This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 7 genes and 10 molecular subtypes across 80 patients, 33 significant findings detected with P value < 0.05 and Q value < 0.25.
-
EIF1AX mutation correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
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BAP1 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
-
GNAQ mutation correlated to 'CN_CNMF'.
-
GNA11 mutation correlated to 'CN_CNMF'.
-
SF3B1 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.
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SRSF2 mutation correlated to 'MRNA_CNMF'.
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CYSLTR2 mutation correlated to 'CN_CNMF'.
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, 33 significant findings detected.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
LINCRNA CNMF |
LINCRNA CHIERARCHICAL |
MIR MATURE CNMF |
MIR MATURE CHIERARCHICAL |
CN CNMF |
CN THRESHOLDED CNMF |
METHYLATION CNMF |
METHYLATION 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 | |
BAP1 | 20 (25%) | 60 |
1e-05 (0.000117) |
1e-05 (0.000117) |
0.0036 (0.0133) |
1e-05 (0.000117) |
0.0144 (0.0348) |
0.00165 (0.00877) |
1e-05 (0.000117) |
1e-05 (0.000117) |
9e-05 (0.000787) |
1e-05 (0.000117) |
SF3B1 | 18 (22%) | 62 |
0.0431 (0.0915) |
0.00444 (0.0141) |
0.00321 (0.0125) |
0.0193 (0.0451) |
0.00403 (0.0139) |
0.0105 (0.0283) |
0.00299 (0.0123) |
0.00021 (0.00134) |
9e-05 (0.000787) |
0.00188 (0.00877) |
EIF1AX | 10 (12%) | 70 |
0.068 (0.126) |
0.00654 (0.0199) |
0.00418 (0.0139) |
0.00184 (0.00877) |
0.0101 (0.0283) |
0.00206 (0.00901) |
0.00938 (0.0274) |
0.00021 (0.00134) |
0.00016 (0.00124) |
0.00073 (0.00426) |
GNAQ | 40 (50%) | 40 |
0.557 (0.696) |
0.0851 (0.149) |
0.501 (0.65) |
0.0684 (0.126) |
0.151 (0.24) |
0.0579 (0.116) |
0.0247 (0.0541) |
0.154 (0.24) |
0.517 (0.658) |
0.0778 (0.14) |
GNA11 | 35 (44%) | 45 |
0.781 (0.882) |
0.141 (0.231) |
0.332 (0.467) |
0.0672 (0.126) |
0.618 (0.736) |
0.334 (0.467) |
0.0137 (0.0341) |
0.207 (0.315) |
0.592 (0.727) |
0.142 (0.231) |
SRSF2 | 3 (4%) | 77 |
0.0234 (0.0529) |
0.05 (0.103) |
0.901 (0.986) |
0.621 (0.736) |
1 (1.00) |
0.671 (0.783) |
1 (1.00) |
0.727 (0.834) |
0.269 (0.4) |
0.434 (0.574) |
CYSLTR2 | 3 (4%) | 77 |
0.0939 (0.16) |
0.329 (0.467) |
0.43 (0.574) |
0.423 (0.574) |
0.889 (0.986) |
1 (1.00) |
0.0136 (0.0341) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
P value = 0.068 (Fisher's exact test), Q value = 0.13
Table S1. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
EIF1AX MUTATED | 0 | 1 | 8 | 1 | 0 |
EIF1AX WILD-TYPE | 11 | 10 | 21 | 20 | 8 |
P value = 0.00654 (Fisher's exact test), Q value = 0.02
Table S2. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
EIF1AX MUTATED | 0 | 3 | 7 | 0 |
EIF1AX WILD-TYPE | 15 | 12 | 20 | 23 |
Figure S1. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.00418 (Fisher's exact test), Q value = 0.014
Table S3. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
EIF1AX MUTATED | 0 | 4 | 2 | 1 | 3 |
EIF1AX WILD-TYPE | 18 | 3 | 26 | 10 | 13 |
Figure S2. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.0088
Table S4. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
EIF1AX MUTATED | 0 | 7 | 0 | 3 |
EIF1AX WILD-TYPE | 21 | 17 | 20 | 12 |
Figure S3. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.028
Table S5. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
EIF1AX MUTATED | 1 | 0 | 5 | 2 | 2 |
EIF1AX WILD-TYPE | 12 | 21 | 13 | 22 | 2 |
Figure S4. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.009
Table S6. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
