This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 7 genes and 8 molecular subtypes across 80 patients, 30 significant findings detected with P value < 0.05 and Q value < 0.25.
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GNAQ mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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EIF1AX mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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SF3B1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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BAP1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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CYSLTR2 mutation correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Table 1. Get Full Table Overview of the association between mutation status of 7 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, 30 significant findings detected.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
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 | |
SF3B1 | 18 (22%) | 62 |
0.00084 (0.00433) |
0.00082 (0.00433) |
0.00045 (0.0042) |
0.00201 (0.00804) |
0.0004 (0.0042) |
0.0188 (0.0457) |
0.00085 (0.00433) |
0.0108 (0.0275) |
BAP1 | 16 (20%) | 64 |
4e-05 (0.00224) |
0.00018 (0.00336) |
0.00083 (0.00433) |
0.00017 (0.00336) |
0.00135 (0.0063) |
0.0004 (0.0042) |
0.00298 (0.0111) |
0.0107 (0.0275) |
GNAQ | 40 (50%) | 40 |
0.0306 (0.0714) |
0.0415 (0.083) |
0.0462 (0.0862) |
0.0378 (0.0814) |
0.0393 (0.0815) |
0.093 (0.149) |
0.0523 (0.0945) |
0.00743 (0.0231) |
EIF1AX | 10 (12%) | 70 |
0.00079 (0.00433) |
0.00159 (0.00685) |
0.00967 (0.0271) |
0.00847 (0.025) |
0.00345 (0.0121) |
0.00479 (0.0158) |
0.0648 (0.11) |
0.171 (0.239) |
CYSLTR2 | 3 (4%) | 77 |
0.0375 (0.0814) |
1 (1.00) |
0.0443 (0.0856) |
0.107 (0.167) |
0.795 (0.89) |
0.272 (0.346) |
1 (1.00) |
0.574 (0.67) |
GNA11 | 36 (45%) | 44 |
0.0767 (0.126) |
0.0625 (0.109) |
0.188 (0.257) |
0.135 (0.2) |
0.146 (0.209) |
0.27 (0.346) |
0.235 (0.313) |
0.31 (0.386) |
PRMT8 | 5 (6%) | 75 |
0.857 (0.941) |
0.626 (0.715) |
0.499 (0.608) |
0.531 (0.633) |
1 (1.00) |
0.924 (0.995) |
0.126 (0.191) |
1 (1.00) |
P value = 0.0306 (Fisher's exact test), Q value = 0.071
Table S1. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 36 | 22 |
GNAQ MUTATED | 8 | 24 | 8 |
GNAQ WILD-TYPE | 14 | 12 | 14 |
Figure S1. Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.083
Table S2. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 29 |
GNAQ MUTATED | 13 | 7 | 20 |
GNAQ WILD-TYPE | 20 | 11 | 9 |
Figure S2. Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.086
Table S3. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 30 | 15 | 35 |
GNAQ MUTATED | 12 | 5 | 23 |
GNAQ WILD-TYPE | 18 | 10 | 12 |
Figure S3. Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.081
Table S4. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 33 | 18 |
GNAQ MUTATED | 10 | 22 | 8 |
GNAQ WILD-TYPE | 19 | 11 | 10 |
Figure S4. Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

P value = 0.0393 (Fisher's exact test), Q value = 0.082
Table S5. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 17 | 29 |
GNAQ MUTATED | 13 | 7 | 20 |
GNAQ WILD-TYPE | 21 | 10 | 9 |
Figure S5. Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

