Correlation between copy number variation genes and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1JQ0ZCS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1JQ0ZCS
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 46 peak regions and 10 molecular subtypes across 197 patients, 61 significant findings detected with Q value < 0.25.

- Amp Peak 1(1q21.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 2(3q26.2) cnvs correlated to 'CN_CNMF'.

- Amp Peak 3(7p15.3) cnvs correlated to 'CN_CNMF'.

- Amp Peak 4(7q34) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- Amp Peak 5(8p11.22) cnvs correlated to 'CN_CNMF'.

- Amp Peak 6(8q24.21) cnvs correlated to 'CN_CNMF'.

- Amp Peak 7(9q34.3) cnvs correlated to 'CN_CNMF'.

- Amp Peak 8(11q13.2) cnvs correlated to 'CN_CNMF'.

- Amp Peak 11(20q13.33) cnvs correlated to 'METHLYATION_CNMF'.

- Del Peak 1(1p31.3) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 3(2q22.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- Del Peak 6(4q28.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 7(5q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 8(5q21.1) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 9(6q15) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 11(8p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- Del Peak 12(8p11.21) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- Del Peak 13(9p22.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 14(10q23.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 17(13q14.13) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 18(16q22.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 19(16q24.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 20(17p13.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- Del Peak 21(17q21.31) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- Del Peak 22(18q23) cnvs correlated to 'CN_CNMF'.

