Correlation between gene mutation status and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1HM56JG
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 gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1HM56JG
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 32 genes and 10 molecular subtypes across 323 patients, 26 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 32 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 26 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE 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 | Fisher's exact test | Fisher's exact test
BRAF | 183 (57%) | 140 | 0.0194 (1.00) | 9.33e-39 (2.63e-36) | 9.4e-07 (0.000256) | 2.51e-11 (6.89e-09) | 7.79e-49 (2.24e-46) | 1.22e-48 (3.5e-46) | 2.35e-40 (6.66e-38) | 3.32e-43 (9.42e-41) | 5.44e-44 (1.55e-41) | 1.44e-45 (4.12e-43)
HRAS | 12 (4%) | 311 | 0.000222 (0.0586) | 2.28e-06 (0.000613) | 9.23e-05 (0.0245) | 0.00529 (1.00) | 1.46e-05 (0.00389) | 3.74e-06 (0.001) | 1.69e-06 (0.000455) | 9.25e-06 (0.00247) | 1.22e-06 (0.000331) | 3.38e-07 (9.23e-05)
NRAS | 26 (8%) | 297 | 0.00692 (1.00) | 7.17e-14 (2.01e-11) | 1 (1.00) | 0.000583 (0.153) | 8.63e-13 (2.39e-10) | 7.02e-14 (1.97e-11) | 1.87e-12 (5.16e-10) | 3.3e-12 (9.09e-10) | 8.08e-13 (2.25e-10) | 2.01e-13 (5.62e-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) | 1 (1.00) | 1 (1.00) | 1 (1.00)
PTTG1IP | 4 (1%) | 319 | 1 (1.00) | 1 (1.00) |  |  | 0.199 (1.00) | 0.418 (1.00) | 0.471 (1.00) | 0.396 (1.00) | 0.467 (1.00) | 0.556 (1.00)
RPTN | 8 (2%) | 315 | 0.805 (1.00) | 0.436 (1.00) | 0.265 (1.00) | 0.801 (1.00) | 0.0385 (1.00) | 0.22 (1.00) | 0.74 (1.00) | 0.672 (1.00) | 0.821 (1.00) | 1 (1.00)
TG | 16 (5%) | 307 | 1 (1.00) | 0.0226 (1.00) | 0.34 (1.00) | 0.492 (1.00) | 0.129 (1.00) | 0.0519 (1.00) | 0.0453 (1.00) | 0.021 (1.00) | 0.0428 (1.00) | 0.0235 (1.00)
TMCO2 | 3 (1%) | 320 | 1 (1.00) | 0.41 (1.00) | 0.778 (1.00) | 0.2 (1.00) | 0.508 (1.00) | 0.325 (1.00) | 0.418 (1.00) | 0.778 (1.00) | 0.394 (1.00) | 0.778 (1.00)
R3HDM2 | 4 (1%) | 319 | 0.0124 (1.00) | 0.0607 (1.00) |  |  | 0.136 (1.00) | 0.0869 (1.00) | 0.021 (1.00) | 0.00694 (1.00) | 0.0184 (1.00) | 0.00788 (1.00)
PRB2 | 6 (2%) | 317 | 1 (1.00) | 0.633 (1.00) | 0.0801 (1.00) | 0.851 (1.00) | 0.374 (1.00) | 0.572 (1.00) | 0.529 (1.00) | 0.518 (1.00) | 0.52 (1.00) | 0.523 (1.00)
LYPD3 | 3 (1%) | 320 | 0.547 (1.00) | 0.41 (1.00) |  |  | 0.508 (1.00) | 0.439 (1.00) | 0.653 (1.00) | 0.778 (1.00) | 0.64 (1.00) | 0.778 (1.00)
IL32 | 3 (1%) | 320 | 1 (1.00) | 0.569 (1.00) |  |  | 1 (1.00) | 0.858 (1.00) | 0.209 (1.00) | 1 (1.00) | 1 (1.00) | 0.644 (1.00)
PPM1D | 5 (2%) | 318 | 1 (1.00) | 1 (1.00) | 0.778 (1.00) | 0.125 (1.00) | 0.455 (1.00) | 0.249 (1.00) | 0.869 (1.00) | 0.328 (1.00) | 0.864 (1.00) | 0.329 (1.00)
