Correlation between copy number variations of arm-level result and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
21 April 2013 | analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C13J39ZX
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Thyroid Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13J39ZX
Overview
Introduction

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

Summary

Testing the association between copy number variation 45 arm-level results and 8 molecular subtypes across 497 patients, 102 significant findings detected with Q value < 0.25.

- 1q gain cnv correlated to 'CN_CNMF'.

- 4p gain cnv correlated to 'CN_CNMF'.

- 4q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

- 11q gain cnv correlated to 'CN_CNMF'.

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

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

- 13q gain cnv correlated to 'CN_CNMF'.

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

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

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

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

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

- 19p gain cnv correlated to 'CN_CNMF'.

- 19q gain cnv correlated to 'CN_CNMF'.

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

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

- 1p loss cnv correlated to 'CN_CNMF'.

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

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

- 3q loss cnv correlated to 'CN_CNMF'.

- 8p loss cnv correlated to 'CN_CNMF'.

- 8q loss cnv correlated to 'CN_CNMF'.

- 9p loss cnv correlated to 'CN_CNMF'.

- 9q loss cnv correlated to 'CN_CNMF'.

- 10p loss cnv correlated to 'CN_CNMF'.

- 10q loss cnv correlated to 'CN_CNMF'.

- 11p loss cnv correlated to 'CN_CNMF'.

- 11q loss cnv correlated to 'CN_CNMF'.

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

- 18p loss cnv correlated to 'CN_CNMF'.

- 18q loss cnv correlated to 'CN_CNMF'.

- 21q loss cnv correlated to 'CN_CNMF'.

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

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 45 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 102 significant findings detected.

