Correlation between copy number variations of arm-level result and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C15X27MN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C15X27MN
Overview
Introduction

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

Summary

Testing the association between copy number variation 57 arm-level events and 10 molecular subtypes across 494 patients, 166 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 3p 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', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

- 8p gain cnv correlated to 'CN_CNMF'.

- 8q gain cnv correlated to 'CN_CNMF'.

- 11p gain cnv correlated to 'CN_CNMF'.

- 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', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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'.

- 18p gain cnv correlated to 'CN_CNMF'.

- 18q gain cnv correlated to 'CN_CNMF'.

- 19p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 19q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

- 21q gain cnv correlated to 'CN_CNMF'.

- xq gain cnv correlated to 'CN_CNMF'.

- 1p loss cnv correlated to 'CN_CNMF'.

- 1q 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_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 3p loss cnv correlated to 'CN_CNMF'.

- 3q loss cnv correlated to 'CN_CNMF'.

- 6q 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' and 'MIRSEQ_CNMF'.

- 15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_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_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 57 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 166 significant findings detected.

|  | Clinical Features | 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 | 20 (4%) | 474 | 6.92e-25 (3.69e-22) | 9.82e-06 (0.00451) | 0.571 (1.00) | 0.000676 (0.249) | 0.000166 (0.067) | 7.82e-06 (0.00368) | 0.000144 (0.0585) | 1.15e-05 (0.00527) | 4.38e-05 (0.0189) | 9.06e-06 (0.00419)
5q gain | 17 (3%) | 477 | 1.76e-22 (9.35e-20) | 3.39e-05 (0.0147) | 0.85 (1.00) | 0.00745 (1.00) | 0.000345 (0.132) | 1.56e-05 (0.00709) | 0.000344 (0.132) | 4.11e-05 (0.0178) | 9.6e-05 (0.0395) | 3.18e-05 (0.0139)
12p gain | 14 (3%) | 480 | 1.48e-16 (7.82e-14) | 3.71e-06 (0.00178) | 0.85 (1.00) | 0.00745 (1.00) | 1.56e-05 (0.00709) | 6.26e-07 (0.000315) | 6.05e-05 (0.0256) | 8.86e-06 (0.0041) | 9.65e-06 (0.00445) | 8.52e-06 (0.00396)
12q gain | 15 (3%) | 479 | 2.14e-16 (1.12e-13) | 1.32e-06 (0.000645) | 0.85 (1.00) | 0.00745 (1.00) | 8.44e-06 (0.00395) | 1.55e-07 (7.87e-05) | 2.24e-05 (0.00988) | 2.87e-06 (0.00139) | 3.63e-06 (0.00175) | 2.66e-06 (0.00129)
16p gain | 15 (3%) | 479 | 6.94e-18 (3.67e-15) | 1.85e-05 (0.0083) | 0.633 (1.00) | 0.0106 (1.00) | 0.000187 (0.0751) | 8.24e-06 (0.00386) | 0.000192 (0.0765) | 4.25e-05 (0.0184) | 3.07e-05 (0.0134) | 3.96e-05 (0.0172)
17p gain | 16 (3%) | 478 | 4.23e-13 (2.2e-10) | 5.64e-07 (0.000285) | 0.538 (1.00) | 0.00327 (1.00) | 4.05e-06 (0.00194) | 4.72e-08 (2.42e-05) | 8.06e-06 (0.00379) | 8.97e-07 (0.00045) | 1.33e-06 (0.000649) | 8.04e-07 (0.000404)
17q gain | 18 (4%) | 476 | 5.03e-14 (2.62e-11) | 1.13e-06 (0.000563) | 0.633 (1.00) | 0.00271 (0.906) | 1.47e-05 (0.0067) | 3.38e-07 (0.000171) | 1.17e-05 (0.00533) | 1.46e-06 (0.00071) | 3.69e-06 (0.00177) | 1.09e-06 (0.000544)
19p gain | 8 (2%) | 486 | 2.19e-10 (1.13e-07) | 0.000139 (0.0568) |  |  | 0.000585 (0.217) | 5.96e-05 (0.0253) | 6.43e-05 (0.027) | 1.99e-05 (0.0088) | 0.000242 (0.0955) | 1.75e-05 (0.00787)
19q gain | 10 (2%) | 484 | 1.92e-11 (9.93e-09) | 8.44e-06 (0.00395) | 0.636 (1.00) | 0.0523 (1.00) | 7.31e-05 (0.0305) | 6.66e-06 (0.00315) | 5.49e-06 (0.00262) | 1.25e-06 (0.000613) | 2.43e-05 (0.0107) | 1.06e-06 (0.000533)
2p loss | 10 (2%) | 484 | 1.92e-11 (9.93e-09) | 8.44e-06 (0.00395) | 0.773 (1.00) | 0.0122 (1.00) | 7.31e-05 (0.0305) | 6.66e-06 (0.00315) | 5.49e-06 (0.00262) | 1.25e-06 (0.000613) | 2.43e-05 (0.0107) | 1.06e-06 (0.000533)
2q loss | 10 (2%) | 484 | 6.03e-13 (3.13e-10) | 8.44e-06 (0.00395) | 0.773 (1.00) | 0.0122 (1.00) | 7.31e-05 (0.0305) | 6.66e-06 (0.00315) | 5.49e-06 (0.00262) | 1.25e-06 (0.000613) | 2.43e-05 (0.0107) | 1.06e-06 (0.000533)
