Brain Lower Grade Glioma: 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 51 arm-level results and 8 molecular subtypes across 220 patients, 53 significant findings detected with Q value < 0.25.

- 1p gain cnv correlated to 'MRNASEQ_CNMF'.

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

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

- 10p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 19p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 19q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

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

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

- 1p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- 1q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 4p loss cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

- 4q loss cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.

- 10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

- 14q loss cnv correlated to 'METHLYATION_CNMF'.

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

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

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 51 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 53 significant findings detected.

|  | Molecular subtypes | MRNA CNMF | MRNA CHIERARCHICAL | CN CNMF | METHLYATION CNMF | 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 | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test
1p loss | 67 (30%) | 153 | 0.00361 (0.97) | 0.00862 (1.00) | 4.56e-47 (1.57e-44) | 2.38e-51 (8.19e-49) | 1.61e-24 (5.43e-22) | 1.37e-30 (4.67e-28) | 1.41e-19 (4.71e-17) | 3.05e-05 (0.00951)
19q loss | 76 (35%) | 144 | 0.247 (1.00) | 0.145 (1.00) | 1.4e-45 (4.79e-43) | 1.01e-36 (3.43e-34) | 9.57e-22 (3.22e-19) | 4.5e-27 (1.53e-24) | 3.01e-17 (9.91e-15) | 3.32e-05 (0.0103)
7p gain | 37 (17%) | 183 | 0.175 (1.00) | 0.162 (1.00) | 1.86e-17 (6.15e-15) | 6.22e-11 (2.02e-08) | 8.17e-12 (2.66e-09) | 0.000204 (0.0609) | 0.000552 (0.162) | 0.0071 (1.00)
4p loss | 15 (7%) | 205 | 0.415 (1.00) | 0.329 (1.00) | 0.000882 (0.257) | 0.000144 (0.0433) | 0.000108 (0.0325) | 0.000418 (0.123) | 4.98e-06 (0.00159) | 0.833 (1.00)
7q gain | 51 (23%) | 169 | 0.282 (1.00) | 0.144 (1.00) | 6.78e-15 (2.22e-12) | 2.14e-09 (6.93e-07) | 6.56e-08 (2.12e-05) | 0.00139 (0.393) | 0.00423 (1.00) | 0.128 (1.00)
19q gain | 9 (4%) | 211 |  |  | 0.00034 (0.101) | 0.000707 (0.207) | 0.000336 (0.1) | 0.0217 (1.00) | 0.115 (1.00) | 0.162 (1.00)
20p gain | 17 (8%) | 203 |  |  | 1.66e-05 (0.00528) | 7.69e-05 (0.0234) | 1.7e-05 (0.00537) | 0.259 (1.00) | 0.0281 (1.00) | 0.267 (1.00)
20q gain | 16 (7%) | 204 |  |  | 8.04e-05 (0.0244) | 5.24e-05 (0.0162) | 7.35e-08 (2.37e-05) | 0.0252 (1.00) | 0.00356 (0.963) | 0.0462 (1.00)