|  | Molecular subtypes | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
7q gain | 0 (0%) | 478 | 1.76e-23 (5.65e-21) | 3.64e-05 (0.00969) | 0.689 (1.00) | 0.00298 (0.597) | 4.87e-05 (0.0128) | 6.26e-06 (0.00177) | 0.000289 (0.0691) | 2.87e-05 (0.00773)
12p gain | 0 (0%) | 486 | 1.03e-12 (3.22e-10) | 3.14e-06 (0.000912) | 0.901 (1.00) | 0.0299 (1.00) | 1.59e-05 (0.00446) | 3.43e-06 (0.000987) | 5.19e-05 (0.0136) | 1.7e-05 (0.00472)
12q gain | 0 (0%) | 485 | 1.27e-12 (3.98e-10) | 6.85e-07 (0.000204) | 0.901 (1.00) | 0.0299 (1.00) | 3.88e-06 (0.00111) | 7.94e-07 (0.000235) | 1.64e-05 (0.00459) | 4.85e-06 (0.00138)
16p gain | 0 (0%) | 485 | 5.51e-14 (1.75e-11) | 2.82e-05 (0.0076) | 1 (1.00) | 0.0445 (1.00) | 0.000128 (0.0323) | 3.37e-05 (0.00899) | 0.000214 (0.052) | 5.88e-05 (0.0152)
17p gain | 0 (0%) | 485 | 2e-09 (6.13e-07) | 6.85e-07 (0.000204) | 0.772 (1.00) | 0.0179 (1.00) | 3.88e-06 (0.00111) | 7.94e-07 (0.000235) | 5.19e-05 (0.0136) | 1.7e-05 (0.00472)
17q gain | 0 (0%) | 484 | 3.83e-09 (1.17e-06) | 1.58e-07 (4.73e-05) | 0.795 (1.00) | 0.0206 (1.00) | 1.36e-06 (0.000398) | 1.92e-07 (5.74e-05) | 1.64e-05 (0.00459) | 4.85e-06 (0.00138)
2p loss | 0 (0%) | 489 | 5.02e-09 (1.53e-06) | 8.94e-05 (0.0229) | 1 (1.00) | 0.0817 (1.00) | 0.000496 (0.114) | 0.000164 (0.041) | 5.53e-05 (0.0144) | 2.27e-05 (0.00615)
22q loss | 0 (0%) | 431 | 6.79e-58 (2.19e-55) | 0.00013 (0.0328) | 0.114 (1.00) | 0.0835 (1.00) | 8.4e-11 (2.6e-08) | 1.98e-10 (6.11e-08) | 4.33e-05 (0.0114) | 9.51e-06 (0.00268)
5q gain | 0 (0%) | 483 | 2.6e-18 (8.27e-16) | 3.16e-05 (0.00847) | 0.901 (1.00) | 0.0299 (1.00) | 0.000163 (0.0408) | 4.26e-05 (0.0113) | 0.00146 (0.309) | 0.000106 (0.0269)
7p gain | 0 (0%) | 480 | 1.59e-22 (5.09e-20) | 0.000218 (0.0529) | 1 (1.00) | 0.0129 (1.00) | 0.000389 (0.0906) | 6.9e-05 (0.0178) | 0.00232 (0.478) | 0.000272 (0.0652)
2q loss | 0 (0%) | 490 | 3.78e-09 (1.16e-06) | 0.000378 (0.0884) | 0.837 (1.00) | 0.0549 (1.00) | 0.00144 (0.307) | 0.00065 (0.146) | 0.000192 (0.0475) | 8.85e-05 (0.0227)
5p gain | 0 (0%) | 480 | 6.97e-20 (2.22e-17) | 0.000747 (0.166) | 1 (1.00) | 0.125 (1.00) | 0.00247 (0.499) | 0.000522 (0.119) | 0.00691 (1.00) | 0.000541 (0.123)
14q gain | 0 (0%) | 489 | 5.02e-09 (1.53e-06) | 8.94e-05 (0.0229) | 1 (1.00) | 0.256 (1.00) | 0.000496 (0.114) | 0.000164 (0.041) | 0.00467 (0.906) | 0.00229 (0.475)
16q gain | 0 (0%) | 487 | 5.67e-13 (1.79e-10) | 0.000247 (0.0595) | 0.856 (1.00) | 0.129 (1.00) | 0.00144 (0.308) | 0.000429 (0.0995) | 0.00169 (0.355) | 0.000547 (0.124)
15q loss | 0 (0%) | 490 | 0.000464 (0.107) | 0.00241 (0.494) | 0.458 (1.00) | 0.256 (1.00) | 0.00491 (0.948) | 0.00175 (0.367) | 0.000664 (0.149) | 0.000342 (0.0805)
20p gain | 0 (0%) | 488 | 1.11e-11 (3.44e-09) | 0.000767 (0.17) | 1 (1.00) | 0.0817 (1.00) | 0.00397 (0.789) | 0.00123 (0.27) | 0.0124 (1.00) | 0.00619 (1.00)
20q gain | 0 (0%) | 488 | 1.11e-11 (3.44e-09) | 0.000767 (0.17) | 1 (1.00) | 0.0817 (1.00) | 0.00397 (0.789) | 0.00123 (0.27) | 0.0124 (1.00) | 0.00619 (1.00)
1q gain | 0 (0%) | 476 | 3.29e-06 (0.000951) | 0.0812 (1.00) | 0.0153 (1.00) | 0.0826 (1.00) | 0.0148 (1.00) | 0.00133 (0.288) | 0.224 (1.00) | 0.204 (1.00)
4p gain | 0 (0%) | 493 | 1.85e-05 (0.0051) | 0.0192 (1.00) |  |  | 0.0366 (1.00) | 0.0186 (1.00) | 0.112 (1.00) | 0.0975 (1.00)
4q gain | 0 (0%) | 493 | 1.85e-05 (0.0051) | 0.0192 (1.00) |  |  | 0.0366 (1.00) | 0.0186 (1.00) | 0.112 (1.00) | 0.0975 (1.00)
