Correlation between gene mutation status and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
21 April 2013 | analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1V122S2
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Thyroid Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1V122S2
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 (1.01e-35) | 9.4e-07 (0.000255) | 2.51e-11 (6.84e-09) | 3.88e-49 (1.09e-46) | 7.76e-49 (2.18e-46) | 2.35e-40 (6.57e-38) | 3.32e-43 (9.29e-41)
HRAS | 12 (4%) | 311 | 0.000222 (0.0586) | 1.48e-06 (0.000399) | 9.23e-05 (0.0245) | 0.00529 (1.00) | 1.71e-05 (0.00454) | 5.23e-06 (0.0014) | 1.69e-06 (0.000453) | 9.25e-06 (0.00247)
NRAS | 26 (8%) | 297 | 0.00692 (1.00) | 6.06e-14 (1.68e-11) | 1 (1.00) | 0.000583 (0.153) | 1.63e-12 (4.47e-10) | 1.11e-13 (3.08e-11) | 1.87e-12 (5.13e-10) | 3.3e-12 (9.02e-10)
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) | 1 (1.00)
PTTG1IP | 4 (1%) | 319 | 1 (1.00) | 1 (1.00) |  |  | 0.223 (1.00) | 0.451 (1.00) | 0.471 (1.00) | 0.396 (1.00)
RPTN | 8 (2%) | 315 | 0.805 (1.00) | 0.442 (1.00) | 0.265 (1.00) | 0.801 (1.00) | 0.0267 (1.00) | 0.663 (1.00) | 0.74 (1.00) | 0.672 (1.00)
EIF1AX | 5 (2%) | 318 | 0.731 (1.00) | 0.0278 (1.00) | 0.444 (1.00) | 0.132 (1.00) | 0.0654 (1.00) | 0.0257 (1.00) | 0.0634 (1.00) | 0.199 (1.00)
CCDC15 | 5 (2%) | 318 | 0.731 (1.00) | 0.115 (1.00) | 1 (1.00) | 0.381 (1.00) | 0.211 (1.00) | 0.327 (1.00) | 0.627 (1.00) | 0.108 (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) | 0.552 (1.00) | 0.875 (1.00) | 0.334 (1.00)
ZNF878 | 4 (1%) | 319 | 1 (1.00) | 0.487 (1.00) |  |  | 0.0475 (1.00) | 0.561 (1.00) | 0.694 (1.00) | 1 (1.00)
TG | 16 (5%) | 307 | 1 (1.00) | 0.0205 (1.00) | 0.34 (1.00) | 0.492 (1.00) | 0.145 (1.00) | 0.0643 (1.00) | 0.0453 (1.00) | 0.021 (1.00)
PRB2 | 6 (2%) | 317 | 1 (1.00) | 0.637 (1.00) | 0.0801 (1.00) | 0.851 (1.00) | 0.415 (1.00) | 0.623 (1.00) | 0.529 (1.00) | 0.518 (1.00)
R3HDM2 | 4 (1%) | 319 | 0.0124 (1.00) | 0.063 (1.00) |  |  | 0.0598 (1.00) | 0.0654 (1.00) | 0.021 (1.00) | 0.00694 (1.00)
IL32 | 3 (1%) | 320 | 1 (1.00) | 0.742 (1.00) |  |  | 1 (1.00) | 1 (1.00) | 0.209 (1.00) | 1 (1.00)
TMCO2 | 3 (1%) | 320 | 1 (1.00) | 0.416 (1.00) | 0.778 (1.00) | 0.2 (1.00) | 0.5 (1.00) | 0.214 (1.00) | 0.418 (1.00) | 0.778 (1.00)
PPTC7 | 3 (1%) | 320 | 0.0791 (1.00) | 0.0627 (1.00) |  |  | 0.174 (1.00) | 0.0688 (1.00) | 0.312 (1.00) | 0.292 (1.00)
MUC7 | 5 (2%) | 318 | 0.731 (1.00) | 0.372 (1.00) | 0.683 (1.00) | 0.26 (1.00) | 0.806 (1.00) | 0.908 (1.00) | 0.869 (1.00) | 0.631 (1.00)
LYPD3 | 3 (1%) | 320 | 0.547 (1.00) | 0.416 (1.00) |  |  | 0.5 (1.00) | 0.427 (1.00) | 0.653 (1.00) | 0.778 (1.00)
