Thyroid Adenocarcinoma: Correlation between gene mutation status 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 significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 41 genes and 8 molecular subtypes across 323 patients, 20 significant findings detected with P value < 0.05 and Q value < 0.25.

- BRAF mutation correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- HRAS mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- NRAS mutation correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 41 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 20 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL
| nMutated (%) | 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
BRAF | 183 (57%) | 140 | 0.0194 (1.00) | 3.62e-38 (9.99e-36) | 9.4e-07 (0.000252) | 2.51e-11 (6.84e-09) | 4.03e-46 (1.13e-43) | 1.56e-39 (4.31e-37) | 9.88e-42 (2.75e-39) | 1.03e-43 (2.86e-41)
HRAS | 12 (4%) | 311 | 0.000222 (0.0582) | 1.48e-06 (0.000393) | 9.23e-05 (0.0243) | 0.00529 (1.00) | 1.37e-05 (0.00362) | 6.79e-06 (0.0018) | 1.31e-06 (0.00035) | 3.85e-07 (0.000104)
NRAS | 26 (8%) | 297 | 0.00692 (1.00) | 6.06e-14 (1.67e-11) | 1 (1.00) | 0.000583 (0.152) | 4.7e-11 (1.27e-08) | 4.03e-11 (1.09e-08) | 9.19e-13 (2.51e-10) | 2.47e-13 (6.78e-11)
EMG1 | 6 (2%) | 317 | 0.548 (1.00) | 1 (1.00) | 0.327 (1.00) | 0.0846 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.778 (1.00)
PTTG1IP | 4 (1%) | 319 | 1 (1.00) | 1 (1.00) |  |  | 0.242 (1.00) | 0.252 (1.00) | 0.469 (1.00) | 0.393 (1.00)
RPTN | 8 (2%) | 315 | 0.805 (1.00) | 0.442 (1.00) | 0.265 (1.00) | 0.801 (1.00) | 0.0249 (1.00) | 0.415 (1.00) | 0.82 (1.00) | 0.666 (1.00)
EIF1AX | 5 (2%) | 318 | 0.731 (1.00) | 0.0278 (1.00) | 0.444 (1.00) | 0.132 (1.00) | 0.0621 (1.00) | 0.0109 (1.00) | 0.0581 (1.00) | 0.236 (1.00)
CCDC15 | 5 (2%) | 318 | 0.731 (1.00) | 0.115 (1.00) | 1 (1.00) | 0.381 (1.00) | 0.132 (1.00) | 0.136 (1.00) | 0.63 (1.00) | 0.53 (1.00)
ZNF845 | 6 (2%) | 317 | 0.42 (1.00) | 0.637 (1.00) | 0.639 (1.00) | 0.125 (1.00) | 0.943 (1.00) | 0.166 (1.00) | 0.777 (1.00) | 0.328 (1.00)
ZNF878 | 4 (1%) | 319 | 1 (1.00) | 0.487 (1.00) |  |  | 0.0454 (1.00) | 0.833 (1.00) | 0.691 (1.00) | 1 (1.00)
TG | 16 (5%) | 307 | 1 (1.00) | 0.0205 (1.00) | 0.34 (1.00) | 0.492 (1.00) | 0.406 (1.00) | 0.293 (1.00) | 0.0452 (1.00) | 0.0253 (1.00)
PRB2 | 6 (2%) | 317 | 1 (1.00) | 0.637 (1.00) | 0.0801 (1.00) | 0.851 (1.00) | 0.474 (1.00) | 0.723 (1.00) | 0.522 (1.00) | 0.598 (1.00)
R3HDM2 | 4 (1%) | 319 | 0.0124 (1.00) | 0.063 (1.00) |  |  | 0.0699 (1.00) | 0.0388 (1.00) | 0.0191 (1.00) | 0.00822 (1.00)
IL32 | 3 (1%) | 320 | 1 (1.00) | 0.742 (1.00) |  |  | 1 (1.00) | 0.78 (1.00) | 0.202 (1.00) | 0.645 (1.00)
TMCO2 | 3 (1%) | 320 | 1 (1.00) | 0.416 (1.00) | 0.778 (1.00) | 0.2 (1.00) | 0.492 (1.00) | 0.303 (1.00) | 0.401 (1.00) | 0.778 (1.00)
PPTC7 | 3 (1%) | 320 | 0.0791 (1.00) | 0.0627 (1.00) |  |  | 0.172 (1.00) | 0.0916 (1.00) | 0.299 (1.00) | 0.403 (1.00)
