Correlation between copy number variation genes and molecular subtypes
Colon Adenocarcinoma (Primary solid tumor)
21 April 2013 | analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C12F7KCS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Colon Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C12F7KCS
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 68 peak regions and 10 molecular subtypes across 413 patients, 150 significant findings detected with Q value < 0.25.

- Amp Peak 1(2q33.1) cnvs correlated to 'CN_CNMF'.

- Amp Peak 2(5p13.2) cnvs correlated to 'CN_CNMF'.

- Amp Peak 4(6p21.1) cnvs correlated to 'CN_CNMF'.

- Amp Peak 5(8p11.23) cnvs correlated to 'CN_CNMF'.

- Amp Peak 6(8p11.21) cnvs correlated to 'CN_CNMF'.

- Amp Peak 7(8q12.1) cnvs correlated to 'CN_CNMF'.

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

- Amp Peak 9(11p15.5) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

- Amp Peak 11(13q12.13) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 12(13q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 13(16p11.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.

- Amp Peak 14(16q12.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

- Amp Peak 15(17q12) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- Amp Peak 16(17q24.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- Amp Peak 17(19p13.2) cnvs correlated to 'CN_CNMF'.

- Amp Peak 19(20p12.3) cnvs correlated to 'CN_CNMF'.

- Amp Peak 20(20p11.23) cnvs correlated to 'CN_CNMF'.

- Amp Peak 21(20p11.21) cnvs correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 22(20q11.21) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 23(20q12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Amp Peak 24(20q13.32) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 1(1p36.11) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', and 'MRNASEQ_CNMF'.

- Del Peak 2(1p33) cnvs correlated to 'CN_CNMF'.

- Del Peak 3(1p13.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 4(1q43) cnvs correlated to 'CN_CNMF'.

- Del Peak 6(3p26.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 9(4p16.2) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 10(4q22.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 11(4q35.1) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- Del Peak 12(5q11.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 13(5q21.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 14(5q23.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 15(6p25.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 18(8p23.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- Del Peak 19(8p22) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.

- Del Peak 20(8p11.22) cnvs correlated to 'CN_CNMF'.

- Del Peak 21(8p11.21) cnvs correlated to 'CN_CNMF'.

- Del Peak 22(9p21.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 23(10p15.3) cnvs correlated to 'CN_CNMF'.

- Del Peak 24(10q21.1) cnvs correlated to 'CN_CNMF'.

- Del Peak 25(10q23.31) cnvs correlated to 'CN_CNMF'.

- Del Peak 26(10q25.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 27(12p13.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 28(13q14.13) cnvs correlated to 'CN_CNMF'.

- Del Peak 29(14q32.11) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CNMF'.

- Del Peak 30(15q11.2) cnvs correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 31(15q21.1) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 32(15q22.33) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 35(17p12) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 37(18p11.31) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 38(18q12.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 39(18q21.2) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 40(18q22.1) cnvs correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- Del Peak 42(20p12.1) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- Del Peak 43(21q11.2) cnvs correlated to 'CN_CNMF'.

- Del Peak 44(22q13.32) cnvs correlated to 'MRNA_CNMF' and 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 68 regions and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 150 significant findings detected.

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

'Amp Peak 1(2q33.1)' versus 'CN_CNMF'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.017

Table S1. Gene #1: 'Amp Peak 1(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 1(2Q33.1) CNV | 49 | 18 | 8 | 4
AMP PEAK 1(2Q33.1) WILD-TYPE | 121 | 169 | 24 | 20

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(2q33.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 2(5p13.2)' versus 'CN_CNMF'

P value = 0.000202 (Fisher's exact test), Q value = 0.11

Table S2. Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 2(5P13.2) CNV | 46 | 20 | 10 | 5
AMP PEAK 2(5P13.2) WILD-TYPE | 124 | 167 | 22 | 19

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(5p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 4(6p21.1)' versus 'CN_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.1e-06

Table S3. Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 4(6P21.1) CNV | 61 | 16 | 8 | 4
AMP PEAK 4(6P21.1) WILD-TYPE | 109 | 171 | 24 | 20

Figure S3. Get High-res Image Gene #4: 'Amp Peak 4(6p21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 5(8p11.23)' versus 'CN_CNMF'

P value = 2.99e-13 (Fisher's exact test), Q value = 1.9e-10

Table S4. Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 5(8P11.23) CNV | 56 | 47 | 17 | 24
AMP PEAK 5(8P11.23) WILD-TYPE | 114 | 140 | 15 | 0

Figure S4. Get High-res Image Gene #5: 'Amp Peak 5(8p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 6(8p11.21)' versus 'CN_CNMF'

P value = 4.51e-10 (Fisher's exact test), Q value = 2.8e-07

Table S5. Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 6(8P11.21) CNV | 75 | 55 | 21 | 22
AMP PEAK 6(8P11.21) WILD-TYPE | 95 | 132 | 11 | 2

Figure S5. Get High-res Image Gene #6: 'Amp Peak 6(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 7(8q12.1)' versus 'CN_CNMF'

P value = 9.31e-12 (Fisher's exact test), Q value = 5.9e-09

Table S6. Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 7(8Q12.1) CNV | 106 | 64 | 23 | 22
AMP PEAK 7(8Q12.1) WILD-TYPE | 64 | 123 | 9 | 2

Figure S6. Get High-res Image Gene #7: 'Amp Peak 7(8q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 7.86e-14 (Fisher's exact test), Q value = 5.1e-11

Table S7. Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 8(8Q24.21) CNV | 119 | 73 | 23 | 24
AMP PEAK 8(8Q24.21) WILD-TYPE | 51 | 114 | 9 | 0

Figure S7. Get High-res Image Gene #8: 'Amp Peak 8(8q24.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 9(11p15.5)' versus 'MRNA_CNMF'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0079

Table S8. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
AMP PEAK 9(11P15.5) CNV | 1 | 17 | 3 | 13
AMP PEAK 9(11P15.5) WILD-TYPE | 30 | 45 | 27 | 10

Figure S8. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 9(11p15.5)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000201 (Fisher's exact test), Q value = 0.11

Table S9. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
AMP PEAK 9(11P15.5) CNV | 14 | 2 | 18
AMP PEAK 9(11P15.5) WILD-TYPE | 42 | 42 | 28

Figure S9. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 9(11p15.5)' versus 'CN_CNMF'

P value = 1.54e-09 (Fisher's exact test), Q value = 9.5e-07

Table S10. Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 9(11P15.5) CNV | 54 | 17 | 14 | 1
AMP PEAK 9(11P15.5) WILD-TYPE | 116 | 170 | 18 | 23

Figure S10. Get High-res Image Gene #9: 'Amp Peak 9(11p15.5)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNA_CNMF'

P value = 7.21e-08 (Fisher's exact test), Q value = 4.3e-05

Table S11. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
AMP PEAK 11(13Q12.13) CNV | 14 | 52 | 8 | 18
AMP PEAK 11(13Q12.13) WILD-TYPE | 17 | 10 | 22 | 5

