 | 162 | 59 | 11 |
Figure S45. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 8.25e-06 (Chi-square test), Q value = 0.0051
Table S46. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 13(8P11.23) CNV | 18 | 45 | 20 | 19 | 5 |
AMP PEAK 13(8P11.23) WILD-TYPE | 72 | 49 | 75 | 81 | 20 |
Figure S46. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 7.16e-06 (Fisher's exact test), Q value = 0.0044
Table S47. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 13(8P11.23) CNV | 28 | 27 | 56 |
AMP PEAK 13(8P11.23) WILD-TYPE | 130 | 78 | 72 |
Figure S47. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000479 (Fisher's exact test), Q value = 0.25
Table S48. Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 13(8P11.23) CNV | 27 | 82 | 15 |
AMP PEAK 13(8P11.23) WILD-TYPE | 137 | 162 | 44 |
Figure S48. Get High-res Image Gene #13: 'Amp Peak 13(8p11.23)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 3.42e-21 (Fisher's exact test), Q value = 2.8e-18
Table S49. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 14(8P11.21) CNV | 47 | 32 | 39 | 44 |
AMP PEAK 14(8P11.21) WILD-TYPE | 101 | 156 | 48 | 5 |
Figure S49. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000128 (Chi-square test), Q value = 0.07
Table S50. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 14(8P11.21) CNV | 21 | 51 | 32 | 29 | 7 |
AMP PEAK 14(8P11.21) WILD-TYPE | 69 | 43 | 63 | 71 | 18 |
Figure S50. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.59e-05 (Chi-square test), Q value = 0.0095
Table S51. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 14(8P11.21) CNV | 27 | 13 | 32 | 16 | 8 | 27 | 7 | 6 | 3 |
AMP PEAK 14(8P11.21) WILD-TYPE | 48 | 42 | 24 | 26 | 21 | 21 | 32 | 18 | 20 |
Figure S51. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.9e-07 (Fisher's exact test), Q value = 0.00033
Table S52. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 14(8P11.21) CNV | 33 | 41 | 65 |
AMP PEAK 14(8P11.21) WILD-TYPE | 125 | 64 | 63 |
Figure S52. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 4.19e-05 (Fisher's exact test), Q value = 0.024
Table S53. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 14(8P11.21) CNV | 39 | 89 | 33 |
AMP PEAK 14(8P11.21) WILD-TYPE | 132 | 109 | 65 |
Figure S53. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 6.3e-06 (Fisher's exact test), Q value = 0.0039
Table S54. Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 14(8P11.21) CNV | 34 | 107 | 20 |
AMP PEAK 14(8P11.21) WILD-TYPE | 130 | 137 | 39 |
Figure S54. Get High-res Image Gene #14: 'Amp Peak 14(8p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 3.04e-22 (Fisher's exact test), Q value = 2.5e-19
Table S55. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 15(8Q11.1) CNV | 85 | 39 | 46 | 44 |
AMP PEAK 15(8Q11.1) WILD-TYPE | 63 | 149 | 41 | 5 |
Figure S55. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.14e-07 (Chi-square test), Q value = 8.1e-05
Table S56. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 15(8Q11.1) CNV | 25 | 62 | 52 | 32 | 12 |
AMP PEAK 15(8Q11.1) WILD-TYPE | 65 | 32 | 43 | 68 | 13 |
Figure S56. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 5.35e-06 (Chi-square test), Q value = 0.0033
Table S57. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 15(8Q11.1) CNV | 38 | 22 | 33 | 18 | 10 | 34 | 7 | 11 | 4 |
AMP PEAK 15(8Q11.1) WILD-TYPE | 37 | 33 | 23 | 24 | 19 | 14 | 32 | 13 | 19 |
Figure S57. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.26e-05 (Fisher's exact test), Q value = 0.013
Table S58. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 15(8Q11.1) CNV | 50 | 53 | 74 |
AMP PEAK 15(8Q11.1) WILD-TYPE | 108 | 52 | 54 |
Figure S58. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.94e-07 (Fisher's exact test), Q value = 0.00014
Table S59. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 15(8Q11.1) CNV | 50 | 114 | 48 |
AMP PEAK 15(8Q11.1) WILD-TYPE | 121 | 84 | 50 |
Figure S59. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 8.84e-07 (Fisher's exact test), Q value = 0.00059
Table S60. Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 15(8Q11.1) CNV | 49 | 137 | 26 |
AMP PEAK 15(8Q11.1) WILD-TYPE | 115 | 107 | 33 |
Figure S60. Get High-res Image Gene #15: 'Amp Peak 15(8q11.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 8.4e-20 (Fisher's exact test), Q value = 6.8e-17
Table S61. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 16(8Q24.21) CNV | 113 | 73 | 65 | 47 |
AMP PEAK 16(8Q24.21) WILD-TYPE | 35 | 115 | 22 | 2 |
Figure S61. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.72e-08 (Chi-square test), Q value = 2.7e-05
Table S62. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 16(8Q24.21) CNV | 39 | 76 | 71 | 50 | 16 |
AMP PEAK 16(8Q24.21) WILD-TYPE | 51 | 18 | 24 | 50 | 9 |
Figure S62. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 6.65e-05 (Chi-square test), Q value = 0.038
Table S63. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 16(8Q24.21) CNV | 55 | 34 | 37 | 27 | 11 | 41 | 20 | 13 | 8 |
AMP PEAK 16(8Q24.21) WILD-TYPE | 20 | 21 | 19 | 15 | 18 | 7 | 19 | 11 | 15 |
Figure S63. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.27e-06 (Fisher's exact test), Q value = 0.0021
Table S64. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 16(8Q24.21) CNV | 76 | 79 | 91 |
AMP PEAK 16(8Q24.21) WILD-TYPE | 82 | 26 | 37 |
Figure S64. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 8.41e-07 (Fisher's exact test), Q value = 0.00056
Table S65. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 16(8Q24.21) CNV | 82 | 147 | 66 |
AMP PEAK 16(8Q24.21) WILD-TYPE | 89 | 51 | 32 |
Figure S65. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.26e-05 (Fisher's exact test), Q value = 0.0076
Table S66. Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 16(8Q24.21) CNV | 81 | 177 | 37 |
AMP PEAK 16(8Q24.21) WILD-TYPE | 83 | 67 | 22 |
Figure S66. Get High-res Image Gene #16: 'Amp Peak 16(8q24.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 4.17e-06 (Fisher's exact test), Q value = 0.0026
Table S67. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 17(10P15.1) CNV | 39 | 29 | 34 | 22 |
AMP PEAK 17(10P15.1) WILD-TYPE | 109 | 159 | 53 | 27 |
Figure S67. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.59e-07 (Chi-square test), Q value = 0.00018
Table S68. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 17(10P15.1) CNV | 7 | 39 | 35 | 20 | 4 |
AMP PEAK 17(10P15.1) WILD-TYPE | 83 | 55 | 60 | 80 | 21 |
Figure S68. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 6.78e-05 (Chi-square test), Q value = 0.038
Table S69. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 17(10P15.1) CNV | 24 | 2 | 25 | 14 | 10 | 15 | 9 | 4 | 2 |
AMP PEAK 17(10P15.1) WILD-TYPE | 51 | 53 | 31 | 28 | 19 | 33 | 30 | 20 | 21 |
Figure S69. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.08e-08 (Fisher's exact test), Q value = 1.5e-05
Table S70. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 17(10P15.1) CNV | 21 | 27 | 57 |
AMP PEAK 17(10P15.1) WILD-TYPE | 137 | 78 | 71 |
Figure S70. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000237 (Fisher's exact test), Q value = 0.13
Table S71. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 17(10P15.1) CNV | 28 | 69 | 24 |
AMP PEAK 17(10P15.1) WILD-TYPE | 143 | 129 | 74 |
Figure S71. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 6.08e-05 (Fisher's exact test), Q value = 0.035
Table S72. Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 17(10P15.1) CNV | 27 | 84 | 10 |
AMP PEAK 17(10P15.1) WILD-TYPE | 137 | 160 | 49 |
Figure S72. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 5.94e-14 (Fisher's exact test), Q value = 4.8e-11
Table S73. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 18(11Q13.3) CNV | 69 | 24 | 42 | 22 |
AMP PEAK 18(11Q13.3) WILD-TYPE | 79 | 164 | 45 | 27 |
Figure S73. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.94e-05 (Chi-square test), Q value = 0.011
Table S74. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 18(11Q13.3) CNV | 15 | 43 | 43 | 25 | 8 |
AMP PEAK 18(11Q13.3) WILD-TYPE | 75 | 51 | 52 | 75 | 17 |
Figure S74. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3.07e-08 (Chi-square test), Q value = 2.2e-05
Table S75. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 18(11Q13.3) CNV | 34 | 21 | 23 | 4 | 9 | 30 | 7 | 3 | 2 |
AMP PEAK 18(11Q13.3) WILD-TYPE | 41 | 34 | 33 | 38 | 20 | 18 | 32 | 21 | 21 |
Figure S75. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 9.49e-07 (Fisher's exact test), Q value = 0.00063
Table S76. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 18(11Q13.3) CNV | 30 | 47 | 56 |
AMP PEAK 18(11Q13.3) WILD-TYPE | 128 | 58 | 72 |
Figure S76. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.08e-10 (Fisher's exact test), Q value = 1.6e-07
Table S77. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 18(11Q13.3) CNV | 26 | 93 | 35 |
AMP PEAK 18(11Q13.3) WILD-TYPE | 145 | 105 | 63 |
Figure S77. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 2.03e-07 (Fisher's exact test), Q value = 0.00014
Table S78. Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 18(11Q13.3) CNV | 29 | 106 | 19 |
AMP PEAK 18(11Q13.3) WILD-TYPE | 135 | 138 | 40 |
Figure S78. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 5.45e-22 (Fisher's exact test), Q value = 4.5e-19
Table S79. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 19(12P12.1) CNV | 42 | 36 | 70 | 15 |
AMP PEAK 19(12P12.1) WILD-TYPE | 106 | 152 | 17 | 34 |
Figure S79. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.14e-06 (Chi-square test), Q value = 0.0026