15q loss | 8 (2%) | 486 | 5.63e-05 (0.0241) | 0.000139 (0.0568) | 0.193 (1.00) | 0.126 (1.00) | 0.000585 (0.217) | 5.96e-05 (0.0253) | 6.43e-05 (0.027) | 1.99e-05 (0.0088) | 0.000242 (0.0955) | 1.75e-05 (0.00787)
14q gain | 11 (2%) | 483 | 3.23e-10 (1.66e-07) | 0.000161 (0.0652) | 1 (1.00) | 0.079 (1.00) | 0.000557 (0.207) | 6.26e-05 (0.0264) | 0.000461 (0.174) | 0.000151 (0.0611) | 0.00123 (0.434) | 0.000114 (0.0468)
22q loss | 86 (17%) | 408 | 7.48e-90 (4e-87) | 1.1e-05 (0.00502) | 0.123 (1.00) | 0.15 (1.00) | 3.38e-09 (1.74e-06) | 8.03e-08 (4.09e-05) | 0.000956 (0.35) | 0.000342 (0.132) | 3.12e-06 (0.00151) | 0.000206 (0.0821)
7p gain | 18 (4%) | 476 | 6.29e-24 (3.35e-21) | 7.19e-05 (0.03) | 0.66 (1.00) | 0.00219 (0.746) | 0.00088 (0.324) | 6.17e-05 (0.026) | 0.00105 (0.379) | 0.000121 (0.0498) | 0.000259 (0.102) | 7.61e-05 (0.0314)
16q gain | 13 (3%) | 481 | 6.49e-17 (3.43e-14) | 0.000121 (0.0498) | 0.795 (1.00) | 0.0363 (1.00) | 0.00105 (0.379) | 7.59e-05 (0.0314) | 0.00171 (0.602) | 0.000387 (0.146) | 0.000182 (0.073) | 0.000336 (0.13)
5p gain | 21 (4%) | 473 | 4.18e-23 (2.22e-20) | 0.00093 (0.341) | 0.53 (1.00) | 0.0969 (1.00) | 0.00705 (1.00) | 0.000485 (0.182) | 0.00411 (1.00) | 0.000523 (0.195) | 0.0011 (0.396) | 0.00031 (0.12)
20p gain | 12 (2%) | 482 | 1.42e-15 (7.47e-13) | 0.000376 (0.143) | 0.795 (1.00) | 0.0193 (1.00) | 0.003 (0.993) | 0.00026 (0.102) | 0.00466 (1.00) | 0.00111 (0.397) | 0.000508 (0.19) | 0.000981 (0.358)
20q gain | 12 (2%) | 482 | 1.42e-15 (7.47e-13) | 0.000376 (0.143) | 0.795 (1.00) | 0.0193 (1.00) | 0.003 (0.993) | 0.00026 (0.102) | 0.00466 (1.00) | 0.00111 (0.397) | 0.000508 (0.19) | 0.000981 (0.358)
1q gain | 24 (5%) | 470 | 9.81e-06 (0.00451) | 0.0289 (1.00) | 0.00112 (0.4) | 0.0319 (1.00) | 0.000993 (0.36) | 5.04e-05 (0.0216) | 0.146 (1.00) | 0.0524 (1.00) | 0.0941 (1.00) | 0.0219 (1.00)
11q loss | 9 (2%) | 485 | 3.28e-06 (0.00158) | 0.0106 (1.00) | 0.321 (1.00) | 0.794 (1.00) | 0.0176 (1.00) | 0.00994 (1.00) | 0.000352 (0.134) | 0.00336 (1.00) | 0.00122 (0.432) | 0.00275 (0.914)
3p gain | 3 (1%) | 491 | 0.0003 (0.117) | 0.582 (1.00) |  |  | 0.488 (1.00) | 0.195 (1.00) | 0.207 (1.00) | 0.355 (1.00) | 0.323 (1.00) | 0.27 (1.00)
4p gain | 5 (1%) | 489 | 1.16e-06 (0.000575) | 0.00581 (1.00) |  |  | 0.0181 (1.00) | 0.00529 (1.00) | 0.0268 (1.00) | 0.0215 (1.00) | 0.0687 (1.00) | 0.0216 (1.00)
4q gain | 5 (1%) | 489 | 1.16e-06 (0.000575) | 0.00581 (1.00) |  |  | 0.0181 (1.00) | 0.00529 (1.00) | 0.0268 (1.00) | 0.0215 (1.00) | 0.0687 (1.00) | 0.0216 (1.00)
8p gain | 6 (1%) | 488 | 0.000364 (0.139) | 0.551 (1.00) | 0.457 (1.00) | 0.655 (1.00) | 0.625 (1.00) | 0.301 (1.00) | 0.526 (1.00) | 0.294 (1.00) | 0.334 (1.00) | 0.341 (1.00)
8q gain | 7 (1%) | 487 | 4.62e-05 (0.0199) | 0.378 (1.00) | 0.457 (1.00) | 0.655 (1.00) | 0.866 (1.00) | 0.561 (1.00) | 0.799 (1.00) | 0.561 (1.00) | 0.318 (1.00) | 0.629 (1.00)
11p gain | 6 (1%) | 488 | 0.000191 (0.0764) | 0.0263 (1.00) | 0.78 (1.00) | 0.284 (1.00) | 0.053 (1.00) | 0.0106 (1.00) | 0.0146 (1.00) | 0.00351 (1.00) | 0.00237 (0.801) | 0.00392 (1.00)
11q gain | 5 (1%) | 489 | 1.6e-05 (0.00724) | 0.0757 (1.00) | 0.78 (1.00) | 0.284 (1.00) | 0.116 (1.00) | 0.0275 (1.00) | 0.0415 (1.00) | 0.0115 (1.00) | 0.00735 (1.00) | 0.0127 (1.00)
13q gain | 5 (1%) | 489 | 1.16e-06 (0.000575) | 0.0173 (1.00) | 0.384 (1.00) | 0.0523 (1.00) | 0.046 (1.00) | 0.0196 (1.00) | 0.169 (1.00) | 0.139 (1.00) | 0.21 (1.00) | 0.148 (1.00)
18p gain | 6 (1%) | 488 | 1.16e-06 (0.000575) | 0.0973 (1.00) |  |  | 0.108 (1.00) | 0.0489 (1.00) | 0.255 (1.00) | 0.0841 (1.00) | 0.0259 (1.00) | 0.107 (1.00)
18q gain | 6 (1%) | 488 | 1.16e-06 (0.000575) | 0.0973 (1.00) |  |  | 0.108 (1.00) | 0.0489 (1.00) | 0.255 (1.00) | 0.0841 (1.00) | 0.0259 (1.00) | 0.107 (1.00)
21q gain | 5 (1%) | 489 | 1.6e-05 (0.00724) | 0.249 (1.00) |  |  | 0.217 (1.00) | 0.111 (1.00) | 0.451 (1.00) | 0.229 (1.00) | 0.0687 (1.00) | 0.318 (1.00)
xq gain | 9 (2%) | 485 | 2.7e-07 (0.000137) | 0.0217 (1.00) | 0.839 (1.00) | 0.25 (1.00) | 0.0976 (1.00) | 0.0414 (1.00) | 0.337 (1.00) | 0.207 (1.00) | 0.483 (1.00) | 0.196 (1.00)
