Correlation between copy number variations of arm-level result and molecular subtypes
Brain Lower Grade Glioma (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C19S1P81
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C19S1P81
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, 49 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'.

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

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

- 20q gain cnv correlated to 'CN_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'.

- 11p 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, 49 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 (0.974) | 0.00862 (1.00) | 4.56e-47 (1.57e-44) | 1.46e-42 (4.96e-40) | 1.61e-24 (5.41e-22) | 1.37e-30 (4.66e-28) | 1.41e-19 (4.72e-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) | 9.63e-33 (3.27e-30) | 9.57e-22 (3.22e-19) | 4.5e-27 (1.52e-24) | 3.01e-17 (9.94e-15) | 3.32e-05 (0.0103)
7p gain | 37 (17%) | 183 | 0.175 (1.00) | 0.162 (1.00) | 1.86e-17 (6.17e-15) | 3.65e-07 (0.000118) | 8.17e-12 (2.65e-09) | 0.000204 (0.0615) | 0.000552 (0.164) | 0.0071 (1.00)
4p loss | 15 (7%) | 205 | 0.415 (1.00) | 0.329 (1.00) | 0.000882 (0.259) | 0.000169 (0.0513) | 0.000108 (0.0328) | 0.000418 (0.125) | 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 (2.21e-12) | 6.01e-06 (0.00192) | 6.56e-08 (2.13e-05) | 0.00139 (0.396) | 0.00423 (1.00) | 0.128 (1.00)
1q loss | 9 (4%) | 211 | 0.0889 (1.00) | 0.0971 (1.00) | 8.38e-05 (0.0256) | 3.23e-05 (0.01) | 0.00603 (1.00) | 0.00013 (0.0397) | 0.0106 (1.00) | 0.715 (1.00)
10p loss | 31 (14%) | 189 | 0.271 (1.00) | 0.241 (1.00) | 2.3e-17 (7.62e-15) | 7.92e-17 (2.61e-14) | 4.79e-19 (1.59e-16) | 0.0016 (0.454) | 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) | 6.63e-16 (2.17e-13) | 3.81e-20 (1.28e-17) | 0.00109 (0.318) | 0.0128 (1.00) | 0.0178 (1.00)
22q loss | 15 (7%) | 205 | 1 (1.00) | 0.763 (1.00) | 7.15e-06 (0.00227) | 0.00075 (0.221) | 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) | 2.89e-05 (0.00905) | 0.0175 (1.00) | 0.094 (1.00) | 0.54 (1.00) | 0.93 (1.00)
19q gain | 9 (4%) | 211 |  |  | 0.00034 (0.102) | 0.0103 (1.00) | 0.000336 (0.101) | 0.0217 (1.00) | 0.115 (1.00) | 0.162 (1.00)
20p gain | 17 (8%) | 203 |  |  | 1.66e-05 (0.00528) | 0.00225 (0.627) | 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 (0.0247) | 0.00128 (0.365) | 7.35e-08 (2.37e-05) | 0.0252 (1.00) | 0.00356 (0.966) | 0.0462 (1.00)
4q loss | 24 (11%) | 196 | 0.839 (1.00) | 0.828 (1.00) | 0.0049 (1.00) | 0.000613 (0.181) | 0.002 (0.56) | 0.00355 (0.966) | 6.65e-05 (0.0205) | 0.6 (1.00)
1p gain | 6 (3%) | 214 |  |  | 0.0272 (1.00) | 0.115 (1.00) | 3.39e-05 (0.0105) | 0.103 (1.00) | 0.234 (1.00) | 0.208 (1.00)
19p gain | 11 (5%) | 209 |  |  | 2.25e-05 (0.00708) | 0.00124 (0.356) | 0.00122 (0.353) | 0.0102 (1.00) | 0.0861 (1.00) | 0.0595 (1.00)
11p loss | 20 (9%) | 200 | 0.815 (1.00) | 0.526 (1.00) | 0.00199 (0.56) | 0.000474 (0.141) | 0.0162 (1.00) | 0.00897 (1.00) | 0.0113 (1.00) | 0.0469 (1.00)
1q gain | 8 (4%) | 212 |  |  | 0.00126 (0.362) | 0.0898 (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) | 0.426 (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) | 0.26 (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) | 0.0872 (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) | 0.355 (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) | 0.274 (1.00) | 0.00231 (0.642) | 0.519 (1.00) | 0.747 (1.00) | 0.37 (1.00)
11p gain | 9 (4%) | 211 |  |  | 0.5 (1.00) | 0.192 (1.00) | 0.00395 (1.00) | 0.00261 (0.717) | 0.138 (1.00) | 0.426 (1.00)
11q gain | 14 (6%) | 206 |  |  | 0.353 (1.00) | 0.301 (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) | 0.179 (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) | 0.885 (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) | 0.504 (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) | 0.709 (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) | 0.504 (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) | 0.109 (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) | 0.0317 (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) | 0.0734 (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) | 0.0431 (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) | 0.0237 (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) |  | 0.571 (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 (0.791) | 0.0555 (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) | 0.0542 (1.00) | 0.0111 (1.00) | 0.000882 (0.259) | 0.00806 (1.00) | 0.795 (1.00)
11q loss | 4 (2%) | 216 |  |  | 0.00243 (0.669) | 0.238 (1.00) | 0.00187 (0.527) | 0.279 (1.00) | 0.697 (1.00) | 0.0958 (1.00)
12q loss | 8 (4%) | 212 |  |  | 0.0444 (1.00) | 0.153 (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) | 0.171 (1.00) | 0.86 (1.00) | 0.537 (1.00) | 0.914 (1.00) | 0.364 (1.00)
14q loss | 24 (11%) | 196 |  |  | 0.00111 (0.322) | 0.0183 (1.00) | 0.00126 (0.362) | 0.452 (1.00) | 0.0127 (1.00) | 0.103 (1.00)
15q loss | 12 (5%) | 208 |  |  | 0.00582 (1.00) | 0.0161 (1.00) | 0.000977 (0.285) | 0.00504 (1.00) | 0.248 (1.00) | 0.89 (1.00)
16q loss | 6 (3%) | 214 |  |  | 0.662 (1.00) | 0.115 (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) | 0.0484 (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 (0.807) | 0.00953 (1.00) | 0.0024 (0.664) | 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) | 0.0581 (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) | 0.423 (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) | 0.203 (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 = 6.2e-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 = 3.65e-07 (Fisher's exact test), Q value = 0.00012

