Correlation between copy number variations of arm-level result and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1S46Q10
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1S46Q10
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.

Summary

Testing the association between copy number variation 45 arm-level results and 10 molecular subtypes across 497 patients, 128 significant findings detected with Q value < 0.25.

- 1q gain cnv correlated to 'CN_CNMF'.

- 4p gain cnv correlated to 'CN_CNMF'.

- 4q gain cnv correlated to 'CN_CNMF'.

- 5p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 5q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 11q gain cnv correlated to 'CN_CNMF'.

- 12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 12q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 13q gain cnv correlated to 'CN_CNMF'.

- 14q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 16p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 16q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 17p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 19p gain cnv correlated to 'CN_CNMF'.

- 19q gain cnv correlated to 'CN_CNMF'.

- 20p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 20q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 1p loss cnv correlated to 'CN_CNMF'.

- 2p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 2q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 3q loss cnv correlated to 'CN_CNMF'.

- 8p loss cnv correlated to 'CN_CNMF'.

- 8q loss cnv correlated to 'CN_CNMF'.

- 9p loss cnv correlated to 'CN_CNMF'.

- 9q loss cnv correlated to 'CN_CNMF'.

- 10p loss cnv correlated to 'CN_CNMF'.

- 10q loss cnv correlated to 'CN_CNMF'.

- 11p loss cnv correlated to 'CN_CNMF'.

- 11q loss cnv correlated to 'CN_CNMF'.

- 15q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 18p loss cnv correlated to 'CN_CNMF'.

- 18q loss cnv correlated to 'CN_CNMF'.

- 21q loss cnv correlated to 'CN_CNMF'.

- 22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 45 arm-level results and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 128 significant findings detected.