Figure S11. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNA_CHIERARCHICAL'

P value = 5.27e-06 (Fisher's exact test), Q value = 0.0031

Table S12. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
AMP PEAK 11(13Q12.13) CNV | 39 | 15 | 38
AMP PEAK 11(13Q12.13) WILD-TYPE | 17 | 29 | 8

Figure S12. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 11(13q12.13)' versus 'CN_CNMF'

P value = 5.04e-36 (Fisher's exact test), Q value = 3.4e-33

Table S13. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 11(13Q12.13) CNV | 158 | 57 | 18 | 17
AMP PEAK 11(13Q12.13) WILD-TYPE | 12 | 130 | 14 | 7

Figure S13. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 11(13q12.13)' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.15

Table S14. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
AMP PEAK 11(13Q12.13) CNV | 79 | 42 | 33
AMP PEAK 11(13Q12.13) WILD-TYPE | 26 | 44 | 30

Figure S14. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNASEQ_CNMF'

P value = 1.27e-06 (Fisher's exact test), Q value = 0.00075

Table S15. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
AMP PEAK 11(13Q12.13) CNV | 22 | 46 | 26 | 16
AMP PEAK 11(13Q12.13) WILD-TYPE | 9 | 13 | 21 | 38

Figure S15. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 11(13q12.13)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000196 (Fisher's exact test), Q value = 0.11

Table S16. Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
AMP PEAK 11(13Q12.13) CNV | 16 | 43 | 51
AMP PEAK 11(13Q12.13) WILD-TYPE | 33 | 19 | 29

Figure S16. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 12(13q22.1)' versus 'MRNA_CNMF'

P value = 6.34e-05 (Fisher's exact test), Q value = 0.036

Table S17. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
AMP PEAK 12(13Q22.1) CNV | 15 | 49 | 10 | 17
AMP PEAK 12(13Q22.1) WILD-TYPE | 16 | 13 | 20 | 6

Figure S17. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 5.43e-05 (Fisher's exact test), Q value = 0.031

Table S18. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
AMP PEAK 12(13Q22.1) CNV | 38 | 16 | 37
AMP PEAK 12(13Q22.1) WILD-TYPE | 18 | 28 | 9

Figure S18. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 12(13q22.1)' versus 'CN_CNMF'

P value = 7.2e-33 (Fisher's exact test), Q value = 4.8e-30

Table S19. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 12(13Q22.1) CNV | 158 | 63 | 17 | 16
AMP PEAK 12(13Q22.1) WILD-TYPE | 12 | 124 | 15 | 8

Figure S19. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNASEQ_CNMF'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00067

Table S20. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
AMP PEAK 12(13Q22.1) CNV | 22 | 49 | 25 | 19
AMP PEAK 12(13Q22.1) WILD-TYPE | 9 | 10 | 22 | 35

Figure S20. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 12(13q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.67e-05 (Fisher's exact test), Q value = 0.043

Table S21. Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
AMP PEAK 12(13Q22.1) CNV | 17 | 46 | 52
AMP PEAK 12(13Q22.1) WILD-TYPE | 32 | 16 | 28

Figure S21. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 13(16p11.2)' versus 'MRNA_CNMF'

P value = 0.000447 (Fisher's exact test), Q value = 0.24

Table S22. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
AMP PEAK 13(16P11.2) CNV | 5 | 23 | 3 | 13
AMP PEAK 13(16P11.2) WILD-TYPE | 26 | 39 | 27 | 10

Figure S22. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 13(16p11.2)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000375 (Fisher's exact test), Q value = 0.2

Table S23. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
AMP PEAK 13(16P11.2) CNV | 13 | 7 | 24
AMP PEAK 13(16P11.2) WILD-TYPE | 43 | 37 | 22

Figure S23. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 13(16p11.2)' versus 'CN_CNMF'

P value = 8.55e-19 (Fisher's exact test), Q value = 5.7e-16

Table S24. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 13(16P11.2) CNV | 88 | 18 | 8 | 2
AMP PEAK 13(16P11.2) WILD-TYPE | 82 | 169 | 24 | 22

Figure S24. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 13(16p11.2)' versus 'MRNASEQ_CNMF'

P value = 0.000429 (Fisher's exact test), Q value = 0.23

Table S25. Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
AMP PEAK 13(16P11.2) CNV | 8 | 24 | 13 | 4
AMP PEAK 13(16P11.2) WILD-TYPE | 23 | 35 | 34 | 50

Figure S25. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 14(16q12.1)' versus 'MRNA_CNMF'

P value = 3.02e-05 (Fisher's exact test), Q value = 0.017

Table S26. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
AMP PEAK 14(16Q12.1) CNV | 3 | 21 | 2 | 13
AMP PEAK 14(16Q12.1) WILD-TYPE | 28 | 41 | 28 | 10

Figure S26. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 14(16q12.1)' versus 'MRNA_CHIERARCHICAL'

P value = 0.000126 (Fisher's exact test), Q value = 0.07

Table S27. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
AMP PEAK 14(16Q12.1) CNV | 13 | 4 | 22
AMP PEAK 14(16Q12.1) WILD-TYPE | 43 | 40 | 24

Figure S27. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 14(16q12.1)' versus 'CN_CNMF'

P value = 1.67e-20 (Fisher's exact test), Q value = 1.1e-17

Table S28. Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 14(16Q12.1) CNV | 82 | 12 | 7 | 1
AMP PEAK 14(16Q12.1) WILD-TYPE | 88 | 175 | 25 | 23

Figure S28. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(17q12)' versus 'CN_CNMF'

P value = 7.53e-07 (Fisher's exact test), Q value = 0.00044

Table S29. Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 15(17Q12) CNV | 62 | 23 | 8 | 8
AMP PEAK 15(17Q12) WILD-TYPE | 108 | 164 | 24 | 16

Figure S29. Get High-res Image Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 15(17q12)' versus 'MRNASEQ_CNMF'

P value = 4.59e-05 (Fisher's exact test), Q value = 0.026

Table S30. Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
AMP PEAK 15(17Q12) CNV | 8 | 26 | 6 | 5
AMP PEAK 15(17Q12) WILD-TYPE | 23 | 33 | 41 | 49

Figure S30. Get High-res Image Gene #15: 'Amp Peak 15(17q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 16(17q24.1)' versus 'CN_CNMF'

P value = 1.61e-08 (Fisher's exact test), Q value = 9.7e-06

Table S31. Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 16(17Q24.1) CNV | 59 | 17 | 8 | 8
AMP PEAK 16(17Q24.1) WILD-TYPE | 111 | 170 | 24 | 16

Figure S31. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 16(17q24.1)' versus 'MRNASEQ_CNMF'

P value = 6.04e-06 (Fisher's exact test), Q value = 0.0035

Table S32. Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
AMP PEAK 16(17Q24.1) CNV | 9 | 26 | 4 | 5
AMP PEAK 16(17Q24.1) WILD-TYPE | 22 | 33 | 43 | 49

