Correlation between copy number variation genes (focal events) and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1251GW7
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 variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1251GW7
Overview
Introduction

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

Summary

Testing the association between copy number variation 30 focal events and 10 molecular subtypes across 494 patients, 87 significant findings detected with P value < 0.05 and Q value < 0.25.

- amp_xq22.3 cnv correlated to 'CN_CNMF'.

- del_1q24.2 cnv correlated to 'CN_CNMF'.

- del_2p23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_2q35 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_6q22.31 cnv correlated to 'CN_CNMF'.

- del_8p23.2 cnv correlated to 'CN_CNMF'.

- del_8p22 cnv correlated to 'CN_CNMF'.

- del_8p12 cnv correlated to 'CN_CNMF'.

- del_8q24.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_9q21.13 cnv correlated to 'CN_CNMF'.

- del_10q21.2 cnv correlated to 'CN_CNMF'.

- del_10q23.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_11p15.1 cnv correlated to 'CN_CNMF'.

- del_13q12.3 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

- del_13q21.31 cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- del_15q25.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_18p11.21 cnv correlated to 'CN_CNMF'.

- del_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_21q21.1 cnv correlated to 'CN_CNMF'.

- del_22q13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_22q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- del_22q13.32 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 30 focal 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, 87 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
del 2p23 1 | 12 (2%) | 482 | 3.58e-10 (1.01e-07) | 1.21e-05 (0.00302) | 0.773 (1.00) | 0.0122 (1.00) | 9.75e-06 (0.00249) | 5.26e-06 (0.00135) | 1.13e-06 (0.000301) | 1.29e-07 (3.51e-05) | 3.13e-06 (0.000816) | 1.45e-07 (3.91e-05)
del 2q35 | 12 (2%) | 482 | 3.43e-13 (9.7e-11) | 1.51e-06 (0.000401) | 0.538 (1.00) | 0.00327 (0.604) | 9.75e-06 (0.00249) | 3.05e-07 (8.17e-05) | 1.13e-06 (0.000301) | 1.29e-07 (3.51e-05) | 3.13e-06 (0.000816) | 1.45e-07 (3.91e-05)
del 22q13 1 | 86 (17%) | 408 | 7.48e-90 (2.16e-87) | 1.1e-05 (0.00277) | 0.123 (1.00) | 0.15 (1.00) | 3.38e-09 (9.46e-07) | 8.03e-08 (2.21e-05) | 0.000956 (0.198) | 0.000342 (0.0764) | 3.12e-06 (0.000816) | 0.000206 (0.0479)
del 22q13 2 | 86 (17%) | 408 | 7.48e-90 (2.16e-87) | 1.1e-05 (0.00277) | 0.123 (1.00) | 0.15 (1.00) | 3.38e-09 (9.46e-07) | 8.03e-08 (2.21e-05) | 0.000956 (0.198) | 0.000342 (0.0764) | 3.12e-06 (0.000816) | 0.000206 (0.0479)
del 22q13 31 | 86 (17%) | 408 | 7.48e-90 (2.16e-87) | 1.1e-05 (0.00277) | 0.123 (1.00) | 0.15 (1.00) | 3.38e-09 (9.46e-07) | 8.03e-08 (2.21e-05) | 0.000956 (0.198) | 0.000342 (0.0764) | 3.12e-06 (0.000816) | 0.000206 (0.0479)
del 22q13 32 | 87 (18%) | 407 | 6.22e-88 (1.77e-85) | 5.47e-06 (0.0014) | 0.123 (1.00) | 0.15 (1.00) | 1.75e-09 (4.92e-07) | 3.91e-08 (1.08e-05) | 0.000547 (0.118) | 0.000174 (0.0406) | 1.55e-06 (0.000409) | 9.94e-05 (0.0236)
del 8q24 22 | 7 (1%) | 487 | 4.62e-05 (0.0113) | 0.000343 (0.0764) | 0.839 (1.00) | 0.0521 (1.00) | 0.00169 (0.335) | 0.000221 (0.05) | 0.000219 (0.0498) | 7.85e-05 (0.0188) | 0.000758 (0.159) | 7.02e-05 (0.0169)
del 19p13 2 | 7 (1%) | 487 | 0.000653 (0.138) | 0.000343 (0.0764) | 0.855 (1.00) | 0.126 (1.00) | 0.00169 (0.335) | 0.000221 (0.05) | 0.000219 (0.0498) | 7.85e-05 (0.0188) | 0.000758 (0.159) | 7.02e-05 (0.0169)