|  | Molecular subtypes | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
7q gain | 0 (0%) | 478 | 1.76e-23 (7.13e-21) | 3.65e-05 (0.0124) | 0.689 (1.00) | 0.00298 (0.752) | 5.06e-05 (0.0168) | 6.18e-06 (0.00224) | 0.000289 (0.0879) | 2.87e-05 (0.00992) | 0.0002 (0.0622) | 3.59e-05 (0.0122)
12p gain | 0 (0%) | 486 | 1.03e-12 (4.09e-10) | 2.87e-06 (0.00107) | 0.901 (1.00) | 0.0299 (1.00) | 1.6e-05 (0.00577) | 2.12e-06 (0.000794) | 5.19e-05 (0.0172) | 1.7e-05 (0.00606) | 3.43e-05 (0.0118) | 2e-05 (0.00701)
12q gain | 0 (0%) | 485 | 1.27e-12 (5.04e-10) | 6.48e-07 (0.000248) | 0.901 (1.00) | 0.0299 (1.00) | 4.46e-06 (0.00165) | 6.49e-07 (0.000248) | 1.64e-05 (0.00588) | 4.85e-06 (0.00179) | 6.11e-06 (0.00222) | 5.76e-06 (0.00211)
16p gain | 0 (0%) | 485 | 5.51e-14 (2.21e-11) | 3.21e-05 (0.011) | 1 (1.00) | 0.0445 (1.00) | 0.000132 (0.0422) | 2.69e-05 (0.00935) | 0.000214 (0.0657) | 5.88e-05 (0.0194) | 8.28e-05 (0.0271) | 8.35e-05 (0.0272)
17p gain | 0 (0%) | 485 | 2e-09 (7.81e-07) | 6.48e-07 (0.000248) | 0.772 (1.00) | 0.0179 (1.00) | 4.46e-06 (0.00165) | 6.49e-07 (0.000248) | 5.19e-05 (0.0172) | 1.7e-05 (0.00606) | 3.43e-05 (0.0118) | 2e-05 (0.00701)
17q gain | 0 (0%) | 484 | 3.83e-09 (1.49e-06) | 3.73e-07 (0.000143) | 0.795 (1.00) | 0.0206 (1.00) | 1.51e-06 (0.000569) | 1.6e-07 (6.15e-05) | 1.64e-05 (0.00588) | 4.85e-06 (0.00179) | 6.11e-06 (0.00222) | 5.76e-06 (0.00211)
2p loss | 0 (0%) | 489 | 5.02e-09 (1.95e-06) | 8.76e-05 (0.0285) | 1 (1.00) | 0.0817 (1.00) | 0.000325 (0.0975) | 0.000148 (0.0472) | 5.53e-05 (0.0182) | 2.27e-05 (0.0079) | 4.85e-05 (0.0162) | 2.81e-05 (0.00973)
22q loss | 0 (0%) | 431 | 6.79e-58 (2.76e-55) | 4.45e-05 (0.015) | 0.114 (1.00) | 0.0835 (1.00) | 2.26e-11 (8.89e-09) | 2.59e-11 (1.01e-08) | 4.33e-05 (0.0146) | 9.51e-06 (0.00343) | 3.93e-05 (0.0133) | 4.85e-06 (0.00179)
2q loss | 0 (0%) | 490 | 3.78e-09 (1.47e-06) | 0.000364 (0.108) | 0.837 (1.00) | 0.0549 (1.00) | 0.00153 (0.409) | 0.000534 (0.155) | 0.000192 (0.06) | 8.85e-05 (0.0286) | 0.000171 (0.0538) | 0.000107 (0.0342)
5q gain | 0 (0%) | 483 | 2.6e-18 (1.05e-15) | 4.02e-05 (0.0136) | 0.901 (1.00) | 0.0299 (1.00) | 0.000164 (0.0518) | 4.71e-05 (0.0158) | 0.00146 (0.392) | 0.000106 (0.0341) | 0.000991 (0.275) | 0.000119 (0.0379)
7p gain | 0 (0%) | 480 | 1.59e-22 (6.42e-20) | 0.000169 (0.0531) | 1 (1.00) | 0.0129 (1.00) | 0.00041 (0.121) | 6.05e-05 (0.0199) | 0.00232 (0.601) | 0.000272 (0.0829) | 0.00135 (0.367) | 0.000418 (0.122)
16q gain | 0 (0%) | 487 | 5.67e-13 (2.26e-10) | 0.000224 (0.0686) | 0.856 (1.00) | 0.129 (1.00) | 0.00131 (0.361) | 0.00039 (0.115) | 0.00169 (0.448) | 0.000547 (0.157) | 0.000713 (0.201) | 0.000758 (0.212)
15q loss | 0 (0%) | 490 | 0.000464 (0.135) | 0.00226 (0.594) | 0.458 (1.00) | 0.256 (1.00) | 0.00153 (0.409) | 0.000534 (0.155) | 0.000664 (0.189) | 0.000342 (0.102) | 0.000602 (0.172) | 0.000402 (0.118)
5p gain | 0 (0%) | 480 | 6.97e-20 (2.81e-17) | 0.000873 (0.244) | 1 (1.00) | 0.125 (1.00) | 0.00235 (0.607) | 0.000538 (0.156) | 0.00691 (1.00) | 0.000541 (0.156) | 0.00487 (1.00) | 0.00075 (0.211)
14q gain | 0 (0%) | 489 | 5.02e-09 (1.95e-06) | 8.76e-05 (0.0285) | 1 (1.00) | 0.256 (1.00) | 0.000325 (0.0975) | 0.000148 (0.0472) | 0.00467 (1.00) | 0.00229 (0.599) | 0.00291 (0.735) | 0.00256 (0.65)
20p gain | 0 (0%) | 488 | 1.11e-11 (4.37e-09) | 0.000706 (0.2) | 1 (1.00) | 0.0817 (1.00) | 0.00374 (0.939) | 0.00144 (0.391) | 0.0124 (1.00) | 0.00619 (1.00) | 0.00573 (1.00) | 0.00645 (1.00)
20q gain | 0 (0%) | 488 | 1.11e-11 (4.37e-09) | 0.000706 (0.2) | 1 (1.00) | 0.0817 (1.00) | 0.00374 (0.939) | 0.00144 (0.391) | 0.0124 (1.00) | 0.00619 (1.00) | 0.00573 (1.00) | 0.00645 (1.00)
1q gain | 0 (0%) | 476 | 3.29e-06 (0.00122) | 0.0744 (1.00) | 0.0153 (1.00) | 0.0826 (1.00) | 0.012 (1.00) | 0.00102 (0.283) | 0.224 (1.00) | 0.204 (1.00) | 0.177 (1.00) | 0.216 (1.00)
4p gain | 0 (0%) | 493 | 1.85e-05 (0.00655) | 0.0186 (1.00) |  |  | 0.0378 (1.00) | 0.0215 (1.00) | 0.112 (1.00) | 0.0975 (1.00) | 0.0719 (1.00) | 0.101 (1.00)
4q gain | 0 (0%) | 493 | 1.85e-05 (0.00655) | 0.0186 (1.00) |  |  | 0.0378 (1.00) | 0.0215 (1.00) | 0.112 (1.00) | 0.0975 (1.00) | 0.0719 (1.00) | 0.101 (1.00)