1p loss | 4 (1%) | 490 | 1.89e-05 (0.00846) | 0.22 (1.00) |  |  | 0.237 (1.00) | 0.089 (1.00) | 0.0755 (1.00) | 0.0676 (1.00) | 0.129 (1.00) | 0.0942 (1.00)
1q loss | 3 (1%) | 491 | 0.0003 (0.117) | 0.0585 (1.00) |  |  | 0.0959 (1.00) | 0.0721 (1.00) | 0.0278 (1.00) | 0.018 (1.00) | 0.0701 (1.00) | 0.0172 (1.00)
3p loss | 3 (1%) | 491 | 0.0003 (0.117) | 0.0585 (1.00) |  |  | 0.0959 (1.00) | 0.0721 (1.00) | 0.0278 (1.00) | 0.018 (1.00) | 0.0701 (1.00) | 0.0172 (1.00)
3q loss | 4 (1%) | 490 | 1.89e-05 (0.00846) | 0.0149 (1.00) | 0.495 (1.00) | 0.364 (1.00) | 0.0429 (1.00) | 0.0157 (1.00) | 0.00833 (1.00) | 0.00467 (1.00) | 0.0227 (1.00) | 0.00439 (1.00)
6q loss | 7 (1%) | 487 | 4.62e-05 (0.0199) | 0.0038 (1.00) | 0.0129 (1.00) | 0.364 (1.00) | 0.032 (1.00) | 0.00901 (1.00) | 0.00316 (1.00) | 0.00196 (0.683) | 0.00954 (1.00) | 0.00199 (0.683)
8p loss | 4 (1%) | 490 | 1.89e-05 (0.00846) | 0.0149 (1.00) |  |  | 0.0429 (1.00) | 0.0157 (1.00) | 0.00833 (1.00) | 0.00467 (1.00) | 0.0227 (1.00) | 0.00439 (1.00)
8q loss | 4 (1%) | 490 | 1.89e-05 (0.00846) | 0.0149 (1.00) |  |  | 0.0429 (1.00) | 0.0157 (1.00) | 0.00833 (1.00) | 0.00467 (1.00) | 0.0227 (1.00) | 0.00439 (1.00)
9p loss | 19 (4%) | 475 | 2.94e-12 (1.53e-09) | 0.0258 (1.00) | 0.243 (1.00) | 0.368 (1.00) | 0.0313 (1.00) | 0.0138 (1.00) | 0.00659 (1.00) | 0.00303 (0.996) | 0.00966 (1.00) | 0.00181 (0.635)
9q loss | 24 (5%) | 470 | 9.23e-15 (4.83e-12) | 0.0481 (1.00) | 0.173 (1.00) | 0.0332 (1.00) | 0.106 (1.00) | 0.0204 (1.00) | 0.00917 (1.00) | 0.00675 (1.00) | 0.0117 (1.00) | 0.00437 (1.00)
10p loss | 7 (1%) | 487 | 3.94e-09 (2.02e-06) | 0.00956 (1.00) | 0.495 (1.00) | 0.364 (1.00) | 0.0211 (1.00) | 0.00294 (0.976) | 0.00316 (1.00) | 0.00196 (0.683) | 0.00954 (1.00) | 0.00199 (0.683)
10q loss | 6 (1%) | 488 | 6.87e-08 (3.51e-05) | 0.0263 (1.00) |  |  | 0.053 (1.00) | 0.0106 (1.00) | 0.00929 (1.00) | 0.00658 (1.00) | 0.0259 (1.00) | 0.00664 (1.00)
11p loss | 7 (1%) | 487 | 7.98e-08 (4.07e-05) | 0.00956 (1.00) | 0.495 (1.00) | 1 (1.00) | 0.00675 (1.00) | 0.00901 (1.00) | 0.00316 (1.00) | 0.00196 (0.683) | 0.00954 (1.00) | 0.00199 (0.683)
18p loss | 4 (1%) | 490 | 0.000207 (0.0821) | 0.22 (1.00) | 1 (1.00) | 0.284 (1.00) | 0.237 (1.00) | 0.089 (1.00) | 0.115 (1.00) | 0.037 (1.00) | 0.0227 (1.00) | 0.0402 (1.00)
18q loss | 4 (1%) | 490 | 0.000207 (0.0821) | 0.22 (1.00) | 1 (1.00) | 0.284 (1.00) | 0.237 (1.00) | 0.089 (1.00) | 0.115 (1.00) | 0.037 (1.00) | 0.0227 (1.00) | 0.0402 (1.00)
21q loss | 8 (2%) | 486 | 5.63e-05 (0.0241) | 0.221 (1.00) | 0.384 (1.00) | 0.0523 (1.00) | 0.652 (1.00) | 0.503 (1.00) | 0.0744 (1.00) | 0.307 (1.00) | 0.0974 (1.00) | 0.0642 (1.00)
1p gain | 3 (1%) | 491 | 0.253 (1.00) | 0.745 (1.00) |  |  | 0.559 (1.00) | 1 (1.00) | 0.413 (1.00) | 0.621 (1.00) | 0.216 (1.00) | 0.485 (1.00)
9p gain | 3 (1%) | 491 | 0.00246 (0.83) | 0.582 (1.00) |  |  | 0.488 (1.00) | 0.195 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
9q gain | 4 (1%) | 490 | 0.0101 (1.00) | 0.649 (1.00) |  |  | 0.897 (1.00) | 0.104 (1.00) | 1 (1.00) | 0.822 (1.00) | 1 (1.00) | 0.828 (1.00)
6p loss | 4 (1%) | 490 | 0.00236 (0.801) | 0.0594 (1.00) |  |  | 0.454 (1.00) | 0.289 (1.00) | 0.0755 (1.00) | 0.0676 (1.00) | 0.129 (1.00) | 0.0942 (1.00)
13q loss | 14 (3%) | 480 | 0.00844 (1.00) | 0.02 (1.00) | 0.0614 (1.00) | 0.893 (1.00) | 0.00551 (1.00) | 0.0043 (1.00) | 0.00199 (0.683) | 0.00197 (0.683) | 0.00187 (0.651) | 0.00261 (0.874)
17p loss | 8 (2%) | 486 | 0.00182 (0.636) | 0.335 (1.00) | 1 (1.00) | 0.284 (1.00) | 0.652 (1.00) | 0.452 (1.00) | 0.33 (1.00) | 0.307 (1.00) | 0.672 (1.00) | 0.282 (1.00)
17q loss | 4 (1%) | 490 | 0.0538 (1.00) | 0.649 (1.00) |  |  | 0.897 (1.00) | 0.626 (1.00) | 0.399 (1.00) | 0.689 (1.00) | 0.847 (1.00) | 0.573 (1.00)
19p loss | 5 (1%) | 489 | 0.0251 (1.00) | 0.00581 (1.00) | 0.321 (1.00) | 0.118 (1.00) | 0.0181 (1.00) | 0.00529 (1.00) | 0.00249 (0.836) | 0.0012 (0.427) | 0.00735 (1.00) | 0.00111 (0.397)
xq loss | 3 (1%) | 491 | 0.0219 (1.00) | 0.0585 (1.00) | 0.278 (1.00) | 0.364 (1.00) | 0.0959 (1.00) | 0.0721 (1.00) | 0.0278 (1.00) | 0.018 (1.00) | 0.0701 (1.00) | 0.0172 (1.00)