del 10q23 31 | 12 (2%) | 482 | 2.51e-06 (0.00066) | 0.00426 (0.78) | 0.0519 (1.00) | 0.0237 (1.00) | 0.000648 (0.138) | 0.000386 (0.0841) | 0.00466 (0.82) | 0.00111 (0.224) | 0.000508 (0.11) | 0.000981 (0.2)
del 15q25 3 | 9 (2%) | 485 | 0.00014 (0.0331) | 0.00199 (0.384) | 0.243 (1.00) | 0.0433 (1.00) | 0.00462 (0.818) | 0.000795 (0.165) | 0.000558 (0.12) | 0.000164 (0.0386) | 0.00162 (0.324) | 0.000171 (0.04)
del 13q12 3 | 16 (3%) | 478 | 0.00603 (1.00) | 0.000988 (0.201) | 0.183 (1.00) | 0.257 (1.00) | 0.000653 (0.138) | 0.00929 (1.00) | 0.0335 (1.00) | 0.00877 (1.00) | 0.0127 (1.00) | 0.00614 (1.00)
amp xq22 3 | 15 (3%) | 479 | 1.32e-05 (0.00328) | 0.771 (1.00) | 0.839 (1.00) | 0.25 (1.00) | 0.766 (1.00) | 0.703 (1.00) | 1 (1.00) | 0.818 (1.00) | 0.946 (1.00) | 0.729 (1.00)
del 1q24 2 | 3 (1%) | 491 | 0.0003 (0.0671) | 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)
del 6q22 31 | 7 (1%) | 487 | 4.62e-05 (0.0113) | 0.0038 (0.699) | 0.0129 (1.00) | 0.364 (1.00) | 0.032 (1.00) | 0.00901 (1.00) | 0.00316 (0.592) | 0.00196 (0.383) | 0.00954 (1.00) | 0.00199 (0.384)
del 8p23 2 | 4 (1%) | 490 | 1.89e-05 (0.00469) | 0.0149 (1.00) |  |  | 0.0429 (1.00) | 0.0157 (1.00) | 0.00833 (1.00) | 0.00467 (0.82) | 0.0227 (1.00) | 0.00439 (0.795)
del 8p22 | 4 (1%) | 490 | 1.89e-05 (0.00469) | 0.0149 (1.00) |  |  | 0.0429 (1.00) | 0.0157 (1.00) | 0.00833 (1.00) | 0.00467 (0.82) | 0.0227 (1.00) | 0.00439 (0.795)
del 8p12 | 4 (1%) | 490 | 1.89e-05 (0.00469) | 0.0149 (1.00) |  |  | 0.0429 (1.00) | 0.0157 (1.00) | 0.00833 (1.00) | 0.00467 (0.82) | 0.0227 (1.00) | 0.00439 (0.795)
del 9q21 13 | 24 (5%) | 470 | 9.23e-15 (2.62e-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 (0.795)
del 10q21 2 | 12 (2%) | 482 | 5.17e-05 (0.0126) | 0.108 (1.00) | 0.155 (1.00) | 0.62 (1.00) | 0.0186 (1.00) | 0.00267 (0.502) | 0.141 (1.00) | 0.0382 (1.00) | 0.0375 (1.00) | 0.058 (1.00)
del 11p15 1 | 7 (1%) | 487 | 7.98e-08 (2.2e-05) | 0.00956 (1.00) | 0.495 (1.00) | 1 (1.00) | 0.00675 (1.00) | 0.00901 (1.00) | 0.00316 (0.592) | 0.00196 (0.383) | 0.00954 (1.00) | 0.00199 (0.384)
del 13q21 31 | 18 (4%) | 476 | 0.00548 (0.937) | 0.0215 (1.00) | 0.0531 (1.00) | 0.913 (1.00) | 0.00193 (0.377) | 0.000642 (0.137) | 0.00504 (0.868) | 0.00213 (0.404) | 0.0045 (0.801) | 0.00229 (0.433)
del 18p11 21 | 4 (1%) | 490 | 0.000207 (0.0479) | 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)
del 21q21 1 | 9 (2%) | 485 | 5.66e-05 (0.0137) | 0.486 (1.00) | 0.148 (1.00) | 0.204 (1.00) | 0.739 (1.00) | 0.722 (1.00) | 0.0526 (1.00) | 0.266 (1.00) | 0.0537 (1.00) | 0.0436 (1.00)
del 5p15 2 | 4 (1%) | 490 | 0.348 (1.00) | 0.394 (1.00) |  |  | 0.412 (1.00) | 0.363 (1.00) | 0.555 (1.00) | 0.578 (1.00) | 0.476 (1.00) | 0.684 (1.00)
del 7q34 | 4 (1%) | 490 | 0.64 (1.00) | 0.649 (1.00) |  |  | 0.741 (1.00) | 0.658 (1.00) | 0.691 (1.00) | 0.822 (1.00) | 1 (1.00) | 0.828 (1.00)
del 16q23 3 | 6 (1%) | 488 | 0.0483 (1.00) | 0.0744 (1.00) | 0.444 (1.00) | 0.102 (1.00) | 0.285 (1.00) | 0.239 (1.00) | 0.197 (1.00) | 0.387 (1.00) | 0.294 (1.00) | 0.293 (1.00)
del 17p13 1 | 8 (2%) | 486 | 0.00182 (0.358) | 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)
del 18q22 2 | 5 (1%) | 489 | 0.00134 (0.27) | 0.0757 (1.00) | 1 (1.00) | 0.25 (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)
del xq22 1 | 6 (1%) | 488 | 0.0736 (1.00) | 0.551 (1.00) | 0.0977 (1.00) | 0.118 (1.00) | 0.59 (1.00) | 0.641 (1.00) | 0.526 (1.00) | 0.294 (1.00) | 0.703 (1.00) | 0.341 (1.00)
del xq22 3 | 4 (1%) | 490 | 0.0538 (1.00) | 0.0594 (1.00) | 0.278 (1.00) | 0.364 (1.00) | 0.0924 (1.00) | 0.289 (1.00) | 0.115 (1.00) | 0.037 (1.00) | 0.226 (1.00) | 0.0402 (1.00)

