This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 18 genes and 8 molecular subtypes across 198 patients, 36 significant findings detected with P value < 0.05 and Q value < 0.25.
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TP53 mutation correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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CTNNB1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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RB1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
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AXIN1 mutation correlated to 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
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BAP1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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TSC2 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
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ARID1A mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.
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ALB mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
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HNF1A mutation correlated to 'MIRSEQ_MATURE_CNMF'.
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APOB mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
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GNAS mutation correlated to 'MRNASEQ_CNMF'.
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HIST1H1C mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between mutation status of 18 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 36 significant findings detected.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
CTNNB1 | 51 (26%) | 147 |
0.0377 (0.165) |
0.00087 (0.0114) |
1e-05 (0.000288) |
1e-05 (0.000288) |
0.0465 (0.186) |
1e-05 (0.000288) |
0.00038 (0.00684) |
1e-05 (0.000288) |
BAP1 | 10 (5%) | 188 |
0.706 (0.877) |
0.0075 (0.0635) |
0.00128 (0.0154) |
0.00036 (0.00684) |
5e-05 (0.0012) |
0.0106 (0.0779) |
0.0391 (0.166) |
0.0181 (0.105) |
TP53 | 62 (31%) | 136 |
0.00682 (0.0614) |
0.775 (0.905) |
1e-05 (0.000288) |
0.0205 (0.105) |
0.0197 (0.105) |
0.00054 (0.00864) |
0.232 (0.495) |
0.0115 (0.0787) |
AXIN1 | 9 (5%) | 189 |
0.279 (0.515) |
0.476 (0.711) |
0.0108 (0.0779) |
0.186 (0.438) |
0.00457 (0.0506) |
0.457 (0.7) |
0.00527 (0.0542) |
0.693 (0.876) |
RB1 | 15 (8%) | 183 |
0.727 (0.877) |
0.00081 (0.0114) |
0.00609 (0.0585) |
0.31 (0.531) |
0.213 (0.48) |
0.39 (0.624) |
0.213 (0.48) |
0.303 (0.525) |
TSC2 | 9 (5%) | 189 |
0.907 (0.953) |
0.0189 (0.105) |
0.102 (0.316) |
0.0194 (0.105) |
0.764 (0.901) |
0.567 (0.785) |
0.788 (0.905) |
0.11 (0.316) |
ARID1A | 16 (8%) | 182 |
0.831 (0.907) |
0.29 (0.516) |
0.067 (0.254) |
0.0251 (0.117) |
0.109 (0.316) |
0.671 (0.863) |
0.016 (0.105) |
0.585 (0.795) |
ALB | 18 (9%) | 180 |
0.0412 (0.17) |
0.0218 (0.105) |
0.408 (0.645) |
0.575 (0.788) |
0.824 (0.905) |
0.843 (0.913) |
0.505 (0.724) |
0.253 (0.501) |
HNF1A | 8 (4%) | 190 |
0.162 (0.41) |
0.666 (0.863) |
0.0705 (0.254) |
0.526 (0.742) |
0.0944 (0.316) |
0.152 (0.399) |
0.0105 (0.0779) |
0.287 (0.516) |
APOB | 24 (12%) | 174 |
1 (1.00) |
0.892 (0.944) |
0.132 (0.369) |
0.1 (0.316) |
0.276 (0.515) |
0.0693 (0.254) |
0.219 (0.484) |
0.0201 (0.105) |
GNAS | 7 (4%) | 191 |
0.89 (0.944) |
0.238 (0.495) |
0.0293 (0.132) |
0.172 (0.419) |
0.0781 (0.274) |
0.45 (0.696) |
0.555 (0.777) |
0.725 (0.877) |
HIST1H1C | 5 (3%) | 193 |
0.722 (0.877) |
0.737 (0.877) |
0.471 (0.711) |
0.347 (0.58) |
0.801 (0.905) |
0.247 (0.501) |
0.641 (0.839) |
0.0212 (0.105) |
IL6ST | 7 (4%) | 191 |
0.491 (0.714) |
0.297 (0.521) |
0.17 (0.419) |
0.137 (0.373) |
0.441 (0.691) |
0.107 (0.316) |
0.479 (0.711) |
1 (1.00) |
EEF1A1 | 5 (3%) | 193 |
0.0555 (0.216) |
0.736 (0.877) |
0.254 (0.501) |
0.133 (0.369) |
0.611 (0.818) |
0.261 (0.505) |
0.241 (0.495) |
0.617 (0.818) |
KIF19 | 10 (5%) | 188 |
0.918 (0.958) |
0.104 (0.316) |
0.234 (0.495) |
0.238 (0.495) |
0.383 (0.62) |
0.81 (0.905) |
0.152 (0.399) |
0.1 (0.316) |
F5 | 4 (2%) | 194 |
0.817 (0.905) |
0.18 (0.432) |
0.798 (0.905) |
0.619 (0.818) |
0.102 (0.316) |
0.936 (0.963) |
||
PTEN | 7 (4%) | 191 |
0.49 (0.714) |
0.263 (0.505) |
0.372 (0.615) |
0.508 (0.724) |
0.86 (0.924) |
0.275 (0.515) |
0.783 (0.905) |
0.285 (0.516) |
DLK2 | 4 (2%) | 194 |
0.818 (0.905) |
0.693 (0.876) |
0.735 (0.877) |
0.379 (0.62) |
