This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 75 peak regions and 6 molecular subtypes across 306 patients, 190 significant findings detected with Q value < 0.25.
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Amp Peak 1(1p36.22) cnvs correlated to 'CN_CNMF'.
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Amp Peak 2(1q21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 3(1q42.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 4(3q27.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 5(5p13.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Amp Peak 6(6p21.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 7(6q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 8(6q21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 9(7p22.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 10(7p11.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 11(7q21.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 12(8p23.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 13(8q24.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 15(9q34.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 16(10q22.2) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Amp Peak 17(10q26.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Amp Peak 18(11p13) cnvs correlated to 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 19(11q13.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 20(12p12.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 21(12q15) cnvs correlated to 'METHLYATION_CNMF'.
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Amp Peak 22(13q12.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 23(13q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 24(15q26.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Amp Peak 25(17q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Amp Peak 26(18q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 27(19q12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 28(20q13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Amp Peak 29(Xq27.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 1(1p36.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 5(2q37.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 6(3p26.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 7(3p14.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 8(3q26.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 9(4p16.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 10(4q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 11(4q34.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 13(5q23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 14(6p25.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 15(6q26) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
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Del Peak 16(7q31.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 17(7q36.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 18(8p23.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 19(9p23) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 20(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 21(9q21.11) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 22(10p15.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 23(10q22.3) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 24(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 25(11p15.4) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 26(11q23.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 27(12p13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 28(13q12.11) cnvs correlated to 'CN_CNMF'.
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Del Peak 29(14q21.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 30(14q32.33) cnvs correlated to 'CN_CNMF'.
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Del Peak 31(15q15.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 32(16p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 33(16q23.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 34(17p12) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 35(17q24.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
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Del Peak 36(18q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 37(19p13.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 38(19q13.11) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 39(20p12.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 40(20p12.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 41(21q11.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 42(21q22.13) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 43(22q13.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
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Del Peak 44(Xp22.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 45(Xp21.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 46(Xq21.33) cnvs correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 75 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 190 significant findings detected.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
Amp Peak 2(1q21 3) | 0 (0%) | 198 |
4.55e-20 (2.02e-17) |
5.04e-11 (2.08e-08) |
3.28e-08 (1.26e-05) |
3.6e-05 (0.0114) |
1.31e-05 (0.0044) |
1.78e-05 (0.00588) |
Amp Peak 3(1q42 3) | 0 (0%) | 201 |
5.52e-14 (2.38e-11) |
1.11e-07 (4.21e-05) |
4.49e-07 (0.000166) |
0.000462 (0.13) |
1.58e-06 (0.000569) |
1.77e-06 (0.000637) |
Amp Peak 27(19q12) | 0 (0%) | 216 |
1.67e-15 (7.32e-13) |
4.66e-10 (1.88e-07) |
8.37e-11 (3.43e-08) |
4.59e-06 (0.00161) |
0.000305 (0.088) |
1.71e-10 (6.94e-08) |
Del Peak 12(5q11 2) | 0 (0%) | 203 |
6.54e-28 (2.94e-25) |
1.27e-13 (5.44e-11) |
9.48e-07 (0.000343) |
3.06e-07 (0.000114) |
2.92e-07 (0.000109) |
2.53e-09 (1.01e-06) |
Del Peak 13(5q23 2) | 0 (0%) | 213 |
2.48e-23 (1.11e-20) |
2.5e-12 (1.05e-09) |
2.02e-07 (7.62e-05) |
2.07e-06 (0.000738) |
2.65e-07 (9.94e-05) |
1.11e-08 (4.35e-06) |
Del Peak 37(19p13 3) | 0 (0%) | 207 |
2.35e-27 (1.06e-24) |
2.38e-16 (1.05e-13) |
3.62e-11 (1.5e-08) |
1.34e-12 (5.64e-10) |
2.21e-07 (8.32e-05) |
1.06e-19 (4.7e-17) |
Del Peak 9(4p16 3) | 0 (0%) | 194 |
2.89e-10 (1.17e-07) |
0.000377 (0.107) |
0.000266 (0.078) |
0.007 (1.00) |
0.000848 (0.225) |
3.07e-05 (0.00983) |
Del Peak 31(15q15 1) | 0 (0%) | 227 |
6.44e-13 (2.74e-10) |
5.71e-07 (0.00021) |
1.79e-05 (0.00592) |
7.38e-06 (0.00254) |
0.00132 (0.33) |
8.73e-07 (0.000317) |
Del Peak 34(17p12) | 0 (0%) | 191 |
1.81e-23 (8.11e-21) |
4.44e-11 (1.84e-08) |
9.95e-06 (0.00338) |
1.96e-05 (0.00644) |
0.00284 (0.633) |
6.36e-06 (0.00221) |
Del Peak 43(22q13 31) | 0 (0%) | 205 |
9.68e-15 (4.22e-12) |
0.000142 (0.0431) |
0.000528 (0.146) |
0.000471 (0.131) |
0.00655 (1.00) |
6.56e-06 (0.00227) |
Amp Peak 6(6p21 1) | 0 (0%) | 226 |
3.1e-17 (1.37e-14) |
5.99e-10 (2.41e-07) |
0.000807 (0.216) |
0.00341 (0.747) |
0.00998 (1.00) |
2.45e-05 (0.00799) |
Amp Peak 7(6q12) | 0 (0%) | 246 |
2.98e-09 (1.18e-06) |
1.69e-08 (6.53e-06) |
0.000245 (0.0726) |
0.0112 (1.00) |
0.046 (1.00) |
0.000263 (0.0776) |
Amp Peak 24(15q26 1) | 0 (0%) | 237 |
1.03e-13 (4.43e-11) |
0.00041 (0.116) |
0.000136 (0.0416) |
7.53e-06 (0.00258) |
0.21 (1.00) |
0.196 (1.00) |
Amp Peak 28(20q13 2) | 0 (0%) | 105 |
5.63e-21 (2.51e-18) |
2.06e-11 (8.57e-09) |
6.87e-07 (0.000252) |
0.00828 (1.00) |
0.0141 (1.00) |
8.89e-09 (3.5e-06) |
Del Peak 11(4q34 3) | 0 (0%) | 179 |
1.07e-14 (4.66e-12) |
7.57e-07 (0.000276) |
0.000746 (0.202) |
0.0177 (1.00) |
0.0116 (1.00) |
9.16e-06 (0.00312) |
Del Peak 17(7q36 3) | 0 (0%) | 248 |
1.82e-14 (7.88e-12) |
1.93e-05 (0.00636) |
0.000791 (0.213) |
0.00554 (1.00) |
0.123 (1.00) |
0.000113 (0.0349) |
Del Peak 18(8p23 2) | 0 (0%) | 229 |
4.3e-14 (1.86e-11) |
5.78e-06 (0.00201) |
0.000543 (0.149) |
0.00156 (0.381) |
0.134 (1.00) |
0.00016 (0.0483) |
Del Peak 20(9p21 3) | 0 (0%) | 188 |
6.29e-16 (2.77e-13) |
5.35e-11 (2.2e-08) |
3e-06 (0.00106) |
0.00205 (0.478) |
0.0263 (1.00) |
0.00026 (0.0769) |
Del Peak 27(12p13 31) | 0 (0%) | 256 |
1.49e-10 (6.06e-08) |
1.13e-05 (0.00382) |
2.66e-05 (0.00862) |
0.000281 (0.0817) |
0.0679 (1.00) |
0.0287 (1.00) |
Del Peak 32(16p13 3) | 0 (0%) | 248 |
7.42e-11 (3.05e-08) |
7.03e-05 (0.0219) |
2.03e-05 (0.00665) |
0.000382 (0.108) |
0.00489 (1.00) |
0.0185 (1.00) |
Amp Peak 5(5p13 1) | 0 (0%) | 219 |
1.64e-14 (7.14e-12) |
5.68e-07 (0.000209) |
2.72e-05 (0.00879) |
0.0175 (1.00) |
0.0226 (1.00) |
0.00407 (0.864) |
Amp Peak 17(10q26 13) | 0 (0%) | 245 |
1.18e-05 (0.004) |
0.000754 (0.204) |
0.000929 (0.244) |
0.0573 (1.00) |
0.624 (1.00) |
0.0183 (1.00) |
Amp Peak 23(13q22 1) | 0 (0%) | 185 |
1.54e-08 (5.99e-06) |
3.74e-05 (0.0118) |
0.0133 (1.00) |
0.13 (1.00) |
0.532 (1.00) |
2e-06 (0.000715) |
Amp Peak 25(17q12) | 0 (0%) | 214 |
9.54e-13 (4.04e-10) |
8.07e-06 (0.00276) |
6.85e-06 (0.00236) |
0.00179 (0.428) |
0.0233 (1.00) |
0.000996 (0.258) |
Del Peak 6(3p26 1) | 0 (0%) | 222 |
2.64e-10 (1.07e-07) |
0.0003 (0.0869) |
0.107 (1.00) |
0.166 (1.00) |
0.239 (1.00) |
0.000517 (0.143) |
Del Peak 7(3p14 2) | 0 (0%) | 204 |
9.33e-13 (3.95e-10) |
1.38e-06 (0.000498) |
0.00367 (0.797) |
0.00187 (0.441) |
0.0981 (1.00) |
3.65e-05 (0.0115) |
Del Peak 8(3q26 31) | 0 (0%) | 272 |
4.23e-06 (0.00148) |
8.44e-05 (0.0262) |
0.000956 (0.25) |
0.00675 (1.00) |
0.0163 (1.00) |
0.00183 (0.434) |
Del Peak 10(4q22 1) | 0 (0%) | 171 |
6.72e-19 (2.98e-16) |
1.23e-07 (4.66e-05) |
0.0213 (1.00) |
0.0319 (1.00) |
0.00325 (0.716) |
0.000102 (0.0314) |
Del Peak 14(6p25 3) | 0 (0%) | 237 |
