This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 22 genes and 10 molecular subtypes across 332 patients, 20 significant findings detected with P value < 0.05 and Q value < 0.25.
-
SPOP mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
-
FOXA1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
ATM mutation correlated to 'CN_CNMF'.
-
MED12 mutation correlated to 'CN_CNMF'.
-
KDM6A mutation correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
MLL2 mutation correlated to 'CN_CNMF'.
-
ZMYM3 mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
-
CDK12 mutation correlated to 'CN_CNMF' and 'RPPA_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between mutation status of 22 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, 20 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 | |
SPOP | 37 (11%) | 295 |
1e-05 (0.00055) |
1e-05 (0.00055) |
0.641 (1.00) |
0.9 (1.00) |
1e-05 (0.00055) |
1e-05 (0.00055) |
0.782 (1.00) |
0.108 (0.567) |
0.17 (0.635) |
0.315 (0.786) |
TP53 | 23 (7%) | 309 |
0.00025 (0.00687) |
0.0159 (0.233) |
0.0915 (0.559) |
0.896 (1.00) |
0.0665 (0.515) |
0.018 (0.233) |
0.688 (1.00) |
0.00063 (0.0139) |
0.319 (0.789) |
0.132 (0.611) |
FOXA1 | 13 (4%) | 319 |
3e-05 (0.0011) |
2e-05 (0.00088) |
0.457 (0.94) |
0.11 (0.567) |
0.00023 (0.00687) |
0.00029 (0.00709) |
0.43 (0.901) |
0.0974 (0.564) |
0.567 (0.998) |
0.8 (1.00) |
KDM6A | 6 (2%) | 326 |
0.0201 (0.233) |
0.257 (0.741) |
0.539 (0.974) |
0.928 (1.00) |
0.0266 (0.279) |
0.578 (1.00) |
0.533 (0.974) |
0.356 (0.834) |
0.339 (0.814) |
0.0129 (0.203) |
CDK12 | 6 (2%) | 326 |
0.0119 (0.201) |
0.224 (0.705) |
0.168 (0.635) |
0.00542 (0.108) |
0.878 (1.00) |
0.169 (0.635) |
0.0418 (0.379) |
0.221 (0.705) |
1 (1.00) |
0.824 (1.00) |
ATM | 13 (4%) | 319 |
0.0118 (0.201) |
0.116 (0.568) |
0.557 (0.987) |
0.215 (0.705) |
0.732 (1.00) |
0.21 (0.705) |
0.144 (0.622) |
0.713 (1.00) |
0.506 (0.974) |
0.785 (1.00) |
MED12 | 6 (2%) | 326 |
0.0196 (0.233) |
0.522 (0.974) |
0.54 (0.974) |
0.766 (1.00) |
0.518 (0.974) |
0.144 (0.622) |
1 (1.00) |
0.947 (1.00) |
0.0701 (0.515) |
0.0503 (0.426) |
MLL2 | 11 (3%) | 321 |
0.0227 (0.25) |
0.798 (1.00) |
1 (1.00) |
0.891 (1.00) |
0.201 (0.705) |
0.0946 (0.563) |
0.743 (1.00) |
0.119 (0.57) |
0.395 (0.86) |
0.39 (0.86) |
ZMYM3 | 6 (2%) | 326 |
0.628 (1.00) |
0.599 (1.00) |
0.372 (0.847) |
0.818 (1.00) |
0.879 (1.00) |
0.667 (1.00) |
0.875 (1.00) |
0.532 (0.974) |
0.0702 (0.515) |
0.0174 (0.233) |
BRAF | 8 (2%) | 324 |
0.331 (0.81) |
0.256 (0.741) |
0.258 (0.741) |
0.908 (1.00) |
0.179 (0.656) |
0.477 (0.955) |
0.823 (1.00) |
0.825 (1.00) |
0.829 (1.00) |
0.288 (0.741) |
PTEN | 9 (3%) | 323 |
0.811 (1.00) |
0.164 (0.635) |
0.241 (0.738) |
0.747 (1.00) |
0.224 (0.705) |
0.0288 (0.288) |
0.706 (1.00) |
0.412 (0.888) |
0.955 (1.00) |
0.72 (1.00) |
CTNNB1 | 8 (2%) | 324 |
0.794 (1.00) |
0.0431 (0.379) |
0.168 (0.635) |
0.0872 (0.552) |
0.361 (0.837) |
0.0787 (0.552) |
0.289 (0.741) |
0.133 (0.611) |
0.54 (0.974) |
0.293 (0.741) |
AKT1 | 3 (1%) | 329 |
1 (1.00) |
0.11 (0.567) |
0.112 (0.567) |
0.265 (0.741) |
1 (1.00) |
1 (1.00) |
||||
HRAS | 4 (1%) | 328 |
1 (1.00) |
0.836 (1.00) |
1 (1.00) |
0.252 (0.741) |
0.833 (1.00) |
1 (1.00) |
0.842 (1.00) |
0.222 (0.705) |
0.698 (1.00) |
0.843 (1.00) |
XPO5 | 3 (1%) | 329 |
1 (1.00) |
0.11 (0.567) |
0.113 (0.567) |
0.19 (0.685) |
||||||
KLHL2 | 4 (1%) | 328 |
0.818 (1.00) |
0.692 (1.00) |
0.0341 (0.326) |
0.465 (0.947) |
1 (1.00) |
1 (1.00) |
0.694 (1.00) |
0.374 (0.847) |
0.705 (1.00) |
0.963 (1.00) |
AMFR | 3 (1%) | 329 |
0.139 (0.622) |
1 (1.00) |
0.608 (1.00) |
0.351 (0.831) |
1 (1.00) |
1 (1.00) |
0.537 (0.974) |
0.0819 (0.552) |
||
IL6ST | 3 (1%) | 329 |
0.0847 (0.552) |
1 (1.00) |
0.795 (1.00) |
0.472 (0.953) |
0.291 (0.741) |
0.789 (1.00) |
0.423 (0.901) |
0.856 (1.00) |
||
NKX3-1 | 4 (1%) | 328 |
0.384 (0.86) |
1 (1.00) |
0.0545 (0.444) |
0.504 (0.974) |
0.556 (0.987) |
0.238 (0.738) |
0.169 (0.635) |
0.524 (0.974) |
||
IRF4 | 4 (1%) | 328 |
0.817 (1.00) |
1 (1.00) |
0.792 (1.00) |
0.698 (1.00) |
1 (1.00) |
0.829 (1.00) |
0.22 (0.705) |
0.0878 (0.552) |
0.28 (0.741) |
0.34 (0.814) |
ASH1L | 7 (2%) | 325 |
0.765 (1.00) |
0.64 (1.00) |
0.28 (0.741) |
0.892 (1.00) |
0.163 (0.635) |
0.497 (0.974) |
0.15 (0.635) |
0.452 (0.938) |
1 (1.00) |
0.267 (0.741) |
MLL3 | 13 (4%) | 319 |
0.285 (0.741) |
0.777 (1.00) |
1 (1.00) |
0.279 (0.741) |
0.834 (1.00) |
0.395 (0.86) |
0.427 (0.901) |
0.27 (0.741) |
0.216 (0.705) |
0.776 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00055
Table S1. Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
SPOP MUTATED | 6 | 11 | 20 |
SPOP WILD-TYPE | 179 | 77 | 39 |
Figure S1. Get High-res Image Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
![](D1V1.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00055
Table S2. Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
SPOP MUTATED | 6 | 30 | 1 |
SPOP WILD-TYPE | 101 | 73 | 121 |
Figure S2. Get High-res Image Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D1V2.png)
P value = 0.641 (Fisher's exact test), Q value = 1
Table S3. Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
SPOP MUTATED | 6 | 6 | 11 |
SPOP WILD-TYPE | 82 | 51 | 93 |
P value = 0.9 (Fisher's exact test), Q value = 1
Table S4. Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
SPOP MUTATED | 5 | 8 | 5 | 5 |
SPOP WILD-TYPE | 53 | 74 | 61 | 38 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00055
Table S5. Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
SPOP MUTATED | 7 | 30 | 0 |
SPOP WILD-TYPE | 96 | 73 | 126 |
Figure S3. Get High-res Image Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D1V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00055
