This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.
Testing the association between copy number variation of 71 peak regions and 10 molecular subtypes across 368 patients, 104 significant findings detected with Q value < 0.25.
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Amp Peak 1(1q21.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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Amp Peak 2(2q11.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 3(2q31.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 4(3q26.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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Amp Peak 5(5p15.33) cnvs correlated to 'CN_CNMF'.
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Amp Peak 6(6p12.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 7(6q12) cnvs correlated to 'CN_CNMF'.
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Amp Peak 8(7p11.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 9(7q21.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 11(8q11.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Amp Peak 12(8q24.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Amp Peak 13(9p23) cnvs correlated to 'CN_CNMF'.
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Amp Peak 14(9p13.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 16(11q13.3) cnvs correlated to 'CN_CNMF'.
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Amp Peak 17(12p13.33) cnvs correlated to 'CN_CNMF'.
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Amp Peak 19(13q22.1) cnvs correlated to 'CN_CNMF'.
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Amp Peak 20(15q26.3) cnvs correlated to 'CN_CNMF'.
-
Amp Peak 21(17q12) cnvs correlated to 'CN_CNMF'.
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Amp Peak 22(18p11.31) cnvs correlated to 'CN_CNMF'.
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Amp Peak 23(18q11.2) cnvs correlated to 'CN_CNMF'.
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Amp Peak 24(20q11.22) cnvs correlated to 'CN_CNMF'.
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Del Peak 1(1p36.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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Del Peak 2(1p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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Del Peak 4(2q21.2) cnvs correlated to 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
Del Peak 6(2q36.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 7(3p25.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 8(3p14.2) cnvs correlated to 'CN_CNMF'.
-
Del Peak 9(3p14.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 10(3p12.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 11(4p15.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
-
Del Peak 12(4q22.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 13(4q35.2) cnvs correlated to 'CN_CNMF'.
-
Del Peak 14(5q11.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 15(5q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
-
Del Peak 16(5q35.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
-
Del Peak 21(8p23.2) cnvs correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
Del Peak 22(9p23) cnvs correlated to 'CN_CNMF'.
-
Del Peak 23(9p21.3) cnvs correlated to 'CN_CNMF'.
-
Del Peak 24(9q21.11) cnvs correlated to 'CN_CNMF'.
-
Del Peak 28(10q23.31) cnvs correlated to 'METHLYATION_CNMF'.
-
Del Peak 29(11p15.4) cnvs correlated to 'CN_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
Del Peak 30(11q14.2) cnvs correlated to 'CN_CNMF'.
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Del Peak 31(11q23.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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Del Peak 33(13q12.11) cnvs correlated to 'CN_CNMF'.
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Del Peak 34(13q14.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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Del Peak 36(14q32.32) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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Del Peak 37(15q15.1) cnvs correlated to 'CN_CNMF'.
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Del Peak 38(16q12.1) cnvs correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
Del Peak 39(16q23.3) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
Del Peak 41(18q21.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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Del Peak 42(18q23) cnvs correlated to 'CN_CNMF'.
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Del Peak 43(19p13.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 44(19q13.43) cnvs correlated to 'CN_CNMF'.
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Del Peak 45(Xp21.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 46(Xp11.3) cnvs correlated to 'CN_CNMF'.
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Del Peak 47(Xq21.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 71 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 104 significant findings detected.
Molecular subtypes |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
Del Peak 38(16q12 1) | 0 (0%) | 305 |
0.0522 (1.00) |
4.05e-09 (2.75e-06) |
0.746 (1.00) |
0.0896 (1.00) |
7.1e-08 (4.79e-05) |
3.91e-07 (0.000263) |
0.000157 (0.0983) |
0.013 (1.00) |
8.88e-06 (0.00583) |
3.44e-05 (0.0221) |
Amp Peak 1(1q21 2) | 0 (0%) | 283 |
1.19e-09 (8.15e-07) |
2.12e-05 (0.0138) |
0.473 (1.00) |
0.718 (1.00) |
0.000509 (0.307) |
0.00316 (1.00) |
0.00035 (0.214) |
0.57 (1.00) |
3.36e-05 (0.0217) |
0.000316 (0.194) |
Del Peak 34(13q14 2) | 0 (0%) | 210 |
8.8e-07 (0.000587) |
0.000281 (0.174) |
0.151 (1.00) |
0.275 (1.00) |
5.7e-05 (0.0364) |
6.46e-05 (0.0412) |
0.021 (1.00) |
0.673 (1.00) |
5.29e-05 (0.0339) |
0.0181 (1.00) |
Amp Peak 4(3q26 33) | 0 (0%) | 92 |
1.01e-16 (7.04e-14) |
4.75e-05 (0.0305) |
0.244 (1.00) |
0.193 (1.00) |
0.00128 (0.748) |
0.000468 (0.283) |
0.00152 (0.875) |
0.0706 (1.00) |
9.01e-05 (0.057) |
6.81e-06 (0.00448) |
Amp Peak 12(8q24 21) | 0 (0%) | 101 |
5.27e-09 (3.58e-06) |
2.54e-05 (0.0165) |
0.19 (1.00) |
0.917 (1.00) |
0.000102 (0.0645) |
0.000135 (0.0851) |
0.0313 (1.00) |
0.000509 (0.307) |
0.0435 (1.00) |
0.00403 (1.00) |
Del Peak 1(1p36 13) | 0 (0%) | 297 |
1.15e-13 (7.96e-11) |
2.28e-07 (0.000154) |
0.0225 (1.00) |
0.739 (1.00) |
3.03e-05 (0.0196) |
0.000716 (0.427) |
0.00468 (1.00) |
0.103 (1.00) |
2.14e-05 (0.0139) |
0.00496 (1.00) |
Del Peak 2(1p13 2) | 0 (0%) | 281 |
3.38e-11 (2.33e-08) |
0.000147 (0.0921) |
0.0124 (1.00) |
0.118 (1.00) |
0.00546 (1.00) |
0.0927 (1.00) |
0.000105 (0.066) |
0.967 (1.00) |
1.53e-05 (0.01) |
0.00513 (1.00) |
Del Peak 15(5q15) | 0 (0%) | 216 |
5.86e-16 (4.09e-13) |
4.73e-05 (0.0304) |
0.0337 (1.00) |
0.598 (1.00) |
0.0676 (1.00) |
0.000402 (0.245) |
0.119 (1.00) |
0.441 (1.00) |
0.000403 (0.245) |
0.116 (1.00) |
Del Peak 36(14q32 32) | 0 (0%) | 314 |
0.0418 (1.00) |
6.74e-08 (4.55e-05) |
0.0984 (1.00) |
0.413 (1.00) |
0.000242 (0.15) |