TMEM90B | 3 (1%) | 320 | 0.135 (1.00) | 1 (1.00) |  |  | 1 (1.00) | 1 (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) | 0.598 (1.00) | 0.908 (1.00) | 0.453 (1.00) | 1 (1.00)
PPM1D | 5 (2%) | 318 | 1 (1.00) | 1 (1.00) | 0.778 (1.00) | 0.125 (1.00) | 0.695 (1.00) | 0.212 (1.00) | 0.869 (1.00) | 0.328 (1.00)
MAP3K3 | 4 (1%) | 319 | 0.061 (1.00) | 0.224 (1.00) | 0.459 (1.00) | 0.0846 (1.00) | 0.117 (1.00) | 0.313 (1.00) | 0.471 (1.00) | 0.557 (1.00)
TROAP | 3 (1%) | 320 | 1 (1.00) | 0.742 (1.00) | 0.778 (1.00) | 0.535 (1.00) | 0.751 (1.00) | 0.85 (1.00) | 0.533 (1.00) | 1 (1.00)
SYNPO2L | 3 (1%) | 320 | 0.547 (1.00) | 1 (1.00) |  |  | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
ATAD2 | 4 (1%) | 319 | 1 (1.00) | 0.823 (1.00) |  |  | 0.813 (1.00) | 0.561 (1.00) | 0.694 (1.00) | 1 (1.00)
KRAS | 3 (1%) | 320 | 1 (1.00) | 0.0627 (1.00) |  |  | 0.174 (1.00) | 0.0974 (1.00) | 0.0661 (1.00) | 0.0243 (1.00)
SLC5A11 | 3 (1%) | 320 | 0.547 (1.00) | 0.742 (1.00) |  |  | 0.657 (1.00) | 0.365 (1.00) | 0.312 (1.00) | 0.292 (1.00)
PRG4 | 4 (1%) | 319 | 0.23 (1.00) | 0.104 (1.00) |  |  | 0.0143 (1.00) | 0.028 (1.00) | 0.471 (1.00) | 0.557 (1.00)
SCUBE2 | 3 (1%) | 320 | 1 (1.00) | 0.281 (1.00) |  |  | 0.32 (1.00) | 0.259 (1.00) | 0.653 (1.00) | 0.643 (1.00)
ZNF479 | 3 (1%) | 320 | 1 (1.00) | 0.742 (1.00) |  |  | 1 (1.00) | 1 (1.00) | 0.533 (1.00) | 1 (1.00)
SREBF2 | 3 (1%) | 320 | 1 (1.00) | 0.742 (1.00) |  |  | 0.577 (1.00) | 0.214 (1.00) | 0.418 (1.00) | 0.778 (1.00)
SLC26A11 | 3 (1%) | 320 | 0.0791 (1.00) | 1 (1.00) |  |  | 0.375 (1.00) | 1 (1.00) | 0.776 (1.00) | 0.398 (1.00)
TSC22D1 | 3 (1%) | 320 | 1 (1.00) | 1 (1.00) |  |  | 0.751 (1.00) | 0.85 (1.00) | 1 (1.00) | 0.512 (1.00)
ANKRD30A | 5 (2%) | 318 | 0.731 (1.00) | 0.462 (1.00) |  |  | 0.75 (1.00) | 0.514 (1.00) | 0.743 (1.00) | 0.744 (1.00)
FAM155A | 4 (1%) | 319 | 0.144 (1.00) | 0.156 (1.00) | 0.778 (1.00) | 0.535 (1.00) |  |  | 0.0361 (1.00) | 1 (1.00)
SLA | 3 (1%) | 320 | 0.547 (1.00) | 0.0627 (1.00) | 0.286 (1.00) | 0.285 (1.00) | 0.174 (1.00) | 0.0974 (1.00) | 0.0661 (1.00) | 0.0243 (1.00)
ZFHX3 | 10 (3%) | 313 | 0.171 (1.00) | 0.616 (1.00) | 0.48 (1.00) | 0.632 (1.00) | 0.583 (1.00) | 0.459 (1.00) | 0.617 (1.00) | 0.721 (1.00)
ARMCX3 | 3 (1%) | 320 | 0.547 (1.00) | 0.742 (1.00) |  |  | 0.657 (1.00) | 0.132 (1.00) | 0.533 (1.00) | 0.2 (1.00)
SLC25A45 | 3 (1%) | 320 | 0.135 (1.00) | 1 (1.00) |  |  |  |  | 0.209 (1.00) | 0.292 (1.00)
COL5A3 | 6 (2%) | 317 | 0.752 (1.00) | 0.317 (1.00) | 0.778 (1.00) | 0.758 (1.00) | 0.0513 (1.00) | 0.518 (1.00) | 0.875 (1.00) | 0.596 (1.00)
CDC27 | 3 (1%) | 320 | 1 (1.00) | 1 (1.00) |  |  | 0.375 (1.00) | 0.17 (1.00) | 0.776 (1.00) | 0.398 (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 = 3.88e-49 (Fisher's exact test), Q value = 1.1e-46