'1q gain' versus 'CN_CNMF'

P value = 9.81e-06 (Fisher's exact test), Q value = 0.0045

Table S1. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
1Q GAIN MUTATED | 9 | 14 | 1
1Q GAIN WILD-TYPE | 25 | 369 | 76

Figure S1. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.04e-05 (Fisher's exact test), Q value = 0.022

Table S2. Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
1Q GAIN MUTATED | 21 | 2 | 1 | 0
1Q GAIN WILD-TYPE | 176 | 126 | 95 | 71

Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.12

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
3P GAIN MUTATED | 3 | 0 | 0
3P GAIN WILD-TYPE | 31 | 383 | 77

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

'4p gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00057

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
4P GAIN MUTATED | 5 | 0 | 0
4P GAIN WILD-TYPE | 29 | 383 | 77

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

'4q gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00057

Table S5. Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
4Q GAIN MUTATED | 5 | 0 | 0
4Q GAIN WILD-TYPE | 29 | 383 | 77

Figure S5. Get High-res Image Gene #5: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 4.18e-23 (Fisher's exact test), Q value = 2.2e-20

Table S6. Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
5P GAIN MUTATED | 19 | 2 | 0
5P GAIN WILD-TYPE | 15 | 381 | 77

Figure S6. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000485 (Fisher's exact test), Q value = 0.18

Table S7. Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
5P GAIN MUTATED | 6 | 14 | 1 | 0
5P GAIN WILD-TYPE | 191 | 114 | 95 | 71

Figure S7. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000523 (Fisher's exact test), Q value = 0.2

Table S8. Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
5P GAIN MUTATED | 1 | 13 | 7
5P GAIN WILD-TYPE | 154 | 117 | 201

Figure S8. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.12

Table S9. Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
5P GAIN MUTATED | 7 | 13 | 1
5P GAIN WILD-TYPE | 192 | 115 | 165

Figure S9. Get High-res Image Gene #6: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1.76e-22 (Fisher's exact test), Q value = 9.4e-20

Table S10. Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
5Q GAIN MUTATED | 17 | 0 | 0
5Q GAIN WILD-TYPE | 17 | 383 | 77

Figure S10. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.015

Table S11. Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
5Q GAIN MUTATED | 14 | 1 | 2
5Q GAIN WILD-TYPE | 137 | 82 | 258

Figure S11. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.000345 (Fisher's exact test), Q value = 0.13

Table S12. Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
5Q GAIN MUTATED | 14 | 0 | 1 | 2
5Q GAIN WILD-TYPE | 140 | 55 | 115 | 165

Figure S12. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0071

Table S13. Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
5Q GAIN MUTATED | 2 | 14 | 1 | 0
5Q GAIN WILD-TYPE | 195 | 114 | 95 | 71

Figure S13. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.000344 (Fisher's exact test), Q value = 0.13

Table S14. Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
5Q GAIN MUTATED | 13 | 2 | 2
5Q GAIN WILD-TYPE | 137 | 171 | 168

Figure S14. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.11e-05 (Fisher's exact test), Q value = 0.018

Table S15. Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
5Q GAIN MUTATED | 1 | 13 | 3
5Q GAIN WILD-TYPE | 154 | 117 | 205

Figure S15. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S16. Gene #7: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
5Q GAIN MUTATED | 14 | 1 | 2
5Q GAIN WILD-TYPE | 149 | 168 | 159

Figure S16. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.014

Table S17. Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
5Q GAIN MUTATED | 3 | 13 | 1
5Q GAIN WILD-TYPE | 196 | 115 | 165

Figure S17. Get High-res Image Gene #7: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 6.29e-24 (Fisher's exact test), Q value = 3.3e-21

Table S18. Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
7P GAIN MUTATED | 18 | 0 | 0
7P GAIN WILD-TYPE | 16 | 383 | 77

Figure S18. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 7.19e-05 (Fisher's exact test), Q value = 0.03

Table S19. Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
7P GAIN MUTATED | 14 | 2 | 2
7P GAIN WILD-TYPE | 137 | 81 | 258

Figure S19. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.17e-05 (Fisher's exact test), Q value = 0.026

Table S20. Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
7P GAIN MUTATED | 2 | 14 | 1 | 1
7P GAIN WILD-TYPE | 195 | 114 | 95 | 70

Figure S20. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S21. Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
7P GAIN MUTATED | 1 | 13 | 4
7P GAIN WILD-TYPE | 154 | 117 | 204

Figure S21. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000259 (Fisher's exact test), Q value = 0.1

Table S22. Gene #8: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
7P GAIN MUTATED | 14 | 1 | 3
7P GAIN WILD-TYPE | 149 | 168 | 158

Figure S22. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.61e-05 (Fisher's exact test), Q value = 0.031

Table S23. Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
7P GAIN MUTATED | 4 | 13 | 1
7P GAIN WILD-TYPE | 195 | 115 | 165

Figure S23. Get High-res Image Gene #8: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 6.92e-25 (Fisher's exact test), Q value = 3.7e-22

Table S24. Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
7Q GAIN MUTATED | 19 | 0 | 1
7Q GAIN WILD-TYPE | 15 | 383 | 76

Figure S24. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 9.82e-06 (Fisher's exact test), Q value = 0.0045

Table S25. Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
7Q GAIN MUTATED | 16 | 2 | 2
7Q GAIN WILD-TYPE | 135 | 81 | 258

Figure S25. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.000676 (Fisher's exact test), Q value = 0.25

Table S26. Gene #9: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 94 | 96
7Q GAIN MUTATED | 5 | 0 | 7
7Q GAIN WILD-TYPE | 26 | 94 | 89

Figure S26. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 0.000166 (Fisher's exact test), Q value = 0.067

Table S27. Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
7Q GAIN MUTATED | 16 | 1 | 1 | 2
7Q GAIN WILD-TYPE | 138 | 54 | 115 | 165

Figure S27. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.82e-06 (Fisher's exact test), Q value = 0.0037

Table S28. Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
7Q GAIN MUTATED | 2 | 16 | 1 | 1
7Q GAIN WILD-TYPE | 195 | 112 | 95 | 70

Figure S28. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.000144 (Fisher's exact test), Q value = 0.058

Table S29. Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
7Q GAIN MUTATED | 15 | 2 | 3
7Q GAIN WILD-TYPE | 135 | 171 | 167

Figure S29. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.15e-05 (Fisher's exact test), Q value = 0.0053

Table S30. Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
7Q GAIN MUTATED | 1 | 15 | 4
7Q GAIN WILD-TYPE | 154 | 115 | 204

Figure S30. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.019

Table S31. Gene #9: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
7Q GAIN MUTATED | 16 | 1 | 3
7Q GAIN WILD-TYPE | 147 | 168 | 158

Figure S31. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.06e-06 (Fisher's exact test), Q value = 0.0042

Table S32. Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
7Q GAIN MUTATED | 4 | 15 | 1
7Q GAIN WILD-TYPE | 195 | 113 | 165

Figure S32. Get High-res Image Gene #9: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 0.000364 (Fisher's exact test), Q value = 0.14

Table S33. Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
8P GAIN MUTATED | 4 | 2 | 0
8P GAIN WILD-TYPE | 30 | 381 | 77

Figure S33. Get High-res Image Gene #10: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 4.62e-05 (Fisher's exact test), Q value = 0.02

Table S34. Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
8Q GAIN MUTATED | 5 | 2 | 0
8Q GAIN WILD-TYPE | 29 | 381 | 77

Figure S34. Get High-res Image Gene #11: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.076

Table S35. Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
11P GAIN MUTATED | 4 | 1 | 1
11P GAIN WILD-TYPE | 30 | 382 | 76

Figure S35. Get High-res Image Gene #14: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0072

Table S36. Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
11Q GAIN MUTATED | 4 | 0 | 1
11Q GAIN WILD-TYPE | 30 | 383 | 76

Figure S36. Get High-res Image Gene #15: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.48e-16 (Fisher's exact test), Q value = 7.8e-14

Table S37. Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
12P GAIN MUTATED | 13 | 0 | 1
12P GAIN WILD-TYPE | 21 | 383 | 76

Figure S37. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3.71e-06 (Fisher's exact test), Q value = 0.0018

Table S38. Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
12P GAIN MUTATED | 13 | 0 | 1
12P GAIN WILD-TYPE | 138 | 83 | 259