9.8e-05 (0.0619) |
0.00574 (1.00) |
0.0785 (1.00) |
0.000656 (0.393) |
2.32e-06 (0.00154) |
Del Peak 47(Xq21 33) | 0 (0%) | 309 |
7.56e-07 (0.000506) |
0.000338 (0.207) |
0.0255 (1.00) |
0.444 (1.00) |
0.00131 (0.763) |
0.0123 (1.00) |
2.36e-05 (0.0153) |
0.00563 (1.00) |
0.000164 (0.102) |
0.00044 (0.267) |
Del Peak 4(2q21 2) | 0 (0%) | 322 |
0.511 (1.00) |
0.745 (1.00) |
0.91 (1.00) |
1 (1.00) |
0.0154 (1.00) |
0.00564 (1.00) |
0.000297 (0.183) |
0.29 (1.00) |
0.000268 (0.166) |
0.000159 (0.0992) |
Del Peak 11(4p15 2) | 0 (0%) | 214 |
3.81e-13 (2.64e-10) |
1.94e-05 (0.0127) |
0.0483 (1.00) |
0.13 (1.00) |
0.0406 (1.00) |
0.0129 (1.00) |
0.0253 (1.00) |
0.789 (1.00) |
0.00039 (0.238) |
0.0356 (1.00) |
Del Peak 29(11p15 4) | 0 (0%) | 253 |
4.83e-11 (3.33e-08) |
0.00668 (1.00) |
0.471 (1.00) |
0.458 (1.00) |
0.00228 (1.00) |
0.0071 (1.00) |
0.00211 (1.00) |
0.35 (1.00) |
3.05e-09 (2.08e-06) |
0.000321 (0.197) |
Del Peak 31(11q23 1) | 0 (0%) | 193 |
1.28e-20 (8.98e-18) |
3.94e-06 (0.0026) |
0.169 (1.00) |
0.254 (1.00) |
0.000815 (0.483) |
0.00023 (0.143) |
0.175 (1.00) |
0.277 (1.00) |
0.00148 (0.859) |
0.139 (1.00) |
Amp Peak 11(8q11 21) | 0 (0%) | 148 |
1.93e-06 (0.00128) |
0.000199 (0.123) |
0.0323 (1.00) |
0.518 (1.00) |
0.00113 (0.664) |
0.000664 (0.397) |
0.00954 (1.00) |
0.00141 (0.821) |
0.0111 (1.00) |
0.00172 (0.985) |
Del Peak 6(2q36 2) | 0 (0%) | 261 |
1.28e-08 (8.66e-06) |
7.6e-05 (0.0484) |
0.114 (1.00) |
0.531 (1.00) |
0.000636 (0.382) |
0.00125 (0.734) |
0.00385 (1.00) |
0.165 (1.00) |
0.00334 (1.00) |
0.0523 (1.00) |
Del Peak 16(5q35 3) | 0 (0%) | 227 |
2.14e-14 (1.49e-11) |
2.58e-06 (0.0017) |
0.419 (1.00) |
0.0645 (1.00) |
0.0146 (1.00) |
0.000477 (0.288) |
0.223 (1.00) |
0.657 (1.00) |
0.00732 (1.00) |
0.193 (1.00) |
Del Peak 21(8p23 2) | 0 (0%) | 161 |
3.72e-16 (2.6e-13) |
0.000934 (0.553) |
0.134 (1.00) |
0.188 (1.00) |
0.0166 (1.00) |
0.00353 (1.00) |
0.234 (1.00) |
0.025 (1.00) |
0.0343 (1.00) |
0.000335 (0.205) |
Del Peak 39(16q23 3) | 0 (0%) | 295 |
0.0223 (1.00) |
1.86e-05 (0.0122) |
0.504 (1.00) |
0.0196 (1.00) |
0.000601 (0.361) |
8.88e-05 (0.0563) |
0.00687 (1.00) |
0.142 (1.00) |
0.00115 (0.675) |
0.00171 (0.979) |
Del Peak 41(18q21 2) | 0 (0%) | 177 |
3.89e-20 (2.73e-17) |
0.00016 (0.0999) |
0.603 (1.00) |
0.642 (1.00) |
0.00268 (1.00) |
0.0073 (1.00) |
0.00343 (1.00) |
0.0033 (1.00) |
0.0932 (1.00) |
0.216 (1.00) |
Amp Peak 2(2q11 2) | 0 (0%) | 292 |
1.01e-09 (6.91e-07) |
0.00319 (1.00) |
0.991 (1.00) |
0.295 (1.00) |
0.0119 (1.00) |
0.0807 (1.00) |
0.00184 (1.00) |
0.168 (1.00) |
0.00542 (1.00) |
0.0377 (1.00) |
Amp Peak 3(2q31 2) | 0 (0%) | 292 |
2.38e-12 (1.65e-09) |
0.00152 (0.875) |
0.814 (1.00) |
0.498 (1.00) |
0.308 (1.00) |
0.134 (1.00) |
0.212 (1.00) |
0.274 (1.00) |
0.0177 (1.00) |
0.00832 (1.00) |
Amp Peak 5(5p15 33) | 0 (0%) | 202 |
1.41e-09 (9.59e-07) |
0.158 (1.00) |
0.624 (1.00) |
0.282 (1.00) |
0.683 (1.00) |
0.32 (1.00) |
0.682 (1.00) |
0.337 (1.00) |
0.653 (1.00) |
0.469 (1.00) |
Amp Peak 6(6p12 1) | 0 (0%) | 295 |
1.87e-05 (0.0122) |
0.328 (1.00) |
0.303 (1.00) |
0.47 (1.00) |
0.983 (1.00) |
0.802 (1.00) |
1 (1.00) |
0.0781 (1.00) |
0.834 (1.00) |
0.246 (1.00) |
Amp Peak 7(6q12) | 0 (0%) | 301 |
7.89e-05 (0.0501) |
0.396 (1.00) |
0.811 (1.00) |
0.373 (1.00) |
1 (1.00) |
0.822 (1.00) |
0.795 (1.00) |
0.27 (1.00) |
1 (1.00) |
0.985 (1.00) |
Amp Peak 8(7p11 2) | 0 (0%) | 214 |
9.14e-07 (0.000609) |
0.0109 (1.00) |
0.26 (1.00) |
0.832 (1.00) |
0.5 (1.00) |
0.923 (1.00) |
0.99 (1.00) |
0.282 (1.00) |
0.485 (1.00) |
0.862 (1.00) |
Amp Peak 9(7q21 3) | 0 (0%) | 244 |
3.49e-15 (2.44e-12) |
0.115 (1.00) |
0.238 (1.00) |
0.468 (1.00) |
0.154 (1.00) |
0.128 (1.00) |
0.0472 (1.00) |
0.0724 (1.00) |
0.0738 (1.00) |
0.264 (1.00) |
Amp Peak 13(9p23) | 0 (0%) | 281 |
6.75e-06 (0.00445) |
0.406 (1.00) |
0.655 (1.00) |
0.888 (1.00) |
0.0993 (1.00) |
0.227 (1.00) |
0.402 (1.00) |
1 (1.00) |
0.0311 (1.00) |
0.0242 (1.00) |
Amp Peak 14(9p13 3) | 0 (0%) | 266 |
0.000371 (0.226) |
0.356 (1.00) |
0.39 (1.00) |
0.254 (1.00) |
0.00708 (1.00) |
0.0379 (1.00) |
0.0126 (1.00) |
0.0497 (1.00) |
0.0281 (1.00) |
0.0328 (1.00) |
Amp Peak 16(11q13 3) | 0 (0%) | 198 |
3.83e-30 (2.71e-27) |
0.0812 (1.00) |
0.901 (1.00) |
0.284 (1.00) |
0.361 (1.00) |
0.504 (1.00) |
0.781 (1.00) |
0.17 (1.00) |
0.919 (1.00) |
0.495 (1.00) |
Amp Peak 17(12p13 33) | 0 (0%) | 243 |
1.99e-12 (1.38e-09) |
0.00308 (1.00) |
0.276 (1.00) |
0.352 (1.00) |
0.00912 (1.00) |
0.00101 (0.596) |
0.00302 (1.00) |
0.864 (1.00) |
0.00251 (1.00) |
0.0105 (1.00) |
Amp Peak 19(13q22 1) | 0 (0%) | 291 |
1.18e-06 (0.000783) |
0.186 (1.00) |
0.0181 (1.00) |
0.205 (1.00) |
0.233 (1.00) |
0.0924 (1.00) |
0.138 (1.00) |
0.132 (1.00) |
0.821 (1.00) |
0.381 (1.00) |
Amp Peak 20(15q26 3) | 0 (0%) | 292 |
5.54e-05 (0.0355) |
0.438 (1.00) |
0.263 (1.00) |
0.624 (1.00) |
0.923 (1.00) |
0.416 (1.00) |
0.88 (1.00) |
0.242 (1.00) |
0.264 (1.00) |
0.0521 (1.00) |
Amp Peak 21(17q12) | 0 (0%) | 302 |
8.18e-07 (0.000546) |
0.031 (1.00) |
0.623 (1.00) |
0.73 (1.00) |
0.0168 (1.00) |
0.0308 (1.00) |
0.0196 (1.00) |
0.448 (1.00) |
0.0285 (1.00) |
0.0128 (1.00) |
Amp Peak 22(18p11 31) | 0 (0%) | 257 |
7.52e-07 (0.000504) |
0.000945 (0.558) |
0.962 (1.00) |
0.766 (1.00) |
0.262 (1.00) |
0.206 (1.00) |
0.579 (1.00) |
0.741 (1.00) |
0.0202 (1.00) |
0.0374 (1.00) |
Amp Peak 23(18q11 2) | 0 (0%) | 289 |
7.62e-05 (0.0484) |
0.0304 (1.00) |
0.157 (1.00) |
0.462 (1.00) |
1 (1.00) |
0.689 (1.00) |
0.191 (1.00) |
0.489 (1.00) |
0.00157 (0.9) |
0.0316 (1.00) |
Amp Peak 24(20q11 22) | 0 (0%) | 206 |
5.45e-07 (0.000365) |
0.0804 (1.00) |
0.845 (1.00) |
0.442 (1.00) |
0.0128 (1.00) |
0.0854 (1.00) |
0.298 (1.00) |
0.009 (1.00) |
0.339 (1.00) |
0.0304 (1.00) |
Del Peak 7(3p25 3) | 0 (0%) | 111 |
7.39e-27 (5.21e-24) |
0.00975 (1.00) |
0.213 (1.00) |
0.39 (1.00) |
0.0134 (1.00) |
0.0632 (1.00) |
0.176 (1.00) |
0.00314 (1.00) |
0.0281 (1.00) |
0.258 (1.00) |
Del Peak 8(3p14 2) | 0 (0%) | 96 |
1.1e-39 (7.84e-37) |
0.00151 (0.875) |
0.259 (1.00) |
0.5 (1.00) |
0.115 (1.00) |
0.161 (1.00) |
0.522 (1.00) |
0.127 (1.00) |
0.0541 (1.00) |
0.154 (1.00) |
Del Peak 9(3p14 2) | 0 (0%) | 96 |
1.1e-39 (7.84e-37) |
0.00151 (0.875) |
0.216 (1.00) |
0.386 (1.00) |
0.115 (1.00) |
0.161 (1.00) |
0.522 (1.00) |
0.127 (1.00) |
0.0393 (1.00) |
0.118 (1.00) |
Del Peak 10(3p12 2) | 0 (0%) | 110 |
1.31e-31 (9.27e-29) |
0.00359 (1.00) |
0.853 (1.00) |
0.684 (1.00) |
0.241 (1.00) |
0.463 (1.00) |
0.229 (1.00) |
0.432 (1.00) |
0.0143 (1.00) |
0.446 (1.00) |
Del Peak 12(4q22 1) | 0 (0%) | 247 |
1.21e-13 (8.41e-11) |
0.0231 (1.00) |
0.13 (1.00) |
0.651 (1.00) |
0.371 (1.00) |
0.205 (1.00) |
0.383 (1.00) |
0.341 (1.00) |
0.0048 (1.00) |
0.0695 (1.00) |
Del Peak 13(4q35 2) | 0 (0%) | 219 |
2.03e-10 (1.39e-07) |
0.647 (1.00) |
0.0962 (1.00) |
0.534 (1.00) |
0.275 (1.00) |
0.353 (1.00) |
0.209 (1.00) |
0.32 (1.00) |
0.0399 (1.00) |
0.351 (1.00) |
Del Peak 14(5q11 2) | 0 (0%) | 220 |
7.05e-17 (4.94e-14) |
0.000751 (0.448) |
0.0186 (1.00) |
0.615 (1.00) |
0.0401 (1.00) |
0.000767 (0.457) |
