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 42 arm-level results and 8 molecular subtypes across 432 patients, 95 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', 'MIRSEQ_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', 'MIRSEQ_CNMF', 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'.

- 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', 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'.

- 20q gain cnv correlated to 'CN_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', '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 42 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 95 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 | 13 (3%) | 419 | 3.8e-16 (1.16e-13) | 0.000147 (0.0363) | 0.901 (1.00) | 0.0299 (1.00) | 0.000812 (0.176) | 0.000952 (0.206) | 0.000192 (0.0467) | 8.84e-05 (0.0222)
7p gain | 17 (4%) | 415 | 1.8e-21 (5.53e-19) | 0.000397 (0.0917) | 1 (1.00) | 0.0129 (1.00) | 0.000704 (0.154) | 0.000607 (0.135) | 0.000271 (0.0652) | 0.000103 (0.0257)
7q gain | 19 (4%) | 413 | 2.84e-24 (8.79e-22) | 7.69e-05 (0.0195) | 0.689 (1.00) | 0.00298 (0.594) | 0.000286 (0.0682) | 0.000176 (0.0429) | 3.84e-05 (0.00996) | 9.67e-06 (0.00267)
12p gain | 12 (3%) | 420 | 5.23e-12 (1.59e-09) | 1.01e-06 (0.000292) | 0.901 (1.00) | 0.0299 (1.00) | 7.78e-06 (0.00217) | 4.91e-06 (0.00138) | 1.46e-05 (0.00401) | 3.89e-06 (0.00111)
12q gain | 12 (3%) | 420 | 5.23e-12 (1.59e-09) | 1.01e-06 (0.000292) | 0.901 (1.00) | 0.0299 (1.00) | 7.78e-06 (0.00217) | 4.91e-06 (0.00138) | 1.46e-05 (0.00401) | 3.89e-06 (0.00111)
16p gain | 12 (3%) | 420 | 2.57e-13 (7.84e-11) | 4.7e-05 (0.0121) | 1 (1.00) | 0.0445 (1.00) | 0.000239 (0.0577) | 0.000167 (0.0411) | 0.000137 (0.0341) | 5.08e-05 (0.013)
17p gain | 11 (3%) | 421 | 1.04e-07 (3.05e-05) | 4.25e-06 (0.0012) | 0.772 (1.00) | 0.0179 (1.00) | 1.83e-05 (0.00495) | 1.93e-05 (0.0052) | 4.67e-05 (0.0121) | 1.41e-05 (0.00387)
17q gain | 12 (3%) | 420 | 7.49e-08 (2.2e-05) | 1.01e-06 (0.000292) | 0.795 (1.00) | 0.0206 (1.00) | 7.78e-06 (0.00217) | 4.91e-06 (0.00138) | 1.46e-05 (0.00401) | 3.89e-06 (0.00111)
2p loss | 8 (2%) | 424 | 1.32e-08 (3.91e-06) | 0.000197 (0.0478) | 1 (1.00) | 0.0817 (1.00) | 0.000731 (0.159) | 0.000334 (0.0775) | 4.73e-05 (0.0121) | 2.14e-05 (0.00575)
22q loss | 54 (12%) | 378 | 1.18e-45 (3.64e-43) | 0.00135 (0.286) | 0.114 (1.00) | 0.0835 (1.00) | 3.69e-09 (1.1e-06) | 2.07e-07 (6.01e-05) | 0.000284 (0.0679) | 8.99e-05 (0.0225)
2q loss | 7 (2%) | 425 | 1.01e-08 (3e-06) | 0.000476 (0.108) | 0.837 (1.00) | 0.0549 (1.00) | 0.00213 (0.433) | 0.00122 (0.261) | 0.000168 (0.0411) | 8.4e-05 (0.0212)
5p gain | 16 (4%) | 416 | 1.4e-17 (4.28e-15) | 0.00411 (0.806) | 1 (1.00) | 0.125 (1.00) | 0.00945 (1.00) | 0.01 (1.00) | 0.000633 (0.14) | 0.000544 (0.122)
16q gain | 10 (2%) | 422 | 2.33e-12 (7.1e-10) | 0.000314 (0.0735) | 0.856 (1.00) | 0.129 (1.00) | 0.00204 (0.421) | 0.00146 (0.309) | 0.00165 (0.346) | 0.000643 (0.142)
15q loss | 6 (1%) | 426 | 0.000556 (0.125) | 0.0112 (1.00) | 0.458 (1.00) | 0.256 (1.00) | 0.0173 (1.00) | 0.00933 (1.00) | 0.000592 (0.132) | 0.000328 (0.0764)
14q gain | 7 (2%) | 425 | 1.77e-07 (5.18e-05) | 0.000476 (0.108) | 1 (1.00) | 0.256 (1.00) | 0.00213 (0.433) | 0.00122 (0.261) | 0.00437 (0.853) | 0.00209 (0.426)
1q gain | 16 (4%) | 416 | 5.82e-05 (0.0148) | 0.255 (1.00) | 0.0153 (1.00) | 0.0826 (1.00) | 0.0325 (1.00) | 0.0233 (1.00) | 0.136 (1.00) | 0.0514 (1.00)
4p gain | 4 (1%) | 428 | 3.24e-05 (0.00862) | 0.0212 (1.00) |  |  | 0.0371 (1.00) | 0.0346 (1.00) | 0.109 (1.00) | 0.0989 (1.00)