5.01e-07 (0.000185) |
0.000932 (0.244) |
0.0174 (1.00) |
0.0023 (0.527) |
0.0976 (1.00) |
0.000915 (0.242) |
Del Peak 19(9p23) | 0 (0%) | 186 |
2.66e-15 (1.17e-12) |
2.88e-05 (0.00923) |
0.00032 (0.0918) |
0.0347 (1.00) |
0.0801 (1.00) |
0.00209 (0.482) |
Del Peak 24(10q23 31) | 0 (0%) | 233 |
2.72e-12 (1.14e-09) |
1.2e-05 (0.00404) |
0.144 (1.00) |
0.139 (1.00) |
0.00287 (0.635) |
2.51e-05 (0.00817) |
Del Peak 35(17q24 3) | 0 (0%) | 251 |
1.32e-10 (5.38e-08) |
0.000237 (0.0707) |
0.000463 (0.13) |
0.00182 (0.434) |
0.0246 (1.00) |
0.0144 (1.00) |
Del Peak 38(19q13 11) | 0 (0%) | 263 |
2.69e-09 (1.07e-06) |
6.16e-05 (0.0193) |
0.0142 (1.00) |
0.00155 (0.38) |
0.0165 (1.00) |
2.44e-06 (0.000866) |
Del Peak 41(21q11 2) | 0 (0%) | 198 |
1.39e-10 (5.66e-08) |
5.41e-05 (0.017) |
0.00538 (1.00) |
0.000341 (0.0976) |
0.0197 (1.00) |
0.00116 (0.29) |
Amp Peak 8(6q21) | 0 (0%) | 250 |
4.38e-09 (1.73e-06) |
2.74e-05 (0.00883) |
0.0068 (1.00) |
0.022 (1.00) |
0.247 (1.00) |
0.00427 (0.901) |
Amp Peak 9(7p22 3) | 0 (0%) | 149 |
8.25e-14 (3.55e-11) |
3.2e-05 (0.0102) |
0.0217 (1.00) |
0.118 (1.00) |
0.083 (1.00) |
0.0057 (1.00) |
Amp Peak 13(8q24 21) | 0 (0%) | 101 |
2.63e-06 (0.000932) |
0.000101 (0.0313) |
0.155 (1.00) |
0.211 (1.00) |
0.273 (1.00) |
0.00158 (0.384) |
Amp Peak 16(10q22 2) | 0 (0%) | 250 |
9.41e-08 (3.6e-05) |
0.0748 (1.00) |
0.000796 (0.213) |
0.00252 (0.57) |
0.174 (1.00) |
0.0283 (1.00) |
Amp Peak 22(13q12 3) | 0 (0%) | 190 |
7.07e-10 (2.83e-07) |
1.45e-05 (0.00485) |
0.148 (1.00) |
0.18 (1.00) |
0.281 (1.00) |
0.00227 (0.522) |
Amp Peak 26(18q11 2) | 0 (0%) | 216 |
3.31e-06 (0.00117) |
0.00023 (0.0687) |
0.0413 (1.00) |
0.0733 (1.00) |
0.291 (1.00) |
0.0974 (1.00) |
Del Peak 1(1p36 11) | 0 (0%) | 223 |
4.2e-15 (1.84e-12) |
0.000366 (0.104) |
0.00149 (0.367) |
0.00241 (0.549) |
0.00195 (0.458) |
0.00576 (1.00) |
Del Peak 15(6q26) | 0 (0%) | 244 |
0.000128 (0.039) |
0.0591 (1.00) |
1.51e-05 (0.00502) |
0.00895 (1.00) |
0.389 (1.00) |
0.0772 (1.00) |
Del Peak 21(9q21 11) | 0 (0%) | 233 |
2.97e-08 (1.15e-05) |
0.000163 (0.049) |
0.084 (1.00) |
0.243 (1.00) |
0.0427 (1.00) |
0.00367 (0.797) |
Del Peak 23(10q22 3) | 0 (0%) | 257 |
2.43e-09 (9.68e-07) |
0.00113 (0.285) |
0.0829 (1.00) |
0.0669 (1.00) |
0.0525 (1.00) |
0.000641 (0.176) |
Del Peak 25(11p15 4) | 0 (0%) | 247 |
2.96e-08 (1.14e-05) |
1.55e-05 (0.00515) |
0.0772 (1.00) |
0.0262 (1.00) |
0.707 (1.00) |
0.0303 (1.00) |
Del Peak 36(18q21 2) | 0 (0%) | 173 |
4.49e-13 (1.91e-10) |
0.000846 (0.225) |
0.0141 (1.00) |
0.152 (1.00) |
0.134 (1.00) |
0.00632 (1.00) |
Del Peak 42(21q22 13) | 0 (0%) | 191 |
1.56e-09 (6.23e-07) |
0.000509 (0.142) |
0.00507 (1.00) |
0.00104 (0.268) |
0.34 (1.00) |
0.0017 (0.409) |
Del Peak 44(Xp22 2) | 0 (0%) | 245 |
1.44e-09 (5.77e-07) |
0.000642 (0.176) |
0.00396 (0.848) |
0.0128 (1.00) |
0.173 (1.00) |
0.0306 (1.00) |
Amp Peak 1(1p36 22) | 0 (0%) | 270 |
1.19e-07 (4.53e-05) |
0.00396 (0.848) |
0.0211 (1.00) |
0.00567 (1.00) |
0.718 (1.00) |
0.0894 (1.00) |
Amp Peak 4(3q27 1) | 0 (0%) | 203 |
1.21e-05 (0.00405) |
0.00742 (1.00) |
0.215 (1.00) |
0.865 (1.00) |
0.607 (1.00) |
0.0457 (1.00) |
Amp Peak 10(7p11 2) | 0 (0%) | 163 |
4.23e-12 (1.77e-09) |
0.0145 (1.00) |
0.0807 (1.00) |
0.473 (1.00) |
0.267 (1.00) |
0.0274 (1.00) |
Amp Peak 11(7q21 2) | 0 (0%) | 169 |
2.36e-11 (9.81e-09) |
0.0249 (1.00) |
0.384 (1.00) |
0.267 (1.00) |
0.466 (1.00) |
0.308 (1.00) |
Amp Peak 12(8p23 1) | 0 (0%) | 185 |
3.39e-13 (1.45e-10) |
0.00174 (0.417) |
0.456 (1.00) |
0.0124 (1.00) |
0.753 (1.00) |
0.196 (1.00) |
Amp Peak 15(9q34 3) | 0 (0%) | 232 |
2.86e-07 (0.000107) |
0.00775 (1.00) |
0.00975 (1.00) |
0.014 (1.00) |
0.139 (1.00) |
0.214 (1.00) |
Amp Peak 18(11p13) | 0 (0%) | 252 |
0.00658 (1.00) |
0.109 (1.00) |
0.00516 (1.00) |
0.00537 (1.00) |
0.187 (1.00) |
0.000655 (0.178) |
Amp Peak 19(11q13 3) | 0 (0%) | 238 |
3.27e-05 (0.0104) |
0.188 (1.00) |
0.21 (1.00) |
0.663 (1.00) |
0.00198 (0.464) |
0.0216 (1.00) |
Amp Peak 20(12p12 1) | 0 (0%) | 220 |
0.000304 (0.0877) |
0.0184 (1.00) |
0.343 (1.00) |
0.976 (1.00) |
0.759 (1.00) |
0.397 (1.00) |
Amp Peak 21(12q15) | 0 (0%) | 229 |
0.00803 (1.00) |
0.000278 (0.0812) |
0.171 (1.00) |
0.429 (1.00) |
0.596 (1.00) |
0.282 (1.00) |
Amp Peak 29(Xq27 3) | 0 (0%) | 246 |
0.000155 (0.047) |
0.223 (1.00) |
0.0519 (1.00) |
0.346 (1.00) |
0.259 (1.00) |
0.803 (1.00) |
Del Peak 2(1p13 2) | 0 (0%) | 247 |
5.4e-12 (2.26e-09) |
0.00106 (0.274) |
0.0127 (1.00) |
0.022 (1.00) |
0.0255 (1.00) |
0.0159 (1.00) |
Del Peak 5(2q37 2) | 0 (0%) | 259 |
0.000191 (0.0572) |
0.00393 (0.846) |
0.0612 (1.00) |
0.163 (1.00) |
0.00285 (0.633) |
0.000991 (0.258) |
Del Peak 16(7q31 1) | 0 (0%) | 262 |
3.11e-07 (0.000115) |
0.00141 (0.351) |
0.141 (1.00) |
0.52 (1.00) |
0.00634 (1.00) |
0.152 (1.00) |
Del Peak 22(10p15 1) | 0 (0%) | 268 |
0.000124 (0.0381) |
0.18 (1.00) |
0.349 (1.00) |
0.497 (1.00) |
0.265 (1.00) |
0.103 (1.00) |
Del Peak 26(11q23 2) | 0 (0%) | 244 |
0.000264 (0.0777) |
0.00248 (0.564) |
0.00154 (0.38) |
0.701 (1.00) |
0.488 (1.00) |
0.779 (1.00) |
Del Peak 28(13q12 11) | 0 (0%) | 262 |
2.32e-06 (0.000827) |
0.0715 (1.00) |
0.0695 (1.00) |
0.118 (1.00) |
0.746 (1.00) |
0.14 (1.00) |
Del Peak 29(14q21 1) | 0 (0%) | 235 |
7.69e-07 (0.00028) |
0.00456 (0.949) |
0.00433 (0.909) |
0.00206 (0.478) |
0.0198 (1.00) |
0.00158 (0.384) |
Del Peak 30(14q32 33) | 0 (0%) | 217 |
9.24e-09 (3.62e-06) |
0.015 (1.00) |
0.0362 (1.00) |
0.00132 (0.33) |
0.023 (1.00) |
0.117 (1.00) |
Del Peak 33(16q23 1) | 0 (0%) | 188 |
2.22e-07 (8.34e-05) |
0.00471 (0.974) |
0.0226 (1.00) |
0.00433 (0.909) |
0.667 (1.00) |
0.132 (1.00) |
Del Peak 39(20p12 1) | 0 (0%) | 254 |
1.21e-08 (4.71e-06) |
0.00112 (0.284) |
0.00107 (0.274) |
0.0182 (1.00) |
0.197 (1.00) |
0.00269 (0.606) |
Del Peak 40(20p12 1) | 0 (0%) | 254 |
1.21e-08 (4.71e-06) |
0.00112 (0.284) |
0.00107 (0.274) |
0.0182 (1.00) |
0.197 (1.00) |
0.00269 (0.606) |
Del Peak 45(Xp21 1) | 0 (0%) | 254 |
6.22e-08 (2.38e-05) |
0.00471 (0.974) |
0.243 (1.00) |
0.094 (1.00) |
0.538 (1.00) |
0.807 (1.00) |
Del Peak 46(Xq21 33) | 0 (0%) | 264 |
5.77e-06 (0.00201) |
0.0421 (1.00) |
0.162 (1.00) |
0.174 (1.00) |
0.00365 (0.796) |
0.0377 (1.00) |
Amp Peak 14(9p24 1) | 0 (0%) | 257 |
0.364 (1.00) |
0.102 (1.00) |
0.65 (1.00) |
0.269 (1.00) |
0.792 (1.00) |
0.273 (1.00) |
Del Peak 3(1q44) | 0 (0%) | 283 |
0.0185 (1.00) |
0.01 (1.00) |
0.55 (1.00) |
0.732 (1.00) |
0.42 (1.00) |
0.317 (1.00) |
Del Peak 4(2q32 1) | 0 (0%) | 264 |
0.00895 (1.00) |
0.12 (1.00) |
0.365 (1.00) |
0.929 (1.00) |
0.0849 (1.00) |
0.227 (1.00) |
P value = 1.19e-07 (Fisher's exact test), Q value = 4.5e-05
Table S1. Gene #1: 'Amp Peak 1(1p36.22)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 1(1P36.22) CNV | 2 | 4 | 3 | 27 |
AMP PEAK 1(1P36.22) WILD-TYPE | 135 | 24 | 25 | 86 |
Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p36.22)' versus Molecular Subtype #1: 'CN_CNMF'
![](D1V1.png)
P value = 4.55e-20 (Fisher's exact test), Q value = 2e-17
Table S2. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 2(1Q21.3) CNV | 12 | 12 | 12 | 72 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 125 | 16 | 16 | 41 |
Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D2V1.png)
P value = 5.04e-11 (Fisher's exact test), Q value = 2.1e-08
Table S3. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 2(1Q21.3) CNV | 4 | 25 | 11 | 51 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 33 | 54 | 53 | 27 |
Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D2V2.png)
P value = 3.28e-08 (Chi-square test), Q value = 1.3e-05
Table S4. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
AMP PEAK 2(1Q21.3) CNV | 6 | 6 | 8 | 8 | 33 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 33 | 31 | 20 | 24 | 14 |
Figure S4. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D2V3.png)
P value = 3.6e-05 (Fisher's exact test), Q value = 0.011
Table S5. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
AMP PEAK 2(1Q21.3) CNV | 8 | 25 | 28 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 50 | 48 | 24 |
Figure S5. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D2V4.png)
P value = 1.31e-05 (Fisher's exact test), Q value = 0.0044
Table S6. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 53 | 101 |
AMP PEAK 2(1Q21.3) CNV | 20 | 10 | 52 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 63 | 43 | 49 |
Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D2V5.png)
P value = 1.78e-05 (Fisher's exact test), Q value = 0.0059
Table S7. Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
AMP PEAK 2(1Q21.3) CNV | 34 | 14 | 34 |
AMP PEAK 2(1Q21.3) WILD-TYPE | 22 | 47 | 86 |
Figure S7. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D2V6.png)
P value = 5.52e-14 (Fisher's exact test), Q value = 2.4e-11
Table S8. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 3(1Q42.3) CNV | 16 | 14 | 11 | 64 |
AMP PEAK 3(1Q42.3) WILD-TYPE | 121 | 14 | 17 | 49 |
Figure S8. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D3V1.png)
P value = 1.11e-07 (Fisher's exact test), Q value = 4.2e-05
Table S9. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 3(1Q42.3) CNV | 5 | 23 | 14 | 47 |
AMP PEAK 3(1Q42.3) WILD-TYPE | 32 | 56 | 50 | 31 |
Figure S9. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D3V2.png)
P value = 4.49e-07 (Chi-square test), Q value = 0.00017
Table S10. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
AMP PEAK 3(1Q42.3) CNV | 6 | 7 | 7 | 7 | 31 |
AMP PEAK 3(1Q42.3) WILD-TYPE | 33 | 30 | 21 | 25 | 16 |
Figure S10. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D3V3.png)
