Thyroid Adenocarcinoma: Correlation between copy number variations of arm-level result and molecular subtypes
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 470 patients, 99 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', and 'MIRSEQ_CHIERARCHICAL'.

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

- 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', 'MIRSEQ_CNMF', 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', '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, 99 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
5q gain | 14 (3%) | 456 | 5.75e-18 (1.79e-15) | 3.24e-05 (0.00851) | 0.901 (1.00) | 0.0299 (1.00) | 0.000812 (0.179) | 0.000952 (0.209) | 0.00104 (0.229) | 0.00014 (0.0351)
7q gain | 19 (4%) | 451 | 4.86e-23 (1.53e-20) | 3.72e-05 (0.00968) | 0.689 (1.00) | 0.00298 (0.6) | 0.000286 (0.0687) | 0.000176 (0.0438) | 0.000214 (0.0526) | 4.94e-05 (0.0127)
12p gain | 11 (2%) | 459 | 1.79e-12 (5.52e-10) | 3.2e-06 (0.000926) | 0.901 (1.00) | 0.0299 (1.00) | 1.83e-05 (0.00506) | 1.93e-05 (0.00526) | 3.39e-05 (0.00888) | 1.87e-05 (0.00515)
12q gain | 12 (3%) | 458 | 2.23e-12 (6.85e-10) | 6.84e-07 (2e-04) | 0.901 (1.00) | 0.0299 (1.00) | 7.78e-06 (0.00219) | 4.91e-06 (0.0014) | 1.09e-05 (0.00303) | 5.32e-06 (0.00151)
16p gain | 12 (3%) | 458 | 1.02e-13 (3.17e-11) | 2.89e-05 (0.00764) | 1 (1.00) | 0.0445 (1.00) | 0.000239 (0.0587) | 0.000167 (0.0418) | 9.46e-05 (0.0239) | 7.74e-05 (0.0198)
17p gain | 12 (3%) | 458 | 3.73e-09 (1.13e-06) | 6.84e-07 (2e-04) | 0.772 (1.00) | 0.0179 (1.00) | 1.83e-05 (0.00506) | 1.93e-05 (0.00526) | 3.39e-05 (0.00888) | 1.87e-05 (0.00515)
17q gain | 13 (3%) | 457 | 5.93e-09 (1.78e-06) | 1.53e-07 (4.49e-05) | 0.795 (1.00) | 0.0206 (1.00) | 7.78e-06 (0.00219) | 4.91e-06 (0.0014) | 1.09e-05 (0.00303) | 5.32e-06 (0.00151)
2p loss | 8 (2%) | 462 | 7.39e-09 (2.21e-06) | 8.85e-05 (0.0226) | 1 (1.00) | 0.0817 (1.00) | 0.000731 (0.164) | 0.000334 (0.0799) | 5.28e-05 (0.0136) | 2.87e-05 (0.0076)
22q loss | 62 (13%) | 408 | 7.02e-54 (2.22e-51) | 0.000526 (0.122) | 0.114 (1.00) | 0.0835 (1.00) | 1.79e-09 (5.41e-07) | 1.22e-07 (3.59e-05) | 4.79e-05 (0.0124) | 4.64e-06 (0.00134)
7p gain | 17 (4%) | 453 | 4.17e-22 (1.31e-19) | 0.000198 (0.0489) | 1 (1.00) | 0.0129 (1.00) | 0.000704 (0.16) | 0.000607 (0.14) | 0.00178 (0.377) | 0.000414 (0.0965)
16q gain | 10 (2%) | 460 | 9.96e-13 (3.08e-10) | 0.000255 (0.0615) | 0.856 (1.00) | 0.129 (1.00) | 0.00204 (0.429) | 0.00146 (0.313) | 0.00107 (0.233) | 0.000706 (0.16)
2q loss | 7 (1%) | 463 | 5.6e-09 (1.68e-06) | 0.00038 (0.0892) | 0.837 (1.00) | 0.0549 (1.00) | 0.00213 (0.446) | 0.00122 (0.264) | 0.000185 (0.0458) | 0.000108 (0.0273)
5p gain | 17 (4%) | 453 | 1.72e-19 (5.39e-17) | 0.000766 (0.172) | 1 (1.00) | 0.125 (1.00) | 0.00945 (1.00) | 0.01 (1.00) | 0.00564 (1.00) | 0.000668 (0.152)
15q loss | 6 (1%) | 464 | 0.000427 (0.099) | 0.00547 (1.00) | 0.458 (1.00) | 0.256 (1.00) | 0.0173 (1.00) | 0.00933 (1.00) | 0.000641 (0.147) | 0.000407 (0.0953)
14q gain | 8 (2%) | 462 | 7.39e-09 (2.21e-06) | 8.85e-05 (0.0226) | 1 (1.00) | 0.256 (1.00) | 0.00213 (0.446) | 0.00122 (0.264) | 0.00296 (0.597) | 0.00247 (0.509)
20p gain | 9 (2%) | 461 | 1.84e-11 (5.6e-09) | 0.000789 (0.176) | 1 (1.00) | 0.0817 (1.00) | 0.0134 (1.00) | 0.0136 (1.00) | 0.0101 (1.00) | 0.00804 (1.00)
20q gain | 9 (2%) | 461 | 1.84e-11 (5.6e-09) | 0.000789 (0.176) | 1 (1.00) | 0.0817 (1.00) | 0.0134 (1.00) | 0.0136 (1.00) | 0.0101 (1.00) | 0.00804 (1.00)
1q gain | 21 (4%) | 449 | 4.65e-06 (0.00134) | 0.0818 (1.00) | 0.0153 (1.00) | 0.0826 (1.00) | 0.0325 (1.00) | 0.0233 (1.00) | 0.198 (1.00) | 0.242 (1.00)