11q gain | 0 (0%) | 493 | 0.000204 (0.0633) | 0.0186 (1.00) |  |  | 0.0378 (1.00) | 0.0215 (1.00) | 0.00778 (1.00) | 0.00503 (1.00) | 0.0073 (1.00) | 0.00558 (1.00)
13q gain | 0 (0%) | 494 | 0.000294 (0.0892) | 0.0489 (1.00) |  |  | 0.103 (1.00) | 0.0656 (1.00) |  |  |  |
19p gain | 0 (0%) | 493 | 1.85e-05 (0.00655) | 0.0186 (1.00) |  |  | 0.0378 (1.00) | 0.0215 (1.00) | 0.0264 (1.00) | 0.0191 (1.00) | 0.0252 (1.00) | 0.0206 (1.00)
19q gain | 0 (0%) | 492 | 1.12e-06 (0.000425) | 0.00421 (1.00) | 0.636 (1.00) | 0.0551 (1.00) | 0.0127 (1.00) | 0.00552 (1.00) | 0.00778 (1.00) | 0.00503 (1.00) | 0.0073 (1.00) | 0.00558 (1.00)
1p loss | 0 (0%) | 494 | 0.000294 (0.0892) | 0.554 (1.00) |  |  | 0.503 (1.00) | 0.184 (1.00) | 0.3 (1.00) | 0.276 (1.00) | 0.2 (1.00) | 0.282 (1.00)
3q loss | 0 (0%) | 494 | 0.000294 (0.0892) | 0.0489 (1.00) |  |  | 0.103 (1.00) | 0.0656 (1.00) | 0.0264 (1.00) | 0.0191 (1.00) | 0.0252 (1.00) | 0.0206 (1.00)
8p loss | 0 (0%) | 493 | 1.85e-05 (0.00655) | 0.0457 (1.00) |  |  | 0.0378 (1.00) | 0.0215 (1.00) | 0.00778 (1.00) | 0.00503 (1.00) | 0.0073 (1.00) | 0.00558 (1.00)
8q loss | 0 (0%) | 493 | 1.85e-05 (0.00655) | 0.0457 (1.00) |  |  | 0.0378 (1.00) | 0.0215 (1.00) | 0.00778 (1.00) | 0.00503 (1.00) | 0.0073 (1.00) | 0.00558 (1.00)
9p loss | 0 (0%) | 485 | 1.08e-11 (4.26e-09) | 0.267 (1.00) | 0.559 (1.00) | 0.206 (1.00) | 0.0911 (1.00) | 0.0944 (1.00) | 0.185 (1.00) | 0.159 (1.00) | 0.15 (1.00) | 0.176 (1.00)
9q loss | 0 (0%) | 480 | 1.58e-13 (6.32e-11) | 0.177 (1.00) | 0.21 (1.00) | 0.00441 (1.00) | 0.19 (1.00) | 0.139 (1.00) | 0.235 (1.00) | 0.228 (1.00) | 0.168 (1.00) | 0.241 (1.00)
10p loss | 0 (0%) | 491 | 6.62e-08 (2.56e-05) | 0.0944 (1.00) |  |  | 0.0479 (1.00) | 0.0142 (1.00) | 0.0399 (1.00) | 0.0333 (1.00) | 0.0251 (1.00) | 0.0348 (1.00)
10q loss | 0 (0%) | 492 | 1.12e-06 (0.000425) | 0.171 (1.00) |  |  | 0.104 (1.00) | 0.0415 (1.00) | 0.112 (1.00) | 0.0975 (1.00) | 0.0719 (1.00) | 0.101 (1.00)
11p loss | 0 (0%) | 490 | 7.74e-08 (2.98e-05) | 0.0116 (1.00) | 0.499 (1.00) | 1 (1.00) | 0.00603 (1.00) | 0.0143 (1.00) | 0.0399 (1.00) | 0.0333 (1.00) | 0.0251 (1.00) | 0.0348 (1.00)
11q loss | 0 (0%) | 488 | 3.24e-06 (0.00121) | 0.0142 (1.00) | 0.388 (1.00) | 0.798 (1.00) | 0.0143 (1.00) | 0.0148 (1.00) | 0.0138 (1.00) | 0.0075 (1.00) | 0.00862 (1.00) | 0.0117 (1.00)
18p loss | 0 (0%) | 493 | 0.000204 (0.0633) | 0.186 (1.00) | 1 (1.00) | 0.369 (1.00) | 0.224 (1.00) | 0.0814 (1.00) | 0.0743 (1.00) | 0.0671 (1.00) | 0.109 (1.00) | 0.0681 (1.00)
18q loss | 0 (0%) | 493 | 0.000204 (0.0633) | 0.186 (1.00) | 1 (1.00) | 0.369 (1.00) | 0.224 (1.00) | 0.0814 (1.00) | 0.0743 (1.00) | 0.0671 (1.00) | 0.109 (1.00) | 0.0681 (1.00)
21q loss | 0 (0%) | 491 | 0.000192 (0.06) | 0.0944 (1.00) | 0.384 (1.00) | 0.0551 (1.00) | 0.209 (1.00) | 0.222 (1.00) | 0.0399 (1.00) | 0.0333 (1.00) | 0.0251 (1.00) | 0.0348 (1.00)
11p gain | 0 (0%) | 492 | 0.00134 (0.366) | 0.00421 (1.00) |  |  | 0.0127 (1.00) | 0.00552 (1.00) | 0.00228 (0.597) | 0.00132 (0.361) | 0.0021 (0.555) | 0.0015 (0.403)
18p gain | 0 (0%) | 494 | 0.00245 (0.629) | 0.0489 (1.00) |  |  | 0.103 (1.00) | 0.0656 (1.00) |  |  |  |
18q gain | 0 (0%) | 494 | 0.00245 (0.629) | 0.0489 (1.00) |  |  | 0.103 (1.00) | 0.0656 (1.00) |  |  |  |
21q gain | 0 (0%) | 494 | 0.00245 (0.629) | 0.0489 (1.00) |  |  | 0.103 (1.00) | 0.0656 (1.00) | 0.0264 (1.00) | 0.0191 (1.00) | 0.0252 (1.00) | 0.0206 (1.00)
6q loss | 0 (0%) | 494 | 0.0218 (1.00) | 0.0489 (1.00) |  |  | 0.103 (1.00) | 0.0656 (1.00) | 0.0264 (1.00) | 0.0191 (1.00) | 0.0252 (1.00) | 0.0206 (1.00)
13q loss | 0 (0%) | 486 | 0.0123 (1.00) | 0.0227 (1.00) | 0.0779 (1.00) | 1 (1.00) | 0.0208 (1.00) | 0.0129 (1.00) | 0.00774 (1.00) | 0.0164 (1.00) | 0.0086 (1.00) | 0.0023 (0.599)
17p loss | 0 (0%) | 490 | 0.00118 (0.326) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.79 (1.00) | 0.755 (1.00) | 0.518 (1.00) | 0.499 (1.00) | 0.799 (1.00) | 0.5 (1.00)
19p loss | 0 (0%) | 493 | 0.132 (1.00) | 0.0186 (1.00) | 0.281 (1.00) | 0.369 (1.00) | 0.0378 (1.00) | 0.0215 (1.00) | 0.00778 (1.00) | 0.00503 (1.00) | 0.0073 (1.00) | 0.00558 (1.00)