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
7P GAIN MUTATED | 10 | 17 | 2 | 2
7P GAIN WILD-TYPE | 66 | 14 | 17 | 47

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 = 0.062

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 = 6.01e-06 (Fisher's exact test), Q value = 0.0019

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
7Q GAIN MUTATED | 16 | 19 | 3 | 5
7Q GAIN WILD-TYPE | 60 | 12 | 16 | 44

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 = 2.89e-05 (Fisher's exact test), Q value = 0.009

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
10P GAIN MUTATED | 17 | 0 | 1 | 0
10P GAIN WILD-TYPE | 59 | 31 | 18 | 49

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'

'19q gain mutation analysis' versus 'CN_CNMF'

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

Table S13. 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 S13. Get High-res Image Gene #17: '19q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'19q gain mutation analysis' versus 'MRNASEQ_CNMF'

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

Table S14. 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 S14. 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 S15. 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 S15. Get High-res Image Gene #18: '20p gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20p gain mutation analysis' versus 'MRNASEQ_CNMF'

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

Table S16. 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 S16. 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 = 0.025

Table S17. 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 S17. Get High-res Image Gene #19: '20q gain mutation analysis' versus Clinical Feature #3: 'CN_CNMF'

'20q gain mutation analysis' versus 'MRNASEQ_CNMF'

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

Table S18. 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 S18. 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 S19. 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 S19. 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 = 1.46e-42 (Fisher's exact test), Q value = 5e-40

Table S20. Gene #21: '1p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
1P LOSS MUTATED | 0 | 0 | 4 | 49
1P LOSS WILD-TYPE | 76 | 31 | 15 | 0

Figure S20. 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 S21. 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 S21. 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 S22. 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 S22. 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 S23. 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 S23. 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 S24. 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 S24. 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 = 0.026

Table S25. 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 S25. 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 = 3.23e-05 (Fisher's exact test), Q value = 0.01

Table S26. Gene #22: '1q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
1Q LOSS MUTATED | 0 | 0 | 0 | 9
1Q LOSS WILD-TYPE | 76 | 31 | 19 | 40

Figure S26. 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 = 0.04

Table S27. 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 S27. 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 = 0.000169 (Fisher's exact test), Q value = 0.051

Table S28. Gene #27: '4p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
4P LOSS MUTATED | 3 | 0 | 0 | 12
4P LOSS WILD-TYPE | 73 | 31 | 19 | 37

Figure S28. 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 = 0.033

Table S29. 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 S29. 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 = 0.13

Table S30. 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 S30. 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 S31. 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 S31. 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 = 0.000613 (Fisher's exact test), Q value = 0.18

Table S32. Gene #28: '4q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
4Q LOSS MUTATED | 8 | 1 | 0 | 15
4Q LOSS WILD-TYPE | 68 | 30 | 19 | 34

Figure S32. 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 S33. 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 S33. 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 S34. 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 S34. 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 = 7.92e-17 (Fisher's exact test), Q value = 2.6e-14

Table S35. Gene #36: '10p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
10P LOSS MUTATED | 1 | 22 | 0 | 3
10P LOSS WILD-TYPE | 75 | 9 | 19 | 46

Figure S35. 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 S36. 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 S36. 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 S37. 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 S37. 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 = 6.63e-16 (Fisher's exact test), Q value = 2.2e-13

Table S38. Gene #37: '10q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
10Q LOSS MUTATED | 2 | 22 | 0 | 3
10Q LOSS WILD-TYPE | 74 | 9 | 19 | 46

Figure S38. 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 S39. 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 S39. Get High-res Image Gene #37: '10q loss mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'11p loss mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000474 (Fisher's exact test), Q value = 0.14

Table S40. Gene #38: '11p loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
11P LOSS MUTATED | 15 | 2 | 0 | 0
11P LOSS WILD-TYPE | 61 | 29 | 19 | 49

Figure S40. Get High-res Image Gene #38: '11p 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 S41. 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 S41. 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 = 9.63e-33 (Fisher's exact test), Q value = 3.3e-30

Table S42. Gene #48: '19q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
19Q LOSS MUTATED | 7 | 1 | 4 | 49
19Q LOSS WILD-TYPE | 69 | 30 | 15 | 0

Figure S42. 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 S43. 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 S43. 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 S44. 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 S44. 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 S45. 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 S45. 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 S46. 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 S46. 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 S47. 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 S47. 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 = 0.00075 (Fisher's exact test), Q value = 0.22

Table S48. Gene #50: '22q loss mutation analysis' versus Clinical Feature #4: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 31 | 19 | 49
22Q LOSS MUTATED | 5 | 8 | 1 | 0
22Q LOSS WILD-TYPE | 71 | 23 | 18 | 49

Figure S48. 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 S49. 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 S49. 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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