4p gain | 4 (1%) | 466 | 2.31e-05 (0.00624) | 0.0195 (1.00) |  |  | 0.0371 (1.00) | 0.0346 (1.00) | 0.073 (1.00) | 0.137 (1.00)
4q gain | 4 (1%) | 466 | 2.31e-05 (0.00624) | 0.0195 (1.00) |  |  | 0.0371 (1.00) | 0.0346 (1.00) | 0.073 (1.00) | 0.137 (1.00)
11q gain | 4 (1%) | 466 | 0.000241 (0.0587) | 0.0195 (1.00) |  |  | 0.0371 (1.00) | 0.0346 (1.00) | 0.00761 (1.00) | 0.00564 (1.00)
13q gain | 3 (1%) | 467 | 0.000348 (0.0828) | 0.0496 (1.00) |  |  |  |  |  |
19p gain | 4 (1%) | 466 | 2.31e-05 (0.00624) | 0.0195 (1.00) |  |  | 0.101 (1.00) | 0.0821 (1.00) | 0.026 (1.00) | 0.0208 (1.00)
19q gain | 5 (1%) | 465 | 1.49e-06 (0.000433) | 0.00437 (0.874) | 0.636 (1.00) | 0.0551 (1.00) | 0.0371 (1.00) | 0.0346 (1.00) | 0.00761 (1.00) | 0.00564 (1.00)
1p loss | 3 (1%) | 467 | 0.000348 (0.0828) | 0.412 (1.00) |  |  | 0.487 (1.00) | 0.195 (1.00) | 0.202 (1.00) | 0.367 (1.00)
3q loss | 3 (1%) | 467 | 0.000348 (0.0828) | 0.0496 (1.00) |  |  | 0.101 (1.00) | 0.0821 (1.00) | 0.026 (1.00) | 0.0208 (1.00)
8p loss | 4 (1%) | 466 | 2.31e-05 (0.00624) | 0.0474 (1.00) |  |  | 0.0371 (1.00) | 0.0346 (1.00) | 0.00761 (1.00) | 0.00564 (1.00)
8q loss | 4 (1%) | 466 | 2.31e-05 (0.00624) | 0.0474 (1.00) |  |  | 0.0371 (1.00) | 0.0346 (1.00) | 0.00761 (1.00) | 0.00564 (1.00)
9p loss | 11 (2%) | 459 | 1.04e-11 (3.19e-09) | 0.365 (1.00) | 0.559 (1.00) | 0.206 (1.00) | 0.249 (1.00) | 0.527 (1.00) | 0.151 (1.00) | 0.192 (1.00)
9q loss | 16 (3%) | 454 | 1.1e-13 (3.41e-11) | 0.288 (1.00) | 0.21 (1.00) | 0.00441 (0.874) | 0.441 (1.00) | 0.823 (1.00) | 0.193 (1.00) | 0.274 (1.00)
10p loss | 6 (1%) | 464 | 9.28e-08 (2.75e-05) | 0.0793 (1.00) |  |  | 0.12 (1.00) | 0.0427 (1.00) | 0.0256 (1.00) | 0.0361 (1.00)
10q loss | 5 (1%) | 465 | 1.49e-06 (0.000433) | 0.177 (1.00) |  |  | 0.242 (1.00) | 0.0893 (1.00) | 0.073 (1.00) | 0.137 (1.00)
11p loss | 6 (1%) | 464 | 9.28e-08 (2.75e-05) | 0.0202 (1.00) | 0.499 (1.00) | 1 (1.00) | 0.0495 (1.00) | 0.166 (1.00) | 0.0256 (1.00) | 0.0361 (1.00)
11q loss | 8 (2%) | 462 | 4.79e-06 (0.00137) | 0.0278 (1.00) | 0.388 (1.00) | 0.798 (1.00) | 0.0186 (1.00) | 0.0672 (1.00) | 0.00877 (1.00) | 0.00798 (1.00)
18p loss | 4 (1%) | 466 | 0.000241 (0.0587) | 0.191 (1.00) | 1 (1.00) | 0.369 (1.00) | 0.242 (1.00) | 0.0893 (1.00) | 0.111 (1.00) | 0.0414 (1.00)
18q loss | 4 (1%) | 466 | 0.000241 (0.0587) | 0.191 (1.00) | 1 (1.00) | 0.369 (1.00) | 0.242 (1.00) | 0.0893 (1.00) | 0.111 (1.00) | 0.0414 (1.00)
21q loss | 5 (1%) | 465 | 1.96e-05 (0.00531) | 0.0132 (1.00) | 0.384 (1.00) | 0.0551 (1.00) | 0.0495 (1.00) | 0.166 (1.00) | 0.0256 (1.00) | 0.0361 (1.00)
11p gain | 5 (1%) | 465 | 0.00151 (0.321) | 0.00437 (0.874) |  |  | 0.0173 (1.00) | 0.00933 (1.00) | 0.00222 (0.459) | 0.00152 (0.322)
18p gain | 3 (1%) | 467 | 0.00273 (0.56) | 0.0496 (1.00) |  |  |  |  |  |
18q gain | 3 (1%) | 467 | 0.00273 (0.56) | 0.0496 (1.00) |  |  |  |  |  |
21q gain | 3 (1%) | 467 | 0.00273 (0.56) | 0.0496 (1.00) |  |  | 0.101 (1.00) | 0.0821 (1.00) | 0.026 (1.00) | 0.0208 (1.00)
6q loss | 3 (1%) | 467 | 0.0234 (1.00) | 0.0496 (1.00) |  |  | 0.101 (1.00) | 0.0821 (1.00) | 0.026 (1.00) | 0.0208 (1.00)
13q loss | 11 (2%) | 459 | 0.0136 (1.00) | 0.0184 (1.00) | 0.0779 (1.00) | 1 (1.00) | 0.0941 (1.00) | 0.116 (1.00) | 0.00769 (1.00) | 0.0142 (1.00)
17p loss | 7 (1%) | 463 | 0.00134 (0.288) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.826 (1.00) | 0.886 (1.00) | 0.403 (1.00) | 0.495 (1.00)
19p loss | 4 (1%) | 466 | 0.138 (1.00) | 0.0195 (1.00) | 0.281 (1.00) | 0.369 (1.00) | 0.0371 (1.00) | 0.0346 (1.00) | 0.00761 (1.00) | 0.00564 (1.00)