'amp_xq22.3' versus 'CN_CNMF'

P value = 1.32e-05 (Fisher's exact test), Q value = 0.0033

Table S1. Gene #1: 'amp_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
AMP PEAK 1(XQ22.3) MUTATED | 7 | 8 | 0
AMP PEAK 1(XQ22.3) WILD-TYPE | 27 | 375 | 77

Figure S1. Get High-res Image Gene #1: 'amp_xq22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q24.2' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.067

Table S2. Gene #2: 'del_1q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 1(1Q24.2) MUTATED | 3 | 0 | 0
DEL PEAK 1(1Q24.2) WILD-TYPE | 31 | 383 | 77

Figure S2. Get High-res Image Gene #2: 'del_1q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p23.1' versus 'CN_CNMF'

P value = 3.58e-10 (Fisher's exact test), Q value = 1e-07

Table S3. Gene #3: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 2(2P23.1) MUTATED | 9 | 1 | 2
DEL PEAK 2(2P23.1) WILD-TYPE | 25 | 382 | 75

Figure S3. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2p23.1' versus 'METHLYATION_CNMF'

P value = 1.21e-05 (Fisher's exact test), Q value = 0.003

Table S4. Gene #3: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 2(2P23.1) MUTATED | 11 | 1 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 140 | 82 | 260

Figure S4. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2p23.1' versus 'MRNASEQ_CNMF'

P value = 9.75e-06 (Fisher's exact test), Q value = 0.0025

Table S5. Gene #3: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
DEL PEAK 2(2P23.1) MUTATED | 12 | 0 | 0 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 142 | 55 | 116 | 167

Figure S5. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.26e-06 (Fisher's exact test), Q value = 0.0014

Table S6. Gene #3: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
DEL PEAK 2(2P23.1) MUTATED | 0 | 11 | 0 | 1
DEL PEAK 2(2P23.1) WILD-TYPE | 197 | 117 | 96 | 70

Figure S6. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2p23.1' versus 'MIRSEQ_CNMF'

P value = 1.13e-06 (Fisher's exact test), Q value = 3e-04

Table S7. Gene #3: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 2(2P23.1) MUTATED | 12 | 0 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 138 | 173 | 170

Figure S7. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.29e-07 (Fisher's exact test), Q value = 3.5e-05

Table S8. Gene #3: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 2(2P23.1) MUTATED | 0 | 12 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 155 | 118 | 208

Figure S8. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2p23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.13e-06 (Fisher's exact test), Q value = 0.00082

Table S9. Gene #3: 'del_2p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 2(2P23.1) MUTATED | 12 | 0 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 151 | 169 | 161

Figure S9. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2p23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.45e-07 (Fisher's exact test), Q value = 3.9e-05

Table S10. Gene #3: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 2(2P23.1) MUTATED | 0 | 12 | 0
DEL PEAK 2(2P23.1) WILD-TYPE | 199 | 116 | 166

Figure S10. Get High-res Image Gene #3: 'del_2p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q35' versus 'CN_CNMF'

P value = 3.43e-13 (Fisher's exact test), Q value = 9.7e-11

Table S11. Gene #4: 'del_2q35' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 3(2Q35) MUTATED | 11 | 1 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 23 | 382 | 77