EIF1AX MUTATED | 0 | 0 | 3 | 4 | 3 |
EIF1AX WILD-TYPE | 21 | 20 | 5 | 13 | 11 |
Figure S5. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 0.00938 (Fisher's exact test), Q value = 0.027
Table S7. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
EIF1AX MUTATED | 0 | 0 | 10 | 0 | 0 |
EIF1AX WILD-TYPE | 18 | 21 | 27 | 2 | 2 |
Figure S6. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0013
Table S8. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
EIF1AX MUTATED | 0 | 0 | 10 | 0 | 0 | 0 | 0 | 0 |
EIF1AX WILD-TYPE | 16 | 7 | 12 | 12 | 2 | 14 | 5 | 2 |
Figure S7. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0012
Table S9. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
EIF1AX MUTATED | 0 | 6 | 0 | 4 |
EIF1AX WILD-TYPE | 28 | 7 | 16 | 19 |
Figure S8. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0043
Table S10. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
EIF1AX MUTATED | 0 | 4 | 6 |
EIF1AX WILD-TYPE | 40 | 11 | 19 |
Figure S9. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S11. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
BAP1 MUTATED | 8 | 1 | 0 | 8 | 3 |
BAP1 WILD-TYPE | 3 | 10 | 29 | 13 | 5 |
Figure S10. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S12. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
BAP1 MUTATED | 8 | 1 | 0 | 11 |
BAP1 WILD-TYPE | 7 | 14 | 27 | 12 |
Figure S11. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.0036 (Fisher's exact test), Q value = 0.013
Table S13. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
BAP1 MUTATED | 9 | 0 | 8 | 3 | 0 |
BAP1 WILD-TYPE | 9 | 7 | 20 | 8 | 16 |
Figure S12. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S14. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
BAP1 MUTATED | 11 | 0 | 9 | 0 |
BAP1 WILD-TYPE | 10 | 24 | 11 | 15 |
Figure S13. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.035
Table S15. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
BAP1 MUTATED | 5 | 10 | 3 | 2 | 0 |
BAP1 WILD-TYPE | 8 | 11 | 15 | 22 | 4 |
Figure S14. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0088
Table S16. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
BAP1 MUTATED | 8 | 10 | 0 | 1 | 1 |
BAP1 WILD-TYPE | 13 | 10 | 8 | 16 | 13 |
Figure S15. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S17. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
BAP1 MUTATED | 7 | 11 | 0 | 1 | 1 |
BAP1 WILD-TYPE | 11 | 10 | 37 | 1 | 1 |
Figure S16. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S18. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
BAP1 MUTATED | 5 | 5 | 0 | 0 | 0 | 9 | 1 | 0 |
BAP1 WILD-TYPE | 11 | 2 | 22 | 12 | 2 | 5 | 4 | 2 |
Figure S17. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00079
Table S19. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
BAP1 MUTATED | 13 | 1 | 6 | 0 |
BAP1 WILD-TYPE | 15 | 12 | 10 | 23 |
Figure S18. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012
Table S20. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
BAP1 MUTATED | 20 | 0 | 0 |
BAP1 WILD-TYPE | 20 | 15 | 25 |
Figure S19. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 0.557 (Fisher's exact test), Q value = 0.7
Table S21. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
GNAQ MUTATED | 5 | 4 | 18 | 10 | 3 |
GNAQ WILD-TYPE | 6 | 7 | 11 | 11 | 5 |
P value = 0.0851 (Fisher's exact test), Q value = 0.15
Table S22. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
GNAQ MUTATED | 6 | 6 | 19 | 9 |
GNAQ WILD-TYPE | 9 | 9 | 8 | 14 |
P value = 0.501 (Fisher's exact test), Q value = 0.65
Table S23. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