- Del Peak 25(21q22.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 46 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 61 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test
Del Peak 11(8p21 3) | 0 (0%) | 85 | 2.84e-06 (0.00124) | 5.31e-08 (2.36e-05) | 0.00364 (1.00) | 0.014 (1.00) | 1.79e-05 (0.00761) | 5.65e-06 (0.00243) | 3.79e-06 (0.00165) | 0.0246 (1.00) | 2.67e-06 (0.00116) | 0.00106 (0.416)
Del Peak 9(6q15) | 0 (0%) | 134 | 7.92e-13 (3.61e-10) | 3.43e-12 (1.56e-09) | 0.000189 (0.0775) | 0.0155 (1.00) | 1.11e-06 (0.000485) | 7.99e-07 (0.000352) | 0.000661 (0.262) | 0.00123 (0.477) | 0.00146 (0.56) | 0.504 (1.00)
Del Peak 25(21q22 3) | 0 (0%) | 133 | 1.11e-05 (0.00477) | 1.2e-11 (5.42e-09) | 0.105 (1.00) | 0.206 (1.00) | 3.79e-14 (1.73e-11) | 2.89e-10 (1.29e-07) | 0.307 (1.00) | 0.000581 (0.233) | 0.0469 (1.00) | 0.0516 (1.00)
Del Peak 14(10q23 31) | 0 (0%) | 128 | 3.88e-06 (0.00168) | 1.03e-06 (0.000451) | 0.0971 (1.00) | 0.222 (1.00) | 1.68e-10 (7.55e-08) | 6.28e-06 (0.0027) | 0.143 (1.00) | 0.0922 (1.00) | 0.00339 (1.00) | 0.193 (1.00)
Del Peak 17(13q14 13) | 0 (0%) | 108 | 0.000107 (0.0443) | 1.23e-05 (0.00525) | 0.0975 (1.00) | 0.133 (1.00) | 6.55e-05 (0.0274) | 4.43e-05 (0.0186) | 0.122 (1.00) | 0.156 (1.00) | 0.28 (1.00) | 0.357 (1.00)
Amp Peak 4(7q34) | 0 (0%) | 162 | 8.59e-08 (3.8e-05) | 4.98e-05 (0.0209) | 0.655 (1.00) | 0.636 (1.00) | 0.000377 (0.151) | 0.00783 (1.00) | 0.0836 (1.00) | 0.00369 (1.00) | 0.0197 (1.00) | 0.385 (1.00)
Del Peak 3(2q22 1) | 0 (0%) | 173 | 5.22e-06 (0.00226) | 0.000289 (0.117) | 0.00293 (1.00) | 0.00946 (1.00) | 0.0533 (1.00) | 0.00705 (1.00) | 0.142 (1.00) | 0.000193 (0.0788) | 0.00697 (1.00) | 0.00487 (1.00)
Del Peak 12(8p11 21) | 0 (0%) | 135 | 0.000318 (0.129) | 2.71e-05 (0.0114) | 0.82 (1.00) | 0.709 (1.00) | 0.000359 (0.145) | 0.00678 (1.00) | 0.00119 (0.461) | 0.568 (1.00) | 0.000893 (0.351) | 0.0518 (1.00)
Del Peak 20(17p13 1) | 0 (0%) | 143 | 5.83e-11 (2.63e-08) | 0.0408 (1.00) | 0.0139 (1.00) | 0.0164 (1.00) | 0.00218 (0.821) | 2.25e-05 (0.00951) | 0.0427 (1.00) | 0.00109 (0.424) | 0.00037 (0.149) | 0.88 (1.00)
Del Peak 21(17q21 31) | 0 (0%) | 158 | 0.000171 (0.0701) | 2.19e-06 (0.000961) | 0.514 (1.00) | 0.877 (1.00) | 1.42e-05 (0.00604) | 0.00159 (0.61) | 0.029 (1.00) | 0.217 (1.00) | 0.0354 (1.00) | 0.699 (1.00)
Amp Peak 1(1q21 3) | 0 (0%) | 180 | 1.87e-05 (0.00792) | 0.00184 (0.7) | 0.000652 (0.259) | 0.00838 (1.00) | 0.00458 (1.00) | 0.000216 (0.0881) | 0.102 (1.00) | 0.053 (1.00) | 0.00541 (1.00) | 0.938 (1.00)
Del Peak 1(1p31 3) | 0 (0%) | 172 | 0.0688 (1.00) | 0.000156 (0.0643) | 0.558 (1.00) | 0.823 (1.00) | 0.00196 (0.741) | 7.24e-05 (0.0302) | 0.0707 (1.00) | 0.142 (1.00) | 0.0819 (1.00) | 0.367 (1.00)
Del Peak 6(4q28 2) | 0 (0%) | 178 | 4.46e-06 (0.00193) | 3.26e-05 (0.0137) | 0.0725 (1.00) | 0.0645 (1.00) | 0.00745 (1.00) | 0.0479 (1.00) | 0.0933 (1.00) | 0.06 (1.00) | 0.00192 (0.728) | 0.243 (1.00)
Del Peak 7(5q11 2) | 0 (0%) | 164 | 0.000606 (0.242) | 0.000121 (0.0499) | 0.00256 (0.955) | 0.0144 (1.00) | 0.0289 (1.00) | 0.00272 (1.00) | 0.0789 (1.00) | 0.0213 (1.00) | 0.309 (1.00) | 0.717 (1.00)
Del Peak 8(5q21 1) | 0 (0%) | 162 | 1.08e-11 (4.89e-09) | 5.81e-09 (2.59e-06) | 0.1 (1.00) | 0.123 (1.00) | 0.00346 (1.00) | 0.00889 (1.00) | 0.0293 (1.00) | 0.136 (1.00) | 0.274 (1.00) | 0.527 (1.00)
Del Peak 18(16q22 3) | 0 (0%) | 133 | 4.34e-12 (1.97e-09) | 0.003 (1.00) | 0.728 (1.00) | 0.285 (1.00) | 0.00203 (0.767) | 7.67e-05 (0.0319) | 0.0942 (1.00) | 0.00492 (1.00) | 0.0152 (1.00) | 0.382 (1.00)
Amp Peak 2(3q26 2) | 0 (0%) | 166 | 0.000195 (0.0794) | 0.0744 (1.00) | 0.0468 (1.00) | 0.158 (1.00) | 0.169 (1.00) | 0.147 (1.00) | 0.29 (1.00) | 0.0477 (1.00) | 0.00644 (1.00) | 0.27 (1.00)
Amp Peak 3(7p15 3) | 0 (0%) | 159 | 3.35e-09 (1.5e-06) | 0.0014 (0.539) | 0.245 (1.00) | 0.274 (1.00) | 0.0016 (0.611) | 0.0309 (1.00) | 0.246 (1.00) | 0.00724 (1.00) | 0.0309 (1.00) | 0.393 (1.00)
Amp Peak 5(8p11 22) | 0 (0%) | 177 | 7.39e-08 (3.27e-05) | 0.0674 (1.00) | 0.191 (1.00) | 0.186 (1.00) | 0.0195 (1.00) | 0.0317 (1.00) | 0.22 (1.00) | 0.0749 (1.00) | 0.0152 (1.00) | 0.533 (1.00)
Amp Peak 6(8q24 21) | 0 (0%) | 145 | 5.34e-12 (2.42e-09) | 0.0438 (1.00) | 0.0177 (1.00) | 0.014 (1.00) | 0.00243 (0.907) | 0.00132 (0.509) | 0.0744 (1.00) | 0.0193 (1.00) | 0.00265 (0.987) | 0.589 (1.00)
Amp Peak 7(9q34 3) | 0 (0%) | 177 | 7.37e-06 (0.00316) | 0.171 (1.00) | 0.0866 (1.00) | 0.0639 (1.00) | 0.535 (1.00) | 0.166 (1.00) | 0.183 (1.00) | 0.0303 (1.00) | 0.132 (1.00) | 0.634 (1.00)
