This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 16 genes and 9 molecular subtypes across 154 patients, 7 significant findings detected with P value < 0.05 and Q value < 0.25.
-
BRAF mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
-
KRAS mutation correlated to 'MRNA_CHIERARCHICAL'.
-
TP53 mutation correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
-
FBXW7 mutation correlated to 'CN_CNMF'.
Table 1. Get Full Table Overview of the association between mutation status of 16 genes and 9 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 7 significant findings detected.
Clinical Features |
MRNA CNMF |
MRNA CHIERARCHICAL |
CN CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
||
nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
BRAF | 20 (13%) | 134 |
4.96e-07 (6.65e-05) |
1.22e-07 (1.64e-05) |
0.000101 (0.0134) |
0.722 (1.00) |
0.926 (1.00) |
0.0103 (1.00) |
0.146 (1.00) |
0.462 (1.00) |
1 (1.00) |
TP53 | 74 (48%) | 80 |
0.00233 (0.3) |
0.0127 (1.00) |
2.17e-08 (2.95e-06) |
0.268 (1.00) |
0.38 (1.00) |
0.000112 (0.0148) |
0.83 (1.00) |
0.62 (1.00) |
1 (1.00) |
KRAS | 58 (38%) | 96 |
0.025 (1.00) |
0.000725 (0.095) |
0.836 (1.00) |
0.704 (1.00) |
0.752 (1.00) |
0.303 (1.00) |
0.596 (1.00) |
0.626 (1.00) |
0.283 (1.00) |
FBXW7 | 29 (19%) | 125 |
0.226 (1.00) |
0.093 (1.00) |
0.00183 (0.237) |
0.0038 (0.486) |
0.233 (1.00) |
0.132 (1.00) |
1 (1.00) |
1 (1.00) |
0.474 (1.00) |
APC | 103 (67%) | 51 |
0.171 (1.00) |
0.0198 (1.00) |
0.0374 (1.00) |
0.218 (1.00) |
0.388 (1.00) |
0.87 (1.00) |
0.141 (1.00) |
0.601 (1.00) |
0.258 (1.00) |
PIK3CA | 26 (17%) | 128 |
0.335 (1.00) |
0.321 (1.00) |
0.0338 (1.00) |
0.116 (1.00) |
0.332 (1.00) |
0.0435 (1.00) |
1 (1.00) |
0.514 (1.00) |
0.416 (1.00) |
NRAS | 15 (10%) | 139 |
0.0773 (1.00) |
0.38 (1.00) |
0.867 (1.00) |
0.465 (1.00) |
0.332 (1.00) |
0.229 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
SMAD4 | 18 (12%) | 136 |
0.303 (1.00) |
0.587 (1.00) |
0.00721 (0.908) |
0.852 (1.00) |
0.495 (1.00) |
0.582 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
FAM123B | 19 (12%) | 135 |
0.21 (1.00) |
0.00698 (0.886) |
0.0249 (1.00) |
0.286 (1.00) |
0.422 (1.00) |
0.214 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.338 (1.00) |
SOX9 | 9 (6%) | 145 |
0.235 (1.00) |
0.214 (1.00) |
0.398 (1.00) |
0.231 (1.00) |
0.461 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
ACVR2A | 8 (5%) | 146 |
0.045 (1.00) |
0.296 (1.00) |
0.0542 (1.00) |
0.199 (1.00) |
0.668 (1.00) |
0.665 (1.00) |
1 (1.00) |
1 (1.00) |
0.162 (1.00) |
TNFRSF10C | 6 (4%) | 148 |
0.381 (1.00) |
0.676 (1.00) |
0.119 (1.00) |
0.68 (1.00) |
0.169 (1.00) |
0.0967 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
ACOT4 | 3 (2%) | 151 |
0.665 (1.00) |
0.391 (1.00) |
0.75 (1.00) |
0.81 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
SMAD2 | 10 (6%) | 144 |
0.0995 (1.00) |
0.19 (1.00) |
0.0497 (1.00) |
1 (1.00) |
0.377 (1.00) |
0.126 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
PCBP1 | 4 (3%) | 150 |
0.33 (1.00) |
0.552 (1.00) |
0.368 (1.00) |
0.852 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
GGT1 | 3 (2%) | 151 |
0.355 (1.00) |
0.81 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
P value = 0.171 (Fisher's exact test), Q value = 1
Table S1. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
APC MUTATED | 18 | 42 | 21 | 14 |
APC WILD-TYPE | 16 | 15 | 7 | 8 |
P value = 0.0198 (Fisher's exact test), Q value = 1
Table S2. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
APC MUTATED | 40 | 21 | 34 |
APC WILD-TYPE | 13 | 21 | 12 |
Figure S1. Get High-res Image Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D1V2.png)
P value = 0.0374 (Fisher's exact test), Q value = 1
Table S3. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