0.0809 (1.00) |
0.325 (1.00) |
0.00377 (1.00) |
0.0109 (1.00) |
Del Peak 22(9p23) | 0 (0%) | 199 |
9.87e-14 (6.86e-11) |
0.0581 (1.00) |
0.538 (1.00) |
0.851 (1.00) |
0.74 (1.00) |
0.493 (1.00) |
0.677 (1.00) |
0.385 (1.00) |
0.0341 (1.00) |
0.333 (1.00) |
Del Peak 23(9p21 3) | 0 (0%) | 156 |
3.41e-10 (2.33e-07) |
0.0126 (1.00) |
0.707 (1.00) |
0.423 (1.00) |
0.39 (1.00) |
0.462 (1.00) |
0.824 (1.00) |
0.2 (1.00) |
0.573 (1.00) |
0.666 (1.00) |
Del Peak 24(9q21 11) | 0 (0%) | 301 |
1.33e-05 (0.00871) |
0.00187 (1.00) |
0.96 (1.00) |
0.926 (1.00) |
0.882 (1.00) |
0.673 (1.00) |
0.588 (1.00) |
0.00252 (1.00) |
0.582 (1.00) |
0.0693 (1.00) |
Del Peak 28(10q23 31) | 0 (0%) | 277 |
0.00565 (1.00) |
0.000159 (0.0992) |
0.179 (1.00) |
0.548 (1.00) |
0.0249 (1.00) |
0.0128 (1.00) |
0.0843 (1.00) |
0.905 (1.00) |
0.00143 (0.828) |
0.0601 (1.00) |
Del Peak 30(11q14 2) | 0 (0%) | 232 |
2.56e-20 (1.8e-17) |
0.0012 (0.701) |
0.232 (1.00) |
0.803 (1.00) |
0.00101 (0.596) |
0.0121 (1.00) |
0.632 (1.00) |
0.457 (1.00) |
0.0137 (1.00) |
0.425 (1.00) |
Del Peak 33(13q12 11) | 0 (0%) | 200 |
7.7e-11 (5.29e-08) |
0.00693 (1.00) |
0.272 (1.00) |
0.371 (1.00) |
0.053 (1.00) |
0.0289 (1.00) |
0.498 (1.00) |
0.624 (1.00) |
0.00224 (1.00) |
0.214 (1.00) |
Del Peak 37(15q15 1) | 0 (0%) | 286 |
1.19e-06 (0.000792) |
0.723 (1.00) |
0.293 (1.00) |
0.161 (1.00) |
0.0226 (1.00) |
0.0628 (1.00) |
0.179 (1.00) |
0.183 (1.00) |
0.266 (1.00) |
0.411 (1.00) |
Del Peak 42(18q23) | 0 (0%) | 161 |
1.08e-22 (7.63e-20) |
0.00193 (1.00) |
0.183 (1.00) |
0.385 (1.00) |
0.00216 (1.00) |
0.00333 (1.00) |
0.0145 (1.00) |
0.0191 (1.00) |
0.252 (1.00) |
0.362 (1.00) |
Del Peak 43(19p13 3) | 0 (0%) | 249 |
0.000105 (0.0658) |
0.528 (1.00) |
0.31 (1.00) |
0.0817 (1.00) |
0.0853 (1.00) |
0.679 (1.00) |
0.441 (1.00) |
0.11 (1.00) |
0.581 (1.00) |
0.406 (1.00) |
Del Peak 44(19q13 43) | 0 (0%) | 297 |
8.73e-06 (0.00573) |
0.0423 (1.00) |
0.256 (1.00) |
0.0841 (1.00) |
0.584 (1.00) |
0.262 (1.00) |
0.0674 (1.00) |
0.839 (1.00) |
0.0563 (1.00) |
0.87 (1.00) |
Del Peak 45(Xp21 3) | 0 (0%) | 247 |
2.14e-07 (0.000144) |
0.0609 (1.00) |
0.424 (1.00) |
0.0649 (1.00) |
0.275 (1.00) |
0.0415 (1.00) |
0.199 (1.00) |
0.52 (1.00) |
0.568 (1.00) |
0.664 (1.00) |
Del Peak 46(Xp11 3) | 0 (0%) | 249 |
1.29e-08 (8.7e-06) |
0.0276 (1.00) |
0.346 (1.00) |
0.00914 (1.00) |
0.211 (1.00) |
0.0598 (1.00) |
0.102 (1.00) |
0.79 (1.00) |
0.0478 (1.00) |
0.714 (1.00) |
Amp Peak 10(8p11 23) | 0 (0%) | 249 |
0.00368 (1.00) |
0.0827 (1.00) |
0.897 (1.00) |
0.629 (1.00) |
0.15 (1.00) |
0.0182 (1.00) |
0.0102 (1.00) |
0.0711 (1.00) |
0.0437 (1.00) |
0.191 (1.00) |
Amp Peak 15(11p13) | 0 (0%) | 296 |
0.0134 (1.00) |
0.331 (1.00) |
0.187 (1.00) |
0.0539 (1.00) |
0.631 (1.00) |
0.163 (1.00) |
0.523 (1.00) |
0.134 (1.00) |
0.781 (1.00) |
0.783 (1.00) |
Amp Peak 18(12q15) | 0 (0%) | 293 |
0.00193 (1.00) |
0.486 (1.00) |
0.0609 (1.00) |
0.193 (1.00) |
0.09 (1.00) |
0.0459 (1.00) |
0.471 (1.00) |
0.695 (1.00) |
0.326 (1.00) |
0.752 (1.00) |
Del Peak 3(1q44) | 0 (0%) | 337 |
0.568 (1.00) |
0.0115 (1.00) |
0.859 (1.00) |
0.931 (1.00) |
0.0628 (1.00) |
0.0133 (1.00) |
0.00659 (1.00) |
0.213 (1.00) |
0.0906 (1.00) |
0.0169 (1.00) |
Del Peak 5(2q22 1) | 0 (0%) | 289 |
0.0342 (1.00) |
0.165 (1.00) |
0.29 (1.00) |
0.522 (1.00) |
0.0513 (1.00) |
0.0292 (1.00) |
0.0573 (1.00) |
0.0192 (1.00) |
0.0538 (1.00) |
0.0476 (1.00) |
Del Peak 17(6p25 3) | 0 (0%) | 299 |
0.00185 (1.00) |
0.00731 (1.00) |
0.0727 (1.00) |
0.133 (1.00) |
0.00752 (1.00) |
0.38 (1.00) |
0.099 (1.00) |
0.842 (1.00) |
0.101 (1.00) |
0.474 (1.00) |
Del Peak 18(6q12) | 0 (0%) | 305 |
0.0132 (1.00) |
0.0233 (1.00) |
0.052 (1.00) |
0.153 (1.00) |
0.949 (1.00) |
0.949 (1.00) |
0.206 (1.00) |
0.464 (1.00) |
0.338 (1.00) |
0.222 (1.00) |
Del Peak 19(7q31 1) | 0 (0%) | 312 |
0.0487 (1.00) |
0.213 (1.00) |
0.17 (1.00) |
0.581 (1.00) |
0.363 (1.00) |
0.609 (1.00) |
0.571 (1.00) |
0.273 (1.00) |
0.901 (1.00) |
0.194 (1.00) |
Del Peak 20(7q36 1) | 0 (0%) | 278 |
0.0257 (1.00) |
0.693 (1.00) |
0.00511 (1.00) |
0.277 (1.00) |
0.957 (1.00) |
0.674 (1.00) |
0.815 (1.00) |
0.254 (1.00) |
0.781 (1.00) |
0.397 (1.00) |
Del Peak 25(9q34 3) | 0 (0%) | 310 |
0.00081 (0.481) |
0.0206 (1.00) |
0.712 (1.00) |
0.108 (1.00) |
0.851 (1.00) |
0.409 (1.00) |
0.276 (1.00) |
0.0275 (1.00) |
0.583 (1.00) |
0.326 (1.00) |
Del Peak 26(10p15 3) | 0 (0%) | 251 |
0.00337 (1.00) |
0.227 (1.00) |
0.504 (1.00) |
0.155 (1.00) |
0.327 (1.00) |
0.307 (1.00) |
0.271 (1.00) |
0.703 (1.00) |
0.0166 (1.00) |
0.332 (1.00) |
Del Peak 27(10p11 21) | 0 (0%) | 258 |
0.00132 (0.767) |
0.0495 (1.00) |
0.225 (1.00) |
0.0652 (1.00) |
0.702 (1.00) |
0.975 (1.00) |
0.542 (1.00) |
0.831 (1.00) |
0.0675 (1.00) |
0.458 (1.00) |
Del Peak 32(12q24 33) | 0 (0%) | 327 |
0.0202 (1.00) |
0.208 (1.00) |
0.082 (1.00) |
0.748 (1.00) |
0.859 (1.00) |
0.775 (1.00) |
0.931 (1.00) |
0.358 (1.00) |
0.366 (1.00) |
0.509 (1.00) |
Del Peak 35(14q11 2) | 0 (0%) | 316 |
0.0288 (1.00) |
0.113 (1.00) |
0.38 (1.00) |
0.515 (1.00) |
0.463 (1.00) |
0.329 (1.00) |
0.111 (1.00) |
0.154 (1.00) |
0.0401 (1.00) |
0.0328 (1.00) |
Del Peak 40(17q25 3) | 0 (0%) | 324 |
0.321 (1.00) |
0.0923 (1.00) |
0.474 (1.00) |
1 (1.00) |
0.037 (1.00) |
0.0612 (1.00) |
0.0204 (1.00) |
0.0941 (1.00) |
0.00228 (1.00) |
0.0789 (1.00) |
P value = 1.19e-09 (Chi-square test), Q value = 8.2e-07
Table S1. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 1(1Q21.2) CNV | 31 | 24 | 5 | 2 | 8 | 4 | 2 | 9 |
AMP PEAK 1(1Q21.2) WILD-TYPE | 55 | 32 | 72 | 29 | 68 | 14 | 7 | 6 |
Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D1V1.png)
P value = 2.12e-05 (Fisher's exact test), Q value = 0.014
Table S2. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
AMP PEAK 1(1Q21.2) CNV | 20 | 40 | 11 |
AMP PEAK 1(1Q21.2) WILD-TYPE | 79 | 66 | 90 |
Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D1V2.png)
P value = 0.00035 (Fisher's exact test), Q value = 0.21
Table S3. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 134 | 104 |
AMP PEAK 1(1Q21.2) CNV | 15 | 46 | 21 |
AMP PEAK 1(1Q21.2) WILD-TYPE | 98 | 88 | 83 |
Figure S3. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
![](D1V7.png)
P value = 3.36e-05 (Fisher's exact test), Q value = 0.022
Table S4. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 117 | 96 |
AMP PEAK 1(1Q21.2) CNV | 14 | 46 | 19 |
AMP PEAK 1(1Q21.2) WILD-TYPE | 88 | 71 | 77 |
Figure S4. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D1V9.png)
P value = 0.000316 (Fisher's exact test), Q value = 0.19
Table S5. Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 5 | 93 | 92 | 125 |
AMP PEAK 1(1Q21.2) CNV | 1 | 37 | 12 | 29 |
AMP PEAK 1(1Q21.2) WILD-TYPE | 4 | 56 | 80 | 96 |
Figure S5. Get High-res Image Gene #1: 'Amp Peak 1(1q21.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D1V10.png)
P value = 1.01e-09 (Chi-square test), Q value = 6.9e-07
Table S6. Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 2(2Q11.2) CNV | 25 | 23 | 1 | 2 | 11 | 4 | 1 | 9 |
AMP PEAK 2(2Q11.2) WILD-TYPE | 61 | 33 | 76 | 29 | 65 | 14 | 8 | 6 |