Table S6. Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
SPOP MUTATED | 3 | 34 | 0 |
SPOP WILD-TYPE | 113 | 98 | 84 |
Figure S4. Get High-res Image Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D1V6.png)
P value = 0.782 (Fisher's exact test), Q value = 1
Table S7. Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
SPOP MUTATED | 11 | 11 | 15 |
SPOP WILD-TYPE | 94 | 98 | 100 |
P value = 0.108 (Fisher's exact test), Q value = 0.57
Table S8. Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
SPOP MUTATED | 8 | 8 | 1 | 12 | 8 |
SPOP WILD-TYPE | 92 | 60 | 38 | 60 | 42 |
P value = 0.17 (Fisher's exact test), Q value = 0.64
Table S9. Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
SPOP MUTATED | 2 | 8 | 2 | 9 |
SPOP WILD-TYPE | 48 | 42 | 34 | 66 |
P value = 0.315 (Fisher's exact test), Q value = 0.79
Table S10. Gene #1: 'SPOP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
SPOP MUTATED | 3 | 3 | 1 | 7 | 0 | 7 |
SPOP WILD-TYPE | 36 | 20 | 20 | 38 | 25 | 51 |
P value = 0.00025 (Fisher's exact test), Q value = 0.0069
Table S11. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
TP53 MUTATED | 6 | 15 | 2 |
TP53 WILD-TYPE | 179 | 73 | 57 |
Figure S5. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
![](D2V1.png)
P value = 0.0159 (Fisher's exact test), Q value = 0.23
Table S12. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
TP53 MUTATED | 5 | 3 | 15 |
TP53 WILD-TYPE | 102 | 100 | 107 |
Figure S6. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D2V2.png)
P value = 0.0915 (Fisher's exact test), Q value = 0.56
Table S13. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
TP53 MUTATED | 3 | 2 | 11 |
TP53 WILD-TYPE | 85 | 55 | 93 |
P value = 0.896 (Fisher's exact test), Q value = 1
Table S14. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
TP53 MUTATED | 4 | 4 | 5 | 3 |
TP53 WILD-TYPE | 54 | 78 | 61 | 40 |
P value = 0.0665 (Fisher's exact test), Q value = 0.51
Table S15. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
TP53 MUTATED | 4 | 5 | 14 |
TP53 WILD-TYPE | 99 | 98 | 112 |
P value = 0.018 (Fisher's exact test), Q value = 0.23
Table S16. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
TP53 MUTATED | 5 | 6 | 12 |
TP53 WILD-TYPE | 111 | 126 | 72 |
Figure S7. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D2V6.png)
P value = 0.688 (Fisher's exact test), Q value = 1
Table S17. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
TP53 MUTATED | 6 | 7 | 10 |
TP53 WILD-TYPE | 99 | 102 | 105 |
P value = 0.00063 (Fisher's exact test), Q value = 0.014
Table S18. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
TP53 MUTATED | 3 | 1 | 9 | 6 | 4 |
TP53 WILD-TYPE | 97 | 67 | 30 | 66 | 46 |
Figure S8. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
![](D2V8.png)
P value = 0.319 (Fisher's exact test), Q value = 0.79
Table S19. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
TP53 MUTATED | 1 | 4 | 2 | 8 |
TP53 WILD-TYPE | 49 | 46 | 34 | 67 |
P value = 0.132 (Fisher's exact test), Q value = 0.61
Table S20. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
TP53 MUTATED | 2 | 0 | 4 | 4 | 0 | 5 |
TP53 WILD-TYPE | 37 | 23 | 17 | 41 | 25 | 53 |
P value = 3e-05 (Fisher's exact test), Q value = 0.0011
Table S21. Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
FOXA1 MUTATED | 0 | 7 | 6 |
FOXA1 WILD-TYPE | 185 | 81 | 53 |
Figure S9. Get High-res Image Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
![](D3V1.png)
P value = 2e-05 (Fisher's exact test), Q value = 0.00088
Table S22. Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
FOXA1 MUTATED | 1 | 12 | 0 |
FOXA1 WILD-TYPE | 106 | 91 | 122 |
Figure S10. Get High-res Image Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D3V2.png)
P value = 0.457 (Fisher's exact test), Q value = 0.94
Table S23. Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
FOXA1 MUTATED | 2 | 2 | 6 |
FOXA1 WILD-TYPE | 86 | 55 | 98 |
P value = 0.11 (Fisher's exact test), Q value = 0.57
Table S24. Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
FOXA1 MUTATED | 0 | 3 | 3 | 4 |
FOXA1 WILD-TYPE | 58 | 79 | 63 | 39 |
P value = 0.00023 (Fisher's exact test), Q value = 0.0069
Table S25. Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
FOXA1 MUTATED | 3 | 10 | 0 |
FOXA1 WILD-TYPE | 100 | 93 | 126 |
Figure S11. Get High-res Image Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D3V5.png)
P value = 0.00029 (Fisher's exact test), Q value = 0.0071
Table S26. Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
FOXA1 MUTATED | 1 | 12 | 0 |
FOXA1 WILD-TYPE | 115 | 120 | 84 |
Figure S12. Get High-res Image Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D3V6.png)
P value = 0.43 (Fisher's exact test), Q value = 0.9
Table S27. Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
FOXA1 MUTATED | 3 | 3 | 7 |
FOXA1 WILD-TYPE | 102 | 106 | 108 |
P value = 0.0974 (Fisher's exact test), Q value = 0.56
Table S28. Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
FOXA1 MUTATED | 1 | 4 | 0 | 5 | 3 |
FOXA1 WILD-TYPE | 99 | 64 | 39 | 67 | 47 |
P value = 0.567 (Fisher's exact test), Q value = 1
Table S29. Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
FOXA1 MUTATED | 1 | 1 | 1 | 5 |
FOXA1 WILD-TYPE | 49 | 49 | 35 | 70 |
P value = 0.8 (Fisher's exact test), Q value = 1
Table S30. Gene #3: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
FOXA1 MUTATED | 1 | 1 | 0 | 2 | 0 | 4 |
FOXA1 WILD-TYPE | 38 | 22 | 21 | 43 | 25 | 54 |
P value = 0.331 (Fisher's exact test), Q value = 0.81
Table S31. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
BRAF MUTATED | 4 | 1 | 3 |
BRAF WILD-TYPE | 181 | 87 | 56 |
P value = 0.256 (Fisher's exact test), Q value = 0.74