0.333 (0.564) |
0.936 (0.963) |
0.189 (0.438) |
0.162 (0.41) |
P value = 0.00682 (Fisher's exact test), Q value = 0.061
Table S1. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
TP53 MUTATED | 9 | 29 | 24 |
TP53 WILD-TYPE | 37 | 33 | 61 |
Figure S1. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
![](D1V1.png)
P value = 0.775 (Fisher's exact test), Q value = 0.91
Table S2. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
TP53 MUTATED | 19 | 27 | 16 |
TP53 WILD-TYPE | 38 | 56 | 42 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00029
Table S3. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
TP53 MUTATED | 30 | 16 | 3 | 5 | 7 |
TP53 WILD-TYPE | 13 | 39 | 26 | 31 | 25 |
Figure S2. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D1V3.png)
P value = 0.0205 (Fisher's exact test), Q value = 0.1
Table S4. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
TP53 MUTATED | 18 | 10 | 20 | 6 | 7 |
TP53 WILD-TYPE | 16 | 19 | 47 | 30 | 22 |
Figure S3. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D1V4.png)
P value = 0.0197 (Fisher's exact test), Q value = 0.1
Table S5. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
TP53 MUTATED | 16 | 25 | 10 | 10 |
TP53 WILD-TYPE | 22 | 43 | 17 | 50 |
Figure S4. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D1V5.png)
P value = 0.00054 (Fisher's exact test), Q value = 0.0086
Table S6. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
TP53 MUTATED | 14 | 25 | 6 | 14 | 2 |
TP53 WILD-TYPE | 10 | 33 | 18 | 52 | 19 |
Figure S5. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D1V6.png)
P value = 0.232 (Fisher's exact test), Q value = 0.49
Table S7. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
TP53 MUTATED | 22 | 10 | 17 | 10 |
TP53 WILD-TYPE | 35 | 31 | 39 | 11 |
P value = 0.0115 (Fisher's exact test), Q value = 0.079
Table S8. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
TP53 MUTATED | 13 | 23 | 10 | 10 | 3 |
TP53 WILD-TYPE | 19 | 30 | 40 | 10 | 17 |
Figure S6. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D1V8.png)
P value = 0.0377 (Fisher's exact test), Q value = 0.16
Table S9. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
CTNNB1 MUTATED | 19 | 13 | 19 |
CTNNB1 WILD-TYPE | 27 | 49 | 66 |
Figure S7. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
![](D2V1.png)
P value = 0.00087 (Fisher's exact test), Q value = 0.011
Table S10. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
CTNNB1 MUTATED | 9 | 33 | 9 |
CTNNB1 WILD-TYPE | 48 | 50 | 49 |
Figure S8. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D2V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00029
Table S11. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
CTNNB1 MUTATED | 9 | 8 | 1 | 5 | 28 |
CTNNB1 WILD-TYPE | 34 | 47 | 28 | 31 | 4 |
Figure S9. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D2V3.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00029
Table S12. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
CTNNB1 MUTATED | 3 | 7 | 9 | 7 | 25 |
CTNNB1 WILD-TYPE | 31 | 22 | 58 | 29 | 4 |
Figure S10. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D2V4.png)
P value = 0.0465 (Fisher's exact test), Q value = 0.19
Table S13. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
CTNNB1 MUTATED | 9 | 25 | 7 | 9 |
CTNNB1 WILD-TYPE | 29 | 43 | 20 | 51 |
Figure S11. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D2V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00029
Table S14. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
CTNNB1 MUTATED | 8 | 11 | 2 | 11 | 18 |
CTNNB1 WILD-TYPE | 16 | 47 | 22 | 55 | 3 |
Figure S12. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D2V6.png)
P value = 0.00038 (Fisher's exact test), Q value = 0.0068
Table S15. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
CTNNB1 MUTATED | 8 | 5 | 25 | 5 |
CTNNB1 WILD-TYPE | 49 | 36 | 31 | 16 |
Figure S13. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
![](D2V7.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.00029
Table S16. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
CTNNB1 MUTATED | 3 | 10 | 7 | 7 | 16 |
CTNNB1 WILD-TYPE | 29 | 43 | 43 | 13 | 4 |
Figure S14. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D2V8.png)
P value = 0.727 (Fisher's exact test), Q value = 0.88
Table S17. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
RB1 MUTATED | 3 | 6 | 5 |
RB1 WILD-TYPE | 43 | 56 | 80 |
P value = 0.00081 (Fisher's exact test), Q value = 0.011