MUC7 | 5 (2%) | 318 | 0.731 (1.00) | 0.372 (1.00) | 0.683 (1.00) | 0.26 (1.00) | 0.805 (1.00) | 0.848 (1.00) | 0.866 (1.00) | 0.629 (1.00)
LYPD3 | 3 (1%) | 320 | 0.547 (1.00) | 0.416 (1.00) |  |  | 0.492 (1.00) | 0.303 (1.00) | 0.644 (1.00) | 0.778 (1.00)
TMEM90B | 3 (1%) | 320 | 0.135 (1.00) | 1 (1.00) |  |  | 1 (1.00) | 0.78 (1.00) | 1 (1.00) | 1 (1.00)
ZNF799 | 5 (2%) | 318 | 0.465 (1.00) | 1 (1.00) | 0.505 (1.00) | 1 (1.00) | 0.592 (1.00) | 0.848 (1.00) | 0.451 (1.00) | 1 (1.00)
PPM1D | 5 (2%) | 318 | 1 (1.00) | 1 (1.00) | 0.778 (1.00) | 0.125 (1.00) | 0.693 (1.00) | 0.848 (1.00) | 0.866 (1.00) | 0.329 (1.00)
MAP3K3 | 4 (1%) | 319 | 0.061 (1.00) | 0.224 (1.00) | 0.459 (1.00) | 0.0846 (1.00) | 0.274 (1.00) | 0.184 (1.00) | 0.469 (1.00) | 0.555 (1.00)
TROAP | 3 (1%) | 320 | 1 (1.00) | 0.742 (1.00) | 0.778 (1.00) | 0.535 (1.00) | 0.746 (1.00) | 1 (1.00) | 0.519 (1.00) | 0.403 (1.00)
SYNPO2L | 3 (1%) | 320 | 0.547 (1.00) | 1 (1.00) |  |  | 1 (1.00) | 0.78 (1.00) | 1 (1.00) | 1 (1.00)
ATAD2 | 4 (1%) | 319 | 1 (1.00) | 0.823 (1.00) |  |  | 0.808 (1.00) | 1 (1.00) | 0.691 (1.00) | 1 (1.00)
KRAS | 3 (1%) | 320 | 1 (1.00) | 0.0627 (1.00) |  |  | 0.172 (1.00) | 0.0916 (1.00) | 0.0616 (1.00) | 0.0276 (1.00)
SLC5A11 | 3 (1%) | 320 | 0.547 (1.00) | 0.742 (1.00) |  |  |  |  | 0.299 (1.00) | 0.403 (1.00)
PRG4 | 4 (1%) | 319 | 0.23 (1.00) | 0.104 (1.00) |  |  | 0.0128 (1.00) | 0.142 (1.00) | 0.469 (1.00) | 0.555 (1.00)
SCUBE2 | 3 (1%) | 320 | 1 (1.00) | 0.281 (1.00) |  |  | 0.314 (1.00) | 0.303 (1.00) | 0.644 (1.00) | 0.522 (1.00)
ZNF479 | 3 (1%) | 320 | 1 (1.00) | 0.742 (1.00) |  |  | 1 (1.00) | 0.78 (1.00) | 0.519 (1.00) | 1 (1.00)
SREBF2 | 3 (1%) | 320 | 1 (1.00) | 0.742 (1.00) |  |  | 0.568 (1.00) | 1 (1.00) | 0.401 (1.00) | 0.778 (1.00)
SLC26A11 | 3 (1%) | 320 | 0.0791 (1.00) | 1 (1.00) |  |  | 0.368 (1.00) | 0.78 (1.00) | 0.778 (1.00) | 0.301 (1.00)
TSC22D1 | 3 (1%) | 320 | 1 (1.00) | 1 (1.00) |  |  | 0.746 (1.00) | 1 (1.00) | 0.778 (1.00) | 0.645 (1.00)
ANKRD30A | 5 (2%) | 318 | 0.731 (1.00) | 0.462 (1.00) |  |  | 0.749 (1.00) | 0.507 (1.00) | 0.74 (1.00) | 0.865 (1.00)
FAM155A | 4 (1%) | 319 | 0.144 (1.00) | 0.156 (1.00) | 0.778 (1.00) | 0.535 (1.00) |  |  | 0.0372 (1.00) | 0.555 (1.00)
SLA | 3 (1%) | 320 | 0.547 (1.00) | 0.0627 (1.00) | 0.286 (1.00) | 0.285 (1.00) | 0.172 (1.00) | 0.0916 (1.00) | 0.0616 (1.00) | 0.0276 (1.00)
ZFHX3 | 10 (3%) | 313 | 0.171 (1.00) | 0.616 (1.00) | 0.48 (1.00) | 0.632 (1.00) | 0.794 (1.00) | 0.437 (1.00) | 0.613 (1.00) | 0.723 (1.00)
ARMCX3 | 3 (1%) | 320 | 0.547 (1.00) | 0.742 (1.00) |  |  | 0.646 (1.00) | 0.213 (1.00) | 0.519 (1.00) | 0.202 (1.00)
SLC25A45 | 3 (1%) | 320 | 0.135 (1.00) | 1 (1.00) |  |  |  |  | 0.202 (1.00) | 0.403 (1.00)
COL5A3 | 6 (2%) | 317 | 0.752 (1.00) | 0.317 (1.00) | 0.778 (1.00) | 0.758 (1.00) | 0.044 (1.00) | 0.753 (1.00) | 0.877 (1.00) | 0.523 (1.00)
CDC27 | 3 (1%) | 320 | 1 (1.00) | 1 (1.00) |  |  | 0.368 (1.00) | 0.0446 (1.00) | 0.778 (1.00) | 0.301 (1.00)