P value = 0.000462 (Fisher's exact test), Q value = 0.13
Table S11. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
AMP PEAK 3(1Q42.3) CNV | 10 | 21 | 27 |
AMP PEAK 3(1Q42.3) WILD-TYPE | 48 | 52 | 25 |
Figure S11. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D3V4.png)
P value = 1.58e-06 (Fisher's exact test), Q value = 0.00057
Table S12. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 53 | 101 |
AMP PEAK 3(1Q42.3) CNV | 16 | 13 | 54 |
AMP PEAK 3(1Q42.3) WILD-TYPE | 67 | 40 | 47 |
Figure S12. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D3V5.png)
P value = 1.77e-06 (Fisher's exact test), Q value = 0.00064
Table S13. Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
AMP PEAK 3(1Q42.3) CNV | 36 | 16 | 31 |
AMP PEAK 3(1Q42.3) WILD-TYPE | 20 | 45 | 89 |
Figure S13. Get High-res Image Gene #3: 'Amp Peak 3(1q42.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D3V6.png)
P value = 1.21e-05 (Fisher's exact test), Q value = 0.0041
Table S14. Gene #4: 'Amp Peak 4(3q27.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 4(3Q27.1) CNV | 26 | 12 | 14 | 51 |
AMP PEAK 4(3Q27.1) WILD-TYPE | 111 | 16 | 14 | 62 |
Figure S14. Get High-res Image Gene #4: 'Amp Peak 4(3q27.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D4V1.png)
P value = 1.64e-14 (Fisher's exact test), Q value = 7.1e-12
Table S15. Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 5(5P13.1) CNV | 12 | 9 | 5 | 61 |
AMP PEAK 5(5P13.1) WILD-TYPE | 125 | 19 | 23 | 52 |
Figure S15. Get High-res Image Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D5V1.png)
P value = 5.68e-07 (Fisher's exact test), Q value = 0.00021
Table S16. Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 5(5P13.1) CNV | 7 | 20 | 6 | 39 |
AMP PEAK 5(5P13.1) WILD-TYPE | 30 | 59 | 58 | 39 |
Figure S16. Get High-res Image Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D5V2.png)
P value = 2.72e-05 (Chi-square test), Q value = 0.0088
Table S17. Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
AMP PEAK 5(5P13.1) CNV | 8 | 8 | 6 | 7 | 29 |
AMP PEAK 5(5P13.1) WILD-TYPE | 31 | 29 | 22 | 25 | 18 |
Figure S17. Get High-res Image Gene #5: 'Amp Peak 5(5p13.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D5V3.png)
P value = 3.1e-17 (Fisher's exact test), Q value = 1.4e-14
Table S18. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 6(6P21.1) CNV | 6 | 7 | 9 | 58 |
AMP PEAK 6(6P21.1) WILD-TYPE | 131 | 21 | 19 | 55 |
Figure S18. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D6V1.png)
P value = 5.99e-10 (Fisher's exact test), Q value = 2.4e-07
Table S19. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 6(6P21.1) CNV | 1 | 20 | 5 | 38 |
AMP PEAK 6(6P21.1) WILD-TYPE | 36 | 59 | 59 | 40 |
Figure S19. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D6V2.png)
P value = 0.000807 (Chi-square test), Q value = 0.22
Table S20. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
AMP PEAK 6(6P21.1) CNV | 5 | 6 | 6 | 7 | 23 |
AMP PEAK 6(6P21.1) WILD-TYPE | 34 | 31 | 22 | 25 | 24 |
Figure S20. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D6V3.png)
P value = 2.45e-05 (Fisher's exact test), Q value = 0.008
Table S21. Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
AMP PEAK 6(6P21.1) CNV | 29 | 11 | 24 |
AMP PEAK 6(6P21.1) WILD-TYPE | 27 | 50 | 96 |
Figure S21. Get High-res Image Gene #6: 'Amp Peak 6(6p21.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D6V6.png)
P value = 2.98e-09 (Fisher's exact test), Q value = 1.2e-06
Table S22. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 7(6Q12) CNV | 7 | 5 | 7 | 41 |
AMP PEAK 7(6Q12) WILD-TYPE | 130 | 23 | 21 | 72 |
Figure S22. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #1: 'CN_CNMF'
![](D7V1.png)
P value = 1.69e-08 (Fisher's exact test), Q value = 6.5e-06
Table S23. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 7(6Q12) CNV | 1 | 13 | 2 | 30 |
AMP PEAK 7(6Q12) WILD-TYPE | 36 | 66 | 62 | 48 |
Figure S23. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D7V2.png)
P value = 0.000245 (Chi-square test), Q value = 0.073
Table S24. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
AMP PEAK 7(6Q12) CNV | 3 | 4 | 6 | 4 | 20 |
AMP PEAK 7(6Q12) WILD-TYPE | 36 | 33 | 22 | 28 | 27 |
Figure S24. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D7V3.png)
P value = 0.000263 (Fisher's exact test), Q value = 0.078
Table S25. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
AMP PEAK 7(6Q12) CNV | 22 | 8 | 16 |
AMP PEAK 7(6Q12) WILD-TYPE | 34 | 53 | 104 |
Figure S25. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D7V6.png)
P value = 4.38e-09 (Fisher's exact test), Q value = 1.7e-06
Table S26. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 8(6Q21) CNV | 6 | 4 | 9 | 37 |
AMP PEAK 8(6Q21) WILD-TYPE | 131 | 24 | 19 | 76 |
Figure S26. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #1: 'CN_CNMF'
![](D8V1.png)
P value = 2.74e-05 (Fisher's exact test), Q value = 0.0088
Table S27. Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 8(6Q21) CNV | 1 | 13 | 4 | 25 |
AMP PEAK 8(6Q21) WILD-TYPE | 36 | 66 | 60 | 53 |
Figure S27. Get High-res Image Gene #8: 'Amp Peak 8(6q21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D8V2.png)
P value = 8.25e-14 (Fisher's exact test), Q value = 3.5e-11
Table S28. Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 9(7P22.3) CNV | 40 | 26 | 14 | 77 |
AMP PEAK 9(7P22.3) WILD-TYPE | 97 | 2 | 14 | 36 |
Figure S28. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D9V1.png)
P value = 3.2e-05 (Fisher's exact test), Q value = 0.01
Table S29. Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 9(7P22.3) CNV | 17 | 46 | 18 | 52 |
AMP PEAK 9(7P22.3) WILD-TYPE | 20 | 33 | 46 | 26 |
Figure S29. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D9V2.png)
P value = 4.23e-12 (Fisher's exact test), Q value = 1.8e-09
Table S30. Gene #10: 'Amp Peak 10(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 10(7P11.2) CNV | 39 | 27 | 14 | 63 |
AMP PEAK 10(7P11.2) WILD-TYPE | 98 | 1 | 14 | 50 |
Figure S30. Get High-res Image Gene #10: 'Amp Peak 10(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D10V1.png)
P value = 2.36e-11 (Fisher's exact test), Q value = 9.8e-09
Table S31. Gene #11: 'Amp Peak 11(7q21.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 11(7Q21.2) CNV | 39 | 27 | 13 | 58 |
AMP PEAK 11(7Q21.2) WILD-TYPE | 98 | 1 | 15 | 55 |
Figure S31. Get High-res Image Gene #11: 'Amp Peak 11(7q21.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D11V1.png)
P value = 3.39e-13 (Fisher's exact test), Q value = 1.4e-10
Table S32. Gene #12: 'Amp Peak 12(8p23.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 12(8P23.1) CNV | 52 | 13 | 28 | 28 |
AMP PEAK 12(8P23.1) WILD-TYPE | 85 | 15 | 0 | 85 |
Figure S32. Get High-res Image Gene #12: 'Amp Peak 12(8p23.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D12V1.png)
P value = 2.63e-06 (Fisher's exact test), Q value = 0.00093
Table S33. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 13(8Q24.21) CNV | 71 | 19 | 24 | 91 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 66 | 9 | 4 | 22 |
Figure S33. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'
![](D13V1.png)
P value = 0.000101 (Fisher's exact test), Q value = 0.031
Table S34. Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 13(8Q24.21) CNV | 18 | 57 | 31 | 62 |
AMP PEAK 13(8Q24.21) WILD-TYPE | 19 | 22 | 33 | 16 |
Figure S34. Get High-res Image Gene #13: 'Amp Peak 13(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D13V2.png)
P value = 2.86e-07 (Fisher's exact test), Q value = 0.00011
Table S35. Gene #15: 'Amp Peak 15(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 15(9Q34.3) CNV | 15 | 7 | 5 | 47 |
AMP PEAK 15(9Q34.3) WILD-TYPE | 122 | 21 | 23 | 66 |
Figure S35. Get High-res Image Gene #15: 'Amp Peak 15(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D15V1.png)
P value = 9.41e-08 (Fisher's exact test), Q value = 3.6e-05
Table S36. Gene #16: 'Amp Peak 16(10q22.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 16(10Q22.2) CNV | 8 | 3 | 10 | 35 |
AMP PEAK 16(10Q22.2) WILD-TYPE | 129 | 25 | 18 | 78 |
Figure S36. Get High-res Image Gene #16: 'Amp Peak 16(10q22.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D16V1.png)
P value = 0.000796 (Chi-square test), Q value = 0.21
Table S37. Gene #16: 'Amp Peak 16(10q22.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
AMP PEAK 16(10Q22.2) CNV | 2 | 6 | 4 | 2 | 17 |
AMP PEAK 16(10Q22.2) WILD-TYPE | 37 | 31 | 24 | 30 | 30 |
Figure S37. Get High-res Image Gene #16: 'Amp Peak 16(10q22.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D16V3.png)
P value = 1.18e-05 (Fisher's exact test), Q value = 0.004
Table S38. Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 17(10Q26.13) CNV | 12 | 4 | 8 | 37 |
AMP PEAK 17(10Q26.13) WILD-TYPE | 125 | 24 | 20 | 76 |
Figure S38. Get High-res Image Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #1: 'CN_CNMF'
![](D17V1.png)
P value = 0.000754 (Fisher's exact test), Q value = 0.2
Table S39. Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 17(10Q26.13) CNV | 3 | 11 | 8 | 27 |
AMP PEAK 17(10Q26.13) WILD-TYPE | 34 | 68 | 56 | 51 |
Figure S39. Get High-res Image Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D17V2.png)
P value = 0.000929 (Chi-square test), Q value = 0.24
Table S40. Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
AMP PEAK 17(10Q26.13) CNV | 3 | 10 | 3 | 4 | 19 |
AMP PEAK 17(10Q26.13) WILD-TYPE | 36 | 27 | 25 | 28 | 28 |
Figure S40. Get High-res Image Gene #17: 'Amp Peak 17(10q26.13)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D17V3.png)