Table S32. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
BRAF MUTATED | 3 | 4 | 1 |
BRAF WILD-TYPE | 104 | 99 | 121 |
P value = 0.258 (Fisher's exact test), Q value = 0.74
Table S33. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
BRAF MUTATED | 4 | 2 | 1 |
BRAF WILD-TYPE | 84 | 55 | 103 |
P value = 0.908 (Fisher's exact test), Q value = 1
Table S34. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
BRAF MUTATED | 2 | 3 | 1 | 1 |
BRAF WILD-TYPE | 56 | 79 | 65 | 42 |
P value = 0.179 (Fisher's exact test), Q value = 0.66
Table S35. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
BRAF MUTATED | 2 | 5 | 1 |
BRAF WILD-TYPE | 101 | 98 | 125 |
P value = 0.477 (Fisher's exact test), Q value = 0.95
Table S36. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
BRAF MUTATED | 2 | 5 | 1 |
BRAF WILD-TYPE | 114 | 127 | 83 |
P value = 0.823 (Fisher's exact test), Q value = 1
Table S37. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
BRAF MUTATED | 3 | 3 | 2 |
BRAF WILD-TYPE | 102 | 106 | 113 |
P value = 0.825 (Fisher's exact test), Q value = 1
Table S38. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
BRAF MUTATED | 4 | 1 | 0 | 2 | 1 |
BRAF WILD-TYPE | 96 | 67 | 39 | 70 | 49 |
P value = 0.829 (Fisher's exact test), Q value = 1
Table S39. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
BRAF MUTATED | 1 | 0 | 1 | 2 |
BRAF WILD-TYPE | 49 | 50 | 35 | 73 |
P value = 0.288 (Fisher's exact test), Q value = 0.74
Table S40. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
BRAF MUTATED | 0 | 1 | 1 | 0 | 1 | 1 |
BRAF WILD-TYPE | 39 | 22 | 20 | 45 | 24 | 57 |
P value = 0.811 (Fisher's exact test), Q value = 1
Table S41. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
PTEN MUTATED | 5 | 3 | 1 |
PTEN WILD-TYPE | 180 | 85 | 58 |
P value = 0.164 (Fisher's exact test), Q value = 0.64
Table S42. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
PTEN MUTATED | 1 | 2 | 6 |
PTEN WILD-TYPE | 106 | 101 | 116 |
P value = 0.241 (Fisher's exact test), Q value = 0.74
Table S43. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
PTEN MUTATED | 2 | 4 | 2 |
PTEN WILD-TYPE | 86 | 53 | 102 |
P value = 0.747 (Fisher's exact test), Q value = 1
Table S44. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
PTEN MUTATED | 2 | 4 | 1 | 1 |
PTEN WILD-TYPE | 56 | 78 | 65 | 42 |
P value = 0.224 (Fisher's exact test), Q value = 0.71
Table S45. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
PTEN MUTATED | 1 | 2 | 6 |
PTEN WILD-TYPE | 102 | 101 | 120 |
P value = 0.0288 (Fisher's exact test), Q value = 0.29
Table S46. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
PTEN MUTATED | 1 | 2 | 6 |
PTEN WILD-TYPE | 115 | 130 | 78 |
Figure S13. Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
![](D5V6.png)
P value = 0.706 (Fisher's exact test), Q value = 1
Table S47. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
PTEN MUTATED | 4 | 2 | 3 |
PTEN WILD-TYPE | 101 | 107 | 112 |
P value = 0.412 (Fisher's exact test), Q value = 0.89
Table S48. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
PTEN MUTATED | 4 | 1 | 0 | 1 | 3 |
PTEN WILD-TYPE | 96 | 67 | 39 | 71 | 47 |
P value = 0.955 (Fisher's exact test), Q value = 1
Table S49. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
PTEN MUTATED | 1 | 2 | 1 | 3 |
PTEN WILD-TYPE | 49 | 48 | 35 | 72 |
P value = 0.72 (Fisher's exact test), Q value = 1
Table S50. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
PTEN MUTATED | 1 | 0 | 0 | 3 | 0 | 3 |
PTEN WILD-TYPE | 38 | 23 | 21 | 42 | 25 | 55 |
P value = 0.0118 (Fisher's exact test), Q value = 0.2
Table S51. Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
ATM MUTATED | 3 | 8 | 2 |
ATM WILD-TYPE | 182 | 80 | 57 |
Figure S14. Get High-res Image Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
![](D6V1.png)
P value = 0.116 (Fisher's exact test), Q value = 0.57
Table S52. Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
ATM MUTATED | 1 | 6 | 6 |
ATM WILD-TYPE | 106 | 97 | 116 |
P value = 0.557 (Fisher's exact test), Q value = 0.99
Table S53. Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
ATM MUTATED | 3 | 2 | 7 |
ATM WILD-TYPE | 85 | 55 | 97 |
P value = 0.215 (Fisher's exact test), Q value = 0.71
Table S54. Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
ATM MUTATED | 2 | 3 | 2 | 5 |
ATM WILD-TYPE | 56 | 79 | 64 | 38 |
P value = 0.732 (Fisher's exact test), Q value = 1
Table S55. Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
ATM MUTATED | 3 | 5 | 5 |
ATM WILD-TYPE | 100 | 98 | 121 |
P value = 0.21 (Fisher's exact test), Q value = 0.71
Table S56. Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
ATM MUTATED | 2 | 8 | 3 |
ATM WILD-TYPE | 114 | 124 | 81 |
P value = 0.144 (Fisher's exact test), Q value = 0.62
Table S57. Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
ATM MUTATED | 1 | 6 | 6 |
ATM WILD-TYPE | 104 | 103 | 109 |
P value = 0.713 (Fisher's exact test), Q value = 1
Table S58. Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
ATM MUTATED | 2 | 4 | 2 | 3 | 2 |
ATM WILD-TYPE | 98 | 64 | 37 | 69 | 48 |
P value = 0.506 (Fisher's exact test), Q value = 0.97
Table S59. Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
ATM MUTATED | 1 | 3 | 0 | 4 |
ATM WILD-TYPE | 49 | 47 | 36 | 71 |
P value = 0.785 (Fisher's exact test), Q value = 1
Table S60. Gene #6: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
ATM MUTATED | 0 | 1 | 1 | 2 | 1 | 3 |
ATM WILD-TYPE | 39 | 22 | 20 | 43 | 24 | 55 |
P value = 0.794 (Fisher's exact test), Q value = 1
Table S61. Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
CTNNB1 MUTATED | 4 | 3 | 1 |
CTNNB1 WILD-TYPE | 181 | 85 | 58 |
P value = 0.0431 (Fisher's exact test), Q value = 0.38