4q gain | 4 (1%) | 428 | 3.24e-05 (0.00862) | 0.0212 (1.00) |  |  | 0.0371 (1.00) | 0.0346 (1.00) | 0.109 (1.00) | 0.0989 (1.00)
11q gain | 4 (1%) | 428 | 0.000308 (0.0731) | 0.0212 (1.00) |  |  | 0.0371 (1.00) | 0.0346 (1.00) | 0.00722 (1.00) | 0.00489 (0.944)
19p gain | 3 (1%) | 429 | 0.000448 (0.103) | 0.0552 (1.00) |  |  | 0.101 (1.00) | 0.0821 (1.00) | 0.025 (1.00) | 0.0187 (1.00)
19q gain | 4 (1%) | 428 | 3.24e-05 (0.00862) | 0.0212 (1.00) | 0.636 (1.00) | 0.0551 (1.00) | 0.0371 (1.00) | 0.0346 (1.00) | 0.00722 (1.00) | 0.00489 (0.944)
20p gain | 8 (2%) | 424 | 6.44e-10 (1.93e-07) | 0.00221 (0.445) | 1 (1.00) | 0.0817 (1.00) | 0.0134 (1.00) | 0.0136 (1.00) | 0.0122 (1.00) | 0.00562 (1.00)
20q gain | 8 (2%) | 424 | 6.44e-10 (1.93e-07) | 0.00221 (0.445) | 1 (1.00) | 0.0817 (1.00) | 0.0134 (1.00) | 0.0136 (1.00) | 0.0122 (1.00) | 0.00562 (1.00)
1p loss | 3 (1%) | 429 | 0.000448 (0.103) | 0.729 (1.00) |  |  | 0.487 (1.00) | 0.195 (1.00) | 0.295 (1.00) | 0.359 (1.00)
3q loss | 3 (1%) | 429 | 0.000448 (0.103) | 0.0552 (1.00) |  |  | 0.101 (1.00) | 0.0821 (1.00) | 0.025 (1.00) | 0.0187 (1.00)
8p loss | 4 (1%) | 428 | 3.24e-05 (0.00862) | 0.0532 (1.00) |  |  | 0.0371 (1.00) | 0.0346 (1.00) | 0.00722 (1.00) | 0.00489 (0.944)
8q loss | 4 (1%) | 428 | 3.24e-05 (0.00862) | 0.0532 (1.00) |  |  | 0.0371 (1.00) | 0.0346 (1.00) | 0.00722 (1.00) | 0.00489 (0.944)
9p loss | 10 (2%) | 422 | 3.74e-10 (1.12e-07) | 0.609 (1.00) | 0.559 (1.00) | 0.206 (1.00) | 0.249 (1.00) | 0.527 (1.00) | 0.182 (1.00) | 0.143 (1.00)
9q loss | 14 (3%) | 418 | 8.23e-11 (2.48e-08) | 0.212 (1.00) | 0.21 (1.00) | 0.00441 (0.855) | 0.441 (1.00) | 0.823 (1.00) | 0.193 (1.00) | 0.256 (1.00)
10p loss | 4 (1%) | 428 | 3.24e-05 (0.00862) | 0.473 (1.00) |  |  | 0.242 (1.00) | 0.0893 (1.00) | 0.109 (1.00) | 0.0989 (1.00)
10q loss | 4 (1%) | 428 | 3.24e-05 (0.00862) | 0.473 (1.00) |  |  | 0.242 (1.00) | 0.0893 (1.00) | 0.109 (1.00) | 0.0989 (1.00)
11p loss | 5 (1%) | 427 | 2.27e-06 (0.000652) | 0.0689 (1.00) | 0.499 (1.00) | 1 (1.00) | 0.0495 (1.00) | 0.166 (1.00) | 0.0383 (1.00) | 0.0225 (1.00)
11q loss | 6 (1%) | 426 | 2.33e-05 (0.00624) | 0.024 (1.00) | 0.388 (1.00) | 0.798 (1.00) | 0.0186 (1.00) | 0.0672 (1.00) | 0.0131 (1.00) | 0.00695 (1.00)
18p loss | 4 (1%) | 428 | 0.000308 (0.0731) | 0.204 (1.00) | 1 (1.00) | 0.369 (1.00) | 0.242 (1.00) | 0.0893 (1.00) | 0.109 (1.00) | 0.0389 (1.00)
18q loss | 4 (1%) | 428 | 0.000308 (0.0731) | 0.204 (1.00) | 1 (1.00) | 0.369 (1.00) | 0.242 (1.00) | 0.0893 (1.00) | 0.109 (1.00) | 0.0389 (1.00)
21q loss | 5 (1%) | 427 | 2.73e-05 (0.00728) | 0.0225 (1.00) | 0.384 (1.00) | 0.0551 (1.00) | 0.0495 (1.00) | 0.166 (1.00) | 0.0383 (1.00) | 0.0225 (1.00)
11p gain | 5 (1%) | 427 | 0.00181 (0.377) | 0.00503 (0.946) |  |  | 0.0173 (1.00) | 0.00933 (1.00) | 0.00207 (0.425) | 0.00127 (0.271)
21q gain | 3 (1%) | 429 | 0.00322 (0.635) | 0.0552 (1.00) |  |  | 0.101 (1.00) | 0.0821 (1.00) | 0.025 (1.00) | 0.0187 (1.00)
6q loss | 3 (1%) | 429 | 0.0261 (1.00) | 0.0552 (1.00) |  |  | 0.101 (1.00) | 0.0821 (1.00) | 0.025 (1.00) | 0.0187 (1.00)
13q loss | 11 (3%) | 421 | 0.00193 (0.399) | 0.0337 (1.00) | 0.0779 (1.00) | 1 (1.00) | 0.0941 (1.00) | 0.116 (1.00) | 0.0161 (1.00) | 0.00298 (0.594)
17p loss | 7 (2%) | 425 | 0.00165 (0.346) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.826 (1.00) | 0.886 (1.00) | 0.112 (1.00) | 0.493 (1.00)
19p loss | 4 (1%) | 428 | 0.23 (1.00) | 0.0212 (1.00) | 0.281 (1.00) | 0.369 (1.00) | 0.0371 (1.00) | 0.0346 (1.00) | 0.00722 (1.00) | 0.00489 (0.944)