'1q gain mutation analysis' versus 'CN_CNMF'

P value = 4.65e-06 (Fisher's exact test), Q value = 0.0013

Table S1. Gene #1: '1q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
1Q GAIN MUTATED | 9 | 11 | 1
1Q GAIN WILD-TYPE | 25 | 352 | 72

Figure S1. Get High-res Image Gene #1: '1q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'4p gain mutation analysis' versus 'CN_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0062

Table S2. Gene #2: '4p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
4P GAIN MUTATED | 4 | 0 | 0
4P GAIN WILD-TYPE | 30 | 363 | 73

Figure S2. Get High-res Image Gene #2: '4p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'4q gain mutation analysis' versus 'CN_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0062

Table S3. Gene #3: '4q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
4Q GAIN MUTATED | 4 | 0 | 0
4Q GAIN WILD-TYPE | 30 | 363 | 73

Figure S3. Get High-res Image Gene #3: '4q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5p gain mutation analysis' versus 'CN_CNMF'

P value = 1.72e-19 (Fisher's exact test), Q value = 5.4e-17

Table S4. Gene #4: '5p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
5P GAIN MUTATED | 16 | 1 | 0
5P GAIN WILD-TYPE | 18 | 362 | 73

Figure S4. Get High-res Image Gene #4: '5p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000766 (Fisher's exact test), Q value = 0.17

Table S5. Gene #4: '5p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
5P GAIN MUTATED | 12 | 2 | 3
5P GAIN WILD-TYPE | 128 | 69 | 256

Figure S5. Get High-res Image Gene #4: '5p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'5p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000668 (Fisher's exact test), Q value = 0.15

Table S6. Gene #4: '5p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
5P GAIN MUTATED | 6 | 0 | 10
5P GAIN WILD-TYPE | 167 | 133 | 107

Figure S6. Get High-res Image Gene #4: '5p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain mutation analysis' versus 'CN_CNMF'

P value = 5.75e-18 (Fisher's exact test), Q value = 1.8e-15

Table S7. Gene #5: '5q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
5Q GAIN MUTATED | 14 | 0 | 0
5Q GAIN WILD-TYPE | 20 | 363 | 73

Figure S7. Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'5q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.0085

Table S8. Gene #5: '5q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
5Q GAIN MUTATED | 12 | 1 | 1
5Q GAIN WILD-TYPE | 128 | 70 | 258

Figure S8. Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'5q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000812 (Fisher's exact test), Q value = 0.18

Table S9. Gene #5: '5q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
5Q GAIN MUTATED | 11 | 0 | 0 | 2
5Q GAIN WILD-TYPE | 119 | 50 | 89 | 136

Figure S9. Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'5q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000952 (Fisher's exact test), Q value = 0.21

Table S10. Gene #5: '5q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
5Q GAIN MUTATED | 11 | 2 | 0
5Q GAIN WILD-TYPE | 131 | 189 | 74