Table S18. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
RB1 MUTATED | 1 | 3 | 11 |
RB1 WILD-TYPE | 56 | 80 | 47 |
Figure S15. Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D3V2.png)
P value = 0.00609 (Fisher's exact test), Q value = 0.058
Table S19. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
RB1 MUTATED | 3 | 6 | 6 | 0 | 0 |
RB1 WILD-TYPE | 40 | 49 | 23 | 36 | 32 |
Figure S16. Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D3V3.png)
P value = 0.31 (Fisher's exact test), Q value = 0.53
Table S20. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
RB1 MUTATED | 3 | 1 | 8 | 3 | 0 |
RB1 WILD-TYPE | 31 | 28 | 59 | 33 | 29 |
P value = 0.213 (Fisher's exact test), Q value = 0.48
Table S21. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
RB1 MUTATED | 0 | 6 | 2 | 6 |
RB1 WILD-TYPE | 38 | 62 | 25 | 54 |
P value = 0.39 (Fisher's exact test), Q value = 0.62
Table S22. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
RB1 MUTATED | 1 | 3 | 2 | 8 | 0 |
RB1 WILD-TYPE | 23 | 55 | 22 | 58 | 21 |
P value = 0.213 (Fisher's exact test), Q value = 0.48
Table S23. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
RB1 MUTATED | 6 | 4 | 1 | 1 |
RB1 WILD-TYPE | 51 | 37 | 55 | 20 |
P value = 0.303 (Fisher's exact test), Q value = 0.52
Table S24. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
RB1 MUTATED | 5 | 3 | 3 | 1 | 0 |
RB1 WILD-TYPE | 27 | 50 | 47 | 19 | 20 |
P value = 0.279 (Fisher's exact test), Q value = 0.51
Table S25. Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
AXIN1 MUTATED | 2 | 5 | 2 |
AXIN1 WILD-TYPE | 44 | 57 | 83 |
P value = 0.476 (Fisher's exact test), Q value = 0.71
Table S26. Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
AXIN1 MUTATED | 1 | 4 | 4 |
AXIN1 WILD-TYPE | 56 | 79 | 54 |
P value = 0.0108 (Fisher's exact test), Q value = 0.078
Table S27. Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
AXIN1 MUTATED | 1 | 3 | 5 | 0 | 0 |
AXIN1 WILD-TYPE | 42 | 52 | 24 | 36 | 32 |
Figure S17. Get High-res Image Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D4V3.png)
P value = 0.186 (Fisher's exact test), Q value = 0.44
Table S28. Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
AXIN1 MUTATED | 1 | 0 | 4 | 4 | 0 |
AXIN1 WILD-TYPE | 33 | 29 | 63 | 32 | 29 |
P value = 0.00457 (Fisher's exact test), Q value = 0.051
Table S29. Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
AXIN1 MUTATED | 0 | 4 | 4 | 0 |
AXIN1 WILD-TYPE | 38 | 64 | 23 | 60 |
Figure S18. Get High-res Image Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D4V5.png)
P value = 0.457 (Fisher's exact test), Q value = 0.7
Table S30. Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
AXIN1 MUTATED | 1 | 1 | 2 | 4 | 0 |
AXIN1 WILD-TYPE | 23 | 57 | 22 | 62 | 21 |
P value = 0.00527 (Fisher's exact test), Q value = 0.054
Table S31. Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
AXIN1 MUTATED | 1 | 0 | 2 | 4 |
AXIN1 WILD-TYPE | 56 | 41 | 54 | 17 |
Figure S19. Get High-res Image Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
![](D4V7.png)
P value = 0.693 (Fisher's exact test), Q value = 0.88
Table S32. Gene #4: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
AXIN1 MUTATED | 0 | 2 | 3 | 1 | 1 |
AXIN1 WILD-TYPE | 32 | 51 | 47 | 19 | 19 |
P value = 0.706 (Fisher's exact test), Q value = 0.88
Table S33. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
BAP1 MUTATED | 2 | 2 | 6 |
BAP1 WILD-TYPE | 44 | 60 | 79 |
P value = 0.0075 (Fisher's exact test), Q value = 0.064
Table S34. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
BAP1 MUTATED | 5 | 0 | 5 |
BAP1 WILD-TYPE | 52 | 83 | 53 |
Figure S20. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D5V2.png)
P value = 0.00128 (Fisher's exact test), Q value = 0.015
Table S35. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
BAP1 MUTATED | 1 | 0 | 4 | 5 | 0 |
BAP1 WILD-TYPE | 42 | 55 | 25 | 31 | 32 |
Figure S21. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D5V3.png)
P value = 0.00036 (Fisher's exact test), Q value = 0.0068
Table S36. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
BAP1 MUTATED | 5 | 0 | 0 | 5 | 0 |
BAP1 WILD-TYPE | 29 | 29 | 67 | 31 | 29 |
Figure S22. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D5V4.png)
P value = 5e-05 (Fisher's exact test), Q value = 0.0012
Table S37. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
BAP1 MUTATED | 0 | 0 | 0 | 10 |