Table S80. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 19(12P12.1) CNV | 10 | 44 | 35 | 40 | 7 |
AMP PEAK 19(12P12.1) WILD-TYPE | 80 | 50 | 60 | 60 | 18 |
Figure S80. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.44e-05 (Chi-square test), Q value = 0.0086
Table S81. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 19(12P12.1) CNV | 29 | 12 | 24 | 7 | 16 | 26 | 16 | 6 | 1 |
AMP PEAK 19(12P12.1) WILD-TYPE | 46 | 43 | 32 | 35 | 13 | 22 | 23 | 18 | 22 |
Figure S81. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.74e-07 (Fisher's exact test), Q value = 0.00019
Table S82. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 19(12P12.1) CNV | 32 | 40 | 65 |
AMP PEAK 19(12P12.1) WILD-TYPE | 126 | 65 | 63 |
Figure S82. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 6.05e-06 (Fisher's exact test), Q value = 0.0038
Table S83. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 19(12P12.1) CNV | 39 | 92 | 29 |
AMP PEAK 19(12P12.1) WILD-TYPE | 132 | 106 | 69 |
Figure S83. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.01e-05 (Fisher's exact test), Q value = 0.0062
Table S84. Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 19(12P12.1) CNV | 40 | 108 | 12 |
AMP PEAK 19(12P12.1) WILD-TYPE | 124 | 136 | 47 |
Figure S84. Get High-res Image Gene #19: 'Amp Peak 19(12p12.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2.65e-24 (Fisher's exact test), Q value = 2.2e-21
Table S85. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 20(12Q14.1) CNV | 29 | 32 | 68 | 19 |
AMP PEAK 20(12Q14.1) WILD-TYPE | 119 | 156 | 19 | 30 |
Figure S85. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.45e-07 (Chi-square test), Q value = 1e-04
Table S86. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 20(12Q14.1) CNV | 11 | 49 | 25 | 34 | 5 |
AMP PEAK 20(12Q14.1) WILD-TYPE | 79 | 45 | 70 | 66 | 20 |
Figure S86. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 2.93e-07 (Chi-square test), Q value = 2e-04
Table S87. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 20(12Q14.1) CNV | 18 | 12 | 23 | 7 | 13 | 30 | 13 | 4 | 1 |
AMP PEAK 20(12Q14.1) WILD-TYPE | 57 | 43 | 33 | 35 | 16 | 18 | 26 | 20 | 22 |
Figure S87. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.88e-10 (Fisher's exact test), Q value = 3e-07
Table S88. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 20(12Q14.1) CNV | 26 | 28 | 67 |
AMP PEAK 20(12Q14.1) WILD-TYPE | 132 | 77 | 61 |
Figure S88. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 6.24e-09 (Fisher's exact test), Q value = 4.7e-06
Table S89. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 20(12Q14.1) CNV | 29 | 91 | 26 |
AMP PEAK 20(12Q14.1) WILD-TYPE | 142 | 107 | 72 |
Figure S89. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 4.09e-09 (Fisher's exact test), Q value = 3.1e-06
Table S90. Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 20(12Q14.1) CNV | 28 | 107 | 11 |
AMP PEAK 20(12Q14.1) WILD-TYPE | 136 | 137 | 48 |
Figure S90. Get High-res Image Gene #20: 'Amp Peak 20(12q14.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.49e-21 (Fisher's exact test), Q value = 1.2e-18
Table S91. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 21(12Q15) CNV | 31 | 34 | 66 | 20 |
AMP PEAK 21(12Q15) WILD-TYPE | 117 | 154 | 21 | 29 |
Figure S91. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.35e-08 (Chi-square test), Q value = 1.7e-05
Table S92. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 21(12Q15) CNV | 11 | 52 | 25 | 32 | 8 |
AMP PEAK 21(12Q15) WILD-TYPE | 79 | 42 | 70 | 68 | 17 |
Figure S92. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 7.24e-08 (Chi-square test), Q value = 5.2e-05
Table S93. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 21(12Q15) CNV | 17 | 13 | 23 | 7 | 15 | 31 | 12 | 6 | 1 |
AMP PEAK 21(12Q15) WILD-TYPE | 58 | 42 | 33 | 35 | 14 | 17 | 27 | 18 | 22 |
Figure S93. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.39e-09 (Fisher's exact test), Q value = 3.3e-06
Table S94. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 21(12Q15) CNV | 32 | 25 | 68 |
AMP PEAK 21(12Q15) WILD-TYPE | 126 | 80 | 60 |
Figure S94. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.17e-09 (Fisher's exact test), Q value = 1.6e-06
Table S95. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 21(12Q15) CNV | 30 | 94 | 26 |
AMP PEAK 21(12Q15) WILD-TYPE | 141 | 104 | 72 |
Figure S95. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.1e-07 (Fisher's exact test), Q value = 7.9e-05
Table S96. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 21(12Q15) CNV | 29 | 106 | 15 |
AMP PEAK 21(12Q15) WILD-TYPE | 135 | 138 | 44 |
Figure S96. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2.03e-11 (Fisher's exact test), Q value = 1.6e-08
Table S97. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 23(14Q13.3) CNV | 80 | 48 | 48 | 35 |
AMP PEAK 23(14Q13.3) WILD-TYPE | 68 | 140 | 39 | 14 |
Figure S97. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.73e-06 (Chi-square test), Q value = 0.003
Table S98. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 23(14Q13.3) CNV | 29 | 56 | 47 | 31 | 18 |
AMP PEAK 23(14Q13.3) WILD-TYPE | 61 | 38 | 48 | 69 | 7 |
Figure S98. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.28e-09 (Chi-square test), Q value = 9.8e-07
Table S99. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 23(14Q13.3) CNV | 40 | 22 | 31 | 9 | 6 | 40 | 11 | 8 | 7 |
AMP PEAK 23(14Q13.3) WILD-TYPE | 35 | 33 | 25 | 33 | 23 | 8 | 28 | 16 | 16 |
Figure S99. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.84e-05 (Fisher's exact test), Q value = 0.022
Table S100. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 23(14Q13.3) CNV | 49 | 59 | 66 |
AMP PEAK 23(14Q13.3) WILD-TYPE | 109 | 46 | 62 |
Figure S100. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 8.7e-08 (Fisher's exact test), Q value = 6.2e-05
Table S101. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 23(14Q13.3) CNV | 47 | 108 | 53 |
AMP PEAK 23(14Q13.3) WILD-TYPE | 124 | 90 | 45 |
Figure S101. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 2.61e-09 (Fisher's exact test), Q value = 2e-06
Table S102. Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 23(14Q13.3) CNV | 42 | 138 | 28 |
AMP PEAK 23(14Q13.3) WILD-TYPE | 122 | 106 | 31 |
Figure S102. Get High-res Image Gene #23: 'Amp Peak 23(14q13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 6.08e-14 (Fisher's exact test), Q value = 4.9e-11
Table S103. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 24(17Q12) CNV | 90 | 42 | 52 | 24 |
AMP PEAK 24(17Q12) WILD-TYPE | 58 | 146 | 35 | 25 |
Figure S103. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 8.27e-07 (Chi-square test), Q value = 0.00055
Table S104. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 24(17Q12) CNV | 22 | 51 | 54 | 31 | 15 |
AMP PEAK 24(17Q12) WILD-TYPE | 68 | 43 | 41 | 69 | 10 |
Figure S104. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.086
Table S105. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 89 | 65 | 58 |
AMP PEAK 24(17Q12) CNV | 3 | 52 | 33 | 20 |
AMP PEAK 24(17Q12) WILD-TYPE | 20 | 37 | 32 | 38 |
Figure S105. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 9.56e-11 (Chi-square test), Q value = 7.5e-08
Table S106. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 24(17Q12) CNV | 53 | 30 | 30 | 6 | 9 | 23 | 10 | 11 | 1 |
AMP PEAK 24(17Q12) WILD-TYPE | 22 | 25 | 26 | 36 | 20 | 25 | 29 | 13 | 22 |
Figure S106. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.02e-06 (Fisher's exact test), Q value = 0.0013
Table S107. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 24(17Q12) CNV | 48 | 65 | 60 |
AMP PEAK 24(17Q12) WILD-TYPE | 110 | 40 | 68 |
Figure S107. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 7.33e-07 (Fisher's exact test), Q value = 0.00049
Table S108. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 24(17Q12) CNV | 50 | 112 | 44 |
AMP PEAK 24(17Q12) WILD-TYPE | 121 | 86 | 54 |
Figure S108. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.1e-06 (Fisher's exact test), Q value = 0.00072
Table S109. Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 24(17Q12) CNV | 49 | 135 | 22 |
AMP PEAK 24(17Q12) WILD-TYPE | 115 | 109 | 37 |
Figure S109. Get High-res Image Gene #24: 'Amp Peak 24(17q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2.25e-14 (Fisher's exact test), Q value = 1.8e-11
Table S110. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 25(17Q23.1) CNV | 100 | 51 | 56 | 23 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 48 | 137 | 31 | 26 |
Figure S110. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.11e-08 (Chi-square test), Q value = 1.6e-05
Table S111. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 25(17Q23.1) CNV | 24 | 52 | 65 | 36 | 15 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 66 | 42 | 30 | 64 | 10 |
Figure S111. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 4.12e-07 (Fisher's exact test), Q value = 0.00028
Table S112. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 89 | 65 | 58 |
AMP PEAK 25(17Q23.1) CNV | 3 | 57 | 38 | 17 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 20 | 32 | 27 | 41 |
Figure S112. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 2.7e-13 (Chi-square test), Q value = 2.2e-10
Table S113. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 25(17Q23.1) CNV | 61 | 32 | 32 | 8 | 6 | 23 | 15 | 10 | 2 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 14 | 23 | 24 | 34 | 23 | 25 | 24 | 14 | 21 |
Figure S113. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 5.99e-10 (Fisher's exact test), Q value = 4.6e-07
Table S114. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 25(17Q23.1) CNV | 49 | 75 | 65 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 109 | 30 | 63 |