Figure S10. Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.23

Table S11. Gene #5: '5q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
5Q GAIN MUTATED | 10 | 1 | 2
5Q GAIN WILD-TYPE | 116 | 152 | 142

Figure S11. Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'5q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.035

Table S12. Gene #5: '5q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
5Q GAIN MUTATED | 3 | 0 | 10
5Q GAIN WILD-TYPE | 170 | 133 | 107

Figure S12. Get High-res Image Gene #5: '5q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 4.17e-22 (Fisher's exact test), Q value = 1.3e-19

Table S13. Gene #6: '7p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
7P GAIN MUTATED | 17 | 0 | 0
7P GAIN WILD-TYPE | 17 | 363 | 73

Figure S13. Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000198 (Fisher's exact test), Q value = 0.049

Table S14. Gene #6: '7p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
7P GAIN MUTATED | 12 | 3 | 2
7P GAIN WILD-TYPE | 128 | 68 | 257

Figure S14. Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000704 (Fisher's exact test), Q value = 0.16

Table S15. Gene #6: '7p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
7P GAIN MUTATED | 13 | 0 | 1 | 2
7P GAIN WILD-TYPE | 117 | 50 | 88 | 136

Figure S15. Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000607 (Fisher's exact test), Q value = 0.14

Table S16. Gene #6: '7p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
7P GAIN MUTATED | 13 | 2 | 1
7P GAIN WILD-TYPE | 129 | 189 | 73

Figure S16. Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000414 (Fisher's exact test), Q value = 0.097

Table S17. Gene #6: '7p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
7P GAIN MUTATED | 4 | 1 | 12
7P GAIN WILD-TYPE | 169 | 132 | 105

Figure S17. Get High-res Image Gene #6: '7p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 4.86e-23 (Fisher's exact test), Q value = 1.5e-20

Table S18. Gene #7: '7q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
7Q GAIN MUTATED | 18 | 0 | 1
7Q GAIN WILD-TYPE | 16 | 363 | 72

Figure S18. Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'7q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.72e-05 (Fisher's exact test), Q value = 0.0097

Table S19. Gene #7: '7q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
7Q GAIN MUTATED | 14 | 3 | 2
7Q GAIN WILD-TYPE | 126 | 68 | 257

Figure S19. Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000286 (Fisher's exact test), Q value = 0.069

Table S20. Gene #7: '7q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
7Q GAIN MUTATED | 14 | 0 | 1 | 2
7Q GAIN WILD-TYPE | 116 | 50 | 88 | 136

Figure S20. Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000176 (Fisher's exact test), Q value = 0.044

Table S21. Gene #7: '7q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
7Q GAIN MUTATED | 14 | 2 | 1
7Q GAIN WILD-TYPE | 128 | 189 | 73

Figure S21. Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.053

Table S22. Gene #7: '7q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
7Q GAIN MUTATED | 14 | 2 | 3
7Q GAIN WILD-TYPE | 112 | 151 | 141

Figure S22. Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'7q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.94e-05 (Fisher's exact test), Q value = 0.013

Table S23. Gene #7: '7q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
7Q GAIN MUTATED | 4 | 1 | 14
7Q GAIN WILD-TYPE | 169 | 132 | 103

Figure S23. Get High-res Image Gene #7: '7q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.059

Table S24. Gene #9: '11q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
11Q GAIN MUTATED | 3 | 0 | 1
11Q GAIN WILD-TYPE | 31 | 363 | 72

Figure S24. Get High-res Image Gene #9: '11q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'12p gain mutation analysis' versus 'CN_CNMF'

P value = 1.79e-12 (Fisher's exact test), Q value = 5.5e-10

Table S25. Gene #10: '12p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
12P GAIN MUTATED | 10 | 0 | 1
12P GAIN WILD-TYPE | 24 | 363 | 72

Figure S25. Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'12p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.2e-06 (Fisher's exact test), Q value = 0.00093

Table S26. Gene #10: '12p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
12P GAIN MUTATED | 11 | 0 | 0
12P GAIN WILD-TYPE | 129 | 71 | 259

Figure S26. Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'12p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.0051

Table S27. Gene #10: '12p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
12P GAIN MUTATED | 11 | 0 | 0 | 0
12P GAIN WILD-TYPE | 119 | 50 | 89 | 138

Figure S27. Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'12p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0053

Table S28. Gene #10: '12p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
12P GAIN MUTATED | 11 | 0 | 0
12P GAIN WILD-TYPE | 131 | 191 | 74

Figure S28. Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.0089

Table S29. Gene #10: '12p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
12P GAIN MUTATED | 10 | 0 | 1
12P GAIN WILD-TYPE | 116 | 153 | 143

Figure S29. Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'12p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.87e-05 (Fisher's exact test), Q value = 0.0052

Table S30. Gene #10: '12p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
12P GAIN MUTATED | 1 | 0 | 10
12P GAIN WILD-TYPE | 172 | 133 | 107

Figure S30. Get High-res Image Gene #10: '12p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain mutation analysis' versus 'CN_CNMF'