Amp Peak 8(11q13 2) | 0 (0%) | 185 | 0.000532 (0.214) | 0.134 (1.00) | 0.476 (1.00) | 0.35 (1.00) | 0.05 (1.00) | 0.222 (1.00) | 0.999 (1.00) | 0.259 (1.00) | 0.504 (1.00) | 0.631 (1.00)
Amp Peak 11(20q13 33) | 0 (0%) | 184 | 0.013 (1.00) | 0.000612 (0.244) | 0.561 (1.00) | 0.652 (1.00) | 0.0263 (1.00) | 0.0102 (1.00) | 0.992 (1.00) | 0.0977 (1.00) | 0.656 (1.00) | 0.856 (1.00)
Del Peak 13(9p22 3) | 0 (0%) | 181 | 9.6e-05 (0.0398) | 0.412 (1.00) | 0.00509 (1.00) | 0.00622 (1.00) | 0.131 (1.00) | 0.021 (1.00) | 0.711 (1.00) | 0.615 (1.00) | 0.726 (1.00) | 0.756 (1.00)
Del Peak 19(16q24 1) | 0 (0%) | 119 | 8.31e-16 (3.8e-13) | 0.00124 (0.481) | 0.855 (1.00) | 0.658 (1.00) | 0.00957 (1.00) | 0.00428 (1.00) | 0.107 (1.00) | 0.00996 (1.00) | 0.0113 (1.00) | 0.366 (1.00)
Del Peak 22(18q23) | 0 (0%) | 142 | 6.8e-08 (3.02e-05) | 0.571 (1.00) | 0.974 (1.00) | 0.69 (1.00) | 0.143 (1.00) | 0.142 (1.00) | 0.673 (1.00) | 0.958 (1.00) | 0.582 (1.00) | 0.632 (1.00)
Amp Peak 9(12q24 32) | 0 (0%) | 190 | 0.0109 (1.00) | 0.233 (1.00) | 0.231 (1.00) | 0.229 (1.00) | 1 (1.00) | 0.108 (1.00) | 0.498 (1.00) | 0.534 (1.00) | 0.216 (1.00) | 0.116 (1.00)
Amp Peak 10(14q21 1) | 0 (0%) | 185 | 0.00112 (0.437) | 0.0152 (1.00) | 0.139 (1.00) | 0.104 (1.00) | 0.000723 (0.286) | 0.19 (1.00) | 0.139 (1.00) | 0.00416 (1.00) | 0.166 (1.00) | 0.64 (1.00)
Amp Peak 12(Xp22 11) | 0 (0%) | 190 | 0.0787 (1.00) | 1 (1.00) |  |  | 0.4 (1.00) | 0.796 (1.00) | 0.159 (1.00) | 0.0234 (1.00) | 0.0441 (1.00) | 0.0328 (1.00)
Amp Peak 13(Xp22 11) | 0 (0%) | 190 | 0.0787 (1.00) | 0.891 (1.00) | 0.126 (1.00) | 0.322 (1.00) | 0.511 (1.00) | 0.796 (1.00) | 0.0374 (1.00) | 0.193 (1.00) | 0.235 (1.00) | 0.351 (1.00)
Amp Peak 14(Xp21 1) | 0 (0%) | 191 | 0.186 (1.00) | 0.188 (1.00) | 0.636 (1.00) | 0.628 (1.00) | 0.874 (1.00) | 0.766 (1.00) | 0.178 (1.00) | 0.254 (1.00) | 0.117 (1.00) | 0.147 (1.00)
Amp Peak 15(Xq12) | 0 (0%) | 193 | 0.187 (1.00) | 0.105 (1.00) | 0.561 (1.00) | 0.46 (1.00) | 0.0353 (1.00) | 0.178 (1.00) | 0.532 (1.00) | 0.307 (1.00) | 0.00709 (1.00) | 0.789 (1.00)
Amp Peak 16(Xq21 1) | 0 (0%) | 190 | 0.038 (1.00) | 0.138 (1.00) | 0.488 (1.00) | 0.497 (1.00) | 0.181 (1.00) | 0.381 (1.00) | 0.0822 (1.00) | 0.727 (1.00) | 0.288 (1.00) | 0.248 (1.00)
Amp Peak 17(Xq21 1) | 0 (0%) | 192 | 0.171 (1.00) | 0.00178 (0.679) | 0.452 (1.00) | 1 (1.00) | 0.624 (1.00) | 0.63 (1.00) | 0.815 (1.00) | 0.847 (1.00) | 0.769 (1.00) | 1 (1.00)
Amp Peak 18(Xq21 31) | 0 (0%) | 192 | 0.0598 (1.00) | 0.86 (1.00) | 0.636 (1.00) | 0.628 (1.00) | 0.376 (1.00) | 0.118 (1.00) | 0.548 (1.00) | 0.728 (1.00) | 0.553 (1.00) | 0.693 (1.00)
Amp Peak 19(Xq25) | 0 (0%) | 193 | 0.187 (1.00) | 0.254 (1.00) | 0.631 (1.00) | 1 (1.00) | 0.465 (1.00) | 1 (1.00) | 0.151 (1.00) | 0.152 (1.00) | 0.285 (1.00) | 0.19 (1.00)
Amp Peak 20(Xq25) | 0 (0%) | 191 | 0.42 (1.00) | 0.586 (1.00) | 0.88 (1.00) | 0.77 (1.00) | 0.169 (1.00) | 0.661 (1.00) | 0.794 (1.00) | 0.436 (1.00) | 0.423 (1.00) | 0.506 (1.00)
Amp Peak 21(Xq27 1) | 0 (0%) | 188 | 0.642 (1.00) | 0.292 (1.00) | 0.425 (1.00) | 0.347 (1.00) | 0.912 (1.00) | 0.91 (1.00) | 0.0178 (1.00) | 0.028 (1.00) | 0.0367 (1.00) | 0.0068 (1.00)
Del Peak 2(1q42 13) | 0 (0%) | 179 | 0.421 (1.00) | 0.00285 (1.00) | 0.875 (1.00) | 0.121 (1.00) | 0.711 (1.00) | 0.706 (1.00) | 0.0632 (1.00) | 0.471 (1.00) | 0.39 (1.00) | 0.256 (1.00)
Del Peak 4(3p13) | 0 (0%) | 168 | 0.359 (1.00) | 0.0162 (1.00) | 0.685 (1.00) | 0.96 (1.00) | 0.105 (1.00) | 0.107 (1.00) | 0.264 (1.00) | 0.883 (1.00) | 0.124 (1.00) | 0.0244 (1.00)
Del Peak 5(3q29) | 0 (0%) | 183 | 0.861 (1.00) | 0.0398 (1.00) | 0.846 (1.00) | 0.6 (1.00) | 0.0361 (1.00) | 0.315 (1.00) | 0.0462 (1.00) | 0.445 (1.00) | 0.129 (1.00) | 0.505 (1.00)
Del Peak 10(7q36 1) | 0 (0%) | 187 | 0.434 (1.00) | 0.781 (1.00) | 0.0761 (1.00) | 0.192 (1.00) | 0.779 (1.00) | 0.708 (1.00) | 0.731 (1.00) | 0.371 (1.00) | 0.945 (1.00) | 0.9 (1.00)
Del Peak 15(11q23 2) | 0 (0%) | 173 | 0.154 (1.00) | 0.0871 (1.00) | 0.198 (1.00) | 0.137 (1.00) | 0.482 (1.00) | 0.533 (1.00) | 0.423 (1.00) | 0.343 (1.00) | 0.123 (1.00) | 1 (1.00)
Del Peak 16(12p13 2) | 0 (0%) | 156 | 0.000725 (0.286) | 0.00299 (1.00) | 0.0701 (1.00) | 0.462 (1.00) | 0.274 (1.00) | 0.0569 (1.00) | 0.023 (1.00) | 0.357 (1.00) | 0.0507 (1.00) | 0.241 (1.00)
Del Peak 23(19q13 2) | 0 (0%) | 180 | 0.0305 (1.00) | 0.0513 (1.00) | 0.349 (1.00) | 0.392 (1.00) | 0.0658 (1.00) | 0.133 (1.00) | 0.103 (1.00) | 0.0196 (1.00) | 0.0152 (1.00) | 0.166 (1.00)
Del Peak 24(21q22 2) | 0 (0%) | 179 | 0.0662 (1.00) | 0.318 (1.00) | 0.508 (1.00) | 0.895 (1.00) | 0.0532 (1.00) | 0.00226 (0.847) | 0.784 (1.00) | 0.351 (1.00) | 0.749 (1.00) | 0.881 (1.00)