Table S62. Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
CTNNB1 MUTATED | 0 | 2 | 6 |
CTNNB1 WILD-TYPE | 107 | 101 | 116 |
Figure S15. Get High-res Image Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D7V2.png)
P value = 0.168 (Fisher's exact test), Q value = 0.64
Table S63. Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
CTNNB1 MUTATED | 0 | 1 | 4 |
CTNNB1 WILD-TYPE | 88 | 56 | 100 |
P value = 0.0872 (Fisher's exact test), Q value = 0.55
Table S64. Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
CTNNB1 MUTATED | 0 | 1 | 1 | 3 |
CTNNB1 WILD-TYPE | 58 | 81 | 65 | 40 |
P value = 0.361 (Fisher's exact test), Q value = 0.84
Table S65. Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
CTNNB1 MUTATED | 1 | 2 | 5 |
CTNNB1 WILD-TYPE | 102 | 101 | 121 |
P value = 0.0787 (Fisher's exact test), Q value = 0.55
Table S66. Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
CTNNB1 MUTATED | 1 | 2 | 5 |
CTNNB1 WILD-TYPE | 115 | 130 | 79 |
P value = 0.289 (Fisher's exact test), Q value = 0.74
Table S67. Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
CTNNB1 MUTATED | 1 | 2 | 5 |
CTNNB1 WILD-TYPE | 104 | 107 | 110 |
P value = 0.133 (Fisher's exact test), Q value = 0.61
Table S68. Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
CTNNB1 MUTATED | 1 | 0 | 1 | 3 | 3 |
CTNNB1 WILD-TYPE | 99 | 68 | 38 | 69 | 47 |
P value = 0.54 (Fisher's exact test), Q value = 0.97
Table S69. Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
CTNNB1 MUTATED | 1 | 3 | 0 | 3 |
CTNNB1 WILD-TYPE | 49 | 47 | 36 | 72 |
P value = 0.293 (Fisher's exact test), Q value = 0.74
Table S70. Gene #7: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
CTNNB1 MUTATED | 0 | 0 | 0 | 4 | 1 | 2 |
CTNNB1 WILD-TYPE | 39 | 23 | 21 | 41 | 24 | 56 |
P value = 0.0196 (Fisher's exact test), Q value = 0.23
Table S71. Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
MED12 MUTATED | 2 | 0 | 4 |
MED12 WILD-TYPE | 183 | 88 | 55 |
Figure S16. Get High-res Image Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
![](D8V1.png)
P value = 0.522 (Fisher's exact test), Q value = 0.97
Table S72. Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
MED12 MUTATED | 3 | 2 | 1 |
MED12 WILD-TYPE | 104 | 101 | 121 |
P value = 0.54 (Fisher's exact test), Q value = 0.97
Table S73. Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
MED12 MUTATED | 3 | 1 | 1 |
MED12 WILD-TYPE | 85 | 56 | 103 |
P value = 0.766 (Fisher's exact test), Q value = 1
Table S74. Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
MED12 MUTATED | 2 | 2 | 1 | 0 |
MED12 WILD-TYPE | 56 | 80 | 65 | 43 |
P value = 0.518 (Fisher's exact test), Q value = 0.97
Table S75. Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
MED12 MUTATED | 2 | 3 | 1 |
MED12 WILD-TYPE | 101 | 100 | 125 |
P value = 0.144 (Fisher's exact test), Q value = 0.62
Table S76. Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
MED12 MUTATED | 1 | 5 | 0 |
MED12 WILD-TYPE | 115 | 127 | 84 |
P value = 1 (Fisher's exact test), Q value = 1
Table S77. Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
MED12 MUTATED | 2 | 2 | 2 |
MED12 WILD-TYPE | 103 | 107 | 113 |
P value = 0.947 (Fisher's exact test), Q value = 1
Table S78. Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
MED12 MUTATED | 2 | 2 | 0 | 1 | 1 |
MED12 WILD-TYPE | 98 | 66 | 39 | 71 | 49 |
P value = 0.0701 (Fisher's exact test), Q value = 0.51
Table S79. Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
MED12 MUTATED | 0 | 1 | 2 | 0 |
MED12 WILD-TYPE | 50 | 49 | 34 | 75 |
P value = 0.0503 (Fisher's exact test), Q value = 0.43
Table S80. Gene #8: 'MED12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
MED12 MUTATED | 1 | 2 | 0 | 0 | 0 | 0 |
MED12 WILD-TYPE | 38 | 21 | 21 | 45 | 25 | 58 |
P value = 0.0201 (Fisher's exact test), Q value = 0.23
Table S81. Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
KDM6A MUTATED | 2 | 0 | 4 |
KDM6A WILD-TYPE | 183 | 88 | 55 |
Figure S17. Get High-res Image Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
![](D9V1.png)
P value = 0.257 (Fisher's exact test), Q value = 0.74
Table S82. Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
KDM6A MUTATED | 1 | 4 | 1 |
KDM6A WILD-TYPE | 106 | 99 | 121 |
P value = 0.539 (Fisher's exact test), Q value = 0.97
Table S83. Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
KDM6A MUTATED | 3 | 1 | 1 |
KDM6A WILD-TYPE | 85 | 56 | 103 |
P value = 0.928 (Fisher's exact test), Q value = 1
Table S84. Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
KDM6A MUTATED | 1 | 1 | 2 | 1 |
KDM6A WILD-TYPE | 57 | 81 | 64 | 42 |
P value = 0.0266 (Fisher's exact test), Q value = 0.28
Table S85. Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
KDM6A MUTATED | 0 | 5 | 1 |
KDM6A WILD-TYPE | 103 | 98 | 125 |
Figure S18. Get High-res Image Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
![](D9V5.png)
P value = 0.578 (Fisher's exact test), Q value = 1
Table S86. Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
KDM6A MUTATED | 1 | 4 | 1 |
KDM6A WILD-TYPE | 115 | 128 | 83 |
P value = 0.533 (Fisher's exact test), Q value = 0.97
Table S87. Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
KDM6A MUTATED | 2 | 3 | 1 |
KDM6A WILD-TYPE | 103 | 106 | 114 |
P value = 0.356 (Fisher's exact test), Q value = 0.83
Table S88. Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
KDM6A MUTATED | 2 | 3 | 0 | 0 | 1 |
KDM6A WILD-TYPE | 98 | 65 | 39 | 72 | 49 |
P value = 0.339 (Fisher's exact test), Q value = 0.81
Table S89. Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
KDM6A MUTATED | 0 | 0 | 1 | 3 |
KDM6A WILD-TYPE | 50 | 50 | 35 | 72 |
P value = 0.0129 (Fisher's exact test), Q value = 0.2