P value = 2.23e-12 (Fisher's exact test), Q value = 6.9e-10

Table S31. Gene #11: '12q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
12Q GAIN MUTATED | 10 | 0 | 2
12Q GAIN WILD-TYPE | 24 | 363 | 71

Figure S31. Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'12q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.84e-07 (Fisher's exact test), Q value = 2e-04

Table S32. Gene #11: '12q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
12Q GAIN MUTATED | 12 | 0 | 0
12Q GAIN WILD-TYPE | 128 | 71 | 259

Figure S32. Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'12q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.78e-06 (Fisher's exact test), Q value = 0.0022

Table S33. Gene #11: '12q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
12Q GAIN MUTATED | 12 | 0 | 0 | 0
12Q GAIN WILD-TYPE | 118 | 50 | 89 | 138

Figure S33. Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'12q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.91e-06 (Fisher's exact test), Q value = 0.0014

Table S34. Gene #11: '12q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
12Q GAIN MUTATED | 12 | 0 | 0
12Q GAIN WILD-TYPE | 130 | 191 | 74

Figure S34. Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.003

Table S35. Gene #11: '12q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
12Q GAIN MUTATED | 11 | 0 | 1
12Q GAIN WILD-TYPE | 115 | 153 | 143

Figure S35. Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'12q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.32e-06 (Fisher's exact test), Q value = 0.0015

Table S36. Gene #11: '12q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
12Q GAIN MUTATED | 1 | 0 | 11
12Q GAIN WILD-TYPE | 172 | 133 | 106

Figure S36. Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain mutation analysis' versus 'CN_CNMF'

P value = 0.000348 (Fisher's exact test), Q value = 0.083

Table S37. Gene #12: '13q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
13Q GAIN MUTATED | 3 | 0 | 0
13Q GAIN WILD-TYPE | 31 | 363 | 73

Figure S37. Get High-res Image Gene #12: '13q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'14q gain mutation analysis' versus 'CN_CNMF'

P value = 7.39e-09 (Fisher's exact test), Q value = 2.2e-06

Table S38. Gene #13: '14q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
14Q GAIN MUTATED | 7 | 0 | 1
14Q GAIN WILD-TYPE | 27 | 363 | 72

Figure S38. Get High-res Image Gene #13: '14q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'14q gain mutation analysis' versus 'METHLYATION_CNMF'

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

Table S39. Gene #13: '14q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
14Q GAIN MUTATED | 8 | 0 | 0
14Q GAIN WILD-TYPE | 132 | 71 | 259

Figure S39. Get High-res Image Gene #13: '14q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16p gain mutation analysis' versus 'CN_CNMF'

P value = 1.02e-13 (Fisher's exact test), Q value = 3.2e-11

Table S40. Gene #14: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
16P GAIN MUTATED | 11 | 0 | 1
16P GAIN WILD-TYPE | 23 | 363 | 72

Figure S40. Get High-res Image Gene #14: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.89e-05 (Fisher's exact test), Q value = 0.0076

Table S41. Gene #14: '16p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
16P GAIN MUTATED | 10 | 2 | 0
16P GAIN WILD-TYPE | 130 | 69 | 259

Figure S41. Get High-res Image Gene #14: '16p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000239 (Fisher's exact test), Q value = 0.059

Table S42. Gene #14: '16p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
16P GAIN MUTATED | 11 | 0 | 0 | 1
16P GAIN WILD-TYPE | 119 | 50 | 89 | 137

Figure S42. Get High-res Image Gene #14: '16p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'16p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000167 (Fisher's exact test), Q value = 0.042

Table S43. Gene #14: '16p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
16P GAIN MUTATED | 11 | 1 | 0
16P GAIN WILD-TYPE | 131 | 190 | 74

Figure S43. Get High-res Image Gene #14: '16p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.46e-05 (Fisher's exact test), Q value = 0.024

Table S44. Gene #14: '16p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
16P GAIN MUTATED | 10 | 0 | 2
16P GAIN WILD-TYPE | 116 | 153 | 142

Figure S44. Get High-res Image Gene #14: '16p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'16p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7.74e-05 (Fisher's exact test), Q value = 0.02

Table S45. Gene #14: '16p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
16P GAIN MUTATED | 2 | 0 | 10
16P GAIN WILD-TYPE | 171 | 133 | 107

Figure S45. Get High-res Image Gene #14: '16p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain mutation analysis' versus 'CN_CNMF'

P value = 9.96e-13 (Fisher's exact test), Q value = 3.1e-10

Table S46. Gene #15: '16q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
16Q GAIN MUTATED | 10 | 0 | 0
16Q GAIN WILD-TYPE | 24 | 363 | 73

Figure S46. Get High-res Image Gene #15: '16q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000255 (Fisher's exact test), Q value = 0.061

Table S47. Gene #15: '16q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
16Q GAIN MUTATED | 8 | 2 | 0
16Q GAIN WILD-TYPE | 132 | 69 | 259

Figure S47. Get High-res Image Gene #15: '16q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.23

Table S48. Gene #15: '16q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
16Q GAIN MUTATED | 8 | 0 | 2
16Q GAIN WILD-TYPE | 118 | 153 | 142