'Amp Peak 1(1q21.3)' versus 'CN_CNMF'

P value = 1.87e-05 (Fisher's exact test), Q value = 0.0079

Table S1. Gene #1: 'Amp Peak 1(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
AMP PEAK 1(1Q21.3) CNV | 1 | 2 | 14
AMP PEAK 1(1Q21.3) WILD-TYPE | 27 | 106 | 47

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1q21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 1(1q21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000216 (Fisher's exact test), Q value = 0.088

Table S2. Gene #1: 'Amp Peak 1(1q21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 68 | 77
AMP PEAK 1(1Q21.3) CNV | 6 | 11 | 0
AMP PEAK 1(1Q21.3) WILD-TYPE | 43 | 57 | 77

Figure S2. Get High-res Image Gene #1: 'Amp Peak 1(1q21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 2(3q26.2)' versus 'CN_CNMF'

P value = 0.000195 (Fisher's exact test), Q value = 0.079

Table S3. Gene #2: 'Amp Peak 2(3q26.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
AMP PEAK 2(3Q26.2) CNV | 6 | 7 | 18
AMP PEAK 2(3Q26.2) WILD-TYPE | 22 | 101 | 43

Figure S3. Get High-res Image Gene #2: 'Amp Peak 2(3q26.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 3(7p15.3)' versus 'CN_CNMF'

P value = 3.35e-09 (Fisher's exact test), Q value = 1.5e-06

Table S4. Gene #3: 'Amp Peak 3(7p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
AMP PEAK 3(7P15.3) CNV | 7 | 5 | 26
AMP PEAK 3(7P15.3) WILD-TYPE | 21 | 103 | 35

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(7p15.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(7q34)' versus 'CN_CNMF'

P value = 8.59e-08 (Fisher's exact test), Q value = 3.8e-05

Table S5. Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
AMP PEAK 4(7Q34) CNV | 7 | 5 | 23
AMP PEAK 4(7Q34) WILD-TYPE | 21 | 103 | 38

Figure S5. Get High-res Image Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 4(7q34)' versus 'METHLYATION_CNMF'

P value = 4.98e-05 (Fisher's exact test), Q value = 0.021

Table S6. Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
AMP PEAK 4(7Q34) CNV | 20 | 3 | 12
AMP PEAK 4(7Q34) WILD-TYPE | 37 | 62 | 63

Figure S6. Get High-res Image Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Amp Peak 4(7q34)' versus 'MRNASEQ_CNMF'

P value = 0.000377 (Fisher's exact test), Q value = 0.15

Table S7. Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 60 | 67
AMP PEAK 4(7Q34) CNV | 21 | 3 | 11
AMP PEAK 4(7Q34) WILD-TYPE | 46 | 57 | 56

Figure S7. Get High-res Image Gene #4: 'Amp Peak 4(7q34)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Amp Peak 5(8p11.22)' versus 'CN_CNMF'