Figure S11. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q35' versus 'METHLYATION_CNMF'

P value = 1.51e-06 (Fisher's exact test), Q value = 4e-04

Table S12. Gene #4: 'del_2q35' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 3(2Q35) MUTATED | 12 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 139 | 83 | 260

Figure S12. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q35' versus 'MRNASEQ_CNMF'

P value = 9.75e-06 (Fisher's exact test), Q value = 0.0025

Table S13. Gene #4: 'del_2q35' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
DEL PEAK 3(2Q35) MUTATED | 12 | 0 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 142 | 55 | 116 | 167

Figure S13. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q35' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.05e-07 (Fisher's exact test), Q value = 8.2e-05

Table S14. Gene #4: 'del_2q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
DEL PEAK 3(2Q35) MUTATED | 0 | 12 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 197 | 116 | 96 | 71

Figure S14. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q35' versus 'MIRSEQ_CNMF'

P value = 1.13e-06 (Fisher's exact test), Q value = 3e-04

Table S15. Gene #4: 'del_2q35' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 3(2Q35) MUTATED | 12 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 138 | 173 | 170

Figure S15. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q35' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.29e-07 (Fisher's exact test), Q value = 3.5e-05

Table S16. Gene #4: 'del_2q35' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 3(2Q35) MUTATED | 0 | 12 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 155 | 118 | 208

Figure S16. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q35' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.13e-06 (Fisher's exact test), Q value = 0.00082

Table S17. Gene #4: 'del_2q35' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 3(2Q35) MUTATED | 12 | 0 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 151 | 169 | 161

Figure S17. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q35' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.45e-07 (Fisher's exact test), Q value = 3.9e-05

Table S18. Gene #4: 'del_2q35' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 3(2Q35) MUTATED | 0 | 12 | 0
DEL PEAK 3(2Q35) WILD-TYPE | 199 | 116 | 166

Figure S18. Get High-res Image Gene #4: 'del_2q35' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 4.62e-05 (Fisher's exact test), Q value = 0.011

Table S19. Gene #6: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 6(6Q22.31) MUTATED | 5 | 2 | 0
DEL PEAK 6(6Q22.31) WILD-TYPE | 29 | 381 | 77

Figure S19. Get High-res Image Gene #6: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0047

Table S20. Gene #8: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 9(8P23.2) MUTATED | 4 | 0 | 0
DEL PEAK 9(8P23.2) WILD-TYPE | 30 | 383 | 77

Figure S20. Get High-res Image Gene #8: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p22' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0047

Table S21. Gene #9: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 10(8P22) MUTATED | 4 | 0 | 0
DEL PEAK 10(8P22) WILD-TYPE | 30 | 383 | 77

Figure S21. Get High-res Image Gene #9: 'del_8p22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p12' versus 'CN_CNMF'

P value = 1.89e-05 (Fisher's exact test), Q value = 0.0047

Table S22. Gene #10: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 11(8P12) MUTATED | 4 | 0 | 0
DEL PEAK 11(8P12) WILD-TYPE | 30 | 383 | 77

Figure S22. Get High-res Image Gene #10: 'del_8p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_8q24.22' versus 'CN_CNMF'

P value = 4.62e-05 (Fisher's exact test), Q value = 0.011

Table S23. Gene #11: 'del_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 12(8Q24.22) MUTATED | 5 | 2 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 29 | 381 | 77

Figure S23. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #1: 'CN_CNMF'

'del_8q24.22' versus 'METHLYATION_CNMF'

P value = 0.000343 (Fisher's exact test), Q value = 0.076

Table S24. Gene #11: 'del_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 12(8Q24.22) MUTATED | 7 | 0 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 144 | 83 | 260

Figure S24. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8q24.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000221 (Fisher's exact test), Q value = 0.05

Table S25. Gene #11: 'del_8q24.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
DEL PEAK 12(8Q24.22) MUTATED | 0 | 7 | 0 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 197 | 121 | 96 | 71

Figure S25. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8q24.22' versus 'MIRSEQ_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.05

Table S26. Gene #11: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 12(8Q24.22) MUTATED | 7 | 0 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 143 | 173 | 170

Figure S26. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8q24.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.85e-05 (Fisher's exact test), Q value = 0.019

Table S27. Gene #11: 'del_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 12(8Q24.22) MUTATED | 0 | 7 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 155 | 123 | 208

Figure S27. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8q24.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000758 (Fisher's exact test), Q value = 0.16

Table S28. Gene #11: 'del_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 12(8Q24.22) MUTATED | 7 | 0 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 156 | 169 | 161