Table S90. Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
KDM6A MUTATED | 0 | 3 | 0 | 0 | 0 | 1 |
KDM6A WILD-TYPE | 39 | 20 | 21 | 45 | 25 | 57 |
Figure S19. Get High-res Image Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D9V10.png)
P value = 0.0227 (Fisher's exact test), Q value = 0.25
Table S91. Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
MLL2 MUTATED | 2 | 5 | 4 |
MLL2 WILD-TYPE | 183 | 83 | 55 |
Figure S20. Get High-res Image Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
![](D10V1.png)
P value = 0.798 (Fisher's exact test), Q value = 1
Table S92. Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
MLL2 MUTATED | 4 | 4 | 3 |
MLL2 WILD-TYPE | 103 | 99 | 119 |
P value = 1 (Fisher's exact test), Q value = 1
Table S93. Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
MLL2 MUTATED | 3 | 2 | 3 |
MLL2 WILD-TYPE | 85 | 55 | 101 |
P value = 0.891 (Fisher's exact test), Q value = 1
Table S94. Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
MLL2 MUTATED | 1 | 3 | 3 | 1 |
MLL2 WILD-TYPE | 57 | 79 | 63 | 42 |
P value = 0.201 (Fisher's exact test), Q value = 0.71
Table S95. Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
MLL2 MUTATED | 3 | 6 | 2 |
MLL2 WILD-TYPE | 100 | 97 | 124 |
P value = 0.0946 (Fisher's exact test), Q value = 0.56
Table S96. Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
MLL2 MUTATED | 6 | 5 | 0 |
MLL2 WILD-TYPE | 110 | 127 | 84 |
P value = 0.743 (Fisher's exact test), Q value = 1
Table S97. Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
MLL2 MUTATED | 3 | 5 | 3 |
MLL2 WILD-TYPE | 102 | 104 | 112 |
P value = 0.119 (Fisher's exact test), Q value = 0.57
Table S98. Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
MLL2 MUTATED | 3 | 4 | 3 | 0 | 1 |
MLL2 WILD-TYPE | 97 | 64 | 36 | 72 | 49 |
P value = 0.395 (Fisher's exact test), Q value = 0.86
Table S99. Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
MLL2 MUTATED | 0 | 2 | 2 | 2 |
MLL2 WILD-TYPE | 50 | 48 | 34 | 73 |
P value = 0.39 (Fisher's exact test), Q value = 0.86
Table S100. Gene #10: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
MLL2 MUTATED | 0 | 2 | 0 | 2 | 0 | 2 |
MLL2 WILD-TYPE | 39 | 21 | 21 | 43 | 25 | 56 |
P value = 1 (Fisher's exact test), Q value = 1
Table S101. Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
AKT1 MUTATED | 2 | 1 | 0 |
AKT1 WILD-TYPE | 183 | 87 | 59 |
P value = 0.11 (Fisher's exact test), Q value = 0.57
Table S102. Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
AKT1 MUTATED | 0 | 0 | 3 |
AKT1 WILD-TYPE | 107 | 103 | 119 |
P value = 0.112 (Fisher's exact test), Q value = 0.57
Table S103. Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
AKT1 MUTATED | 0 | 0 | 3 |
AKT1 WILD-TYPE | 103 | 103 | 123 |
P value = 0.265 (Fisher's exact test), Q value = 0.74
Table S104. Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
AKT1 MUTATED | 0 | 1 | 2 |
AKT1 WILD-TYPE | 116 | 131 | 82 |
P value = 1 (Fisher's exact test), Q value = 1
Table S105. Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
AKT1 MUTATED | 1 | 1 | 1 |
AKT1 WILD-TYPE | 104 | 108 | 114 |
P value = 1 (Fisher's exact test), Q value = 1
Table S106. Gene #11: 'AKT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
AKT1 MUTATED | 1 | 1 | 0 | 1 | 0 |
AKT1 WILD-TYPE | 99 | 67 | 39 | 71 | 50 |
P value = 1 (Fisher's exact test), Q value = 1
Table S107. Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
HRAS MUTATED | 3 | 1 | 0 |
HRAS WILD-TYPE | 182 | 87 | 59 |
P value = 0.836 (Fisher's exact test), Q value = 1
Table S108. Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
HRAS MUTATED | 2 | 1 | 1 |
HRAS WILD-TYPE | 105 | 102 | 121 |
P value = 1 (Fisher's exact test), Q value = 1
Table S109. Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
HRAS MUTATED | 1 | 1 | 1 |
HRAS WILD-TYPE | 87 | 56 | 103 |
P value = 0.252 (Fisher's exact test), Q value = 0.74
Table S110. Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
HRAS MUTATED | 2 | 0 | 1 | 0 |
HRAS WILD-TYPE | 56 | 82 | 65 | 43 |
P value = 0.833 (Fisher's exact test), Q value = 1
Table S111. Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
HRAS MUTATED | 1 | 2 | 1 |
HRAS WILD-TYPE | 102 | 101 | 125 |
P value = 1 (Fisher's exact test), Q value = 1
Table S112. Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
HRAS MUTATED | 1 | 2 | 1 |
HRAS WILD-TYPE | 115 | 130 | 83 |
P value = 0.842 (Fisher's exact test), Q value = 1
Table S113. Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
HRAS MUTATED | 1 | 2 | 1 |
HRAS WILD-TYPE | 104 | 107 | 114 |
P value = 0.222 (Fisher's exact test), Q value = 0.71
Table S114. Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
HRAS MUTATED | 1 | 0 | 0 | 3 | 0 |
HRAS WILD-TYPE | 99 | 68 | 39 | 69 | 50 |
P value = 0.698 (Fisher's exact test), Q value = 1
Table S115. Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
HRAS MUTATED | 1 | 0 | 1 | 1 |
HRAS WILD-TYPE | 49 | 50 | 35 | 74 |
P value = 0.843 (Fisher's exact test), Q value = 1
Table S116. Gene #12: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
HRAS MUTATED | 1 | 0 | 0 | 0 | 0 | 2 |
HRAS WILD-TYPE | 38 | 23 | 21 | 45 | 25 | 56 |
P value = 1 (Fisher's exact test), Q value = 1
Table S117. Gene #13: 'XPO5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
XPO5 MUTATED | 2 | 1 | 0 |
XPO5 WILD-TYPE | 183 | 87 | 59 |
P value = 0.11 (Fisher's exact test), Q value = 0.57
Table S118. Gene #13: 'XPO5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
XPO5 MUTATED | 0 | 0 | 3 |
XPO5 WILD-TYPE | 107 | 103 | 119 |
P value = 0.113 (Fisher's exact test), Q value = 0.57
Table S119. Gene #13: 'XPO5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
XPO5 MUTATED | 0 | 0 | 3 |