'1q gain mutation analysis' versus 'CN_CNMF'

P value = 5.82e-05 (Fisher's exact test), Q value = 0.015

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
1Q GAIN MUTATED | 7 | 9 | 0
1Q GAIN WILD-TYPE | 27 | 323 | 66

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 = 3.24e-05 (Fisher's exact test), Q value = 0.0086

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
4P GAIN MUTATED | 4 | 0 | 0
4P GAIN WILD-TYPE | 30 | 332 | 66

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 = 3.24e-05 (Fisher's exact test), Q value = 0.0086

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
4Q GAIN MUTATED | 4 | 0 | 0
4Q GAIN WILD-TYPE | 30 | 332 | 66

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 = 1.4e-17 (Fisher's exact test), Q value = 4.3e-15

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
5P GAIN MUTATED | 15 | 1 | 0
5P GAIN WILD-TYPE | 19 | 331 | 66

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

'5p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000633 (Fisher's exact test), Q value = 0.14

Table S5. Gene #4: '5p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
5P GAIN MUTATED | 10 | 0 | 6
5P GAIN WILD-TYPE | 110 | 144 | 138

Figure S5. Get High-res Image Gene #4: '5p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'5p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000544 (Fisher's exact test), Q value = 0.12

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
5P GAIN MUTATED | 10 | 6 | 0
5P GAIN WILD-TYPE | 99 | 163 | 130