Figure S6. Get High-res Image Gene #2: 'Amp Peak 2(2q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D2V1.png)
P value = 2.38e-12 (Chi-square test), Q value = 1.6e-09
Table S7. Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 3(2Q31.2) CNV | 28 | 26 | 2 | 2 | 6 | 4 | 0 | 8 |
AMP PEAK 3(2Q31.2) WILD-TYPE | 58 | 30 | 75 | 29 | 70 | 14 | 9 | 7 |
Figure S7. Get High-res Image Gene #3: 'Amp Peak 3(2q31.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D3V1.png)
P value = 1.01e-16 (Chi-square test), Q value = 7e-14
Table S8. Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 4(3Q26.33) CNV | 76 | 53 | 27 | 23 | 60 | 16 | 7 | 14 |
AMP PEAK 4(3Q26.33) WILD-TYPE | 10 | 3 | 50 | 8 | 16 | 2 | 2 | 1 |
Figure S8. Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #1: 'CN_CNMF'
![](D4V1.png)
P value = 4.75e-05 (Fisher's exact test), Q value = 0.031
Table S9. Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
AMP PEAK 4(3Q26.33) CNV | 70 | 94 | 64 |
AMP PEAK 4(3Q26.33) WILD-TYPE | 29 | 12 | 37 |
Figure S9. Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D4V2.png)
P value = 9.01e-05 (Fisher's exact test), Q value = 0.057
Table S10. Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 117 | 96 |
AMP PEAK 4(3Q26.33) CNV | 61 | 100 | 70 |
AMP PEAK 4(3Q26.33) WILD-TYPE | 41 | 17 | 26 |
Figure S10. Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D4V9.png)
P value = 6.81e-06 (Fisher's exact test), Q value = 0.0045
Table S11. Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 5 | 93 | 92 | 125 |
AMP PEAK 4(3Q26.33) CNV | 2 | 82 | 53 | 94 |
AMP PEAK 4(3Q26.33) WILD-TYPE | 3 | 11 | 39 | 31 |
Figure S11. Get High-res Image Gene #4: 'Amp Peak 4(3q26.33)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D4V10.png)
P value = 1.41e-09 (Chi-square test), Q value = 9.6e-07
Table S12. Gene #5: 'Amp Peak 5(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 5(5P15.33) CNV | 52 | 29 | 19 | 10 | 25 | 16 | 2 | 13 |
AMP PEAK 5(5P15.33) WILD-TYPE | 34 | 27 | 58 | 21 | 51 | 2 | 7 | 2 |
Figure S12. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33)' versus Molecular Subtype #1: 'CN_CNMF'
![](D5V1.png)
P value = 1.87e-05 (Chi-square test), Q value = 0.012
Table S13. Gene #6: 'Amp Peak 6(6p12.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 6(6P12.1) CNV | 27 | 13 | 4 | 1 | 14 | 9 | 2 | 3 |
AMP PEAK 6(6P12.1) WILD-TYPE | 59 | 43 | 73 | 30 | 62 | 9 | 7 | 12 |
Figure S13. Get High-res Image Gene #6: 'Amp Peak 6(6p12.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D6V1.png)
P value = 7.89e-05 (Chi-square test), Q value = 0.05
Table S14. Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 7(6Q12) CNV | 20 | 13 | 3 | 1 | 16 | 9 | 2 | 3 |
AMP PEAK 7(6Q12) WILD-TYPE | 66 | 43 | 74 | 30 | 60 | 9 | 7 | 12 |
Figure S14. Get High-res Image Gene #7: 'Amp Peak 7(6q12)' versus Molecular Subtype #1: 'CN_CNMF'
![](D7V1.png)
P value = 9.14e-07 (Chi-square test), Q value = 0.00061
Table S15. Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 8(7P11.2) CNV | 49 | 28 | 17 | 5 | 31 | 11 | 2 | 11 |
AMP PEAK 8(7P11.2) WILD-TYPE | 37 | 28 | 60 | 26 | 45 | 7 | 7 | 4 |
Figure S15. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D8V1.png)
P value = 3.49e-15 (Chi-square test), Q value = 2.4e-12
Table S16. Gene #9: 'Amp Peak 9(7q21.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 9(7Q21.3) CNV | 48 | 31 | 11 | 3 | 12 | 4 | 2 | 13 |
AMP PEAK 9(7Q21.3) WILD-TYPE | 38 | 25 | 66 | 28 | 64 | 14 | 7 | 2 |
Figure S16. Get High-res Image Gene #9: 'Amp Peak 9(7q21.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D9V1.png)
P value = 1.93e-06 (Chi-square test), Q value = 0.0013
Table S17. Gene #11: 'Amp Peak 11(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 11(8Q11.21) CNV | 56 | 29 | 30 | 14 | 54 | 18 | 7 | 12 |
AMP PEAK 11(8Q11.21) WILD-TYPE | 30 | 27 | 47 | 17 | 22 | 0 | 2 | 3 |
Figure S17. Get High-res Image Gene #11: 'Amp Peak 11(8q11.21)' versus Molecular Subtype #1: 'CN_CNMF'
![](D11V1.png)
P value = 0.000199 (Fisher's exact test), Q value = 0.12
Table S18. Gene #11: 'Amp Peak 11(8q11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
AMP PEAK 11(8Q11.21) CNV | 68 | 44 | 63 |
AMP PEAK 11(8Q11.21) WILD-TYPE | 31 | 62 | 38 |
Figure S18. Get High-res Image Gene #11: 'Amp Peak 11(8q11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D11V2.png)
P value = 5.27e-09 (Chi-square test), Q value = 3.6e-06
Table S19. Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 12(8Q24.21) CNV | 74 | 36 | 37 | 18 | 61 | 18 | 8 | 15 |
AMP PEAK 12(8Q24.21) WILD-TYPE | 12 | 20 | 40 | 13 | 15 | 0 | 1 | 0 |
Figure S19. Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'
![](D12V1.png)
P value = 2.54e-05 (Fisher's exact test), Q value = 0.016
Table S20. Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
AMP PEAK 12(8Q24.21) CNV | 82 | 58 | 77 |
AMP PEAK 12(8Q24.21) WILD-TYPE | 17 | 48 | 24 |
Figure S20. Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D12V2.png)
P value = 0.000102 (Fisher's exact test), Q value = 0.065
Table S21. Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 91 | 90 |
AMP PEAK 12(8Q24.21) CNV | 69 | 77 | 68 |
AMP PEAK 12(8Q24.21) WILD-TYPE | 49 | 14 | 22 |
Figure S21. Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D12V5.png)
P value = 0.000135 (Fisher's exact test), Q value = 0.085
Table S22. Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 84 | 120 |
AMP PEAK 12(8Q24.21) CNV | 79 | 65 | 70 |
AMP PEAK 12(8Q24.21) WILD-TYPE | 16 | 19 | 50 |
Figure S22. Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D12V6.png)
P value = 6.75e-06 (Chi-square test), Q value = 0.0044
Table S23. Gene #13: 'Amp Peak 13(9p23)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 13(9P23) CNV | 19 | 14 | 17 | 8 | 11 | 7 | 9 | 2 |
AMP PEAK 13(9P23) WILD-TYPE | 67 | 42 | 60 | 23 | 65 | 11 | 0 | 13 |
Figure S23. Get High-res Image Gene #13: 'Amp Peak 13(9p23)' versus Molecular Subtype #1: 'CN_CNMF'
![](D13V1.png)
P value = 0.000371 (Chi-square test), Q value = 0.23
Table S24. Gene #14: 'Amp Peak 14(9p13.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 14(9P13.3) CNV | 21 | 17 | 16 | 7 | 22 | 6 | 9 | 4 |
AMP PEAK 14(9P13.3) WILD-TYPE | 65 | 39 | 61 | 24 | 54 | 12 | 0 | 11 |
Figure S24. Get High-res Image Gene #14: 'Amp Peak 14(9p13.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D14V1.png)
P value = 3.83e-30 (Chi-square test), Q value = 2.7e-27
Table S25. Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 16(11Q13.3) CNV | 86 | 19 | 8 | 5 | 34 | 8 | 4 | 6 |
AMP PEAK 16(11Q13.3) WILD-TYPE | 0 | 37 | 69 | 26 | 42 | 10 | 5 | 9 |
Figure S25. Get High-res Image Gene #16: 'Amp Peak 16(11q13.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D16V1.png)
P value = 1.99e-12 (Chi-square test), Q value = 1.4e-09
Table S26. Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 17(12P13.33) CNV | 33 | 36 | 8 | 4 | 20 | 14 | 2 | 8 |
AMP PEAK 17(12P13.33) WILD-TYPE | 53 | 20 | 69 | 27 | 56 | 4 | 7 | 7 |
Figure S26. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33)' versus Molecular Subtype #1: 'CN_CNMF'
![](D17V1.png)