1q loss | 9 (4%) | 211 | 0.0889 (1.00) | 0.0971 (1.00) | 8.38e-05 (0.0254) | 2.66e-05 (0.00833) | 0.00603 (1.00) | 0.00013 (0.0393) | 0.0106 (1.00) | 0.715 (1.00)
10p loss | 31 (14%) | 189 | 0.271 (1.00) | 0.241 (1.00) | 2.3e-17 (7.59e-15) | 2.62e-22 (8.84e-20) | 4.79e-19 (1.59e-16) | 0.0016 (0.45) | 0.0191 (1.00) | 0.0066 (1.00)
10q loss | 32 (15%) | 188 | 0.271 (1.00) | 0.241 (1.00) | 3.46e-16 (1.14e-13) | 2.77e-21 (9.27e-19) | 3.81e-20 (1.27e-17) | 0.00109 (0.315) | 0.0128 (1.00) | 0.0178 (1.00)
22q loss | 15 (7%) | 205 | 1 (1.00) | 0.763 (1.00) | 7.15e-06 (0.00228) | 6.34e-05 (0.0195) | 1.92e-05 (0.00605) | 0.0451 (1.00) | 0.149 (1.00) | 0.149 (1.00)
10p gain | 21 (10%) | 199 |  |  | 6.41e-07 (0.000206) | 1.43e-05 (0.00455) | 0.0175 (1.00) | 0.094 (1.00) | 0.54 (1.00) | 0.93 (1.00)
19p gain | 11 (5%) | 209 |  |  | 2.25e-05 (0.00708) | 5.91e-05 (0.0182) | 0.00122 (0.348) | 0.0102 (1.00) | 0.0861 (1.00) | 0.0595 (1.00)
4q loss | 24 (11%) | 196 | 0.839 (1.00) | 0.828 (1.00) | 0.0049 (1.00) | 0.000399 (0.118) | 0.002 (0.556) | 0.00355 (0.963) | 6.65e-05 (0.0204) | 0.6 (1.00)
1p gain | 6 (3%) | 214 |  |  | 0.0272 (1.00) | 0.0843 (1.00) | 3.39e-05 (0.0105) | 0.103 (1.00) | 0.234 (1.00) | 0.208 (1.00)
14q loss | 24 (11%) | 196 |  |  | 0.00111 (0.319) | 0.000835 (0.244) | 0.00126 (0.359) | 0.452 (1.00) | 0.0127 (1.00) | 0.103 (1.00)
1q gain | 8 (4%) | 212 |  |  | 0.00126 (0.359) | 0.103 (1.00) | 0.0312 (1.00) | 0.618 (1.00) | 0.851 (1.00) | 0.569 (1.00)
6p gain | 4 (2%) | 216 |  |  | 0.213 (1.00) | 0.427 (1.00) | 0.0517 (1.00) | 0.279 (1.00) | 0.0922 (1.00) | 0.717 (1.00)
8p gain | 14 (6%) | 206 |  |  | 0.0337 (1.00) | 0.235 (1.00) | 0.606 (1.00) | 0.464 (1.00) | 0.205 (1.00) | 0.459 (1.00)
8q gain | 17 (8%) | 203 |  |  | 0.00467 (1.00) | 0.0606 (1.00) | 0.377 (1.00) | 0.203 (1.00) | 0.125 (1.00) | 0.172 (1.00)
9p gain | 4 (2%) | 216 |  |  | 0.213 (1.00) | 0.543 (1.00) | 0.0715 (1.00) | 1 (1.00) | 1 (1.00) | 0.159 (1.00)
9q gain | 6 (3%) | 214 |  |  | 0.0272 (1.00) | 0.273 (1.00) | 0.00231 (0.639) | 0.519 (1.00) | 0.747 (1.00) | 0.37 (1.00)
11p gain | 9 (4%) | 211 |  |  | 0.5 (1.00) | 0.233 (1.00) | 0.00395 (1.00) | 0.00261 (0.714) | 0.138 (1.00) | 0.426 (1.00)
11q gain | 14 (6%) | 206 |  |  | 0.353 (1.00) | 0.347 (1.00) | 0.172 (1.00) | 0.107 (1.00) | 0.708 (1.00) | 0.521 (1.00)
12p gain | 11 (5%) | 209 |  |  | 0.0368 (1.00) | 0.106 (1.00) | 0.286 (1.00) | 0.17 (1.00) | 0.0299 (1.00) | 0.05 (1.00)
12q gain | 5 (2%) | 215 |  |  | 0.848 (1.00) | 0.763 (1.00) | 0.934 (1.00) | 0.346 (1.00) | 0.0605 (1.00) | 0.157 (1.00)
18p gain | 4 (2%) | 216 |  |  | 0.213 (1.00) | 0.543 (1.00) | 0.569 (1.00) | 0.279 (1.00) | 0.37 (1.00) | 0.0958 (1.00)
21q gain | 3 (1%) | 217 |  |  | 0.328 (1.00) | 0.6 (1.00) | 0.158 (1.00) | 0.0879 (1.00) | 1 (1.00) | 1 (1.00)
2p loss | 4 (2%) | 216 |  |  | 0.825 (1.00) | 1 (1.00) | 0.464 (1.00) | 0.37 (1.00) | 0.37 (1.00) | 0.0958 (1.00)