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 = 3.8e-16 (Fisher's exact test), Q value = 1.2e-13

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
5Q GAIN MUTATED | 13 | 0 | 0
5Q GAIN WILD-TYPE | 21 | 332 | 66

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 = 0.000147 (Fisher's exact test), Q value = 0.036

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
5Q GAIN MUTATED | 11 | 1 | 1
5Q GAIN WILD-TYPE | 125 | 64 | 230

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 = 0.000192 (Fisher's exact test), Q value = 0.047

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
5Q GAIN MUTATED | 10 | 0 | 3
5Q GAIN WILD-TYPE | 110 | 144 | 141

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 = 8.84e-05 (Fisher's exact test), Q value = 0.022

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
5Q GAIN MUTATED | 10 | 3 | 0
5Q GAIN WILD-TYPE | 99 | 166 | 130

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 = 1.8e-21 (Fisher's exact test), Q value = 5.5e-19

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
7P GAIN MUTATED | 17 | 0 | 0
7P GAIN WILD-TYPE | 17 | 332 | 66

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 = 0.000397 (Fisher's exact test), Q value = 0.092

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
7P GAIN MUTATED | 12 | 3 | 2
7P GAIN WILD-TYPE | 124 | 62 | 229

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 = 0.15

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 = 0.13

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_CNMF'

P value = 0.000271 (Fisher's exact test), Q value = 0.065

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
7P GAIN MUTATED | 12 | 1 | 3
7P GAIN WILD-TYPE | 108 | 143 | 141

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

'7p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000103 (Fisher's exact test), Q value = 0.026

Table S18. Gene #6: '7p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
7P GAIN MUTATED | 12 | 3 | 1
7P GAIN WILD-TYPE | 97 | 166 | 129

Figure S18. 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 = 2.84e-24 (Fisher's exact test), Q value = 8.8e-22

Table S19. Gene #7: '7q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
7Q GAIN MUTATED | 19 | 0 | 0
7Q GAIN WILD-TYPE | 15 | 332 | 66

Figure S19. 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 = 7.69e-05 (Fisher's exact test), Q value = 0.019

Table S20. Gene #7: '7q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
7Q GAIN MUTATED | 14 | 3 | 2
7Q GAIN WILD-TYPE | 122 | 62 | 229

Figure S20. 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 = 0.068

Table S21. 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 S21. 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 = 0.043

Table S22. 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 S22. 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 = 3.84e-05 (Fisher's exact test), Q value = 0.01

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
7Q GAIN MUTATED | 14 | 1 | 3
7Q GAIN WILD-TYPE | 106 | 143 | 141

Figure S23. 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 = 9.67e-06 (Fisher's exact test), Q value = 0.0027

Table S24. Gene #7: '7q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
7Q GAIN MUTATED | 14 | 3 | 1
7Q GAIN WILD-TYPE | 95 | 166 | 129

Figure S24. 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 = 0.000308 (Fisher's exact test), Q value = 0.073

Table S25. Gene #9: '11q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
11Q GAIN MUTATED | 3 | 0 | 1
11Q GAIN WILD-TYPE | 31 | 332 | 65

Figure S25. 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 = 5.23e-12 (Fisher's exact test), Q value = 1.6e-09

Table S26. Gene #10: '12p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
12P GAIN MUTATED | 10 | 0 | 2
12P GAIN WILD-TYPE | 24 | 332 | 64

Figure S26. 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 = 1.01e-06 (Fisher's exact test), Q value = 0.00029

Table S27. Gene #10: '12p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
12P GAIN MUTATED | 12 | 0 | 0
12P GAIN WILD-TYPE | 124 | 65 | 231

Figure S27. 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 = 7.78e-06 (Fisher's exact test), Q value = 0.0022

Table S28. 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 | 12 | 0 | 0 | 0
12P GAIN WILD-TYPE | 118 | 50 | 89 | 138

Figure S28. 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 = 4.91e-06 (Fisher's exact test), Q value = 0.0014

Table S29. 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 | 12 | 0 | 0
12P GAIN WILD-TYPE | 130 | 191 | 74

Figure S29. 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 = 1.46e-05 (Fisher's exact test), Q value = 0.004

Table S30. Gene #10: '12p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
12P GAIN MUTATED | 11 | 0 | 1
12P GAIN WILD-TYPE | 109 | 144 | 143