Figure S48. Get High-res Image Gene #15: '16q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'16q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000706 (Fisher's exact test), Q value = 0.16

Table S49. Gene #15: '16q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
16Q GAIN MUTATED | 2 | 0 | 8
16Q GAIN WILD-TYPE | 171 | 133 | 109

Figure S49. Get High-res Image Gene #15: '16q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain mutation analysis' versus 'CN_CNMF'

P value = 3.73e-09 (Fisher's exact test), Q value = 1.1e-06

Table S50. Gene #16: '17p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
17P GAIN MUTATED | 9 | 2 | 1
17P GAIN WILD-TYPE | 25 | 361 | 72

Figure S50. Get High-res Image Gene #16: '17p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'17p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.84e-07 (Fisher's exact test), Q value = 2e-04

Table S51. Gene #16: '17p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
17P GAIN MUTATED | 12 | 0 | 0
17P GAIN WILD-TYPE | 128 | 71 | 259

Figure S51. Get High-res Image Gene #16: '17p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'17p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.0051

Table S52. Gene #16: '17p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
17P GAIN MUTATED | 11 | 0 | 0 | 0
17P GAIN WILD-TYPE | 119 | 50 | 89 | 138

Figure S52. Get High-res Image Gene #16: '17p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'17p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.93e-05 (Fisher's exact test), Q value = 0.0053

Table S53. Gene #16: '17p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
17P GAIN MUTATED | 11 | 0 | 0
17P GAIN WILD-TYPE | 131 | 191 | 74

Figure S53. Get High-res Image Gene #16: '17p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.39e-05 (Fisher's exact test), Q value = 0.0089

Table S54. Gene #16: '17p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
17P GAIN MUTATED | 10 | 0 | 1
17P GAIN WILD-TYPE | 116 | 153 | 143

Figure S54. Get High-res Image Gene #16: '17p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'17p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.87e-05 (Fisher's exact test), Q value = 0.0052

Table S55. Gene #16: '17p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
17P GAIN MUTATED | 1 | 0 | 10
17P GAIN WILD-TYPE | 172 | 133 | 107

Figure S55. Get High-res Image Gene #16: '17p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain mutation analysis' versus 'CN_CNMF'

P value = 5.93e-09 (Fisher's exact test), Q value = 1.8e-06

Table S56. Gene #17: '17q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
17Q GAIN MUTATED | 9 | 2 | 2
17Q GAIN WILD-TYPE | 25 | 361 | 71

Figure S56. Get High-res Image Gene #17: '17q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'17q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.53e-07 (Fisher's exact test), Q value = 4.5e-05

Table S57. Gene #17: '17q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
17Q GAIN MUTATED | 13 | 0 | 0
17Q GAIN WILD-TYPE | 127 | 71 | 259

Figure S57. Get High-res Image Gene #17: '17q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'17q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.78e-06 (Fisher's exact test), Q value = 0.0022

Table S58. Gene #17: '17q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
17Q GAIN MUTATED | 12 | 0 | 0 | 0
17Q GAIN WILD-TYPE | 118 | 50 | 89 | 138

Figure S58. Get High-res Image Gene #17: '17q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'17q gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.91e-06 (Fisher's exact test), Q value = 0.0014

Table S59. Gene #17: '17q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
17Q GAIN MUTATED | 12 | 0 | 0
17Q GAIN WILD-TYPE | 130 | 191 | 74

Figure S59. Get High-res Image Gene #17: '17q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.003

Table S60. Gene #17: '17q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
17Q GAIN MUTATED | 11 | 0 | 1
17Q GAIN WILD-TYPE | 115 | 153 | 143

Figure S60. Get High-res Image Gene #17: '17q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'17q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.32e-06 (Fisher's exact test), Q value = 0.0015

Table S61. Gene #17: '17q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
17Q GAIN MUTATED | 1 | 0 | 11
17Q GAIN WILD-TYPE | 172 | 133 | 106

Figure S61. Get High-res Image Gene #17: '17q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0062

Table S62. Gene #20: '19p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
19P GAIN MUTATED | 4 | 0 | 0
19P GAIN WILD-TYPE | 30 | 363 | 73

Figure S62. Get High-res Image Gene #20: '19p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'19q gain mutation analysis' versus 'CN_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.00043

Table S63. Gene #21: '19q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
19Q GAIN MUTATED | 5 | 0 | 0
19Q GAIN WILD-TYPE | 29 | 363 | 73

Figure S63. Get High-res Image Gene #21: '19q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 1.84e-11 (Fisher's exact test), Q value = 5.6e-09

Table S64. Gene #22: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
20P GAIN MUTATED | 9 | 0 | 0
20P GAIN WILD-TYPE | 25 | 363 | 73

Figure S64. Get High-res Image Gene #22: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000789 (Fisher's exact test), Q value = 0.18

Table S65. Gene #22: '20p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
20P GAIN MUTATED | 7 | 2 | 0
20P GAIN WILD-TYPE | 133 | 69 | 259