XPO5 WILD-TYPE | 103 | 103 | 123 |
P value = 0.19 (Fisher's exact test), Q value = 0.68
Table S120. Gene #13: 'XPO5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
XPO5 MUTATED | 1 | 0 | 2 |
XPO5 WILD-TYPE | 115 | 132 | 82 |
P value = 0.818 (Fisher's exact test), Q value = 1
Table S121. Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
KLHL2 MUTATED | 2 | 1 | 1 |
KLHL2 WILD-TYPE | 183 | 87 | 58 |
P value = 0.692 (Fisher's exact test), Q value = 1
Table S122. Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
KLHL2 MUTATED | 1 | 2 | 1 |
KLHL2 WILD-TYPE | 106 | 101 | 121 |
P value = 0.0341 (Fisher's exact test), Q value = 0.33
Table S123. Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
KLHL2 MUTATED | 1 | 3 | 0 |
KLHL2 WILD-TYPE | 87 | 54 | 104 |
Figure S21. Get High-res Image Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
![](D14V3.png)
P value = 0.465 (Fisher's exact test), Q value = 0.95
Table S124. Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
KLHL2 MUTATED | 2 | 1 | 0 | 1 |
KLHL2 WILD-TYPE | 56 | 81 | 66 | 42 |
P value = 1 (Fisher's exact test), Q value = 1
Table S125. Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
KLHL2 MUTATED | 1 | 1 | 2 |
KLHL2 WILD-TYPE | 102 | 102 | 124 |
P value = 1 (Fisher's exact test), Q value = 1
Table S126. Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
KLHL2 MUTATED | 1 | 2 | 1 |
KLHL2 WILD-TYPE | 115 | 130 | 83 |
P value = 0.694 (Fisher's exact test), Q value = 1
Table S127. Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
KLHL2 MUTATED | 2 | 1 | 1 |
KLHL2 WILD-TYPE | 103 | 108 | 114 |
P value = 0.374 (Fisher's exact test), Q value = 0.85
Table S128. Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
KLHL2 MUTATED | 1 | 0 | 0 | 1 | 2 |
KLHL2 WILD-TYPE | 99 | 68 | 39 | 71 | 48 |
P value = 0.705 (Fisher's exact test), Q value = 1
Table S129. Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
KLHL2 MUTATED | 2 | 1 | 0 | 1 |
KLHL2 WILD-TYPE | 48 | 49 | 36 | 74 |
P value = 0.963 (Fisher's exact test), Q value = 1
Table S130. Gene #14: 'KLHL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
KLHL2 MUTATED | 1 | 0 | 0 | 1 | 1 | 1 |
KLHL2 WILD-TYPE | 38 | 23 | 21 | 44 | 24 | 57 |
P value = 0.628 (Fisher's exact test), Q value = 1
Table S131. Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
ZMYM3 MUTATED | 3 | 1 | 2 |
ZMYM3 WILD-TYPE | 182 | 87 | 57 |
P value = 0.599 (Fisher's exact test), Q value = 1
Table S132. Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
ZMYM3 MUTATED | 1 | 3 | 2 |
ZMYM3 WILD-TYPE | 106 | 100 | 120 |
P value = 0.372 (Fisher's exact test), Q value = 0.85
Table S133. Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
ZMYM3 MUTATED | 3 | 0 | 2 |
ZMYM3 WILD-TYPE | 85 | 57 | 102 |
P value = 0.818 (Fisher's exact test), Q value = 1
Table S134. Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
ZMYM3 MUTATED | 2 | 1 | 1 | 1 |
ZMYM3 WILD-TYPE | 56 | 81 | 65 | 42 |
P value = 0.879 (Fisher's exact test), Q value = 1
Table S135. Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
ZMYM3 MUTATED | 2 | 1 | 3 |
ZMYM3 WILD-TYPE | 101 | 102 | 123 |
P value = 0.667 (Fisher's exact test), Q value = 1
Table S136. Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
ZMYM3 MUTATED | 1 | 3 | 2 |
ZMYM3 WILD-TYPE | 115 | 129 | 82 |
P value = 0.875 (Fisher's exact test), Q value = 1
Table S137. Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
ZMYM3 MUTATED | 1 | 2 | 3 |
ZMYM3 WILD-TYPE | 104 | 107 | 112 |
P value = 0.532 (Fisher's exact test), Q value = 0.97
Table S138. Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
ZMYM3 MUTATED | 2 | 1 | 2 | 1 | 0 |
ZMYM3 WILD-TYPE | 98 | 67 | 37 | 71 | 50 |
P value = 0.0702 (Fisher's exact test), Q value = 0.51
Table S139. Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
ZMYM3 MUTATED | 3 | 2 | 0 | 0 |
ZMYM3 WILD-TYPE | 47 | 48 | 36 | 75 |
P value = 0.0174 (Fisher's exact test), Q value = 0.23
Table S140. Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
ZMYM3 MUTATED | 0 | 0 | 0 | 2 | 3 | 0 |
ZMYM3 WILD-TYPE | 39 | 23 | 21 | 43 | 22 | 58 |
Figure S22. Get High-res Image Gene #15: 'ZMYM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D15V10.png)
P value = 0.139 (Fisher's exact test), Q value = 0.62
Table S141. Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
AMFR MUTATED | 1 | 0 | 2 |
AMFR WILD-TYPE | 184 | 88 | 57 |
P value = 1 (Fisher's exact test), Q value = 1
Table S142. Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
AMFR MUTATED | 1 | 1 | 1 |
AMFR WILD-TYPE | 106 | 102 | 121 |
P value = 0.608 (Fisher's exact test), Q value = 1
Table S143. Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
AMFR MUTATED | 2 | 0 | 1 |
AMFR WILD-TYPE | 86 | 57 | 103 |
P value = 0.351 (Fisher's exact test), Q value = 0.83
Table S144. Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
AMFR MUTATED | 2 | 1 | 0 | 0 |
AMFR WILD-TYPE | 56 | 81 | 66 | 43 |
P value = 1 (Fisher's exact test), Q value = 1
Table S145. Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
AMFR MUTATED | 1 | 1 | 1 |
AMFR WILD-TYPE | 102 | 102 | 125 |
P value = 1 (Fisher's exact test), Q value = 1
Table S146. Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
AMFR MUTATED | 1 | 1 | 1 |
AMFR WILD-TYPE | 115 | 131 | 83 |
P value = 0.537 (Fisher's exact test), Q value = 0.97
Table S147. Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
AMFR MUTATED | 0 | 2 | 1 |
AMFR WILD-TYPE | 105 | 107 | 114 |
P value = 0.0819 (Fisher's exact test), Q value = 0.55
Table S148. Gene #16: 'AMFR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
AMFR MUTATED | 0 | 1 | 0 | 0 | 2 |
AMFR WILD-TYPE | 100 | 67 | 39 | 72 | 48 |
P value = 0.0847 (Fisher's exact test), Q value = 0.55