11q gain | 0 (0%) | 493 | 0.000204 (0.0503) | 0.0192 (1.00) |  |  | 0.0366 (1.00) | 0.0186 (1.00) | 0.00778 (1.00) | 0.00503 (0.965)
13q gain | 0 (0%) | 494 | 0.000294 (0.07) | 0.0495 (1.00) |  |  | 0.101 (1.00) | 0.0769 (1.00) |  |
19p gain | 0 (0%) | 493 | 1.85e-05 (0.0051) | 0.0192 (1.00) |  |  | 0.0366 (1.00) | 0.0186 (1.00) | 0.0264 (1.00) | 0.0191 (1.00)
19q gain | 0 (0%) | 492 | 1.12e-06 (0.00033) | 0.00434 (0.855) | 0.636 (1.00) | 0.0551 (1.00) | 0.0147 (1.00) | 0.00587 (1.00) | 0.00778 (1.00) | 0.00503 (0.965)
1p loss | 0 (0%) | 494 | 0.000294 (0.07) | 0.559 (1.00) |  |  | 0.495 (1.00) | 0.214 (1.00) | 0.3 (1.00) | 0.276 (1.00)
3q loss | 0 (0%) | 494 | 0.000294 (0.07) | 0.0495 (1.00) |  |  | 0.101 (1.00) | 0.0769 (1.00) | 0.0264 (1.00) | 0.0191 (1.00)
8p loss | 0 (0%) | 493 | 1.85e-05 (0.0051) | 0.047 (1.00) |  |  | 0.0366 (1.00) | 0.0186 (1.00) | 0.00778 (1.00) | 0.00503 (0.965)
8q loss | 0 (0%) | 493 | 1.85e-05 (0.0051) | 0.047 (1.00) |  |  | 0.0366 (1.00) | 0.0186 (1.00) | 0.00778 (1.00) | 0.00503 (0.965)
9p loss | 0 (0%) | 485 | 1.08e-11 (3.36e-09) | 0.272 (1.00) | 0.559 (1.00) | 0.206 (1.00) | 0.157 (1.00) | 0.206 (1.00) | 0.185 (1.00) | 0.159 (1.00)
9q loss | 0 (0%) | 480 | 1.58e-13 (4.99e-11) | 0.204 (1.00) | 0.21 (1.00) | 0.00441 (0.86) | 0.268 (1.00) | 0.295 (1.00) | 0.235 (1.00) | 0.228 (1.00)
10p loss | 0 (0%) | 491 | 6.62e-08 (2e-05) | 0.0979 (1.00) |  |  | 0.047 (1.00) | 0.0135 (1.00) | 0.0399 (1.00) | 0.0333 (1.00)
10q loss | 0 (0%) | 492 | 1.12e-06 (0.00033) | 0.175 (1.00) |  |  | 0.102 (1.00) | 0.0405 (1.00) | 0.112 (1.00) | 0.0975 (1.00)
11p loss | 0 (0%) | 490 | 7.74e-08 (2.33e-05) | 0.00947 (1.00) | 0.499 (1.00) | 1 (1.00) | 0.0148 (1.00) | 0.0419 (1.00) | 0.0399 (1.00) | 0.0333 (1.00)
11q loss | 0 (0%) | 488 | 3.24e-06 (0.00094) | 0.0149 (1.00) | 0.388 (1.00) | 0.798 (1.00) | 0.044 (1.00) | 0.039 (1.00) | 0.0138 (1.00) | 0.0075 (1.00)
18p loss | 0 (0%) | 493 | 0.000204 (0.0503) | 0.19 (1.00) | 1 (1.00) | 0.369 (1.00) | 0.22 (1.00) | 0.12 (1.00) | 0.0743 (1.00) | 0.0671 (1.00)
18q loss | 0 (0%) | 493 | 0.000204 (0.0503) | 0.19 (1.00) | 1 (1.00) | 0.369 (1.00) | 0.22 (1.00) | 0.12 (1.00) | 0.0743 (1.00) | 0.0671 (1.00)
21q loss | 0 (0%) | 491 | 0.000192 (0.0475) | 0.0979 (1.00) | 0.384 (1.00) | 0.0551 (1.00) | 0.0439 (1.00) | 0.112 (1.00) | 0.0399 (1.00) | 0.0333 (1.00)
11p gain | 0 (0%) | 492 | 0.00134 (0.288) | 0.00434 (0.855) |  |  | 0.0147 (1.00) | 0.00587 (1.00) | 0.00228 (0.474) | 0.00132 (0.286)
18p gain | 0 (0%) | 494 | 0.00245 (0.499) | 0.0495 (1.00) |  |  | 0.101 (1.00) | 0.0769 (1.00) |  |
18q gain | 0 (0%) | 494 | 0.00245 (0.499) | 0.0495 (1.00) |  |  | 0.101 (1.00) | 0.0769 (1.00) |  |
21q gain | 0 (0%) | 494 | 0.00245 (0.499) | 0.0495 (1.00) |  |  | 0.101 (1.00) | 0.0769 (1.00) | 0.0264 (1.00) | 0.0191 (1.00)
6q loss | 0 (0%) | 494 | 0.0218 (1.00) | 0.0495 (1.00) |  |  | 0.101 (1.00) | 0.0769 (1.00) | 0.0264 (1.00) | 0.0191 (1.00)
13q loss | 0 (0%) | 486 | 0.0123 (1.00) | 0.0182 (1.00) | 0.0779 (1.00) | 1 (1.00) | 0.0182 (1.00) | 0.00154 (0.325) | 0.00774 (1.00) | 0.0164 (1.00)
17p loss | 0 (0%) | 490 | 0.00118 (0.26) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.79 (1.00) | 0.819 (1.00) | 0.518 (1.00) | 0.499 (1.00)
19p loss | 0 (0%) | 493 | 0.132 (1.00) | 0.0192 (1.00) | 0.281 (1.00) | 0.369 (1.00) | 0.0366 (1.00) | 0.0186 (1.00) | 0.00778 (1.00) | 0.00503 (0.965)