P value = 7.39e-08 (Fisher's exact test), Q value = 3.3e-05

Table S8. Gene #5: 'Amp Peak 5(8p11.22)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
AMP PEAK 5(8P11.22) CNV | 6 | 0 | 14
AMP PEAK 5(8P11.22) WILD-TYPE | 22 | 108 | 47

Figure S8. Get High-res Image Gene #5: 'Amp Peak 5(8p11.22)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 6(8q24.21)' versus 'CN_CNMF'

P value = 5.34e-12 (Fisher's exact test), Q value = 2.4e-09

Table S9. Gene #6: 'Amp Peak 6(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
AMP PEAK 6(8Q24.21) CNV | 7 | 9 | 36
AMP PEAK 6(8Q24.21) WILD-TYPE | 21 | 99 | 25

Figure S9. Get High-res Image Gene #6: 'Amp Peak 6(8q24.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 7(9q34.3)' versus 'CN_CNMF'

P value = 7.37e-06 (Fisher's exact test), Q value = 0.0032

Table S10. Gene #7: 'Amp Peak 7(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
AMP PEAK 7(9Q34.3) CNV | 1 | 3 | 16
AMP PEAK 7(9Q34.3) WILD-TYPE | 27 | 105 | 45

Figure S10. Get High-res Image Gene #7: 'Amp Peak 7(9q34.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 8(11q13.2)' versus 'CN_CNMF'

P value = 0.000532 (Fisher's exact test), Q value = 0.21

Table S11. Gene #8: 'Amp Peak 8(11q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
AMP PEAK 8(11Q13.2) CNV | 0 | 2 | 10
AMP PEAK 8(11Q13.2) WILD-TYPE | 28 | 106 | 51

Figure S11. Get High-res Image Gene #8: 'Amp Peak 8(11q13.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Amp Peak 11(20q13.33)' versus 'METHLYATION_CNMF'

P value = 0.000612 (Fisher's exact test), Q value = 0.24

Table S12. Gene #11: 'Amp Peak 11(20q13.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
AMP PEAK 11(20Q13.33) CNV | 10 | 1 | 2
AMP PEAK 11(20Q13.33) WILD-TYPE | 47 | 64 | 73

Figure S12. Get High-res Image Gene #11: 'Amp Peak 11(20q13.33)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 1(1p31.3)' versus 'METHLYATION_CNMF'

P value = 0.000156 (Fisher's exact test), Q value = 0.064

Table S13. Gene #22: 'Del Peak 1(1p31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 1(1P31.3) CNV | 6 | 1 | 18
DEL PEAK 1(1P31.3) WILD-TYPE | 51 | 64 | 57

Figure S13. Get High-res Image Gene #22: 'Del Peak 1(1p31.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 1(1p31.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.24e-05 (Fisher's exact test), Q value = 0.03

Table S14. Gene #22: 'Del Peak 1(1p31.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 68 | 77
DEL PEAK 1(1P31.3) CNV | 5 | 18 | 2
DEL PEAK 1(1P31.3) WILD-TYPE | 44 | 50 | 75

Figure S14. Get High-res Image Gene #22: 'Del Peak 1(1p31.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 3(2q22.1)' versus 'CN_CNMF'

P value = 5.22e-06 (Fisher's exact test), Q value = 0.0023

Table S15. Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 3(2Q22.1) CNV | 9 | 3 | 12
DEL PEAK 3(2Q22.1) WILD-TYPE | 19 | 105 | 49

Figure S15. Get High-res Image Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 3(2q22.1)' versus 'METHLYATION_CNMF'

P value = 0.000289 (Fisher's exact test), Q value = 0.12

Table S16. Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 3(2Q22.1) CNV | 14 | 1 | 9
DEL PEAK 3(2Q22.1) WILD-TYPE | 43 | 64 | 66

Figure S16. Get High-res Image Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 3(2q22.1)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000193 (Fisher's exact test), Q value = 0.079

Table S17. Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 21 | 74 | 67
DEL PEAK 3(2Q22.1) CNV | 2 | 4 | 17 | 1
DEL PEAK 3(2Q22.1) WILD-TYPE | 32 | 17 | 57 | 66

Figure S17. Get High-res Image Gene #24: 'Del Peak 3(2q22.1)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 6(4q28.2)' versus 'CN_CNMF'

P value = 4.46e-06 (Fisher's exact test), Q value = 0.0019

Table S18. Gene #27: 'Del Peak 6(4q28.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 6(4Q28.2) CNV | 5 | 1 | 13
DEL PEAK 6(4Q28.2) WILD-TYPE | 23 | 107 | 48

Figure S18. Get High-res Image Gene #27: 'Del Peak 6(4q28.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 6(4q28.2)' versus 'METHLYATION_CNMF'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.014

Table S19. Gene #27: 'Del Peak 6(4q28.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 6(4Q28.2) CNV | 13 | 0 | 6
DEL PEAK 6(4Q28.2) WILD-TYPE | 44 | 65 | 69

Figure S19. Get High-res Image Gene #27: 'Del Peak 6(4q28.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 7(5q11.2)' versus 'CN_CNMF'

P value = 0.000606 (Fisher's exact test), Q value = 0.24

Table S20. Gene #28: 'Del Peak 7(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 7(5Q11.2) CNV | 5 | 9 | 19
DEL PEAK 7(5Q11.2) WILD-TYPE | 23 | 99 | 42