P value = 1.18e-06 (Chi-square test), Q value = 0.00078
Table S27. Gene #19: 'Amp Peak 19(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 19(13Q22.1) CNV | 24 | 8 | 3 | 6 | 17 | 7 | 2 | 10 |
AMP PEAK 19(13Q22.1) WILD-TYPE | 62 | 48 | 74 | 25 | 59 | 11 | 7 | 5 |
Figure S27. Get High-res Image Gene #19: 'Amp Peak 19(13q22.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D19V1.png)
P value = 5.54e-05 (Chi-square test), Q value = 0.035
Table S28. Gene #20: 'Amp Peak 20(15q26.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 20(15Q26.3) CNV | 29 | 13 | 5 | 2 | 17 | 3 | 0 | 7 |
AMP PEAK 20(15Q26.3) WILD-TYPE | 57 | 43 | 72 | 29 | 59 | 15 | 9 | 8 |
Figure S28. Get High-res Image Gene #20: 'Amp Peak 20(15q26.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D20V1.png)
P value = 8.18e-07 (Chi-square test), Q value = 0.00055
Table S29. Gene #21: 'Amp Peak 21(17q12)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 21(17Q12) CNV | 25 | 20 | 1 | 2 | 10 | 2 | 1 | 5 |
AMP PEAK 21(17Q12) WILD-TYPE | 61 | 36 | 76 | 29 | 66 | 16 | 8 | 10 |
Figure S29. Get High-res Image Gene #21: 'Amp Peak 21(17q12)' versus Molecular Subtype #1: 'CN_CNMF'
![](D21V1.png)
P value = 7.52e-07 (Chi-square test), Q value = 5e-04
Table S30. Gene #22: 'Amp Peak 22(18p11.31)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 22(18P11.31) CNV | 32 | 29 | 9 | 5 | 17 | 11 | 4 | 4 |
AMP PEAK 22(18P11.31) WILD-TYPE | 54 | 27 | 68 | 26 | 59 | 7 | 5 | 11 |
Figure S30. Get High-res Image Gene #22: 'Amp Peak 22(18p11.31)' versus Molecular Subtype #1: 'CN_CNMF'
![](D22V1.png)
P value = 7.62e-05 (Chi-square test), Q value = 0.048
Table S31. Gene #23: 'Amp Peak 23(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 23(18Q11.2) CNV | 16 | 26 | 8 | 3 | 16 | 5 | 1 | 4 |
AMP PEAK 23(18Q11.2) WILD-TYPE | 70 | 30 | 69 | 28 | 60 | 13 | 8 | 11 |
Figure S31. Get High-res Image Gene #23: 'Amp Peak 23(18q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D23V1.png)
P value = 5.45e-07 (Chi-square test), Q value = 0.00037
Table S32. Gene #24: 'Amp Peak 24(20q11.22)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
AMP PEAK 24(20Q11.22) CNV | 39 | 22 | 18 | 12 | 39 | 18 | 4 | 10 |
AMP PEAK 24(20Q11.22) WILD-TYPE | 47 | 34 | 59 | 19 | 37 | 0 | 5 | 5 |
Figure S32. Get High-res Image Gene #24: 'Amp Peak 24(20q11.22)' versus Molecular Subtype #1: 'CN_CNMF'
![](D24V1.png)
P value = 1.15e-13 (Chi-square test), Q value = 8e-11
Table S33. Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 1(1P36.13) CNV | 17 | 29 | 5 | 1 | 10 | 0 | 0 | 9 |
DEL PEAK 1(1P36.13) WILD-TYPE | 69 | 27 | 72 | 30 | 66 | 18 | 9 | 6 |
Figure S33. Get High-res Image Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #1: 'CN_CNMF'
![](D25V1.png)
P value = 2.28e-07 (Fisher's exact test), Q value = 0.00015
Table S34. Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 1(1P36.13) CNV | 14 | 41 | 9 |
DEL PEAK 1(1P36.13) WILD-TYPE | 85 | 65 | 92 |
Figure S34. Get High-res Image Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D25V2.png)
P value = 3.03e-05 (Fisher's exact test), Q value = 0.02
Table S35. Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 91 | 90 |
DEL PEAK 1(1P36.13) CNV | 39 | 17 | 7 |
DEL PEAK 1(1P36.13) WILD-TYPE | 79 | 74 | 83 |
Figure S35. Get High-res Image Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D25V5.png)
P value = 2.14e-05 (Fisher's exact test), Q value = 0.014
Table S36. Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 117 | 96 |
DEL PEAK 1(1P36.13) CNV | 10 | 39 | 13 |
DEL PEAK 1(1P36.13) WILD-TYPE | 92 | 78 | 83 |
Figure S36. Get High-res Image Gene #25: 'Del Peak 1(1p36.13)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D25V9.png)
P value = 3.38e-11 (Chi-square test), Q value = 2.3e-08
Table S37. Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 2(1P13.2) CNV | 21 | 31 | 4 | 2 | 15 | 4 | 1 | 9 |
DEL PEAK 2(1P13.2) WILD-TYPE | 65 | 25 | 73 | 29 | 61 | 14 | 8 | 6 |
Figure S37. Get High-res Image Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D26V1.png)
P value = 0.000147 (Fisher's exact test), Q value = 0.092
Table S38. Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 2(1P13.2) CNV | 22 | 40 | 13 |
DEL PEAK 2(1P13.2) WILD-TYPE | 77 | 66 | 88 |
Figure S38. Get High-res Image Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D26V2.png)
P value = 0.000105 (Fisher's exact test), Q value = 0.066
Table S39. Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 134 | 104 |
DEL PEAK 2(1P13.2) CNV | 16 | 49 | 20 |
DEL PEAK 2(1P13.2) WILD-TYPE | 97 | 85 | 84 |
Figure S39. Get High-res Image Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
![](D26V7.png)
P value = 1.53e-05 (Fisher's exact test), Q value = 0.01
Table S40. Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 117 | 96 |
DEL PEAK 2(1P13.2) CNV | 13 | 46 | 19 |
DEL PEAK 2(1P13.2) WILD-TYPE | 89 | 71 | 77 |
Figure S40. Get High-res Image Gene #26: 'Del Peak 2(1p13.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D26V9.png)
P value = 0.000297 (Fisher's exact test), Q value = 0.18
Table S41. Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 134 | 104 |
DEL PEAK 4(2Q21.2) CNV | 26 | 15 | 5 |
DEL PEAK 4(2Q21.2) WILD-TYPE | 87 | 119 | 99 |
Figure S41. Get High-res Image Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
![](D28V7.png)
P value = 0.000268 (Fisher's exact test), Q value = 0.17
Table S42. Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 117 | 96 |
DEL PEAK 4(2Q21.2) CNV | 23 | 11 | 4 |
DEL PEAK 4(2Q21.2) WILD-TYPE | 79 | 106 | 92 |
Figure S42. Get High-res Image Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D28V9.png)
P value = 0.000159 (Fisher's exact test), Q value = 0.099
Table S43. Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 5 | 93 | 92 | 125 |
DEL PEAK 4(2Q21.2) CNV | 1 | 6 | 23 | 8 |
DEL PEAK 4(2Q21.2) WILD-TYPE | 4 | 87 | 69 | 117 |
Figure S43. Get High-res Image Gene #28: 'Del Peak 4(2q21.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D28V10.png)
P value = 1.28e-08 (Chi-square test), Q value = 8.7e-06
Table S44. Gene #30: 'Del Peak 6(2q36.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 6(2Q36.2) CNV | 25 | 34 | 11 | 4 | 17 | 3 | 4 | 9 |
DEL PEAK 6(2Q36.2) WILD-TYPE | 61 | 22 | 66 | 27 | 59 | 15 | 5 | 6 |
Figure S44. Get High-res Image Gene #30: 'Del Peak 6(2q36.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D30V1.png)
P value = 7.6e-05 (Fisher's exact test), Q value = 0.048
Table S45. Gene #30: 'Del Peak 6(2q36.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 6(2Q36.2) CNV | 27 | 48 | 18 |
DEL PEAK 6(2Q36.2) WILD-TYPE | 72 | 58 | 83 |
Figure S45. Get High-res Image Gene #30: 'Del Peak 6(2q36.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D30V2.png)
P value = 7.39e-27 (Chi-square test), Q value = 5.2e-24
Table S46. Gene #31: 'Del Peak 7(3p25.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 7(3P25.3) CNV | 76 | 44 | 12 | 24 | 63 | 16 | 8 | 14 |
DEL PEAK 7(3P25.3) WILD-TYPE | 10 | 12 | 65 | 7 | 13 | 2 | 1 | 1 |
Figure S46. Get High-res Image Gene #31: 'Del Peak 7(3p25.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D31V1.png)