Figure S65. Get High-res Image Gene #22: '20p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 1.84e-11 (Fisher's exact test), Q value = 5.6e-09

Table S66. Gene #23: '20q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
20Q GAIN MUTATED | 9 | 0 | 0
20Q GAIN WILD-TYPE | 25 | 363 | 73

Figure S66. Get High-res Image Gene #23: '20q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000789 (Fisher's exact test), Q value = 0.18

Table S67. Gene #23: '20q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
20Q GAIN MUTATED | 7 | 2 | 0
20Q GAIN WILD-TYPE | 133 | 69 | 259

Figure S67. Get High-res Image Gene #23: '20q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000348 (Fisher's exact test), Q value = 0.083

Table S68. Gene #25: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
1P LOSS MUTATED | 3 | 0 | 0
1P LOSS WILD-TYPE | 31 | 363 | 73

Figure S68. Get High-res Image Gene #25: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2p loss mutation analysis' versus 'CN_CNMF'

P value = 7.39e-09 (Fisher's exact test), Q value = 2.2e-06

Table S69. Gene #26: '2p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
2P LOSS MUTATED | 7 | 0 | 1
2P LOSS WILD-TYPE | 27 | 363 | 72

Figure S69. Get High-res Image Gene #26: '2p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2p loss mutation analysis' versus 'METHLYATION_CNMF'

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

Table S70. Gene #26: '2p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
2P LOSS MUTATED | 8 | 0 | 0
2P LOSS WILD-TYPE | 132 | 71 | 259

Figure S70. Get High-res Image Gene #26: '2p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'2p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000731 (Fisher's exact test), Q value = 0.16

Table S71. Gene #26: '2p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
2P LOSS MUTATED | 8 | 0 | 0 | 0
2P LOSS WILD-TYPE | 122 | 50 | 89 | 138

Figure S71. Get High-res Image Gene #26: '2p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'2p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000334 (Fisher's exact test), Q value = 0.08

Table S72. Gene #26: '2p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
2P LOSS MUTATED | 8 | 0 | 0
2P LOSS WILD-TYPE | 134 | 191 | 74

Figure S72. Get High-res Image Gene #26: '2p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 5.28e-05 (Fisher's exact test), Q value = 0.014

Table S73. Gene #26: '2p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
2P LOSS MUTATED | 8 | 0 | 0
2P LOSS WILD-TYPE | 118 | 153 | 144

Figure S73. Get High-res Image Gene #26: '2p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'2p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.0076

Table S74. Gene #26: '2p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
2P LOSS MUTATED | 0 | 0 | 8
2P LOSS WILD-TYPE | 173 | 133 | 109

Figure S74. Get High-res Image Gene #26: '2p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss mutation analysis' versus 'CN_CNMF'

P value = 5.6e-09 (Fisher's exact test), Q value = 1.7e-06

Table S75. Gene #27: '2q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
2Q LOSS MUTATED | 7 | 0 | 0
2Q LOSS WILD-TYPE | 27 | 363 | 73

Figure S75. Get High-res Image Gene #27: '2q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.089

Table S76. Gene #27: '2q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
2Q LOSS MUTATED | 7 | 0 | 0
2Q LOSS WILD-TYPE | 133 | 71 | 259

Figure S76. Get High-res Image Gene #27: '2q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'2q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000185 (Fisher's exact test), Q value = 0.046

Table S77. Gene #27: '2q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
2Q LOSS MUTATED | 7 | 0 | 0
2Q LOSS WILD-TYPE | 119 | 153 | 144

Figure S77. Get High-res Image Gene #27: '2q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'2q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000108 (Fisher's exact test), Q value = 0.027

Table S78. Gene #27: '2q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
2Q LOSS MUTATED | 0 | 0 | 7
2Q LOSS WILD-TYPE | 173 | 133 | 110

Figure S78. Get High-res Image Gene #27: '2q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000348 (Fisher's exact test), Q value = 0.083

Table S79. Gene #28: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
3Q LOSS MUTATED | 3 | 0 | 0
3Q LOSS WILD-TYPE | 31 | 363 | 73

Figure S79. Get High-res Image Gene #28: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0062

Table S80. Gene #30: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
8P LOSS MUTATED | 4 | 0 | 0
8P LOSS WILD-TYPE | 30 | 363 | 73

Figure S80. Get High-res Image Gene #30: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8q loss mutation analysis' versus 'CN_CNMF'

P value = 2.31e-05 (Fisher's exact test), Q value = 0.0062

Table S81. Gene #31: '8q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
8Q LOSS MUTATED | 4 | 0 | 0
8Q LOSS WILD-TYPE | 30 | 363 | 73

Figure S81. Get High-res Image Gene #31: '8q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 1.04e-11 (Fisher's exact test), Q value = 3.2e-09

Table S82. Gene #32: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
9P LOSS MUTATED | 10 | 1 | 0
9P LOSS WILD-TYPE | 24 | 362 | 73

Figure S82. Get High-res Image Gene #32: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 1.1e-13 (Fisher's exact test), Q value = 3.4e-11