Figure S20. Get High-res Image Gene #28: 'Del Peak 7(5q11.2)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 7(5q11.2)' versus 'METHLYATION_CNMF'

P value = 0.000121 (Fisher's exact test), Q value = 0.05

Table S21. Gene #28: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 7(5Q11.2) CNV | 17 | 2 | 14
DEL PEAK 7(5Q11.2) WILD-TYPE | 40 | 63 | 61

Figure S21. Get High-res Image Gene #28: 'Del Peak 7(5q11.2)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 8(5q21.1)' versus 'CN_CNMF'

P value = 1.08e-11 (Fisher's exact test), Q value = 4.9e-09

Table S22. Gene #29: 'Del Peak 8(5q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 8(5Q21.1) CNV | 14 | 2 | 19
DEL PEAK 8(5Q21.1) WILD-TYPE | 14 | 106 | 42

Figure S22. Get High-res Image Gene #29: 'Del Peak 8(5q21.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 8(5q21.1)' versus 'METHLYATION_CNMF'

P value = 5.81e-09 (Fisher's exact test), Q value = 2.6e-06

Table S23. Gene #29: 'Del Peak 8(5q21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 8(5Q21.1) CNV | 25 | 2 | 8
DEL PEAK 8(5Q21.1) WILD-TYPE | 32 | 63 | 67

Figure S23. Get High-res Image Gene #29: 'Del Peak 8(5q21.1)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 9(6q15)' versus 'CN_CNMF'

P value = 7.92e-13 (Fisher's exact test), Q value = 3.6e-10

Table S24. Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 9(6Q15) CNV | 21 | 12 | 30
DEL PEAK 9(6Q15) WILD-TYPE | 7 | 96 | 31

Figure S24. Get High-res Image Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 9(6q15)' versus 'METHLYATION_CNMF'

P value = 3.43e-12 (Fisher's exact test), Q value = 1.6e-09

Table S25. Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 9(6Q15) CNV | 36 | 3 | 24
DEL PEAK 9(6Q15) WILD-TYPE | 21 | 62 | 51

Figure S25. Get High-res Image Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 9(6q15)' versus 'RPPA_CNMF'

P value = 0.000189 (Fisher's exact test), Q value = 0.077

Table S26. Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 56 | 57
DEL PEAK 9(6Q15) CNV | 14 | 7 | 27
DEL PEAK 9(6Q15) WILD-TYPE | 27 | 49 | 30

Figure S26. Get High-res Image Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #3: 'RPPA_CNMF'

'Del Peak 9(6q15)' versus 'MRNASEQ_CNMF'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00049

Table S27. Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 60 | 67
DEL PEAK 9(6Q15) CNV | 35 | 6 | 22
DEL PEAK 9(6Q15) WILD-TYPE | 32 | 54 | 45

Figure S27. Get High-res Image Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 9(6q15)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.99e-07 (Fisher's exact test), Q value = 0.00035

Table S28. Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 68 | 77
DEL PEAK 9(6Q15) CNV | 25 | 29 | 9
DEL PEAK 9(6Q15) WILD-TYPE | 24 | 39 | 68

Figure S28. Get High-res Image Gene #30: 'Del Peak 9(6q15)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(8p21.3)' versus 'CN_CNMF'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.0012

Table S29. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 11(8P21.3) CNV | 10 | 52 | 50
DEL PEAK 11(8P21.3) WILD-TYPE | 18 | 56 | 11

Figure S29. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 11(8p21.3)' versus 'METHLYATION_CNMF'

P value = 5.31e-08 (Fisher's exact test), Q value = 2.4e-05

Table S30. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 11(8P21.3) CNV | 31 | 21 | 60
DEL PEAK 11(8P21.3) WILD-TYPE | 26 | 44 | 15

Figure S30. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 11(8p21.3)' versus 'MRNASEQ_CNMF'

P value = 1.79e-05 (Fisher's exact test), Q value = 0.0076

Table S31. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 60 | 67
DEL PEAK 11(8P21.3) CNV | 35 | 24 | 53
DEL PEAK 11(8P21.3) WILD-TYPE | 32 | 36 | 14

Figure S31. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 11(8p21.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.65e-06 (Fisher's exact test), Q value = 0.0024

Table S32. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 68 | 77
DEL PEAK 11(8P21.3) CNV | 23 | 55 | 34
DEL PEAK 11(8P21.3) WILD-TYPE | 26 | 13 | 43

Figure S32. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(8p21.3)' versus 'MIRSEQ_CNMF'

P value = 3.79e-06 (Chi-square test), Q value = 0.0016

Table S33. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 52 | 39 | 17 | 14 | 74
DEL PEAK 11(8P21.3) CNV | 42 | 14 | 8 | 2 | 45
DEL PEAK 11(8P21.3) WILD-TYPE | 10 | 25 | 9 | 12 | 29

Figure S33. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'Del Peak 11(8p21.3)' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.67e-06 (Chi-square test), Q value = 0.0012

Table S34. Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 73 | 18 | 12 | 15 | 78
DEL PEAK 11(8P21.3) CNV | 50 | 2 | 2 | 6 | 51
DEL PEAK 11(8P21.3) WILD-TYPE | 23 | 16 | 10 | 9 | 27