BAP1 WILD-TYPE | 38 | 68 | 27 | 50 |
Figure S23. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
![](D5V5.png)
P value = 0.0106 (Fisher's exact test), Q value = 0.078
Table S38. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
BAP1 MUTATED | 0 | 0 | 2 | 8 | 0 |
BAP1 WILD-TYPE | 24 | 58 | 22 | 58 | 21 |
Figure S24. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
![](D5V6.png)
P value = 0.0391 (Fisher's exact test), Q value = 0.17
Table S39. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
BAP1 MUTATED | 4 | 5 | 0 | 1 |
BAP1 WILD-TYPE | 53 | 36 | 56 | 20 |
Figure S25. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
![](D5V7.png)
P value = 0.0181 (Fisher's exact test), Q value = 0.1
Table S40. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
BAP1 MUTATED | 1 | 1 | 8 | 0 | 0 |
BAP1 WILD-TYPE | 31 | 52 | 42 | 20 | 20 |
Figure S26. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D5V8.png)
P value = 0.907 (Fisher's exact test), Q value = 0.95
Table S41. Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
TSC2 MUTATED | 2 | 2 | 5 |
TSC2 WILD-TYPE | 44 | 60 | 80 |
P value = 0.0189 (Fisher's exact test), Q value = 0.1
Table S42. Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
TSC2 MUTATED | 6 | 3 | 0 |
TSC2 WILD-TYPE | 51 | 80 | 58 |
Figure S27. Get High-res Image Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D6V2.png)
P value = 0.102 (Fisher's exact test), Q value = 0.32
Table S43. Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
TSC2 MUTATED | 5 | 1 | 2 | 1 | 0 |
TSC2 WILD-TYPE | 38 | 54 | 27 | 35 | 32 |
P value = 0.0194 (Fisher's exact test), Q value = 0.1
Table S44. Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
TSC2 MUTATED | 5 | 0 | 4 | 0 | 0 |
TSC2 WILD-TYPE | 29 | 29 | 63 | 36 | 29 |
Figure S28. Get High-res Image Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D6V4.png)
P value = 0.764 (Fisher's exact test), Q value = 0.9
Table S45. Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
TSC2 MUTATED | 2 | 4 | 0 | 3 |
TSC2 WILD-TYPE | 36 | 64 | 27 | 57 |
P value = 0.567 (Fisher's exact test), Q value = 0.78
Table S46. Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
TSC2 MUTATED | 2 | 2 | 2 | 2 | 1 |
TSC2 WILD-TYPE | 22 | 56 | 22 | 64 | 20 |
P value = 0.788 (Fisher's exact test), Q value = 0.91
Table S47. Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
TSC2 MUTATED | 4 | 2 | 3 | 0 |
TSC2 WILD-TYPE | 53 | 39 | 53 | 21 |
P value = 0.11 (Fisher's exact test), Q value = 0.32
Table S48. Gene #6: 'TSC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
TSC2 MUTATED | 4 | 1 | 1 | 1 | 2 |
TSC2 WILD-TYPE | 28 | 52 | 49 | 19 | 18 |
P value = 0.831 (Fisher's exact test), Q value = 0.91
Table S49. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
ARID1A MUTATED | 3 | 6 | 6 |
ARID1A WILD-TYPE | 43 | 56 | 79 |
P value = 0.29 (Fisher's exact test), Q value = 0.52
Table S50. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
ARID1A MUTATED | 5 | 4 | 7 |
ARID1A WILD-TYPE | 52 | 79 | 51 |
P value = 0.067 (Fisher's exact test), Q value = 0.25
Table S51. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
ARID1A MUTATED | 2 | 2 | 6 | 2 | 4 |
ARID1A WILD-TYPE | 41 | 53 | 23 | 34 | 28 |
P value = 0.0251 (Fisher's exact test), Q value = 0.12
Table S52. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
ARID1A MUTATED | 1 | 2 | 2 | 7 | 4 |
ARID1A WILD-TYPE | 33 | 27 | 65 | 29 | 25 |
Figure S29. Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
![](D7V4.png)
P value = 0.109 (Fisher's exact test), Q value = 0.32
Table S53. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
ARID1A MUTATED | 4 | 5 | 5 | 2 |
ARID1A WILD-TYPE | 34 | 63 | 22 | 58 |
P value = 0.671 (Fisher's exact test), Q value = 0.86
Table S54. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
ARID1A MUTATED | 3 | 3 | 3 | 6 | 1 |
ARID1A WILD-TYPE | 21 | 55 | 21 | 60 | 20 |
P value = 0.016 (Fisher's exact test), Q value = 0.1
Table S55. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
ARID1A MUTATED | 4 | 3 | 2 | 6 |
ARID1A WILD-TYPE | 53 | 38 | 54 | 15 |
Figure S30. Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
![](D7V7.png)
P value = 0.585 (Fisher's exact test), Q value = 0.79
Table S56. Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
ARID1A MUTATED | 2 | 3 | 6 | 3 | 1 |
ARID1A WILD-TYPE | 30 | 50 | 44 | 17 | 19 |
P value = 0.491 (Fisher's exact test), Q value = 0.71
Table S57. Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