P value = 0.093 (Fisher's exact test), Q value = 0.15
Table S6. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 17 | 13 | 28 | 22 |
GNAQ MUTATED | 5 | 8 | 18 | 9 |
GNAQ WILD-TYPE | 12 | 5 | 10 | 13 |
P value = 0.0523 (Fisher's exact test), Q value = 0.094
Table S7. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 28 | 14 |
GNAQ MUTATED | 12 | 19 | 6 |
GNAQ WILD-TYPE | 20 | 9 | 8 |
P value = 0.00743 (Fisher's exact test), Q value = 0.023
Table S8. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 5 | 12 | 16 | 16 | 15 | 10 |
GNAQ MUTATED | 1 | 2 | 11 | 12 | 5 | 6 |
GNAQ WILD-TYPE | 4 | 10 | 5 | 4 | 10 | 4 |
Figure S6. Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0767 (Fisher's exact test), Q value = 0.13
Table S9. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 36 | 22 |
GNA11 MUTATED | 14 | 12 | 10 |
GNA11 WILD-TYPE | 8 | 24 | 12 |
P value = 0.0625 (Fisher's exact test), Q value = 0.11
Table S10. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 29 |
GNA11 MUTATED | 18 | 10 | 8 |
GNA11 WILD-TYPE | 15 | 8 | 21 |
P value = 0.188 (Fisher's exact test), Q value = 0.26
Table S11. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 30 | 15 | 35 |
GNA11 MUTATED | 17 | 7 | 12 |
GNA11 WILD-TYPE | 13 | 8 | 23 |
P value = 0.135 (Fisher's exact test), Q value = 0.2
Table S12. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 33 | 18 |
GNA11 MUTATED | 17 | 11 | 8 |
GNA11 WILD-TYPE | 12 | 22 | 10 |
P value = 0.146 (Fisher's exact test), Q value = 0.21
Table S13. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 17 | 29 |
GNA11 MUTATED | 17 | 10 | 9 |
GNA11 WILD-TYPE | 17 | 7 | 20 |
P value = 0.27 (Fisher's exact test), Q value = 0.35
Table S14. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 17 | 13 | 28 | 22 |
GNA11 MUTATED | 10 | 4 | 10 | 12 |
GNA11 WILD-TYPE | 7 | 9 | 18 | 10 |
P value = 0.235 (Fisher's exact test), Q value = 0.31
Table S15. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 28 | 14 |
GNA11 MUTATED | 16 | 9 | 8 |
GNA11 WILD-TYPE | 16 | 19 | 6 |
P value = 0.31 (Fisher's exact test), Q value = 0.39
Table S16. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 5 | 12 | 16 | 16 | 15 | 10 |
GNA11 MUTATED | 4 | 7 | 6 | 5 | 8 | 3 |
GNA11 WILD-TYPE | 1 | 5 | 10 | 11 | 7 | 7 |
P value = 0.00079 (Fisher's exact test), Q value = 0.0043
Table S17. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 36 | 22 |
EIF1AX MUTATED | 0 | 10 | 0 |
EIF1AX WILD-TYPE | 22 | 26 | 22 |
Figure S7. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.0068
Table S18. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 29 |
EIF1AX MUTATED | 0 | 2 | 8 |
EIF1AX WILD-TYPE | 33 | 16 | 21 |
Figure S8. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00967 (Fisher's exact test), Q value = 0.027
Table S19. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 30 | 15 | 35 |
EIF1AX MUTATED | 0 | 2 | 8 |
EIF1AX WILD-TYPE | 30 | 13 | 27 |
Figure S9. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

P value = 0.00847 (Fisher's exact test), Q value = 0.025
Table S20. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 33 | 18 |
EIF1AX MUTATED | 0 | 8 | 2 |
EIF1AX WILD-TYPE | 29 | 25 | 16 |
Figure S10. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00345 (Fisher's exact test), Q value = 0.012
Table S21. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 17 | 29 |
EIF1AX MUTATED | 0 | 3 | 7 |
EIF1AX WILD-TYPE | 34 | 14 | 22 |
Figure S11. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

P value = 0.00479 (Fisher's exact test), Q value = 0.016
Table S22. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 17 | 13 | 28 | 22 |
EIF1AX MUTATED | 0 | 3 | 7 | 0 |
EIF1AX WILD-TYPE | 17 | 10 | 21 | 22 |
Figure S12. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