EIF1AX | 5 (2%) | 318 | 0.731 (1.00) | 0.0268 (1.00) | 0.444 (1.00) | 0.132 (1.00) | 0.0584 (1.00) | 0.0304 (1.00) | 0.0634 (1.00) | 0.199 (1.00) | 0.056 (1.00) | 0.235 (1.00)
PPTC7 | 3 (1%) | 320 | 0.0791 (1.00) | 0.0615 (1.00) |  |  | 0.173 (1.00) | 0.108 (1.00) | 0.312 (1.00) | 0.292 (1.00) | 0.294 (1.00) | 0.301 (1.00)
SCUBE2 | 3 (1%) | 320 | 1 (1.00) | 0.273 (1.00) |  |  | 0.322 (1.00) | 0.608 (1.00) | 0.653 (1.00) | 0.643 (1.00) | 0.64 (1.00) | 0.522 (1.00)
MUC7 | 5 (2%) | 318 | 0.731 (1.00) | 0.362 (1.00) | 0.683 (1.00) | 0.26 (1.00) | 0.805 (1.00) | 0.915 (1.00) | 0.869 (1.00) | 0.631 (1.00) | 0.864 (1.00) | 0.63 (1.00)
TMEM90B | 3 (1%) | 320 | 0.135 (1.00) | 1 (1.00) |  |  | 1 (1.00) | 0.858 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00)
CCDC15 | 5 (2%) | 318 | 0.731 (1.00) | 0.147 (1.00) | 1 (1.00) | 0.381 (1.00) | 0.143 (1.00) | 0.271 (1.00) | 0.627 (1.00) | 0.108 (1.00) | 0.632 (1.00) | 0.531 (1.00)
ATAD2 | 4 (1%) | 319 | 1 (1.00) | 0.645 (1.00) |  |  | 0.814 (1.00) | 1 (1.00) | 0.694 (1.00) | 1 (1.00) | 0.689 (1.00) | 1 (1.00)
ZNF878 | 4 (1%) | 319 | 1 (1.00) | 0.48 (1.00) |  |  | 0.048 (1.00) | 0.643 (1.00) | 0.694 (1.00) | 1 (1.00) | 0.689 (1.00) | 1 (1.00)
ARMCX3 | 3 (1%) | 320 | 0.547 (1.00) | 0.569 (1.00) |  |  | 0.443 (1.00) | 0.181 (1.00) | 0.533 (1.00) | 0.2 (1.00) | 0.514 (1.00) | 0.202 (1.00)
TSC22D1 | 3 (1%) | 320 | 1 (1.00) | 1 (1.00) |  |  | 0.753 (1.00) | 1 (1.00) | 1 (1.00) | 0.512 (1.00) | 0.779 (1.00) | 0.644 (1.00)
TROAP | 3 (1%) | 320 | 1 (1.00) | 0.569 (1.00) | 0.778 (1.00) | 0.535 (1.00) | 0.753 (1.00) | 1 (1.00) | 0.533 (1.00) | 1 (1.00) | 0.294 (1.00) | 0.301 (1.00)
SYNPO2L | 3 (1%) | 320 | 0.547 (1.00) | 1 (1.00) |  |  | 1 (1.00) | 0.858 (1.00) | 1 (1.00) | 1 (1.00) | 0.779 (1.00) | 1 (1.00)
ZNF443 | 4 (1%) | 319 | 0.144 (1.00) | 0.29 (1.00) | 1 (1.00) | 1 (1.00) | 0.515 (1.00) | 0.371 (1.00) | 0.167 (1.00) | 0.107 (1.00) | 0.152 (1.00) | 0.113 (1.00)
SLC26A11 | 3 (1%) | 320 | 0.0791 (1.00) | 1 (1.00) |  |  | 0.382 (1.00) | 0.858 (1.00) | 0.776 (1.00) | 0.398 (1.00) | 0.779 (1.00) | 0.401 (1.00)
CDC27 | 3 (1%) | 320 | 1 (1.00) | 1 (1.00) |  |  | 0.382 (1.00) | 0.143 (1.00) | 0.776 (1.00) | 0.398 (1.00) | 0.779 (1.00) | 0.401 (1.00)
CHD2 | 4 (1%) | 319 | 1 (1.00) | 0.376 (1.00) | 0.639 (1.00) | 0.535 (1.00) | 0.74 (1.00) | 0.0637 (1.00) | 1 (1.00) | 0.84 (1.00) | 1 (1.00) | 0.837 (1.00)
SREBF2 | 3 (1%) | 320 | 1 (1.00) | 0.569 (1.00) |  |  | 0.583 (1.00) | 0.325 (1.00) | 0.418 (1.00) | 0.778 (1.00) | 0.394 (1.00) | 0.778 (1.00)
ACD | 3 (1%) | 320 | 0.547 (1.00) | 1 (1.00) |  |  | 0.382 (1.00) | 0.143 (1.00) | 0.209 (1.00) | 1 (1.00) | 0.199 (1.00) | 0.644 (1.00)
DNMT3A | 5 (2%) | 318 | 0.465 (1.00) | 1 (1.00) | 0.505 (1.00) | 1 (1.00) | 0.484 (1.00) | 0.782 (1.00) | 0.743 (1.00) | 0.861 (1.00) | 0.74 (1.00) | 0.864 (1.00)