IL6ST MUTATED | 0 | 2 | 4 |
IL6ST WILD-TYPE | 46 | 60 | 81 |
P value = 0.297 (Fisher's exact test), Q value = 0.52
Table S58. Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
IL6ST MUTATED | 3 | 1 | 3 |
IL6ST WILD-TYPE | 54 | 82 | 55 |
P value = 0.17 (Fisher's exact test), Q value = 0.42
Table S59. Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
IL6ST MUTATED | 1 | 1 | 2 | 0 | 3 |
IL6ST WILD-TYPE | 42 | 54 | 27 | 36 | 29 |
P value = 0.137 (Fisher's exact test), Q value = 0.37
Table S60. Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
IL6ST MUTATED | 0 | 1 | 1 | 2 | 3 |
IL6ST WILD-TYPE | 34 | 28 | 66 | 34 | 26 |
P value = 0.441 (Fisher's exact test), Q value = 0.69
Table S61. Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
IL6ST MUTATED | 0 | 3 | 2 | 2 |
IL6ST WILD-TYPE | 38 | 65 | 25 | 58 |
P value = 0.107 (Fisher's exact test), Q value = 0.32
Table S62. Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
IL6ST MUTATED | 0 | 0 | 1 | 4 | 2 |
IL6ST WILD-TYPE | 24 | 58 | 23 | 62 | 19 |
P value = 0.479 (Fisher's exact test), Q value = 0.71
Table S63. Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
IL6ST MUTATED | 2 | 0 | 3 | 1 |
IL6ST WILD-TYPE | 55 | 41 | 53 | 20 |
P value = 1 (Fisher's exact test), Q value = 1
Table S64. Gene #8: 'IL6ST MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
IL6ST MUTATED | 1 | 2 | 2 | 0 | 1 |
IL6ST WILD-TYPE | 31 | 51 | 48 | 20 | 19 |
P value = 0.0412 (Fisher's exact test), Q value = 0.17
Table S65. Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
ALB MUTATED | 8 | 2 | 7 |
ALB WILD-TYPE | 38 | 60 | 78 |
Figure S31. Get High-res Image Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
![](D9V1.png)
P value = 0.0218 (Fisher's exact test), Q value = 0.1
Table S66. Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
ALB MUTATED | 5 | 12 | 1 |
ALB WILD-TYPE | 52 | 71 | 57 |
Figure S32. Get High-res Image Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
![](D9V2.png)
P value = 0.408 (Fisher's exact test), Q value = 0.64
Table S67. Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
ALB MUTATED | 4 | 6 | 0 | 4 | 3 |
ALB WILD-TYPE | 39 | 49 | 29 | 32 | 29 |
P value = 0.575 (Fisher's exact test), Q value = 0.79
Table S68. Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
ALB MUTATED | 3 | 4 | 6 | 1 | 3 |
ALB WILD-TYPE | 31 | 25 | 61 | 35 | 26 |
P value = 0.824 (Fisher's exact test), Q value = 0.91
Table S69. Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
ALB MUTATED | 4 | 6 | 1 | 5 |
ALB WILD-TYPE | 34 | 62 | 26 | 55 |
P value = 0.843 (Fisher's exact test), Q value = 0.91
Table S70. Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
ALB MUTATED | 3 | 5 | 2 | 4 | 2 |
ALB WILD-TYPE | 21 | 53 | 22 | 62 | 19 |
P value = 0.505 (Fisher's exact test), Q value = 0.72
Table S71. Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
ALB MUTATED | 4 | 4 | 6 | 0 |
ALB WILD-TYPE | 53 | 37 | 50 | 21 |
P value = 0.253 (Fisher's exact test), Q value = 0.5
Table S72. Gene #9: 'ALB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
ALB MUTATED | 1 | 5 | 2 | 3 | 3 |
ALB WILD-TYPE | 31 | 48 | 48 | 17 | 17 |
P value = 0.162 (Fisher's exact test), Q value = 0.41
Table S73. Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
HNF1A MUTATED | 0 | 2 | 6 |
HNF1A WILD-TYPE | 46 | 60 | 79 |
P value = 0.666 (Fisher's exact test), Q value = 0.86
Table S74. Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
HNF1A MUTATED | 3 | 4 | 1 |
HNF1A WILD-TYPE | 54 | 79 | 57 |
P value = 0.0705 (Fisher's exact test), Q value = 0.25
Table S75. Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
HNF1A MUTATED | 1 | 6 | 0 | 0 | 1 |
HNF1A WILD-TYPE | 42 | 49 | 29 | 36 | 31 |
P value = 0.526 (Fisher's exact test), Q value = 0.74
Table S76. Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
HNF1A MUTATED | 1 | 1 | 5 | 0 | 1 |
HNF1A WILD-TYPE | 33 | 28 | 62 | 36 | 28 |
P value = 0.0944 (Fisher's exact test), Q value = 0.32
Table S77. Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
HNF1A MUTATED | 1 | 5 | 2 | 0 |
HNF1A WILD-TYPE | 37 | 63 | 25 | 60 |
P value = 0.152 (Fisher's exact test), Q value = 0.4
Table S78. Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
HNF1A MUTATED | 0 | 6 | 0 | 2 | 0 |
HNF1A WILD-TYPE | 24 | 52 | 24 | 64 | 21 |
P value = 0.0105 (Fisher's exact test), Q value = 0.078
Table S79. Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