P value = 1.1e-39 (Chi-square test), Q value = 7.8e-37
Table S47. Gene #32: 'Del Peak 8(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 8(3P14.2) CNV | 83 | 49 | 9 | 29 | 64 | 15 | 9 | 14 |
DEL PEAK 8(3P14.2) WILD-TYPE | 3 | 7 | 68 | 2 | 12 | 3 | 0 | 1 |
Figure S47. Get High-res Image Gene #32: 'Del Peak 8(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D32V1.png)
P value = 1.1e-39 (Chi-square test), Q value = 7.8e-37
Table S48. Gene #33: 'Del Peak 9(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 9(3P14.2) CNV | 83 | 49 | 9 | 29 | 64 | 15 | 9 | 14 |
DEL PEAK 9(3P14.2) WILD-TYPE | 3 | 7 | 68 | 2 | 12 | 3 | 0 | 1 |
Figure S48. Get High-res Image Gene #33: 'Del Peak 9(3p14.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D33V1.png)
P value = 1.31e-31 (Chi-square test), Q value = 9.3e-29
Table S49. Gene #34: 'Del Peak 10(3p12.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 10(3P12.2) CNV | 79 | 48 | 9 | 26 | 61 | 14 | 8 | 13 |
DEL PEAK 10(3P12.2) WILD-TYPE | 7 | 8 | 68 | 5 | 15 | 4 | 1 | 2 |
Figure S49. Get High-res Image Gene #34: 'Del Peak 10(3p12.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D34V1.png)
P value = 3.81e-13 (Chi-square test), Q value = 2.6e-10
Table S50. Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 11(4P15.2) CNV | 51 | 40 | 9 | 8 | 31 | 3 | 2 | 10 |
DEL PEAK 11(4P15.2) WILD-TYPE | 35 | 16 | 68 | 23 | 45 | 15 | 7 | 5 |
Figure S50. Get High-res Image Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D35V1.png)
P value = 1.94e-05 (Fisher's exact test), Q value = 0.013
Table S51. Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 11(4P15.2) CNV | 42 | 62 | 27 |
DEL PEAK 11(4P15.2) WILD-TYPE | 57 | 44 | 74 |
Figure S51. Get High-res Image Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D35V2.png)
P value = 0.00039 (Fisher's exact test), Q value = 0.24
Table S52. Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 117 | 96 |
DEL PEAK 11(4P15.2) CNV | 29 | 64 | 38 |
DEL PEAK 11(4P15.2) WILD-TYPE | 73 | 53 | 58 |
Figure S52. Get High-res Image Gene #35: 'Del Peak 11(4p15.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D35V9.png)
P value = 1.21e-13 (Chi-square test), Q value = 8.4e-11
Table S53. Gene #36: 'Del Peak 12(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 12(4Q22.1) CNV | 31 | 39 | 7 | 1 | 24 | 7 | 2 | 10 |
DEL PEAK 12(4Q22.1) WILD-TYPE | 55 | 17 | 70 | 30 | 52 | 11 | 7 | 5 |
Figure S53. Get High-res Image Gene #36: 'Del Peak 12(4q22.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D36V1.png)
P value = 2.03e-10 (Chi-square test), Q value = 1.4e-07
Table S54. Gene #37: 'Del Peak 13(4q35.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 13(4Q35.2) CNV | 34 | 35 | 11 | 3 | 40 | 10 | 5 | 11 |
DEL PEAK 13(4Q35.2) WILD-TYPE | 52 | 21 | 66 | 28 | 36 | 8 | 4 | 4 |
Figure S54. Get High-res Image Gene #37: 'Del Peak 13(4q35.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D37V1.png)
P value = 7.05e-17 (Chi-square test), Q value = 4.9e-14
Table S55. Gene #38: 'Del Peak 14(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 14(5Q11.2) CNV | 43 | 36 | 5 | 1 | 37 | 11 | 2 | 13 |
DEL PEAK 14(5Q11.2) WILD-TYPE | 43 | 20 | 72 | 30 | 39 | 7 | 7 | 2 |
Figure S55. Get High-res Image Gene #38: 'Del Peak 14(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D38V1.png)
P value = 5.86e-16 (Chi-square test), Q value = 4.1e-13
Table S56. Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 15(5Q15) CNV | 44 | 36 | 8 | 1 | 36 | 11 | 2 | 14 |
DEL PEAK 15(5Q15) WILD-TYPE | 42 | 20 | 69 | 30 | 40 | 7 | 7 | 1 |
Figure S56. Get High-res Image Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #1: 'CN_CNMF'
![](D39V1.png)
P value = 4.73e-05 (Fisher's exact test), Q value = 0.03
Table S57. Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 15(5Q15) CNV | 55 | 50 | 26 |
DEL PEAK 15(5Q15) WILD-TYPE | 44 | 56 | 75 |
Figure S57. Get High-res Image Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D39V2.png)
P value = 0.000402 (Fisher's exact test), Q value = 0.24
Table S58. Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 84 | 120 |
DEL PEAK 15(5Q15) CNV | 44 | 22 | 64 |
DEL PEAK 15(5Q15) WILD-TYPE | 51 | 62 | 56 |
Figure S58. Get High-res Image Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D39V6.png)
P value = 0.000403 (Fisher's exact test), Q value = 0.24
Table S59. Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 117 | 96 |
DEL PEAK 15(5Q15) CNV | 29 | 64 | 39 |
DEL PEAK 15(5Q15) WILD-TYPE | 73 | 53 | 57 |
Figure S59. Get High-res Image Gene #39: 'Del Peak 15(5q15)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D39V9.png)
P value = 2.14e-14 (Chi-square test), Q value = 1.5e-11
Table S60. Gene #40: 'Del Peak 16(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 16(5Q35.3) CNV | 34 | 40 | 8 | 1 | 34 | 10 | 3 | 11 |
DEL PEAK 16(5Q35.3) WILD-TYPE | 52 | 16 | 69 | 30 | 42 | 8 | 6 | 4 |
Figure S60. Get High-res Image Gene #40: 'Del Peak 16(5q35.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D40V1.png)
P value = 2.58e-06 (Fisher's exact test), Q value = 0.0017
Table S61. Gene #40: 'Del Peak 16(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 16(5Q35.3) CNV | 54 | 46 | 21 |
DEL PEAK 16(5Q35.3) WILD-TYPE | 45 | 60 | 80 |
Figure S61. Get High-res Image Gene #40: 'Del Peak 16(5q35.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D40V2.png)
P value = 3.72e-16 (Chi-square test), Q value = 2.6e-13
Table S62. Gene #45: 'Del Peak 21(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 21(8P23.2) CNV | 68 | 21 | 17 | 12 | 53 | 15 | 7 | 14 |
DEL PEAK 21(8P23.2) WILD-TYPE | 18 | 35 | 60 | 19 | 23 | 3 | 2 | 1 |
Figure S62. Get High-res Image Gene #45: 'Del Peak 21(8p23.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D45V1.png)
P value = 0.000335 (Fisher's exact test), Q value = 0.21
Table S63. Gene #45: 'Del Peak 21(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 5 | 93 | 92 | 125 |
DEL PEAK 21(8P23.2) CNV | 2 | 37 | 61 | 80 |
DEL PEAK 21(8P23.2) WILD-TYPE | 3 | 56 | 31 | 45 |
Figure S63. Get High-res Image Gene #45: 'Del Peak 21(8p23.2)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D45V10.png)
P value = 9.87e-14 (Chi-square test), Q value = 6.9e-11
Table S64. Gene #46: 'Del Peak 22(9p23)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 22(9P23) CNV | 51 | 33 | 7 | 10 | 48 | 9 | 0 | 11 |
DEL PEAK 22(9P23) WILD-TYPE | 35 | 23 | 70 | 21 | 28 | 9 | 9 | 4 |
Figure S64. Get High-res Image Gene #46: 'Del Peak 22(9p23)' versus Molecular Subtype #1: 'CN_CNMF'
![](D46V1.png)
P value = 3.41e-10 (Chi-square test), Q value = 2.3e-07
Table S65. Gene #47: 'Del Peak 23(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 23(9P21.3) CNV | 66 | 37 | 21 | 14 | 55 | 8 | 2 | 9 |
DEL PEAK 23(9P21.3) WILD-TYPE | 20 | 19 | 56 | 17 | 21 | 10 | 7 | 6 |
Figure S65. Get High-res Image Gene #47: 'Del Peak 23(9p21.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D47V1.png)
P value = 1.33e-05 (Chi-square test), Q value = 0.0087