P value = 0.000655 (Fisher's exact test), Q value = 0.18
Table S41. Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
AMP PEAK 18(11P13) CNV | 20 | 11 | 13 |
AMP PEAK 18(11P13) WILD-TYPE | 36 | 50 | 107 |
Figure S41. Get High-res Image Gene #18: 'Amp Peak 18(11p13)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D18V6.png)
P value = 3.27e-05 (Fisher's exact test), Q value = 0.01
Table S42. Gene #19: 'Amp Peak 19(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 19(11Q13.3) CNV | 15 | 5 | 8 | 40 |
AMP PEAK 19(11Q13.3) WILD-TYPE | 122 | 23 | 20 | 73 |
Figure S42. Get High-res Image Gene #19: 'Amp Peak 19(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D19V1.png)
P value = 0.000304 (Fisher's exact test), Q value = 0.088
Table S43. Gene #20: 'Amp Peak 20(12p12.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 20(12P12.1) CNV | 24 | 6 | 9 | 47 |
AMP PEAK 20(12P12.1) WILD-TYPE | 113 | 22 | 19 | 66 |
Figure S43. Get High-res Image Gene #20: 'Amp Peak 20(12p12.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D20V1.png)
P value = 0.000278 (Fisher's exact test), Q value = 0.081
Table S44. Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 21(12Q15) CNV | 15 | 12 | 9 | 29 |
AMP PEAK 21(12Q15) WILD-TYPE | 22 | 67 | 55 | 49 |
Figure S44. Get High-res Image Gene #21: 'Amp Peak 21(12q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D21V2.png)
P value = 7.07e-10 (Fisher's exact test), Q value = 2.8e-07
Table S45. Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 22(13Q12.3) CNV | 31 | 21 | 5 | 59 |
AMP PEAK 22(13Q12.3) WILD-TYPE | 106 | 7 | 23 | 54 |
Figure S45. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D22V1.png)
P value = 1.45e-05 (Fisher's exact test), Q value = 0.0049
Table S46. Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 22(13Q12.3) CNV | 8 | 25 | 17 | 47 |
AMP PEAK 22(13Q12.3) WILD-TYPE | 29 | 54 | 47 | 31 |
Figure S46. Get High-res Image Gene #22: 'Amp Peak 22(13q12.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D22V2.png)
P value = 1.54e-08 (Fisher's exact test), Q value = 6e-06
Table S47. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 23(13Q22.1) CNV | 35 | 20 | 5 | 61 |
AMP PEAK 23(13Q22.1) WILD-TYPE | 102 | 8 | 23 | 52 |
Figure S47. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D23V1.png)
P value = 3.74e-05 (Fisher's exact test), Q value = 0.012
Table S48. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 23(13Q22.1) CNV | 11 | 23 | 17 | 47 |
AMP PEAK 23(13Q22.1) WILD-TYPE | 26 | 56 | 47 | 31 |
Figure S48. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D23V2.png)
P value = 2e-06 (Fisher's exact test), Q value = 0.00072
Table S49. Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
AMP PEAK 23(13Q22.1) CNV | 38 | 18 | 35 |
AMP PEAK 23(13Q22.1) WILD-TYPE | 18 | 43 | 85 |
Figure S49. Get High-res Image Gene #23: 'Amp Peak 23(13q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D23V6.png)
P value = 1.03e-13 (Fisher's exact test), Q value = 4.4e-11
Table S50. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 24(15Q26.1) CNV | 10 | 5 | 1 | 53 |
AMP PEAK 24(15Q26.1) WILD-TYPE | 127 | 23 | 27 | 60 |
Figure S50. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D24V1.png)
P value = 0.00041 (Fisher's exact test), Q value = 0.12
Table S51. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 24(15Q26.1) CNV | 1 | 20 | 11 | 27 |
AMP PEAK 24(15Q26.1) WILD-TYPE | 36 | 59 | 53 | 51 |
Figure S51. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D24V2.png)
P value = 0.000136 (Chi-square test), Q value = 0.042
Table S52. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
AMP PEAK 24(15Q26.1) CNV | 6 | 2 | 11 | 6 | 21 |
AMP PEAK 24(15Q26.1) WILD-TYPE | 33 | 35 | 17 | 26 | 26 |
Figure S52. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D24V3.png)
P value = 7.53e-06 (Fisher's exact test), Q value = 0.0026
Table S53. Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
AMP PEAK 24(15Q26.1) CNV | 4 | 18 | 24 |
AMP PEAK 24(15Q26.1) WILD-TYPE | 54 | 55 | 28 |
Figure S53. Get High-res Image Gene #24: 'Amp Peak 24(15q26.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D24V4.png)
P value = 9.54e-13 (Fisher's exact test), Q value = 4e-10
Table S54. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 25(17Q12) CNV | 16 | 9 | 5 | 62 |
AMP PEAK 25(17Q12) WILD-TYPE | 121 | 19 | 23 | 51 |
Figure S54. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #1: 'CN_CNMF'
![](D25V1.png)
P value = 8.07e-06 (Fisher's exact test), Q value = 0.0028
Table S55. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 25(17Q12) CNV | 11 | 16 | 11 | 41 |
AMP PEAK 25(17Q12) WILD-TYPE | 26 | 63 | 53 | 37 |
Figure S55. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D25V2.png)
P value = 6.85e-06 (Chi-square test), Q value = 0.0024
Table S56. Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
AMP PEAK 25(17Q12) CNV | 6 | 3 | 12 | 6 | 25 |
AMP PEAK 25(17Q12) WILD-TYPE | 33 | 34 | 16 | 26 | 22 |
Figure S56. Get High-res Image Gene #25: 'Amp Peak 25(17q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D25V3.png)
P value = 3.31e-06 (Fisher's exact test), Q value = 0.0012
Table S57. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 26(18Q11.2) CNV | 23 | 8 | 6 | 53 |
AMP PEAK 26(18Q11.2) WILD-TYPE | 114 | 20 | 22 | 60 |
Figure S57. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D26V1.png)
P value = 0.00023 (Fisher's exact test), Q value = 0.069
Table S58. Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 26(18Q11.2) CNV | 4 | 18 | 15 | 36 |
AMP PEAK 26(18Q11.2) WILD-TYPE | 33 | 61 | 49 | 42 |
Figure S58. Get High-res Image Gene #26: 'Amp Peak 26(18q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D26V2.png)
P value = 1.67e-15 (Fisher's exact test), Q value = 7.3e-13
Table S59. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 27(19Q12) CNV | 14 | 9 | 3 | 64 |
AMP PEAK 27(19Q12) WILD-TYPE | 123 | 19 | 25 | 49 |
Figure S59. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #1: 'CN_CNMF'
![](D27V1.png)
P value = 4.66e-10 (Fisher's exact test), Q value = 1.9e-07
Table S60. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 27(19Q12) CNV | 8 | 13 | 10 | 47 |
AMP PEAK 27(19Q12) WILD-TYPE | 29 | 66 | 54 | 31 |
Figure S60. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D27V2.png)
P value = 8.37e-11 (Chi-square test), Q value = 3.4e-08
Table S61. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
AMP PEAK 27(19Q12) CNV | 5 | 4 | 5 | 6 | 33 |
AMP PEAK 27(19Q12) WILD-TYPE | 34 | 33 | 23 | 26 | 14 |
Figure S61. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D27V3.png)
P value = 4.59e-06 (Fisher's exact test), Q value = 0.0016
Table S62. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
AMP PEAK 27(19Q12) CNV | 9 | 15 | 29 |
AMP PEAK 27(19Q12) WILD-TYPE | 49 | 58 | 23 |
Figure S62. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D27V4.png)
P value = 0.000305 (Fisher's exact test), Q value = 0.088
Table S63. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 53 | 101 |
AMP PEAK 27(19Q12) CNV | 18 | 8 | 43 |
AMP PEAK 27(19Q12) WILD-TYPE | 65 | 45 | 58 |
Figure S63. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D27V5.png)
P value = 1.71e-10 (Fisher's exact test), Q value = 6.9e-08
Table S64. Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
AMP PEAK 27(19Q12) CNV | 37 | 11 | 21 |
AMP PEAK 27(19Q12) WILD-TYPE | 19 | 50 | 99 |
Figure S64. Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D27V6.png)
P value = 5.63e-21 (Fisher's exact test), Q value = 2.5e-18
Table S65. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 28(20Q13.2) CNV | 52 | 27 | 20 | 102 |
AMP PEAK 28(20Q13.2) WILD-TYPE | 85 | 1 | 8 | 11 |
Figure S65. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D28V1.png)
P value = 2.06e-11 (Fisher's exact test), Q value = 8.6e-09
Table S66. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
AMP PEAK 28(20Q13.2) CNV | 27 | 41 | 29 | 73 |
AMP PEAK 28(20Q13.2) WILD-TYPE | 10 | 38 | 35 | 5 |
Figure S66. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D28V2.png)
P value = 6.87e-07 (Chi-square test), Q value = 0.00025
Table S67. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
AMP PEAK 28(20Q13.2) CNV | 15 | 19 | 18 | 20 | 45 |
AMP PEAK 28(20Q13.2) WILD-TYPE | 24 | 18 | 10 | 12 | 2 |
Figure S67. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D28V3.png)
P value = 8.89e-09 (Fisher's exact test), Q value = 3.5e-06
Table S68. Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
AMP PEAK 28(20Q13.2) CNV | 54 | 34 | 69 |
AMP PEAK 28(20Q13.2) WILD-TYPE | 2 | 27 | 51 |
Figure S68. Get High-res Image Gene #28: 'Amp Peak 28(20q13.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D28V6.png)
P value = 0.000155 (Fisher's exact test), Q value = 0.047
Table S69. Gene #29: 'Amp Peak 29(Xq27.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
AMP PEAK 29(XQ27.3) CNV | 13 | 10 | 5 | 32 |
AMP PEAK 29(XQ27.3) WILD-TYPE | 124 | 18 | 23 | 81 |
Figure S69. Get High-res Image Gene #29: 'Amp Peak 29(Xq27.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D29V1.png)
P value = 4.2e-15 (Fisher's exact test), Q value = 1.8e-12
Table S70. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 1(1P36.11) CNV | 10 | 7 | 6 | 60 |
DEL PEAK 1(1P36.11) WILD-TYPE | 127 | 21 | 22 | 53 |
Figure S70. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'CN_CNMF'
![](D30V1.png)
P value = 0.000366 (Fisher's exact test), Q value = 0.1
Table S71. Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 1(1P36.11) CNV | 4 | 20 | 9 | 32 |