Figure S32. Get High-res Image Gene #16: 'Amp Peak 16(17q24.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 17(19p13.2)' versus 'CN_CNMF'

P value = 4.82e-05 (Fisher's exact test), Q value = 0.027

Table S33. Gene #17: 'Amp Peak 17(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 17(19P13.2) CNV | 39 | 13 | 8 | 5
AMP PEAK 17(19P13.2) WILD-TYPE | 131 | 174 | 24 | 19

Figure S33. Get High-res Image Gene #17: 'Amp Peak 17(19p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 19(20p12.3)' versus 'CN_CNMF'

P value = 1.86e-12 (Fisher's exact test), Q value = 1.2e-09

Table S34. Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 19(20P12.3) CNV | 83 | 58 | 31 | 12
AMP PEAK 19(20P12.3) WILD-TYPE | 87 | 129 | 1 | 12

Figure S34. Get High-res Image Gene #19: 'Amp Peak 19(20p12.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 20(20p11.23)' versus 'CN_CNMF'

P value = 1.26e-16 (Fisher's exact test), Q value = 8.3e-14

Table S35. Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 20(20P11.23) CNV | 102 | 58 | 32 | 13
AMP PEAK 20(20P11.23) WILD-TYPE | 68 | 129 | 0 | 11

Figure S35. Get High-res Image Gene #20: 'Amp Peak 20(20p11.23)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(20p11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 4.27e-05 (Fisher's exact test), Q value = 0.024

Table S36. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
AMP PEAK 21(20P11.21) CNV | 38 | 12 | 31
AMP PEAK 21(20P11.21) WILD-TYPE | 18 | 32 | 15

Figure S36. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 21(20p11.21)' versus 'CN_CNMF'

P value = 4e-23 (Fisher's exact test), Q value = 2.7e-20

Table S37. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 21(20P11.21) CNV | 126 | 58 | 32 | 14
AMP PEAK 21(20P11.21) WILD-TYPE | 44 | 129 | 0 | 10

Figure S37. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 21(20p11.21)' versus 'MRNASEQ_CNMF'

P value = 2.41e-07 (Fisher's exact test), Q value = 0.00014

Table S38. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
AMP PEAK 21(20P11.21) CNV | 19 | 44 | 24 | 12
AMP PEAK 21(20P11.21) WILD-TYPE | 12 | 15 | 23 | 42

Figure S38. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 21(20p11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.39e-06 (Fisher's exact test), Q value = 0.00081

Table S39. Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
AMP PEAK 21(20P11.21) CNV | 10 | 40 | 49
AMP PEAK 21(20P11.21) WILD-TYPE | 39 | 22 | 31

Figure S39. Get High-res Image Gene #21: 'Amp Peak 21(20p11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'MRNA_CNMF'

P value = 1.07e-10 (Fisher's exact test), Q value = 6.7e-08

Table S40. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
AMP PEAK 22(20Q11.21) CNV | 12 | 59 | 14 | 20
AMP PEAK 22(20Q11.21) WILD-TYPE | 19 | 3 | 16 | 3

Figure S40. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 22(20q11.21)' versus 'MRNA_CHIERARCHICAL'

P value = 2.86e-11 (Fisher's exact test), Q value = 1.8e-08

Table S41. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
AMP PEAK 22(20Q11.21) CNV | 50 | 14 | 41
AMP PEAK 22(20Q11.21) WILD-TYPE | 6 | 30 | 5

Figure S41. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'CN_CNMF'

P value = 1.54e-43 (Fisher's exact test), Q value = 1e-40

Table S42. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 22(20Q11.21) CNV | 167 | 74 | 32 | 23
AMP PEAK 22(20Q11.21) WILD-TYPE | 3 | 113 | 0 | 1

Figure S42. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 22(20q11.21)' versus 'METHLYATION_CNMF'

P value = 2.19e-09 (Fisher's exact test), Q value = 1.3e-06

Table S43. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
AMP PEAK 22(20Q11.21) CNV | 96 | 46 | 40
AMP PEAK 22(20Q11.21) WILD-TYPE | 9 | 40 | 23

Figure S43. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 22(20q11.21)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.06

Table S44. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 56 | 63 | 180
AMP PEAK 22(20Q11.21) CNV | 13 | 29 | 53 | 133
AMP PEAK 22(20Q11.21) WILD-TYPE | 13 | 27 | 10 | 47

Figure S44. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 22(20q11.21)' versus 'MRNASEQ_CNMF'

P value = 1.47e-14 (Fisher's exact test), Q value = 9.6e-12

Table S45. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
AMP PEAK 22(20Q11.21) CNV | 23 | 58 | 34 | 17
AMP PEAK 22(20Q11.21) WILD-TYPE | 8 | 1 | 13 | 37

Figure S45. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 22(20q11.21)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.85e-12 (Fisher's exact test), Q value = 2.5e-09

Table S46. Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
AMP PEAK 22(20Q11.21) CNV | 14 | 56 | 62
AMP PEAK 22(20Q11.21) WILD-TYPE | 35 | 6 | 18

Figure S46. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'MRNA_CNMF'

P value = 9.28e-12 (Fisher's exact test), Q value = 5.9e-09

Table S47. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
AMP PEAK 23(20Q12) CNV | 11 | 59 | 13 | 20
AMP PEAK 23(20Q12) WILD-TYPE | 20 | 3 | 17 | 3

Figure S47. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 23(20q12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.82e-11 (Fisher's exact test), Q value = 1.1e-08

Table S48. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
AMP PEAK 23(20Q12) CNV | 49 | 13 | 41
AMP PEAK 23(20Q12) WILD-TYPE | 7 | 31 | 5

Figure S48. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'CN_CNMF'

P value = 6.28e-43 (Fisher's exact test), Q value = 4.2e-40

Table S49. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 23(20Q12) CNV | 167 | 75 | 32 | 23
AMP PEAK 23(20Q12) WILD-TYPE | 3 | 112 | 0 | 1

Figure S49. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 23(20q12)' versus 'METHLYATION_CNMF'

P value = 1.58e-08 (Fisher's exact test), Q value = 9.6e-06

Table S50. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
AMP PEAK 23(20Q12) CNV | 96 | 48 | 41
AMP PEAK 23(20Q12) WILD-TYPE | 9 | 38 | 22

Figure S50. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 23(20q12)' versus 'RPPA_CHIERARCHICAL'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.012

Table S51. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 56 | 63 | 180
AMP PEAK 23(20Q12) CNV | 13 | 29 | 55 | 132
AMP PEAK 23(20Q12) WILD-TYPE | 13 | 27 | 8 | 48

Figure S51. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 23(20q12)' versus 'MRNASEQ_CNMF'

P value = 5.48e-14 (Fisher's exact test), Q value = 3.6e-11

Table S52. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
AMP PEAK 23(20Q12) CNV | 23 | 58 | 35 | 18
AMP PEAK 23(20Q12) WILD-TYPE | 8 | 1 | 12 | 36

Figure S52. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 23(20q12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-11 (Fisher's exact test), Q value = 8.5e-09