APC MUTATED | 49 | 37 | 15 |
APC WILD-TYPE | 16 | 30 | 5 |
Figure S2. Get High-res Image Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
![](D1V3.png)
P value = 0.218 (Fisher's exact test), Q value = 1
Table S4. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
APC MUTATED | 19 | 28 | 12 | 9 |
APC WILD-TYPE | 4 | 19 | 6 | 7 |
P value = 0.388 (Fisher's exact test), Q value = 1
Table S5. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
APC MUTATED | 4 | 5 | 9 | 50 |
APC WILD-TYPE | 3 | 3 | 1 | 29 |
P value = 0.87 (Chi-square test), Q value = 1
Table S6. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
APC MUTATED | 4 | 13 | 3 | 13 | 68 |
APC WILD-TYPE | 4 | 7 | 1 | 7 | 32 |
P value = 0.141 (Fisher's exact test), Q value = 1
Table S7. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
APC MUTATED | 99 | 0 | 2 |
APC WILD-TYPE | 47 | 1 | 3 |
P value = 0.601 (Fisher's exact test), Q value = 1
Table S8. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
APC MUTATED | 2 | 92 |
APC WILD-TYPE | 2 | 45 |
P value = 0.258 (Fisher's exact test), Q value = 1
Table S9. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
APC MUTATED | 1 | 93 | 0 |
APC WILD-TYPE | 1 | 45 | 1 |
P value = 0.335 (Fisher's exact test), Q value = 1
Table S10. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
PIK3CA MUTATED | 6 | 5 | 6 | 4 |
PIK3CA WILD-TYPE | 28 | 52 | 22 | 18 |
P value = 0.321 (Fisher's exact test), Q value = 1
Table S11. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
PIK3CA MUTATED | 9 | 8 | 4 |
PIK3CA WILD-TYPE | 44 | 34 | 42 |
P value = 0.0338 (Fisher's exact test), Q value = 1
Table S12. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
PIK3CA MUTATED | 6 | 17 | 2 |
PIK3CA WILD-TYPE | 59 | 50 | 18 |
Figure S3. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
![](D2V3.png)
P value = 0.116 (Fisher's exact test), Q value = 1
Table S13. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
PIK3CA MUTATED | 8 | 8 | 1 | 4 |
PIK3CA WILD-TYPE | 15 | 39 | 17 | 12 |
P value = 0.332 (Fisher's exact test), Q value = 1
Table S14. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
PIK3CA MUTATED | 1 | 2 | 4 | 14 |
PIK3CA WILD-TYPE | 6 | 6 | 6 | 65 |
P value = 0.0435 (Chi-square test), Q value = 1
Table S15. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
PIK3CA MUTATED | 2 | 2 | 1 | 8 | 13 |
PIK3CA WILD-TYPE | 6 | 18 | 3 | 12 | 87 |
Figure S4. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
![](D2V6.png)
P value = 1 (Fisher's exact test), Q value = 1
Table S16. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
PIK3CA MUTATED | 25 | 0 | 1 |
PIK3CA WILD-TYPE | 121 | 1 | 4 |
P value = 0.514 (Fisher's exact test), Q value = 1
Table S17. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
PIK3CA MUTATED | 1 | 22 |
PIK3CA WILD-TYPE | 3 | 115 |
P value = 0.416 (Fisher's exact test), Q value = 1
Table S18. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
PIK3CA MUTATED | 1 | 22 | 0 |
PIK3CA WILD-TYPE | 1 | 116 | 1 |
P value = 4.96e-07 (Fisher's exact test), Q value = 6.6e-05
Table S19. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
BRAF MUTATED | 14 | 1 | 3 | 0 |
BRAF WILD-TYPE | 20 | 56 | 25 | 22 |
Figure S5. Get High-res Image Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D3V1.png)
P value = 1.22e-07 (Fisher's exact test), Q value = 1.6e-05
Table S20. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
BRAF MUTATED | 1 | 16 | 1 |
BRAF WILD-TYPE | 52 | 26 | 45 |
Figure S6. Get High-res Image Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D3V2.png)
P value = 0.000101 (Fisher's exact test), Q value = 0.013
Table S21. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
BRAF MUTATED | 1 | 17 | 2 |