Figure S30. 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 = 3.89e-06 (Fisher's exact test), Q value = 0.0011

Table S31. Gene #10: '12p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
12P GAIN MUTATED | 11 | 1 | 0
12P GAIN WILD-TYPE | 98 | 168 | 130

Figure S31. 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 = 5.23e-12 (Fisher's exact test), Q value = 1.6e-09

Table S32. Gene #11: '12q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
12Q GAIN MUTATED | 10 | 0 | 2
12Q GAIN WILD-TYPE | 24 | 332 | 64

Figure S32. 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 = 1.01e-06 (Fisher's exact test), Q value = 0.00029

Table S33. Gene #11: '12q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
12Q GAIN MUTATED | 12 | 0 | 0
12Q GAIN WILD-TYPE | 124 | 65 | 231

Figure S33. 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 S34. 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 S34. 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 S35. 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 S35. 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 = 1.46e-05 (Fisher's exact test), Q value = 0.004

Table S36. Gene #11: '12q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
12Q GAIN MUTATED | 11 | 0 | 1
12Q GAIN WILD-TYPE | 109 | 144 | 143

Figure S36. 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 = 3.89e-06 (Fisher's exact test), Q value = 0.0011

Table S37. Gene #11: '12q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
12Q GAIN MUTATED | 11 | 1 | 0
12Q GAIN WILD-TYPE | 98 | 168 | 130

Figure S37. Get High-res Image Gene #11: '12q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain mutation analysis' versus 'CN_CNMF'

P value = 1.77e-07 (Fisher's exact test), Q value = 5.2e-05

Table S38. Gene #12: '14q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
14Q GAIN MUTATED | 6 | 0 | 1
14Q GAIN WILD-TYPE | 28 | 332 | 65

Figure S38. Get High-res Image Gene #12: '14q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'14q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000476 (Fisher's exact test), Q value = 0.11

Table S39. Gene #12: '14q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
14Q GAIN MUTATED | 7 | 0 | 0
14Q GAIN WILD-TYPE | 129 | 65 | 231

Figure S39. Get High-res Image Gene #12: '14q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16p gain mutation analysis' versus 'CN_CNMF'

P value = 2.57e-13 (Fisher's exact test), Q value = 7.8e-11

Table S40. Gene #13: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
16P GAIN MUTATED | 11 | 0 | 1
16P GAIN WILD-TYPE | 23 | 332 | 65

Figure S40. Get High-res Image Gene #13: '16p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.7e-05 (Fisher's exact test), Q value = 0.012

Table S41. Gene #13: '16p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
16P GAIN MUTATED | 10 | 2 | 0
16P GAIN WILD-TYPE | 126 | 63 | 231

Figure S41. Get High-res Image Gene #13: '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 = 0.058

Table S42. Gene #13: '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 #13: '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 = 0.041

Table S43. Gene #13: '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 #13: '16p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000137 (Fisher's exact test), Q value = 0.034

Table S44. Gene #13: '16p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
16P GAIN MUTATED | 10 | 0 | 2
16P GAIN WILD-TYPE | 110 | 144 | 142

Figure S44. Get High-res Image Gene #13: '16p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'16p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5.08e-05 (Fisher's exact test), Q value = 0.013

Table S45. Gene #13: '16p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
16P GAIN MUTATED | 10 | 2 | 0
16P GAIN WILD-TYPE | 99 | 167 | 130

Figure S45. Get High-res Image Gene #13: '16p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain mutation analysis' versus 'CN_CNMF'

P value = 2.33e-12 (Fisher's exact test), Q value = 7.1e-10

Table S46. Gene #14: '16q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
16Q GAIN MUTATED | 10 | 0 | 0
16Q GAIN WILD-TYPE | 24 | 332 | 66

Figure S46. Get High-res Image Gene #14: '16q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'16q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000314 (Fisher's exact test), Q value = 0.073

Table S47. Gene #14: '16q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
16Q GAIN MUTATED | 8 | 2 | 0
16Q GAIN WILD-TYPE | 128 | 63 | 231

Figure S47. Get High-res Image Gene #14: '16q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'16q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000643 (Fisher's exact test), Q value = 0.14

Table S48. Gene #14: '16q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
16Q GAIN MUTATED | 8 | 2 | 0
16Q GAIN WILD-TYPE | 101 | 167 | 130