HNF1A MUTATED | 0 | 0 | 5 | 2 |
HNF1A WILD-TYPE | 57 | 41 | 51 | 19 |
Figure S33. Get High-res Image Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
![](D10V7.png)
P value = 0.287 (Fisher's exact test), Q value = 0.52
Table S80. Gene #10: 'HNF1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
HNF1A MUTATED | 1 | 5 | 1 | 0 | 0 |
HNF1A WILD-TYPE | 31 | 48 | 49 | 20 | 20 |
P value = 1 (Fisher's exact test), Q value = 1
Table S81. Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
APOB MUTATED | 5 | 7 | 10 |
APOB WILD-TYPE | 41 | 55 | 75 |
P value = 0.892 (Fisher's exact test), Q value = 0.94
Table S82. Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
APOB MUTATED | 6 | 10 | 8 |
APOB WILD-TYPE | 51 | 73 | 50 |
P value = 0.132 (Fisher's exact test), Q value = 0.37
Table S83. Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
APOB MUTATED | 3 | 6 | 4 | 2 | 8 |
APOB WILD-TYPE | 40 | 49 | 25 | 34 | 24 |
P value = 0.1 (Fisher's exact test), Q value = 0.32
Table S84. Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
APOB MUTATED | 4 | 2 | 7 | 2 | 8 |
APOB WILD-TYPE | 30 | 27 | 60 | 34 | 21 |
P value = 0.276 (Fisher's exact test), Q value = 0.51
Table S85. Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
APOB MUTATED | 8 | 6 | 4 | 6 |
APOB WILD-TYPE | 30 | 62 | 23 | 54 |
P value = 0.0693 (Fisher's exact test), Q value = 0.25
Table S86. Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
APOB MUTATED | 3 | 7 | 0 | 8 | 6 |
APOB WILD-TYPE | 21 | 51 | 24 | 58 | 15 |
P value = 0.219 (Fisher's exact test), Q value = 0.48
Table S87. Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
APOB MUTATED | 6 | 3 | 11 | 1 |
APOB WILD-TYPE | 51 | 38 | 45 | 20 |
P value = 0.0201 (Fisher's exact test), Q value = 0.1
Table S88. Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
APOB MUTATED | 1 | 5 | 5 | 3 | 7 |
APOB WILD-TYPE | 31 | 48 | 45 | 17 | 13 |
Figure S34. Get High-res Image Gene #11: 'APOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D11V8.png)
P value = 0.0555 (Fisher's exact test), Q value = 0.22
Table S89. Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
EEF1A1 MUTATED | 0 | 0 | 5 |
EEF1A1 WILD-TYPE | 46 | 62 | 80 |
P value = 0.736 (Fisher's exact test), Q value = 0.88
Table S90. Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
EEF1A1 MUTATED | 1 | 3 | 1 |
EEF1A1 WILD-TYPE | 56 | 80 | 57 |
P value = 0.254 (Fisher's exact test), Q value = 0.5
Table S91. Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
EEF1A1 MUTATED | 0 | 1 | 0 | 2 | 2 |
EEF1A1 WILD-TYPE | 43 | 54 | 29 | 34 | 30 |
P value = 0.133 (Fisher's exact test), Q value = 0.37
Table S92. Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
EEF1A1 MUTATED | 0 | 2 | 1 | 0 | 2 |
EEF1A1 WILD-TYPE | 34 | 27 | 66 | 36 | 27 |
P value = 0.611 (Fisher's exact test), Q value = 0.82
Table S93. Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
EEF1A1 MUTATED | 1 | 1 | 0 | 3 |
EEF1A1 WILD-TYPE | 37 | 67 | 27 | 57 |
P value = 0.261 (Fisher's exact test), Q value = 0.5
Table S94. Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
EEF1A1 MUTATED | 1 | 2 | 1 | 0 | 1 |
EEF1A1 WILD-TYPE | 23 | 56 | 23 | 66 | 20 |
P value = 0.241 (Fisher's exact test), Q value = 0.49
Table S95. Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
EEF1A1 MUTATED | 0 | 2 | 3 | 0 |
EEF1A1 WILD-TYPE | 57 | 39 | 53 | 21 |
P value = 0.617 (Fisher's exact test), Q value = 0.82
Table S96. Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
EEF1A1 MUTATED | 0 | 2 | 1 | 1 | 1 |
EEF1A1 WILD-TYPE | 32 | 51 | 49 | 19 | 19 |
P value = 0.918 (Fisher's exact test), Q value = 0.96
Table S97. Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
KIF19 MUTATED | 2 | 4 | 4 |
KIF19 WILD-TYPE | 44 | 58 | 81 |
P value = 0.104 (Fisher's exact test), Q value = 0.32
Table S98. Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
KIF19 MUTATED | 0 | 6 | 4 |
KIF19 WILD-TYPE | 57 | 77 | 54 |
P value = 0.234 (Fisher's exact test), Q value = 0.49
Table S99. Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
KIF19 MUTATED | 4 | 3 | 0 | 0 | 2 |
KIF19 WILD-TYPE | 39 | 52 | 29 | 36 | 30 |
P value = 0.238 (Fisher's exact test), Q value = 0.49
Table S100. Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
KIF19 MUTATED | 3 | 0 | 4 | 0 | 2 |
KIF19 WILD-TYPE | 31 | 29 | 63 | 36 | 27 |
P value = 0.383 (Fisher's exact test), Q value = 0.62
Table S101. Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