DEL PEAK 1(1P36.11) WILD-TYPE | 33 | 59 | 55 | 46 |
Figure S71. Get High-res Image Gene #30: 'Del Peak 1(1p36.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D30V2.png)
P value = 5.4e-12 (Fisher's exact test), Q value = 2.3e-09
Table S72. Gene #31: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 2(1P13.2) CNV | 6 | 6 | 2 | 45 |
DEL PEAK 2(1P13.2) WILD-TYPE | 131 | 22 | 26 | 68 |
Figure S72. Get High-res Image Gene #31: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D31V1.png)
P value = 0.000191 (Fisher's exact test), Q value = 0.057
Table S73. Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 5(2Q37.2) CNV | 9 | 3 | 6 | 29 |
DEL PEAK 5(2Q37.2) WILD-TYPE | 128 | 25 | 22 | 84 |
Figure S73. Get High-res Image Gene #34: 'Del Peak 5(2q37.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D34V1.png)
P value = 2.64e-10 (Fisher's exact test), Q value = 1.1e-07
Table S74. Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 6(3P26.1) CNV | 13 | 11 | 8 | 52 |
DEL PEAK 6(3P26.1) WILD-TYPE | 124 | 17 | 20 | 61 |
Figure S74. Get High-res Image Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D35V1.png)
P value = 3e-04 (Fisher's exact test), Q value = 0.087
Table S75. Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 6(3P26.1) CNV | 7 | 21 | 8 | 34 |
DEL PEAK 6(3P26.1) WILD-TYPE | 30 | 58 | 56 | 44 |
Figure S75. Get High-res Image Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D35V2.png)
P value = 0.000517 (Fisher's exact test), Q value = 0.14
Table S76. Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 6(3P26.1) CNV | 27 | 14 | 24 |
DEL PEAK 6(3P26.1) WILD-TYPE | 29 | 47 | 96 |
Figure S76. Get High-res Image Gene #35: 'Del Peak 6(3p26.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D35V6.png)
P value = 9.33e-13 (Fisher's exact test), Q value = 4e-10
Table S77. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 7(3P14.2) CNV | 17 | 11 | 10 | 64 |
DEL PEAK 7(3P14.2) WILD-TYPE | 120 | 17 | 18 | 49 |
Figure S77. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D36V1.png)
P value = 1.38e-06 (Fisher's exact test), Q value = 5e-04
Table S78. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 7(3P14.2) CNV | 13 | 25 | 8 | 43 |
DEL PEAK 7(3P14.2) WILD-TYPE | 24 | 54 | 56 | 35 |
Figure S78. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D36V2.png)
P value = 3.65e-05 (Fisher's exact test), Q value = 0.012
Table S79. Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 7(3P14.2) CNV | 32 | 13 | 31 |
DEL PEAK 7(3P14.2) WILD-TYPE | 24 | 48 | 89 |
Figure S79. Get High-res Image Gene #36: 'Del Peak 7(3p14.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D36V6.png)
P value = 4.23e-06 (Fisher's exact test), Q value = 0.0015
Table S80. Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 8(3Q26.31) CNV | 4 | 3 | 1 | 26 |
DEL PEAK 8(3Q26.31) WILD-TYPE | 133 | 25 | 27 | 87 |
Figure S80. Get High-res Image Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #1: 'CN_CNMF'
![](D37V1.png)
P value = 8.44e-05 (Fisher's exact test), Q value = 0.026
Table S81. Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 8(3Q26.31) CNV | 2 | 10 | 0 | 17 |
DEL PEAK 8(3Q26.31) WILD-TYPE | 35 | 69 | 64 | 61 |
Figure S81. Get High-res Image Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D37V2.png)
P value = 0.000956 (Chi-square test), Q value = 0.25
Table S82. Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 8(3Q26.31) CNV | 1 | 0 | 1 | 5 | 11 |
DEL PEAK 8(3Q26.31) WILD-TYPE | 38 | 37 | 27 | 27 | 36 |
Figure S82. Get High-res Image Gene #37: 'Del Peak 8(3q26.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D37V3.png)
P value = 2.89e-10 (Fisher's exact test), Q value = 1.2e-07
Table S83. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 9(4P16.3) CNV | 24 | 12 | 10 | 66 |
DEL PEAK 9(4P16.3) WILD-TYPE | 113 | 16 | 18 | 47 |
Figure S83. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D38V1.png)
P value = 0.000377 (Fisher's exact test), Q value = 0.11
Table S84. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 9(4P16.3) CNV | 6 | 25 | 20 | 42 |
DEL PEAK 9(4P16.3) WILD-TYPE | 31 | 54 | 44 | 36 |
Figure S84. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D38V2.png)
P value = 0.000266 (Chi-square test), Q value = 0.078
Table S85. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 9(4P16.3) CNV | 7 | 14 | 8 | 8 | 29 |
DEL PEAK 9(4P16.3) WILD-TYPE | 32 | 23 | 20 | 24 | 18 |
Figure S85. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D38V3.png)
P value = 0.000848 (Fisher's exact test), Q value = 0.23
Table S86. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 53 | 101 |
DEL PEAK 9(4P16.3) CNV | 19 | 19 | 50 |
DEL PEAK 9(4P16.3) WILD-TYPE | 64 | 34 | 51 |
Figure S86. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D38V5.png)
P value = 3.07e-05 (Fisher's exact test), Q value = 0.0098
Table S87. Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 9(4P16.3) CNV | 35 | 21 | 32 |
DEL PEAK 9(4P16.3) WILD-TYPE | 21 | 40 | 88 |
Figure S87. Get High-res Image Gene #38: 'Del Peak 9(4p16.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D38V6.png)
P value = 6.72e-19 (Fisher's exact test), Q value = 3e-16
Table S88. Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 10(4Q22.1) CNV | 24 | 18 | 11 | 82 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 113 | 10 | 17 | 31 |
Figure S88. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D39V1.png)
P value = 1.23e-07 (Fisher's exact test), Q value = 4.7e-05
Table S89. Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 10(4Q22.1) CNV | 6 | 35 | 20 | 53 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 31 | 44 | 44 | 25 |
Figure S89. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D39V2.png)
P value = 0.000102 (Fisher's exact test), Q value = 0.031
Table S90. Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 10(4Q22.1) CNV | 39 | 23 | 44 |
DEL PEAK 10(4Q22.1) WILD-TYPE | 17 | 38 | 76 |
Figure S90. Get High-res Image Gene #39: 'Del Peak 10(4q22.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D39V6.png)
P value = 1.07e-14 (Fisher's exact test), Q value = 4.7e-12
Table S91. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 11(4Q34.3) CNV | 26 | 15 | 9 | 77 |
DEL PEAK 11(4Q34.3) WILD-TYPE | 111 | 13 | 19 | 36 |
Figure S91. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D40V1.png)
P value = 7.57e-07 (Fisher's exact test), Q value = 0.00028
Table S92. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 11(4Q34.3) CNV | 4 | 31 | 24 | 49 |
DEL PEAK 11(4Q34.3) WILD-TYPE | 33 | 48 | 40 | 29 |
Figure S92. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D40V2.png)
P value = 0.000746 (Chi-square test), Q value = 0.2
Table S93. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 11(4Q34.3) CNV | 8 | 14 | 13 | 12 | 31 |
DEL PEAK 11(4Q34.3) WILD-TYPE | 31 | 23 | 15 | 20 | 16 |
Figure S93. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D40V3.png)
P value = 9.16e-06 (Fisher's exact test), Q value = 0.0031
Table S94. Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 11(4Q34.3) CNV | 39 | 23 | 38 |
DEL PEAK 11(4Q34.3) WILD-TYPE | 17 | 38 | 82 |
Figure S94. Get High-res Image Gene #40: 'Del Peak 11(4q34.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D40V6.png)
P value = 6.54e-28 (Fisher's exact test), Q value = 2.9e-25
Table S95. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 12(5Q11.2) CNV | 6 | 11 | 9 | 77 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 131 | 17 | 19 | 36 |
Figure S95. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D41V1.png)
P value = 1.27e-13 (Fisher's exact test), Q value = 5.4e-11
Table S96. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 12(5Q11.2) CNV | 3 | 28 | 7 | 51 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 34 | 51 | 57 | 27 |
Figure S96. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D41V2.png)
P value = 9.48e-07 (Chi-square test), Q value = 0.00034
Table S97. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 12(5Q11.2) CNV | 10 | 2 | 6 | 11 | 29 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 29 | 35 | 22 | 21 | 18 |
Figure S97. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D41V3.png)
P value = 3.06e-07 (Fisher's exact test), Q value = 0.00011
Table S98. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
DEL PEAK 12(5Q11.2) CNV | 5 | 24 | 29 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 53 | 49 | 23 |
Figure S98. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D41V4.png)
P value = 2.92e-07 (Fisher's exact test), Q value = 0.00011
Table S99. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 53 | 101 |
DEL PEAK 12(5Q11.2) CNV | 23 | 5 | 51 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 60 | 48 | 50 |
Figure S99. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D41V5.png)
P value = 2.53e-09 (Fisher's exact test), Q value = 1e-06
Table S100. Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 12(5Q11.2) CNV | 38 | 10 | 31 |
DEL PEAK 12(5Q11.2) WILD-TYPE | 18 | 51 | 89 |
Figure S100. Get High-res Image Gene #41: 'Del Peak 12(5q11.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D41V6.png)
P value = 2.48e-23 (Fisher's exact test), Q value = 1.1e-20
Table S101. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 13(5Q23.2) CNV | 5 | 12 | 9 | 67 |
DEL PEAK 13(5Q23.2) WILD-TYPE | 132 | 16 | 19 | 46 |
Figure S101. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D42V1.png)
P value = 2.5e-12 (Fisher's exact test), Q value = 1.1e-09
Table S102. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 13(5Q23.2) CNV | 5 | 22 | 5 | 48 |