Table S53. Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
AMP PEAK 23(20Q12) CNV | 15 | 56 | 63
AMP PEAK 23(20Q12) WILD-TYPE | 34 | 6 | 17

Figure S53. Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'MRNA_CNMF'

P value = 2.87e-10 (Fisher's exact test), Q value = 1.8e-07

Table S54. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
AMP PEAK 24(20Q13.32) CNV | 12 | 59 | 15 | 20
AMP PEAK 24(20Q13.32) WILD-TYPE | 19 | 3 | 15 | 3

Figure S54. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Amp Peak 24(20q13.32)' versus 'MRNA_CHIERARCHICAL'

P value = 6.27e-12 (Fisher's exact test), Q value = 4e-09

Table S55. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
AMP PEAK 24(20Q13.32) CNV | 51 | 14 | 41
AMP PEAK 24(20Q13.32) WILD-TYPE | 5 | 30 | 5

Figure S55. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'CN_CNMF'

P value = 3.18e-43 (Fisher's exact test), Q value = 2.1e-40

Table S56. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
AMP PEAK 24(20Q13.32) CNV | 168 | 77 | 32 | 23
AMP PEAK 24(20Q13.32) WILD-TYPE | 2 | 110 | 0 | 1

Figure S56. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

'Amp Peak 24(20q13.32)' versus 'METHLYATION_CNMF'

P value = 1.58e-08 (Fisher's exact test), Q value = 9.6e-06

Table S57. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
AMP PEAK 24(20Q13.32) CNV | 96 | 48 | 41
AMP PEAK 24(20Q13.32) WILD-TYPE | 9 | 38 | 22

Figure S57. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Amp Peak 24(20q13.32)' versus 'RPPA_CHIERARCHICAL'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0075

Table S58. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 56 | 63 | 180
AMP PEAK 24(20Q13.32) CNV | 13 | 29 | 55 | 135
AMP PEAK 24(20Q13.32) WILD-TYPE | 13 | 27 | 8 | 45

Figure S58. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Amp Peak 24(20q13.32)' versus 'MRNASEQ_CNMF'

P value = 5.48e-14 (Fisher's exact test), Q value = 3.6e-11

Table S59. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
AMP PEAK 24(20Q13.32) CNV | 23 | 58 | 35 | 18
AMP PEAK 24(20Q13.32) WILD-TYPE | 8 | 1 | 12 | 36

Figure S59. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Amp Peak 24(20q13.32)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.34e-11 (Fisher's exact test), Q value = 8.5e-09

Table S60. Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
AMP PEAK 24(20Q13.32) CNV | 15 | 56 | 63
AMP PEAK 24(20Q13.32) WILD-TYPE | 34 | 6 | 17

Figure S60. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 1(1p36.11)' versus 'MRNA_CNMF'

P value = 6.81e-05 (Fisher's exact test), Q value = 0.038

Table S61. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
DEL PEAK 1(1P36.11) CNV | 9 | 35 | 3 | 11
DEL PEAK 1(1P36.11) WILD-TYPE | 22 | 27 | 27 | 12

Figure S61. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 1(1p36.11)' versus 'CN_CNMF'

P value = 6.32e-17 (Fisher's exact test), Q value = 4.2e-14

Table S62. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 1(1P36.11) CNV | 91 | 28 | 22 | 9
DEL PEAK 1(1P36.11) WILD-TYPE | 79 | 159 | 10 | 15

Figure S62. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 1(1p36.11)' versus 'MRNASEQ_CNMF'

P value = 0.000347 (Fisher's exact test), Q value = 0.19

Table S63. Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 1(1P36.11) CNV | 11 | 31 | 17 | 8
DEL PEAK 1(1P36.11) WILD-TYPE | 20 | 28 | 30 | 46

Figure S63. Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 2(1p33)' versus 'CN_CNMF'

P value = 1.09e-11 (Fisher's exact test), Q value = 6.9e-09

Table S64. Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 2(1P33) CNV | 69 | 20 | 15 | 3
DEL PEAK 2(1P33) WILD-TYPE | 101 | 167 | 17 | 21

Figure S64. Get High-res Image Gene #26: 'Del Peak 2(1p33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 3(1p13.1)' versus 'CN_CNMF'

P value = 6.85e-10 (Fisher's exact test), Q value = 4.3e-07

Table S65. Gene #27: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 3(1P13.1) CNV | 66 | 23 | 13 | 1
DEL PEAK 3(1P13.1) WILD-TYPE | 104 | 164 | 19 | 23

Figure S65. Get High-res Image Gene #27: 'Del Peak 3(1p13.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 4(1q43)' versus 'CN_CNMF'

P value = 6.98e-06 (Fisher's exact test), Q value = 0.004

Table S66. Gene #28: 'Del Peak 4(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 4(1Q43) CNV | 32 | 7 | 5 | 0
DEL PEAK 4(1Q43) WILD-TYPE | 138 | 180 | 27 | 24

Figure S66. Get High-res Image Gene #28: 'Del Peak 4(1q43)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 6(3p26.1)' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.23

Table S67. Gene #30: 'Del Peak 6(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 6(3P26.1) CNV | 36 | 14 | 8 | 2
DEL PEAK 6(3P26.1) WILD-TYPE | 134 | 173 | 24 | 22

Figure S67. Get High-res Image Gene #30: 'Del Peak 6(3p26.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4p16.2)' versus 'CN_CNMF'

P value = 1.16e-12 (Fisher's exact test), Q value = 7.5e-10

Table S68. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 9(4P16.2) CNV | 73 | 23 | 19 | 6
DEL PEAK 9(4P16.2) WILD-TYPE | 97 | 164 | 13 | 18

Figure S68. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 9(4p16.2)' versus 'MRNASEQ_CNMF'

P value = 0.000237 (Fisher's exact test), Q value = 0.13

Table S69. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 9(4P16.2) CNV | 9 | 24 | 16 | 4
DEL PEAK 9(4P16.2) WILD-TYPE | 22 | 35 | 31 | 50

Figure S69. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 9(4p16.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.059

Table S70. Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
DEL PEAK 9(4P16.2) CNV | 3 | 23 | 27
DEL PEAK 9(4P16.2) WILD-TYPE | 46 | 39 | 53

Figure S70. Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 10(4q22.1)' versus 'CN_CNMF'

P value = 8.5e-12 (Fisher's exact test), Q value = 5.4e-09

Table S71. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 10(4Q22.1) CNV | 77 | 28 | 18 | 3
DEL PEAK 10(4Q22.1) WILD-TYPE | 93 | 159 | 14 | 21

Figure S71. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 10(4q22.1)' versus 'MRNASEQ_CNMF'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.052

Table S72. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 10(4Q22.1) CNV | 9 | 28 | 15 | 5
DEL PEAK 10(4Q22.1) WILD-TYPE | 22 | 31 | 32 | 49

Figure S72. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 10(4q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.016

Table S73. Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
DEL PEAK 10(4Q22.1) CNV | 3 | 25 | 29
DEL PEAK 10(4Q22.1) WILD-TYPE | 46 | 37 | 51