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 106 | 39 | 74 | 96
BRAF MUTATED | 5 | 22 | 60 | 91
BRAF WILD-TYPE | 101 | 17 | 14 | 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 = 7.76e-49 (Fisher's exact test), Q value = 2.2e-46

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 97 | 125 | 29 | 64
BRAF MUTATED | 1 | 112 | 17 | 48
BRAF WILD-TYPE | 96 | 13 | 12 | 16

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 = 2.35e-40 (Fisher's exact test), Q value = 6.6e-38

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 106 | 114 | 102
BRAF MUTATED | 7 | 98 | 77
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 = 3.32e-43 (Fisher's exact test), Q value = 9.3e-41

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 116 | 112
BRAF MUTATED | 1 | 92 | 89
BRAF WILD-TYPE | 93 | 24 | 23

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 = 0.059

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 = 4e-04

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 = 1.71e-05 (Fisher's exact test), Q value = 0.0045

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 106 | 39 | 74 | 96
HRAS MUTATED | 12 | 0 | 0 | 0
HRAS WILD-TYPE | 94 | 39 | 74 | 96

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 = 5.23e-06 (Fisher's exact test), Q value = 0.0014

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 97 | 125 | 29 | 64
HRAS MUTATED | 12 | 0 | 0 | 0
HRAS WILD-TYPE | 85 | 125 | 29 | 64

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 = 1.69e-06 (Fisher's exact test), Q value = 0.00045

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 106 | 114 | 102
HRAS MUTATED | 12 | 0 | 0
HRAS WILD-TYPE | 94 | 114 | 102

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 = 9.25e-06 (Fisher's exact test), Q value = 0.0025

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 116 | 112
HRAS MUTATED | 11 | 0 | 1
HRAS WILD-TYPE | 83 | 116 | 111

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 = 1.63e-12 (Fisher's exact test), Q value = 4.5e-10

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 106 | 39 | 74 | 96
NRAS MUTATED | 26 | 0 | 0 | 0
NRAS WILD-TYPE | 80 | 39 | 74 | 96

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 = 1.11e-13 (Fisher's exact test), Q value = 3.1e-11

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 97 | 125 | 29 | 64
NRAS MUTATED | 26 | 0 | 0 | 0
NRAS WILD-TYPE | 71 | 125 | 29 | 64

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 = 1.87e-12 (Fisher's exact test), Q value = 5.1e-10

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 106 | 114 | 102
NRAS MUTATED | 25 | 0 | 1
NRAS WILD-TYPE | 81 | 114 | 101

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 = 3.3e-12 (Fisher's exact test), Q value = 9e-10

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 94 | 116 | 112
NRAS MUTATED | 24 | 1 | 1
NRAS WILD-TYPE | 70 | 115 | 111

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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