Figure S34. Get High-res Image Gene #32: 'Del Peak 11(8p21.3)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 12(8p11.21)' versus 'CN_CNMF'

P value = 0.000318 (Fisher's exact test), Q value = 0.13

Table S35. Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 12(8P11.21) CNV | 1 | 35 | 26
DEL PEAK 12(8P11.21) WILD-TYPE | 27 | 73 | 35

Figure S35. Get High-res Image Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 12(8p11.21)' versus 'METHLYATION_CNMF'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.011

Table S36. Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 12(8P11.21) CNV | 16 | 9 | 37
DEL PEAK 12(8P11.21) WILD-TYPE | 41 | 56 | 38

Figure S36. Get High-res Image Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 12(8p11.21)' versus 'MRNASEQ_CNMF'

P value = 0.000359 (Fisher's exact test), Q value = 0.15

Table S37. Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 60 | 67
DEL PEAK 12(8P11.21) CNV | 19 | 10 | 33
DEL PEAK 12(8P11.21) WILD-TYPE | 48 | 50 | 34

Figure S37. Get High-res Image Gene #33: 'Del Peak 12(8p11.21)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 13(9p22.3)' versus 'CN_CNMF'

P value = 9.6e-05 (Fisher's exact test), Q value = 0.04

Table S38. Gene #34: 'Del Peak 13(9p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 13(9P22.3) CNV | 0 | 3 | 13
DEL PEAK 13(9P22.3) WILD-TYPE | 28 | 105 | 48

Figure S38. Get High-res Image Gene #34: 'Del Peak 13(9p22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(10q23.31)' versus 'CN_CNMF'

P value = 3.88e-06 (Fisher's exact test), Q value = 0.0017

Table S39. Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 14(10Q23.31) CNV | 6 | 26 | 37
DEL PEAK 14(10Q23.31) WILD-TYPE | 22 | 82 | 24

Figure S39. Get High-res Image Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 14(10q23.31)' versus 'METHLYATION_CNMF'

P value = 1.03e-06 (Fisher's exact test), Q value = 0.00045

Table S40. Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 14(10Q23.31) CNV | 15 | 11 | 43
DEL PEAK 14(10Q23.31) WILD-TYPE | 42 | 54 | 32

Figure S40. Get High-res Image Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 14(10q23.31)' versus 'MRNASEQ_CNMF'

P value = 1.68e-10 (Fisher's exact test), Q value = 7.5e-08

Table S41. Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 60 | 67
DEL PEAK 14(10Q23.31) CNV | 15 | 9 | 45
DEL PEAK 14(10Q23.31) WILD-TYPE | 52 | 51 | 22

Figure S41. Get High-res Image Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 14(10q23.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.28e-06 (Fisher's exact test), Q value = 0.0027

Table S42. Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 68 | 77
DEL PEAK 14(10Q23.31) CNV | 11 | 40 | 18
DEL PEAK 14(10Q23.31) WILD-TYPE | 38 | 28 | 59

Figure S42. Get High-res Image Gene #35: 'Del Peak 14(10q23.31)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(13q14.13)' versus 'CN_CNMF'

P value = 0.000107 (Fisher's exact test), Q value = 0.044

Table S43. Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 17(13Q14.13) CNV | 17 | 34 | 38
DEL PEAK 17(13Q14.13) WILD-TYPE | 11 | 74 | 23

Figure S43. Get High-res Image Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 17(13q14.13)' versus 'METHLYATION_CNMF'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.0053

Table S44. Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 17(13Q14.13) CNV | 33 | 14 | 42
DEL PEAK 17(13Q14.13) WILD-TYPE | 24 | 51 | 33

Figure S44. Get High-res Image Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 17(13q14.13)' versus 'MRNASEQ_CNMF'

P value = 6.55e-05 (Fisher's exact test), Q value = 0.027

Table S45. Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 60 | 67
DEL PEAK 17(13Q14.13) CNV | 33 | 14 | 41
DEL PEAK 17(13Q14.13) WILD-TYPE | 34 | 46 | 26

Figure S45. Get High-res Image Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 17(13q14.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.43e-05 (Fisher's exact test), Q value = 0.019

Table S46. Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 68 | 77
DEL PEAK 17(13Q14.13) CNV | 27 | 41 | 20
DEL PEAK 17(13Q14.13) WILD-TYPE | 22 | 27 | 57

Figure S46. Get High-res Image Gene #38: 'Del Peak 17(13q14.13)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 18(16q22.3)' versus 'CN_CNMF'

P value = 4.34e-12 (Fisher's exact test), Q value = 2e-09

Table S47. Gene #39: 'Del Peak 18(16q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 18(16Q22.3) CNV | 4 | 18 | 42
DEL PEAK 18(16Q22.3) WILD-TYPE | 24 | 90 | 19

Figure S47. Get High-res Image Gene #39: 'Del Peak 18(16q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 18(16q22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.67e-05 (Fisher's exact test), Q value = 0.032

Table S48. Gene #39: 'Del Peak 18(16q22.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 68 | 77
DEL PEAK 18(16Q22.3) CNV | 9 | 36 | 19
DEL PEAK 18(16Q22.3) WILD-TYPE | 40 | 32 | 58