Figure S114. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.001
Table S115. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 25(17Q23.1) CNV | 58 | 120 | 50 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 113 | 78 | 48 |
Figure S115. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 5.68e-06 (Fisher's exact test), Q value = 0.0035
Table S116. Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 25(17Q23.1) CNV | 58 | 145 | 25 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 106 | 99 | 34 |
Figure S116. Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.07e-08 (Chi-square test), Q value = 7.9e-06
Table S117. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 26(18Q11.2) CNV | 7 | 40 | 19 | 11 | 7 |
AMP PEAK 26(18Q11.2) WILD-TYPE | 83 | 54 | 76 | 89 | 18 |
Figure S117. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 9.61e-05 (Fisher's exact test), Q value = 0.054
Table S118. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 26(18Q11.2) CNV | 19 | 21 | 42 |
AMP PEAK 26(18Q11.2) WILD-TYPE | 139 | 84 | 86 |
Figure S118. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.06e-05 (Fisher's exact test), Q value = 0.0064
Table S119. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 26(18Q11.2) CNV | 16 | 57 | 20 |
AMP PEAK 26(18Q11.2) WILD-TYPE | 155 | 141 | 78 |
Figure S119. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 6.73e-07 (Fisher's exact test), Q value = 0.00045
Table S120. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 26(18Q11.2) CNV | 18 | 71 | 4 |
AMP PEAK 26(18Q11.2) WILD-TYPE | 146 | 173 | 55 |
Figure S120. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.29e-08 (Fisher's exact test), Q value = 9.5e-06
Table S121. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 27(19Q12) CNV | 36 | 28 | 43 | 19 |
AMP PEAK 27(19Q12) WILD-TYPE | 112 | 160 | 44 | 30 |
Figure S121. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000304 (Chi-square test), Q value = 0.16
Table S122. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 27(19Q12) CNV | 15 | 41 | 21 | 25 | 10 |
AMP PEAK 27(19Q12) WILD-TYPE | 75 | 53 | 74 | 75 | 15 |
Figure S122. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000438 (Chi-square test), Q value = 0.23
Table S123. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 27(19Q12) CNV | 21 | 7 | 24 | 14 | 6 | 19 | 8 | 5 | 0 |
AMP PEAK 27(19Q12) WILD-TYPE | 54 | 48 | 32 | 28 | 23 | 29 | 31 | 19 | 23 |
Figure S123. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.22e-08 (Fisher's exact test), Q value = 3.1e-05
Table S124. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 27(19Q12) CNV | 19 | 32 | 53 |
AMP PEAK 27(19Q12) WILD-TYPE | 139 | 73 | 75 |
Figure S124. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.00083
Table S125. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 27(19Q12) CNV | 25 | 76 | 25 |
AMP PEAK 27(19Q12) WILD-TYPE | 146 | 122 | 73 |
Figure S125. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.00096
Table S126. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 27(19Q12) CNV | 29 | 90 | 7 |
AMP PEAK 27(19Q12) WILD-TYPE | 135 | 154 | 52 |
Figure S126. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0067
Table S127. Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 28(20P11.21) CNV | 53 | 52 | 44 | 30 |
AMP PEAK 28(20P11.21) WILD-TYPE | 95 | 136 | 43 | 19 |
Figure S127. Get High-res Image Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000221 (Chi-square test), Q value = 0.12
Table S128. Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 28(20P11.21) CNV | 23 | 24 | 33 | 15 | 9 | 26 | 8 | 9 | 3 |
AMP PEAK 28(20P11.21) WILD-TYPE | 52 | 31 | 23 | 27 | 20 | 22 | 31 | 15 | 20 |
Figure S128. Get High-res Image Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.000145 (Fisher's exact test), Q value = 0.078
Table S129. Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 28(20P11.21) CNV | 44 | 91 | 42 |
AMP PEAK 28(20P11.21) WILD-TYPE | 127 | 107 | 56 |
Figure S129. Get High-res Image Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 7.51e-05 (Fisher's exact test), Q value = 0.042
Table S130. Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 28(20P11.21) CNV | 42 | 114 | 21 |
AMP PEAK 28(20P11.21) WILD-TYPE | 122 | 130 | 38 |
Figure S130. Get High-res Image Gene #28: 'Amp Peak 28(20p11.21)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.03e-07 (Fisher's exact test), Q value = 7.4e-05
Table S131. Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 29(20Q13.33) CNV | 77 | 61 | 52 | 35 |
AMP PEAK 29(20Q13.33) WILD-TYPE | 71 | 127 | 35 | 14 |
Figure S131. Get High-res Image Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.37e-05 (Chi-square test), Q value = 0.0082
Table S132. Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
AMP PEAK 29(20Q13.33) CNV | 37 | 31 | 37 | 15 | 9 | 33 | 14 | 11 | 3 |
AMP PEAK 29(20Q13.33) WILD-TYPE | 38 | 24 | 19 | 27 | 20 | 15 | 25 | 13 | 20 |
Figure S132. Get High-res Image Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.53e-06 (Fisher's exact test), Q value = 0.0016
Table S133. Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
AMP PEAK 29(20Q13.33) CNV | 58 | 119 | 44 |
AMP PEAK 29(20Q13.33) WILD-TYPE | 113 | 79 | 54 |
Figure S133. Get High-res Image Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 4.24e-07 (Fisher's exact test), Q value = 0.00029
Table S134. Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
AMP PEAK 29(20Q13.33) CNV | 51 | 142 | 28 |
AMP PEAK 29(20Q13.33) WILD-TYPE | 113 | 102 | 31 |
Figure S134. Get High-res Image Gene #29: 'Amp Peak 29(20q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 3.01e-10 (Fisher's exact test), Q value = 2.3e-07
Table S135. Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
AMP PEAK 31(XQ28) CNV | 73 | 29 | 31 | 18 |
AMP PEAK 31(XQ28) WILD-TYPE | 75 | 159 | 56 | 31 |
Figure S135. Get High-res Image Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 5.94e-05 (Chi-square test), Q value = 0.034
Table S136. Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
AMP PEAK 31(XQ28) CNV | 15 | 34 | 43 | 22 | 11 |
AMP PEAK 31(XQ28) WILD-TYPE | 75 | 60 | 52 | 78 | 14 |
Figure S136. Get High-res Image Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 9.71e-05 (Fisher's exact test), Q value = 0.054
Table S137. Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
AMP PEAK 31(XQ28) CNV | 35 | 50 | 42 |
AMP PEAK 31(XQ28) WILD-TYPE | 123 | 55 | 86 |
Figure S137. Get High-res Image Gene #31: 'Amp Peak 31(Xq28)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.59e-06 (Fisher's exact test), Q value = 0.001
Table S138. Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 1(1P36.13) CNV | 19 | 38 | 27 | 24 |
DEL PEAK 1(1P36.13) WILD-TYPE | 129 | 150 | 60 | 25 |
Figure S138. Get High-res Image Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.18e-05 (Chi-square test), Q value = 0.013
Table S139. Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 1(1P36.13) CNV | 11 | 38 | 22 | 15 | 4 |
DEL PEAK 1(1P36.13) WILD-TYPE | 79 | 56 | 73 | 85 | 21 |
Figure S139. Get High-res Image Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 8.06e-06 (Chi-square test), Q value = 0.005
Table S140. Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 1(1P36.13) CNV | 17 | 4 | 13 | 8 | 8 | 25 | 10 | 1 | 3 |
DEL PEAK 1(1P36.13) WILD-TYPE | 58 | 51 | 43 | 34 | 21 | 23 | 29 | 23 | 20 |
Figure S140. Get High-res Image Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 8.99e-06 (Fisher's exact test), Q value = 0.0055
Table S141. Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 1(1P36.13) CNV | 19 | 24 | 46 |
DEL PEAK 1(1P36.13) WILD-TYPE | 139 | 81 | 82 |
Figure S141. Get High-res Image Gene #32: 'Del Peak 1(1p36.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 9.97e-07 (Fisher's exact test), Q value = 0.00066
Table S142. Gene #33: 'Del Peak 2(1p13.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 2(1P13.3) CNV | 29 | 46 | 37 | 27 |
DEL PEAK 2(1P13.3) WILD-TYPE | 119 | 142 | 50 | 22 |
Figure S142. Get High-res Image Gene #33: 'Del Peak 2(1p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 9.81e-05 (Chi-square test), Q value = 0.055
Table S143. Gene #33: 'Del Peak 2(1p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 2(1P13.3) CNV | 25 | 41 | 27 | 13 | 5 |
DEL PEAK 2(1P13.3) WILD-TYPE | 65 | 53 | 68 | 87 | 20 |
Figure S143. Get High-res Image Gene #33: 'Del Peak 2(1p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.93e-06 (Fisher's exact test), Q value = 0.0013
Table S144. Gene #34: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 3(1P13.1) CNV | 31 | 42 | 40 | 24 |
DEL PEAK 3(1P13.1) WILD-TYPE | 117 | 146 | 47 | 25 |
Figure S144. Get High-res Image Gene #34: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.2e-05 (Chi-square test), Q value = 0.013
Table S145. Gene #34: 'Del Peak 3(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 3(1P13.1) CNV | 22 | 40 | 32 | 12 | 4 |
DEL PEAK 3(1P13.1) WILD-TYPE | 68 | 54 | 63 | 88 | 21 |
Figure S145. Get High-res Image Gene #34: 'Del Peak 3(1p13.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.17
Table S146. Gene #36: 'Del Peak 5(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 5(2Q37.3) CNV | 30 | 12 | 10 | 11 |
DEL PEAK 5(2Q37.3) WILD-TYPE | 118 | 176 | 77 | 38 |
Figure S146. Get High-res Image Gene #36: 'Del Peak 5(2q37.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000153 (Fisher's exact test), Q value = 0.083
Table S147. Gene #36: 'Del Peak 5(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 5(2Q37.3) CNV | 10 | 48 | 5 |