P value = 0.0648 (Fisher's exact test), Q value = 0.11
Table S23. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 28 | 14 |
EIF1AX MUTATED | 1 | 6 | 1 |
EIF1AX WILD-TYPE | 31 | 22 | 13 |
P value = 0.171 (Fisher's exact test), Q value = 0.24
Table S24. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 5 | 12 | 16 | 16 | 15 | 10 |
EIF1AX MUTATED | 0 | 1 | 4 | 3 | 0 | 0 |
EIF1AX WILD-TYPE | 5 | 11 | 12 | 13 | 15 | 10 |
P value = 0.00084 (Fisher's exact test), Q value = 0.0043
Table S25. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 36 | 22 |
SF3B1 MUTATED | 0 | 14 | 4 |
SF3B1 WILD-TYPE | 22 | 22 | 18 |
Figure S13. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0043
Table S26. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 29 |
SF3B1 MUTATED | 1 | 6 | 11 |
SF3B1 WILD-TYPE | 32 | 12 | 18 |
Figure S14. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0042
Table S27. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 30 | 15 | 35 |
SF3B1 MUTATED | 3 | 0 | 15 |
SF3B1 WILD-TYPE | 27 | 15 | 20 |
Figure S15. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

P value = 0.00201 (Fisher's exact test), Q value = 0.008
Table S28. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 33 | 18 |
SF3B1 MUTATED | 2 | 14 | 2 |
SF3B1 WILD-TYPE | 27 | 19 | 16 |
Figure S16. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0042
Table S29. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 17 | 29 |
SF3B1 MUTATED | 1 | 5 | 12 |
SF3B1 WILD-TYPE | 33 | 12 | 17 |
Figure S17. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.046
Table S30. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 17 | 13 | 28 | 22 |
SF3B1 MUTATED | 1 | 5 | 10 | 2 |
SF3B1 WILD-TYPE | 16 | 8 | 18 | 20 |
Figure S18. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.0043
Table S31. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 28 | 14 |
SF3B1 MUTATED | 1 | 11 | 5 |
SF3B1 WILD-TYPE | 31 | 17 | 9 |
Figure S19. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.028
Table S32. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 5 | 12 | 16 | 16 | 15 | 10 |
SF3B1 MUTATED | 0 | 1 | 6 | 8 | 2 | 0 |
SF3B1 WILD-TYPE | 5 | 11 | 10 | 8 | 13 | 10 |
Figure S20. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0022
Table S33. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 36 | 22 |
BAP1 MUTATED | 9 | 0 | 7 |
BAP1 WILD-TYPE | 13 | 36 | 15 |
Figure S21. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0034
Table S34. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 29 |
BAP1 MUTATED | 13 | 3 | 0 |
BAP1 WILD-TYPE | 20 | 15 | 29 |
Figure S22. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0043
Table S35. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 30 | 15 | 35 |
BAP1 MUTATED | 11 | 4 | 1 |
BAP1 WILD-TYPE | 19 | 11 | 34 |
Figure S23. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0034
Table S36. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 33 | 18 |
BAP1 MUTATED | 10 | 0 | 6 |
BAP1 WILD-TYPE | 19 | 33 | 12 |
Figure S24. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0063
Table S37. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 17 | 29 |
BAP1 MUTATED | 13 | 2 | 1 |
BAP1 WILD-TYPE | 21 | 15 | 28 |
Figure S25. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0042
Table S38. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 17 | 13 | 28 | 22 |
BAP1 MUTATED | 7 | 0 | 1 | 8 |
BAP1 WILD-TYPE | 10 | 13 | 27 | 14 |
Figure S26. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