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.62e-38 (Fisher's exact test), Q value = 1e-35

Table S1. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 52 | 166
BRAF MUTATED | 10 | 30 | 143
BRAF WILD-TYPE | 95 | 22 | 23

Figure S1. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 9.4e-07 (Fisher's exact test), Q value = 0.00025

Table S2. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 62 | 76 | 79
BRAF MUTATED | 19 | 57 | 42
BRAF WILD-TYPE | 43 | 19 | 37

Figure S2. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 2.51e-11 (Fisher's exact test), Q value = 6.8e-09

Table S3. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 96 | 32 | 89
BRAF MUTATED | 30 | 16 | 72
BRAF WILD-TYPE | 66 | 16 | 17

Figure S3. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.03e-46 (Fisher's exact test), Q value = 1.1e-43

Table S4. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 102 | 36 | 70 | 95
BRAF MUTATED | 6 | 20 | 57 | 90
BRAF WILD-TYPE | 96 | 16 | 13 | 5

Figure S4. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.56e-39 (Fisher's exact test), Q value = 4.3e-37

Table S5. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 110 | 136 | 57
BRAF MUTATED | 11 | 120 | 42
BRAF WILD-TYPE | 99 | 16 | 15

Figure S5. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 9.88e-42 (Fisher's exact test), Q value = 2.7e-39

Table S6. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 119 | 98
BRAF MUTATED | 6 | 103 | 73
BRAF WILD-TYPE | 99 | 16 | 25

Figure S6. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.03e-43 (Fisher's exact test), Q value = 2.9e-41

Table S7. Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 118 | 106 | 98
BRAF MUTATED | 94 | 86 | 2
BRAF WILD-TYPE | 24 | 20 | 96

Figure S7. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000222 (Fisher's exact test), Q value = 0.058

Table S8. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 25 | 246 | 49
HRAS MUTATED | 0 | 4 | 8
HRAS WILD-TYPE | 25 | 242 | 41

Figure S8. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.48e-06 (Fisher's exact test), Q value = 0.00039

Table S9. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 52 | 166
HRAS MUTATED | 12 | 0 | 0
HRAS WILD-TYPE | 93 | 52 | 166

Figure S9. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.024

Table S10. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 62 | 76 | 79
HRAS MUTATED | 9 | 2 | 0
HRAS WILD-TYPE | 53 | 74 | 79

Figure S10. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.37e-05 (Fisher's exact test), Q value = 0.0036

Table S11. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 102 | 36 | 70 | 95
HRAS MUTATED | 12 | 0 | 0 | 0
HRAS WILD-TYPE | 90 | 36 | 70 | 95

Figure S11. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.79e-06 (Fisher's exact test), Q value = 0.0018

Table S12. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 110 | 136 | 57
HRAS MUTATED | 12 | 0 | 0
HRAS WILD-TYPE | 98 | 136 | 57

Figure S12. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.00035

Table S13. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 119 | 98
HRAS MUTATED | 12 | 0 | 0
HRAS WILD-TYPE | 93 | 119 | 98

Figure S13. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.85e-07 (Fisher's exact test), Q value = 1e-04

Table S14. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 118 | 106 | 98
HRAS MUTATED | 0 | 0 | 12
HRAS WILD-TYPE | 118 | 106 | 86

Figure S14. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.06e-14 (Fisher's exact test), Q value = 1.7e-11

Table S15. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 52 | 166
NRAS MUTATED | 26 | 0 | 0
NRAS WILD-TYPE | 79 | 52 | 166

Figure S15. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.000583 (Fisher's exact test), Q value = 0.15

Table S16. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 96 | 32 | 89
NRAS MUTATED | 9 | 5 | 0
NRAS WILD-TYPE | 87 | 27 | 89

Figure S16. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.7e-11 (Fisher's exact test), Q value = 1.3e-08

Table S17. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 102 | 36 | 70 | 95
NRAS MUTATED | 23 | 0 | 0 | 0
NRAS WILD-TYPE | 79 | 36 | 70 | 95

Figure S17. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.03e-11 (Fisher's exact test), Q value = 1.1e-08

Table S18. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 110 | 136 | 57
NRAS MUTATED | 23 | 0 | 0
NRAS WILD-TYPE | 87 | 136 | 57

Figure S18. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 9.19e-13 (Fisher's exact test), Q value = 2.5e-10

Table S19. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 119 | 98
NRAS MUTATED | 25 | 0 | 1
NRAS WILD-TYPE | 80 | 119 | 97

Figure S19. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.47e-13 (Fisher's exact test), Q value = 6.8e-11

Table S20. Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 118 | 106 | 98
NRAS MUTATED | 1 | 0 | 25
NRAS WILD-TYPE | 117 | 106 | 73

Figure S20. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data
Input

- Mutation data file = THCA-TP.mutsig.cluster.txt

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

- Number of patients = 323

- Number of significantly mutated genes = 41

- 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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