DEL PEAK 5(2Q37.3) WILD-TYPE | 154 | 196 | 54 |
Figure S147. Get High-res Image Gene #36: 'Del Peak 5(2q37.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 7.53e-06 (Fisher's exact test), Q value = 0.0046
Table S148. Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 6(3P21.31) CNV | 77 | 65 | 53 | 32 |
DEL PEAK 6(3P21.31) WILD-TYPE | 71 | 123 | 34 | 17 |
Figure S148. Get High-res Image Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.21e-06 (Chi-square test), Q value = 0.0021
Table S149. Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 6(3P21.31) CNV | 32 | 67 | 43 | 39 | 15 |
DEL PEAK 6(3P21.31) WILD-TYPE | 58 | 27 | 52 | 61 | 10 |
Figure S149. Get High-res Image Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3.35e-05 (Chi-square test), Q value = 0.019
Table S150. Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 6(3P21.31) CNV | 32 | 26 | 42 | 15 | 12 | 29 | 19 | 12 | 3 |
DEL PEAK 6(3P21.31) WILD-TYPE | 43 | 29 | 14 | 27 | 17 | 19 | 20 | 12 | 20 |
Figure S150. Get High-res Image Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 6.23e-09 (Fisher's exact test), Q value = 4.7e-06
Table S151. Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 6(3P21.31) CNV | 53 | 48 | 89 |
DEL PEAK 6(3P21.31) WILD-TYPE | 105 | 57 | 39 |
Figure S151. Get High-res Image Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.0071
Table S152. Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 6(3P21.31) CNV | 57 | 110 | 56 |
DEL PEAK 6(3P21.31) WILD-TYPE | 114 | 88 | 42 |
Figure S152. Get High-res Image Gene #37: 'Del Peak 6(3p21.31)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 8.11e-05 (Chi-square test), Q value = 0.046
Table S153. Gene #39: 'Del Peak 8(3q29)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 8(3Q29) CNV | 35 | 36 | 29 | 11 | 7 |
DEL PEAK 8(3Q29) WILD-TYPE | 55 | 58 | 66 | 89 | 18 |
Figure S153. Get High-res Image Gene #39: 'Del Peak 8(3q29)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3.27e-08 (Chi-square test), Q value = 2.4e-05
Table S154. Gene #39: 'Del Peak 8(3q29)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 8(3Q29) CNV | 18 | 17 | 9 | 18 | 8 | 30 | 2 | 4 | 4 |
DEL PEAK 8(3Q29) WILD-TYPE | 57 | 38 | 47 | 24 | 21 | 18 | 37 | 20 | 19 |
Figure S154. Get High-res Image Gene #39: 'Del Peak 8(3q29)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0093
Table S155. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 9(4P16.3) CNV | 37 | 28 | 28 | 23 |
DEL PEAK 9(4P16.3) WILD-TYPE | 111 | 160 | 59 | 26 |
Figure S155. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.31e-05 (Chi-square test), Q value = 0.014
Table S156. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 9(4P16.3) CNV | 7 | 38 | 22 | 26 | 7 |
DEL PEAK 9(4P16.3) WILD-TYPE | 83 | 56 | 73 | 74 | 18 |
Figure S156. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 8.4e-07 (Chi-square test), Q value = 0.00056
Table S157. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 9(4P16.3) CNV | 11 | 12 | 26 | 3 | 8 | 23 | 7 | 7 | 2 |
DEL PEAK 9(4P16.3) WILD-TYPE | 64 | 43 | 30 | 39 | 21 | 25 | 32 | 17 | 21 |
Figure S157. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 6.36e-11 (Fisher's exact test), Q value = 5e-08
Table S158. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 9(4P16.3) CNV | 16 | 25 | 58 |
DEL PEAK 9(4P16.3) WILD-TYPE | 142 | 80 | 70 |
Figure S158. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.82e-07 (Fisher's exact test), Q value = 0.00019
Table S159. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 9(4P16.3) CNV | 20 | 71 | 24 |
DEL PEAK 9(4P16.3) WILD-TYPE | 151 | 127 | 74 |
Figure S159. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.11e-07 (Fisher's exact test), Q value = 7.9e-05
Table S160. Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 9(4P16.3) CNV | 20 | 86 | 9 |
DEL PEAK 9(4P16.3) WILD-TYPE | 144 | 158 | 50 |
Figure S160. Get High-res Image Gene #40: 'Del Peak 9(4p16.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 0.000214 (Fisher's exact test), Q value = 0.11
Table S161. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 5 | 9 | 12 | 6 |
DEL PEAK 10(4Q22.1) CNV | 3 | 1 | 0 | 5 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 2 | 8 | 12 | 1 |
Figure S161. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 9.89e-05 (Fisher's exact test), Q value = 0.055
Table S162. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 7 | 13 | 12 |
DEL PEAK 10(4Q22.1) CNV | 6 | 0 | 3 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 1 | 13 | 9 |
Figure S162. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 3.67e-07 (Fisher's exact test), Q value = 0.00025
Table S163. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 10(4Q22.1) CNV | 48 | 32 | 42 | 20 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 100 | 156 | 45 | 29 |
Figure S163. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 9.89e-08 (Chi-square test), Q value = 7.1e-05
Table S164. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 10(4Q22.1) CNV | 8 | 45 | 25 | 29 | 12 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 82 | 49 | 70 | 71 | 13 |
Figure S164. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3.81e-06 (Chi-square test), Q value = 0.0024
Table S165. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 10(4Q22.1) CNV | 12 | 17 | 27 | 6 | 9 | 25 | 11 | 8 | 1 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 63 | 38 | 29 | 36 | 20 | 23 | 28 | 16 | 22 |
Figure S165. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 9.97e-14 (Fisher's exact test), Q value = 8e-11
Table S166. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 10(4Q22.1) CNV | 21 | 25 | 70 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 137 | 80 | 58 |
Figure S166. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.66e-08 (Fisher's exact test), Q value = 1.2e-05
Table S167. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 10(4Q22.1) CNV | 25 | 84 | 32 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 146 | 114 | 66 |
Figure S167. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.54e-06 (Fisher's exact test), Q value = 0.001
Table S168. Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 10(4Q22.1) CNV | 30 | 99 | 12 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 134 | 145 | 47 |
Figure S168. Get High-res Image Gene #41: 'Del Peak 10(4q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 7.48e-10 (Fisher's exact test), Q value = 5.7e-07
Table S169. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 11(4Q35.1) CNV | 58 | 38 | 50 | 26 |
DEL PEAK 11(4Q35.1) WILD-TYPE | 90 | 150 | 37 | 23 |
Figure S169. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.36e-11 (Chi-square test), Q value = 1.1e-08
Table S170. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 11(4Q35.1) CNV | 8 | 58 | 35 | 35 | 12 |
DEL PEAK 11(4Q35.1) WILD-TYPE | 82 | 36 | 60 | 65 | 13 |
Figure S170. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000196 (Fisher's exact test), Q value = 0.1
Table S171. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 89 | 65 | 58 |
DEL PEAK 11(4Q35.1) CNV | 11 | 32 | 39 | 13 |
DEL PEAK 11(4Q35.1) WILD-TYPE | 12 | 57 | 26 | 45 |
Figure S171. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 2.47e-09 (Chi-square test), Q value = 1.9e-06
Table S172. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 11(4Q35.1) CNV | 18 | 14 | 35 | 7 | 10 | 31 | 13 | 10 | 2 |
DEL PEAK 11(4Q35.1) WILD-TYPE | 57 | 41 | 21 | 35 | 19 | 17 | 26 | 14 | 21 |
Figure S172. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 7.36e-18 (Fisher's exact test), Q value = 5.9e-15
Table S173. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 11(4Q35.1) CNV | 28 | 27 | 85 |
DEL PEAK 11(4Q35.1) WILD-TYPE | 130 | 78 | 43 |
Figure S173. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.57e-10 (Fisher's exact test), Q value = 1.2e-07
Table S174. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 11(4Q35.1) CNV | 34 | 105 | 32 |
DEL PEAK 11(4Q35.1) WILD-TYPE | 137 | 93 | 66 |
Figure S174. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1e-10 (Fisher's exact test), Q value = 7.8e-08
Table S175. Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 11(4Q35.1) CNV | 37 | 124 | 10 |
DEL PEAK 11(4Q35.1) WILD-TYPE | 127 | 120 | 49 |
Figure S175. Get High-res Image Gene #42: 'Del Peak 11(4q35.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.9e-12 (Fisher's exact test), Q value = 1.5e-09
Table S176. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 12(5Q11.2) CNV | 70 | 29 | 44 | 23 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 78 | 159 | 43 | 26 |
Figure S176. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.02e-07 (Chi-square test), Q value = 0.00014
Table S177. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 12(5Q11.2) CNV | 12 | 47 | 35 | 29 | 15 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 78 | 47 | 60 | 71 | 10 |
Figure S177. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.35e-06 (Chi-square test), Q value = 0.00089
Table S178. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 12(5Q11.2) CNV | 32 | 18 | 36 | 6 | 11 | 20 | 8 | 8 | 2 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 43 | 37 | 20 | 36 | 18 | 28 | 31 | 16 | 21 |
Figure S178. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.57e-09 (Fisher's exact test), Q value = 1.9e-06
Table S179. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 12(5Q11.2) CNV | 30 | 42 | 69 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 128 | 63 | 59 |
Figure S179. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 4.53e-08 (Fisher's exact test), Q value = 3.3e-05