2q loss | 3 (1%) | 217 |  |  | 0.796 (1.00) | 1 (1.00) | 0.513 (1.00) | 0.259 (1.00) | 0.0543 (1.00) | 0.387 (1.00)
3p loss | 4 (2%) | 216 |  |  | 0.553 (1.00) | 0.543 (1.00) | 0.356 (1.00) | 0.279 (1.00) | 0.191 (1.00) | 0.241 (1.00)
3q loss | 9 (4%) | 211 | 0.175 (1.00) | 1 (1.00) | 0.128 (1.00) | 0.0699 (1.00) | 0.547 (1.00) | 0.453 (1.00) | 0.96 (1.00) | 0.849 (1.00)
5p loss | 11 (5%) | 209 | 1 (1.00) | 0.388 (1.00) | 0.0162 (1.00) | 0.0233 (1.00) | 0.847 (1.00) | 0.36 (1.00) | 0.161 (1.00) | 0.766 (1.00)
5q loss | 9 (4%) | 211 | 0.615 (1.00) | 0.0971 (1.00) | 0.0453 (1.00) | 0.0699 (1.00) | 0.0439 (1.00) | 0.0217 (1.00) | 0.00506 (1.00) | 0.139 (1.00)
6p loss | 7 (3%) | 213 |  |  | 0.12 (1.00) | 0.0239 (1.00) | 0.139 (1.00) | 1 (1.00) | 0.693 (1.00) | 0.157 (1.00)
6q loss | 21 (10%) | 199 |  |  | 0.00431 (1.00) | 0.0122 (1.00) | 0.362 (1.00) | 0.332 (1.00) | 0.0529 (1.00) | 0.32 (1.00)
8p loss | 3 (1%) | 217 |  |  | 0.17 (1.00) | 0.167 (1.00) | 0.571 (1.00) | 1 (1.00) | 0.125 (1.00) | 0.387 (1.00)
9p loss | 38 (17%) | 182 | 0.384 (1.00) | 0.828 (1.00) | 0.00289 (0.788) | 0.0642 (1.00) | 0.692 (1.00) | 0.245 (1.00) | 0.804 (1.00) | 0.915 (1.00)
9q loss | 6 (3%) | 214 |  |  | 0.0702 (1.00) | 0.0431 (1.00) | 0.0111 (1.00) | 0.000882 (0.257) | 0.00806 (1.00) | 0.795 (1.00)
11p loss | 20 (9%) | 200 | 0.815 (1.00) | 0.526 (1.00) | 0.00199 (0.556) | 0.00111 (0.319) | 0.0162 (1.00) | 0.00897 (1.00) | 0.0113 (1.00) | 0.0469 (1.00)
11q loss | 4 (2%) | 216 |  |  | 0.00243 (0.667) | 0.177 (1.00) | 0.00187 (0.523) | 0.279 (1.00) | 0.697 (1.00) | 0.0958 (1.00)
12q loss | 8 (4%) | 212 |  |  | 0.0444 (1.00) | 0.198 (1.00) | 0.686 (1.00) | 0.618 (1.00) | 0.182 (1.00) | 0.833 (1.00)
13q loss | 28 (13%) | 192 | 1 (1.00) | 0.388 (1.00) | 0.635 (1.00) | 0.17 (1.00) | 0.86 (1.00) | 0.537 (1.00) | 0.914 (1.00) | 0.364 (1.00)
15q loss | 12 (5%) | 208 |  |  | 0.00582 (1.00) | 0.00428 (1.00) | 0.000977 (0.282) | 0.00504 (1.00) | 0.248 (1.00) | 0.89 (1.00)
16q loss | 6 (3%) | 214 |  |  | 0.662 (1.00) | 0.0843 (1.00) | 0.302 (1.00) | 0.519 (1.00) | 0.549 (1.00) | 1 (1.00)
18p loss | 15 (7%) | 205 | 0.344 (1.00) | 0.413 (1.00) | 0.144 (1.00) | 0.0623 (1.00) | 0.119 (1.00) | 0.117 (1.00) | 0.0755 (1.00) | 0.354 (1.00)
18q loss | 16 (7%) | 204 | 0.0889 (1.00) | 0.0971 (1.00) | 0.00296 (0.804) | 0.0055 (1.00) | 0.0024 (0.662) | 0.0264 (1.00) | 0.0111 (1.00) | 0.51 (1.00)
19p loss | 10 (5%) | 210 | 0.302 (1.00) | 0.0773 (1.00) | 0.0618 (1.00) | 0.149 (1.00) | 0.0747 (1.00) | 0.0204 (1.00) | 0.0118 (1.00) | 0.744 (1.00)
21q loss | 8 (4%) | 212 |  |  | 0.588 (1.00) | 0.605 (1.00) | 0.46 (1.00) | 0.618 (1.00) | 0.33 (1.00) | 0.197 (1.00)
Xq loss | 6 (3%) | 214 |  |  | 0.132 (1.00) | 0.35 (1.00) | 0.698 (1.00) | 0.103 (1.00) | 0.234 (1.00) | 0.208 (1.00)

