This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.
Testing the association between mutation status of 7 genes and 10 molecular subtypes across 249 patients, 9 significant findings detected with P value < 0.05 and Q value < 0.25.
-
SPOP mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
-
FOXA1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
-
TP53 mutation correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Table 1. Get Full Table Overview of the association between mutation status of 7 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 9 significant findings detected.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
SPOP | 24 (10%) | 225 |
0.000575 (0.0379) |
2.68e-08 (1.88e-06) |
0.538 (1.00) |
0.769 (1.00) |
5.99e-05 (0.00401) |
1.07e-07 (7.27e-06) |
0.155 (1.00) |
0.253 (1.00) |
0.0173 (1.00) |
0.0214 (1.00) |
TP53 | 20 (8%) | 229 |
3.88e-08 (2.68e-06) |
0.355 (1.00) |
0.0102 (0.625) |
0.025 (1.00) |
0.00267 (0.168) |
0.00309 (0.192) |
0.456 (1.00) |
0.802 (1.00) |
0.644 (1.00) |
0.749 (1.00) |
FOXA1 | 11 (4%) | 238 |
0.156 (1.00) |
0.000691 (0.0449) |
1 (1.00) |
0.68 (1.00) |
0.0768 (1.00) |
0.00255 (0.163) |
0.299 (1.00) |
0.0728 (1.00) |
0.212 (1.00) |
0.235 (1.00) |
CTNNB1 | 9 (4%) | 240 |
0.481 (1.00) |
0.0431 (1.00) |
0.0208 (1.00) |
0.0357 (1.00) |
0.0126 (0.756) |
0.368 (1.00) |
0.674 (1.00) |
0.75 (1.00) |
0.58 (1.00) |
0.761 (1.00) |
PTEN | 13 (5%) | 236 |
0.0581 (1.00) |
0.291 (1.00) |
0.196 (1.00) |
0.658 (1.00) |
0.025 (1.00) |
0.0815 (1.00) |
0.527 (1.00) |
0.761 (1.00) |
0.556 (1.00) |
0.559 (1.00) |
PCDHAC2 | 26 (10%) | 223 |
0.547 (1.00) |
0.105 (1.00) |
0.93 (1.00) |
0.546 (1.00) |
0.212 (1.00) |
0.158 (1.00) |
0.683 (1.00) |
0.527 (1.00) |
0.584 (1.00) |
0.651 (1.00) |
TMEM216 | 4 (2%) | 245 |
1 (1.00) |
0.836 (1.00) |
0.781 (1.00) |
0.0272 (1.00) |
1 (1.00) |
1 (1.00) |
0.792 (1.00) |
1 (1.00) |
0.839 (1.00) |
0.832 (1.00) |
P value = 0.481 (Fisher's exact test), Q value = 1
Table S1. Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 130 | 74 |
CTNNB1 MUTATED | 2 | 3 | 4 |
CTNNB1 WILD-TYPE | 40 | 127 | 70 |
P value = 0.0431 (Fisher's exact test), Q value = 1
Table S2. Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 73 | 84 | 92 |
CTNNB1 MUTATED | 3 | 0 | 6 |
CTNNB1 WILD-TYPE | 70 | 84 | 86 |
Figure S1. Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 1
Table S3. Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 57 | 56 |
CTNNB1 MUTATED | 0 | 0 | 4 |
CTNNB1 WILD-TYPE | 41 | 57 | 52 |
Figure S2. Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 1
Table S4. Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 57 | 47 |
CTNNB1 MUTATED | 0 | 4 | 0 |
CTNNB1 WILD-TYPE | 50 | 53 | 47 |
Figure S3. Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.76
Table S5. Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 63 | 68 | 50 |
CTNNB1 MUTATED | 3 | 0 | 6 | 0 |
CTNNB1 WILD-TYPE | 63 | 63 | 62 | 50 |
Figure S4. Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 1
Table S6. Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 76 | 62 | 33 |
CTNNB1 MUTATED | 1 | 5 | 2 | 1 |
CTNNB1 WILD-TYPE | 75 | 71 | 60 | 32 |
P value = 0.674 (Chi-square test), Q value = 1
Table S7. Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 62 | 23 | 15 | 70 | 77 |
CTNNB1 MUTATED | 2 | 0 | 0 | 4 | 3 |