DEL PEAK 13(5Q23.2) WILD-TYPE | 32 | 57 | 59 | 30 |
Figure S102. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D42V2.png)
P value = 2.02e-07 (Chi-square test), Q value = 7.6e-05
Table S103. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 13(5Q23.2) CNV | 11 | 1 | 4 | 9 | 28 |
DEL PEAK 13(5Q23.2) WILD-TYPE | 28 | 36 | 24 | 23 | 19 |
Figure S103. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D42V3.png)
P value = 2.07e-06 (Fisher's exact test), Q value = 0.00074
Table S104. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
DEL PEAK 13(5Q23.2) CNV | 5 | 21 | 27 |
DEL PEAK 13(5Q23.2) WILD-TYPE | 53 | 52 | 25 |
Figure S104. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D42V4.png)
P value = 2.65e-07 (Fisher's exact test), Q value = 9.9e-05
Table S105. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 53 | 101 |
DEL PEAK 13(5Q23.2) CNV | 18 | 4 | 47 |
DEL PEAK 13(5Q23.2) WILD-TYPE | 65 | 49 | 54 |
Figure S105. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D42V5.png)
P value = 1.11e-08 (Fisher's exact test), Q value = 4.3e-06
Table S106. Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 13(5Q23.2) CNV | 34 | 7 | 28 |
DEL PEAK 13(5Q23.2) WILD-TYPE | 22 | 54 | 92 |
Figure S106. Get High-res Image Gene #42: 'Del Peak 13(5q23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D42V6.png)
P value = 5.01e-07 (Fisher's exact test), Q value = 0.00018
Table S107. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 14(6P25.3) CNV | 15 | 6 | 3 | 45 |
DEL PEAK 14(6P25.3) WILD-TYPE | 122 | 22 | 25 | 68 |
Figure S107. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D43V1.png)
P value = 0.000932 (Fisher's exact test), Q value = 0.24
Table S108. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 14(6P25.3) CNV | 3 | 20 | 9 | 29 |
DEL PEAK 14(6P25.3) WILD-TYPE | 34 | 59 | 55 | 49 |
Figure S108. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D43V2.png)
P value = 0.000915 (Fisher's exact test), Q value = 0.24
Table S109. Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 14(6P25.3) CNV | 22 | 7 | 22 |
DEL PEAK 14(6P25.3) WILD-TYPE | 34 | 54 | 98 |
Figure S109. Get High-res Image Gene #43: 'Del Peak 14(6p25.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D43V6.png)
P value = 0.000128 (Fisher's exact test), Q value = 0.039
Table S110. Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 15(6Q26) CNV | 14 | 9 | 4 | 35 |
DEL PEAK 15(6Q26) WILD-TYPE | 123 | 19 | 24 | 78 |
Figure S110. Get High-res Image Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #1: 'CN_CNMF'
![](D44V1.png)
P value = 1.51e-05 (Chi-square test), Q value = 0.005
Table S111. Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 15(6Q26) CNV | 8 | 3 | 16 | 3 | 16 |
DEL PEAK 15(6Q26) WILD-TYPE | 31 | 34 | 12 | 29 | 31 |
Figure S111. Get High-res Image Gene #44: 'Del Peak 15(6q26)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D44V3.png)
P value = 3.11e-07 (Fisher's exact test), Q value = 0.00012
Table S112. Gene #45: 'Del Peak 16(7q31.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 16(7Q31.1) CNV | 6 | 1 | 5 | 32 |
DEL PEAK 16(7Q31.1) WILD-TYPE | 131 | 27 | 23 | 81 |
Figure S112. Get High-res Image Gene #45: 'Del Peak 16(7q31.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D45V1.png)
P value = 1.82e-14 (Fisher's exact test), Q value = 7.9e-12
Table S113. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 17(7Q36.3) CNV | 4 | 2 | 5 | 47 |
DEL PEAK 17(7Q36.3) WILD-TYPE | 133 | 26 | 23 | 66 |
Figure S113. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D46V1.png)
P value = 1.93e-05 (Fisher's exact test), Q value = 0.0064
Table S114. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 17(7Q36.3) CNV | 0 | 19 | 6 | 24 |
DEL PEAK 17(7Q36.3) WILD-TYPE | 37 | 60 | 58 | 54 |
Figure S114. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D46V2.png)
P value = 0.000791 (Chi-square test), Q value = 0.21
Table S115. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 17(7Q36.3) CNV | 4 | 6 | 5 | 2 | 19 |
DEL PEAK 17(7Q36.3) WILD-TYPE | 35 | 31 | 23 | 30 | 28 |
Figure S115. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D46V3.png)
P value = 0.000113 (Fisher's exact test), Q value = 0.035
Table S116. Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 17(7Q36.3) CNV | 22 | 6 | 17 |
DEL PEAK 17(7Q36.3) WILD-TYPE | 34 | 55 | 103 |
Figure S116. Get High-res Image Gene #46: 'Del Peak 17(7q36.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D46V6.png)
P value = 4.3e-14 (Fisher's exact test), Q value = 1.9e-11
Table S117. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 18(8P23.2) CNV | 13 | 9 | 0 | 55 |
DEL PEAK 18(8P23.2) WILD-TYPE | 124 | 19 | 28 | 58 |
Figure S117. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D47V1.png)
P value = 5.78e-06 (Fisher's exact test), Q value = 0.002
Table S118. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 18(8P23.2) CNV | 3 | 16 | 10 | 36 |
DEL PEAK 18(8P23.2) WILD-TYPE | 34 | 63 | 54 | 42 |
Figure S118. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D47V2.png)
P value = 0.000543 (Chi-square test), Q value = 0.15
Table S119. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 18(8P23.2) CNV | 5 | 5 | 7 | 7 | 23 |
DEL PEAK 18(8P23.2) WILD-TYPE | 34 | 32 | 21 | 25 | 24 |
Figure S119. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D47V3.png)
P value = 0.00016 (Fisher's exact test), Q value = 0.048
Table S120. Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 18(8P23.2) CNV | 27 | 13 | 22 |
DEL PEAK 18(8P23.2) WILD-TYPE | 29 | 48 | 98 |
Figure S120. Get High-res Image Gene #47: 'Del Peak 18(8p23.2)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D47V6.png)
P value = 2.66e-15 (Fisher's exact test), Q value = 1.2e-12
Table S121. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 19(9P23) CNV | 22 | 10 | 13 | 75 |
DEL PEAK 19(9P23) WILD-TYPE | 115 | 18 | 15 | 38 |
Figure S121. Get High-res Image Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #1: 'CN_CNMF'
![](D48V1.png)
P value = 2.88e-05 (Fisher's exact test), Q value = 0.0092
Table S122. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 19(9P23) CNV | 7 | 28 | 19 | 47 |
DEL PEAK 19(9P23) WILD-TYPE | 30 | 51 | 45 | 31 |
Figure S122. Get High-res Image Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D48V2.png)
P value = 0.00032 (Chi-square test), Q value = 0.092
Table S123. Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 19(9P23) CNV | 12 | 13 | 17 | 8 | 31 |
DEL PEAK 19(9P23) WILD-TYPE | 27 | 24 | 11 | 24 | 16 |
Figure S123. Get High-res Image Gene #48: 'Del Peak 19(9p23)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D48V3.png)
P value = 6.29e-16 (Fisher's exact test), Q value = 2.8e-13
Table S124. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 20(9P21.3) CNV | 22 | 8 | 12 | 76 |
DEL PEAK 20(9P21.3) WILD-TYPE | 115 | 20 | 16 | 37 |
Figure S124. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D49V1.png)
P value = 5.35e-11 (Fisher's exact test), Q value = 2.2e-08
Table S125. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 20(9P21.3) CNV | 1 | 28 | 20 | 51 |
DEL PEAK 20(9P21.3) WILD-TYPE | 36 | 51 | 44 | 27 |
Figure S125. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D49V2.png)
P value = 3e-06 (Chi-square test), Q value = 0.0011
Table S126. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 20(9P21.3) CNV | 7 | 11 | 16 | 10 | 33 |
DEL PEAK 20(9P21.3) WILD-TYPE | 32 | 26 | 12 | 22 | 14 |
Figure S126. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D49V3.png)
P value = 0.00026 (Fisher's exact test), Q value = 0.077
Table S127. Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 20(9P21.3) CNV | 36 | 22 | 39 |
DEL PEAK 20(9P21.3) WILD-TYPE | 20 | 39 | 81 |
Figure S127. Get High-res Image Gene #49: 'Del Peak 20(9p21.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D49V6.png)
P value = 2.97e-08 (Fisher's exact test), Q value = 1.1e-05
Table S128. Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 21(9Q21.11) CNV | 12 | 7 | 8 | 46 |
DEL PEAK 21(9Q21.11) WILD-TYPE | 125 | 21 | 20 | 67 |
Figure S128. Get High-res Image Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'
![](D50V1.png)
P value = 0.000163 (Fisher's exact test), Q value = 0.049
Table S129. Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 21(9Q21.11) CNV | 2 | 17 | 13 | 32 |
DEL PEAK 21(9Q21.11) WILD-TYPE | 35 | 62 | 51 | 46 |
Figure S129. Get High-res Image Gene #50: 'Del Peak 21(9q21.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D50V2.png)
P value = 0.000124 (Fisher's exact test), Q value = 0.038
Table S130. Gene #51: 'Del Peak 22(10p15.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 22(10P15.1) CNV | 6 | 3 | 3 | 26 |
DEL PEAK 22(10P15.1) WILD-TYPE | 131 | 25 | 25 | 87 |
Figure S130. Get High-res Image Gene #51: 'Del Peak 22(10p15.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D51V1.png)
P value = 2.43e-09 (Fisher's exact test), Q value = 9.7e-07
Table S131. Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 23(10Q22.3) CNV | 4 | 9 | 3 | 33 |
DEL PEAK 23(10Q22.3) WILD-TYPE | 133 | 19 | 25 | 80 |
Figure S131. Get High-res Image Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D52V1.png)
P value = 0.000641 (Fisher's exact test), Q value = 0.18
Table S132. Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 23(10Q22.3) CNV | 17 | 3 | 17 |
DEL PEAK 23(10Q22.3) WILD-TYPE | 39 | 58 | 103 |
Figure S132. Get High-res Image Gene #52: 'Del Peak 23(10q22.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D52V6.png)
P value = 2.72e-12 (Fisher's exact test), Q value = 1.1e-09