'1q gain' versus 'CN_CNMF'

P value = 3.29e-06 (Fisher's exact test), Q value = 0.0012

Table S1. Gene #1: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
1Q GAIN CNV | 9 | 11 | 1
1Q GAIN WILD-TYPE | 25 | 374 | 77

Figure S1. Get High-res Image Gene #1: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0066

Table S2. Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
4P GAIN CNV | 4 | 0 | 0
4P GAIN WILD-TYPE | 30 | 385 | 78

Figure S2. Get High-res Image Gene #2: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0066

Table S3. Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
4Q GAIN CNV | 4 | 0 | 0
4Q GAIN WILD-TYPE | 30 | 385 | 78

Figure S3. Get High-res Image Gene #3: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 6.97e-20 (Fisher's exact test), Q value = 2.8e-17

Table S4. Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
5P GAIN CNV | 16 | 1 | 0
5P GAIN WILD-TYPE | 18 | 384 | 78

Figure S4. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.000873 (Fisher's exact test), Q value = 0.24

Table S5. Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
5P GAIN CNV | 12 | 2 | 3
5P GAIN WILD-TYPE | 138 | 70 | 272

Figure S5. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000538 (Fisher's exact test), Q value = 0.16

Table S6. Gene #4: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
5P GAIN CNV | 0 | 5 | 12 | 0
5P GAIN WILD-TYPE | 89 | 194 | 118 | 65

Figure S6. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000541 (Fisher's exact test), Q value = 0.16

Table S7. Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
5P GAIN CNV | 10 | 6 | 0
5P GAIN WILD-TYPE | 104 | 162 | 142

Figure S7. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.21

Table S8. Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
5P GAIN CNV | 6 | 10 | 0
5P GAIN WILD-TYPE | 161 | 107 | 140

Figure S8. Get High-res Image Gene #4: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 2.6e-18 (Fisher's exact test), Q value = 1e-15

Table S9. Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
5Q GAIN CNV | 14 | 0 | 0
5Q GAIN WILD-TYPE | 20 | 385 | 78

Figure S9. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 4.02e-05 (Fisher's exact test), Q value = 0.014

Table S10. Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
5Q GAIN CNV | 12 | 1 | 1
5Q GAIN WILD-TYPE | 138 | 71 | 274

Figure S10. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.000164 (Fisher's exact test), Q value = 0.052

Table S11. Gene #5: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 59 | 115 | 161
5Q GAIN CNV | 12 | 0 | 0 | 2
5Q GAIN WILD-TYPE | 136 | 59 | 115 | 159

Figure S11. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.71e-05 (Fisher's exact test), Q value = 0.016

Table S12. Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
5Q GAIN CNV | 0 | 2 | 12 | 0
5Q GAIN WILD-TYPE | 89 | 197 | 118 | 65

Figure S12. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000106 (Fisher's exact test), Q value = 0.034

Table S13. Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
5Q GAIN CNV | 10 | 3 | 0
5Q GAIN WILD-TYPE | 104 | 165 | 142

Figure S13. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000119 (Fisher's exact test), Q value = 0.038

Table S14. Gene #5: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
5Q GAIN CNV | 3 | 10 | 0
5Q GAIN WILD-TYPE | 164 | 107 | 140

Figure S14. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1.59e-22 (Fisher's exact test), Q value = 6.4e-20

Table S15. Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
7P GAIN CNV | 17 | 0 | 0
7P GAIN WILD-TYPE | 17 | 385 | 78

Figure S15. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.000169 (Fisher's exact test), Q value = 0.053

Table S16. Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
7P GAIN CNV | 12 | 3 | 2
7P GAIN WILD-TYPE | 138 | 69 | 273

Figure S16. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.12

Table S17. Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 59 | 115 | 161
7P GAIN CNV | 13 | 0 | 1 | 2
7P GAIN WILD-TYPE | 135 | 59 | 114 | 159

Figure S17. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.05e-05 (Fisher's exact test), Q value = 0.02

Table S18. Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
7P GAIN CNV | 1 | 2 | 13 | 0
7P GAIN WILD-TYPE | 88 | 197 | 117 | 65

Figure S18. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000272 (Fisher's exact test), Q value = 0.083

Table S19. Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
7P GAIN CNV | 12 | 4 | 1
7P GAIN WILD-TYPE | 102 | 164 | 141

Figure S19. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000418 (Fisher's exact test), Q value = 0.12

Table S20. Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
7P GAIN CNV | 4 | 12 | 1
7P GAIN WILD-TYPE | 163 | 105 | 139

Figure S20. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1.76e-23 (Fisher's exact test), Q value = 7.1e-21

Table S21. Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
7Q GAIN CNV | 18 | 0 | 1
7Q GAIN WILD-TYPE | 16 | 385 | 77

Figure S21. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 3.65e-05 (Fisher's exact test), Q value = 0.012

Table S22. Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
7Q GAIN CNV | 14 | 3 | 2
7Q GAIN WILD-TYPE | 136 | 69 | 273

Figure S22. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 5.06e-05 (Fisher's exact test), Q value = 0.017

Table S23. Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 59 | 115 | 161
7Q GAIN CNV | 15 | 0 | 1 | 2
7Q GAIN WILD-TYPE | 133 | 59 | 114 | 159

Figure S23. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.18e-06 (Fisher's exact test), Q value = 0.0022

Table S24. Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
7Q GAIN CNV | 1 | 2 | 15 | 0
7Q GAIN WILD-TYPE | 88 | 197 | 115 | 65

Figure S24. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.000289 (Fisher's exact test), Q value = 0.088

Table S25. Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 148 | 149
7Q GAIN CNV | 14 | 2 | 3
7Q GAIN WILD-TYPE | 113 | 146 | 146

Figure S25. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.0099

Table S26. Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
7Q GAIN CNV | 14 | 4 | 1
7Q GAIN WILD-TYPE | 100 | 164 | 141

Figure S26. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.062

Table S27. Gene #7: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 125 | 157 | 142
7Q GAIN CNV | 14 | 2 | 3
7Q GAIN WILD-TYPE | 111 | 155 | 139