Figure S73. Get High-res Image Gene #34: 'Del Peak 10(4q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 11(4q35.1)' versus 'MRNA_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.07

Table S74. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
DEL PEAK 11(4Q35.1) CNV | 7 | 30 | 3 | 13
DEL PEAK 11(4Q35.1) WILD-TYPE | 24 | 32 | 27 | 10

Figure S74. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 11(4q35.1)' versus 'CN_CNMF'

P value = 1.05e-13 (Fisher's exact test), Q value = 6.8e-11

Table S75. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 11(4Q35.1) CNV | 88 | 28 | 16 | 5
DEL PEAK 11(4Q35.1) WILD-TYPE | 82 | 159 | 16 | 19

Figure S75. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 11(4q35.1)' versus 'METHLYATION_CNMF'

P value = 7.69e-05 (Fisher's exact test), Q value = 0.043

Table S76. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
DEL PEAK 11(4Q35.1) CNV | 46 | 13 | 20
DEL PEAK 11(4Q35.1) WILD-TYPE | 59 | 73 | 43

Figure S76. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 11(4q35.1)' versus 'MRNASEQ_CNMF'

P value = 0.000239 (Fisher's exact test), Q value = 0.13

Table S77. Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 11(4Q35.1) CNV | 11 | 30 | 15 | 7
DEL PEAK 11(4Q35.1) WILD-TYPE | 20 | 29 | 32 | 47

Figure S77. Get High-res Image Gene #35: 'Del Peak 11(4q35.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 12(5q11.2)' versus 'CN_CNMF'

P value = 4.94e-09 (Fisher's exact test), Q value = 3e-06

Table S78. Gene #36: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 12(5Q11.2) CNV | 60 | 16 | 9 | 6
DEL PEAK 12(5Q11.2) WILD-TYPE | 110 | 171 | 23 | 18

Figure S78. Get High-res Image Gene #36: 'Del Peak 12(5q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 13(5q21.3)' versus 'CN_CNMF'

P value = 1.14e-09 (Fisher's exact test), Q value = 7e-07

Table S79. Gene #37: 'Del Peak 13(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 13(5Q21.3) CNV | 71 | 24 | 14 | 8
DEL PEAK 13(5Q21.3) WILD-TYPE | 99 | 163 | 18 | 16

Figure S79. Get High-res Image Gene #37: 'Del Peak 13(5q21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 14(5q23.1)' versus 'CN_CNMF'

P value = 1.57e-08 (Fisher's exact test), Q value = 9.5e-06

Table S80. Gene #38: 'Del Peak 14(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 14(5Q23.1) CNV | 64 | 22 | 13 | 8
DEL PEAK 14(5Q23.1) WILD-TYPE | 106 | 165 | 19 | 16

Figure S80. Get High-res Image Gene #38: 'Del Peak 14(5q23.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 15(6p25.3)' versus 'CN_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.057

Table S81. Gene #39: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 15(6P25.3) CNV | 13 | 23 | 9 | 9
DEL PEAK 15(6P25.3) WILD-TYPE | 157 | 164 | 23 | 15

Figure S81. Get High-res Image Gene #39: 'Del Peak 15(6p25.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p23.3)' versus 'CN_CNMF'

P value = 6.84e-26 (Fisher's exact test), Q value = 4.6e-23

Table S82. Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 18(8P23.3) CNV | 119 | 32 | 6 | 14
DEL PEAK 18(8P23.3) WILD-TYPE | 51 | 155 | 26 | 10

Figure S82. Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 18(8p23.3)' versus 'METHLYATION_CNMF'

P value = 3.61e-06 (Fisher's exact test), Q value = 0.0021

Table S83. Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
DEL PEAK 18(8P23.3) CNV | 62 | 21 | 22
DEL PEAK 18(8P23.3) WILD-TYPE | 43 | 65 | 41

Figure S83. Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(8p22)' versus 'CN_CNMF'

P value = 2.41e-30 (Fisher's exact test), Q value = 1.6e-27

Table S84. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 19(8P22) CNV | 129 | 33 | 8 | 15
DEL PEAK 19(8P22) WILD-TYPE | 41 | 154 | 24 | 9

Figure S84. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 19(8p22)' versus 'METHLYATION_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00021

Table S85. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
DEL PEAK 19(8P22) CNV | 69 | 24 | 24
DEL PEAK 19(8P22) WILD-TYPE | 36 | 62 | 39

Figure S85. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 19(8p22)' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.071

Table S86. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 56 | 63 | 180
DEL PEAK 19(8P22) CNV | 5 | 15 | 38 | 82
DEL PEAK 19(8P22) WILD-TYPE | 21 | 41 | 25 | 98

Figure S86. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 19(8p22)' versus 'MRNASEQ_CNMF'

P value = 2.16e-05 (Fisher's exact test), Q value = 0.012

Table S87. Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 19(8P22) CNV | 17 | 38 | 21 | 11
DEL PEAK 19(8P22) WILD-TYPE | 14 | 21 | 26 | 43

Figure S87. Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 20(8p11.22)' versus 'CN_CNMF'

P value = 8.88e-09 (Fisher's exact test), Q value = 5.4e-06

Table S88. Gene #44: 'Del Peak 20(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 20(8P11.22) CNV | 58 | 18 | 3 | 1
DEL PEAK 20(8P11.22) WILD-TYPE | 112 | 169 | 29 | 23

Figure S88. Get High-res Image Gene #44: 'Del Peak 20(8p11.22)' versus Molecular Subtype #3: 'CN_CNMF'

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

P value = 5.81e-07 (Fisher's exact test), Q value = 0.00034

Table S89. Gene #45: 'Del Peak 21(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 21(8P11.21) CNV | 35 | 7 | 1 | 0
DEL PEAK 21(8P11.21) WILD-TYPE | 135 | 180 | 31 | 24

Figure S89. Get High-res Image Gene #45: 'Del Peak 21(8p11.21)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 22(9p21.3)' versus 'CN_CNMF'

P value = 4.51e-05 (Fisher's exact test), Q value = 0.026

Table S90. Gene #46: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 22(9P21.3) CNV | 35 | 10 | 7 | 4
DEL PEAK 22(9P21.3) WILD-TYPE | 135 | 177 | 25 | 20

Figure S90. Get High-res Image Gene #46: 'Del Peak 22(9p21.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 23(10p15.3)' versus 'CN_CNMF'

P value = 2.25e-08 (Fisher's exact test), Q value = 1.4e-05

Table S91. Gene #47: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 23(10P15.3) CNV | 38 | 12 | 15 | 3
DEL PEAK 23(10P15.3) WILD-TYPE | 132 | 175 | 17 | 21

Figure S91. Get High-res Image Gene #47: 'Del Peak 23(10p15.3)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 24(10q21.1)' versus 'CN_CNMF'