'1p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.39e-05 (Chi-square test), Q value = 0.01

Table S1. Gene #1: '1p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
1P GAIN MUTATED | 0 | 6 | 0 | 0 | 0
1P GAIN WILD-TYPE | 60 | 36 | 35 | 70 | 11

Figure S1. Get High-res Image Gene #1: '1p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'7p gain mutation analysis' versus 'CN_CNMF'

P value = 1.86e-17 (Fisher's exact test), Q value = 6.1e-15

Table S2. Gene #4: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
7P GAIN MUTATED | 5 | 30 | 2
7P GAIN WILD-TYPE | 89 | 20 | 74

Figure S2. Get High-res Image Gene #4: '7p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.22e-11 (Fisher's exact test), Q value = 2e-08

Table S3. Gene #4: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
7P GAIN MUTATED | 12 | 21 | 2 | 1
7P GAIN WILD-TYPE | 88 | 13 | 56 | 22

Figure S3. Get High-res Image Gene #4: '7p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.17e-12 (Chi-square test), Q value = 2.7e-09

Table S4. Gene #4: '7p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
7P GAIN MUTATED | 10 | 23 | 2 | 2 | 0
7P GAIN WILD-TYPE | 50 | 19 | 33 | 68 | 11

Figure S4. Get High-res Image Gene #4: '7p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'7p gain mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.061

Table S5. Gene #4: '7p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 117 | 69
7P GAIN MUTATED | 2 | 31 | 4
7P GAIN WILD-TYPE | 30 | 86 | 65

Figure S5. Get High-res Image Gene #4: '7p gain mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000552 (Fisher's exact test), Q value = 0.16

Table S6. Gene #4: '7p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 50 | 50 | 32 | 87
7P GAIN MUTATED | 14 | 14 | 1 | 8
7P GAIN WILD-TYPE | 36 | 36 | 31 | 79

Figure S6. Get High-res Image Gene #4: '7p gain mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'7q gain mutation analysis' versus 'CN_CNMF'

P value = 6.78e-15 (Fisher's exact test), Q value = 2.2e-12

Table S7. Gene #5: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
7Q GAIN MUTATED | 10 | 34 | 7
7Q GAIN WILD-TYPE | 84 | 16 | 69

Figure S7. Get High-res Image Gene #5: '7q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'7q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.14e-09 (Fisher's exact test), Q value = 6.9e-07

Table S8. Gene #5: '7q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
7Q GAIN MUTATED | 20 | 23 | 6 | 1
7Q GAIN WILD-TYPE | 80 | 11 | 52 | 22

Figure S8. Get High-res Image Gene #5: '7q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'7q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 6.56e-08 (Chi-square test), Q value = 2.1e-05

Table S9. Gene #5: '7q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
7Q GAIN MUTATED | 17 | 23 | 4 | 6 | 0
7Q GAIN WILD-TYPE | 43 | 19 | 31 | 64 | 11

Figure S9. Get High-res Image Gene #5: '7q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'10p gain mutation analysis' versus 'CN_CNMF'

P value = 6.41e-07 (Fisher's exact test), Q value = 0.00021

Table S10. Gene #10: '10p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
10P GAIN MUTATED | 20 | 0 | 1
10P GAIN WILD-TYPE | 74 | 50 | 75

Figure S10. Get High-res Image Gene #10: '10p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.0046

Table S11. Gene #10: '10p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
10P GAIN MUTATED | 20 | 0 | 0 | 1
10P GAIN WILD-TYPE | 80 | 34 | 58 | 22

Figure S11. Get High-res Image Gene #10: '10p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19p gain mutation analysis' versus 'CN_CNMF'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.0071

Table S12. Gene #16: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
19P GAIN MUTATED | 2 | 9 | 0
19P GAIN WILD-TYPE | 92 | 41 | 76

Figure S12. Get High-res Image Gene #16: '19p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.91e-05 (Fisher's exact test), Q value = 0.018

Table S13. Gene #16: '19p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
19P GAIN MUTATED | 3 | 8 | 0 | 0
19P GAIN WILD-TYPE | 97 | 26 | 58 | 23