'1q gain' versus 'CN_CNMF'

P value = 3.29e-06 (Fisher's exact test), Q value = 0.00095

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

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

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

'4p gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0051

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

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

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

'4q gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0051

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

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

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

'5p gain' versus 'CN_CNMF'

P value = 6.97e-20 (Fisher's exact test), Q value = 2.2e-17

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

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

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

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.000747 (Fisher's exact test), Q value = 0.17

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
5P GAIN CNV | 12 | 2 | 3
5P GAIN WILD-TYPE | 137 | 72 | 271

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

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000522 (Fisher's exact test), Q value = 0.12

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
5P GAIN CNV | 12 | 5 | 0 | 0
5P GAIN WILD-TYPE | 111 | 186 | 53 | 91

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000541 (Fisher's exact test), Q value = 0.12

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

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

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

'5q gain' versus 'CN_CNMF'

P value = 2.6e-18 (Fisher's exact test), Q value = 8.3e-16

Table S8. Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S8. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 3.16e-05 (Fisher's exact test), Q value = 0.0085

Table S9. Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
5Q GAIN CNV | 12 | 1 | 1
5Q GAIN WILD-TYPE | 137 | 73 | 273

Figure S9. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.000163 (Fisher's exact test), Q value = 0.041

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 140 | 56 | 106 | 156
5Q GAIN CNV | 12 | 0 | 0 | 2
5Q GAIN WILD-TYPE | 128 | 56 | 106 | 154

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

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.26e-05 (Fisher's exact test), Q value = 0.011

Table S11. Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
5Q GAIN CNV | 12 | 2 | 0 | 0
5Q GAIN WILD-TYPE | 111 | 189 | 53 | 91

Figure S11. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000106 (Fisher's exact test), Q value = 0.027

Table S12. Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S12. Get High-res Image Gene #5: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1.59e-22 (Fisher's exact test), Q value = 5.1e-20

Table S13. Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S13. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.000218 (Fisher's exact test), Q value = 0.053

Table S14. Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
7P GAIN CNV | 12 | 3 | 2
7P GAIN WILD-TYPE | 137 | 71 | 272

Figure S14. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.000389 (Fisher's exact test), Q value = 0.091

Table S15. Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 140 | 56 | 106 | 156
7P GAIN CNV | 13 | 0 | 1 | 2
7P GAIN WILD-TYPE | 127 | 56 | 105 | 154

Figure S15. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.9e-05 (Fisher's exact test), Q value = 0.018

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
7P GAIN CNV | 13 | 2 | 0 | 1
7P GAIN WILD-TYPE | 110 | 189 | 53 | 90

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

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000272 (Fisher's exact test), Q value = 0.065

Table S17. Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S17. Get High-res Image Gene #6: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1.76e-23 (Fisher's exact test), Q value = 5.7e-21

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

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

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

'7q gain' versus 'METHLYATION_CNMF'

P value = 3.64e-05 (Fisher's exact test), Q value = 0.0097

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
7Q GAIN CNV | 14 | 3 | 2
7Q GAIN WILD-TYPE | 135 | 71 | 272

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

'7q gain' versus 'MRNASEQ_CNMF'