CTNNB1 WILD-TYPE | 60 | 23 | 15 | 66 | 74 |
P value = 0.75 (Fisher's exact test), Q value = 1
Table S8. Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 111 | 69 |
CTNNB1 MUTATED | 3 | 3 | 3 |
CTNNB1 WILD-TYPE | 64 | 108 | 66 |
P value = 0.58 (Fisher's exact test), Q value = 1
Table S9. Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 89 | 78 |
CTNNB1 MUTATED | 3 | 2 | 4 |
CTNNB1 WILD-TYPE | 77 | 87 | 74 |
P value = 0.761 (Fisher's exact test), Q value = 1
Table S10. Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 77 | 93 | 77 |
CTNNB1 MUTATED | 2 | 3 | 4 |
CTNNB1 WILD-TYPE | 75 | 90 | 73 |
P value = 0.000575 (Fisher's exact test), Q value = 0.038
Table S11. Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 130 | 74 |
SPOP MUTATED | 11 | 6 | 6 |
SPOP WILD-TYPE | 31 | 124 | 68 |
Figure S5. Get High-res Image Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

P value = 2.68e-08 (Fisher's exact test), Q value = 1.9e-06
Table S12. Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 73 | 84 | 92 |
SPOP MUTATED | 20 | 3 | 1 |
SPOP WILD-TYPE | 53 | 81 | 91 |
Figure S6. Get High-res Image Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 1
Table S13. Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 57 | 56 |
SPOP MUTATED | 4 | 3 | 6 |
SPOP WILD-TYPE | 37 | 54 | 50 |
P value = 0.769 (Fisher's exact test), Q value = 1
Table S14. Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 57 | 47 |
SPOP MUTATED | 4 | 6 | 3 |
SPOP WILD-TYPE | 46 | 51 | 44 |
P value = 5.99e-05 (Fisher's exact test), Q value = 0.004
Table S15. Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 63 | 68 | 50 |
SPOP MUTATED | 15 | 5 | 0 | 3 |
SPOP WILD-TYPE | 51 | 58 | 68 | 47 |
Figure S7. Get High-res Image Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 1.07e-07 (Fisher's exact test), Q value = 7.3e-06
Table S16. Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 76 | 62 | 33 |
SPOP MUTATED | 3 | 0 | 18 | 2 |
SPOP WILD-TYPE | 73 | 76 | 44 | 31 |
Figure S8. Get High-res Image Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.155 (Chi-square test), Q value = 1
Table S17. Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 62 | 23 | 15 | 70 | 77 |
SPOP MUTATED | 3 | 1 | 0 | 10 | 10 |
SPOP WILD-TYPE | 59 | 22 | 15 | 60 | 67 |
P value = 0.253 (Fisher's exact test), Q value = 1
Table S18. Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 111 | 69 |
SPOP MUTATED | 4 | 10 | 10 |
SPOP WILD-TYPE | 63 | 101 | 59 |
P value = 0.0173 (Fisher's exact test), Q value = 1
Table S19. Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 89 | 78 |
SPOP MUTATED | 2 | 12 | 10 |
SPOP WILD-TYPE | 78 | 77 | 68 |
Figure S9. Get High-res Image Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 1
Table S20. Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 77 | 93 | 77 |
SPOP MUTATED | 2 | 11 | 11 |
SPOP WILD-TYPE | 75 | 82 | 66 |
Figure S10. Get High-res Image Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0581 (Fisher's exact test), Q value = 1
Table S21. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 130 | 74 |
PTEN MUTATED | 4 | 3 | 6 |
PTEN WILD-TYPE | 38 | 127 | 68 |
P value = 0.291 (Fisher's exact test), Q value = 1
Table S22. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 73 | 84 | 92 |
PTEN MUTATED | 4 | 2 | 7 |
PTEN WILD-TYPE | 69 | 82 | 85 |
P value = 0.196 (Fisher's exact test), Q value = 1