Table S180. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 12(5Q11.2) CNV | 34 | 96 | 33 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 137 | 102 | 65 |
Figure S180. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 2.11e-06 (Fisher's exact test), Q value = 0.0014
Table S181. Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 12(5Q11.2) CNV | 36 | 111 | 16 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 128 | 133 | 43 |
Figure S181. Get High-res Image Gene #43: 'Del Peak 12(5q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.08e-12 (Fisher's exact test), Q value = 8.6e-10
Table S182. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 13(5Q22.1) CNV | 75 | 37 | 52 | 25 |
DEL PEAK 13(5Q22.1) WILD-TYPE | 73 | 151 | 35 | 24 |
Figure S182. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.56e-08 (Chi-square test), Q value = 1.9e-05
Table S183. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 13(5Q22.1) CNV | 14 | 52 | 43 | 37 | 17 |
DEL PEAK 13(5Q22.1) WILD-TYPE | 76 | 42 | 52 | 63 | 8 |
Figure S183. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.55e-08 (Chi-square test), Q value = 1.1e-05
Table S184. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 13(5Q22.1) CNV | 40 | 14 | 41 | 8 | 11 | 24 | 11 | 9 | 4 |
DEL PEAK 13(5Q22.1) WILD-TYPE | 35 | 41 | 15 | 34 | 18 | 24 | 28 | 15 | 19 |
Figure S184. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.56e-10 (Fisher's exact test), Q value = 2.7e-07
Table S185. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 13(5Q22.1) CNV | 36 | 49 | 77 |
DEL PEAK 13(5Q22.1) WILD-TYPE | 122 | 56 | 51 |
Figure S185. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 5.97e-10 (Fisher's exact test), Q value = 4.6e-07
Table S186. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 13(5Q22.1) CNV | 38 | 109 | 39 |
DEL PEAK 13(5Q22.1) WILD-TYPE | 133 | 89 | 59 |
Figure S186. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 8.43e-09 (Fisher's exact test), Q value = 6.3e-06
Table S187. Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 13(5Q22.1) CNV | 40 | 129 | 17 |
DEL PEAK 13(5Q22.1) WILD-TYPE | 124 | 115 | 42 |
Figure S187. Get High-res Image Gene #44: 'Del Peak 13(5q22.1)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.29e-06 (Chi-square test), Q value = 0.00085
Table S188. Gene #46: 'Del Peak 15(6q22.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 15(6Q22.31) CNV | 51 | 52 | 62 | 28 | 9 |
DEL PEAK 15(6Q22.31) WILD-TYPE | 39 | 42 | 33 | 72 | 16 |
Figure S188. Get High-res Image Gene #46: 'Del Peak 15(6q22.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 8.64e-05 (Chi-square test), Q value = 0.049
Table S189. Gene #47: 'Del Peak 16(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 16(6Q26) CNV | 49 | 54 | 58 | 31 | 9 |
DEL PEAK 16(6Q26) WILD-TYPE | 41 | 40 | 37 | 69 | 16 |
Figure S189. Get High-res Image Gene #47: 'Del Peak 16(6q26)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 7.67e-17 (Fisher's exact test), Q value = 6.2e-14
Table S190. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 17(8P23.2) CNV | 107 | 49 | 51 | 22 |
DEL PEAK 17(8P23.2) WILD-TYPE | 41 | 139 | 36 | 27 |
Figure S190. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 9.17e-05 (Chi-square test), Q value = 0.051
Table S191. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 17(8P23.2) CNV | 26 | 45 | 58 | 47 | 17 |
DEL PEAK 17(8P23.2) WILD-TYPE | 64 | 49 | 37 | 53 | 8 |
Figure S191. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000354 (Fisher's exact test), Q value = 0.18
Table S192. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 89 | 65 | 58 |
DEL PEAK 17(8P23.2) CNV | 10 | 56 | 34 | 16 |
DEL PEAK 17(8P23.2) WILD-TYPE | 13 | 33 | 31 | 42 |
Figure S192. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 8.22e-09 (Chi-square test), Q value = 6.1e-06
Table S193. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 17(8P23.2) CNV | 55 | 33 | 35 | 8 | 7 | 20 | 17 | 10 | 6 |
DEL PEAK 17(8P23.2) WILD-TYPE | 20 | 22 | 21 | 34 | 22 | 28 | 22 | 14 | 17 |
Figure S193. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 2.29e-07 (Fisher's exact test), Q value = 0.00016
Table S194. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 17(8P23.2) CNV | 57 | 74 | 60 |
DEL PEAK 17(8P23.2) WILD-TYPE | 101 | 31 | 68 |
Figure S194. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 3.58e-06 (Fisher's exact test), Q value = 0.0023
Table S195. Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 17(8P23.2) CNV | 57 | 111 | 58 |
DEL PEAK 17(8P23.2) WILD-TYPE | 114 | 87 | 40 |
Figure S195. Get High-res Image Gene #48: 'Del Peak 17(8p23.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.83e-15 (Fisher's exact test), Q value = 1.5e-12
Table S196. Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 18(8P12) CNV | 101 | 45 | 43 | 16 |
DEL PEAK 18(8P12) WILD-TYPE | 47 | 143 | 44 | 33 |
Figure S196. Get High-res Image Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.95e-05 (Chi-square test), Q value = 0.012
Table S197. Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 18(8P12) CNV | 23 | 39 | 54 | 43 | 18 |
DEL PEAK 18(8P12) WILD-TYPE | 67 | 55 | 41 | 57 | 7 |
Figure S197. Get High-res Image Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 4.61e-05 (Chi-square test), Q value = 0.027
Table S198. Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 18(8P12) CNV | 48 | 29 | 28 | 9 | 7 | 20 | 15 | 9 | 5 |
DEL PEAK 18(8P12) WILD-TYPE | 27 | 26 | 28 | 33 | 22 | 28 | 24 | 15 | 18 |
Figure S198. Get High-res Image Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 5.37e-06 (Fisher's exact test), Q value = 0.0033
Table S199. Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 18(8P12) CNV | 51 | 66 | 53 |
DEL PEAK 18(8P12) WILD-TYPE | 107 | 39 | 75 |
Figure S199. Get High-res Image Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 5.26e-05 (Fisher's exact test), Q value = 0.03
Table S200. Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 18(8P12) CNV | 52 | 105 | 45 |
DEL PEAK 18(8P12) WILD-TYPE | 119 | 93 | 53 |
Figure S200. Get High-res Image Gene #49: 'Del Peak 18(8p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 2.79e-11 (Fisher's exact test), Q value = 2.2e-08
Table S201. Gene #50: 'Del Peak 19(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 19(8P11.21) CNV | 59 | 27 | 21 | 0 |
DEL PEAK 19(8P11.21) WILD-TYPE | 89 | 161 | 66 | 49 |
Figure S201. Get High-res Image Gene #50: 'Del Peak 19(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.22e-07 (Fisher's exact test), Q value = 0.00022
Table S202. Gene #52: 'Del Peak 21(9p23)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 21(9P23) CNV | 88 | 85 | 67 | 18 |
DEL PEAK 21(9P23) WILD-TYPE | 60 | 103 | 20 | 31 |
Figure S202. Get High-res Image Gene #52: 'Del Peak 21(9p23)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.0012
Table S203. Gene #53: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 22(9P21.3) CNV | 91 | 89 | 66 | 18 |
DEL PEAK 22(9P21.3) WILD-TYPE | 57 | 99 | 21 | 31 |
Figure S203. Get High-res Image Gene #53: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.49e-07 (Fisher's exact test), Q value = 0.00011
Table S204. Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 23(9Q21.11) CNV | 73 | 66 | 61 | 31 |
DEL PEAK 23(9Q21.11) WILD-TYPE | 75 | 122 | 26 | 18 |
Figure S204. Get High-res Image Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 5.08e-05 (Chi-square test), Q value = 0.029
Table S205. Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 23(9Q21.11) CNV | 36 | 66 | 36 | 46 | 13 |
DEL PEAK 23(9Q21.11) WILD-TYPE | 54 | 28 | 59 | 54 | 12 |
Figure S205. Get High-res Image Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000116 (Chi-square test), Q value = 0.064
Table S206. Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 23(9Q21.11) CNV | 36 | 34 | 40 | 14 | 13 | 29 | 15 | 9 | 5 |
DEL PEAK 23(9Q21.11) WILD-TYPE | 39 | 21 | 16 | 28 | 16 | 19 | 24 | 15 | 18 |
Figure S206. Get High-res Image Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.67e-07 (Fisher's exact test), Q value = 0.00012
Table S207. Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 23(9Q21.11) CNV | 59 | 47 | 89 |
DEL PEAK 23(9Q21.11) WILD-TYPE | 99 | 58 | 39 |
Figure S207. Get High-res Image Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000126 (Fisher's exact test), Q value = 0.069
Table S208. Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 23(9Q21.11) CNV | 63 | 142 | 23 |
DEL PEAK 23(9Q21.11) WILD-TYPE | 101 | 102 | 36 |
Figure S208. Get High-res Image Gene #54: 'Del Peak 23(9q21.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 4.78e-06 (Fisher's exact test), Q value = 0.003
Table S209. Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 25(10Q26.3) CNV | 63 | 32 | 21 | 14 |
DEL PEAK 25(10Q26.3) WILD-TYPE | 85 | 156 | 66 | 35 |
Figure S209. Get High-res Image Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000256 (Chi-square test), Q value = 0.13
Table S210. Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 25(10Q26.3) CNV | 18 | 31 | 29 | 16 | 14 |
DEL PEAK 25(10Q26.3) WILD-TYPE | 72 | 63 | 66 | 84 | 11 |
Figure S210. Get High-res Image Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 5.65e-05 (Chi-square test), Q value = 0.032
Table S211. Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 25(10Q26.3) CNV | 27 | 24 | 20 | 0 | 11 | 9 | 11 | 4 | 4 |
DEL PEAK 25(10Q26.3) WILD-TYPE | 48 | 31 | 36 | 42 | 18 | 39 | 28 | 20 | 19 |
Figure S211. Get High-res Image Gene #56: 'Del Peak 25(10q26.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.04e-06 (Fisher's exact test), Q value = 0.0026