P value = 4.87e-05 (Fisher's exact test), Q value = 0.013

Table S20. Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 140 | 56 | 106 | 156
7Q GAIN CNV | 15 | 0 | 1 | 2
7Q GAIN WILD-TYPE | 125 | 56 | 105 | 154

Figure S20. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.26e-06 (Fisher's exact test), Q value = 0.0018

Table S21. Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
7Q GAIN CNV | 15 | 2 | 0 | 1
7Q GAIN WILD-TYPE | 108 | 189 | 53 | 90

Figure S21. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.000289 (Fisher's exact test), Q value = 0.069

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

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

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

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.0077

Table S23. Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S23. Get High-res Image Gene #7: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.05

Table S24. Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S24. Get High-res Image Gene #9: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1.03e-12 (Fisher's exact test), Q value = 3.2e-10

Table S25. Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S25. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3.14e-06 (Fisher's exact test), Q value = 0.00091

Table S26. Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
12P GAIN CNV | 11 | 0 | 0
12P GAIN WILD-TYPE | 138 | 74 | 274

Figure S26. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.0045

Table S27. Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 140 | 56 | 106 | 156
12P GAIN CNV | 11 | 0 | 0 | 0
12P GAIN WILD-TYPE | 129 | 56 | 106 | 156

Figure S27. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.43e-06 (Fisher's exact test), Q value = 0.00099

Table S28. Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
12P GAIN CNV | 11 | 0 | 0 | 0
12P GAIN WILD-TYPE | 112 | 191 | 53 | 91

Figure S28. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.014

Table S29. Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

Figure S29. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.0047

Table S30. Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S30. Get High-res Image Gene #10: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1.27e-12 (Fisher's exact test), Q value = 4e-10

Table S31. Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S31. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 6.85e-07 (Fisher's exact test), Q value = 2e-04

Table S32. Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
12Q GAIN CNV | 12 | 0 | 0
12Q GAIN WILD-TYPE | 137 | 74 | 274

Figure S32. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 3.88e-06 (Fisher's exact test), Q value = 0.0011

Table S33. Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 140 | 56 | 106 | 156
12Q GAIN CNV | 12 | 0 | 0 | 0
12Q GAIN WILD-TYPE | 128 | 56 | 106 | 156

Figure S33. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.94e-07 (Fisher's exact test), Q value = 0.00023

Table S34. Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
12Q GAIN CNV | 12 | 0 | 0 | 0
12Q GAIN WILD-TYPE | 111 | 191 | 53 | 91

Figure S34. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.0046

Table S35. Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

Figure S35. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0014

Table S36. Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S36. Get High-res Image Gene #11: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.07

Table S37. Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S37. Get High-res Image Gene #12: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 5.02e-09 (Fisher's exact test), Q value = 1.5e-06

Table S38. Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S38. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 8.94e-05 (Fisher's exact test), Q value = 0.023

Table S39. Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
14Q GAIN CNV | 8 | 0 | 0
14Q GAIN WILD-TYPE | 141 | 74 | 274

Figure S39. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.000496 (Fisher's exact test), Q value = 0.11

Table S40. Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 140 | 56 | 106 | 156
14Q GAIN CNV | 8 | 0 | 0 | 0
14Q GAIN WILD-TYPE | 132 | 56 | 106 | 156

Figure S40. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000164 (Fisher's exact test), Q value = 0.041

Table S41. Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
14Q GAIN CNV | 8 | 0 | 0 | 0
14Q GAIN WILD-TYPE | 115 | 191 | 53 | 91

Figure S41. Get High-res Image Gene #13: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 5.51e-14 (Fisher's exact test), Q value = 1.7e-11

Table S42. Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S42. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.0076

Table S43. Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
16P GAIN CNV | 10 | 2 | 0
16P GAIN WILD-TYPE | 139 | 72 | 274

Figure S43. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.000128 (Fisher's exact test), Q value = 0.032

Table S44. Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 140 | 56 | 106 | 156
16P GAIN CNV | 11 | 0 | 0 | 1
16P GAIN WILD-TYPE | 129 | 56 | 106 | 155

Figure S44. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.009

Table S45. Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
16P GAIN CNV | 11 | 1 | 0 | 0
16P GAIN WILD-TYPE | 112 | 190 | 53 | 91

Figure S45. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.052

Table S46. Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

Figure S46. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.88e-05 (Fisher's exact test), Q value = 0.015

