This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 6 genes and 10 molecular subtypes across 401 patients, 29 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'.
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EIF1AX mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
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, 29 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) |
3.06e-53 (1.68e-51) |
1.2e-53 (6.74e-52) |
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) |
2.59e-06 (9.08e-05) |
3.86e-08 (1.51e-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) |
3.71e-16 (1.67e-14) |
1.03e-19 (5.05e-18) |
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) |
0.054 (1.00) |
0.00672 (0.188) |
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) |
0.503 (1.00) |
1 (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) |
0.422 (1.00) |
0.698 (1.00) |
0.777 (1.00) |
0.0536 (1.00) |
0.533 (1.00) |
0.0614 (1.00) |
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'

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'

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 |
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'

P value = 3.71e-16 (Fisher's exact test), Q value = 1.7e-14
Table S5. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 127 | 44 | 95 | 128 |
NRAS MUTATED | 34 | 0 | 0 | 0 |
NRAS WILD-TYPE | 93 | 44 | 95 | 128 |
Figure S4. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1.03e-19 (Fisher's exact test), Q value = 5e-18
Table S6. Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 114 | 232 | 48 |
NRAS MUTATED | 34 | 0 | 0 |
NRAS WILD-TYPE | 80 | 232 | 48 |
Figure S5. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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'

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'

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'

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'

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'

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'

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'

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'

P value = 3.06e-53 (Fisher's exact test), Q value = 1.7e-51
Table S15. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 127 | 44 | 95 | 128 |
BRAF MUTATED | 11 | 27 | 80 | 119 |
BRAF WILD-TYPE | 116 | 17 | 15 | 9 |
Figure S14. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1.2e-53 (Fisher's exact test), Q value = 6.7e-52
Table S16. Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 114 | 232 | 48 |
BRAF MUTATED | 5 | 201 | 31 |
BRAF WILD-TYPE | 109 | 31 | 17 |
Figure S15. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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'

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'

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'

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'

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'

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'

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'

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'

P value = 2.59e-06 (Fisher's exact test), Q value = 9.1e-05
Table S25. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 127 | 44 | 95 | 128 |
HRAS MUTATED | 14 | 0 | 0 | 0 |
HRAS WILD-TYPE | 113 | 44 | 95 | 128 |
Figure S24. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 3.86e-08 (Fisher's exact test), Q value = 1.5e-06
Table S26. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 114 | 232 | 48 |
HRAS MUTATED | 14 | 0 | 0 |
HRAS WILD-TYPE | 100 | 232 | 48 |
Figure S25. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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'

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'

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'

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'

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 |
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 |
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 |
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 |
P value = 0.054 (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 | 127 | 44 | 95 | 128 |
EIF1AX MUTATED | 5 | 0 | 1 | 0 |
EIF1AX WILD-TYPE | 122 | 44 | 94 | 128 |
P value = 0.00672 (Fisher's exact test), Q value = 0.19
Table S36. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 114 | 232 | 48 |
EIF1AX MUTATED | 4 | 0 | 2 |
EIF1AX WILD-TYPE | 110 | 232 | 46 |
Figure S30. Get High-res Image Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

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 |
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 |
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 |
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 |
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 |
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 |
P value = 0.503 (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 | 127 | 44 | 95 | 128 |
NUP93 MUTATED | 1 | 0 | 0 | 3 |
NUP93 WILD-TYPE | 126 | 44 | 95 | 125 |
P value = 1 (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 |
---|---|---|---|
ALL | 114 | 232 | 48 |
NUP93 MUTATED | 1 | 3 | 0 |
NUP93 WILD-TYPE | 113 | 229 | 48 |
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 |
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 |
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 |
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 |
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 |
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 |
P value = 0.422 (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 | 127 | 44 | 95 | 128 |
NLRP6 MUTATED | 0 | 0 | 2 | 1 |
NLRP6 WILD-TYPE | 127 | 44 | 93 | 127 |
P value = 0.698 (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 |
---|---|---|---|
ALL | 114 | 232 | 48 |
NLRP6 MUTATED | 0 | 3 | 0 |
NLRP6 WILD-TYPE | 114 | 229 | 48 |
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 |
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 |
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 |
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 |
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Mutation data file = transformed.cor.cli.txt
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Molecular subtypes file = THCA-TP.transferedmergedcluster.txt
-
Number of patients = 401
-
Number of significantly mutated genes = 6
-
Number of Molecular subtypes = 10
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Exclude genes that fewer than K tumors have mutations, K = 3
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
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.
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.