Table S149. Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
IL6ST MUTATED | 0 | 2 | 1 |
IL6ST WILD-TYPE | 185 | 86 | 58 |
P value = 1 (Fisher's exact test), Q value = 1
Table S150. Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
IL6ST MUTATED | 1 | 1 | 1 |
IL6ST WILD-TYPE | 106 | 102 | 121 |
P value = 0.795 (Fisher's exact test), Q value = 1
Table S151. Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
IL6ST MUTATED | 1 | 0 | 2 |
IL6ST WILD-TYPE | 87 | 57 | 102 |
P value = 0.472 (Fisher's exact test), Q value = 0.95
Table S152. Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
IL6ST MUTATED | 1 | 0 | 1 | 1 |
IL6ST WILD-TYPE | 57 | 82 | 65 | 42 |
P value = 0.291 (Fisher's exact test), Q value = 0.74
Table S153. Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
IL6ST MUTATED | 2 | 1 | 0 |
IL6ST WILD-TYPE | 101 | 102 | 126 |
P value = 0.789 (Fisher's exact test), Q value = 1
Table S154. Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
IL6ST MUTATED | 1 | 2 | 0 |
IL6ST WILD-TYPE | 115 | 130 | 84 |
P value = 0.423 (Fisher's exact test), Q value = 0.9
Table S155. Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
IL6ST MUTATED | 2 | 0 | 1 |
IL6ST WILD-TYPE | 103 | 109 | 114 |
P value = 0.856 (Fisher's exact test), Q value = 1
Table S156. Gene #17: 'IL6ST MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
IL6ST MUTATED | 2 | 0 | 0 | 1 | 0 |
IL6ST WILD-TYPE | 98 | 68 | 39 | 71 | 50 |
P value = 0.0119 (Fisher's exact test), Q value = 0.2
Table S157. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
CDK12 MUTATED | 1 | 5 | 0 |
CDK12 WILD-TYPE | 184 | 83 | 59 |
Figure S23. Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
![](D18V1.png)
P value = 0.224 (Fisher's exact test), Q value = 0.71
Table S158. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
CDK12 MUTATED | 0 | 3 | 3 |
CDK12 WILD-TYPE | 107 | 100 | 119 |
P value = 0.168 (Fisher's exact test), Q value = 0.64
Table S159. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
CDK12 MUTATED | 0 | 1 | 4 |
CDK12 WILD-TYPE | 88 | 56 | 100 |
P value = 0.00542 (Fisher's exact test), Q value = 0.11
Table S160. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
CDK12 MUTATED | 0 | 1 | 0 | 4 |
CDK12 WILD-TYPE | 58 | 81 | 66 | 39 |
Figure S24. Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
![](D18V4.png)
P value = 0.878 (Fisher's exact test), Q value = 1
Table S161. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
CDK12 MUTATED | 1 | 2 | 3 |
CDK12 WILD-TYPE | 102 | 101 | 123 |
P value = 0.169 (Fisher's exact test), Q value = 0.64
Table S162. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
CDK12 MUTATED | 0 | 4 | 2 |
CDK12 WILD-TYPE | 116 | 128 | 82 |
P value = 0.0418 (Fisher's exact test), Q value = 0.38
Table S163. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
CDK12 MUTATED | 1 | 0 | 5 |
CDK12 WILD-TYPE | 104 | 109 | 110 |
Figure S25. Get High-res Image Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
![](D18V7.png)
P value = 0.221 (Fisher's exact test), Q value = 0.71
Table S164. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
CDK12 MUTATED | 0 | 1 | 1 | 3 | 1 |
CDK12 WILD-TYPE | 100 | 67 | 38 | 69 | 49 |
P value = 1 (Fisher's exact test), Q value = 1
Table S165. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
CDK12 MUTATED | 1 | 1 | 0 | 2 |
CDK12 WILD-TYPE | 49 | 49 | 36 | 73 |
P value = 0.824 (Fisher's exact test), Q value = 1
Table S166. Gene #18: 'CDK12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
CDK12 MUTATED | 0 | 0 | 0 | 1 | 1 | 2 |
CDK12 WILD-TYPE | 39 | 23 | 21 | 44 | 24 | 56 |
P value = 0.384 (Fisher's exact test), Q value = 0.86
Table S167. Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
NKX3-1 MUTATED | 4 | 0 | 0 |
NKX3-1 WILD-TYPE | 181 | 88 | 59 |
P value = 1 (Fisher's exact test), Q value = 1
Table S168. Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
NKX3-1 MUTATED | 1 | 1 | 2 |
NKX3-1 WILD-TYPE | 106 | 102 | 120 |
P value = 0.0545 (Fisher's exact test), Q value = 0.44
Table S169. Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
NKX3-1 MUTATED | 0 | 3 | 1 |
NKX3-1 WILD-TYPE | 88 | 54 | 103 |
P value = 0.504 (Fisher's exact test), Q value = 0.97
Table S170. Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
NKX3-1 MUTATED | 0 | 3 | 1 | 0 |
NKX3-1 WILD-TYPE | 58 | 79 | 65 | 43 |
P value = 0.556 (Fisher's exact test), Q value = 0.99
Table S171. Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
NKX3-1 MUTATED | 0 | 2 | 2 |
NKX3-1 WILD-TYPE | 103 | 101 | 124 |
P value = 0.238 (Fisher's exact test), Q value = 0.74
Table S172. Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
NKX3-1 MUTATED | 0 | 2 | 2 |
NKX3-1 WILD-TYPE | 116 | 130 | 82 |
P value = 0.169 (Fisher's exact test), Q value = 0.64
Table S173. Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
NKX3-1 MUTATED | 1 | 3 | 0 |
NKX3-1 WILD-TYPE | 104 | 106 | 115 |
P value = 0.524 (Fisher's exact test), Q value = 0.97
Table S174. Gene #19: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
NKX3-1 MUTATED | 1 | 2 | 0 | 0 | 1 |
NKX3-1 WILD-TYPE | 99 | 66 | 39 | 72 | 49 |
P value = 0.817 (Fisher's exact test), Q value = 1
Table S175. Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
IRF4 MUTATED | 2 | 1 | 1 |
IRF4 WILD-TYPE | 183 | 87 | 58 |
P value = 1 (Fisher's exact test), Q value = 1
Table S176. Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
IRF4 MUTATED | 1 | 1 | 2 |
IRF4 WILD-TYPE | 106 | 102 | 120 |
P value = 0.792 (Fisher's exact test), Q value = 1
Table S177. Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
IRF4 MUTATED | 1 | 0 | 2 |
IRF4 WILD-TYPE | 87 | 57 | 102 |
P value = 0.698 (Fisher's exact test), Q value = 1