Figure S13. Get High-res Image Gene #16: '19p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19q gain mutation analysis' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.1

Table S14. Gene #17: '19q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
19Q GAIN MUTATED | 2 | 7 | 0
19Q GAIN WILD-TYPE | 92 | 43 | 76

Figure S14. Get High-res Image Gene #17: '19q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000707 (Fisher's exact test), Q value = 0.21

Table S15. Gene #17: '19q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
19Q GAIN MUTATED | 2 | 6 | 0 | 0
19Q GAIN WILD-TYPE | 98 | 28 | 58 | 23

Figure S15. Get High-res Image Gene #17: '19q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000336 (Chi-square test), Q value = 0.1

Table S16. Gene #17: '19q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
19Q GAIN MUTATED | 1 | 7 | 0 | 1 | 0
19Q GAIN WILD-TYPE | 59 | 35 | 35 | 69 | 11

Figure S16. Get High-res Image Gene #17: '19q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'20p gain mutation analysis' versus 'CN_CNMF'

P value = 1.66e-05 (Fisher's exact test), Q value = 0.0053

Table S17. Gene #18: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
20P GAIN MUTATED | 4 | 12 | 1
20P GAIN WILD-TYPE | 90 | 38 | 75

Figure S17. Get High-res Image Gene #18: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 7.69e-05 (Fisher's exact test), Q value = 0.023

Table S18. Gene #18: '20p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
20P GAIN MUTATED | 6 | 10 | 1 | 0
20P GAIN WILD-TYPE | 94 | 24 | 57 | 23

Figure S18. Get High-res Image Gene #18: '20p gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.7e-05 (Chi-square test), Q value = 0.0054

Table S19. Gene #18: '20p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
20P GAIN MUTATED | 2 | 11 | 1 | 2 | 0
20P GAIN WILD-TYPE | 58 | 31 | 34 | 68 | 11

Figure S19. Get High-res Image Gene #18: '20p gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'20q gain mutation analysis' versus 'CN_CNMF'

P value = 8.04e-05 (Fisher's exact test), Q value = 0.024

Table S20. Gene #19: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
20Q GAIN MUTATED | 4 | 11 | 1
20Q GAIN WILD-TYPE | 90 | 39 | 75

Figure S20. Get High-res Image Gene #19: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.24e-05 (Fisher's exact test), Q value = 0.016

Table S21. Gene #19: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
20Q GAIN MUTATED | 5 | 10 | 1 | 0
20Q GAIN WILD-TYPE | 95 | 24 | 57 | 23

Figure S21. Get High-res Image Gene #19: '20q gain mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.35e-08 (Chi-square test), Q value = 2.4e-05

Table S22. Gene #19: '20q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
20Q GAIN MUTATED | 2 | 12 | 1 | 0 | 0
20Q GAIN WILD-TYPE | 58 | 30 | 34 | 70 | 11

Figure S22. Get High-res Image Gene #19: '20q gain mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'1p loss mutation analysis' versus 'CN_CNMF'

P value = 4.56e-47 (Fisher's exact test), Q value = 1.6e-44

Table S23. Gene #21: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
1P LOSS MUTATED | 0 | 0 | 67
1P LOSS WILD-TYPE | 94 | 50 | 9

Figure S23. Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.38e-51 (Fisher's exact test), Q value = 8.2e-49

Table S24. Gene #21: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
1P LOSS MUTATED | 0 | 0 | 58 | 6
1P LOSS WILD-TYPE | 100 | 34 | 0 | 17

Figure S24. Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'1p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.61e-24 (Chi-square test), Q value = 5.4e-22

Table S25. Gene #21: '1p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
1P LOSS MUTATED | 0 | 0 | 33 | 31 | 3
1P LOSS WILD-TYPE | 60 | 42 | 2 | 39 | 8

Figure S25. Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'1p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-30 (Fisher's exact test), Q value = 4.7e-28

Table S26. Gene #21: '1p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 117 | 69
1P LOSS MUTATED | 32 | 4 | 31
1P LOSS WILD-TYPE | 0 | 113 | 38

Figure S26. Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 1.41e-19 (Fisher's exact test), Q value = 4.7e-17

Table S27. Gene #21: '1p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 50 | 50 | 32 | 87
1P LOSS MUTATED | 3 | 0 | 25 | 39
1P LOSS WILD-TYPE | 47 | 50 | 7 | 48