P value = 2.24e-11 (Fisher's exact test), Q value = 1.4e-08

Table S92. Gene #48: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 24(10Q21.1) CNV | 48 | 12 | 17 | 5
DEL PEAK 24(10Q21.1) WILD-TYPE | 122 | 175 | 15 | 19

Figure S92. Get High-res Image Gene #48: 'Del Peak 24(10q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 25(10q23.31)' versus 'CN_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00021

Table S93. Gene #49: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 25(10Q23.31) CNV | 53 | 21 | 15 | 5
DEL PEAK 25(10Q23.31) WILD-TYPE | 117 | 166 | 17 | 19

Figure S93. Get High-res Image Gene #49: 'Del Peak 25(10q23.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 26(10q25.2)' versus 'CN_CNMF'

P value = 1.91e-11 (Fisher's exact test), Q value = 1.2e-08

Table S94. Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 26(10Q25.2) CNV | 57 | 16 | 17 | 3
DEL PEAK 26(10Q25.2) WILD-TYPE | 113 | 171 | 15 | 21

Figure S94. Get High-res Image Gene #50: 'Del Peak 26(10q25.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 27(12p13.2)' versus 'CN_CNMF'

P value = 9.87e-08 (Fisher's exact test), Q value = 5.9e-05

Table S95. Gene #51: 'Del Peak 27(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 27(12P13.2) CNV | 34 | 4 | 5 | 1
DEL PEAK 27(12P13.2) WILD-TYPE | 136 | 183 | 27 | 23

Figure S95. Get High-res Image Gene #51: 'Del Peak 27(12p13.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 28(13q14.13)' versus 'CN_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.07

Table S96. Gene #52: 'Del Peak 28(13q14.13)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 28(13Q14.13) CNV | 1 | 9 | 6 | 2
DEL PEAK 28(13Q14.13) WILD-TYPE | 169 | 178 | 26 | 22

Figure S96. Get High-res Image Gene #52: 'Del Peak 28(13q14.13)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNA_CNMF'

P value = 2.12e-05 (Fisher's exact test), Q value = 0.012

Table S97. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
DEL PEAK 29(14Q32.11) CNV | 7 | 35 | 3 | 11
DEL PEAK 29(14Q32.11) WILD-TYPE | 24 | 27 | 27 | 12

Figure S97. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.061

Table S98. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
DEL PEAK 29(14Q32.11) CNV | 22 | 7 | 27
DEL PEAK 29(14Q32.11) WILD-TYPE | 34 | 37 | 19

Figure S98. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 29(14q32.11)' versus 'CN_CNMF'

P value = 1.61e-20 (Fisher's exact test), Q value = 1.1e-17

Table S99. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 29(14Q32.11) CNV | 98 | 22 | 10 | 3
DEL PEAK 29(14Q32.11) WILD-TYPE | 72 | 165 | 22 | 21

Figure S99. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 29(14q32.11)' versus 'MRNASEQ_CNMF'

P value = 7.3e-05 (Fisher's exact test), Q value = 0.041

Table S100. Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 29(14Q32.11) CNV | 11 | 28 | 13 | 5
DEL PEAK 29(14Q32.11) WILD-TYPE | 20 | 31 | 34 | 49

Figure S100. Get High-res Image Gene #53: 'Del Peak 29(14q32.11)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(15q11.2)' versus 'MRNA_CNMF'

P value = 0.000422 (Fisher's exact test), Q value = 0.23

Table S101. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
DEL PEAK 30(15Q11.2) CNV | 8 | 35 | 5 | 12
DEL PEAK 30(15Q11.2) WILD-TYPE | 23 | 27 | 25 | 11

Figure S101. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 30(15q11.2)' versus 'CN_CNMF'

P value = 1.2e-21 (Fisher's exact test), Q value = 8e-19

Table S102. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 30(15Q11.2) CNV | 104 | 29 | 22 | 5
DEL PEAK 30(15Q11.2) WILD-TYPE | 66 | 158 | 10 | 19

Figure S102. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 30(15q11.2)' versus 'MRNASEQ_CNMF'

P value = 2.09e-06 (Fisher's exact test), Q value = 0.0012

Table S103. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 30(15Q11.2) CNV | 13 | 32 | 19 | 5
DEL PEAK 30(15Q11.2) WILD-TYPE | 18 | 27 | 28 | 49

Figure S103. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 30(15q11.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000117 (Fisher's exact test), Q value = 0.065

Table S104. Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
DEL PEAK 30(15Q11.2) CNV | 6 | 29 | 34
DEL PEAK 30(15Q11.2) WILD-TYPE | 43 | 33 | 46

Figure S104. Get High-res Image Gene #54: 'Del Peak 30(15q11.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 31(15q21.1)' versus 'CN_CNMF'

P value = 8.15e-18 (Fisher's exact test), Q value = 5.4e-15

Table S105. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 31(15Q21.1) CNV | 97 | 30 | 20 | 4
DEL PEAK 31(15Q21.1) WILD-TYPE | 73 | 157 | 12 | 20

Figure S105. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 31(15q21.1)' versus 'MRNASEQ_CNMF'

P value = 2.03e-07 (Fisher's exact test), Q value = 0.00012

Table S106. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 31(15Q21.1) CNV | 12 | 31 | 17 | 3
DEL PEAK 31(15Q21.1) WILD-TYPE | 19 | 28 | 30 | 51

Figure S106. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 31(15q21.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.05e-05 (Fisher's exact test), Q value = 0.012

Table S107. Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
DEL PEAK 31(15Q21.1) CNV | 4 | 28 | 31
DEL PEAK 31(15Q21.1) WILD-TYPE | 45 | 34 | 49

Figure S107. Get High-res Image Gene #55: 'Del Peak 31(15q21.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 32(15q22.33)' versus 'CN_CNMF'

P value = 2.48e-21 (Fisher's exact test), Q value = 1.7e-18

Table S108. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 32(15Q22.33) CNV | 96 | 23 | 21 | 5
DEL PEAK 32(15Q22.33) WILD-TYPE | 74 | 164 | 11 | 19

Figure S108. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 32(15q22.33)' versus 'METHLYATION_CNMF'

P value = 0.000435 (Fisher's exact test), Q value = 0.23

Table S109. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
DEL PEAK 32(15Q22.33) CNV | 49 | 17 | 22
DEL PEAK 32(15Q22.33) WILD-TYPE | 56 | 69 | 41

Figure S109. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 32(15q22.33)' versus 'MRNASEQ_CNMF'

P value = 3.07e-08 (Fisher's exact test), Q value = 1.8e-05

Table S110. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 32(15Q22.33) CNV | 13 | 33 | 17 | 3
DEL PEAK 32(15Q22.33) WILD-TYPE | 18 | 26 | 30 | 51

Figure S110. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 32(15q22.33)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.55e-06 (Fisher's exact test), Q value = 0.0044

Table S111. Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
DEL PEAK 32(15Q22.33) CNV | 4 | 29 | 33
DEL PEAK 32(15Q22.33) WILD-TYPE | 45 | 33 | 47

Figure S111. Get High-res Image Gene #56: 'Del Peak 32(15q22.33)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'MRNA_CNMF'