BRAF WILD-TYPE | 64 | 50 | 18 |
Figure S7. Get High-res Image Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
![](D3V3.png)
P value = 0.722 (Fisher's exact test), Q value = 1
Table S22. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
BRAF MUTATED | 3 | 4 | 3 | 1 |
BRAF WILD-TYPE | 20 | 43 | 15 | 15 |
P value = 0.926 (Fisher's exact test), Q value = 1
Table S23. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
BRAF MUTATED | 1 | 1 | 1 | 8 |
BRAF WILD-TYPE | 6 | 7 | 9 | 71 |
P value = 0.0103 (Chi-square test), Q value = 1
Table S24. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
BRAF MUTATED | 0 | 0 | 1 | 7 | 12 |
BRAF WILD-TYPE | 8 | 20 | 3 | 13 | 88 |
Figure S8. Get High-res Image Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
![](D3V6.png)
P value = 0.146 (Fisher's exact test), Q value = 1
Table S25. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
BRAF MUTATED | 19 | 1 | 0 |
BRAF WILD-TYPE | 127 | 0 | 5 |
P value = 0.462 (Fisher's exact test), Q value = 1
Table S26. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
BRAF MUTATED | 1 | 19 |
BRAF WILD-TYPE | 3 | 118 |
P value = 1 (Fisher's exact test), Q value = 1
Table S27. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
BRAF MUTATED | 0 | 20 | 0 |
BRAF WILD-TYPE | 2 | 118 | 1 |
P value = 0.025 (Fisher's exact test), Q value = 1
Table S28. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
KRAS MUTATED | 10 | 16 | 17 | 7 |
KRAS WILD-TYPE | 24 | 41 | 11 | 15 |
Figure S9. Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D4V1.png)
P value = 0.000725 (Fisher's exact test), Q value = 0.095
Table S29. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
KRAS MUTATED | 27 | 16 | 7 |
KRAS WILD-TYPE | 26 | 26 | 39 |
Figure S10. Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D4V2.png)
P value = 0.836 (Fisher's exact test), Q value = 1
Table S30. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
KRAS MUTATED | 23 | 27 | 7 |
KRAS WILD-TYPE | 42 | 40 | 13 |
P value = 0.704 (Fisher's exact test), Q value = 1
Table S31. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
KRAS MUTATED | 9 | 22 | 6 | 8 |
KRAS WILD-TYPE | 14 | 25 | 12 | 8 |
P value = 0.752 (Fisher's exact test), Q value = 1
Table S32. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
KRAS MUTATED | 3 | 2 | 5 | 35 |
KRAS WILD-TYPE | 4 | 6 | 5 | 44 |
P value = 0.303 (Chi-square test), Q value = 1
Table S33. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
KRAS MUTATED | 2 | 5 | 2 | 11 | 36 |
KRAS WILD-TYPE | 6 | 15 | 2 | 9 | 64 |
P value = 0.596 (Fisher's exact test), Q value = 1
Table S34. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
KRAS MUTATED | 53 | 0 | 3 |
KRAS WILD-TYPE | 93 | 1 | 2 |
P value = 0.626 (Fisher's exact test), Q value = 1
Table S35. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
KRAS MUTATED | 2 | 50 |
KRAS WILD-TYPE | 2 | 87 |
P value = 0.283 (Fisher's exact test), Q value = 1
Table S36. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
KRAS MUTATED | 0 | 51 | 1 |
KRAS WILD-TYPE | 2 | 87 | 0 |
P value = 0.00233 (Fisher's exact test), Q value = 0.3
Table S37. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
TP53 MUTATED | 12 | 39 | 9 | 10 |
TP53 WILD-TYPE | 22 | 18 | 19 | 12 |
Figure S11. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D5V1.png)
P value = 0.0127 (Fisher's exact test), Q value = 1
Table S38. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
TP53 MUTATED | 29 | 13 | 28 |
TP53 WILD-TYPE | 24 | 29 | 18 |
Figure S12. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D5V2.png)
P value = 2.17e-08 (Fisher's exact test), Q value = 2.9e-06
Table S39. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
TP53 MUTATED | 47 | 15 | 11 |
TP53 WILD-TYPE | 18 | 52 | 9 |