Table S66. Gene #48: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 24(9Q21.11) CNV | 30 | 7 | 4 | 3 | 13 | 4 | 0 | 6 |
DEL PEAK 24(9Q21.11) WILD-TYPE | 56 | 49 | 73 | 28 | 63 | 14 | 9 | 9 |
Figure S66. Get High-res Image Gene #48: 'Del Peak 24(9q21.11)' versus Molecular Subtype #1: 'CN_CNMF'
![](D48V1.png)
P value = 0.000159 (Fisher's exact test), Q value = 0.099
Table S67. Gene #52: 'Del Peak 28(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 28(10Q23.31) CNV | 28 | 40 | 13 |
DEL PEAK 28(10Q23.31) WILD-TYPE | 71 | 66 | 88 |
Figure S67. Get High-res Image Gene #52: 'Del Peak 28(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D52V2.png)
P value = 4.83e-11 (Chi-square test), Q value = 3.3e-08
Table S68. Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 29(11P15.4) CNV | 45 | 30 | 12 | 3 | 11 | 7 | 0 | 7 |
DEL PEAK 29(11P15.4) WILD-TYPE | 41 | 26 | 65 | 28 | 65 | 11 | 9 | 8 |
Figure S68. Get High-res Image Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #1: 'CN_CNMF'
![](D53V1.png)
P value = 3.05e-09 (Fisher's exact test), Q value = 2.1e-06
Table S69. Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 117 | 96 |
DEL PEAK 29(11P15.4) CNV | 14 | 60 | 23 |
DEL PEAK 29(11P15.4) WILD-TYPE | 88 | 57 | 73 |
Figure S69. Get High-res Image Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D53V9.png)
P value = 0.000321 (Fisher's exact test), Q value = 0.2
Table S70. Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 5 | 93 | 92 | 125 |
DEL PEAK 29(11P15.4) CNV | 2 | 44 | 19 | 32 |
DEL PEAK 29(11P15.4) WILD-TYPE | 3 | 49 | 73 | 93 |
Figure S70. Get High-res Image Gene #53: 'Del Peak 29(11p15.4)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D53V10.png)
P value = 2.56e-20 (Chi-square test), Q value = 1.8e-17
Table S71. Gene #54: 'Del Peak 30(11q14.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 30(11Q14.2) CNV | 70 | 22 | 16 | 9 | 8 | 5 | 3 | 3 |
DEL PEAK 30(11Q14.2) WILD-TYPE | 16 | 34 | 61 | 22 | 68 | 13 | 6 | 12 |
Figure S71. Get High-res Image Gene #54: 'Del Peak 30(11q14.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D54V1.png)
P value = 1.28e-20 (Chi-square test), Q value = 9e-18
Table S72. Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 31(11Q23.1) CNV | 78 | 30 | 22 | 16 | 14 | 9 | 4 | 2 |
DEL PEAK 31(11Q23.1) WILD-TYPE | 8 | 26 | 55 | 15 | 62 | 9 | 5 | 13 |
Figure S72. Get High-res Image Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D55V1.png)
P value = 3.94e-06 (Fisher's exact test), Q value = 0.0026
Table S73. Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 31(11Q23.1) CNV | 41 | 72 | 36 |
DEL PEAK 31(11Q23.1) WILD-TYPE | 58 | 34 | 65 |
Figure S73. Get High-res Image Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D55V2.png)
P value = 0.00023 (Fisher's exact test), Q value = 0.14
Table S74. Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 84 | 120 |
DEL PEAK 31(11Q23.1) CNV | 37 | 33 | 76 |
DEL PEAK 31(11Q23.1) WILD-TYPE | 58 | 51 | 44 |
Figure S74. Get High-res Image Gene #55: 'Del Peak 31(11q23.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D55V6.png)
P value = 7.7e-11 (Chi-square test), Q value = 5.3e-08
Table S75. Gene #57: 'Del Peak 33(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 33(13Q12.11) CNV | 45 | 41 | 11 | 7 | 43 | 11 | 4 | 6 |
DEL PEAK 33(13Q12.11) WILD-TYPE | 41 | 15 | 66 | 24 | 33 | 7 | 5 | 9 |
Figure S75. Get High-res Image Gene #57: 'Del Peak 33(13q12.11)' versus Molecular Subtype #1: 'CN_CNMF'
![](D57V1.png)
P value = 8.8e-07 (Chi-square test), Q value = 0.00059
Table S76. Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 34(13Q14.2) CNV | 42 | 38 | 18 | 8 | 38 | 10 | 2 | 2 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 44 | 18 | 59 | 23 | 38 | 8 | 7 | 13 |
Figure S76. Get High-res Image Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D58V1.png)
P value = 0.000281 (Fisher's exact test), Q value = 0.17
Table S77. Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 34(13Q14.2) CNV | 47 | 56 | 27 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 52 | 50 | 74 |
Figure S77. Get High-res Image Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D58V2.png)
P value = 5.7e-05 (Fisher's exact test), Q value = 0.036
Table S78. Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 91 | 90 |
DEL PEAK 34(13Q14.2) CNV | 66 | 39 | 23 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 52 | 52 | 67 |
Figure S78. Get High-res Image Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D58V5.png)
P value = 6.46e-05 (Fisher's exact test), Q value = 0.041
Table S79. Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 84 | 120 |
DEL PEAK 34(13Q14.2) CNV | 38 | 22 | 68 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 57 | 62 | 52 |
Figure S79. Get High-res Image Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D58V6.png)
P value = 5.29e-05 (Fisher's exact test), Q value = 0.034
Table S80. Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 117 | 96 |
DEL PEAK 34(13Q14.2) CNV | 29 | 67 | 36 |
DEL PEAK 34(13Q14.2) WILD-TYPE | 73 | 50 | 60 |
Figure S80. Get High-res Image Gene #58: 'Del Peak 34(13q14.2)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D58V9.png)
P value = 6.74e-08 (Fisher's exact test), Q value = 4.6e-05
Table S81. Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 36(14Q32.32) CNV | 7 | 34 | 6 |
DEL PEAK 36(14Q32.32) WILD-TYPE | 92 | 72 | 95 |
Figure S81. Get High-res Image Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D60V2.png)
P value = 0.000242 (Fisher's exact test), Q value = 0.15
Table S82. Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 91 | 90 |
DEL PEAK 36(14Q32.32) CNV | 30 | 11 | 5 |
DEL PEAK 36(14Q32.32) WILD-TYPE | 88 | 80 | 85 |
Figure S82. Get High-res Image Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D60V5.png)
P value = 9.8e-05 (Fisher's exact test), Q value = 0.062
Table S83. Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 84 | 120 |
DEL PEAK 36(14Q32.32) CNV | 11 | 4 | 31 |
DEL PEAK 36(14Q32.32) WILD-TYPE | 84 | 80 | 89 |
Figure S83. Get High-res Image Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D60V6.png)
P value = 2.32e-06 (Fisher's exact test), Q value = 0.0015
Table S84. Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 5 | 93 | 92 | 125 |
DEL PEAK 36(14Q32.32) CNV | 0 | 28 | 3 | 15 |
DEL PEAK 36(14Q32.32) WILD-TYPE | 5 | 65 | 89 | 110 |
Figure S84. Get High-res Image Gene #60: 'Del Peak 36(14q32.32)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D60V10.png)
P value = 1.19e-06 (Chi-square test), Q value = 0.00079
Table S85. Gene #61: 'Del Peak 37(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 37(15Q15.1) CNV | 18 | 9 | 6 | 11 | 16 | 8 | 7 | 7 |
DEL PEAK 37(15Q15.1) WILD-TYPE | 68 | 47 | 71 | 20 | 60 | 10 | 2 | 8 |
Figure S85. Get High-res Image Gene #61: 'Del Peak 37(15q15.1)' versus Molecular Subtype #1: 'CN_CNMF'
![](D61V1.png)
P value = 4.05e-09 (Fisher's exact test), Q value = 2.8e-06
Table S86. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 38(16Q12.1) CNV | 7 | 38 | 7 |
DEL PEAK 38(16Q12.1) WILD-TYPE | 92 | 68 | 94 |