Figure S38. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.56e-05 (Fisher's exact test), Q value = 0.0071

Table S39. Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
12P GAIN MUTATED | 13 | 0 | 1 | 0
12P GAIN WILD-TYPE | 141 | 55 | 115 | 167

Figure S39. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-07 (Fisher's exact test), Q value = 0.00032

Table S40. Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
12P GAIN MUTATED | 0 | 13 | 1 | 0
12P GAIN WILD-TYPE | 197 | 115 | 95 | 71

Figure S40. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 6.05e-05 (Fisher's exact test), Q value = 0.026

Table S41. Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
12P GAIN MUTATED | 12 | 1 | 1
12P GAIN WILD-TYPE | 138 | 172 | 169

Figure S41. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.86e-06 (Fisher's exact test), Q value = 0.0041

Table S42. Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
12P GAIN MUTATED | 1 | 12 | 1
12P GAIN WILD-TYPE | 154 | 118 | 207

Figure S42. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9.65e-06 (Fisher's exact test), Q value = 0.0044

Table S43. Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
12P GAIN MUTATED | 13 | 0 | 1
12P GAIN WILD-TYPE | 150 | 169 | 160

Figure S43. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.52e-06 (Fisher's exact test), Q value = 0.004

Table S44. Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
12P GAIN MUTATED | 1 | 12 | 1
12P GAIN WILD-TYPE | 198 | 116 | 165

Figure S44. Get High-res Image Gene #16: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 2.14e-16 (Fisher's exact test), Q value = 1.1e-13

Table S45. Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
12Q GAIN MUTATED | 13 | 0 | 2
12Q GAIN WILD-TYPE | 21 | 383 | 75

Figure S45. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1.32e-06 (Fisher's exact test), Q value = 0.00064

Table S46. Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
12Q GAIN MUTATED | 14 | 0 | 1
12Q GAIN WILD-TYPE | 137 | 83 | 259

Figure S46. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.0039

Table S47. Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
12Q GAIN MUTATED | 14 | 0 | 1 | 0
12Q GAIN WILD-TYPE | 140 | 55 | 115 | 167

Figure S47. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.55e-07 (Fisher's exact test), Q value = 7.9e-05

Table S48. Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
12Q GAIN MUTATED | 0 | 14 | 1 | 0
12Q GAIN WILD-TYPE | 197 | 114 | 95 | 71

Figure S48. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.0099

Table S49. Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
12Q GAIN MUTATED | 13 | 1 | 1
12Q GAIN WILD-TYPE | 137 | 172 | 169

Figure S49. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.0014

Table S50. Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
12Q GAIN MUTATED | 1 | 13 | 1
12Q GAIN WILD-TYPE | 154 | 117 | 207

Figure S50. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.63e-06 (Fisher's exact test), Q value = 0.0017

Table S51. Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
12Q GAIN MUTATED | 14 | 0 | 1
12Q GAIN WILD-TYPE | 149 | 169 | 160

Figure S51. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.66e-06 (Fisher's exact test), Q value = 0.0013

Table S52. Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
12Q GAIN MUTATED | 1 | 13 | 1
12Q GAIN WILD-TYPE | 198 | 115 | 165

Figure S52. Get High-res Image Gene #17: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00057

Table S53. Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
13Q GAIN MUTATED | 5 | 0 | 0
13Q GAIN WILD-TYPE | 29 | 383 | 77

Figure S53. Get High-res Image Gene #18: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 3.23e-10 (Fisher's exact test), Q value = 1.7e-07

Table S54. Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
14Q GAIN MUTATED | 9 | 1 | 1
14Q GAIN WILD-TYPE | 25 | 382 | 76

Figure S54. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.000161 (Fisher's exact test), Q value = 0.065

Table S55. Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
14Q GAIN MUTATED | 10 | 0 | 1
14Q GAIN WILD-TYPE | 141 | 83 | 259

Figure S55. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.000557 (Fisher's exact test), Q value = 0.21

Table S56. Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
14Q GAIN MUTATED | 10 | 0 | 0 | 1
14Q GAIN WILD-TYPE | 144 | 55 | 116 | 166

Figure S56. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-05 (Fisher's exact test), Q value = 0.026

Table S57. Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
14Q GAIN MUTATED | 1 | 10 | 0 | 0
14Q GAIN WILD-TYPE | 196 | 118 | 96 | 71

Figure S57. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.000461 (Fisher's exact test), Q value = 0.17

Table S58. Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
14Q GAIN MUTATED | 9 | 0 | 2
14Q GAIN WILD-TYPE | 141 | 173 | 168

Figure S58. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000151 (Fisher's exact test), Q value = 0.061

Table S59. Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
14Q GAIN MUTATED | 0 | 9 | 2
14Q GAIN WILD-TYPE | 155 | 121 | 206

Figure S59. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000114 (Fisher's exact test), Q value = 0.047

Table S60. Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
14Q GAIN MUTATED | 2 | 9 | 0
14Q GAIN WILD-TYPE | 197 | 119 | 166

Figure S60. Get High-res Image Gene #19: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 6.94e-18 (Fisher's exact test), Q value = 3.7e-15

Table S61. Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
16P GAIN MUTATED | 14 | 0 | 1
16P GAIN WILD-TYPE | 20 | 383 | 76

Figure S61. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0083

Table S62. Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
16P GAIN MUTATED | 13 | 1 | 1
16P GAIN WILD-TYPE | 138 | 82 | 259

Figure S62. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000187 (Fisher's exact test), Q value = 0.075

Table S63. Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
16P GAIN MUTATED | 13 | 0 | 1 | 1
16P GAIN WILD-TYPE | 141 | 55 | 115 | 166

Figure S63. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.24e-06 (Fisher's exact test), Q value = 0.0039

Table S64. Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
16P GAIN MUTATED | 1 | 13 | 1 | 0
16P GAIN WILD-TYPE | 196 | 115 | 95 | 71

Figure S64. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.077

Table S65. Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
16P GAIN MUTATED | 12 | 1 | 2
16P GAIN WILD-TYPE | 138 | 172 | 168

Figure S65. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.25e-05 (Fisher's exact test), Q value = 0.018

Table S66. Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
16P GAIN MUTATED | 1 | 12 | 2
16P GAIN WILD-TYPE | 154 | 118 | 206

Figure S66. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.013

Table S67. Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
16P GAIN MUTATED | 13 | 0 | 2
16P GAIN WILD-TYPE | 150 | 169 | 159

Figure S67. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.96e-05 (Fisher's exact test), Q value = 0.017

Table S68. Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
16P GAIN MUTATED | 2 | 12 | 1
16P GAIN WILD-TYPE | 197 | 116 | 165

Figure S68. Get High-res Image Gene #20: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 6.49e-17 (Fisher's exact test), Q value = 3.4e-14

Table S69. Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
16Q GAIN MUTATED | 13 | 0 | 0
16Q GAIN WILD-TYPE | 21 | 383 | 77

Figure S69. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

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

Table S70. Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
16Q GAIN MUTATED | 11 | 1 | 1
16Q GAIN WILD-TYPE | 140 | 82 | 259

Figure S70. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.59e-05 (Fisher's exact test), Q value = 0.031