Figure S13. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
![](D5V3.png)
P value = 0.268 (Fisher's exact test), Q value = 1
Table S40. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
TP53 MUTATED | 8 | 24 | 8 | 4 |
TP53 WILD-TYPE | 15 | 23 | 10 | 12 |
P value = 0.38 (Fisher's exact test), Q value = 1
Table S41. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
TP53 MUTATED | 3 | 1 | 4 | 36 |
TP53 WILD-TYPE | 4 | 7 | 6 | 43 |
P value = 0.000112 (Chi-square test), Q value = 0.015
Table S42. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
TP53 MUTATED | 3 | 12 | 0 | 1 | 57 |
TP53 WILD-TYPE | 5 | 8 | 4 | 19 | 43 |
Figure S14. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
![](D5V6.png)
P value = 0.83 (Fisher's exact test), Q value = 1
Table S43. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
TP53 MUTATED | 70 | 0 | 3 |
TP53 WILD-TYPE | 76 | 1 | 2 |
P value = 0.62 (Fisher's exact test), Q value = 1
Table S44. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
TP53 MUTATED | 1 | 68 |
TP53 WILD-TYPE | 3 | 69 |
P value = 1 (Fisher's exact test), Q value = 1
Table S45. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
TP53 MUTATED | 1 | 68 | 0 |
TP53 WILD-TYPE | 1 | 70 | 1 |
P value = 0.226 (Fisher's exact test), Q value = 1
Table S46. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
FBXW7 MUTATED | 10 | 7 | 5 | 3 |
FBXW7 WILD-TYPE | 24 | 50 | 23 | 19 |
P value = 0.093 (Fisher's exact test), Q value = 1
Table S47. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
FBXW7 MUTATED | 8 | 12 | 5 |
FBXW7 WILD-TYPE | 45 | 30 | 41 |
P value = 0.00183 (Fisher's exact test), Q value = 0.24
Table S48. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
FBXW7 MUTATED | 5 | 21 | 3 |
FBXW7 WILD-TYPE | 60 | 46 | 17 |
Figure S15. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
![](D6V3.png)
P value = 0.0038 (Fisher's exact test), Q value = 0.49
Table S49. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
FBXW7 MUTATED | 4 | 8 | 1 | 9 |
FBXW7 WILD-TYPE | 19 | 39 | 17 | 7 |
Figure S16. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
![](D6V4.png)
P value = 0.233 (Fisher's exact test), Q value = 1
Table S50. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
FBXW7 MUTATED | 1 | 4 | 2 | 15 |
FBXW7 WILD-TYPE | 6 | 4 | 8 | 64 |
P value = 0.132 (Chi-square test), Q value = 1
Table S51. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
FBXW7 MUTATED | 1 | 1 | 0 | 7 | 20 |
FBXW7 WILD-TYPE | 7 | 19 | 4 | 13 | 80 |
P value = 1 (Fisher's exact test), Q value = 1
Table S52. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
FBXW7 MUTATED | 28 | 0 | 1 |
FBXW7 WILD-TYPE | 118 | 1 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
Table S53. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
FBXW7 MUTATED | 0 | 27 |
FBXW7 WILD-TYPE | 4 | 110 |
P value = 0.474 (Fisher's exact test), Q value = 1
Table S54. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
FBXW7 MUTATED | 1 | 26 | 0 |
FBXW7 WILD-TYPE | 1 | 112 | 1 |
P value = 0.0773 (Fisher's exact test), Q value = 1
Table S55. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
NRAS MUTATED | 0 | 8 | 4 | 2 |
NRAS WILD-TYPE | 34 | 49 | 24 | 20 |
P value = 0.38 (Fisher's exact test), Q value = 1
Table S56. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
NRAS MUTATED | 7 | 2 | 5 |
NRAS WILD-TYPE | 46 | 40 | 41 |
P value = 0.867 (Fisher's exact test), Q value = 1
Table S57. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
NRAS MUTATED | 7 | 7 | 1 |
NRAS WILD-TYPE | 58 | 60 | 19 |
P value = 0.465 (Fisher's exact test), Q value = 1
Table S58. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
NRAS MUTATED | 1 | 8 | 1 | 2 |
NRAS WILD-TYPE | 22 | 39 | 17 | 14 |
P value = 0.332 (Fisher's exact test), Q value = 1
