Correlation between gene mutation status and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1H130DK
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/C1H130DK
Overview
Introduction

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

Summary

Testing the association between mutation status of 7 genes and 10 molecular subtypes across 401 patients, 30 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'.

- OTUD4 mutation correlated to 'MRNASEQ_CNMF'.

- EIF1AX mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 7 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, 30 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 | 0.000423 (0.0161) | 1.56e-41 (9.04e-40) | 1.51e-05 (0.000618) | 6.5e-10 (3.25e-08) | 8.11e-54 (5.19e-52) | 1.54e-51 (9.73e-50) | 9.16e-45 (5.5e-43) | 2.33e-49 (1.44e-47) | 6.03e-42 (3.56e-40) | 9.72e-48 (5.93e-46)
HRAS | 14 (3%) | 387 | 7.2e-06 (0.000302) | 1.13e-07 (5.32e-06) | 7.6e-05 (0.00304) | 0.00362 (0.134) | 9.11e-07 (3.92e-05) | 1.94e-07 (8.72e-06) | 1.79e-07 (8.22e-06) | 1.12e-08 (5.38e-07) | 4.91e-07 (2.16e-05) | 8.59e-09 (4.21e-07)
NRAS | 34 (8%) | 367 | 0.0106 (0.361) | 8.51e-19 (4.6e-17) | 1 (1.00) | 0.000377 (0.0147) | 1.44e-17 (7.65e-16) | 2.64e-19 (1.48e-17) | 1.04e-16 (5.41e-15) | 4.4e-19 (2.42e-17) | 3.09e-15 (1.57e-13) | 2.21e-19 (1.26e-17)
OTUD4 | 5 (1%) | 396 | 1 (1.00) | 0.32 (1.00) |  |  | 0.00555 (0.194) | 0.0182 (0.601) | 1 (1.00) | 0.0707 (1.00) | 0.168 (1.00) | 0.384 (1.00)
EIF1AX | 6 (1%) | 395 | 0.73 (1.00) | 0.13 (1.00) | 0.324 (1.00) | 0.13 (1.00) | 0.137 (1.00) | 0.00381 (0.137) | 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) |  |  | 0.504 (1.00) | 0.87 (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) |  |  | 0.37 (1.00) | 0.686 (1.00) | 0.777 (1.00) | 0.0536 (1.00) | 0.533 (1.00) | 0.0614 (1.00)

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 8.51e-19 (Fisher's exact test), Q value = 4.6e-17

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

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.000377 (Fisher's exact test), Q value = 0.015

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

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.44e-17 (Fisher's exact test), Q value = 7.7e-16

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 125 | 46 | 91 | 128
NRAS MUTATED | 34 | 0 | 0 | 0
NRAS WILD-TYPE | 91 | 46 | 91 | 128

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 = 2.64e-19 (Fisher's exact test), Q value = 1.5e-17

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 112 | 171 | 76 | 31
NRAS MUTATED | 34 | 0 | 0 | 0
NRAS WILD-TYPE | 78 | 171 | 76 | 31

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 = 1.04e-16 (Fisher's exact test), Q value = 5.4e-15

Table S5. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #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 S5. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.4e-19 (Fisher's exact test), Q value = 2.4e-17

Table S6. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #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 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 = 3.09e-15 (Fisher's exact test), Q value = 1.6e-13

Table S7. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #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 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 = 2.21e-19 (Fisher's exact test), Q value = 1.3e-17

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

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000423 (Fisher's exact test), Q value = 0.016

Table S9. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S9. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.56e-41 (Fisher's exact test), Q value = 9e-40

Table S10. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S10. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1.51e-05 (Fisher's exact test), Q value = 0.00062

Table S11. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S11. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 6.5e-10 (Fisher's exact test), Q value = 3.3e-08

Table S12. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S12. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8.11e-54 (Fisher's exact test), Q value = 5.2e-52

Table S13. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 125 | 46 | 91 | 128
BRAF MUTATED | 10 | 29 | 76 | 119
BRAF WILD-TYPE | 115 | 17 | 15 | 9

Figure S13. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.54e-51 (Fisher's exact test), Q value = 9.7e-50

Table S14. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 112 | 171 | 76 | 31
BRAF MUTATED | 5 | 151 | 58 | 20
BRAF WILD-TYPE | 107 | 20 | 18 | 11

Figure S14. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 9.16e-45 (Fisher's exact test), Q value = 5.5e-43

Table S15. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S15. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.33e-49 (Fisher's exact test), Q value = 1.4e-47

Table S16. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S16. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.03e-42 (Fisher's exact test), Q value = 3.6e-40

Table S17. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S17. 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 = 9.72e-48 (Fisher's exact test), Q value = 5.9e-46

Table S18. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S18. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 7.2e-06 (Fisher's exact test), Q value = 3e-04

Table S19. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S19. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 5.3e-06

Table S20. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S20. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 7.6e-05 (Fisher's exact test), Q value = 0.003

Table S21. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S21. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00362 (Fisher's exact test), Q value = 0.13

Table S22. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S22. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9.11e-07 (Fisher's exact test), Q value = 3.9e-05

Table S23. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 125 | 46 | 91 | 128
HRAS MUTATED | 14 | 0 | 0 | 0
HRAS WILD-TYPE | 111 | 46 | 91 | 128

Figure S23. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.94e-07 (Fisher's exact test), Q value = 8.7e-06

Table S24. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 112 | 171 | 76 | 31
HRAS MUTATED | 14 | 0 | 0 | 0
HRAS WILD-TYPE | 98 | 171 | 76 | 31

Figure S24. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.79e-07 (Fisher's exact test), Q value = 8.2e-06

Table S25. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S25. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-08 (Fisher's exact test), Q value = 5.4e-07

Table S26. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S26. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.91e-07 (Fisher's exact test), Q value = 2.2e-05

Table S27. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S27. 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 = 8.59e-09 (Fisher's exact test), Q value = 4.2e-07

Table S28. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S28. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'OTUD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00555 (Fisher's exact test), Q value = 0.19

Table S29. Gene #4: 'OTUD4 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 125 | 46 | 91 | 128
OTUD4 MUTATED | 0 | 1 | 4 | 0
OTUD4 WILD-TYPE | 125 | 45 | 87 | 128

Figure S29. Get High-res Image Gene #4: 'OTUD4 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.14

Table S30. Gene #5: 'EIF1AX MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 112 | 171 | 76 | 31
EIF1AX MUTATED | 4 | 0 | 0 | 2
EIF1AX WILD-TYPE | 108 | 171 | 76 | 29

Figure S30. Get High-res Image Gene #5: 'EIF1AX MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

- Number of patients = 401

- Number of significantly mutated genes = 7

- 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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