Figure S28. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8q24.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.02e-05 (Fisher's exact test), Q value = 0.017

Table S29. Gene #11: 'del_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 12(8Q24.22) MUTATED | 0 | 7 | 0
DEL PEAK 12(8Q24.22) WILD-TYPE | 199 | 121 | 166

Figure S29. Get High-res Image Gene #11: 'del_8q24.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.13' versus 'CN_CNMF'

P value = 9.23e-15 (Fisher's exact test), Q value = 2.6e-12

Table S30. Gene #12: 'del_9q21.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 13(9Q21.13) MUTATED | 16 | 7 | 1
DEL PEAK 13(9Q21.13) WILD-TYPE | 18 | 376 | 76

Figure S30. Get High-res Image Gene #12: 'del_9q21.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.2' versus 'CN_CNMF'

P value = 5.17e-05 (Fisher's exact test), Q value = 0.013

Table S31. Gene #13: 'del_10q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 14(10Q21.2) MUTATED | 6 | 6 | 0
DEL PEAK 14(10Q21.2) WILD-TYPE | 28 | 377 | 77

Figure S31. Get High-res Image Gene #13: 'del_10q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'CN_CNMF'

P value = 2.51e-06 (Fisher's exact test), Q value = 0.00066

Table S32. Gene #14: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 15(10Q23.31) MUTATED | 7 | 5 | 0
DEL PEAK 15(10Q23.31) WILD-TYPE | 27 | 378 | 77

Figure S32. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.000648 (Fisher's exact test), Q value = 0.14

Table S33. Gene #14: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
DEL PEAK 15(10Q23.31) MUTATED | 10 | 0 | 2 | 0
DEL PEAK 15(10Q23.31) WILD-TYPE | 144 | 55 | 114 | 167

Figure S33. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000386 (Fisher's exact test), Q value = 0.084

Table S34. Gene #14: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
DEL PEAK 15(10Q23.31) MUTATED | 0 | 9 | 2 | 1
DEL PEAK 15(10Q23.31) WILD-TYPE | 197 | 119 | 94 | 70

Figure S34. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.22

Table S35. Gene #14: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 15(10Q23.31) MUTATED | 1 | 9 | 2
DEL PEAK 15(10Q23.31) WILD-TYPE | 154 | 121 | 206

Figure S35. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000508 (Fisher's exact test), Q value = 0.11

Table S36. Gene #14: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 15(10Q23.31) MUTATED | 10 | 0 | 2
DEL PEAK 15(10Q23.31) WILD-TYPE | 153 | 169 | 159

Figure S36. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000981 (Fisher's exact test), Q value = 0.2

Table S37. Gene #14: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 15(10Q23.31) MUTATED | 2 | 9 | 1
DEL PEAK 15(10Q23.31) WILD-TYPE | 197 | 119 | 165

Figure S37. Get High-res Image Gene #14: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.1' versus 'CN_CNMF'

P value = 7.98e-08 (Fisher's exact test), Q value = 2.2e-05

Table S38. Gene #15: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 16(11P15.1) MUTATED | 6 | 0 | 1
DEL PEAK 16(11P15.1) WILD-TYPE | 28 | 383 | 76

Figure S38. Get High-res Image Gene #15: 'del_11p15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.3' versus 'METHLYATION_CNMF'

P value = 0.000988 (Fisher's exact test), Q value = 0.2

Table S39. Gene #16: 'del_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 17(13Q12.3) MUTATED | 11 | 3 | 2
DEL PEAK 17(13Q12.3) WILD-TYPE | 140 | 80 | 258

Figure S39. Get High-res Image Gene #16: 'del_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.3' versus 'MRNASEQ_CNMF'

P value = 0.000653 (Fisher's exact test), Q value = 0.14

Table S40. Gene #16: 'del_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
DEL PEAK 17(13Q12.3) MUTATED | 11 | 3 | 2 | 0
DEL PEAK 17(13Q12.3) WILD-TYPE | 143 | 52 | 114 | 167

Figure S40. Get High-res Image Gene #16: 'del_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000642 (Fisher's exact test), Q value = 0.14

Table S41. Gene #17: 'del_13q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
DEL PEAK 18(13Q21.31) MUTATED | 1 | 11 | 5 | 1
DEL PEAK 18(13Q21.31) WILD-TYPE | 196 | 117 | 91 | 70

Figure S41. Get High-res Image Gene #17: 'del_13q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q25.3' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.033

Table S42. Gene #18: 'del_15q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 19(15Q25.3) MUTATED | 5 | 3 | 1
DEL PEAK 19(15Q25.3) WILD-TYPE | 29 | 380 | 76