GNAQ MUTATED | 8 | 3 | 14 | 4 | 11 |
GNAQ WILD-TYPE | 10 | 4 | 14 | 7 | 5 |
P value = 0.0684 (Fisher's exact test), Q value = 0.13
Table S24. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
GNAQ MUTATED | 6 | 15 | 9 | 10 |
GNAQ WILD-TYPE | 15 | 9 | 11 | 5 |
P value = 0.151 (Fisher's exact test), Q value = 0.24
Table S25. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
GNAQ MUTATED | 3 | 9 | 11 | 15 | 2 |
GNAQ WILD-TYPE | 10 | 12 | 7 | 9 | 2 |
P value = 0.0579 (Fisher's exact test), Q value = 0.12
Table S26. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
GNAQ MUTATED | 6 | 8 | 5 | 11 | 10 |
GNAQ WILD-TYPE | 15 | 12 | 3 | 6 | 4 |
P value = 0.0247 (Fisher's exact test), Q value = 0.054
Table S27. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
GNAQ MUTATED | 7 | 7 | 25 | 1 | 0 |
GNAQ WILD-TYPE | 11 | 14 | 12 | 1 | 2 |
Figure S20. Get High-res Image Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.24
Table S28. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
GNAQ MUTATED | 6 | 2 | 15 | 7 | 1 | 4 | 3 | 2 |
GNAQ WILD-TYPE | 10 | 5 | 7 | 5 | 1 | 10 | 2 | 0 |
P value = 0.517 (Fisher's exact test), Q value = 0.66
Table S29. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
GNAQ MUTATED | 11 | 8 | 8 | 13 |
GNAQ WILD-TYPE | 17 | 5 | 8 | 10 |
P value = 0.0778 (Fisher's exact test), Q value = 0.14
Table S30. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
GNAQ MUTATED | 15 | 10 | 15 |
GNAQ WILD-TYPE | 25 | 5 | 10 |
P value = 0.781 (Fisher's exact test), Q value = 0.88
Table S31. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
GNA11 MUTATED | 6 | 5 | 10 | 10 | 4 |
GNA11 WILD-TYPE | 5 | 6 | 19 | 11 | 4 |
P value = 0.141 (Fisher's exact test), Q value = 0.23
Table S32. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
GNA11 MUTATED | 8 | 8 | 7 | 12 |
GNA11 WILD-TYPE | 7 | 7 | 20 | 11 |
P value = 0.332 (Fisher's exact test), Q value = 0.47
Table S33. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
GNA11 MUTATED | 10 | 4 | 11 | 6 | 4 |
GNA11 WILD-TYPE | 8 | 3 | 17 | 5 | 12 |
P value = 0.0672 (Fisher's exact test), Q value = 0.13
Table S34. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
GNA11 MUTATED | 14 | 8 | 9 | 4 |
GNA11 WILD-TYPE | 7 | 16 | 11 | 11 |
P value = 0.618 (Fisher's exact test), Q value = 0.74
Table S35. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
GNA11 MUTATED | 7 | 11 | 8 | 8 | 1 |
GNA11 WILD-TYPE | 6 | 10 | 10 | 16 | 3 |
P value = 0.334 (Fisher's exact test), Q value = 0.47
Table S36. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
GNA11 MUTATED | 13 | 9 | 3 | 5 | 5 |
GNA11 WILD-TYPE | 8 | 11 | 5 | 12 | 9 |
P value = 0.0137 (Fisher's exact test), Q value = 0.034
Table S37. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
GNA11 MUTATED | 8 | 14 | 11 | 0 | 2 |
GNA11 WILD-TYPE | 10 | 7 | 26 | 2 | 0 |
Figure S21. Get High-res Image Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 0.32
Table S38. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
GNA11 MUTATED | 8 | 5 | 6 | 4 | 1 | 9 | 2 | 0 |
GNA11 WILD-TYPE | 8 | 2 | 16 | 8 | 1 | 5 | 3 | 2 |
P value = 0.592 (Fisher's exact test), Q value = 0.73
Table S39. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
GNA11 MUTATED | 15 | 5 | 7 | 8 |
GNA11 WILD-TYPE | 13 | 8 | 9 | 15 |
P value = 0.142 (Fisher's exact test), Q value = 0.23
Table S40. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
GNA11 MUTATED | 22 | 5 | 8 |
GNA11 WILD-TYPE | 18 | 10 | 17 |
P value = 0.0431 (Fisher's exact test), Q value = 0.092
Table S41. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