P value = 6.12e-08 (Fisher's exact test), Q value = 3.7e-05

Table S112. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
DEL PEAK 35(17P12) CNV | 10 | 49 | 7 | 16
DEL PEAK 35(17P12) WILD-TYPE | 21 | 13 | 23 | 7

Figure S112. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 35(17p12)' versus 'MRNA_CHIERARCHICAL'

P value = 1.6e-06 (Fisher's exact test), Q value = 0.00093

Table S113. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
DEL PEAK 35(17P12) CNV | 36 | 11 | 35
DEL PEAK 35(17P12) WILD-TYPE | 20 | 33 | 11

Figure S113. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'CN_CNMF'

P value = 2.81e-35 (Fisher's exact test), Q value = 1.9e-32

Table S114. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 35(17P12) CNV | 146 | 43 | 24 | 16
DEL PEAK 35(17P12) WILD-TYPE | 24 | 144 | 8 | 8

Figure S114. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 35(17p12)' versus 'METHLYATION_CNMF'

P value = 1.8e-09 (Fisher's exact test), Q value = 1.1e-06

Table S115. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
DEL PEAK 35(17P12) CNV | 82 | 30 | 29
DEL PEAK 35(17P12) WILD-TYPE | 23 | 56 | 34

Figure S115. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 35(17p12)' versus 'RPPA_CHIERARCHICAL'

P value = 7.42e-05 (Fisher's exact test), Q value = 0.042

Table S116. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 56 | 63 | 180
DEL PEAK 35(17P12) CNV | 8 | 19 | 43 | 106
DEL PEAK 35(17P12) WILD-TYPE | 18 | 37 | 20 | 74

Figure S116. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 35(17p12)' versus 'MRNASEQ_CNMF'

P value = 1.06e-10 (Fisher's exact test), Q value = 6.6e-08

Table S117. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 35(17P12) CNV | 20 | 49 | 23 | 11
DEL PEAK 35(17P12) WILD-TYPE | 11 | 10 | 24 | 43

Figure S117. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 35(17p12)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.2e-08 (Fisher's exact test), Q value = 1.9e-05

Table S118. Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
DEL PEAK 35(17P12) CNV | 11 | 48 | 44
DEL PEAK 35(17P12) WILD-TYPE | 38 | 14 | 36

Figure S118. Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 37(18p11.31)' versus 'MRNA_CNMF'

P value = 1.51e-12 (Fisher's exact test), Q value = 9.7e-10

Table S119. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
DEL PEAK 37(18P11.31) CNV | 6 | 51 | 5 | 16
DEL PEAK 37(18P11.31) WILD-TYPE | 25 | 11 | 25 | 7

Figure S119. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNA_CHIERARCHICAL'

P value = 3.65e-09 (Fisher's exact test), Q value = 2.2e-06

Table S120. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
DEL PEAK 37(18P11.31) CNV | 36 | 7 | 35
DEL PEAK 37(18P11.31) WILD-TYPE | 20 | 37 | 11

Figure S120. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 37(18p11.31)' versus 'CN_CNMF'

P value = 1.93e-42 (Fisher's exact test), Q value = 1.3e-39

Table S121. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 37(18P11.31) CNV | 145 | 34 | 28 | 13
DEL PEAK 37(18P11.31) WILD-TYPE | 25 | 153 | 4 | 11

Figure S121. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 37(18p11.31)' versus 'METHLYATION_CNMF'

P value = 3.11e-13 (Fisher's exact test), Q value = 2e-10

Table S122. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
DEL PEAK 37(18P11.31) CNV | 83 | 22 | 31
DEL PEAK 37(18P11.31) WILD-TYPE | 22 | 64 | 32

Figure S122. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNASEQ_CNMF'

P value = 3.11e-17 (Fisher's exact test), Q value = 2.1e-14

Table S123. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 37(18P11.31) CNV | 17 | 52 | 24 | 5
DEL PEAK 37(18P11.31) WILD-TYPE | 14 | 7 | 23 | 49

Figure S123. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 37(18p11.31)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.19e-10 (Fisher's exact test), Q value = 5.1e-07

Table S124. Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
DEL PEAK 37(18P11.31) CNV | 7 | 45 | 46
DEL PEAK 37(18P11.31) WILD-TYPE | 42 | 17 | 34

Figure S124. Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'MRNA_CNMF'

P value = 8.37e-11 (Fisher's exact test), Q value = 5.2e-08

Table S125. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
DEL PEAK 38(18Q12.2) CNV | 8 | 53 | 8 | 17
DEL PEAK 38(18Q12.2) WILD-TYPE | 23 | 9 | 22 | 6

Figure S125. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 38(18q12.2)' versus 'MRNA_CHIERARCHICAL'

P value = 1.08e-09 (Fisher's exact test), Q value = 6.7e-07

Table S126. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
DEL PEAK 38(18Q12.2) CNV | 39 | 9 | 38
DEL PEAK 38(18Q12.2) WILD-TYPE | 17 | 35 | 8

Figure S126. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'CN_CNMF'

P value = 1.87e-45 (Fisher's exact test), Q value = 1.3e-42

Table S127. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 38(18Q12.2) CNV | 157 | 44 | 27 | 19
DEL PEAK 38(18Q12.2) WILD-TYPE | 13 | 143 | 5 | 5

Figure S127. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 38(18q12.2)' versus 'METHLYATION_CNMF'

P value = 8.98e-16 (Fisher's exact test), Q value = 5.9e-13

Table S128. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
DEL PEAK 38(18Q12.2) CNV | 93 | 29 | 31
DEL PEAK 38(18Q12.2) WILD-TYPE | 12 | 57 | 32

Figure S128. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 38(18q12.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000421 (Fisher's exact test), Q value = 0.23

Table S129. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 56 | 63 | 180
DEL PEAK 38(18Q12.2) CNV | 9 | 22 | 43 | 113
DEL PEAK 38(18Q12.2) WILD-TYPE | 17 | 34 | 20 | 67

Figure S129. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 38(18q12.2)' versus 'MRNASEQ_CNMF'

P value = 7.66e-16 (Fisher's exact test), Q value = 5e-13

Table S130. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 38(18Q12.2) CNV | 21 | 53 | 28 | 8
DEL PEAK 38(18Q12.2) WILD-TYPE | 10 | 6 | 19 | 46

Figure S130. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 38(18q12.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-08 (Fisher's exact test), Q value = 6.5e-06

Table S131. Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
DEL PEAK 38(18Q12.2) CNV | 11 | 48 | 51
DEL PEAK 38(18Q12.2) WILD-TYPE | 38 | 14 | 29

Figure S131. Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'MRNA_CNMF'

P value = 3.06e-10 (Fisher's exact test), Q value = 1.9e-07

Table S132. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
DEL PEAK 39(18Q21.2) CNV | 8 | 53 | 9 | 17
DEL PEAK 39(18Q21.2) WILD-TYPE | 23 | 9 | 21 | 6