Figure S48. Get High-res Image Gene #14: '16q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain mutation analysis' versus 'CN_CNMF'

P value = 1.04e-07 (Fisher's exact test), Q value = 3.1e-05

Table S49. Gene #15: '17p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
17P GAIN MUTATED | 8 | 2 | 1
17P GAIN WILD-TYPE | 26 | 330 | 65

Figure S49. Get High-res Image Gene #15: '17p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'17p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.25e-06 (Fisher's exact test), Q value = 0.0012

Table S50. Gene #15: '17p gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
17P GAIN MUTATED | 11 | 0 | 0
17P GAIN WILD-TYPE | 125 | 65 | 231

Figure S50. Get High-res Image Gene #15: '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 = 0.0049

Table S51. Gene #15: '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 S51. Get High-res Image Gene #15: '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 = 0.0052

Table S52. Gene #15: '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 S52. Get High-res Image Gene #15: '17p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.67e-05 (Fisher's exact test), Q value = 0.012

Table S53. Gene #15: '17p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
17P GAIN MUTATED | 10 | 0 | 1
17P GAIN WILD-TYPE | 110 | 144 | 143

Figure S53. Get High-res Image Gene #15: '17p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'17p gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.0039

Table S54. Gene #15: '17p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
17P GAIN MUTATED | 10 | 1 | 0
17P GAIN WILD-TYPE | 99 | 168 | 130

Figure S54. Get High-res Image Gene #15: '17p gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain mutation analysis' versus 'CN_CNMF'

P value = 7.49e-08 (Fisher's exact test), Q value = 2.2e-05

Table S55. Gene #16: '17q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
17Q GAIN MUTATED | 8 | 2 | 2
17Q GAIN WILD-TYPE | 26 | 330 | 64

Figure S55. Get High-res Image Gene #16: '17q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'17q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00029

Table S56. Gene #16: '17q gain mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
17Q GAIN MUTATED | 12 | 0 | 0
17Q GAIN WILD-TYPE | 124 | 65 | 231

Figure S56. Get High-res Image Gene #16: '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 S57. Gene #16: '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 S57. Get High-res Image Gene #16: '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 S58. Gene #16: '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 S58. Get High-res Image Gene #16: '17q gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.004

Table S59. Gene #16: '17q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
17Q GAIN MUTATED | 11 | 0 | 1
17Q GAIN WILD-TYPE | 109 | 144 | 143

Figure S59. Get High-res Image Gene #16: '17q gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'17q gain mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.89e-06 (Fisher's exact test), Q value = 0.0011

Table S60. Gene #16: '17q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
17Q GAIN MUTATED | 11 | 1 | 0
17Q GAIN WILD-TYPE | 98 | 168 | 130

Figure S60. Get High-res Image Gene #16: '17q gain mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 0.000448 (Fisher's exact test), Q value = 0.1

Table S61. Gene #17: '19p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
19P GAIN MUTATED | 3 | 0 | 0
19P GAIN WILD-TYPE | 31 | 332 | 66

Figure S61. Get High-res Image Gene #17: '19p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'19q gain mutation analysis' versus 'CN_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.0086

Table S62. Gene #18: '19q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
19Q GAIN MUTATED | 4 | 0 | 0
19Q GAIN WILD-TYPE | 30 | 332 | 66

Figure S62. Get High-res Image Gene #18: '19q gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 6.44e-10 (Fisher's exact test), Q value = 1.9e-07

Table S63. Gene #19: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
20P GAIN MUTATED | 8 | 0 | 0
20P GAIN WILD-TYPE | 26 | 332 | 66

Figure S63. Get High-res Image Gene #19: '20p gain mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 6.44e-10 (Fisher's exact test), Q value = 1.9e-07

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
20Q GAIN MUTATED | 8 | 0 | 0
20Q GAIN WILD-TYPE | 26 | 332 | 66

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

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000448 (Fisher's exact test), Q value = 0.1

Table S65. Gene #22: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
1P LOSS MUTATED | 3 | 0 | 0
1P LOSS WILD-TYPE | 31 | 332 | 66

Figure S65. Get High-res Image Gene #22: '1p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2p loss mutation analysis' versus 'CN_CNMF'

P value = 1.32e-08 (Fisher's exact test), Q value = 3.9e-06

Table S66. Gene #23: '2p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
2P LOSS MUTATED | 7 | 0 | 1
2P LOSS WILD-TYPE | 27 | 332 | 65