KIF19 MUTATED | 1 | 6 | 0 | 3 |
KIF19 WILD-TYPE | 37 | 62 | 27 | 57 |
P value = 0.81 (Fisher's exact test), Q value = 0.91
Table S102. Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
KIF19 MUTATED | 2 | 3 | 0 | 4 | 1 |
KIF19 WILD-TYPE | 22 | 55 | 24 | 62 | 20 |
P value = 0.152 (Fisher's exact test), Q value = 0.4
Table S103. Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
KIF19 MUTATED | 5 | 0 | 4 | 0 |
KIF19 WILD-TYPE | 52 | 41 | 52 | 21 |
P value = 0.1 (Fisher's exact test), Q value = 0.32
Table S104. Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
KIF19 MUTATED | 4 | 3 | 0 | 1 | 1 |
KIF19 WILD-TYPE | 28 | 50 | 50 | 19 | 19 |
P value = 0.89 (Fisher's exact test), Q value = 0.94
Table S105. Gene #14: 'GNAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
GNAS MUTATED | 1 | 2 | 4 |
GNAS WILD-TYPE | 45 | 60 | 81 |
P value = 0.238 (Fisher's exact test), Q value = 0.49
Table S106. Gene #14: 'GNAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
GNAS MUTATED | 2 | 1 | 4 |
GNAS WILD-TYPE | 55 | 82 | 54 |
P value = 0.0293 (Fisher's exact test), Q value = 0.13
Table S107. Gene #14: 'GNAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
GNAS MUTATED | 0 | 1 | 2 | 4 | 0 |
GNAS WILD-TYPE | 43 | 54 | 27 | 32 | 32 |
Figure S35. Get High-res Image Gene #14: 'GNAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
![](D14V3.png)
P value = 0.172 (Fisher's exact test), Q value = 0.42
Table S108. Gene #14: 'GNAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
GNAS MUTATED | 1 | 3 | 1 | 2 | 0 |
GNAS WILD-TYPE | 33 | 26 | 66 | 34 | 29 |
P value = 0.0781 (Fisher's exact test), Q value = 0.27
Table S109. Gene #14: 'GNAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
GNAS MUTATED | 0 | 1 | 0 | 5 |
GNAS WILD-TYPE | 38 | 67 | 27 | 55 |
P value = 0.45 (Fisher's exact test), Q value = 0.7
Table S110. Gene #14: 'GNAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
GNAS MUTATED | 0 | 1 | 2 | 3 | 0 |
GNAS WILD-TYPE | 24 | 57 | 22 | 63 | 21 |
P value = 0.555 (Fisher's exact test), Q value = 0.78
Table S111. Gene #14: 'GNAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
GNAS MUTATED | 2 | 3 | 1 | 0 |
GNAS WILD-TYPE | 55 | 38 | 55 | 21 |
P value = 0.725 (Fisher's exact test), Q value = 0.88
Table S112. Gene #14: 'GNAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
GNAS MUTATED | 1 | 1 | 3 | 0 | 1 |
GNAS WILD-TYPE | 31 | 52 | 47 | 20 | 19 |
P value = 0.817 (Fisher's exact test), Q value = 0.91
Table S113. Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
F5 MUTATED | 1 | 2 | 1 |
F5 WILD-TYPE | 45 | 60 | 84 |
P value = 0.18 (Fisher's exact test), Q value = 0.43
Table S114. Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
F5 MUTATED | 0 | 1 | 3 |
F5 WILD-TYPE | 57 | 82 | 55 |
P value = 0.798 (Fisher's exact test), Q value = 0.91
Table S115. Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
F5 MUTATED | 1 | 2 | 1 | 0 | 0 |
F5 WILD-TYPE | 42 | 53 | 28 | 36 | 32 |
P value = 0.619 (Fisher's exact test), Q value = 0.82
Table S116. Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
F5 MUTATED | 0 | 0 | 3 | 1 | 0 |
F5 WILD-TYPE | 34 | 29 | 64 | 35 | 29 |
P value = 0.102 (Fisher's exact test), Q value = 0.32
Table S117. Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
F5 MUTATED | 0 | 4 | 0 | 0 |
F5 WILD-TYPE | 38 | 64 | 27 | 60 |
P value = 0.936 (Fisher's exact test), Q value = 0.96
Table S118. Gene #15: 'F5 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
F5 MUTATED | 0 | 1 | 1 | 2 | 0 |
F5 WILD-TYPE | 24 | 57 | 23 | 64 | 21 |
P value = 0.49 (Fisher's exact test), Q value = 0.71
Table S119. Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
PTEN MUTATED | 0 | 2 | 4 |
PTEN WILD-TYPE | 46 | 60 | 81 |
P value = 0.263 (Fisher's exact test), Q value = 0.5
Table S120. Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
PTEN MUTATED | 0 | 4 | 3 |
PTEN WILD-TYPE | 57 | 79 | 55 |
P value = 0.372 (Fisher's exact test), Q value = 0.62
Table S121. Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
PTEN MUTATED | 1 | 4 | 0 | 0 | 1 |
PTEN WILD-TYPE | 42 | 51 | 29 | 36 | 31 |
P value = 0.508 (Fisher's exact test), Q value = 0.72
Table S122. Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
PTEN MUTATED | 1 | 0 | 4 | 0 | 1 |
PTEN WILD-TYPE | 33 | 29 | 63 | 36 | 28 |
P value = 0.86 (Fisher's exact test), Q value = 0.92
Table S123. Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