Table S133. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 24(10Q23.31) CNV | 7 | 10 | 9 | 47 |
DEL PEAK 24(10Q23.31) WILD-TYPE | 130 | 18 | 19 | 66 |
Figure S133. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'
![](D53V1.png)
P value = 1.2e-05 (Fisher's exact test), Q value = 0.004
Table S134. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 24(10Q23.31) CNV | 4 | 12 | 9 | 34 |
DEL PEAK 24(10Q23.31) WILD-TYPE | 33 | 67 | 55 | 44 |
Figure S134. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D53V2.png)
P value = 2.51e-05 (Fisher's exact test), Q value = 0.0082
Table S135. Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 24(10Q23.31) CNV | 25 | 5 | 30 |
DEL PEAK 24(10Q23.31) WILD-TYPE | 31 | 56 | 90 |
Figure S135. Get High-res Image Gene #53: 'Del Peak 24(10q23.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D53V6.png)
P value = 2.96e-08 (Fisher's exact test), Q value = 1.1e-05
Table S136. Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 25(11P15.4) CNV | 9 | 3 | 6 | 41 |
DEL PEAK 25(11P15.4) WILD-TYPE | 128 | 25 | 22 | 72 |
Figure S136. Get High-res Image Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'
![](D54V1.png)
P value = 1.55e-05 (Fisher's exact test), Q value = 0.0051
Table S137. Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 25(11P15.4) CNV | 2 | 9 | 6 | 28 |
DEL PEAK 25(11P15.4) WILD-TYPE | 35 | 70 | 58 | 50 |
Figure S137. Get High-res Image Gene #54: 'Del Peak 25(11p15.4)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D54V2.png)
P value = 0.000264 (Fisher's exact test), Q value = 0.078
Table S138. Gene #55: 'Del Peak 26(11q23.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 26(11Q23.2) CNV | 15 | 6 | 4 | 37 |
DEL PEAK 26(11Q23.2) WILD-TYPE | 122 | 22 | 24 | 76 |
Figure S138. Get High-res Image Gene #55: 'Del Peak 26(11q23.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D55V1.png)
P value = 1.49e-10 (Fisher's exact test), Q value = 6.1e-08
Table S139. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 27(12P13.31) CNV | 3 | 5 | 5 | 37 |
DEL PEAK 27(12P13.31) WILD-TYPE | 134 | 23 | 23 | 76 |
Figure S139. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #1: 'CN_CNMF'
![](D56V1.png)
P value = 1.13e-05 (Fisher's exact test), Q value = 0.0038
Table S140. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 27(12P13.31) CNV | 2 | 10 | 4 | 27 |
DEL PEAK 27(12P13.31) WILD-TYPE | 35 | 69 | 60 | 51 |
Figure S140. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D56V2.png)
P value = 2.66e-05 (Chi-square test), Q value = 0.0086
Table S141. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 27(12P13.31) CNV | 1 | 2 | 5 | 2 | 17 |
DEL PEAK 27(12P13.31) WILD-TYPE | 38 | 35 | 23 | 30 | 30 |
Figure S141. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D56V3.png)
P value = 0.000281 (Fisher's exact test), Q value = 0.082
Table S142. Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
DEL PEAK 27(12P13.31) CNV | 2 | 9 | 16 |
DEL PEAK 27(12P13.31) WILD-TYPE | 56 | 64 | 36 |
Figure S142. Get High-res Image Gene #56: 'Del Peak 27(12p13.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D56V4.png)
P value = 2.32e-06 (Fisher's exact test), Q value = 0.00083
Table S143. Gene #57: 'Del Peak 28(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 28(13Q12.11) CNV | 6 | 2 | 6 | 30 |
DEL PEAK 28(13Q12.11) WILD-TYPE | 131 | 26 | 22 | 83 |
Figure S143. Get High-res Image Gene #57: 'Del Peak 28(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'
![](D57V1.png)
P value = 7.69e-07 (Fisher's exact test), Q value = 0.00028
Table S144. Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 29(14Q21.1) CNV | 13 | 8 | 7 | 43 |
DEL PEAK 29(14Q21.1) WILD-TYPE | 124 | 20 | 21 | 70 |
Figure S144. Get High-res Image Gene #58: 'Del Peak 29(14q21.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D58V1.png)
P value = 9.24e-09 (Fisher's exact test), Q value = 3.6e-06
Table S145. Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 30(14Q32.33) CNV | 17 | 9 | 9 | 54 |
DEL PEAK 30(14Q32.33) WILD-TYPE | 120 | 19 | 19 | 59 |
Figure S145. Get High-res Image Gene #59: 'Del Peak 30(14q32.33)' versus Molecular Subtype #1: 'CN_CNMF'
![](D59V1.png)
P value = 6.44e-13 (Fisher's exact test), Q value = 2.7e-10
Table S146. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 31(15Q15.1) CNV | 9 | 10 | 7 | 53 |
DEL PEAK 31(15Q15.1) WILD-TYPE | 128 | 18 | 21 | 60 |
Figure S146. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D60V1.png)
P value = 5.71e-07 (Fisher's exact test), Q value = 0.00021
Table S147. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 31(15Q15.1) CNV | 5 | 16 | 7 | 38 |
DEL PEAK 31(15Q15.1) WILD-TYPE | 32 | 63 | 57 | 40 |
Figure S147. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D60V2.png)
P value = 1.79e-05 (Chi-square test), Q value = 0.0059
Table S148. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 31(15Q15.1) CNV | 7 | 2 | 11 | 6 | 24 |
DEL PEAK 31(15Q15.1) WILD-TYPE | 32 | 35 | 17 | 26 | 23 |
Figure S148. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D60V3.png)
P value = 7.38e-06 (Fisher's exact test), Q value = 0.0025
Table S149. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
DEL PEAK 31(15Q15.1) CNV | 4 | 22 | 24 |
DEL PEAK 31(15Q15.1) WILD-TYPE | 54 | 51 | 28 |
Figure S149. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D60V4.png)
P value = 8.73e-07 (Fisher's exact test), Q value = 0.00032
Table S150. Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 31(15Q15.1) CNV | 29 | 6 | 26 |
DEL PEAK 31(15Q15.1) WILD-TYPE | 27 | 55 | 94 |
Figure S150. Get High-res Image Gene #60: 'Del Peak 31(15q15.1)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D60V6.png)
P value = 7.42e-11 (Fisher's exact test), Q value = 3e-08
Table S151. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 32(16P13.3) CNV | 7 | 2 | 5 | 44 |
DEL PEAK 32(16P13.3) WILD-TYPE | 130 | 26 | 23 | 69 |
Figure S151. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D61V1.png)
P value = 7.03e-05 (Fisher's exact test), Q value = 0.022
Table S152. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 32(16P13.3) CNV | 1 | 14 | 7 | 27 |
DEL PEAK 32(16P13.3) WILD-TYPE | 36 | 65 | 57 | 51 |
Figure S152. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D61V2.png)
P value = 2.03e-05 (Chi-square test), Q value = 0.0067
Table S153. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 32(16P13.3) CNV | 3 | 4 | 2 | 2 | 19 |
DEL PEAK 32(16P13.3) WILD-TYPE | 36 | 33 | 26 | 30 | 28 |
Figure S153. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D61V3.png)
P value = 0.000382 (Fisher's exact test), Q value = 0.11
Table S154. Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
DEL PEAK 32(16P13.3) CNV | 5 | 7 | 18 |
DEL PEAK 32(16P13.3) WILD-TYPE | 53 | 66 | 34 |
Figure S154. Get High-res Image Gene #61: 'Del Peak 32(16p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D61V4.png)
P value = 2.22e-07 (Fisher's exact test), Q value = 8.3e-05
Table S155. Gene #62: 'Del Peak 33(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 33(16Q23.1) CNV | 33 | 12 | 7 | 66 |
DEL PEAK 33(16Q23.1) WILD-TYPE | 104 | 16 | 21 | 47 |
Figure S155. Get High-res Image Gene #62: 'Del Peak 33(16q23.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D62V1.png)
P value = 1.81e-23 (Fisher's exact test), Q value = 8.1e-21
Table S156. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 34(17P12) CNV | 13 | 14 | 9 | 79 |
DEL PEAK 34(17P12) WILD-TYPE | 124 | 14 | 19 | 34 |
Figure S156. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #1: 'CN_CNMF'
![](D63V1.png)
P value = 4.44e-11 (Fisher's exact test), Q value = 1.8e-08
Table S157. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 34(17P12) CNV | 4 | 29 | 13 | 53 |
DEL PEAK 34(17P12) WILD-TYPE | 33 | 50 | 51 | 25 |
Figure S157. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D63V2.png)
P value = 9.95e-06 (Chi-square test), Q value = 0.0034
Table S158. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 34(17P12) CNV | 10 | 5 | 13 | 11 | 31 |
DEL PEAK 34(17P12) WILD-TYPE | 29 | 32 | 15 | 21 | 16 |
Figure S158. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D63V3.png)
P value = 1.96e-05 (Fisher's exact test), Q value = 0.0064
Table S159. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
DEL PEAK 34(17P12) CNV | 10 | 29 | 31 |
DEL PEAK 34(17P12) WILD-TYPE | 48 | 44 | 21 |
Figure S159. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D63V4.png)
P value = 6.36e-06 (Fisher's exact test), Q value = 0.0022
Table S160. Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 34(17P12) CNV | 36 | 13 | 42 |
DEL PEAK 34(17P12) WILD-TYPE | 20 | 48 | 78 |
Figure S160. Get High-res Image Gene #63: 'Del Peak 34(17p12)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D63V6.png)
P value = 1.32e-10 (Fisher's exact test), Q value = 5.4e-08
Table S161. Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 35(17Q24.3) CNV | 4 | 6 | 6 | 39 |
DEL PEAK 35(17Q24.3) WILD-TYPE | 133 | 22 | 22 | 74 |
Figure S161. Get High-res Image Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D64V1.png)
P value = 0.000237 (Fisher's exact test), Q value = 0.071
Table S162. Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 35(17Q24.3) CNV | 0 | 16 | 6 | 21 |
DEL PEAK 35(17Q24.3) WILD-TYPE | 37 | 63 | 58 | 57 |
Figure S162. Get High-res Image Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D64V2.png)
P value = 0.000463 (Chi-square test), Q value = 0.13
Table S163. Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 35(17Q24.3) CNV | 5 | 1 | 1 | 7 | 16 |
DEL PEAK 35(17Q24.3) WILD-TYPE | 34 | 36 | 27 | 25 | 31 |