Figure S27. Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'1p loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.0095

Table S28. Gene #21: '1p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 88 | 13 | 118
1P LOSS MUTATED | 42 | 3 | 22
1P LOSS WILD-TYPE | 46 | 10 | 96

Figure S28. Get High-res Image Gene #21: '1p loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'1q loss mutation analysis' versus 'CN_CNMF'

P value = 8.38e-05 (Fisher's exact test), Q value = 0.025

Table S29. Gene #22: '1q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
1Q LOSS MUTATED | 0 | 0 | 9
1Q LOSS WILD-TYPE | 94 | 50 | 67

Figure S29. Get High-res Image Gene #22: '1q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'1q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.0083

Table S30. Gene #22: '1q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
1Q LOSS MUTATED | 0 | 0 | 9 | 0
1Q LOSS WILD-TYPE | 100 | 34 | 49 | 23

Figure S30. Get High-res Image Gene #22: '1q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'1q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.039

Table S31. Gene #22: '1q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 117 | 69
1Q LOSS MUTATED | 5 | 0 | 4
1Q LOSS WILD-TYPE | 27 | 117 | 65

Figure S31. Get High-res Image Gene #22: '1q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000144 (Fisher's exact test), Q value = 0.043

Table S32. Gene #27: '4p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
4P LOSS MUTATED | 3 | 0 | 12 | 0
4P LOSS WILD-TYPE | 97 | 34 | 46 | 23

Figure S32. Get High-res Image Gene #27: '4p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000108 (Chi-square test), Q value = 0.032

Table S33. Gene #27: '4p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
4P LOSS MUTATED | 0 | 0 | 8 | 7 | 0
4P LOSS WILD-TYPE | 60 | 42 | 27 | 63 | 11

Figure S33. Get High-res Image Gene #27: '4p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'4p loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000418 (Fisher's exact test), Q value = 0.12

Table S34. Gene #27: '4p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 117 | 69
4P LOSS MUTATED | 7 | 2 | 6
4P LOSS WILD-TYPE | 25 | 115 | 63

Figure S34. Get High-res Image Gene #27: '4p loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 4.98e-06 (Fisher's exact test), Q value = 0.0016

Table S35. Gene #27: '4p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 50 | 50 | 32 | 87
4P LOSS MUTATED | 0 | 0 | 9 | 6
4P LOSS WILD-TYPE | 50 | 50 | 23 | 81

Figure S35. Get High-res Image Gene #27: '4p loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'4q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000399 (Fisher's exact test), Q value = 0.12

Table S36. Gene #28: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
4Q LOSS MUTATED | 8 | 0 | 15 | 1
4Q LOSS WILD-TYPE | 92 | 34 | 43 | 22

Figure S36. Get High-res Image Gene #28: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'4q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 6.65e-05 (Fisher's exact test), Q value = 0.02

Table S37. Gene #28: '4q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 50 | 50 | 32 | 87
4Q LOSS MUTATED | 1 | 2 | 11 | 10
4Q LOSS WILD-TYPE | 49 | 48 | 21 | 77

Figure S37. Get High-res Image Gene #28: '4q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'10p loss mutation analysis' versus 'CN_CNMF'

P value = 2.3e-17 (Fisher's exact test), Q value = 7.6e-15

Table S38. Gene #36: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
10P LOSS MUTATED | 1 | 27 | 3
10P LOSS WILD-TYPE | 93 | 23 | 73

Figure S38. Get High-res Image Gene #36: '10p loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.62e-22 (Fisher's exact test), Q value = 8.8e-20

Table S39. Gene #36: '10p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
10P LOSS MUTATED | 1 | 26 | 3 | 0
10P LOSS WILD-TYPE | 99 | 8 | 55 | 23

Figure S39. Get High-res Image Gene #36: '10p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'10p loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 4.79e-19 (Chi-square test), Q value = 1.6e-16

Table S40. Gene #36: '10p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
10P LOSS MUTATED | 1 | 25 | 1 | 3 | 0
10P LOSS WILD-TYPE | 59 | 17 | 34 | 67 | 11

Figure S40. Get High-res Image Gene #36: '10p loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'10q loss mutation analysis' versus 'CN_CNMF'

P value = 3.46e-16 (Fisher's exact test), Q value = 1.1e-13

Table S41. Gene #37: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
10Q LOSS MUTATED | 2 | 27 | 3
10Q LOSS WILD-TYPE | 92 | 23 | 73