P value = 0.00298 (Fisher's exact test), Q value = 0.011
Table S39. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 28 | 14 |
BAP1 MUTATED | 12 | 1 | 2 |
BAP1 WILD-TYPE | 20 | 27 | 12 |
Figure S27. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.028
Table S40. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 5 | 12 | 16 | 16 | 15 | 10 |
BAP1 MUTATED | 2 | 4 | 2 | 0 | 2 | 5 |
BAP1 WILD-TYPE | 3 | 8 | 14 | 16 | 13 | 5 |
Figure S28. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.857 (Fisher's exact test), Q value = 0.94
Table S41. Gene #6: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 36 | 22 |
PRMT8 MUTATED | 1 | 2 | 2 |
PRMT8 WILD-TYPE | 21 | 34 | 20 |
P value = 0.626 (Fisher's exact test), Q value = 0.72
Table S42. Gene #6: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 29 |
PRMT8 MUTATED | 3 | 0 | 2 |
PRMT8 WILD-TYPE | 30 | 18 | 27 |
P value = 0.499 (Fisher's exact test), Q value = 0.61
Table S43. Gene #6: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 30 | 15 | 35 |
PRMT8 MUTATED | 3 | 1 | 1 |
PRMT8 WILD-TYPE | 27 | 14 | 34 |
P value = 0.531 (Fisher's exact test), Q value = 0.63
Table S44. Gene #6: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 33 | 18 |
PRMT8 MUTATED | 3 | 1 | 1 |
PRMT8 WILD-TYPE | 26 | 32 | 17 |
P value = 1 (Fisher's exact test), Q value = 1
Table S45. Gene #6: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 17 | 29 |
PRMT8 MUTATED | 2 | 1 | 2 |
PRMT8 WILD-TYPE | 32 | 16 | 27 |
P value = 0.924 (Fisher's exact test), Q value = 1
Table S46. Gene #6: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 17 | 13 | 28 | 22 |
PRMT8 MUTATED | 1 | 0 | 2 | 2 |
PRMT8 WILD-TYPE | 16 | 13 | 26 | 20 |
P value = 0.126 (Fisher's exact test), Q value = 0.19
Table S47. Gene #6: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 28 | 14 |
PRMT8 MUTATED | 3 | 0 | 2 |
PRMT8 WILD-TYPE | 29 | 28 | 12 |
P value = 1 (Fisher's exact test), Q value = 1
Table S48. Gene #6: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 5 | 12 | 16 | 16 | 15 | 10 |
PRMT8 MUTATED | 0 | 1 | 1 | 1 | 1 | 1 |
PRMT8 WILD-TYPE | 5 | 11 | 15 | 15 | 14 | 9 |
P value = 0.0375 (Fisher's exact test), Q value = 0.081
Table S49. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 22 | 36 | 22 |
CYSLTR2 MUTATED | 0 | 0 | 3 |
CYSLTR2 WILD-TYPE | 22 | 36 | 19 |
Figure S29. Get High-res Image Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1
Table S50. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 33 | 18 | 29 |
CYSLTR2 MUTATED | 1 | 1 | 1 |
CYSLTR2 WILD-TYPE | 32 | 17 | 28 |
P value = 0.0443 (Fisher's exact test), Q value = 0.086
Table S51. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 30 | 15 | 35 |
CYSLTR2 MUTATED | 1 | 2 | 0 |
CYSLTR2 WILD-TYPE | 29 | 13 | 35 |
Figure S30. Get High-res Image Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.17
Table S52. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 29 | 33 | 18 |
CYSLTR2 MUTATED | 1 | 0 | 2 |
CYSLTR2 WILD-TYPE | 28 | 33 | 16 |
P value = 0.795 (Fisher's exact test), Q value = 0.89
Table S53. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 34 | 17 | 29 |
CYSLTR2 MUTATED | 2 | 0 | 1 |
CYSLTR2 WILD-TYPE | 32 | 17 | 28 |
P value = 0.272 (Fisher's exact test), Q value = 0.35
Table S54. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 17 | 13 | 28 | 22 |
CYSLTR2 MUTATED | 2 | 0 | 1 | 0 |
CYSLTR2 WILD-TYPE | 15 | 13 | 27 | 22 |
P value = 1 (Fisher's exact test), Q value = 1
Table S55. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 32 | 28 | 14 |
CYSLTR2 MUTATED | 2 | 1 | 0 |
CYSLTR2 WILD-TYPE | 30 | 27 | 14 |
P value = 0.574 (Fisher's exact test), Q value = 0.67
Table S56. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 5 | 12 | 16 | 16 | 15 | 10 |
CYSLTR2 MUTATED | 0 | 1 | 0 | 0 | 1 | 1 |
CYSLTR2 WILD-TYPE | 5 | 11 | 16 | 16 | 14 | 9 |
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Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
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Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/15890468/transformed.cor.cli.txt
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Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/15952300/UVM-TP.transferedmergedcluster.txt
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Number of patients = 80
-
Number of significantly mutated genes = 7
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Number of Molecular subtypes = 8
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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.