Table S47. Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S47. Get High-res Image Gene #14: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 5.67e-13 (Fisher's exact test), Q value = 1.8e-10

Table S48. Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S48. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.000247 (Fisher's exact test), Q value = 0.059

Table S49. Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
16Q GAIN CNV | 8 | 2 | 0
16Q GAIN WILD-TYPE | 141 | 72 | 274

Figure S49. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000429 (Fisher's exact test), Q value = 0.099

Table S50. Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
16Q GAIN CNV | 9 | 1 | 0 | 0
16Q GAIN WILD-TYPE | 114 | 190 | 53 | 91

Figure S50. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S51. Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S51. Get High-res Image Gene #15: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 2e-09 (Fisher's exact test), Q value = 6.1e-07

Table S52. Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S52. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 6.85e-07 (Fisher's exact test), Q value = 2e-04

Table S53. Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
17P GAIN CNV | 12 | 0 | 0
17P GAIN WILD-TYPE | 137 | 74 | 274

Figure S53. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 3.88e-06 (Fisher's exact test), Q value = 0.0011

Table S54. Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 140 | 56 | 106 | 156
17P GAIN CNV | 12 | 0 | 0 | 0
17P GAIN WILD-TYPE | 128 | 56 | 106 | 156

Figure S54. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.94e-07 (Fisher's exact test), Q value = 0.00023

Table S55. Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
17P GAIN CNV | 12 | 0 | 0 | 0
17P GAIN WILD-TYPE | 111 | 191 | 53 | 91

Figure S55. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 5.19e-05 (Fisher's exact test), Q value = 0.014

Table S56. Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

Figure S56. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.7e-05 (Fisher's exact test), Q value = 0.0047

Table S57. Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S57. Get High-res Image Gene #16: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 3.83e-09 (Fisher's exact test), Q value = 1.2e-06

Table S58. Gene #17: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S58. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1.58e-07 (Fisher's exact test), Q value = 4.7e-05

Table S59. Gene #17: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
17Q GAIN CNV | 13 | 0 | 0
17Q GAIN WILD-TYPE | 136 | 74 | 274

Figure S59. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1.36e-06 (Fisher's exact test), Q value = 4e-04

Table S60. Gene #17: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 140 | 56 | 106 | 156
17Q GAIN CNV | 13 | 0 | 0 | 0
17Q GAIN WILD-TYPE | 127 | 56 | 106 | 156

Figure S60. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.92e-07 (Fisher's exact test), Q value = 5.7e-05

Table S61. Gene #17: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
17Q GAIN CNV | 13 | 0 | 0 | 0
17Q GAIN WILD-TYPE | 110 | 191 | 53 | 91

Figure S61. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 1.64e-05 (Fisher's exact test), Q value = 0.0046

Table S62. Gene #17: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

Figure S62. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.85e-06 (Fisher's exact test), Q value = 0.0014

Table S63. Gene #17: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S63. Get High-res Image Gene #17: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0051

Table S64. Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S64. Get High-res Image Gene #20: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00033

Table S65. Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S65. Get High-res Image Gene #21: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1.11e-11 (Fisher's exact test), Q value = 3.4e-09

Table S66. Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S66. Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 0.000767 (Fisher's exact test), Q value = 0.17

Table S67. Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
20P GAIN CNV | 7 | 2 | 0
20P GAIN WILD-TYPE | 142 | 72 | 274

Figure S67. Get High-res Image Gene #22: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.11e-11 (Fisher's exact test), Q value = 3.4e-09

Table S68. Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S68. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 0.000767 (Fisher's exact test), Q value = 0.17

Table S69. Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
20Q GAIN CNV | 7 | 2 | 0
20Q GAIN WILD-TYPE | 142 | 72 | 274

Figure S69. Get High-res Image Gene #23: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.07

Table S70. Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S70. Get High-res Image Gene #25: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 5.02e-09 (Fisher's exact test), Q value = 1.5e-06

Table S71. Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S71. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 8.94e-05 (Fisher's exact test), Q value = 0.023

Table S72. Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
2P LOSS CNV | 8 | 0 | 0
2P LOSS WILD-TYPE | 141 | 74 | 274

Figure S72. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.000496 (Fisher's exact test), Q value = 0.11

Table S73. Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 140 | 56 | 106 | 156
2P LOSS CNV | 8 | 0 | 0 | 0
2P LOSS WILD-TYPE | 132 | 56 | 106 | 156