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 7.17e-14 (Fisher's exact test), Q value = 2e-11

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 106 | 50 | 167
NRAS MUTATED | 26 | 0 | 0
NRAS WILD-TYPE | 80 | 50 | 167

Figure S1. Get High-res Image Gene #1: '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 S2. Gene #1: '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 S2. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8.63e-13 (Fisher's exact test), Q value = 2.4e-10

Table S3. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 105 | 39 | 77 | 94
NRAS MUTATED | 26 | 0 | 0 | 0
NRAS WILD-TYPE | 79 | 39 | 77 | 94

Figure S3. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.02e-14 (Fisher's exact test), Q value = 2e-11

Table S4. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 61 | 124 | 96 | 34
NRAS MUTATED | 0 | 0 | 26 | 0
NRAS WILD-TYPE | 61 | 124 | 70 | 34

Figure S4. Get High-res Image Gene #1: '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 = 5.2e-10

Table S5. Gene #1: '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 S5. Get High-res Image Gene #1: '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 = 9.1e-10

Table S6. Gene #1: '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 S6. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.08e-13 (Fisher's exact test), Q value = 2.2e-10

Table S7. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 121 | 96
NRAS MUTATED | 25 | 0 | 1
NRAS WILD-TYPE | 80 | 121 | 95

Figure S7. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.01e-13 (Fisher's exact test), Q value = 5.6e-11

Table S8. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 118 | 97 | 107
NRAS MUTATED | 1 | 25 | 0
NRAS WILD-TYPE | 117 | 72 | 107

Figure S8. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9.33e-39 (Fisher's exact test), Q value = 2.6e-36

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 106 | 50 | 167
BRAF MUTATED | 10 | 29 | 144
BRAF WILD-TYPE | 96 | 21 | 23

Figure S9. Get High-res Image Gene #2: '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 = 0.00026

Table S10. Gene #2: '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 S10. Get High-res Image Gene #2: '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 = 6.9e-09

Table S11. Gene #2: '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 S11. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 7.79e-49 (Fisher's exact test), Q value = 2.2e-46

Table S12. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 105 | 39 | 77 | 94
BRAF MUTATED | 5 | 21 | 63 | 89
BRAF WILD-TYPE | 100 | 18 | 14 | 5

Figure S12. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.22e-48 (Fisher's exact test), Q value = 3.5e-46

Table S13. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 61 | 124 | 96 | 34
BRAF MUTATED | 47 | 111 | 1 | 19
BRAF WILD-TYPE | 14 | 13 | 95 | 15

Figure S13. Get High-res Image Gene #2: '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 = 6.7e-38

Table S14. Gene #2: '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 S14. Get High-res Image Gene #2: '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 = 9.4e-41

Table S15. Gene #2: '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 S15. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.44e-44 (Fisher's exact test), Q value = 1.5e-41

Table S16. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 121 | 96
BRAF MUTATED | 5 | 106 | 71
BRAF WILD-TYPE | 100 | 15 | 25

Figure S16. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.44e-45 (Fisher's exact test), Q value = 4.1e-43

Table S17. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 118 | 97 | 107
BRAF MUTATED | 92 | 1 | 89
BRAF WILD-TYPE | 26 | 96 | 18

Figure S17. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000222 (Fisher's exact test), Q value = 0.059

Table S18. 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 S18. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.28e-06 (Fisher's exact test), Q value = 0.00061

Table S19. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 106 | 50 | 167
HRAS MUTATED | 12 | 0 | 0
HRAS WILD-TYPE | 94 | 50 | 167

Figure S19. 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 S20. 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 S20. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.0039

Table S21. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 105 | 39 | 77 | 94
HRAS MUTATED | 12 | 0 | 0 | 0
HRAS WILD-TYPE | 93 | 39 | 77 | 94

Figure S21. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.74e-06 (Fisher's exact test), Q value = 0.001

Table S22. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 61 | 124 | 96 | 34
HRAS MUTATED | 0 | 0 | 12 | 0
HRAS WILD-TYPE | 61 | 124 | 84 | 34

Figure S22. 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 S23. 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 S23. 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 S24. 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 S24. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.22e-06 (Fisher's exact test), Q value = 0.00033

Table S25. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 105 | 121 | 96
HRAS MUTATED | 12 | 0 | 0
HRAS WILD-TYPE | 93 | 121 | 96

Figure S25. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.38e-07 (Fisher's exact test), Q value = 9.2e-05

Table S26. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 118 | 97 | 107
HRAS MUTATED | 0 | 12 | 0
HRAS WILD-TYPE | 118 | 85 | 107

Figure S26. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_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 = 32

- Number of Molecular subtypes = 10

- 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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