Table S59. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
NRAS MUTATED | 0 | 2 | 0 | 10 |
NRAS WILD-TYPE | 7 | 6 | 10 | 69 |
P value = 0.229 (Chi-square test), Q value = 1
Table S60. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
NRAS MUTATED | 2 | 3 | 0 | 3 | 6 |
NRAS WILD-TYPE | 6 | 17 | 4 | 17 | 94 |
P value = 1 (Fisher's exact test), Q value = 1
Table S61. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
NRAS MUTATED | 14 | 0 | 0 |
NRAS WILD-TYPE | 132 | 1 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
Table S62. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
NRAS MUTATED | 0 | 13 |
NRAS WILD-TYPE | 4 | 124 |
P value = 1 (Fisher's exact test), Q value = 1
Table S63. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
NRAS MUTATED | 0 | 13 | 0 |
NRAS WILD-TYPE | 2 | 125 | 1 |
P value = 0.303 (Fisher's exact test), Q value = 1
Table S64. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
SMAD4 MUTATED | 6 | 4 | 5 | 2 |
SMAD4 WILD-TYPE | 28 | 53 | 23 | 20 |
P value = 0.587 (Fisher's exact test), Q value = 1
Table S65. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
SMAD4 MUTATED | 5 | 7 | 5 |
SMAD4 WILD-TYPE | 48 | 35 | 41 |
P value = 0.00721 (Fisher's exact test), Q value = 0.91
Table S66. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
SMAD4 MUTATED | 2 | 12 | 4 |
SMAD4 WILD-TYPE | 63 | 55 | 16 |
Figure S17. Get High-res Image Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
![](D8V3.png)
P value = 0.852 (Fisher's exact test), Q value = 1
Table S67. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
SMAD4 MUTATED | 3 | 8 | 2 | 1 |
SMAD4 WILD-TYPE | 20 | 39 | 16 | 15 |
P value = 0.495 (Fisher's exact test), Q value = 1
Table S68. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
SMAD4 MUTATED | 2 | 0 | 1 | 11 |
SMAD4 WILD-TYPE | 5 | 8 | 9 | 68 |
P value = 0.582 (Chi-square test), Q value = 1
Table S69. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
SMAD4 MUTATED | 1 | 1 | 0 | 4 | 11 |
SMAD4 WILD-TYPE | 7 | 19 | 4 | 16 | 89 |
P value = 1 (Fisher's exact test), Q value = 1
Table S70. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
SMAD4 MUTATED | 17 | 0 | 0 |
SMAD4 WILD-TYPE | 129 | 1 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
Table S71. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
SMAD4 MUTATED | 0 | 17 |
SMAD4 WILD-TYPE | 4 | 120 |
P value = 1 (Fisher's exact test), Q value = 1
Table S72. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
SMAD4 MUTATED | 0 | 17 | 0 |
SMAD4 WILD-TYPE | 2 | 121 | 1 |
P value = 0.21 (Fisher's exact test), Q value = 1
Table S73. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
FAM123B MUTATED | 8 | 6 | 4 | 1 |
FAM123B WILD-TYPE | 26 | 51 | 24 | 21 |
P value = 0.00698 (Fisher's exact test), Q value = 0.89
Table S74. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
FAM123B MUTATED | 8 | 10 | 1 |
FAM123B WILD-TYPE | 45 | 32 | 45 |
Figure S18. Get High-res Image Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
![](D9V2.png)
P value = 0.0249 (Fisher's exact test), Q value = 1
Table S75. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
FAM123B MUTATED | 5 | 13 | 0 |
FAM123B WILD-TYPE | 60 | 54 | 20 |
Figure S19. Get High-res Image Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
![](D9V3.png)
P value = 0.286 (Fisher's exact test), Q value = 1
Table S76. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
FAM123B MUTATED | 2 | 4 | 1 | 4 |
FAM123B WILD-TYPE | 21 | 43 | 17 | 12 |
P value = 0.422 (Fisher's exact test), Q value = 1
Table S77. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
FAM123B MUTATED | 0 | 2 | 1 | 8 |
FAM123B WILD-TYPE | 7 | 6 | 9 | 71 |
P value = 0.214 (Chi-square test), Q value = 1