PTEN MUTATED | 1 | 3 | 0 | 3 |
PTEN WILD-TYPE | 37 | 65 | 27 | 57 |
P value = 0.275 (Fisher's exact test), Q value = 0.51
Table S124. Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
PTEN MUTATED | 0 | 5 | 0 | 2 | 0 |
PTEN WILD-TYPE | 24 | 53 | 24 | 64 | 21 |
P value = 0.783 (Fisher's exact test), Q value = 0.91
Table S125. Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
PTEN MUTATED | 3 | 1 | 3 | 0 |
PTEN WILD-TYPE | 54 | 40 | 53 | 21 |
P value = 0.285 (Fisher's exact test), Q value = 0.52
Table S126. Gene #16: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
PTEN MUTATED | 1 | 5 | 1 | 0 | 0 |
PTEN WILD-TYPE | 31 | 48 | 49 | 20 | 20 |
P value = 0.722 (Fisher's exact test), Q value = 0.88
Table S127. Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
HIST1H1C MUTATED | 2 | 1 | 2 |
HIST1H1C WILD-TYPE | 44 | 61 | 83 |
P value = 0.737 (Fisher's exact test), Q value = 0.88
Table S128. Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
HIST1H1C MUTATED | 1 | 3 | 1 |
HIST1H1C WILD-TYPE | 56 | 80 | 57 |
P value = 0.471 (Fisher's exact test), Q value = 0.71
Table S129. Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
HIST1H1C MUTATED | 0 | 1 | 1 | 1 | 2 |
HIST1H1C WILD-TYPE | 43 | 54 | 28 | 35 | 30 |
P value = 0.347 (Fisher's exact test), Q value = 0.58
Table S130. Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
HIST1H1C MUTATED | 1 | 1 | 1 | 0 | 2 |
HIST1H1C WILD-TYPE | 33 | 28 | 66 | 36 | 27 |
P value = 0.801 (Fisher's exact test), Q value = 0.91
Table S131. Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
HIST1H1C MUTATED | 1 | 3 | 0 | 1 |
HIST1H1C WILD-TYPE | 37 | 65 | 27 | 59 |
P value = 0.247 (Fisher's exact test), Q value = 0.5
Table S132. Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
HIST1H1C MUTATED | 0 | 1 | 1 | 1 | 2 |
HIST1H1C WILD-TYPE | 24 | 57 | 23 | 65 | 19 |
P value = 0.641 (Fisher's exact test), Q value = 0.84
Table S133. Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
HIST1H1C MUTATED | 1 | 1 | 3 | 0 |
HIST1H1C WILD-TYPE | 56 | 40 | 53 | 21 |
P value = 0.0212 (Fisher's exact test), Q value = 0.1
Table S134. Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
HIST1H1C MUTATED | 1 | 0 | 1 | 0 | 3 |
HIST1H1C WILD-TYPE | 31 | 53 | 49 | 20 | 17 |
Figure S36. Get High-res Image Gene #17: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
![](D17V8.png)
P value = 0.818 (Fisher's exact test), Q value = 0.91
Table S135. Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 46 | 62 | 85 |
DLK2 MUTATED | 1 | 2 | 1 |
DLK2 WILD-TYPE | 45 | 60 | 84 |
P value = 0.693 (Fisher's exact test), Q value = 0.88
Table S136. Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 57 | 83 | 58 |
DLK2 MUTATED | 2 | 1 | 1 |
DLK2 WILD-TYPE | 55 | 82 | 57 |
P value = 0.735 (Fisher's exact test), Q value = 0.88
Table S137. Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 43 | 55 | 29 | 36 | 32 |
DLK2 MUTATED | 2 | 1 | 0 | 1 | 0 |
DLK2 WILD-TYPE | 41 | 54 | 29 | 35 | 32 |
P value = 0.379 (Fisher's exact test), Q value = 0.62
Table S138. Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 34 | 29 | 67 | 36 | 29 |
DLK2 MUTATED | 2 | 1 | 1 | 0 | 0 |
DLK2 WILD-TYPE | 32 | 28 | 66 | 36 | 29 |
P value = 0.333 (Fisher's exact test), Q value = 0.56
Table S139. Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 38 | 68 | 27 | 60 |
DLK2 MUTATED | 1 | 0 | 1 | 2 |
DLK2 WILD-TYPE | 37 | 68 | 26 | 58 |
P value = 0.936 (Fisher's exact test), Q value = 0.96
Table S140. Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 24 | 58 | 24 | 66 | 21 |
DLK2 MUTATED | 1 | 1 | 0 | 2 | 0 |
DLK2 WILD-TYPE | 23 | 57 | 24 | 64 | 21 |
P value = 0.189 (Fisher's exact test), Q value = 0.44
Table S141. Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 57 | 41 | 56 | 21 |
DLK2 MUTATED | 0 | 2 | 1 | 1 |
DLK2 WILD-TYPE | 57 | 39 | 55 | 20 |
P value = 0.162 (Fisher's exact test), Q value = 0.41
Table S142. Gene #18: 'DLK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 32 | 53 | 50 | 20 | 20 |
DLK2 MUTATED | 0 | 0 | 3 | 1 | 0 |
DLK2 WILD-TYPE | 32 | 53 | 47 | 19 | 20 |
-
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/LIHC-TP/15165528/transformed.cor.cli.txt
-
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/15111045/LIHC-TP.transferedmergedcluster.txt
-
Number of patients = 198
-
Number of significantly mutated genes = 18
-
Number of Molecular subtypes = 8
-
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.