Table S71. Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
16Q GAIN MUTATED | 1 | 11 | 1 | 0
16Q GAIN WILD-TYPE | 196 | 117 | 95 | 71

Figure S71. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000387 (Fisher's exact test), Q value = 0.15

Table S72. Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
16Q GAIN MUTATED | 1 | 10 | 2
16Q GAIN WILD-TYPE | 154 | 120 | 206

Figure S72. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000182 (Fisher's exact test), Q value = 0.073

Table S73. Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
16Q GAIN MUTATED | 11 | 0 | 2
16Q GAIN WILD-TYPE | 152 | 169 | 159

Figure S73. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000336 (Fisher's exact test), Q value = 0.13

Table S74. Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
16Q GAIN MUTATED | 2 | 10 | 1
16Q GAIN WILD-TYPE | 197 | 118 | 165

Figure S74. Get High-res Image Gene #21: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 4.23e-13 (Fisher's exact test), Q value = 2.2e-10

Table S75. Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
17P GAIN MUTATED | 12 | 2 | 2
17P GAIN WILD-TYPE | 22 | 381 | 75

Figure S75. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 5.64e-07 (Fisher's exact test), Q value = 0.00028

Table S76. Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
17P GAIN MUTATED | 15 | 0 | 1
17P GAIN WILD-TYPE | 136 | 83 | 259

Figure S76. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 4.05e-06 (Fisher's exact test), Q value = 0.0019

Table S77. Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
17P GAIN MUTATED | 15 | 0 | 1 | 0
17P GAIN WILD-TYPE | 139 | 55 | 115 | 167

Figure S77. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.72e-08 (Fisher's exact test), Q value = 2.4e-05

Table S78. Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
17P GAIN MUTATED | 0 | 15 | 1 | 0
17P GAIN WILD-TYPE | 197 | 113 | 95 | 71

Figure S78. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 8.06e-06 (Fisher's exact test), Q value = 0.0038

Table S79. Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
17P GAIN MUTATED | 14 | 1 | 1
17P GAIN WILD-TYPE | 136 | 172 | 169

Figure S79. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.97e-07 (Fisher's exact test), Q value = 0.00045

Table S80. Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
17P GAIN MUTATED | 1 | 14 | 1
17P GAIN WILD-TYPE | 154 | 116 | 207

Figure S80. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00065

Table S81. Gene #22: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
17P GAIN MUTATED | 15 | 0 | 1
17P GAIN WILD-TYPE | 148 | 169 | 160

Figure S81. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.04e-07 (Fisher's exact test), Q value = 4e-04

Table S82. Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
17P GAIN MUTATED | 1 | 14 | 1
17P GAIN WILD-TYPE | 198 | 114 | 165

Figure S82. Get High-res Image Gene #22: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 5.03e-14 (Fisher's exact test), Q value = 2.6e-11

Table S83. Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
17Q GAIN MUTATED | 13 | 2 | 3
17Q GAIN WILD-TYPE | 21 | 381 | 74

Figure S83. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.00056

Table S84. Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
17Q GAIN MUTATED | 16 | 0 | 2
17Q GAIN WILD-TYPE | 135 | 83 | 258

Figure S84. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1.47e-05 (Fisher's exact test), Q value = 0.0067

Table S85. Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
17Q GAIN MUTATED | 16 | 0 | 1 | 1
17Q GAIN WILD-TYPE | 138 | 55 | 115 | 166

Figure S85. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.38e-07 (Fisher's exact test), Q value = 0.00017

Table S86. Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
17Q GAIN MUTATED | 1 | 16 | 1 | 0
17Q GAIN WILD-TYPE | 196 | 112 | 95 | 71

Figure S86. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 1.17e-05 (Fisher's exact test), Q value = 0.0053

Table S87. Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
17Q GAIN MUTATED | 15 | 2 | 1
17Q GAIN WILD-TYPE | 135 | 171 | 169

Figure S87. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.00071

Table S88. Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
17Q GAIN MUTATED | 1 | 15 | 2
17Q GAIN WILD-TYPE | 154 | 115 | 206

Figure S88. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.69e-06 (Fisher's exact test), Q value = 0.0018

Table S89. Gene #23: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
17Q GAIN MUTATED | 16 | 1 | 1
17Q GAIN WILD-TYPE | 147 | 168 | 160

Figure S89. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00054

Table S90. Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
17Q GAIN MUTATED | 2 | 15 | 1
17Q GAIN WILD-TYPE | 197 | 113 | 165

Figure S90. Get High-res Image Gene #23: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00057

Table S91. Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
18P GAIN MUTATED | 5 | 0 | 1
18P GAIN WILD-TYPE | 29 | 383 | 76

Figure S91. Get High-res Image Gene #24: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'CN_CNMF'

P value = 1.16e-06 (Fisher's exact test), Q value = 0.00057

Table S92. Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
18Q GAIN MUTATED | 5 | 0 | 1
18Q GAIN WILD-TYPE | 29 | 383 | 76

Figure S92. Get High-res Image Gene #25: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 2.19e-10 (Fisher's exact test), Q value = 1.1e-07

Table S93. Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
19P GAIN MUTATED | 8 | 0 | 0
19P GAIN WILD-TYPE | 26 | 383 | 77

Figure S93. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.057

Table S94. Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
19P GAIN MUTATED | 8 | 0 | 0
19P GAIN WILD-TYPE | 143 | 83 | 260

Figure S94. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.000585 (Fisher's exact test), Q value = 0.22

Table S95. Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
19P GAIN MUTATED | 8 | 0 | 0 | 0
19P GAIN WILD-TYPE | 146 | 55 | 116 | 167

Figure S95. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.96e-05 (Fisher's exact test), Q value = 0.025

Table S96. Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
19P GAIN MUTATED | 0 | 8 | 0 | 0
19P GAIN WILD-TYPE | 197 | 120 | 96 | 71

Figure S96. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.027

Table S97. Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
19P GAIN MUTATED | 8 | 0 | 0
19P GAIN WILD-TYPE | 142 | 173 | 170

Figure S97. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0088

Table S98. Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
19P GAIN MUTATED | 0 | 8 | 0
19P GAIN WILD-TYPE | 155 | 122 | 208

Figure S98. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.095

Table S99. Gene #26: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
19P GAIN MUTATED | 8 | 0 | 0
19P GAIN WILD-TYPE | 155 | 169 | 161

Figure S99. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0079

Table S100. Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
19P GAIN MUTATED | 0 | 8 | 0
19P GAIN WILD-TYPE | 199 | 120 | 166

Figure S100. Get High-res Image Gene #26: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1.92e-11 (Fisher's exact test), Q value = 9.9e-09

Table S101. Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
19Q GAIN MUTATED | 9 | 0 | 1
19Q GAIN WILD-TYPE | 25 | 383 | 76

Figure S101. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.0039

Table S102. Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
19Q GAIN MUTATED | 10 | 0 | 0
19Q GAIN WILD-TYPE | 141 | 83 | 260

Figure S102. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 7.31e-05 (Fisher's exact test), Q value = 0.03

Table S103. Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
19Q GAIN MUTATED | 10 | 0 | 0 | 0
19Q GAIN WILD-TYPE | 144 | 55 | 116 | 167