Figure S66. Get High-res Image Gene #23: '2p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000197 (Fisher's exact test), Q value = 0.048

Table S67. Gene #23: '2p loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
2P LOSS MUTATED | 8 | 0 | 0
2P LOSS WILD-TYPE | 128 | 65 | 231

Figure S67. Get High-res Image Gene #23: '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 S68. Gene #23: '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 S68. Get High-res Image Gene #23: '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 = 0.078

Table S69. Gene #23: '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 S69. Get High-res Image Gene #23: '2p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.73e-05 (Fisher's exact test), Q value = 0.012

Table S70. Gene #23: '2p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
2P LOSS MUTATED | 8 | 0 | 0
2P LOSS WILD-TYPE | 112 | 144 | 144

Figure S70. Get High-res Image Gene #23: '2p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'2p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.14e-05 (Fisher's exact test), Q value = 0.0057

Table S71. Gene #23: '2p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
2P LOSS MUTATED | 8 | 0 | 0
2P LOSS WILD-TYPE | 101 | 169 | 130

Figure S71. Get High-res Image Gene #23: '2p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss mutation analysis' versus 'CN_CNMF'

P value = 1.01e-08 (Fisher's exact test), Q value = 3e-06

Table S72. Gene #24: '2q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
2Q LOSS MUTATED | 7 | 0 | 0
2Q LOSS WILD-TYPE | 27 | 332 | 66

Figure S72. Get High-res Image Gene #24: '2q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'2q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000476 (Fisher's exact test), Q value = 0.11

Table S73. Gene #24: '2q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 136 | 65 | 231
2Q LOSS MUTATED | 7 | 0 | 0
2Q LOSS WILD-TYPE | 129 | 65 | 231

Figure S73. Get High-res Image Gene #24: '2q loss mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'2q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000168 (Fisher's exact test), Q value = 0.041

Table S74. Gene #24: '2q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
2Q LOSS MUTATED | 7 | 0 | 0
2Q LOSS WILD-TYPE | 113 | 144 | 144

Figure S74. Get High-res Image Gene #24: '2q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'2q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.4e-05 (Fisher's exact test), Q value = 0.021

Table S75. Gene #24: '2q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
2Q LOSS MUTATED | 7 | 0 | 0
2Q LOSS WILD-TYPE | 102 | 169 | 130

Figure S75. Get High-res Image Gene #24: '2q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000448 (Fisher's exact test), Q value = 0.1

Table S76. Gene #25: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
3Q LOSS MUTATED | 3 | 0 | 0
3Q LOSS WILD-TYPE | 31 | 332 | 66

Figure S76. Get High-res Image Gene #25: '3q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8p loss mutation analysis' versus 'CN_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.0086

Table S77. Gene #27: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
8P LOSS MUTATED | 4 | 0 | 0
8P LOSS WILD-TYPE | 30 | 332 | 66

Figure S77. Get High-res Image Gene #27: '8p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'8q loss mutation analysis' versus 'CN_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.0086

Table S78. Gene #28: '8q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
8Q LOSS MUTATED | 4 | 0 | 0
8Q LOSS WILD-TYPE | 30 | 332 | 66

Figure S78. Get High-res Image Gene #28: '8q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9p loss mutation analysis' versus 'CN_CNMF'

P value = 3.74e-10 (Fisher's exact test), Q value = 1.1e-07

Table S79. Gene #29: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
9P LOSS MUTATED | 9 | 1 | 0
9P LOSS WILD-TYPE | 25 | 331 | 66

Figure S79. Get High-res Image Gene #29: '9p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'9q loss mutation analysis' versus 'CN_CNMF'

P value = 8.23e-11 (Fisher's exact test), Q value = 2.5e-08

Table S80. Gene #30: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
9Q LOSS MUTATED | 11 | 3 | 0
9Q LOSS WILD-TYPE | 23 | 329 | 66

Figure S80. Get High-res Image Gene #30: '9q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10p loss mutation analysis' versus 'CN_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.0086

Table S81. Gene #31: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
10P LOSS MUTATED | 4 | 0 | 0
10P LOSS WILD-TYPE | 30 | 332 | 66

Figure S81. Get High-res Image Gene #31: '10p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 3.24e-05 (Fisher's exact test), Q value = 0.0086

Table S82. Gene #32: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
10Q LOSS MUTATED | 4 | 0 | 0
10Q LOSS WILD-TYPE | 30 | 332 | 66