Table S78. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
FAM123B MUTATED | 0 | 0 | 1 | 2 | 16 |
FAM123B WILD-TYPE | 8 | 20 | 3 | 18 | 84 |
P value = 1 (Fisher's exact test), Q value = 1
Table S79. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
FAM123B MUTATED | 19 | 0 | 0 |
FAM123B WILD-TYPE | 127 | 1 | 5 |
P value = 0.425 (Fisher's exact test), Q value = 1
Table S80. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
FAM123B MUTATED | 1 | 17 |
FAM123B WILD-TYPE | 3 | 120 |
P value = 0.338 (Fisher's exact test), Q value = 1
Table S81. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
FAM123B MUTATED | 1 | 17 | 0 |
FAM123B WILD-TYPE | 1 | 121 | 1 |
P value = 0.235 (Fisher's exact test), Q value = 1
Table S82. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
SOX9 MUTATED | 2 | 3 | 0 | 3 |
SOX9 WILD-TYPE | 32 | 54 | 28 | 19 |
P value = 0.214 (Fisher's exact test), Q value = 1
Table S83. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
SOX9 MUTATED | 2 | 1 | 5 |
SOX9 WILD-TYPE | 51 | 41 | 41 |
P value = 0.398 (Fisher's exact test), Q value = 1
Table S84. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
SOX9 MUTATED | 2 | 6 | 1 |
SOX9 WILD-TYPE | 63 | 61 | 19 |
P value = 0.231 (Fisher's exact test), Q value = 1
Table S85. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
SOX9 MUTATED | 0 | 3 | 0 | 2 |
SOX9 WILD-TYPE | 23 | 44 | 18 | 14 |
P value = 0.461 (Fisher's exact test), Q value = 1
Table S86. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
SOX9 MUTATED | 1 | 0 | 0 | 4 |
SOX9 WILD-TYPE | 6 | 8 | 10 | 75 |
P value = 0.668 (Chi-square test), Q value = 1
Table S87. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
SOX9 MUTATED | 1 | 0 | 0 | 1 | 7 |
SOX9 WILD-TYPE | 7 | 20 | 4 | 19 | 93 |
P value = 1 (Fisher's exact test), Q value = 1
Table S88. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
SOX9 MUTATED | 9 | 0 | 0 |
SOX9 WILD-TYPE | 137 | 1 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
Table S89. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
SOX9 MUTATED | 0 | 9 |
SOX9 WILD-TYPE | 4 | 128 |
P value = 1 (Fisher's exact test), Q value = 1
Table S90. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
SOX9 MUTATED | 0 | 9 | 0 |
SOX9 WILD-TYPE | 2 | 129 | 1 |
P value = 0.045 (Fisher's exact test), Q value = 1
Table S91. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
ACVR2A MUTATED | 5 | 1 | 1 | 0 |
ACVR2A WILD-TYPE | 29 | 56 | 27 | 22 |
Figure S20. Get High-res Image Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
![](D11V1.png)
P value = 0.296 (Fisher's exact test), Q value = 1
Table S92. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
ACVR2A MUTATED | 2 | 4 | 1 |
ACVR2A WILD-TYPE | 51 | 38 | 45 |
P value = 0.0542 (Fisher's exact test), Q value = 1
Table S93. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
ACVR2A MUTATED | 1 | 7 | 0 |
ACVR2A WILD-TYPE | 64 | 60 | 20 |
P value = 0.199 (Fisher's exact test), Q value = 1
Table S94. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
ACVR2A MUTATED | 0 | 4 | 0 | 2 |
ACVR2A WILD-TYPE | 23 | 43 | 18 | 14 |
P value = 0.668 (Fisher's exact test), Q value = 1
Table S95. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
ACVR2A MUTATED | 0 | 1 | 0 | 5 |
ACVR2A WILD-TYPE | 7 | 7 | 10 | 74 |
P value = 0.665 (Chi-square test), Q value = 1
Table S96. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
ACVR2A MUTATED | 0 | 1 | 0 | 0 | 7 |
ACVR2A WILD-TYPE | 8 | 19 | 4 | 20 | 93 |
P value = 1 (Fisher's exact test), Q value = 1
Table S97. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
ACVR2A MUTATED | 8 | 0 | 0 |
ACVR2A WILD-TYPE | 138 | 1 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
Table S98. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