Figure S27. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.59e-05 (Fisher's exact test), Q value = 0.012

Table S28. Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
7Q GAIN CNV | 4 | 14 | 1
7Q GAIN WILD-TYPE | 163 | 103 | 139

Figure S28. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.063

Table S29. Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
11Q GAIN CNV | 3 | 0 | 1
11Q GAIN WILD-TYPE | 31 | 385 | 77

Figure S29. Get High-res Image Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.03e-12 (Fisher's exact test), Q value = 4.1e-10

Table S30. Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
12P GAIN CNV | 10 | 0 | 1
12P GAIN WILD-TYPE | 24 | 385 | 77

Figure S30. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.0011

Table S31. Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
12P GAIN CNV | 11 | 0 | 0
12P GAIN WILD-TYPE | 139 | 72 | 275

Figure S31. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0058

Table S32. Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 59 | 115 | 161
12P GAIN CNV | 11 | 0 | 0 | 0
12P GAIN WILD-TYPE | 137 | 59 | 115 | 161

Figure S32. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.12e-06 (Fisher's exact test), Q value = 0.00079

Table S33. Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
12P GAIN CNV | 0 | 0 | 11 | 0
12P GAIN WILD-TYPE | 89 | 199 | 119 | 65

Figure S33. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.017

Table S34. Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 148 | 149
12P GAIN CNV | 10 | 0 | 1
12P GAIN WILD-TYPE | 117 | 148 | 148

Figure S34. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.0061

Table S35. Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
12P GAIN CNV | 10 | 1 | 0
12P GAIN WILD-TYPE | 104 | 167 | 142

Figure S35. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.43e-05 (Fisher's exact test), Q value = 0.012

Table S36. Gene #10: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 125 | 157 | 142
12P GAIN CNV | 10 | 0 | 1
12P GAIN WILD-TYPE | 115 | 157 | 141

Figure S36. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.007

Table S37. Gene #10: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
12P GAIN CNV | 1 | 10 | 0
12P GAIN WILD-TYPE | 166 | 107 | 140

Figure S37. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1.27e-12 (Fisher's exact test), Q value = 5e-10

Table S38. Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
12Q GAIN CNV | 10 | 0 | 2
12Q GAIN WILD-TYPE | 24 | 385 | 76

Figure S38. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 6.48e-07 (Fisher's exact test), Q value = 0.00025

Table S39. Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
12Q GAIN CNV | 12 | 0 | 0
12Q GAIN WILD-TYPE | 138 | 72 | 275

Figure S39. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 4.46e-06 (Fisher's exact test), Q value = 0.0017

Table S40. Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 59 | 115 | 161
12Q GAIN CNV | 12 | 0 | 0 | 0
12Q GAIN WILD-TYPE | 136 | 59 | 115 | 161

Figure S40. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.49e-07 (Fisher's exact test), Q value = 0.00025

Table S41. Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
12Q GAIN CNV | 0 | 0 | 12 | 0
12Q GAIN WILD-TYPE | 89 | 199 | 118 | 65

Figure S41. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.0059

Table S42. Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 148 | 149
12Q GAIN CNV | 11 | 0 | 1
12Q GAIN WILD-TYPE | 116 | 148 | 148

Figure S42. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0018

Table S43. Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
12Q GAIN CNV | 11 | 1 | 0
12Q GAIN WILD-TYPE | 103 | 167 | 142

Figure S43. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.11e-06 (Fisher's exact test), Q value = 0.0022

Table S44. Gene #11: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 125 | 157 | 142
12Q GAIN CNV | 11 | 0 | 1
12Q GAIN WILD-TYPE | 114 | 157 | 141

Figure S44. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.76e-06 (Fisher's exact test), Q value = 0.0021

Table S45. Gene #11: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
12Q GAIN CNV | 1 | 11 | 0
12Q GAIN WILD-TYPE | 166 | 106 | 140

Figure S45. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.089

Table S46. Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
13Q GAIN CNV | 3 | 0 | 0
13Q GAIN WILD-TYPE | 31 | 385 | 78

Figure S46. Get High-res Image Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 5.02e-09 (Fisher's exact test), Q value = 1.9e-06

Table S47. Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
14Q GAIN CNV | 7 | 0 | 1
14Q GAIN WILD-TYPE | 27 | 385 | 77

Figure S47. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 8.76e-05 (Fisher's exact test), Q value = 0.028

Table S48. Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
14Q GAIN CNV | 8 | 0 | 0
14Q GAIN WILD-TYPE | 142 | 72 | 275

Figure S48. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.000325 (Fisher's exact test), Q value = 0.098

Table S49. Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 59 | 115 | 161
14Q GAIN CNV | 8 | 0 | 0 | 0
14Q GAIN WILD-TYPE | 140 | 59 | 115 | 161

Figure S49. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000148 (Fisher's exact test), Q value = 0.047

Table S50. Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
14Q GAIN CNV | 0 | 0 | 8 | 0
14Q GAIN WILD-TYPE | 89 | 199 | 122 | 65

Figure S50. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 5.51e-14 (Fisher's exact test), Q value = 2.2e-11

Table S51. Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
16P GAIN CNV | 11 | 0 | 1
16P GAIN WILD-TYPE | 23 | 385 | 77

Figure S51. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 3.21e-05 (Fisher's exact test), Q value = 0.011

Table S52. Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
16P GAIN CNV | 10 | 2 | 0
16P GAIN WILD-TYPE | 140 | 70 | 275

Figure S52. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.042

Table S53. Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 59 | 115 | 161
16P GAIN CNV | 11 | 0 | 0 | 1
16P GAIN WILD-TYPE | 137 | 59 | 115 | 160