Figure S132. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 39(18q21.2)' versus 'MRNA_CHIERARCHICAL'

P value = 6.85e-10 (Fisher's exact test), Q value = 4.3e-07

Table S133. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
DEL PEAK 39(18Q21.2) CNV | 40 | 9 | 38
DEL PEAK 39(18Q21.2) WILD-TYPE | 16 | 35 | 8

Figure S133. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'CN_CNMF'

P value = 1.51e-45 (Fisher's exact test), Q value = 1e-42

Table S134. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 39(18Q21.2) CNV | 161 | 51 | 28 | 20
DEL PEAK 39(18Q21.2) WILD-TYPE | 9 | 136 | 4 | 4

Figure S134. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 39(18q21.2)' versus 'METHLYATION_CNMF'

P value = 3.29e-12 (Fisher's exact test), Q value = 2.1e-09

Table S135. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
DEL PEAK 39(18Q21.2) CNV | 94 | 38 | 33
DEL PEAK 39(18Q21.2) WILD-TYPE | 11 | 48 | 30

Figure S135. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 39(18q21.2)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000225 (Fisher's exact test), Q value = 0.12

Table S136. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 56 | 63 | 180
DEL PEAK 39(18Q21.2) CNV | 10 | 24 | 46 | 120
DEL PEAK 39(18Q21.2) WILD-TYPE | 16 | 32 | 17 | 60

Figure S136. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 39(18q21.2)' versus 'MRNASEQ_CNMF'

P value = 8.74e-13 (Fisher's exact test), Q value = 5.7e-10

Table S137. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 39(18Q21.2) CNV | 21 | 54 | 29 | 13
DEL PEAK 39(18Q21.2) WILD-TYPE | 10 | 5 | 18 | 41

Figure S137. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 39(18q21.2)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.14e-07 (Fisher's exact test), Q value = 0.00042

Table S138. Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
DEL PEAK 39(18Q21.2) CNV | 15 | 49 | 53
DEL PEAK 39(18Q21.2) WILD-TYPE | 34 | 13 | 27

Figure S138. Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'MRNA_CNMF'

P value = 6.92e-11 (Fisher's exact test), Q value = 4.3e-08

Table S139. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
DEL PEAK 40(18Q22.1) CNV | 8 | 54 | 9 | 17
DEL PEAK 40(18Q22.1) WILD-TYPE | 23 | 8 | 21 | 6

Figure S139. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 40(18q22.1)' versus 'MRNA_CHIERARCHICAL'

P value = 3.65e-09 (Fisher's exact test), Q value = 2.2e-06

Table S140. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 56 | 44 | 46
DEL PEAK 40(18Q22.1) CNV | 40 | 10 | 38
DEL PEAK 40(18Q22.1) WILD-TYPE | 16 | 34 | 8

Figure S140. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'CN_CNMF'

P value = 1.58e-47 (Fisher's exact test), Q value = 1.1e-44

Table S141. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 40(18Q22.1) CNV | 162 | 50 | 29 | 19
DEL PEAK 40(18Q22.1) WILD-TYPE | 8 | 137 | 3 | 5

Figure S141. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 40(18q22.1)' versus 'METHLYATION_CNMF'

P value = 2.02e-12 (Fisher's exact test), Q value = 1.3e-09

Table S142. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 86 | 63
DEL PEAK 40(18Q22.1) CNV | 94 | 38 | 32
DEL PEAK 40(18Q22.1) WILD-TYPE | 11 | 48 | 31

Figure S142. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'Del Peak 40(18q22.1)' versus 'RPPA_CHIERARCHICAL'

P value = 0.000224 (Fisher's exact test), Q value = 0.12

Table S143. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 26 | 56 | 63 | 180
DEL PEAK 40(18Q22.1) CNV | 10 | 24 | 45 | 122
DEL PEAK 40(18Q22.1) WILD-TYPE | 16 | 32 | 18 | 58

Figure S143. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'Del Peak 40(18q22.1)' versus 'MRNASEQ_CNMF'

P value = 4.05e-12 (Fisher's exact test), Q value = 2.6e-09

Table S144. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 40(18Q22.1) CNV | 21 | 54 | 29 | 14
DEL PEAK 40(18Q22.1) WILD-TYPE | 10 | 5 | 18 | 40

Figure S144. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 40(18q22.1)' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.76e-07 (Fisher's exact test), Q value = 0.00016

Table S145. Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 49 | 62 | 80
DEL PEAK 40(18Q22.1) CNV | 15 | 50 | 53
DEL PEAK 40(18Q22.1) WILD-TYPE | 34 | 12 | 27

Figure S145. Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 42(20p12.1)' versus 'CN_CNMF'

P value = 1.38e-13 (Fisher's exact test), Q value = 9e-11

Table S146. Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 42(20P12.1) CNV | 61 | 12 | 0 | 6
DEL PEAK 42(20P12.1) WILD-TYPE | 109 | 175 | 32 | 18

Figure S146. Get High-res Image Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 42(20p12.1)' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.082

Table S147. Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 59 | 47 | 54
DEL PEAK 42(20P12.1) CNV | 8 | 24 | 7 | 4
DEL PEAK 42(20P12.1) WILD-TYPE | 23 | 35 | 40 | 50

Figure S147. Get High-res Image Gene #66: 'Del Peak 42(20p12.1)' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'Del Peak 43(21q11.2)' versus 'CN_CNMF'

P value = 3.37e-09 (Fisher's exact test), Q value = 2.1e-06

Table S148. Gene #67: 'Del Peak 43(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 43(21Q11.2) CNV | 72 | 30 | 18 | 5
DEL PEAK 43(21Q11.2) WILD-TYPE | 98 | 157 | 14 | 19

Figure S148. Get High-res Image Gene #67: 'Del Peak 43(21q11.2)' versus Molecular Subtype #3: 'CN_CNMF'

'Del Peak 44(22q13.32)' versus 'MRNA_CNMF'

P value = 0.000428 (Fisher's exact test), Q value = 0.23

Table S149. Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 31 | 62 | 30 | 23
DEL PEAK 44(22Q13.32) CNV | 8 | 34 | 4 | 10
DEL PEAK 44(22Q13.32) WILD-TYPE | 23 | 28 | 26 | 13

Figure S149. Get High-res Image Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #1: 'MRNA_CNMF'

'Del Peak 44(22q13.32)' versus 'CN_CNMF'

P value = 9.76e-13 (Fisher's exact test), Q value = 6.3e-10

Table S150. Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 170 | 187 | 32 | 24
DEL PEAK 44(22Q13.32) CNV | 85 | 28 | 17 | 8
DEL PEAK 44(22Q13.32) WILD-TYPE | 85 | 159 | 15 | 16

Figure S150. Get High-res Image Gene #68: 'Del Peak 44(22q13.32)' versus Molecular Subtype #3: 'CN_CNMF'

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 = COAD-TP.transferedmergedcluster.txt

- Number of patients = 413

- Number of copy number variation regions = 68

- 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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- 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] 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)
[3] GISTIC_version2
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle