Correlation between gene mutation status and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1XG9PTQ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1XG9PTQ
Overview
Introduction

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

Summary

Testing the association between mutation status of 6 genes and 10 molecular subtypes across 401 patients, 28 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 'CN_CNMF', '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', 'RPPA_CHIERARCHICAL', '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 6 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, 28 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 | 240 (60%) | 161 | 0.000429 (0.0133) | 2.44e-41 (1.22e-39) | 1.54e-05 (0.00051) | 6.51e-10 (2.73e-08) | 6.71e-51 (3.69e-49) | 8.55e-53 (4.79e-51) | 1.33e-44 (6.93e-43) | 3.88e-49 (2.09e-47) | 8.54e-42 (4.36e-40) | 1.78e-47 (9.46e-46)
HRAS | 14 (3%) | 387 | 7.2e-06 (0.000245) | 9.42e-08 (3.58e-06) | 7.6e-05 (0.00243) | 0.00362 (0.105) | 2.76e-06 (9.65e-05) | 5.97e-08 (2.33e-06) | 3.4e-07 (1.26e-05) | 3.31e-08 (1.32e-06) | 1.03e-06 (3.71e-05) | 3.01e-08 (1.24e-06)
NRAS | 34 (8%) | 367 | 0.0109 (0.294) | 4.4e-18 (2.03e-16) | 1 (1.00) | 0.00046 (0.0138) | 5.94e-16 (2.67e-14) | 4.71e-19 (2.31e-17) | 6.24e-16 (2.75e-14) | 3.39e-18 (1.6e-16) | 1.85e-14 (7.94e-13) | 1.66e-18 (7.96e-17)
EIF1AX | 6 (1%) | 395 | 0.73 (1.00) | 0.13 (1.00) | 0.324 (1.00) | 0.13 (1.00) | 0.0594 (1.00) | 0.0097 (0.272) | 0.331 (1.00) | 0.586 (1.00) | 0.38 (1.00) | 0.516 (1.00)
NUP93 | 4 (1%) | 397 | 1 (1.00) | 0.827 (1.00) |  |  | 0.59 (1.00) | 0.619 (1.00) | 1 (1.00) | 1 (1.00) | 0.841 (1.00) | 1 (1.00)
NLRP6 | 3 (1%) | 398 | 0.518 (1.00) | 0.295 (1.00) |  |  | 0.41 (1.00) | 0.286 (1.00) | 0.777 (1.00) | 0.0536 (1.00) | 0.533 (1.00) | 0.0614 (1.00)

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.29

Table S1. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 26 | 313 | 60
NRAS MUTATED | 1 | 20 | 11
NRAS WILD-TYPE | 25 | 293 | 49

Figure S1. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.4e-18 (Fisher's exact test), Q value = 2e-16

Table S2. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 70 | 204
NRAS MUTATED | 34 | 0 | 0
NRAS WILD-TYPE | 93 | 70 | 204

Figure S2. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 76 | 77
NRAS MUTATED | 4 | 5 | 5
NRAS WILD-TYPE | 56 | 71 | 72

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.014

Table S4. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 90 | 92
NRAS MUTATED | 5 | 0 | 9
NRAS WILD-TYPE | 26 | 90 | 83

Figure S3. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5.94e-16 (Fisher's exact test), Q value = 2.7e-14

Table S5. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 43 | 93 | 133
NRAS MUTATED | 34 | 0 | 0 | 0
NRAS WILD-TYPE | 96 | 43 | 93 | 133

Figure S4. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.71e-19 (Fisher's exact test), Q value = 2.3e-17

Table S6. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 158 | 109 | 78 | 54
NRAS MUTATED | 0 | 34 | 0 | 0
NRAS WILD-TYPE | 158 | 75 | 78 | 54

Figure S5. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 6.24e-16 (Fisher's exact test), Q value = 2.7e-14

Table S7. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 130 | 140 | 130
NRAS MUTATED | 33 | 0 | 1
NRAS WILD-TYPE | 97 | 140 | 129

Figure S6. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.39e-18 (Fisher's exact test), Q value = 1.6e-16

Table S8. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 113 | 160
NRAS MUTATED | 0 | 33 | 1
NRAS WILD-TYPE | 127 | 80 | 159

Figure S7. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.85e-14 (Fisher's exact test), Q value = 7.9e-13

Table S9. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 131 | 127
NRAS MUTATED | 33 | 0 | 1
NRAS WILD-TYPE | 109 | 131 | 126

Figure S8. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.66e-18 (Fisher's exact test), Q value = 8e-17

Table S10. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 111 | 138
NRAS MUTATED | 1 | 33 | 0
NRAS WILD-TYPE | 150 | 78 | 138

Figure S9. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000429 (Fisher's exact test), Q value = 0.013

Table S11. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 26 | 313 | 60
BRAF MUTATED | 8 | 203 | 29
BRAF WILD-TYPE | 18 | 110 | 31