Table S178. Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
IRF4 MUTATED | 1 | 1 | 0 | 1 |
IRF4 WILD-TYPE | 57 | 81 | 66 | 42 |
P value = 1 (Fisher's exact test), Q value = 1
Table S179. Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
IRF4 MUTATED | 1 | 1 | 2 |
IRF4 WILD-TYPE | 102 | 102 | 124 |
P value = 0.829 (Fisher's exact test), Q value = 1
Table S180. Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
IRF4 MUTATED | 2 | 1 | 1 |
IRF4 WILD-TYPE | 114 | 131 | 83 |
P value = 0.22 (Fisher's exact test), Q value = 0.71
Table S181. Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
IRF4 MUTATED | 0 | 3 | 1 |
IRF4 WILD-TYPE | 105 | 106 | 114 |
P value = 0.0878 (Fisher's exact test), Q value = 0.55
Table S182. Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
IRF4 MUTATED | 0 | 0 | 1 | 1 | 2 |
IRF4 WILD-TYPE | 100 | 68 | 38 | 71 | 48 |
P value = 0.28 (Fisher's exact test), Q value = 0.74
Table S183. Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
IRF4 MUTATED | 0 | 0 | 0 | 3 |
IRF4 WILD-TYPE | 50 | 50 | 36 | 72 |
P value = 0.34 (Fisher's exact test), Q value = 0.81
Table S184. Gene #20: 'IRF4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
IRF4 MUTATED | 0 | 0 | 0 | 0 | 0 | 3 |
IRF4 WILD-TYPE | 39 | 23 | 21 | 45 | 25 | 55 |
P value = 0.765 (Fisher's exact test), Q value = 1
Table S185. Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
ASH1L MUTATED | 4 | 1 | 2 |
ASH1L WILD-TYPE | 181 | 87 | 57 |
P value = 0.64 (Fisher's exact test), Q value = 1
Table S186. Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
ASH1L MUTATED | 1 | 3 | 3 |
ASH1L WILD-TYPE | 106 | 100 | 119 |
P value = 0.28 (Fisher's exact test), Q value = 0.74
Table S187. Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
ASH1L MUTATED | 1 | 3 | 2 |
ASH1L WILD-TYPE | 87 | 54 | 102 |
P value = 0.892 (Fisher's exact test), Q value = 1
Table S188. Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
ASH1L MUTATED | 1 | 3 | 1 | 1 |
ASH1L WILD-TYPE | 57 | 79 | 65 | 42 |
P value = 0.163 (Fisher's exact test), Q value = 0.64
Table S189. Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
ASH1L MUTATED | 0 | 4 | 3 |
ASH1L WILD-TYPE | 103 | 99 | 123 |
P value = 0.497 (Fisher's exact test), Q value = 0.97
Table S190. Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
ASH1L MUTATED | 1 | 4 | 2 |
ASH1L WILD-TYPE | 115 | 128 | 82 |
P value = 0.15 (Fisher's exact test), Q value = 0.64
Table S191. Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
ASH1L MUTATED | 3 | 0 | 4 |
ASH1L WILD-TYPE | 102 | 109 | 111 |
P value = 0.452 (Fisher's exact test), Q value = 0.94
Table S192. Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
ASH1L MUTATED | 3 | 0 | 0 | 2 | 2 |
ASH1L WILD-TYPE | 97 | 68 | 39 | 70 | 48 |
P value = 1 (Fisher's exact test), Q value = 1
Table S193. Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
ASH1L MUTATED | 1 | 1 | 0 | 1 |
ASH1L WILD-TYPE | 49 | 49 | 36 | 74 |
P value = 0.267 (Fisher's exact test), Q value = 0.74
Table S194. Gene #21: 'ASH1L MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
ASH1L MUTATED | 0 | 0 | 0 | 2 | 1 | 0 |
ASH1L WILD-TYPE | 39 | 23 | 21 | 43 | 24 | 58 |
P value = 0.285 (Fisher's exact test), Q value = 0.74
Table S195. Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 185 | 88 | 59 |
MLL3 MUTATED | 6 | 6 | 1 |
MLL3 WILD-TYPE | 179 | 82 | 58 |
P value = 0.777 (Fisher's exact test), Q value = 1
Table S196. Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 107 | 103 | 122 |
MLL3 MUTATED | 4 | 3 | 6 |
MLL3 WILD-TYPE | 103 | 100 | 116 |
P value = 1 (Fisher's exact test), Q value = 1
Table S197. Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 88 | 57 | 104 |
MLL3 MUTATED | 3 | 2 | 4 |
MLL3 WILD-TYPE | 85 | 55 | 100 |
P value = 0.279 (Fisher's exact test), Q value = 0.74
Table S198. Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 58 | 82 | 66 | 43 |
MLL3 MUTATED | 0 | 3 | 4 | 2 |
MLL3 WILD-TYPE | 58 | 79 | 62 | 41 |
P value = 0.834 (Fisher's exact test), Q value = 1
Table S199. Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 103 | 103 | 126 |
MLL3 MUTATED | 3 | 4 | 6 |
MLL3 WILD-TYPE | 100 | 99 | 120 |
P value = 0.395 (Fisher's exact test), Q value = 0.86
Table S200. Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 116 | 132 | 84 |
MLL3 MUTATED | 5 | 3 | 5 |
MLL3 WILD-TYPE | 111 | 129 | 79 |
P value = 0.427 (Fisher's exact test), Q value = 0.9
Table S201. Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 105 | 109 | 115 |
MLL3 MUTATED | 3 | 3 | 7 |
MLL3 WILD-TYPE | 102 | 106 | 108 |
P value = 0.27 (Fisher's exact test), Q value = 0.74
Table S202. Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 100 | 68 | 39 | 72 | 50 |
MLL3 MUTATED | 2 | 3 | 4 | 3 | 1 |
MLL3 WILD-TYPE | 98 | 65 | 35 | 69 | 49 |
P value = 0.216 (Fisher's exact test), Q value = 0.71
Table S203. Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 50 | 50 | 36 | 75 |
MLL3 MUTATED | 2 | 5 | 0 | 3 |
MLL3 WILD-TYPE | 48 | 45 | 36 | 72 |
P value = 0.776 (Fisher's exact test), Q value = 1
Table S204. Gene #22: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 |
---|---|---|---|---|---|---|
ALL | 39 | 23 | 21 | 45 | 25 | 58 |
MLL3 MUTATED | 2 | 0 | 1 | 4 | 1 | 2 |
MLL3 WILD-TYPE | 37 | 23 | 20 | 41 | 24 | 56 |
-
Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
-
Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/20064817/transformed.cor.cli.txt
-
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/20168456/PRAD-TP.transferedmergedcluster.txt
-
Number of patients = 332
-
Number of significantly mutated genes = 22
-
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.
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.