Figure S86. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D62V2.png)
P value = 7.1e-08 (Fisher's exact test), Q value = 4.8e-05
Table S87. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 118 | 91 | 90 |
DEL PEAK 38(16Q12.1) CNV | 38 | 9 | 4 |
DEL PEAK 38(16Q12.1) WILD-TYPE | 80 | 82 | 86 |
Figure S87. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D62V5.png)
P value = 3.91e-07 (Fisher's exact test), Q value = 0.00026
Table S88. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 84 | 120 |
DEL PEAK 38(16Q12.1) CNV | 7 | 6 | 38 |
DEL PEAK 38(16Q12.1) WILD-TYPE | 88 | 78 | 82 |
Figure S88. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D62V6.png)
P value = 0.000157 (Fisher's exact test), Q value = 0.098
Table S89. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 134 | 104 |
DEL PEAK 38(16Q12.1) CNV | 15 | 38 | 9 |
DEL PEAK 38(16Q12.1) WILD-TYPE | 98 | 96 | 95 |
Figure S89. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
![](D62V7.png)
P value = 8.88e-06 (Fisher's exact test), Q value = 0.0058
Table S90. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 117 | 96 |
DEL PEAK 38(16Q12.1) CNV | 8 | 35 | 9 |
DEL PEAK 38(16Q12.1) WILD-TYPE | 94 | 82 | 87 |
Figure S90. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D62V9.png)
P value = 3.44e-05 (Fisher's exact test), Q value = 0.022
Table S91. Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 5 | 93 | 92 | 125 |
DEL PEAK 38(16Q12.1) CNV | 1 | 30 | 8 | 13 |
DEL PEAK 38(16Q12.1) WILD-TYPE | 4 | 63 | 84 | 112 |
Figure S91. Get High-res Image Gene #62: 'Del Peak 38(16q12.1)' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D62V10.png)
P value = 1.86e-05 (Fisher's exact test), Q value = 0.012
Table S92. Gene #63: 'Del Peak 39(16q23.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 39(16Q23.3) CNV | 11 | 37 | 13 |
DEL PEAK 39(16Q23.3) WILD-TYPE | 88 | 69 | 88 |
Figure S92. Get High-res Image Gene #63: 'Del Peak 39(16q23.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D63V2.png)
P value = 8.88e-05 (Fisher's exact test), Q value = 0.056
Table S93. Gene #63: 'Del Peak 39(16q23.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 95 | 84 | 120 |
DEL PEAK 39(16Q23.3) CNV | 11 | 9 | 38 |
DEL PEAK 39(16Q23.3) WILD-TYPE | 84 | 75 | 82 |
Figure S93. Get High-res Image Gene #63: 'Del Peak 39(16q23.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D63V6.png)
P value = 3.89e-20 (Chi-square test), Q value = 2.7e-17
Table S94. Gene #65: 'Del Peak 41(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 41(18Q21.2) CNV | 57 | 24 | 7 | 11 | 62 | 13 | 9 | 8 |
DEL PEAK 41(18Q21.2) WILD-TYPE | 29 | 32 | 70 | 20 | 14 | 5 | 0 | 7 |
Figure S94. Get High-res Image Gene #65: 'Del Peak 41(18q21.2)' versus Molecular Subtype #1: 'CN_CNMF'
![](D65V1.png)
P value = 0.00016 (Fisher's exact test), Q value = 0.1
Table S95. Gene #65: 'Del Peak 41(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 41(18Q21.2) CNV | 66 | 40 | 55 |
DEL PEAK 41(18Q21.2) WILD-TYPE | 33 | 66 | 46 |
Figure S95. Get High-res Image Gene #65: 'Del Peak 41(18q21.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D65V2.png)
P value = 1.08e-22 (Chi-square test), Q value = 7.6e-20
Table S96. Gene #66: 'Del Peak 42(18q23)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 42(18Q23) CNV | 62 | 30 | 7 | 11 | 66 | 13 | 8 | 10 |
DEL PEAK 42(18Q23) WILD-TYPE | 24 | 26 | 70 | 20 | 10 | 5 | 1 | 5 |
Figure S96. Get High-res Image Gene #66: 'Del Peak 42(18q23)' versus Molecular Subtype #1: 'CN_CNMF'
![](D66V1.png)
P value = 0.000105 (Chi-square test), Q value = 0.066
Table S97. Gene #67: 'Del Peak 43(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 43(19P13.3) CNV | 39 | 19 | 6 | 11 | 27 | 7 | 4 | 6 |
DEL PEAK 43(19P13.3) WILD-TYPE | 47 | 37 | 71 | 20 | 49 | 11 | 5 | 9 |
Figure S97. Get High-res Image Gene #67: 'Del Peak 43(19p13.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D67V1.png)
P value = 8.73e-06 (Chi-square test), Q value = 0.0057
Table S98. Gene #68: 'Del Peak 44(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 44(19Q13.43) CNV | 20 | 19 | 3 | 2 | 15 | 2 | 2 | 8 |
DEL PEAK 44(19Q13.43) WILD-TYPE | 66 | 37 | 74 | 29 | 61 | 16 | 7 | 7 |
Figure S98. Get High-res Image Gene #68: 'Del Peak 44(19q13.43)' versus Molecular Subtype #1: 'CN_CNMF'
![](D68V1.png)
P value = 2.14e-07 (Chi-square test), Q value = 0.00014
Table S99. Gene #69: 'Del Peak 45(Xp21.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 45(XP21.3) CNV | 36 | 25 | 9 | 3 | 24 | 9 | 4 | 11 |
DEL PEAK 45(XP21.3) WILD-TYPE | 50 | 31 | 68 | 28 | 52 | 9 | 5 | 4 |
Figure S99. Get High-res Image Gene #69: 'Del Peak 45(Xp21.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D69V1.png)
P value = 1.29e-08 (Chi-square test), Q value = 8.7e-06
Table S100. Gene #70: 'Del Peak 46(Xp11.3)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 46(XP11.3) CNV | 37 | 26 | 8 | 2 | 23 | 7 | 5 | 11 |
DEL PEAK 46(XP11.3) WILD-TYPE | 49 | 30 | 69 | 29 | 53 | 11 | 4 | 4 |
Figure S100. Get High-res Image Gene #70: 'Del Peak 46(Xp11.3)' versus Molecular Subtype #1: 'CN_CNMF'
![](D70V1.png)
P value = 7.56e-07 (Chi-square test), Q value = 0.00051
Table S101. Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 86 | 56 | 77 | 31 | 76 | 18 | 9 | 15 |
DEL PEAK 47(XQ21.33) CNV | 23 | 20 | 4 | 0 | 8 | 1 | 0 | 3 |
DEL PEAK 47(XQ21.33) WILD-TYPE | 63 | 36 | 73 | 31 | 68 | 17 | 9 | 12 |
Figure S101. Get High-res Image Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #1: 'CN_CNMF'
![](D71V1.png)
P value = 0.000338 (Fisher's exact test), Q value = 0.21
Table S102. Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 99 | 106 | 101 |
DEL PEAK 47(XQ21.33) CNV | 21 | 26 | 6 |
DEL PEAK 47(XQ21.33) WILD-TYPE | 78 | 80 | 95 |
Figure S102. Get High-res Image Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D71V2.png)
P value = 2.36e-05 (Fisher's exact test), Q value = 0.015
Table S103. Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 113 | 134 | 104 |
DEL PEAK 47(XQ21.33) CNV | 11 | 37 | 8 |
DEL PEAK 47(XQ21.33) WILD-TYPE | 102 | 97 | 96 |
Figure S103. Get High-res Image Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
![](D71V7.png)
P value = 0.000164 (Fisher's exact test), Q value = 0.1
Table S104. Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 102 | 117 | 96 |
DEL PEAK 47(XQ21.33) CNV | 8 | 31 | 9 |
DEL PEAK 47(XQ21.33) WILD-TYPE | 94 | 86 | 87 |
Figure S104. Get High-res Image Gene #71: 'Del Peak 47(Xq21.33)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
![](D71V9.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 = HNSC-TP.transferedmergedcluster.txt
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Number of patients = 368
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Number of copy number variation regions = 71
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Number of molecular subtypes = 10
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Exclude regions that fewer than K tumors have alterations, K = 3
For 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 binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.