Figure S82. Get High-res Image Gene #32: '10q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11p loss mutation analysis' versus 'CN_CNMF'

P value = 2.27e-06 (Fisher's exact test), Q value = 0.00065

Table S83. Gene #33: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
11P LOSS MUTATED | 5 | 0 | 0
11P LOSS WILD-TYPE | 29 | 332 | 66

Figure S83. Get High-res Image Gene #33: '11p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'11q loss mutation analysis' versus 'CN_CNMF'

P value = 2.33e-05 (Fisher's exact test), Q value = 0.0062

Table S84. Gene #34: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
11Q LOSS MUTATED | 5 | 1 | 0
11Q LOSS WILD-TYPE | 29 | 331 | 66

Figure S84. Get High-res Image Gene #34: '11q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'15q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000556 (Fisher's exact test), Q value = 0.12

Table S85. Gene #36: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
15Q LOSS MUTATED | 4 | 2 | 0
15Q LOSS WILD-TYPE | 30 | 330 | 66

Figure S85. Get High-res Image Gene #36: '15q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'15q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000592 (Fisher's exact test), Q value = 0.13

Table S86. Gene #36: '15q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
15Q LOSS MUTATED | 6 | 0 | 0
15Q LOSS WILD-TYPE | 114 | 144 | 144

Figure S86. Get High-res Image Gene #36: '15q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'15q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000328 (Fisher's exact test), Q value = 0.076

Table S87. Gene #36: '15q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
15Q LOSS MUTATED | 6 | 0 | 0
15Q LOSS WILD-TYPE | 103 | 169 | 130

Figure S87. Get High-res Image Gene #36: '15q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss mutation analysis' versus 'CN_CNMF'

P value = 0.000308 (Fisher's exact test), Q value = 0.073

Table S88. Gene #38: '18p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
18P LOSS MUTATED | 3 | 0 | 1
18P LOSS WILD-TYPE | 31 | 332 | 65

Figure S88. Get High-res Image Gene #38: '18p loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'18q loss mutation analysis' versus 'CN_CNMF'

P value = 0.000308 (Fisher's exact test), Q value = 0.073

Table S89. Gene #39: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
18Q LOSS MUTATED | 3 | 0 | 1
18Q LOSS WILD-TYPE | 31 | 332 | 65

Figure S89. Get High-res Image Gene #39: '18q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'21q loss mutation analysis' versus 'CN_CNMF'

P value = 2.73e-05 (Fisher's exact test), Q value = 0.0073

Table S90. Gene #41: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
21Q LOSS MUTATED | 4 | 0 | 1
21Q LOSS WILD-TYPE | 30 | 332 | 65

Figure S90. Get High-res Image Gene #41: '21q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 1.18e-45 (Fisher's exact test), Q value = 3.6e-43

Table S91. Gene #42: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 332 | 66
22Q LOSS MUTATED | 8 | 0 | 46
22Q LOSS WILD-TYPE | 26 | 332 | 20

Figure S91. Get High-res Image Gene #42: '22q loss mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.69e-09 (Fisher's exact test), Q value = 1.1e-06

Table S92. Gene #42: '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 | 29 | 3 | 16 | 1
22Q LOSS WILD-TYPE | 101 | 47 | 73 | 137

Figure S92. Get High-res Image Gene #42: '22q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.07e-07 (Fisher's exact test), Q value = 6e-05

Table S93. Gene #42: '22q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 191 | 74
22Q LOSS MUTATED | 29 | 6 | 14
22Q LOSS WILD-TYPE | 113 | 185 | 60

Figure S93. Get High-res Image Gene #42: '22q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000284 (Fisher's exact test), Q value = 0.068

Table S94. Gene #42: '22q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 120 | 144 | 144
22Q LOSS MUTATED | 28 | 14 | 10
22Q LOSS WILD-TYPE | 92 | 130 | 134

Figure S94. Get High-res Image Gene #42: '22q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'22q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.99e-05 (Fisher's exact test), Q value = 0.022

Table S95. Gene #42: '22q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 109 | 169 | 130
22Q LOSS MUTATED | 26 | 10 | 16
22Q LOSS WILD-TYPE | 83 | 159 | 114

Figure S95. Get High-res Image Gene #42: '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 = 432

- Number of significantly arm-level cnvs = 42

- 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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