Figure S103. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.66e-06 (Fisher's exact test), Q value = 0.0032

Table S104. Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
19Q GAIN MUTATED | 0 | 10 | 0 | 0
19Q GAIN WILD-TYPE | 197 | 118 | 96 | 71

Figure S104. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026

Table S105. Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
19Q GAIN MUTATED | 10 | 0 | 0
19Q GAIN WILD-TYPE | 140 | 173 | 170

Figure S105. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00061

Table S106. Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
19Q GAIN MUTATED | 0 | 10 | 0
19Q GAIN WILD-TYPE | 155 | 120 | 208

Figure S106. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.011

Table S107. Gene #27: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
19Q GAIN MUTATED | 10 | 0 | 0
19Q GAIN WILD-TYPE | 153 | 169 | 161

Figure S107. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00053

Table S108. Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
19Q GAIN MUTATED | 0 | 10 | 0
19Q GAIN WILD-TYPE | 199 | 118 | 166

Figure S108. Get High-res Image Gene #27: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1.42e-15 (Fisher's exact test), Q value = 7.5e-13

Table S109. Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
20P GAIN MUTATED | 12 | 0 | 0
20P GAIN WILD-TYPE | 22 | 383 | 77

Figure S109. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000376 (Fisher's exact test), Q value = 0.14

Table S110. Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
20P GAIN MUTATED | 10 | 1 | 1
20P GAIN WILD-TYPE | 141 | 82 | 259

Figure S110. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S111. Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
20P GAIN MUTATED | 1 | 10 | 1 | 0
20P GAIN WILD-TYPE | 196 | 118 | 95 | 71

Figure S111. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.19

Table S112. Gene #28: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
20P GAIN MUTATED | 10 | 0 | 2
20P GAIN WILD-TYPE | 153 | 169 | 159

Figure S112. Get High-res Image Gene #28: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.42e-15 (Fisher's exact test), Q value = 7.5e-13

Table S113. Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
20Q GAIN MUTATED | 12 | 0 | 0
20Q GAIN WILD-TYPE | 22 | 383 | 77

Figure S113. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.000376 (Fisher's exact test), Q value = 0.14

Table S114. Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
20Q GAIN MUTATED | 10 | 1 | 1
20Q GAIN WILD-TYPE | 141 | 82 | 259

Figure S114. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S115. Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
20Q GAIN MUTATED | 1 | 10 | 1 | 0
20Q GAIN WILD-TYPE | 196 | 118 | 95 | 71

Figure S115. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.19

Table S116. Gene #29: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
20Q GAIN MUTATED | 10 | 0 | 2
20Q GAIN WILD-TYPE | 153 | 169 | 159

Figure S116. Get High-res Image Gene #29: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'CN_CNMF'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0072

Table S117. Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
21Q GAIN MUTATED | 4 | 0 | 1
21Q GAIN WILD-TYPE | 30 | 383 | 76

Figure S117. Get High-res Image Gene #30: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 2.7e-07 (Fisher's exact test), Q value = 0.00014

Table S118. Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
XQ GAIN MUTATED | 7 | 2 | 0
XQ GAIN WILD-TYPE | 27 | 381 | 77

Figure S118. Get High-res Image Gene #31: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085

Table S119. Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
1P LOSS MUTATED | 4 | 0 | 0
1P LOSS WILD-TYPE | 30 | 383 | 77

Figure S119. Get High-res Image Gene #32: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.12

Table S120. Gene #33: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
1Q LOSS MUTATED | 3 | 0 | 0
1Q LOSS WILD-TYPE | 31 | 383 | 77

Figure S120. Get High-res Image Gene #33: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 1.92e-11 (Fisher's exact test), Q value = 9.9e-09

Table S121. Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
2P LOSS MUTATED | 9 | 0 | 1
2P LOSS WILD-TYPE | 25 | 383 | 76

Figure S121. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.0039

Table S122. Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
2P LOSS MUTATED | 10 | 0 | 0
2P LOSS WILD-TYPE | 141 | 83 | 260

Figure S122. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 7.31e-05 (Fisher's exact test), Q value = 0.03

Table S123. Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
2P LOSS MUTATED | 10 | 0 | 0 | 0
2P LOSS WILD-TYPE | 144 | 55 | 116 | 167

Figure S123. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.66e-06 (Fisher's exact test), Q value = 0.0032

Table S124. Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
2P LOSS MUTATED | 0 | 10 | 0 | 0
2P LOSS WILD-TYPE | 197 | 118 | 96 | 71

Figure S124. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026

Table S125. Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
2P LOSS MUTATED | 10 | 0 | 0
2P LOSS WILD-TYPE | 140 | 173 | 170

Figure S125. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00061

Table S126. Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
2P LOSS MUTATED | 0 | 10 | 0
2P LOSS WILD-TYPE | 155 | 120 | 208

Figure S126. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.011

Table S127. Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
2P LOSS MUTATED | 10 | 0 | 0
2P LOSS WILD-TYPE | 153 | 169 | 161

Figure S127. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00053

Table S128. Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
2P LOSS MUTATED | 0 | 10 | 0
2P LOSS WILD-TYPE | 199 | 118 | 166

Figure S128. Get High-res Image Gene #34: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 6.03e-13 (Fisher's exact test), Q value = 3.1e-10

Table S129. Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
2Q LOSS MUTATED | 10 | 0 | 0
2Q LOSS WILD-TYPE | 24 | 383 | 77

Figure S129. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 8.44e-06 (Fisher's exact test), Q value = 0.0039

Table S130. Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
2Q LOSS MUTATED | 10 | 0 | 0
2Q LOSS WILD-TYPE | 141 | 83 | 260

Figure S130. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 7.31e-05 (Fisher's exact test), Q value = 0.03

Table S131. Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
2Q LOSS MUTATED | 10 | 0 | 0 | 0
2Q LOSS WILD-TYPE | 144 | 55 | 116 | 167

Figure S131. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.66e-06 (Fisher's exact test), Q value = 0.0032

Table S132. Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
2Q LOSS MUTATED | 0 | 10 | 0 | 0
2Q LOSS WILD-TYPE | 197 | 118 | 96 | 71

Figure S132. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 5.49e-06 (Fisher's exact test), Q value = 0.0026

Table S133. Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
2Q LOSS MUTATED | 10 | 0 | 0
2Q LOSS WILD-TYPE | 140 | 173 | 170

Figure S133. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.25e-06 (Fisher's exact test), Q value = 0.00061

Table S134. Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
2Q LOSS MUTATED | 0 | 10 | 0
2Q LOSS WILD-TYPE | 155 | 120 | 208

Figure S134. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.43e-05 (Fisher's exact test), Q value = 0.011

Table S135. Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
2Q LOSS MUTATED | 10 | 0 | 0
2Q LOSS WILD-TYPE | 153 | 169 | 161

Figure S135. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.06e-06 (Fisher's exact test), Q value = 0.00053

Table S136. Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
2Q LOSS MUTATED | 0 | 10 | 0
2Q LOSS WILD-TYPE | 199 | 118 | 166

Figure S136. Get High-res Image Gene #35: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.12