Figure S163. Get High-res Image Gene #64: 'Del Peak 35(17q24.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D64V3.png)
P value = 4.49e-13 (Fisher's exact test), Q value = 1.9e-10
Table S164. Gene #65: 'Del Peak 36(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 36(18Q21.2) CNV | 31 | 20 | 8 | 74 |
DEL PEAK 36(18Q21.2) WILD-TYPE | 106 | 8 | 20 | 39 |
Figure S164. Get High-res Image Gene #65: 'Del Peak 36(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D65V1.png)
P value = 0.000846 (Fisher's exact test), Q value = 0.23
Table S165. Gene #65: 'Del Peak 36(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 36(18Q21.2) CNV | 18 | 30 | 17 | 46 |
DEL PEAK 36(18Q21.2) WILD-TYPE | 19 | 49 | 47 | 32 |
Figure S165. Get High-res Image Gene #65: 'Del Peak 36(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D65V2.png)
P value = 2.35e-27 (Fisher's exact test), Q value = 1.1e-24
Table S166. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 37(19P13.3) CNV | 6 | 10 | 7 | 76 |
DEL PEAK 37(19P13.3) WILD-TYPE | 131 | 18 | 21 | 37 |
Figure S166. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D66V1.png)
P value = 2.38e-16 (Fisher's exact test), Q value = 1.1e-13
Table S167. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 37(19P13.3) CNV | 4 | 18 | 6 | 54 |
DEL PEAK 37(19P13.3) WILD-TYPE | 33 | 61 | 58 | 24 |
Figure S167. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D66V2.png)
P value = 3.62e-11 (Chi-square test), Q value = 1.5e-08
Table S168. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 37(19P13.3) CNV | 8 | 3 | 8 | 7 | 36 |
DEL PEAK 37(19P13.3) WILD-TYPE | 31 | 34 | 20 | 25 | 11 |
Figure S168. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D66V3.png)
P value = 1.34e-12 (Fisher's exact test), Q value = 5.6e-10
Table S169. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
DEL PEAK 37(19P13.3) CNV | 3 | 23 | 36 |
DEL PEAK 37(19P13.3) WILD-TYPE | 55 | 50 | 16 |
Figure S169. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D66V4.png)
P value = 2.21e-07 (Fisher's exact test), Q value = 8.3e-05
Table S170. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 83 | 53 | 101 |
DEL PEAK 37(19P13.3) CNV | 20 | 6 | 52 |
DEL PEAK 37(19P13.3) WILD-TYPE | 63 | 47 | 49 |
Figure S170. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D66V5.png)
P value = 1.06e-19 (Fisher's exact test), Q value = 4.7e-17
Table S171. Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 37(19P13.3) CNV | 47 | 7 | 24 |
DEL PEAK 37(19P13.3) WILD-TYPE | 9 | 54 | 96 |
Figure S171. Get High-res Image Gene #66: 'Del Peak 37(19p13.3)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D66V6.png)
P value = 2.69e-09 (Fisher's exact test), Q value = 1.1e-06
Table S172. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 38(19Q13.11) CNV | 2 | 5 | 5 | 31 |
DEL PEAK 38(19Q13.11) WILD-TYPE | 135 | 23 | 23 | 82 |
Figure S172. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #1: 'CN_CNMF'
![](D67V1.png)
P value = 6.16e-05 (Fisher's exact test), Q value = 0.019
Table S173. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 38(19Q13.11) CNV | 1 | 11 | 2 | 21 |
DEL PEAK 38(19Q13.11) WILD-TYPE | 36 | 68 | 62 | 57 |
Figure S173. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D67V2.png)
P value = 2.44e-06 (Fisher's exact test), Q value = 0.00087
Table S174. Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 38(19Q13.11) CNV | 20 | 3 | 10 |
DEL PEAK 38(19Q13.11) WILD-TYPE | 36 | 58 | 110 |
Figure S174. Get High-res Image Gene #67: 'Del Peak 38(19q13.11)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D67V6.png)
P value = 1.21e-08 (Fisher's exact test), Q value = 4.7e-06
Table S175. Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 39(20P12.1) CNV | 11 | 0 | 2 | 39 |
DEL PEAK 39(20P12.1) WILD-TYPE | 126 | 28 | 26 | 74 |
Figure S175. Get High-res Image Gene #68: 'Del Peak 39(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D68V1.png)
P value = 1.21e-08 (Fisher's exact test), Q value = 4.7e-06
Table S176. Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 40(20P12.1) CNV | 11 | 0 | 2 | 39 |
DEL PEAK 40(20P12.1) WILD-TYPE | 126 | 28 | 26 | 74 |
Figure S176. Get High-res Image Gene #69: 'Del Peak 40(20p12.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D69V1.png)
P value = 1.39e-10 (Fisher's exact test), Q value = 5.7e-08
Table S177. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 41(21Q11.2) CNV | 22 | 9 | 13 | 64 |
DEL PEAK 41(21Q11.2) WILD-TYPE | 115 | 19 | 15 | 49 |
Figure S177. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D70V1.png)
P value = 5.41e-05 (Fisher's exact test), Q value = 0.017
Table S178. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 41(21Q11.2) CNV | 4 | 30 | 18 | 41 |
DEL PEAK 41(21Q11.2) WILD-TYPE | 33 | 49 | 46 | 37 |
Figure S178. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D70V2.png)
P value = 0.000341 (Fisher's exact test), Q value = 0.098
Table S179. Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
DEL PEAK 41(21Q11.2) CNV | 13 | 19 | 29 |
DEL PEAK 41(21Q11.2) WILD-TYPE | 45 | 54 | 23 |
Figure S179. Get High-res Image Gene #70: 'Del Peak 41(21q11.2)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D70V4.png)
P value = 1.56e-09 (Fisher's exact test), Q value = 6.2e-07
Table S180. Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 42(21Q22.13) CNV | 25 | 12 | 14 | 64 |
DEL PEAK 42(21Q22.13) WILD-TYPE | 112 | 16 | 14 | 49 |
Figure S180. Get High-res Image Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #1: 'CN_CNMF'
![](D71V1.png)
P value = 0.000509 (Fisher's exact test), Q value = 0.14
Table S181. Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 42(21Q22.13) CNV | 4 | 34 | 21 | 37 |
DEL PEAK 42(21Q22.13) WILD-TYPE | 33 | 45 | 43 | 41 |
Figure S181. Get High-res Image Gene #71: 'Del Peak 42(21q22.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D71V2.png)
P value = 9.68e-15 (Fisher's exact test), Q value = 4.2e-12
Table S182. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 43(22Q13.31) CNV | 15 | 9 | 11 | 66 |
DEL PEAK 43(22Q13.31) WILD-TYPE | 122 | 19 | 17 | 47 |
Figure S182. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #1: 'CN_CNMF'
![](D72V1.png)
P value = 0.000142 (Fisher's exact test), Q value = 0.043
Table S183. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 43(22Q13.31) CNV | 4 | 27 | 15 | 38 |
DEL PEAK 43(22Q13.31) WILD-TYPE | 33 | 52 | 49 | 40 |
Figure S183. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D72V2.png)
P value = 0.000528 (Chi-square test), Q value = 0.15
Table S184. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 39 | 37 | 28 | 32 | 47 |
DEL PEAK 43(22Q13.31) CNV | 9 | 7 | 12 | 6 | 26 |
DEL PEAK 43(22Q13.31) WILD-TYPE | 30 | 30 | 16 | 26 | 21 |
Figure S184. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D72V3.png)
P value = 0.000471 (Fisher's exact test), Q value = 0.13
Table S185. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 58 | 73 | 52 |
DEL PEAK 43(22Q13.31) CNV | 9 | 25 | 26 |
DEL PEAK 43(22Q13.31) WILD-TYPE | 49 | 48 | 26 |
Figure S185. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D72V4.png)
P value = 6.56e-06 (Fisher's exact test), Q value = 0.0023
Table S186. Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 56 | 61 | 120 |
DEL PEAK 43(22Q13.31) CNV | 34 | 14 | 31 |
DEL PEAK 43(22Q13.31) WILD-TYPE | 22 | 47 | 89 |
Figure S186. Get High-res Image Gene #72: 'Del Peak 43(22q13.31)' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D72V6.png)
P value = 1.44e-09 (Fisher's exact test), Q value = 5.8e-07
Table S187. Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 44(XP22.2) CNV | 10 | 3 | 3 | 45 |
DEL PEAK 44(XP22.2) WILD-TYPE | 127 | 25 | 25 | 68 |
Figure S187. Get High-res Image Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D73V1.png)
P value = 0.000642 (Fisher's exact test), Q value = 0.18
Table S188. Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 37 | 79 | 64 | 78 |
DEL PEAK 44(XP22.2) CNV | 1 | 19 | 9 | 25 |
DEL PEAK 44(XP22.2) WILD-TYPE | 36 | 60 | 55 | 53 |
Figure S188. Get High-res Image Gene #73: 'Del Peak 44(Xp22.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D73V2.png)
P value = 6.22e-08 (Fisher's exact test), Q value = 2.4e-05
Table S189. Gene #74: 'Del Peak 45(Xp21.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 45(XP21.1) CNV | 8 | 4 | 2 | 38 |
DEL PEAK 45(XP21.1) WILD-TYPE | 129 | 24 | 26 | 75 |
Figure S189. Get High-res Image Gene #74: 'Del Peak 45(Xp21.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D74V1.png)
P value = 5.77e-06 (Fisher's exact test), Q value = 0.002
Table S190. Gene #75: 'Del Peak 46(Xq21.33)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 137 | 28 | 28 | 113 |
DEL PEAK 46(XQ21.33) CNV | 7 | 4 | 1 | 30 |
DEL PEAK 46(XQ21.33) WILD-TYPE | 130 | 24 | 27 | 83 |
Figure S190. Get High-res Image Gene #75: 'Del Peak 46(Xq21.33)' versus Molecular Subtype #1: 'CN_CNMF'
![](D75V1.png)
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Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
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Molecular subtype file = STAD-TP.transferedmergedcluster.txt
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Number of patients = 306
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Number of copy number variation regions = 75
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Number of molecular subtypes = 6
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Exclude regions that fewer than K tumors have alterations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.