Figure S10. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.44e-41 (Fisher's exact test), Q value = 1.2e-39

Table S12. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 70 | 204
BRAF MUTATED | 19 | 42 | 179
BRAF WILD-TYPE | 108 | 28 | 25

Figure S11. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1.54e-05 (Fisher's exact test), Q value = 0.00051

Table S13. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 76 | 77
BRAF MUTATED | 21 | 57 | 43
BRAF WILD-TYPE | 39 | 19 | 34

Figure S12. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 6.51e-10 (Fisher's exact test), Q value = 2.7e-08

Table S14. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 90 | 92
BRAF MUTATED | 16 | 73 | 32
BRAF WILD-TYPE | 15 | 17 | 60

Figure S13. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 6.71e-51 (Fisher's exact test), Q value = 3.7e-49

Table S15. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 43 | 93 | 133
BRAF MUTATED | 13 | 27 | 78 | 122
BRAF WILD-TYPE | 117 | 16 | 15 | 11

Figure S14. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.55e-53 (Fisher's exact test), Q value = 4.8e-51

Table S16. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 158 | 109 | 78 | 54
BRAF MUTATED | 143 | 4 | 60 | 33
BRAF WILD-TYPE | 15 | 105 | 18 | 21

Figure S15. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.33e-44 (Fisher's exact test), Q value = 6.9e-43

Table S17. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 130 | 140 | 130
BRAF MUTATED | 15 | 122 | 102
BRAF WILD-TYPE | 115 | 18 | 28

Figure S16. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.88e-49 (Fisher's exact test), Q value = 2.1e-47

Table S18. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 113 | 160
BRAF MUTATED | 107 | 5 | 127
BRAF WILD-TYPE | 20 | 108 | 33

Figure S17. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.54e-42 (Fisher's exact test), Q value = 4.4e-40

Table S19. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 131 | 127
BRAF MUTATED | 23 | 117 | 99
BRAF WILD-TYPE | 119 | 14 | 28

Figure S18. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.78e-47 (Fisher's exact test), Q value = 9.5e-46

Table S20. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 111 | 138
BRAF MUTATED | 122 | 5 | 112
BRAF WILD-TYPE | 29 | 106 | 26

Figure S19. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 7.2e-06 (Fisher's exact test), Q value = 0.00024

Table S21. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 26 | 313 | 60
HRAS MUTATED | 0 | 4 | 10
HRAS WILD-TYPE | 26 | 309 | 50

Figure S20. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9.42e-08 (Fisher's exact test), Q value = 3.6e-06

Table S22. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 70 | 204
HRAS MUTATED | 14 | 0 | 0
HRAS WILD-TYPE | 113 | 70 | 204

Figure S21. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 7.6e-05 (Fisher's exact test), Q value = 0.0024

Table S23. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 76 | 77
HRAS MUTATED | 9 | 1 | 0
HRAS WILD-TYPE | 51 | 75 | 77

Figure S22. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00362 (Fisher's exact test), Q value = 0.11

Table S24. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 90 | 92
HRAS MUTATED | 1 | 0 | 9
HRAS WILD-TYPE | 30 | 90 | 83

Figure S23. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.76e-06 (Fisher's exact test), Q value = 9.7e-05

Table S25. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 43 | 93 | 133
HRAS MUTATED | 14 | 0 | 0 | 0
HRAS WILD-TYPE | 116 | 43 | 93 | 133

Figure S24. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.97e-08 (Fisher's exact test), Q value = 2.3e-06

Table S26. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 158 | 109 | 78 | 54
HRAS MUTATED | 0 | 14 | 0 | 0
HRAS WILD-TYPE | 158 | 95 | 78 | 54

Figure S25. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 3.4e-07 (Fisher's exact test), Q value = 1.3e-05

Table S27. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 130 | 140 | 130
HRAS MUTATED | 14 | 0 | 0
HRAS WILD-TYPE | 116 | 140 | 130

Figure S26. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.31e-08 (Fisher's exact test), Q value = 1.3e-06

Table S28. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 113 | 160
HRAS MUTATED | 0 | 14 | 0
HRAS WILD-TYPE | 127 | 99 | 160

Figure S27. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.03e-06 (Fisher's exact test), Q value = 3.7e-05

Table S29. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 131 | 127
HRAS MUTATED | 14 | 0 | 0
HRAS WILD-TYPE | 128 | 131 | 127

Figure S28. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3.01e-08 (Fisher's exact test), Q value = 1.2e-06

Table S30. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 111 | 138
HRAS MUTATED | 0 | 14 | 0
HRAS WILD-TYPE | 151 | 97 | 138

Figure S29. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 26 | 313 | 60
EIF1AX MUTATED | 0 | 6 | 0
EIF1AX WILD-TYPE | 26 | 307 | 60