Figure S41. Get High-res Image Gene #37: '10q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'10q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.77e-21 (Fisher's exact test), Q value = 9.3e-19

Table S42. Gene #37: '10q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
10Q LOSS MUTATED | 2 | 26 | 3 | 0
10Q LOSS WILD-TYPE | 98 | 8 | 55 | 23

Figure S42. Get High-res Image Gene #37: '10q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'10q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 3.81e-20 (Chi-square test), Q value = 1.3e-17

Table S43. Gene #37: '10q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
10Q LOSS MUTATED | 1 | 26 | 1 | 3 | 0
10Q LOSS WILD-TYPE | 59 | 16 | 34 | 67 | 11

Figure S43. Get High-res Image Gene #37: '10q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'14q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000835 (Fisher's exact test), Q value = 0.24

Table S44. Gene #42: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
14Q LOSS MUTATED | 8 | 11 | 5 | 0
14Q LOSS WILD-TYPE | 92 | 23 | 53 | 23

Figure S44. Get High-res Image Gene #42: '14q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19q loss mutation analysis' versus 'CN_CNMF'

P value = 1.4e-45 (Fisher's exact test), Q value = 4.8e-43

Table S45. Gene #48: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
19Q LOSS MUTATED | 2 | 3 | 71
19Q LOSS WILD-TYPE | 92 | 47 | 5

Figure S45. Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.01e-36 (Fisher's exact test), Q value = 3.4e-34

Table S46. Gene #48: '19q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
19Q LOSS MUTATED | 8 | 2 | 57 | 6
19Q LOSS WILD-TYPE | 92 | 32 | 1 | 17

Figure S46. Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'19q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 9.57e-22 (Chi-square test), Q value = 3.2e-19

Table S47. Gene #48: '19q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
19Q LOSS MUTATED | 4 | 1 | 33 | 36 | 2
19Q LOSS WILD-TYPE | 56 | 41 | 2 | 34 | 9

Figure S47. Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'19q loss mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.5e-27 (Fisher's exact test), Q value = 1.5e-24

Table S48. Gene #48: '19q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 117 | 69
19Q LOSS MUTATED | 32 | 9 | 35
19Q LOSS WILD-TYPE | 0 | 108 | 34

Figure S48. Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss mutation analysis' versus 'MIRSEQ_CNMF'

P value = 3.01e-17 (Fisher's exact test), Q value = 9.9e-15

Table S49. Gene #48: '19q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 50 | 50 | 32 | 87
19Q LOSS MUTATED | 4 | 3 | 26 | 43
19Q LOSS WILD-TYPE | 46 | 47 | 6 | 44

Figure S49. Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'19q loss mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.32e-05 (Fisher's exact test), Q value = 0.01

Table S50. Gene #48: '19q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 88 | 13 | 118
19Q LOSS MUTATED | 46 | 2 | 28
19Q LOSS WILD-TYPE | 42 | 11 | 90

Figure S50. Get High-res Image Gene #48: '19q loss mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss mutation analysis' versus 'CN_CNMF'

P value = 7.15e-06 (Fisher's exact test), Q value = 0.0023

Table S51. Gene #50: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 50 | 76
22Q LOSS MUTATED | 4 | 11 | 0
22Q LOSS WILD-TYPE | 90 | 39 | 76

Figure S51. Get High-res Image Gene #50: '22q loss mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'22q loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.34e-05 (Fisher's exact test), Q value = 0.019

Table S52. Gene #50: '22q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 100 | 34 | 58 | 23
22Q LOSS MUTATED | 6 | 9 | 0 | 0
22Q LOSS WILD-TYPE | 94 | 25 | 58 | 23

Figure S52. Get High-res Image Gene #50: '22q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

'22q loss mutation analysis' versus 'MRNASEQ_CNMF'

P value = 1.92e-05 (Chi-square test), Q value = 0.006

Table S53. Gene #50: '22q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 60 | 42 | 35 | 70 | 11
22Q LOSS MUTATED | 1 | 10 | 0 | 3 | 0
22Q LOSS WILD-TYPE | 59 | 32 | 35 | 67 | 11

Figure S53. Get High-res Image Gene #50: '22q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

Methods & Data
Input

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

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

- Number of patients = 220

- Number of significantly arm-level cnvs = 51

- 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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