Figure S42. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000795 (Fisher's exact test), Q value = 0.17

Table S43. Gene #18: 'del_15q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
DEL PEAK 19(15Q25.3) MUTATED | 1 | 8 | 0 | 0
DEL PEAK 19(15Q25.3) WILD-TYPE | 196 | 120 | 96 | 71

Figure S43. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q25.3' versus 'MIRSEQ_CNMF'

P value = 0.000558 (Fisher's exact test), Q value = 0.12

Table S44. Gene #18: 'del_15q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 19(15Q25.3) MUTATED | 8 | 1 | 0
DEL PEAK 19(15Q25.3) WILD-TYPE | 142 | 172 | 170

Figure S44. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000164 (Fisher's exact test), Q value = 0.039

Table S45. Gene #18: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 19(15Q25.3) MUTATED | 0 | 8 | 1
DEL PEAK 19(15Q25.3) WILD-TYPE | 155 | 122 | 207

Figure S45. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000171 (Fisher's exact test), Q value = 0.04

Table S46. Gene #18: 'del_15q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 19(15Q25.3) MUTATED | 1 | 8 | 0
DEL PEAK 19(15Q25.3) WILD-TYPE | 198 | 120 | 166

Figure S46. Get High-res Image Gene #18: 'del_15q25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18p11.21' versus 'CN_CNMF'

P value = 0.000207 (Fisher's exact test), Q value = 0.048

Table S47. Gene #21: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 23(18P11.21) MUTATED | 3 | 0 | 1
DEL PEAK 23(18P11.21) WILD-TYPE | 31 | 383 | 76

Figure S47. Get High-res Image Gene #21: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.2' versus 'CN_CNMF'

P value = 0.000653 (Fisher's exact test), Q value = 0.14

Table S48. Gene #23: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 25(19P13.2) MUTATED | 4 | 2 | 1
DEL PEAK 25(19P13.2) WILD-TYPE | 30 | 381 | 76

Figure S48. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.000343 (Fisher's exact test), Q value = 0.076

Table S49. Gene #23: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 25(19P13.2) MUTATED | 7 | 0 | 0
DEL PEAK 25(19P13.2) WILD-TYPE | 144 | 83 | 260

Figure S49. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000221 (Fisher's exact test), Q value = 0.05

Table S50. Gene #23: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
DEL PEAK 25(19P13.2) MUTATED | 0 | 7 | 0 | 0
DEL PEAK 25(19P13.2) WILD-TYPE | 197 | 121 | 96 | 71

Figure S50. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.000219 (Fisher's exact test), Q value = 0.05

Table S51. Gene #23: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 25(19P13.2) MUTATED | 7 | 0 | 0
DEL PEAK 25(19P13.2) WILD-TYPE | 143 | 173 | 170

Figure S51. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.85e-05 (Fisher's exact test), Q value = 0.019

Table S52. Gene #23: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 25(19P13.2) MUTATED | 0 | 7 | 0
DEL PEAK 25(19P13.2) WILD-TYPE | 155 | 123 | 208

Figure S52. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000758 (Fisher's exact test), Q value = 0.16

Table S53. Gene #23: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 25(19P13.2) MUTATED | 7 | 0 | 0
DEL PEAK 25(19P13.2) WILD-TYPE | 156 | 169 | 161

Figure S53. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7.02e-05 (Fisher's exact test), Q value = 0.017

Table S54. Gene #23: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 25(19P13.2) MUTATED | 0 | 7 | 0
DEL PEAK 25(19P13.2) WILD-TYPE | 199 | 121 | 166

Figure S54. Get High-res Image Gene #23: 'del_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q21.1' versus 'CN_CNMF'

P value = 5.66e-05 (Fisher's exact test), Q value = 0.014

Table S55. Gene #24: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 28(21Q21.1) MUTATED | 5 | 2 | 2
DEL PEAK 28(21Q21.1) WILD-TYPE | 29 | 381 | 75

Figure S55. Get High-res Image Gene #24: 'del_21q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.1' versus 'CN_CNMF'

P value = 7.48e-90 (Fisher's exact test), Q value = 2.2e-87

Table S56. Gene #25: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 29(22Q13.1) MUTATED | 9 | 0 | 77
DEL PEAK 29(22Q13.1) WILD-TYPE | 25 | 383 | 0

Figure S56. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.1' versus 'METHLYATION_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0028

Table S57. Gene #25: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 29(22Q13.1) MUTATED | 45 | 7 | 34
DEL PEAK 29(22Q13.1) WILD-TYPE | 106 | 76 | 226

Figure S57. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.1' versus 'MRNASEQ_CNMF'