'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 70 | 204
EIF1AX MUTATED | 4 | 1 | 1
EIF1AX WILD-TYPE | 123 | 69 | 203

'EIF1AX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 76 | 77
EIF1AX MUTATED | 3 | 1 | 1
EIF1AX WILD-TYPE | 57 | 75 | 76

'EIF1AX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.13 (Fisher's exact test), Q value = 1

Table S34. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 31 | 90 | 92
EIF1AX MUTATED | 1 | 0 | 4
EIF1AX WILD-TYPE | 30 | 90 | 88

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0594 (Fisher's exact test), Q value = 1

Table S35. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 43 | 93 | 133
EIF1AX MUTATED | 5 | 0 | 1 | 0
EIF1AX WILD-TYPE | 125 | 43 | 92 | 133

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0097 (Fisher's exact test), Q value = 0.27

Table S36. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 158 | 109 | 78 | 54
EIF1AX MUTATED | 0 | 4 | 0 | 2
EIF1AX WILD-TYPE | 158 | 105 | 78 | 52

Figure S30. Get High-res Image Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S37. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 130 | 140 | 130
EIF1AX MUTATED | 4 | 1 | 1
EIF1AX WILD-TYPE | 126 | 139 | 129

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 1

Table S38. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 113 | 160
EIF1AX MUTATED | 1 | 3 | 2
EIF1AX WILD-TYPE | 126 | 110 | 158

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S39. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 131 | 127
EIF1AX MUTATED | 4 | 1 | 1
EIF1AX WILD-TYPE | 138 | 130 | 126

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.516 (Fisher's exact test), Q value = 1

Table S40. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 111 | 138
EIF1AX MUTATED | 2 | 3 | 1
EIF1AX WILD-TYPE | 149 | 108 | 137

'NUP93 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S41. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 26 | 313 | 60
NUP93 MUTATED | 0 | 4 | 0
NUP93 WILD-TYPE | 26 | 309 | 60

'NUP93 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S42. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 70 | 204
NUP93 MUTATED | 1 | 0 | 3
NUP93 WILD-TYPE | 126 | 70 | 201

'NUP93 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S43. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 43 | 93 | 133
NUP93 MUTATED | 1 | 0 | 0 | 3
NUP93 WILD-TYPE | 129 | 43 | 93 | 130

'NUP93 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.619 (Fisher's exact test), Q value = 1

Table S44. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 158 | 109 | 78 | 54
NUP93 MUTATED | 3 | 1 | 0 | 0
NUP93 WILD-TYPE | 155 | 108 | 78 | 54

'NUP93 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S45. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 130 | 140 | 130
NUP93 MUTATED | 1 | 2 | 1
NUP93 WILD-TYPE | 129 | 138 | 129

'NUP93 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S46. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 113 | 160
NUP93 MUTATED | 1 | 1 | 2
NUP93 WILD-TYPE | 126 | 112 | 158

'NUP93 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 1

Table S47. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 131 | 127
NUP93 MUTATED | 1 | 2 | 1
NUP93 WILD-TYPE | 141 | 129 | 126

'NUP93 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S48. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 111 | 138
NUP93 MUTATED | 2 | 1 | 1
NUP93 WILD-TYPE | 149 | 110 | 137

'NLRP6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S49. Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 26 | 313 | 60
NLRP6 MUTATED | 0 | 2 | 1
NLRP6 WILD-TYPE | 26 | 311 | 59

'NLRP6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 1

Table S50. Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 70 | 204
NLRP6 MUTATED | 0 | 0 | 3
NLRP6 WILD-TYPE | 127 | 70 | 201

'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 130 | 43 | 93 | 133
NLRP6 MUTATED | 0 | 0 | 2 | 1
NLRP6 WILD-TYPE | 130 | 43 | 91 | 132

'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S52. Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 158 | 109 | 78 | 54
NLRP6 MUTATED | 1 | 0 | 2 | 0
NLRP6 WILD-TYPE | 157 | 109 | 76 | 54

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S53. Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 130 | 140 | 130
NLRP6 MUTATED | 1 | 2 | 0
NLRP6 WILD-TYPE | 129 | 138 | 130

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0536 (Fisher's exact test), Q value = 1

Table S54. Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 127 | 113 | 160
NLRP6 MUTATED | 3 | 0 | 0
NLRP6 WILD-TYPE | 124 | 113 | 160

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S55. Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 142 | 131 | 127
NLRP6 MUTATED | 1 | 2 | 0
NLRP6 WILD-TYPE | 141 | 129 | 127

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0614 (Fisher's exact test), Q value = 1

Table S56. Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 151 | 111 | 138
NLRP6 MUTATED | 0 | 0 | 3
NLRP6 WILD-TYPE | 151 | 111 | 135

Methods & Data
Input

- Mutation data file = transformed.cor.cli.txt

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

- Number of patients = 401

- Number of significantly mutated genes = 6

- 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- 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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