Figure S53. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.69e-05 (Fisher's exact test), Q value = 0.0093

Table S54. Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
16P GAIN CNV | 0 | 1 | 11 | 0
16P GAIN WILD-TYPE | 89 | 198 | 119 | 65

Figure S54. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.066

Table S55. Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 148 | 149
16P GAIN CNV | 10 | 0 | 2
16P GAIN WILD-TYPE | 117 | 148 | 147

Figure S55. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.019

Table S56. Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
16P GAIN CNV | 10 | 2 | 0
16P GAIN WILD-TYPE | 104 | 166 | 142

Figure S56. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.28e-05 (Fisher's exact test), Q value = 0.027

Table S57. Gene #14: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 125 | 157 | 142
16P GAIN CNV | 10 | 0 | 2
16P GAIN WILD-TYPE | 115 | 157 | 140

Figure S57. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.35e-05 (Fisher's exact test), Q value = 0.027

Table S58. Gene #14: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
16P GAIN CNV | 2 | 10 | 0
16P GAIN WILD-TYPE | 165 | 107 | 140

Figure S58. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 5.67e-13 (Fisher's exact test), Q value = 2.3e-10

Table S59. Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
16Q GAIN CNV | 10 | 0 | 0
16Q GAIN WILD-TYPE | 24 | 385 | 78

Figure S59. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.000224 (Fisher's exact test), Q value = 0.069

Table S60. Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
16Q GAIN CNV | 8 | 2 | 0
16Q GAIN WILD-TYPE | 142 | 70 | 275

Figure S60. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.12

Table S61. Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
16Q GAIN CNV | 0 | 1 | 9 | 0
16Q GAIN WILD-TYPE | 89 | 198 | 121 | 65

Figure S61. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000547 (Fisher's exact test), Q value = 0.16

Table S62. Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
16Q GAIN CNV | 8 | 2 | 0
16Q GAIN WILD-TYPE | 106 | 166 | 142

Figure S62. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000713 (Fisher's exact test), Q value = 0.2

Table S63. Gene #15: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 125 | 157 | 142
16Q GAIN CNV | 8 | 0 | 2
16Q GAIN WILD-TYPE | 117 | 157 | 140

Figure S63. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000758 (Fisher's exact test), Q value = 0.21

Table S64. Gene #15: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
16Q GAIN CNV | 2 | 8 | 0
16Q GAIN WILD-TYPE | 165 | 109 | 140

Figure S64. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 2e-09 (Fisher's exact test), Q value = 7.8e-07

Table S65. Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
17P GAIN CNV | 9 | 2 | 1
17P GAIN WILD-TYPE | 25 | 383 | 77

Figure S65. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 6.48e-07 (Fisher's exact test), Q value = 0.00025

Table S66. Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
17P GAIN CNV | 12 | 0 | 0
17P GAIN WILD-TYPE | 138 | 72 | 275

Figure S66. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 4.46e-06 (Fisher's exact test), Q value = 0.0017

Table S67. Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 59 | 115 | 161
17P GAIN CNV | 12 | 0 | 0 | 0
17P GAIN WILD-TYPE | 136 | 59 | 115 | 161

Figure S67. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.49e-07 (Fisher's exact test), Q value = 0.00025

Table S68. Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
17P GAIN CNV | 0 | 0 | 12 | 0
17P GAIN WILD-TYPE | 89 | 199 | 118 | 65

Figure S68. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.017

Table S69. Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 148 | 149
17P GAIN CNV | 10 | 0 | 1
17P GAIN WILD-TYPE | 117 | 148 | 148

Figure S69. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.0061

Table S70. Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
17P GAIN CNV | 10 | 1 | 0
17P GAIN WILD-TYPE | 104 | 167 | 142

Figure S70. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.43e-05 (Fisher's exact test), Q value = 0.012

Table S71. Gene #16: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 125 | 157 | 142
17P GAIN CNV | 10 | 0 | 1
17P GAIN WILD-TYPE | 115 | 157 | 141

Figure S71. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.007

Table S72. Gene #16: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
17P GAIN CNV | 1 | 10 | 0
17P GAIN WILD-TYPE | 166 | 107 | 140

Figure S72. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 3.83e-09 (Fisher's exact test), Q value = 1.5e-06

Table S73. Gene #17: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
17Q GAIN CNV | 9 | 2 | 2
17Q GAIN WILD-TYPE | 25 | 383 | 76

Figure S73. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 3.73e-07 (Fisher's exact test), Q value = 0.00014

Table S74. Gene #17: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
17Q GAIN CNV | 13 | 0 | 0
17Q GAIN WILD-TYPE | 137 | 72 | 275

Figure S74. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.00057

Table S75. Gene #17: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 59 | 115 | 161
17Q GAIN CNV | 13 | 0 | 0 | 0
17Q GAIN WILD-TYPE | 135 | 59 | 115 | 161

Figure S75. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.6e-07 (Fisher's exact test), Q value = 6.2e-05

Table S76. Gene #17: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
17Q GAIN CNV | 0 | 0 | 13 | 0
17Q GAIN WILD-TYPE | 89 | 199 | 117 | 65

Figure S76. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.0059

Table S77. Gene #17: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 148 | 149
17Q GAIN CNV | 11 | 0 | 1
17Q GAIN WILD-TYPE | 116 | 148 | 148

Figure S77. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0018

Table S78. Gene #17: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
17Q GAIN CNV | 11 | 1 | 0
17Q GAIN WILD-TYPE | 103 | 167 | 142

Figure S78. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.11e-06 (Fisher's exact test), Q value = 0.0022

Table S79. Gene #17: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 125 | 157 | 142
17Q GAIN CNV | 11 | 0 | 1
17Q GAIN WILD-TYPE | 114 | 157 | 141