Table S83. Gene #33: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
9Q LOSS MUTATED | 13 | 3 | 0
9Q LOSS WILD-TYPE | 21 | 360 | 73

Figure S83. Get High-res Image Gene #33: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10p loss mutation analysis' versus 'CN_CNMF'

P value = 9.28e-08 (Fisher's exact test), Q value = 2.8e-05

Table S84. Gene #34: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
10P LOSS MUTATED | 6 | 0 | 0
10P LOSS WILD-TYPE | 28 | 363 | 73

Figure S84. Get High-res Image Gene #34: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.00043

Table S85. Gene #35: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
10Q LOSS MUTATED | 5 | 0 | 0
10Q LOSS WILD-TYPE | 29 | 363 | 73

Figure S85. Get High-res Image Gene #35: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11p loss mutation analysis' versus 'CN_CNMF'

P value = 9.28e-08 (Fisher's exact test), Q value = 2.8e-05

Table S86. Gene #36: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
11P LOSS MUTATED | 6 | 0 | 0
11P LOSS WILD-TYPE | 28 | 363 | 73

Figure S86. Get High-res Image Gene #36: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 4.79e-06 (Fisher's exact test), Q value = 0.0014

Table S87. Gene #37: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
11Q LOSS MUTATED | 6 | 2 | 0
11Q LOSS WILD-TYPE | 28 | 361 | 73

Figure S87. Get High-res Image Gene #37: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000427 (Fisher's exact test), Q value = 0.099

Table S88. Gene #39: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
15Q LOSS MUTATED | 4 | 2 | 0
15Q LOSS WILD-TYPE | 30 | 361 | 73

Figure S88. Get High-res Image Gene #39: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'15q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000641 (Fisher's exact test), Q value = 0.15

Table S89. Gene #39: '15q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
15Q LOSS MUTATED | 6 | 0 | 0
15Q LOSS WILD-TYPE | 120 | 153 | 144

Figure S89. Get High-res Image Gene #39: '15q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'15q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000407 (Fisher's exact test), Q value = 0.095

Table S90. Gene #39: '15q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
15Q LOSS MUTATED | 0 | 0 | 6
15Q LOSS WILD-TYPE | 173 | 133 | 111

Figure S90. Get High-res Image Gene #39: '15q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.059

Table S91. Gene #41: '18p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
18P LOSS MUTATED | 3 | 0 | 1
18P LOSS WILD-TYPE | 31 | 363 | 72

Figure S91. Get High-res Image Gene #41: '18p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000241 (Fisher's exact test), Q value = 0.059

Table S92. Gene #42: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
18Q LOSS MUTATED | 3 | 0 | 1
18Q LOSS WILD-TYPE | 31 | 363 | 72

Figure S92. Get High-res Image Gene #42: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 1.96e-05 (Fisher's exact test), Q value = 0.0053

Table S93. Gene #44: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
21Q LOSS MUTATED | 4 | 0 | 1
21Q LOSS WILD-TYPE | 30 | 363 | 72

Figure S93. Get High-res Image Gene #44: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 7.02e-54 (Fisher's exact test), Q value = 2.2e-51

Table S94. Gene #45: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 363 | 73
22Q LOSS MUTATED | 8 | 0 | 54
22Q LOSS WILD-TYPE | 26 | 363 | 19

Figure S94. Get High-res Image Gene #45: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000526 (Fisher's exact test), Q value = 0.12

Table S95. Gene #45: '22q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 140 | 71 | 259
22Q LOSS MUTATED | 32 | 6 | 24
22Q LOSS WILD-TYPE | 108 | 65 | 235

Figure S95. Get High-res Image Gene #45: '22q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.79e-09 (Fisher's exact test), Q value = 5.4e-07

Table S96. Gene #45: '22q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 50 | 89 | 138
22Q LOSS MUTATED | 30 | 3 | 16 | 1
22Q LOSS WILD-TYPE | 100 | 47 | 73 | 137

Figure S96. Get High-res Image Gene #45: '22q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-07 (Fisher's exact test), Q value = 3.6e-05

Table S97. Gene #45: '22q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
22Q LOSS MUTATED | 30 | 6 | 14
22Q LOSS WILD-TYPE | 112 | 185 | 60

Figure S97. Get High-res Image Gene #45: '22q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.79e-05 (Fisher's exact test), Q value = 0.012

Table S98. Gene #45: '22q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 126 | 153 | 144
22Q LOSS MUTATED | 31 | 14 | 10
22Q LOSS WILD-TYPE | 95 | 139 | 134

Figure S98. Get High-res Image Gene #45: '22q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'22q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.64e-06 (Fisher's exact test), Q value = 0.0013

Table S99. Gene #45: '22q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 173 | 133 | 117
22Q LOSS MUTATED | 11 | 13 | 31
22Q LOSS WILD-TYPE | 162 | 120 | 86

Figure S99. Get High-res Image Gene #45: '22q loss mutation analysis' versus Clinical Feature #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 = 470

- 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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