SF3B1 MUTATED | 2 | 0 | 11 | 5 | 0 |
SF3B1 WILD-TYPE | 9 | 11 | 18 | 16 | 8 |
Figure S22. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.014
Table S42. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
SF3B1 MUTATED | 0 | 3 | 12 | 3 |
SF3B1 WILD-TYPE | 15 | 12 | 15 | 20 |
Figure S23. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

P value = 0.00321 (Fisher's exact test), Q value = 0.012
Table S43. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
SF3B1 MUTATED | 0 | 0 | 7 | 3 | 8 |
SF3B1 WILD-TYPE | 18 | 7 | 21 | 8 | 8 |
Figure S24. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.045
Table S44. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
SF3B1 MUTATED | 3 | 7 | 1 | 7 |
SF3B1 WILD-TYPE | 18 | 17 | 19 | 8 |
Figure S25. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

P value = 0.00403 (Fisher's exact test), Q value = 0.014
Table S45. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
SF3B1 MUTATED | 0 | 1 | 6 | 10 | 1 |
SF3B1 WILD-TYPE | 13 | 20 | 12 | 14 | 3 |
Figure S26. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.028
Table S46. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
SF3B1 MUTATED | 2 | 1 | 2 | 7 | 6 |
SF3B1 WILD-TYPE | 19 | 19 | 6 | 10 | 8 |
Figure S27. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.012
Table S47. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
SF3B1 MUTATED | 3 | 0 | 14 | 0 | 1 |
SF3B1 WILD-TYPE | 15 | 21 | 23 | 2 | 1 |
Figure S28. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0013
Table S48. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
SF3B1 MUTATED | 4 | 0 | 2 | 8 | 1 | 1 | 0 | 2 |
SF3B1 WILD-TYPE | 12 | 7 | 20 | 4 | 1 | 13 | 5 | 0 |
Figure S29. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00079
Table S49. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
SF3B1 MUTATED | 0 | 2 | 5 | 11 |
SF3B1 WILD-TYPE | 28 | 11 | 11 | 12 |
Figure S30. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.0088
Table S50. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
SF3B1 MUTATED | 3 | 4 | 11 |
SF3B1 WILD-TYPE | 37 | 11 | 14 |
Figure S31. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

P value = 0.0234 (Fisher's exact test), Q value = 0.053
Table S51. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
SRSF2 MUTATED | 0 | 2 | 0 | 0 | 1 |
SRSF2 WILD-TYPE | 11 | 9 | 29 | 21 | 7 |
Figure S32. Get High-res Image Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

P value = 0.05 (Fisher's exact test), Q value = 0.1
Table S52. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
SRSF2 MUTATED | 1 | 2 | 0 | 0 |
SRSF2 WILD-TYPE | 14 | 13 | 27 | 23 |
P value = 0.901 (Fisher's exact test), Q value = 0.99
Table S53. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
SRSF2 MUTATED | 1 | 0 | 2 | 0 | 0 |
SRSF2 WILD-TYPE | 17 | 7 | 26 | 11 | 16 |
P value = 0.621 (Fisher's exact test), Q value = 0.74
Table S54. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
SRSF2 MUTATED | 1 | 2 | 0 | 0 |
SRSF2 WILD-TYPE | 20 | 22 | 20 | 15 |
P value = 1 (Fisher's exact test), Q value = 1
Table S55. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
SRSF2 MUTATED | 0 | 1 | 1 | 1 | 0 |
SRSF2 WILD-TYPE | 13 | 20 | 17 | 23 | 4 |
P value = 0.671 (Fisher's exact test), Q value = 0.78
Table S56. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
SRSF2 MUTATED | 1 | 2 | 0 | 0 | 0 |
SRSF2 WILD-TYPE | 20 | 18 | 8 | 17 | 14 |
P value = 1 (Fisher's exact test), Q value = 1
Table S57. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
SRSF2 MUTATED | 1 | 1 | 1 | 0 | 0 |
SRSF2 WILD-TYPE | 17 | 20 | 36 | 2 | 2 |