Table S212. Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 26(11P15.5) CNV | 54 | 27 | 32 | 13 |
DEL PEAK 26(11P15.5) WILD-TYPE | 94 | 161 | 55 | 36 |
Figure S212. Get High-res Image Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.36e-06 (Fisher's exact test), Q value = 0.0028
Table S213. Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 26(11P15.5) CNV | 21 | 30 | 49 |
DEL PEAK 26(11P15.5) WILD-TYPE | 137 | 75 | 79 |
Figure S213. Get High-res Image Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.06
Table S214. Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 26(11P15.5) CNV | 35 | 83 | 6 |
DEL PEAK 26(11P15.5) WILD-TYPE | 129 | 161 | 53 |
Figure S214. Get High-res Image Gene #57: 'Del Peak 26(11p15.5)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 0.000122 (Fisher's exact test), Q value = 0.067
Table S215. Gene #58: 'Del Peak 27(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 27(11Q23.2) CNV | 30 | 29 | 32 | 18 |
DEL PEAK 27(11Q23.2) WILD-TYPE | 118 | 159 | 55 | 31 |
Figure S215. Get High-res Image Gene #58: 'Del Peak 27(11q23.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000172 (Fisher's exact test), Q value = 0.092
Table S216. Gene #60: 'Del Peak 29(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 29(12P13.2) CNV | 59 | 41 | 14 | 12 |
DEL PEAK 29(12P13.2) WILD-TYPE | 89 | 147 | 73 | 37 |
Figure S216. Get High-res Image Gene #60: 'Del Peak 29(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 7.21e-07 (Chi-square test), Q value = 0.00048
Table S217. Gene #60: 'Del Peak 29(12p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 29(12P13.2) CNV | 24 | 17 | 34 | 14 | 16 |
DEL PEAK 29(12P13.2) WILD-TYPE | 66 | 77 | 61 | 86 | 9 |
Figure S217. Get High-res Image Gene #60: 'Del Peak 29(12p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0072
Table S218. Gene #61: 'Del Peak 30(12q12)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 30(12Q12) CNV | 47 | 29 | 6 | 8 |
DEL PEAK 30(12Q12) WILD-TYPE | 101 | 159 | 81 | 41 |
Figure S218. Get High-res Image Gene #61: 'Del Peak 30(12q12)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 6.54e-06 (Fisher's exact test), Q value = 0.004
Table S219. Gene #62: 'Del Peak 31(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 31(12Q24.33) CNV | 55 | 45 | 10 | 5 |
DEL PEAK 31(12Q24.33) WILD-TYPE | 93 | 143 | 77 | 44 |
Figure S219. Get High-res Image Gene #62: 'Del Peak 31(12q24.33)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000306 (Fisher's exact test), Q value = 0.16
Table S220. Gene #62: 'Del Peak 31(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 31(12Q24.33) CNV | 48 | 29 | 15 |
DEL PEAK 31(12Q24.33) WILD-TYPE | 110 | 76 | 113 |
Figure S220. Get High-res Image Gene #62: 'Del Peak 31(12q24.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.38e-19 (Fisher's exact test), Q value = 1.1e-16
Table S221. Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 32(13Q12.11) CNV | 118 | 58 | 59 | 30 |
DEL PEAK 32(13Q12.11) WILD-TYPE | 30 | 130 | 28 | 19 |
Figure S221. Get High-res Image Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.00097
Table S222. Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 89 | 65 | 58 |
DEL PEAK 32(13Q12.11) CNV | 8 | 66 | 39 | 19 |
DEL PEAK 32(13Q12.11) WILD-TYPE | 15 | 23 | 26 | 39 |
Figure S222. Get High-res Image Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 2.73e-07 (Chi-square test), Q value = 0.00019
Table S223. Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 32(13Q12.11) CNV | 53 | 30 | 41 | 14 | 9 | 34 | 21 | 11 | 5 |
DEL PEAK 32(13Q12.11) WILD-TYPE | 22 | 25 | 15 | 28 | 20 | 14 | 18 | 13 | 18 |
Figure S223. Get High-res Image Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.07e-08 (Fisher's exact test), Q value = 3e-05
Table S224. Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 32(13Q12.11) CNV | 60 | 71 | 87 |
DEL PEAK 32(13Q12.11) WILD-TYPE | 98 | 34 | 41 |
Figure S224. Get High-res Image Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 8.51e-05 (Fisher's exact test), Q value = 0.048
Table S225. Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 32(13Q12.11) CNV | 76 | 161 | 27 |
DEL PEAK 32(13Q12.11) WILD-TYPE | 88 | 83 | 32 |
Figure S225. Get High-res Image Gene #63: 'Del Peak 32(13q12.11)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.05e-19 (Fisher's exact test), Q value = 8.5e-17
Table S226. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 33(13Q12.13) CNV | 120 | 59 | 56 | 31 |
DEL PEAK 33(13Q12.13) WILD-TYPE | 28 | 129 | 31 | 18 |
Figure S226. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000107 (Chi-square test), Q value = 0.06
Table S227. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 33(13Q12.13) CNV | 38 | 59 | 66 | 49 | 20 |
DEL PEAK 33(13Q12.13) WILD-TYPE | 52 | 35 | 29 | 51 | 5 |
Figure S227. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 6.68e-07 (Fisher's exact test), Q value = 0.00045
Table S228. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 89 | 65 | 58 |
DEL PEAK 33(13Q12.13) CNV | 8 | 67 | 39 | 19 |
DEL PEAK 33(13Q12.13) WILD-TYPE | 15 | 22 | 26 | 39 |
Figure S228. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 1.2e-07 (Chi-square test), Q value = 8.5e-05
Table S229. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 33(13Q12.13) CNV | 55 | 30 | 38 | 14 | 9 | 36 | 21 | 11 | 5 |
DEL PEAK 33(13Q12.13) WILD-TYPE | 20 | 25 | 18 | 28 | 20 | 12 | 18 | 13 | 18 |
Figure S229. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 8.17e-08 (Fisher's exact test), Q value = 5.9e-05
Table S230. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 33(13Q12.13) CNV | 61 | 72 | 86 |
DEL PEAK 33(13Q12.13) WILD-TYPE | 97 | 33 | 42 |
Figure S230. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000138 (Fisher's exact test), Q value = 0.075
Table S231. Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 33(13Q12.13) CNV | 77 | 161 | 27 |
DEL PEAK 33(13Q12.13) WILD-TYPE | 87 | 83 | 32 |
Figure S231. Get High-res Image Gene #64: 'Del Peak 33(13q12.13)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 7.61e-22 (Fisher's exact test), Q value = 6.2e-19
Table S232. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 34(13Q14.2) CNV | 117 | 52 | 52 | 35 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 31 | 136 | 35 | 14 |
Figure S232. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0064
Table S233. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 89 | 65 | 58 |
DEL PEAK 34(13Q14.2) CNV | 8 | 60 | 40 | 17 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 15 | 29 | 25 | 41 |
Figure S233. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 4.15e-09 (Chi-square test), Q value = 3.1e-06
Table S234. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 34(13Q14.2) CNV | 53 | 32 | 33 | 12 | 7 | 36 | 20 | 11 | 3 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 22 | 23 | 23 | 30 | 22 | 12 | 19 | 13 | 20 |
Figure S234. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.54e-07 (Fisher's exact test), Q value = 0.00011
Table S235. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 34(13Q14.2) CNV | 57 | 71 | 79 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 101 | 34 | 49 |
Figure S235. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000206 (Fisher's exact test), Q value = 0.11
Table S236. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 34(13Q14.2) CNV | 73 | 127 | 53 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 98 | 71 | 45 |
Figure S236. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 4.69e-05 (Fisher's exact test), Q value = 0.027
Table S237. Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 34(13Q14.2) CNV | 73 | 156 | 24 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 91 | 88 | 35 |
Figure S237. Get High-res Image Gene #65: 'Del Peak 34(13q14.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2.2e-15 (Fisher's exact test), Q value = 1.8e-12
Table S238. Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 35(13Q34) CNV | 95 | 43 | 49 | 30 |
DEL PEAK 35(13Q34) WILD-TYPE | 53 | 145 | 38 | 19 |
Figure S238. Get High-res Image Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 3.71e-06 (Chi-square test), Q value = 0.0024
Table S239. Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 35(13Q34) CNV | 45 | 24 | 29 | 13 | 6 | 32 | 16 | 11 | 2 |
DEL PEAK 35(13Q34) WILD-TYPE | 30 | 31 | 27 | 29 | 23 | 16 | 23 | 13 | 21 |
Figure S239. Get High-res Image Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.09e-05 (Fisher's exact test), Q value = 0.018
Table S240. Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 35(13Q34) CNV | 50 | 58 | 70 |
DEL PEAK 35(13Q34) WILD-TYPE | 108 | 47 | 58 |
Figure S240. Get High-res Image Gene #66: 'Del Peak 35(13q34)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 0.000135 (Fisher's exact test), Q value = 0.073
Table S241. Gene #67: 'Del Peak 36(14q32.33)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 36(14Q32.33) CNV | 46 | 46 | 41 | 7 |
DEL PEAK 36(14Q32.33) WILD-TYPE | 102 | 142 | 46 | 42 |
Figure S241. Get High-res Image Gene #67: 'Del Peak 36(14q32.33)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.81e-10 (Fisher's exact test), Q value = 1.4e-07
Table S242. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 37(15Q11.2) CNV | 104 | 63 | 42 | 30 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 44 | 125 | 45 | 19 |
Figure S242. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000193 (Chi-square test), Q value = 0.1
Table S243. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 37(15Q11.2) CNV | 31 | 48 | 59 | 45 | 19 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 59 | 46 | 36 | 55 | 6 |