Table S137. Gene #36: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
3P LOSS MUTATED | 3 | 0 | 0
3P LOSS WILD-TYPE | 31 | 383 | 77

Figure S137. Get High-res Image Gene #36: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085

Table S138. Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
3Q LOSS MUTATED | 4 | 0 | 0
3Q LOSS WILD-TYPE | 30 | 383 | 77

Figure S138. Get High-res Image Gene #37: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 4.62e-05 (Fisher's exact test), Q value = 0.02

Table S139. Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
6Q LOSS MUTATED | 5 | 2 | 0
6Q LOSS WILD-TYPE | 29 | 381 | 77

Figure S139. Get High-res Image Gene #39: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085

Table S140. Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
8P LOSS MUTATED | 4 | 0 | 0
8P LOSS WILD-TYPE | 30 | 383 | 77

Figure S140. Get High-res Image Gene #40: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0085

Table S141. Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
8Q LOSS MUTATED | 4 | 0 | 0
8Q LOSS WILD-TYPE | 30 | 383 | 77

Figure S141. Get High-res Image Gene #41: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 2.94e-12 (Fisher's exact test), Q value = 1.5e-09

Table S142. Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
9P LOSS MUTATED | 13 | 5 | 1
9P LOSS WILD-TYPE | 21 | 378 | 76

Figure S142. Get High-res Image Gene #42: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 9.23e-15 (Fisher's exact test), Q value = 4.8e-12

Table S143. Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
9Q LOSS MUTATED | 16 | 7 | 1
9Q LOSS WILD-TYPE | 18 | 376 | 76

Figure S143. Get High-res Image Gene #43: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 3.94e-09 (Fisher's exact test), Q value = 2e-06

Table S144. Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
10P LOSS MUTATED | 7 | 0 | 0
10P LOSS WILD-TYPE | 27 | 383 | 77

Figure S144. Get High-res Image Gene #44: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 6.87e-08 (Fisher's exact test), Q value = 3.5e-05

Table S145. Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
10Q LOSS MUTATED | 6 | 0 | 0
10Q LOSS WILD-TYPE | 28 | 383 | 77

Figure S145. Get High-res Image Gene #45: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 7.98e-08 (Fisher's exact test), Q value = 4.1e-05

Table S146. Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
11P LOSS MUTATED | 6 | 0 | 1
11P LOSS WILD-TYPE | 28 | 383 | 76

Figure S146. Get High-res Image Gene #46: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.28e-06 (Fisher's exact test), Q value = 0.0016

Table S147. Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
11Q LOSS MUTATED | 6 | 2 | 1
11Q LOSS WILD-TYPE | 28 | 381 | 76

Figure S147. Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.000352 (Fisher's exact test), Q value = 0.13

Table S148. Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
11Q LOSS MUTATED | 8 | 0 | 1
11Q LOSS WILD-TYPE | 142 | 173 | 169

Figure S148. Get High-res Image Gene #47: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 5.63e-05 (Fisher's exact test), Q value = 0.024

Table S149. Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
15Q LOSS MUTATED | 5 | 2 | 1
15Q LOSS WILD-TYPE | 29 | 381 | 76

Figure S149. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 0.000139 (Fisher's exact test), Q value = 0.057

Table S150. Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
15Q LOSS MUTATED | 8 | 0 | 0
15Q LOSS WILD-TYPE | 143 | 83 | 260

Figure S150. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 0.000585 (Fisher's exact test), Q value = 0.22

Table S151. Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
15Q LOSS MUTATED | 8 | 0 | 0 | 0
15Q LOSS WILD-TYPE | 146 | 55 | 116 | 167

Figure S151. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.96e-05 (Fisher's exact test), Q value = 0.025

Table S152. Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
15Q LOSS MUTATED | 0 | 8 | 0 | 0
15Q LOSS WILD-TYPE | 197 | 120 | 96 | 71

Figure S152. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 6.43e-05 (Fisher's exact test), Q value = 0.027

Table S153. Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
15Q LOSS MUTATED | 8 | 0 | 0
15Q LOSS WILD-TYPE | 142 | 173 | 170

Figure S153. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.99e-05 (Fisher's exact test), Q value = 0.0088

Table S154. Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
15Q LOSS MUTATED | 0 | 8 | 0
15Q LOSS WILD-TYPE | 155 | 122 | 208

Figure S154. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000242 (Fisher's exact test), Q value = 0.095

Table S155. Gene #49: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
15Q LOSS MUTATED | 8 | 0 | 0
15Q LOSS WILD-TYPE | 155 | 169 | 161

Figure S155. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.0079

Table S156. Gene #49: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
15Q LOSS MUTATED | 0 | 8 | 0
15Q LOSS WILD-TYPE | 199 | 120 | 166

Figure S156. Get High-res Image Gene #49: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.082

Table S157. Gene #52: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
18P LOSS MUTATED | 3 | 0 | 1
18P LOSS WILD-TYPE | 31 | 383 | 76

Figure S157. Get High-res Image Gene #52: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.082

Table S158. Gene #53: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
18Q LOSS MUTATED | 3 | 0 | 1
18Q LOSS WILD-TYPE | 31 | 383 | 76

Figure S158. Get High-res Image Gene #53: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 5.63e-05 (Fisher's exact test), Q value = 0.024

Table S159. Gene #55: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
21Q LOSS MUTATED | 5 | 2 | 1
21Q LOSS WILD-TYPE | 29 | 381 | 76

Figure S159. Get High-res Image Gene #55: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 7.48e-90 (Fisher's exact test), Q value = 4e-87

Table S160. Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
22Q LOSS MUTATED | 9 | 0 | 77
22Q LOSS WILD-TYPE | 25 | 383 | 0

Figure S160. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.005

Table S161. Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
22Q LOSS MUTATED | 45 | 7 | 34
22Q LOSS WILD-TYPE | 106 | 76 | 226

Figure S161. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 3.38e-09 (Fisher's exact test), Q value = 1.7e-06

Table S162. Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
22Q LOSS MUTATED | 45 | 8 | 26 | 7
22Q LOSS WILD-TYPE | 109 | 47 | 90 | 160

Figure S162. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.03e-08 (Fisher's exact test), Q value = 4.1e-05

Table S163. Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
22Q LOSS MUTATED | 13 | 39 | 23 | 11
22Q LOSS WILD-TYPE | 184 | 89 | 73 | 60

Figure S163. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000342 (Fisher's exact test), Q value = 0.13

Table S164. Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
22Q LOSS MUTATED | 22 | 38 | 26
22Q LOSS WILD-TYPE | 133 | 92 | 182

Figure S164. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.12e-06 (Fisher's exact test), Q value = 0.0015

Table S165. Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
22Q LOSS MUTATED | 49 | 18 | 19
22Q LOSS WILD-TYPE | 114 | 151 | 142

Figure S165. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000206 (Fisher's exact test), Q value = 0.082

Table S166. Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
22Q LOSS MUTATED | 24 | 38 | 24
22Q LOSS WILD-TYPE | 175 | 90 | 142

Figure S166. Get High-res Image Gene #56: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

- Copy number data file = transformed.cor.cli.txt

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

- Number of patients = 494

- Number of significantly arm-level cnvs = 57

- 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

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] 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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