ACVR2A MUTATED | 0 | 8 |
ACVR2A WILD-TYPE | 4 | 129 |
P value = 0.162 (Fisher's exact test), Q value = 1
Table S99. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
ACVR2A MUTATED | 1 | 7 | 0 |
ACVR2A WILD-TYPE | 1 | 131 | 1 |
P value = 0.381 (Fisher's exact test), Q value = 1
Table S100. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
TNFRSF10C MUTATED | 2 | 2 | 0 | 2 |
TNFRSF10C WILD-TYPE | 32 | 55 | 28 | 20 |
P value = 0.676 (Fisher's exact test), Q value = 1
Table S101. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
TNFRSF10C MUTATED | 2 | 1 | 3 |
TNFRSF10C WILD-TYPE | 51 | 41 | 43 |
P value = 0.119 (Fisher's exact test), Q value = 1
Table S102. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
TNFRSF10C MUTATED | 5 | 1 | 0 |
TNFRSF10C WILD-TYPE | 60 | 66 | 20 |
P value = 0.68 (Fisher's exact test), Q value = 1
Table S103. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
TNFRSF10C MUTATED | 2 | 2 | 0 | 1 |
TNFRSF10C WILD-TYPE | 21 | 45 | 18 | 15 |
P value = 0.169 (Fisher's exact test), Q value = 1
Table S104. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
TNFRSF10C MUTATED | 0 | 0 | 2 | 3 |
TNFRSF10C WILD-TYPE | 7 | 8 | 8 | 76 |
P value = 0.0967 (Chi-square test), Q value = 1
Table S105. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
TNFRSF10C MUTATED | 1 | 0 | 1 | 0 | 4 |
TNFRSF10C WILD-TYPE | 7 | 20 | 3 | 20 | 96 |
P value = 1 (Fisher's exact test), Q value = 1
Table S106. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
TNFRSF10C MUTATED | 6 | 0 | 0 |
TNFRSF10C WILD-TYPE | 140 | 1 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
Table S107. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
TNFRSF10C MUTATED | 0 | 6 |
TNFRSF10C WILD-TYPE | 4 | 131 |
P value = 1 (Fisher's exact test), Q value = 1
Table S108. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
TNFRSF10C MUTATED | 0 | 6 | 0 |
TNFRSF10C WILD-TYPE | 2 | 132 | 1 |
P value = 0.665 (Fisher's exact test), Q value = 1
Table S109. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
ACOT4 MUTATED | 1 | 1 | 0 | 1 |
ACOT4 WILD-TYPE | 33 | 56 | 28 | 21 |
P value = 0.391 (Fisher's exact test), Q value = 1
Table S110. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
ACOT4 MUTATED | 1 | 2 | 0 |
ACOT4 WILD-TYPE | 52 | 40 | 46 |
P value = 0.75 (Fisher's exact test), Q value = 1
Table S111. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
ACOT4 MUTATED | 2 | 1 | 0 |
ACOT4 WILD-TYPE | 63 | 66 | 20 |
P value = 0.81 (Chi-square test), Q value = 1
Table S112. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
ACOT4 MUTATED | 0 | 0 | 0 | 1 | 2 |
ACOT4 WILD-TYPE | 8 | 20 | 4 | 19 | 98 |
P value = 1 (Fisher's exact test), Q value = 1
Table S113. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
ACOT4 MUTATED | 3 | 0 | 0 |
ACOT4 WILD-TYPE | 143 | 1 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
Table S114. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
ACOT4 MUTATED | 0 | 3 |
ACOT4 WILD-TYPE | 4 | 134 |
P value = 1 (Fisher's exact test), Q value = 1
Table S115. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
ACOT4 MUTATED | 0 | 3 | 0 |
ACOT4 WILD-TYPE | 2 | 135 | 1 |
P value = 0.0995 (Fisher's exact test), Q value = 1
Table S116. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
SMAD2 MUTATED | 3 | 1 | 4 | 1 |
SMAD2 WILD-TYPE | 31 | 56 | 24 | 21 |
P value = 0.19 (Fisher's exact test), Q value = 1
Table S117. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
SMAD2 MUTATED | 3 | 5 | 1 |
SMAD2 WILD-TYPE | 50 | 37 | 45 |
P value = 0.0497 (Fisher's exact test), Q value = 1
Table S118. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
SMAD2 MUTATED | 1 | 8 | 1 |
SMAD2 WILD-TYPE | 64 | 59 | 19 |
Figure S21. Get High-res Image Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