Figure S243. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.087
Table S244. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 89 | 65 | 58 |
DEL PEAK 37(15Q11.2) CNV | 10 | 59 | 33 | 17 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 13 | 30 | 32 | 41 |
Figure S244. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

P value = 1.91e-13 (Chi-square test), Q value = 1.5e-10
Table S245. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 37(15Q11.2) CNV | 58 | 34 | 30 | 6 | 7 | 34 | 13 | 7 | 6 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 17 | 21 | 26 | 36 | 22 | 14 | 26 | 17 | 17 |
Figure S245. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.4e-05 (Fisher's exact test), Q value = 0.0084
Table S246. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 37(15Q11.2) CNV | 60 | 71 | 64 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 98 | 34 | 64 |
Figure S246. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.016
Table S247. Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 37(15Q11.2) CNV | 63 | 117 | 57 |
DEL PEAK 37(15Q11.2) WILD-TYPE | 108 | 81 | 41 |
Figure S247. Get High-res Image Gene #68: 'Del Peak 37(15q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 2.59e-07 (Fisher's exact test), Q value = 0.00018
Table S248. Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 38(16Q23.1) CNV | 68 | 37 | 40 | 15 |
DEL PEAK 38(16Q23.1) WILD-TYPE | 80 | 151 | 47 | 34 |
Figure S248. Get High-res Image Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.00046 (Chi-square test), Q value = 0.24
Table S249. Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 38(16Q23.1) CNV | 16 | 40 | 43 | 30 | 7 |
DEL PEAK 38(16Q23.1) WILD-TYPE | 74 | 54 | 52 | 70 | 18 |
Figure S249. Get High-res Image Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.73e-06 (Chi-square test), Q value = 0.0011
Table S250. Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 38(16Q23.1) CNV | 38 | 15 | 28 | 5 | 5 | 20 | 16 | 4 | 2 |
DEL PEAK 38(16Q23.1) WILD-TYPE | 37 | 40 | 28 | 37 | 24 | 28 | 23 | 20 | 21 |
Figure S250. Get High-res Image Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.21e-07 (Fisher's exact test), Q value = 0.00022
Table S251. Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 38(16Q23.1) CNV | 30 | 52 | 51 |
DEL PEAK 38(16Q23.1) WILD-TYPE | 128 | 53 | 77 |
Figure S251. Get High-res Image Gene #69: 'Del Peak 38(16q23.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.66e-06 (Fisher's exact test), Q value = 0.0011
Table S252. Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 39(16Q24.3) CNV | 73 | 45 | 43 | 17 |
DEL PEAK 39(16Q24.3) WILD-TYPE | 75 | 143 | 44 | 32 |
Figure S252. Get High-res Image Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.9e-05 (Chi-square test), Q value = 0.017
Table S253. Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 39(16Q24.3) CNV | 43 | 16 | 27 | 8 | 6 | 24 | 15 | 5 | 5 |
DEL PEAK 39(16Q24.3) WILD-TYPE | 32 | 39 | 29 | 34 | 23 | 24 | 24 | 19 | 18 |
Figure S253. Get High-res Image Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.88e-05 (Fisher's exact test), Q value = 0.028
Table S254. Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 39(16Q24.3) CNV | 40 | 53 | 56 |
DEL PEAK 39(16Q24.3) WILD-TYPE | 118 | 52 | 72 |
Figure S254. Get High-res Image Gene #70: 'Del Peak 39(16q24.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.78e-13 (Fisher's exact test), Q value = 2.2e-10
Table S255. Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 40(17P13.3) CNV | 111 | 63 | 53 | 25 |
DEL PEAK 40(17P13.3) WILD-TYPE | 37 | 125 | 34 | 24 |
Figure S255. Get High-res Image Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 7.56e-08 (Chi-square test), Q value = 5.4e-05
Table S256. Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 40(17P13.3) CNV | 29 | 51 | 69 | 44 | 19 |
DEL PEAK 40(17P13.3) WILD-TYPE | 61 | 43 | 26 | 56 | 6 |
Figure S256. Get High-res Image Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 5.6e-08 (Chi-square test), Q value = 4e-05
Table S257. Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 40(17P13.3) CNV | 57 | 38 | 32 | 7 | 14 | 29 | 21 | 9 | 9 |
DEL PEAK 40(17P13.3) WILD-TYPE | 18 | 17 | 24 | 35 | 15 | 19 | 18 | 15 | 14 |
Figure S257. Get High-res Image Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 9.79e-07 (Fisher's exact test), Q value = 0.00065
Table S258. Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 40(17P13.3) CNV | 66 | 78 | 72 |
DEL PEAK 40(17P13.3) WILD-TYPE | 92 | 27 | 56 |
Figure S258. Get High-res Image Gene #71: 'Del Peak 40(17p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 8.58e-10 (Fisher's exact test), Q value = 6.5e-07
Table S259. Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 41(18Q21.32) CNV | 102 | 69 | 48 | 14 |
DEL PEAK 41(18Q21.32) WILD-TYPE | 46 | 119 | 39 | 35 |
Figure S259. Get High-res Image Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 9.08e-09 (Chi-square test), Q value = 6.8e-06
Table S260. Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 41(18Q21.32) CNV | 48 | 39 | 31 | 8 | 15 | 15 | 25 | 9 | 4 |
DEL PEAK 41(18Q21.32) WILD-TYPE | 27 | 16 | 25 | 34 | 14 | 33 | 14 | 15 | 19 |
Figure S260. Get High-res Image Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.066
Table S261. Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 41(18Q21.32) CNV | 64 | 70 | 60 |
DEL PEAK 41(18Q21.32) WILD-TYPE | 94 | 35 | 68 |
Figure S261. Get High-res Image Gene #72: 'Del Peak 41(18q21.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 9.31e-13 (Fisher's exact test), Q value = 7.4e-10
Table S262. Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 42(18Q23) CNV | 104 | 65 | 48 | 11 |
DEL PEAK 42(18Q23) WILD-TYPE | 44 | 123 | 39 | 38 |
Figure S262. Get High-res Image Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.04e-08 (Chi-square test), Q value = 7.7e-06
Table S263. Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 42(18Q23) CNV | 49 | 37 | 28 | 7 | 15 | 15 | 25 | 9 | 4 |
DEL PEAK 42(18Q23) WILD-TYPE | 26 | 18 | 28 | 35 | 14 | 33 | 14 | 15 | 19 |
Figure S263. Get High-res Image Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 1.28e-05 (Fisher's exact test), Q value = 0.0077
Table S264. Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 42(18Q23) CNV | 61 | 71 | 57 |
DEL PEAK 42(18Q23) WILD-TYPE | 97 | 34 | 71 |
Figure S264. Get High-res Image Gene #73: 'Del Peak 42(18q23)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.6e-12 (Fisher's exact test), Q value = 2.1e-09
Table S265. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 43(19P13.3) CNV | 77 | 69 | 70 | 36 |
DEL PEAK 43(19P13.3) WILD-TYPE | 71 | 119 | 17 | 13 |
Figure S265. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.35e-07 (Chi-square test), Q value = 0.00016
Table S266. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 43(19P13.3) CNV | 38 | 73 | 41 | 46 | 18 |
DEL PEAK 43(19P13.3) WILD-TYPE | 52 | 21 | 54 | 54 | 7 |
Figure S266. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3.43e-10 (Chi-square test), Q value = 2.6e-07
Table S267. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 43(19P13.3) CNV | 35 | 28 | 42 | 35 | 16 | 32 | 14 | 5 | 3 |
DEL PEAK 43(19P13.3) WILD-TYPE | 40 | 27 | 14 | 7 | 13 | 16 | 25 | 19 | 20 |
Figure S267. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.14e-07 (Fisher's exact test), Q value = 0.00022
Table S268. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 43(19P13.3) CNV | 65 | 52 | 93 |
DEL PEAK 43(19P13.3) WILD-TYPE | 93 | 53 | 35 |
Figure S268. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 3.65e-06 (Fisher's exact test), Q value = 0.0023
Table S269. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 43(19P13.3) CNV | 71 | 131 | 45 |
DEL PEAK 43(19P13.3) WILD-TYPE | 100 | 67 | 53 |
Figure S269. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.63e-07 (Fisher's exact test), Q value = 0.00011
Table S270. Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 43(19P13.3) CNV | 66 | 159 | 22 |
DEL PEAK 43(19P13.3) WILD-TYPE | 98 | 85 | 37 |
Figure S270. Get High-res Image Gene #74: 'Del Peak 43(19p13.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-11 (Fisher's exact test), Q value = 9.9e-09
Table S271. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 44(19P13.2) CNV | 77 | 66 | 66 | 37 |
DEL PEAK 44(19P13.2) WILD-TYPE | 71 | 122 | 21 | 12 |
Figure S271. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.22e-08 (Chi-square test), Q value = 1.6e-05
Table S272. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 44(19P13.2) CNV | 35 | 74 | 43 | 42 | 17 |
DEL PEAK 44(19P13.2) WILD-TYPE | 55 | 20 | 52 | 58 | 8 |
Figure S272. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3.34e-10 (Chi-square test), Q value = 2.6e-07
Table S273. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 44(19P13.2) CNV | 37 | 26 | 34 | 34 | 15 | 37 | 11 | 5 | 3 |
DEL PEAK 44(19P13.2) WILD-TYPE | 38 | 29 | 22 | 8 | 14 | 11 | 28 | 19 | 20 |
Figure S273. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 4.01e-07 (Fisher's exact test), Q value = 0.00027
Table S274. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 44(19P13.2) CNV | 61 | 51 | 90 |
DEL PEAK 44(19P13.2) WILD-TYPE | 97 | 54 | 38 |
Figure S274. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.46e-06 (Fisher's exact test), Q value = 0.0016
Table S275. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 44(19P13.2) CNV | 69 | 129 | 43 |
DEL PEAK 44(19P13.2) WILD-TYPE | 102 | 69 | 55 |
Figure S275. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 2.87e-07 (Fisher's exact test), Q value = 2e-04
Table S276. Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 44(19P13.2) CNV | 66 | 155 | 20 |