P value = 3.38e-09 (Fisher's exact test), Q value = 9.5e-07

Table S58. Gene #25: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
DEL PEAK 29(22Q13.1) MUTATED | 45 | 8 | 26 | 7
DEL PEAK 29(22Q13.1) WILD-TYPE | 109 | 47 | 90 | 160

Figure S58. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.03e-08 (Fisher's exact test), Q value = 2.2e-05

Table S59. Gene #25: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
DEL PEAK 29(22Q13.1) MUTATED | 13 | 39 | 23 | 11
DEL PEAK 29(22Q13.1) WILD-TYPE | 184 | 89 | 73 | 60

Figure S59. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.1' versus 'MIRSEQ_CNMF'

P value = 0.000956 (Fisher's exact test), Q value = 0.2

Table S60. Gene #25: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 29(22Q13.1) MUTATED | 41 | 24 | 21
DEL PEAK 29(22Q13.1) WILD-TYPE | 109 | 149 | 149

Figure S60. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000342 (Fisher's exact test), Q value = 0.076

Table S61. Gene #25: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 29(22Q13.1) MUTATED | 22 | 38 | 26
DEL PEAK 29(22Q13.1) WILD-TYPE | 133 | 92 | 182

Figure S61. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.12e-06 (Fisher's exact test), Q value = 0.00082

Table S62. Gene #25: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 29(22Q13.1) MUTATED | 49 | 18 | 19
DEL PEAK 29(22Q13.1) WILD-TYPE | 114 | 151 | 142

Figure S62. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000206 (Fisher's exact test), Q value = 0.048

Table S63. Gene #25: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 29(22Q13.1) MUTATED | 24 | 38 | 24
DEL PEAK 29(22Q13.1) WILD-TYPE | 175 | 90 | 142

Figure S63. Get High-res Image Gene #25: 'del_22q13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.2' versus 'CN_CNMF'

P value = 7.48e-90 (Fisher's exact test), Q value = 2.2e-87

Table S64. Gene #26: 'del_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 30(22Q13.2) MUTATED | 9 | 0 | 77
DEL PEAK 30(22Q13.2) WILD-TYPE | 25 | 383 | 0

Figure S64. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.2' versus 'METHLYATION_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0028

Table S65. Gene #26: 'del_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 30(22Q13.2) MUTATED | 45 | 7 | 34
DEL PEAK 30(22Q13.2) WILD-TYPE | 106 | 76 | 226

Figure S65. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.2' versus 'MRNASEQ_CNMF'

P value = 3.38e-09 (Fisher's exact test), Q value = 9.5e-07

Table S66. Gene #26: 'del_22q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
DEL PEAK 30(22Q13.2) MUTATED | 45 | 8 | 26 | 7
DEL PEAK 30(22Q13.2) WILD-TYPE | 109 | 47 | 90 | 160

Figure S66. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.03e-08 (Fisher's exact test), Q value = 2.2e-05

Table S67. Gene #26: 'del_22q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
DEL PEAK 30(22Q13.2) MUTATED | 13 | 39 | 23 | 11
DEL PEAK 30(22Q13.2) WILD-TYPE | 184 | 89 | 73 | 60

Figure S67. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.2' versus 'MIRSEQ_CNMF'

P value = 0.000956 (Fisher's exact test), Q value = 0.2

Table S68. Gene #26: 'del_22q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 30(22Q13.2) MUTATED | 41 | 24 | 21
DEL PEAK 30(22Q13.2) WILD-TYPE | 109 | 149 | 149

Figure S68. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000342 (Fisher's exact test), Q value = 0.076

Table S69. Gene #26: 'del_22q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 30(22Q13.2) MUTATED | 22 | 38 | 26
DEL PEAK 30(22Q13.2) WILD-TYPE | 133 | 92 | 182

Figure S69. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.12e-06 (Fisher's exact test), Q value = 0.00082

Table S70. Gene #26: 'del_22q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 30(22Q13.2) MUTATED | 49 | 18 | 19
DEL PEAK 30(22Q13.2) WILD-TYPE | 114 | 151 | 142

Figure S70. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000206 (Fisher's exact test), Q value = 0.048

Table S71. Gene #26: 'del_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 30(22Q13.2) MUTATED | 24 | 38 | 24
DEL PEAK 30(22Q13.2) WILD-TYPE | 175 | 90 | 142

Figure S71. Get High-res Image Gene #26: 'del_22q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 7.48e-90 (Fisher's exact test), Q value = 2.2e-87

Table S72. Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 31(22Q13.31) MUTATED | 9 | 0 | 77
DEL PEAK 31(22Q13.31) WILD-TYPE | 25 | 383 | 0