![](D14V3.png)
P value = 1 (Fisher's exact test), Q value = 1
Table S119. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 23 | 47 | 18 | 16 |
SMAD2 MUTATED | 2 | 3 | 1 | 1 |
SMAD2 WILD-TYPE | 21 | 44 | 17 | 15 |
P value = 0.377 (Fisher's exact test), Q value = 1
Table S120. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 7 | 8 | 10 | 79 |
SMAD2 MUTATED | 1 | 1 | 0 | 5 |
SMAD2 WILD-TYPE | 6 | 7 | 10 | 74 |
P value = 0.126 (Chi-square test), Q value = 1
Table S121. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
SMAD2 MUTATED | 0 | 1 | 0 | 4 | 5 |
SMAD2 WILD-TYPE | 8 | 19 | 4 | 16 | 95 |
P value = 1 (Fisher's exact test), Q value = 1
Table S122. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
SMAD2 MUTATED | 10 | 0 | 0 |
SMAD2 WILD-TYPE | 136 | 1 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
Table S123. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
SMAD2 MUTATED | 0 | 9 |
SMAD2 WILD-TYPE | 4 | 128 |
P value = 1 (Fisher's exact test), Q value = 1
Table S124. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
SMAD2 MUTATED | 0 | 9 | 0 |
SMAD2 WILD-TYPE | 2 | 129 | 1 |
P value = 0.33 (Fisher's exact test), Q value = 1
Table S125. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 34 | 57 | 28 | 22 |
PCBP1 MUTATED | 0 | 2 | 2 | 0 |
PCBP1 WILD-TYPE | 34 | 55 | 26 | 22 |
P value = 0.552 (Fisher's exact test), Q value = 1
Table S126. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 53 | 42 | 46 |
PCBP1 MUTATED | 2 | 0 | 2 |
PCBP1 WILD-TYPE | 51 | 42 | 44 |
P value = 0.368 (Fisher's exact test), Q value = 1
Table S127. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
PCBP1 MUTATED | 2 | 1 | 1 |
PCBP1 WILD-TYPE | 63 | 66 | 19 |
P value = 0.852 (Chi-square test), Q value = 1
Table S128. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
PCBP1 MUTATED | 0 | 1 | 0 | 0 | 3 |
PCBP1 WILD-TYPE | 8 | 19 | 4 | 20 | 97 |
P value = 1 (Fisher's exact test), Q value = 1
Table S129. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
PCBP1 MUTATED | 4 | 0 | 0 |
PCBP1 WILD-TYPE | 142 | 1 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
Table S130. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
PCBP1 MUTATED | 0 | 3 |
PCBP1 WILD-TYPE | 4 | 134 |
P value = 1 (Fisher's exact test), Q value = 1
Table S131. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
PCBP1 MUTATED | 0 | 3 | 0 |
PCBP1 WILD-TYPE | 2 | 135 | 1 |
P value = 0.355 (Fisher's exact test), Q value = 1
Table S132. Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 65 | 67 | 20 |
GGT1 MUTATED | 0 | 3 | 0 |
GGT1 WILD-TYPE | 65 | 64 | 20 |
P value = 0.81 (Chi-square test), Q value = 1
Table S133. Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 8 | 20 | 4 | 20 | 100 |
GGT1 MUTATED | 0 | 0 | 0 | 0 | 3 |
GGT1 WILD-TYPE | 8 | 20 | 4 | 20 | 97 |
P value = 1 (Fisher's exact test), Q value = 1
Table S134. Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 146 | 1 | 5 |
GGT1 MUTATED | 3 | 0 | 0 |
GGT1 WILD-TYPE | 143 | 1 | 5 |
P value = 1 (Fisher's exact test), Q value = 1
Table S135. Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'
nPatients | CLUS_2 | CLUS_3 |
---|---|---|
ALL | 4 | 137 |
GGT1 MUTATED | 0 | 3 |
GGT1 WILD-TYPE | 4 | 134 |
P value = 1 (Fisher's exact test), Q value = 1
Table S136. Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 2 | 138 | 1 |
GGT1 MUTATED | 0 | 3 | 0 |
GGT1 WILD-TYPE | 2 | 135 | 1 |
-
Mutation data file = transformed.cor.cli.txt
-
Molecular subtypes file = COAD-TP.transferedmergedcluster.txt
-
Number of patients = 154
-
Number of significantly mutated genes = 16
-
Number of Molecular subtypes = 9
-
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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.