P value = 0.727 (Fisher's exact test), Q value = 0.83
Table S58. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
SRSF2 MUTATED | 1 | 0 | 0 | 1 | 0 | 1 | 0 | 0 |
SRSF2 WILD-TYPE | 15 | 7 | 22 | 11 | 2 | 13 | 5 | 2 |
P value = 0.269 (Fisher's exact test), Q value = 0.4
Table S59. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
SRSF2 MUTATED | 1 | 0 | 2 | 0 |
SRSF2 WILD-TYPE | 27 | 13 | 14 | 23 |
P value = 0.434 (Fisher's exact test), Q value = 0.57
Table S60. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
SRSF2 MUTATED | 2 | 1 | 0 |
SRSF2 WILD-TYPE | 38 | 14 | 25 |
P value = 0.0939 (Fisher's exact test), Q value = 0.16
Table S61. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 11 | 11 | 29 | 21 | 8 |
CYSLTR2 MUTATED | 0 | 2 | 0 | 1 | 0 |
CYSLTR2 WILD-TYPE | 11 | 9 | 29 | 20 | 8 |
P value = 0.329 (Fisher's exact test), Q value = 0.47
Table S62. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 15 | 15 | 27 | 23 |
CYSLTR2 MUTATED | 0 | 1 | 0 | 2 |
CYSLTR2 WILD-TYPE | 15 | 14 | 27 | 21 |
P value = 0.43 (Fisher's exact test), Q value = 0.57
Table S63. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 7 | 28 | 11 | 16 |
CYSLTR2 MUTATED | 0 | 0 | 3 | 0 | 0 |
CYSLTR2 WILD-TYPE | 18 | 7 | 25 | 11 | 16 |
P value = 0.423 (Fisher's exact test), Q value = 0.57
Table S64. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 21 | 24 | 20 | 15 |
CYSLTR2 MUTATED | 0 | 1 | 2 | 0 |
CYSLTR2 WILD-TYPE | 21 | 23 | 18 | 15 |
P value = 0.889 (Fisher's exact test), Q value = 0.99
Table S65. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 13 | 21 | 18 | 24 | 4 |
CYSLTR2 MUTATED | 1 | 1 | 0 | 1 | 0 |
CYSLTR2 WILD-TYPE | 12 | 20 | 18 | 23 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
Table S66. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 21 | 20 | 8 | 17 | 14 |
CYSLTR2 MUTATED | 1 | 1 | 0 | 1 | 0 |
CYSLTR2 WILD-TYPE | 20 | 19 | 8 | 16 | 14 |
P value = 0.0136 (Fisher's exact test), Q value = 0.034
Table S67. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 18 | 21 | 37 | 2 | 2 |
CYSLTR2 MUTATED | 2 | 0 | 0 | 1 | 0 |
CYSLTR2 WILD-TYPE | 16 | 21 | 37 | 1 | 2 |
Figure S33. Get High-res Image Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1
Table S68. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8 |
---|---|---|---|---|---|---|---|---|
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2 |
CYSLTR2 MUTATED | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 0 |
CYSLTR2 WILD-TYPE | 15 | 7 | 21 | 12 | 2 | 13 | 5 | 2 |
P value = 1 (Fisher's exact test), Q value = 1
Table S69. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 28 | 13 | 16 | 23 |
CYSLTR2 MUTATED | 1 | 0 | 1 | 1 |
CYSLTR2 WILD-TYPE | 27 | 13 | 15 | 22 |
P value = 1 (Fisher's exact test), Q value = 1
Table S70. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 40 | 15 | 25 |
CYSLTR2 MUTATED | 2 | 0 | 1 |
CYSLTR2 WILD-TYPE | 38 | 15 | 24 |
-
Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
-
Processed Mutation data file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/5947d552-214f-400c-a2a3-61737bb767b7/correlate_genomic_events_all/4e4e215a-e17e-44fb-bf9c-509dde44b76c/call-preprocess_genomic_event/transformed.cor.cli.txt
-
Molecular subtypes file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/9d897bdb-7a9a-423a-ad17-06f28ae98803/aggregate_clusters_workflow/1d8bac82-5a1d-4cd2-aeb1-8ddd0e1e7a20/call-aggregate_clusters/TCGA-UVM-TP.transposedmergedcluster.txt
-
Number of patients = 80
-
Number of significantly mutated genes = 7
-
Number of Molecular subtypes = 10
-
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.