Figure S79. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5.76e-06 (Fisher's exact test), Q value = 0.0021

Table S80. Gene #17: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
17Q GAIN CNV | 1 | 11 | 0
17Q GAIN WILD-TYPE | 166 | 106 | 140

Figure S80. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0066

Table S81. Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
19P GAIN CNV | 4 | 0 | 0
19P GAIN WILD-TYPE | 30 | 385 | 78

Figure S81. Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00042

Table S82. Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
19Q GAIN CNV | 5 | 0 | 0
19Q GAIN WILD-TYPE | 29 | 385 | 78

Figure S82. Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.11e-11 (Fisher's exact test), Q value = 4.4e-09

Table S83. Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
20P GAIN CNV | 9 | 0 | 0
20P GAIN WILD-TYPE | 25 | 385 | 78

Figure S83. Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000706 (Fisher's exact test), Q value = 0.2

Table S84. Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
20P GAIN CNV | 7 | 2 | 0
20P GAIN WILD-TYPE | 143 | 70 | 275

Figure S84. Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.11e-11 (Fisher's exact test), Q value = 4.4e-09

Table S85. Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
20Q GAIN CNV | 9 | 0 | 0
20Q GAIN WILD-TYPE | 25 | 385 | 78

Figure S85. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.000706 (Fisher's exact test), Q value = 0.2

Table S86. Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
20Q GAIN CNV | 7 | 2 | 0
20Q GAIN WILD-TYPE | 143 | 70 | 275

Figure S86. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.089

Table S87. Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
1P LOSS CNV | 3 | 0 | 0
1P LOSS WILD-TYPE | 31 | 385 | 78

Figure S87. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 5.02e-09 (Fisher's exact test), Q value = 1.9e-06

Table S88. Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
2P LOSS CNV | 7 | 0 | 1
2P LOSS WILD-TYPE | 27 | 385 | 77

Figure S88. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 8.76e-05 (Fisher's exact test), Q value = 0.028

Table S89. Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
2P LOSS CNV | 8 | 0 | 0
2P LOSS WILD-TYPE | 142 | 72 | 275

Figure S89. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.000325 (Fisher's exact test), Q value = 0.098

Table S90. Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 59 | 115 | 161
2P LOSS CNV | 8 | 0 | 0 | 0
2P LOSS WILD-TYPE | 140 | 59 | 115 | 161

Figure S90. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000148 (Fisher's exact test), Q value = 0.047

Table S91. Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
2P LOSS CNV | 0 | 0 | 8 | 0
2P LOSS WILD-TYPE | 89 | 199 | 122 | 65

Figure S91. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 5.53e-05 (Fisher's exact test), Q value = 0.018

Table S92. Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 148 | 149
2P LOSS CNV | 8 | 0 | 0
2P LOSS WILD-TYPE | 119 | 148 | 149

Figure S92. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.0079

Table S93. Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
2P LOSS CNV | 8 | 0 | 0
2P LOSS WILD-TYPE | 106 | 168 | 142

Figure S93. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.85e-05 (Fisher's exact test), Q value = 0.016

Table S94. Gene #26: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 125 | 157 | 142
2P LOSS CNV | 8 | 0 | 0
2P LOSS WILD-TYPE | 117 | 157 | 142

Figure S94. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.81e-05 (Fisher's exact test), Q value = 0.0097

Table S95. Gene #26: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
2P LOSS CNV | 0 | 8 | 0
2P LOSS WILD-TYPE | 167 | 109 | 140

Figure S95. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 3.78e-09 (Fisher's exact test), Q value = 1.5e-06

Table S96. Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
2Q LOSS CNV | 7 | 0 | 0
2Q LOSS WILD-TYPE | 27 | 385 | 78

Figure S96. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.000364 (Fisher's exact test), Q value = 0.11

Table S97. Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
2Q LOSS CNV | 7 | 0 | 0
2Q LOSS WILD-TYPE | 143 | 72 | 275

Figure S97. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000534 (Fisher's exact test), Q value = 0.16

Table S98. Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
2Q LOSS CNV | 0 | 0 | 7 | 0
2Q LOSS WILD-TYPE | 89 | 199 | 123 | 65

Figure S98. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.06

Table S99. Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 148 | 149
2Q LOSS CNV | 7 | 0 | 0
2Q LOSS WILD-TYPE | 120 | 148 | 149

Figure S99. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.85e-05 (Fisher's exact test), Q value = 0.029

Table S100. Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
2Q LOSS CNV | 7 | 0 | 0
2Q LOSS WILD-TYPE | 107 | 168 | 142

Figure S100. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000171 (Fisher's exact test), Q value = 0.054

Table S101. Gene #27: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 125 | 157 | 142
2Q LOSS CNV | 7 | 0 | 0
2Q LOSS WILD-TYPE | 118 | 157 | 142

Figure S101. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000107 (Fisher's exact test), Q value = 0.034

Table S102. Gene #27: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
2Q LOSS CNV | 0 | 7 | 0
2Q LOSS WILD-TYPE | 167 | 110 | 140

Figure S102. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.089

Table S103. Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
3Q LOSS CNV | 3 | 0 | 0
3Q LOSS WILD-TYPE | 31 | 385 | 78

Figure S103. Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0066

Table S104. Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
8P LOSS CNV | 4 | 0 | 0
8P LOSS WILD-TYPE | 30 | 385 | 78

Figure S104. Get High-res Image Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0066

Table S105. Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
8Q LOSS CNV | 4 | 0 | 0
8Q LOSS WILD-TYPE | 30 | 385 | 78

Figure S105. Get High-res Image Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1.08e-11 (Fisher's exact test), Q value = 4.3e-09