Figure S48. Get High-res Image Gene #39: 'Del Peak 18(16q22.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 19(16q24.1)' versus 'CN_CNMF'

P value = 8.31e-16 (Fisher's exact test), Q value = 3.8e-13

Table S49. Gene #40: 'Del Peak 19(16q24.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 19(16Q24.1) CNV | 4 | 24 | 50
DEL PEAK 19(16Q24.1) WILD-TYPE | 24 | 84 | 11

Figure S49. Get High-res Image Gene #40: 'Del Peak 19(16q24.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(17p13.1)' versus 'CN_CNMF'

P value = 5.83e-11 (Fisher's exact test), Q value = 2.6e-08

Table S50. Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 20(17P13.1) CNV | 3 | 14 | 37
DEL PEAK 20(17P13.1) WILD-TYPE | 25 | 94 | 24

Figure S50. Get High-res Image Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 20(17p13.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.0095

Table S51. Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 68 | 77
DEL PEAK 20(17P13.1) CNV | 8 | 33 | 13
DEL PEAK 20(17P13.1) WILD-TYPE | 41 | 35 | 64

Figure S51. Get High-res Image Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 20(17p13.1)' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Chi-square test), Q value = 0.15

Table S52. Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 73 | 18 | 12 | 15 | 78
DEL PEAK 20(17P13.1) CNV | 20 | 1 | 0 | 10 | 22
DEL PEAK 20(17P13.1) WILD-TYPE | 53 | 17 | 12 | 5 | 56

Figure S52. Get High-res Image Gene #41: 'Del Peak 20(17p13.1)' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'Del Peak 21(17q21.31)' versus 'CN_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.07

Table S53. Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 21(17Q21.31) CNV | 2 | 14 | 23
DEL PEAK 21(17Q21.31) WILD-TYPE | 26 | 94 | 38

Figure S53. Get High-res Image Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 21(17q21.31)' versus 'METHLYATION_CNMF'

P value = 2.19e-06 (Fisher's exact test), Q value = 0.00096

Table S54. Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 21(17Q21.31) CNV | 4 | 6 | 29
DEL PEAK 21(17Q21.31) WILD-TYPE | 53 | 59 | 46

Figure S54. Get High-res Image Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 21(17q21.31)' versus 'MRNASEQ_CNMF'

P value = 1.42e-05 (Fisher's exact test), Q value = 0.006

Table S55. Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 60 | 67
DEL PEAK 21(17Q21.31) CNV | 9 | 4 | 26
DEL PEAK 21(17Q21.31) WILD-TYPE | 58 | 56 | 41

Figure S55. Get High-res Image Gene #42: 'Del Peak 21(17q21.31)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 22(18q23)' versus 'CN_CNMF'

P value = 6.8e-08 (Fisher's exact test), Q value = 3e-05

Table S56. Gene #43: 'Del Peak 22(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 22(18Q23) CNV | 3 | 18 | 34
DEL PEAK 22(18Q23) WILD-TYPE | 25 | 90 | 27

Figure S56. Get High-res Image Gene #43: 'Del Peak 22(18q23)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(21q22.3)' versus 'CN_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0048

Table S57. Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 108 | 61
DEL PEAK 25(21Q22.3) CNV | 1 | 32 | 31
DEL PEAK 25(21Q22.3) WILD-TYPE | 27 | 76 | 30

Figure S57. Get High-res Image Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #1: 'CN_CNMF'

'Del Peak 25(21q22.3)' versus 'METHLYATION_CNMF'

P value = 1.2e-11 (Fisher's exact test), Q value = 5.4e-09

Table S58. Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 57 | 65 | 75
DEL PEAK 25(21Q22.3) CNV | 7 | 10 | 47
DEL PEAK 25(21Q22.3) WILD-TYPE | 50 | 55 | 28

Figure S58. Get High-res Image Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'Del Peak 25(21q22.3)' versus 'MRNASEQ_CNMF'

P value = 3.79e-14 (Fisher's exact test), Q value = 1.7e-11

Table S59. Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 67 | 60 | 67
DEL PEAK 25(21Q22.3) CNV | 6 | 12 | 46
DEL PEAK 25(21Q22.3) WILD-TYPE | 61 | 48 | 21

Figure S59. Get High-res Image Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'Del Peak 25(21q22.3)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.89e-10 (Fisher's exact test), Q value = 1.3e-07

Table S60. Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 68 | 77
DEL PEAK 25(21Q22.3) CNV | 2 | 40 | 22
DEL PEAK 25(21Q22.3) WILD-TYPE | 47 | 28 | 55

Figure S60. Get High-res Image Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 25(21q22.3)' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000581 (Fisher's exact test), Q value = 0.23

Table S61. Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 34 | 21 | 74 | 67
DEL PEAK 25(21Q22.3) CNV | 4 | 13 | 20 | 26
DEL PEAK 25(21Q22.3) WILD-TYPE | 30 | 8 | 54 | 41

Figure S61. Get High-res Image Gene #46: 'Del Peak 25(21q22.3)' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

- Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

- Molecular subtype file = PRAD-TP.transferedmergedcluster.txt

- Number of patients = 197

- Number of copy number variation regions = 46

- Number of molecular subtypes = 10

- Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

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

Chi-square test

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

Q value calculation

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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
[4] GISTIC_version2
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