Figure S73. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000164 (Fisher's exact test), Q value = 0.041

Table S74. Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
2P LOSS CNV | 8 | 0 | 0 | 0
2P LOSS WILD-TYPE | 115 | 191 | 53 | 91

Figure S74. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 5.53e-05 (Fisher's exact test), Q value = 0.014

Table S75. Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

Figure S75. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.27e-05 (Fisher's exact test), Q value = 0.0062

Table S76. Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S76. Get High-res Image Gene #26: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 3.78e-09 (Fisher's exact test), Q value = 1.2e-06

Table S77. Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S77. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.000378 (Fisher's exact test), Q value = 0.088

Table S78. Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
2Q LOSS CNV | 7 | 0 | 0
2Q LOSS WILD-TYPE | 142 | 74 | 274

Figure S78. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.15

Table S79. Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
2Q LOSS CNV | 7 | 0 | 0 | 0
2Q LOSS WILD-TYPE | 116 | 191 | 53 | 91

Figure S79. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.048

Table S80. Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

Figure S80. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.85e-05 (Fisher's exact test), Q value = 0.023

Table S81. Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S81. Get High-res Image Gene #27: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 0.000294 (Fisher's exact test), Q value = 0.07

Table S82. Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S82. Get High-res Image Gene #28: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0051

Table S83. Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S83. Get High-res Image Gene #30: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'CN_CNMF'

P value = 1.85e-05 (Fisher's exact test), Q value = 0.0051

Table S84. Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S84. Get High-res Image Gene #31: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 1.08e-11 (Fisher's exact test), Q value = 3.4e-09

Table S85. Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S85. Get High-res Image Gene #32: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'CN_CNMF'

P value = 1.58e-13 (Fisher's exact test), Q value = 5e-11

Table S86. Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S86. Get High-res Image Gene #33: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 6.62e-08 (Fisher's exact test), Q value = 2e-05

Table S87. Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S87. Get High-res Image Gene #34: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1.12e-06 (Fisher's exact test), Q value = 0.00033

Table S88. Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S88. Get High-res Image Gene #35: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 7.74e-08 (Fisher's exact test), Q value = 2.3e-05

Table S89. Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S89. Get High-res Image Gene #36: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 3.24e-06 (Fisher's exact test), Q value = 0.00094

Table S90. Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S90. Get High-res Image Gene #37: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'CN_CNMF'

P value = 0.000464 (Fisher's exact test), Q value = 0.11

Table S91. Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S91. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.000664 (Fisher's exact test), Q value = 0.15

Table S92. Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

Figure S92. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000342 (Fisher's exact test), Q value = 0.08

Table S93. Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S93. Get High-res Image Gene #39: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.05

Table S94. Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S94. Get High-res Image Gene #41: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.000204 (Fisher's exact test), Q value = 0.05

Table S95. Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S95. Get High-res Image Gene #42: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 0.000192 (Fisher's exact test), Q value = 0.048

Table S96. Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S96. Get High-res Image Gene #44: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 6.79e-58 (Fisher's exact test), Q value = 2.2e-55

Table S97. Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S97. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.033

Table S98. Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 149 | 74 | 274
22Q LOSS CNV | 35 | 7 | 24
22Q LOSS WILD-TYPE | 114 | 67 | 250

Figure S98. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 8.4e-11 (Fisher's exact test), Q value = 2.6e-08

Table S99. Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 140 | 56 | 106 | 156
22Q LOSS CNV | 33 | 5 | 20 | 1
22Q LOSS WILD-TYPE | 107 | 51 | 86 | 155

Figure S99. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.98e-10 (Fisher's exact test), Q value = 6.1e-08

Table S100. Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 123 | 191 | 53 | 91
22Q LOSS CNV | 33 | 6 | 2 | 18
22Q LOSS WILD-TYPE | 90 | 185 | 51 | 73

Figure S100. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 4.33e-05 (Fisher's exact test), Q value = 0.011

Table S101. Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

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

Figure S101. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.51e-06 (Fisher's exact test), Q value = 0.0027

Table S102. Gene #45: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

Figure S102. Get High-res Image Gene #45: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

- Number of patients = 497

- Number of significantly arm-level cnvs = 45

- Number of molecular subtypes = 8

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

Fisher's exact test

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

Q value calculation

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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