Table S106. Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
9P LOSS CNV | 10 | 1 | 1
9P LOSS WILD-TYPE | 24 | 384 | 77

Figure S106. Get High-res Image Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.58e-13 (Fisher's exact test), Q value = 6.3e-11

Table S107. Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
9Q LOSS CNV | 13 | 3 | 1
9Q LOSS WILD-TYPE | 21 | 382 | 77

Figure S107. Get High-res Image Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 6.62e-08 (Fisher's exact test), Q value = 2.6e-05

Table S108. Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
10P LOSS CNV | 6 | 0 | 0
10P LOSS WILD-TYPE | 28 | 385 | 78

Figure S108. Get High-res Image Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00042

Table S109. Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
10Q LOSS CNV | 5 | 0 | 0
10Q LOSS WILD-TYPE | 29 | 385 | 78

Figure S109. Get High-res Image Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 7.74e-08 (Fisher's exact test), Q value = 3e-05

Table S110. Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
11P LOSS CNV | 6 | 0 | 1
11P LOSS WILD-TYPE | 28 | 385 | 77

Figure S110. Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.24e-06 (Fisher's exact test), Q value = 0.0012

Table S111. Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
11Q LOSS CNV | 6 | 2 | 1
11Q LOSS WILD-TYPE | 28 | 383 | 77

Figure S111. Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.000464 (Fisher's exact test), Q value = 0.14

Table S112. Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
15Q LOSS CNV | 4 | 2 | 1
15Q LOSS WILD-TYPE | 30 | 383 | 77

Figure S112. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000534 (Fisher's exact test), Q value = 0.16

Table S113. Gene #39: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
15Q LOSS CNV | 0 | 0 | 7 | 0
15Q LOSS WILD-TYPE | 89 | 199 | 123 | 65

Figure S113. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.000664 (Fisher's exact test), Q value = 0.19

Table S114. Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 148 | 149
15Q LOSS CNV | 6 | 0 | 0
15Q LOSS WILD-TYPE | 121 | 148 | 149

Figure S114. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000342 (Fisher's exact test), Q value = 0.1

Table S115. Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
15Q LOSS CNV | 6 | 0 | 0
15Q LOSS WILD-TYPE | 108 | 168 | 142

Figure S115. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000602 (Fisher's exact test), Q value = 0.17

Table S116. Gene #39: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 125 | 157 | 142
15Q LOSS CNV | 6 | 0 | 0
15Q LOSS WILD-TYPE | 119 | 157 | 142

Figure S116. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000402 (Fisher's exact test), Q value = 0.12

Table S117. Gene #39: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
15Q LOSS CNV | 0 | 6 | 0
15Q LOSS WILD-TYPE | 167 | 111 | 140

Figure S117. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.063

Table S118. Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
18P LOSS CNV | 3 | 0 | 1
18P LOSS WILD-TYPE | 31 | 385 | 77

Figure S118. Get High-res Image Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.063

Table S119. Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
18Q LOSS CNV | 3 | 0 | 1
18Q LOSS WILD-TYPE | 31 | 385 | 77

Figure S119. Get High-res Image Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.06

Table S120. Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
21Q LOSS CNV | 4 | 1 | 1
21Q LOSS WILD-TYPE | 30 | 384 | 77

Figure S120. Get High-res Image Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 6.79e-58 (Fisher's exact test), Q value = 2.8e-55

Table S121. Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 385 | 78
22Q LOSS CNV | 8 | 0 | 58
22Q LOSS WILD-TYPE | 26 | 385 | 20

Figure S121. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 4.45e-05 (Fisher's exact test), Q value = 0.015

Table S122. Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 72 | 275
22Q LOSS CNV | 36 | 7 | 23
22Q LOSS WILD-TYPE | 114 | 65 | 252

Figure S122. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 2.26e-11 (Fisher's exact test), Q value = 8.9e-09

Table S123. Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 148 | 59 | 115 | 161
22Q LOSS CNV | 36 | 5 | 20 | 1
22Q LOSS WILD-TYPE | 112 | 54 | 95 | 160

Figure S123. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.59e-11 (Fisher's exact test), Q value = 1e-08

Table S124. Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 89 | 199 | 130 | 65
22Q LOSS CNV | 17 | 6 | 36 | 3
22Q LOSS WILD-TYPE | 72 | 193 | 94 | 62

Figure S124. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 4.33e-05 (Fisher's exact test), Q value = 0.015

Table S125. Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 148 | 149
22Q LOSS CNV | 31 | 14 | 10
22Q LOSS WILD-TYPE | 96 | 134 | 139

Figure S125. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.51e-06 (Fisher's exact test), Q value = 0.0034

Table S126. Gene #45: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 114 | 168 | 142
22Q LOSS CNV | 30 | 11 | 14
22Q LOSS WILD-TYPE | 84 | 157 | 128

Figure S126. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.93e-05 (Fisher's exact test), Q value = 0.013

Table S127. Gene #45: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 125 | 157 | 142
22Q LOSS CNV | 31 | 14 | 10
22Q LOSS WILD-TYPE | 94 | 143 | 132

Figure S127. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0018

Table S128. Gene #45: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 167 | 117 | 140
22Q LOSS CNV | 9 | 30 | 16
22Q LOSS WILD-TYPE | 158 | 87 | 124

Figure S128. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

- Mutation data file = broad_values_by_arm.mutsig.cluster.txt

- Molecular subtypes file = THCA-TP.transferedmergedcluster.txt

- Number of patients = 497

- Number of significantly arm-level cnvs = 45

- Number of molecular subtypes = 10

- Exclude genes that fewer than K tumors have mutations, 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)
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