DEL PEAK 44(19P13.2) WILD-TYPE | 98 | 89 | 39 |
Figure S276. Get High-res Image Gene #75: 'Del Peak 44(19p13.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 9.72e-13 (Fisher's exact test), Q value = 7.7e-10
Table S277. Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 45(19P12) CNV | 75 | 41 | 55 | 28 |
DEL PEAK 45(19P12) WILD-TYPE | 73 | 147 | 32 | 21 |
Figure S277. Get High-res Image Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.71e-05 (Chi-square test), Q value = 0.01
Table S278. Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 45(19P12) CNV | 26 | 56 | 40 | 32 | 16 |
DEL PEAK 45(19P12) WILD-TYPE | 64 | 38 | 55 | 68 | 9 |
Figure S278. Get High-res Image Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.066
Table S279. Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 45(19P12) CNV | 45 | 51 | 65 |
DEL PEAK 45(19P12) WILD-TYPE | 113 | 54 | 63 |
Figure S279. Get High-res Image Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.79e-05 (Fisher's exact test), Q value = 0.016
Table S280. Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 45(19P12) CNV | 52 | 106 | 37 |
DEL PEAK 45(19P12) WILD-TYPE | 119 | 92 | 61 |
Figure S280. Get High-res Image Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.27e-05 (Fisher's exact test), Q value = 0.0077
Table S281. Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 45(19P12) CNV | 49 | 127 | 19 |
DEL PEAK 45(19P12) WILD-TYPE | 115 | 117 | 40 |
Figure S281. Get High-res Image Gene #76: 'Del Peak 45(19p12)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2.02e-07 (Fisher's exact test), Q value = 0.00014
Table S282. Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 46(19Q13.33) CNV | 75 | 41 | 39 | 19 |
DEL PEAK 46(19Q13.33) WILD-TYPE | 73 | 147 | 48 | 30 |
Figure S282. Get High-res Image Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 2.52e-05 (Fisher's exact test), Q value = 0.015
Table S283. Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 46(19Q13.33) CNV | 42 | 94 | 34 |
DEL PEAK 46(19Q13.33) WILD-TYPE | 129 | 104 | 64 |
Figure S283. Get High-res Image Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0084
Table S284. Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 46(19Q13.33) CNV | 40 | 113 | 17 |
DEL PEAK 46(19Q13.33) WILD-TYPE | 124 | 131 | 42 |
Figure S284. Get High-res Image Gene #77: 'Del Peak 46(19q13.33)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0015
Table S285. Gene #78: 'Del Peak 47(20p13)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 47(20P13) CNV | 59 | 31 | 25 | 6 |
DEL PEAK 47(20P13) WILD-TYPE | 89 | 157 | 62 | 43 |
Figure S285. Get High-res Image Gene #78: 'Del Peak 47(20p13)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000127 (Chi-square test), Q value = 0.069
Table S286. Gene #78: 'Del Peak 47(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 47(20P13) CNV | 31 | 15 | 9 | 3 | 4 | 9 | 16 | 3 | 5 |
DEL PEAK 47(20P13) WILD-TYPE | 44 | 40 | 47 | 39 | 25 | 39 | 23 | 21 | 18 |
Figure S286. Get High-res Image Gene #78: 'Del Peak 47(20p13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.1e-11 (Fisher's exact test), Q value = 2.4e-08
Table S287. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 48(21Q11.2) CNV | 32 | 46 | 51 | 28 |
DEL PEAK 48(21Q11.2) WILD-TYPE | 116 | 142 | 36 | 21 |
Figure S287. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000131 (Chi-square test), Q value = 0.071
Table S288. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 48(21Q11.2) CNV | 14 | 44 | 34 | 34 | 5 |
DEL PEAK 48(21Q11.2) WILD-TYPE | 76 | 50 | 61 | 66 | 20 |
Figure S288. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3.59e-08 (Chi-square test), Q value = 2.6e-05
Table S289. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 48(21Q11.2) CNV | 27 | 10 | 23 | 8 | 11 | 32 | 19 | 4 | 1 |
DEL PEAK 48(21Q11.2) WILD-TYPE | 48 | 45 | 33 | 34 | 18 | 16 | 20 | 20 | 22 |
Figure S289. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 3.78e-07 (Fisher's exact test), Q value = 0.00026
Table S290. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 48(21Q11.2) CNV | 33 | 36 | 66 |
DEL PEAK 48(21Q11.2) WILD-TYPE | 125 | 69 | 62 |
Figure S290. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.013
Table S291. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 48(21Q11.2) CNV | 38 | 88 | 28 |
DEL PEAK 48(21Q11.2) WILD-TYPE | 133 | 110 | 70 |
Figure S291. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 3.55e-08 (Fisher's exact test), Q value = 2.6e-05
Table S292. Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 48(21Q11.2) CNV | 33 | 110 | 11 |
DEL PEAK 48(21Q11.2) WILD-TYPE | 131 | 134 | 48 |
Figure S292. Get High-res Image Gene #79: 'Del Peak 48(21q11.2)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 9.45e-11 (Fisher's exact test), Q value = 7.4e-08
Table S293. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 49(21Q21.3) CNV | 32 | 44 | 49 | 28 |
DEL PEAK 49(21Q21.3) WILD-TYPE | 116 | 144 | 38 | 21 |
Figure S293. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 1.28e-05 (Chi-square test), Q value = 0.0077
Table S294. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 49(21Q21.3) CNV | 12 | 45 | 28 | 35 | 5 |
DEL PEAK 49(21Q21.3) WILD-TYPE | 78 | 49 | 67 | 65 | 20 |
Figure S294. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 3.24e-10 (Chi-square test), Q value = 2.5e-07
Table S295. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 49(21Q21.3) CNV | 23 | 10 | 25 | 8 | 9 | 35 | 18 | 4 | 1 |
DEL PEAK 49(21Q21.3) WILD-TYPE | 52 | 45 | 31 | 34 | 20 | 13 | 21 | 20 | 22 |
Figure S295. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 5.51e-10 (Fisher's exact test), Q value = 4.2e-07
Table S296. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 49(21Q21.3) CNV | 30 | 32 | 71 |
DEL PEAK 49(21Q21.3) WILD-TYPE | 128 | 73 | 57 |
Figure S296. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0063
Table S297. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 49(21Q21.3) CNV | 34 | 85 | 30 |
DEL PEAK 49(21Q21.3) WILD-TYPE | 137 | 113 | 68 |
Figure S297. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 1.28e-07 (Fisher's exact test), Q value = 9.1e-05
Table S298. Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 49(21Q21.3) CNV | 32 | 106 | 11 |
DEL PEAK 49(21Q21.3) WILD-TYPE | 132 | 138 | 48 |
Figure S298. Get High-res Image Gene #80: 'Del Peak 49(21q21.3)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 6.18e-13 (Fisher's exact test), Q value = 4.9e-10
Table S299. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 50(22Q13.32) CNV | 90 | 49 | 52 | 33 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 58 | 139 | 35 | 16 |
Figure S299. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 4.57e-08 (Chi-square test), Q value = 3.3e-05
Table S300. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 90 | 94 | 95 | 100 | 25 |
DEL PEAK 50(22Q13.32) CNV | 20 | 58 | 57 | 41 | 15 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 70 | 36 | 38 | 59 | 10 |
Figure S300. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

P value = 1.51e-10 (Chi-square test), Q value = 1.2e-07
Table S301. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 | CLUS_9 |
---|---|---|---|---|---|---|---|---|---|
ALL | 75 | 55 | 56 | 42 | 29 | 48 | 39 | 24 | 23 |
DEL PEAK 50(22Q13.32) CNV | 51 | 16 | 33 | 10 | 14 | 36 | 17 | 5 | 4 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 24 | 39 | 23 | 32 | 15 | 12 | 22 | 19 | 19 |
Figure S301. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

P value = 6.29e-11 (Fisher's exact test), Q value = 4.9e-08
Table S302. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 50(22Q13.32) CNV | 44 | 56 | 86 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 114 | 49 | 42 |
Figure S302. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

P value = 1.66e-07 (Fisher's exact test), Q value = 0.00012
Table S303. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 171 | 198 | 98 |
DEL PEAK 50(22Q13.32) CNV | 55 | 121 | 45 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 116 | 77 | 53 |
Figure S303. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

P value = 2.72e-08 (Fisher's exact test), Q value = 2e-05
Table S304. Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 164 | 244 | 59 |
DEL PEAK 50(22Q13.32) CNV | 53 | 147 | 21 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 111 | 97 | 38 |
Figure S304. Get High-res Image Gene #81: 'Del Peak 50(22q13.32)' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-07 (Fisher's exact test), Q value = 0.00014
Table S305. Gene #82: 'Del Peak 51(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 148 | 188 | 87 | 49 |
DEL PEAK 51(XP22.2) CNV | 68 | 32 | 25 | 12 |
DEL PEAK 51(XP22.2) WILD-TYPE | 80 | 156 | 62 | 37 |
Figure S305. Get High-res Image Gene #82: 'Del Peak 51(Xp22.2)' versus Molecular Subtype #3: 'CN_CNMF'

P value = 0.000322 (Fisher's exact test), Q value = 0.17
Table S306. Gene #82: 'Del Peak 51(Xp22.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 158 | 105 | 128 |
DEL PEAK 51(XP22.2) CNV | 33 | 46 | 34 |
DEL PEAK 51(XP22.2) WILD-TYPE | 125 | 59 | 94 |
Figure S306. Get High-res Image Gene #82: 'Del Peak 51(Xp22.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

-
Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
-
Molecular subtype file = LUAD-TP.transferedmergedcluster.txt
-
Number of patients = 472
-
Number of copy number variation regions = 82
-
Number of molecular subtypes = 10
-
Exclude regions that fewer than K tumors have alterations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.