Figure S72. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0028

Table S73. Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 31(22Q13.31) MUTATED | 45 | 7 | 34
DEL PEAK 31(22Q13.31) WILD-TYPE | 106 | 76 | 226

Figure S73. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 3.38e-09 (Fisher's exact test), Q value = 9.5e-07

Table S74. Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
DEL PEAK 31(22Q13.31) MUTATED | 45 | 8 | 26 | 7
DEL PEAK 31(22Q13.31) WILD-TYPE | 109 | 47 | 90 | 160

Figure S74. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.03e-08 (Fisher's exact test), Q value = 2.2e-05

Table S75. Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
DEL PEAK 31(22Q13.31) MUTATED | 13 | 39 | 23 | 11
DEL PEAK 31(22Q13.31) WILD-TYPE | 184 | 89 | 73 | 60

Figure S75. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.000956 (Fisher's exact test), Q value = 0.2

Table S76. Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 31(22Q13.31) MUTATED | 41 | 24 | 21
DEL PEAK 31(22Q13.31) WILD-TYPE | 109 | 149 | 149

Figure S76. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000342 (Fisher's exact test), Q value = 0.076

Table S77. Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 31(22Q13.31) MUTATED | 22 | 38 | 26
DEL PEAK 31(22Q13.31) WILD-TYPE | 133 | 92 | 182

Figure S77. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.12e-06 (Fisher's exact test), Q value = 0.00082

Table S78. Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 31(22Q13.31) MUTATED | 49 | 18 | 19
DEL PEAK 31(22Q13.31) WILD-TYPE | 114 | 151 | 142

Figure S78. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000206 (Fisher's exact test), Q value = 0.048

Table S79. Gene #27: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 31(22Q13.31) MUTATED | 24 | 38 | 24
DEL PEAK 31(22Q13.31) WILD-TYPE | 175 | 90 | 142

Figure S79. Get High-res Image Gene #27: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 6.22e-88 (Fisher's exact test), Q value = 1.8e-85

Table S80. Gene #28: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 383 | 77
DEL PEAK 32(22Q13.32) MUTATED | 9 | 1 | 77
DEL PEAK 32(22Q13.32) WILD-TYPE | 25 | 382 | 0

Figure S80. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 5.47e-06 (Fisher's exact test), Q value = 0.0014

Table S81. Gene #28: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 83 | 260
DEL PEAK 32(22Q13.32) MUTATED | 46 | 7 | 34
DEL PEAK 32(22Q13.32) WILD-TYPE | 105 | 76 | 226

Figure S81. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1.75e-09 (Fisher's exact test), Q value = 4.9e-07

Table S82. Gene #28: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 154 | 55 | 116 | 167
DEL PEAK 32(22Q13.32) MUTATED | 46 | 8 | 26 | 7
DEL PEAK 32(22Q13.32) WILD-TYPE | 108 | 47 | 90 | 160

Figure S82. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.91e-08 (Fisher's exact test), Q value = 1.1e-05

Table S83. Gene #28: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 197 | 128 | 96 | 71
DEL PEAK 32(22Q13.32) MUTATED | 13 | 40 | 23 | 11
DEL PEAK 32(22Q13.32) WILD-TYPE | 184 | 88 | 73 | 60

Figure S83. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.000547 (Fisher's exact test), Q value = 0.12

Table S84. Gene #28: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 150 | 173 | 170
DEL PEAK 32(22Q13.32) MUTATED | 42 | 24 | 21
DEL PEAK 32(22Q13.32) WILD-TYPE | 108 | 149 | 149

Figure S84. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000174 (Fisher's exact test), Q value = 0.041

Table S85. Gene #28: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 155 | 130 | 208
DEL PEAK 32(22Q13.32) MUTATED | 22 | 39 | 26
DEL PEAK 32(22Q13.32) WILD-TYPE | 133 | 91 | 182

Figure S85. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.55e-06 (Fisher's exact test), Q value = 0.00041

Table S86. Gene #28: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 163 | 169 | 161
DEL PEAK 32(22Q13.32) MUTATED | 50 | 18 | 19
DEL PEAK 32(22Q13.32) WILD-TYPE | 113 | 151 | 142

Figure S86. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.94e-05 (Fisher's exact test), Q value = 0.024

Table S87. Gene #28: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 199 | 128 | 166
DEL PEAK 32(22Q13.32) MUTATED | 24 | 39 | 24
DEL PEAK 32(22Q13.32) WILD-TYPE | 175 | 89 | 142

Figure S87. Get High-res Image Gene #28: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

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

- Number of patients = 494

- Number of significantly focal cnvs = 30

- Number of molecular subtypes = 10

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

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

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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