Table S23. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 57 | 56 |
PTEN MUTATED | 4 | 1 | 3 |
PTEN WILD-TYPE | 37 | 56 | 53 |
P value = 0.658 (Fisher's exact test), Q value = 1
Table S24. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 57 | 47 |
PTEN MUTATED | 4 | 2 | 2 |
PTEN WILD-TYPE | 46 | 55 | 45 |
P value = 0.025 (Fisher's exact test), Q value = 1
Table S25. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 63 | 68 | 50 |
PTEN MUTATED | 5 | 1 | 7 | 0 |
PTEN WILD-TYPE | 61 | 62 | 61 | 50 |
Figure S11. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.0815 (Fisher's exact test), Q value = 1
Table S26. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 76 | 62 | 33 |
PTEN MUTATED | 1 | 8 | 3 | 1 |
PTEN WILD-TYPE | 75 | 68 | 59 | 32 |
P value = 0.527 (Chi-square test), Q value = 1
Table S27. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 62 | 23 | 15 | 70 | 77 |
PTEN MUTATED | 3 | 0 | 1 | 6 | 3 |
PTEN WILD-TYPE | 59 | 23 | 14 | 64 | 74 |
P value = 0.761 (Fisher's exact test), Q value = 1
Table S28. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 111 | 69 |
PTEN MUTATED | 3 | 5 | 5 |
PTEN WILD-TYPE | 64 | 106 | 64 |
P value = 0.556 (Fisher's exact test), Q value = 1
Table S29. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 89 | 78 |
PTEN MUTATED | 3 | 4 | 6 |
PTEN WILD-TYPE | 77 | 85 | 72 |
P value = 0.559 (Fisher's exact test), Q value = 1
Table S30. Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 77 | 93 | 77 |
PTEN MUTATED | 3 | 4 | 6 |
PTEN WILD-TYPE | 74 | 89 | 71 |
P value = 0.547 (Fisher's exact test), Q value = 1
Table S31. Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 130 | 74 |
PCDHAC2 MUTATED | 6 | 14 | 6 |
PCDHAC2 WILD-TYPE | 36 | 116 | 68 |
P value = 0.105 (Fisher's exact test), Q value = 1
Table S32. Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 73 | 84 | 92 |
PCDHAC2 MUTATED | 11 | 10 | 5 |
PCDHAC2 WILD-TYPE | 62 | 74 | 87 |
P value = 0.93 (Fisher's exact test), Q value = 1
Table S33. Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 57 | 56 |
PCDHAC2 MUTATED | 4 | 7 | 7 |
PCDHAC2 WILD-TYPE | 37 | 50 | 49 |
P value = 0.546 (Fisher's exact test), Q value = 1
Table S34. Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 57 | 47 |
PCDHAC2 MUTATED | 4 | 7 | 7 |
PCDHAC2 WILD-TYPE | 46 | 50 | 40 |
P value = 0.212 (Fisher's exact test), Q value = 1
Table S35. Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 63 | 68 | 50 |
PCDHAC2 MUTATED | 9 | 7 | 3 | 7 |
PCDHAC2 WILD-TYPE | 57 | 56 | 65 | 43 |
P value = 0.158 (Fisher's exact test), Q value = 1
Table S36. Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 76 | 62 | 33 |
PCDHAC2 MUTATED | 11 | 4 | 9 | 2 |
PCDHAC2 WILD-TYPE | 65 | 72 | 53 | 31 |
P value = 0.683 (Chi-square test), Q value = 1
Table S37. Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 62 | 23 | 15 | 70 | 77 |
PCDHAC2 MUTATED | 6 | 4 | 2 | 5 | 9 |
PCDHAC2 WILD-TYPE | 56 | 19 | 13 | 65 | 68 |
P value = 0.527 (Fisher's exact test), Q value = 1
Table S38. Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 111 | 69 |
PCDHAC2 MUTATED | 7 | 14 | 5 |
PCDHAC2 WILD-TYPE | 60 | 97 | 64 |
P value = 0.584 (Fisher's exact test), Q value = 1
Table S39. Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 89 | 78 |
PCDHAC2 MUTATED | 10 | 10 | 6 |
PCDHAC2 WILD-TYPE | 70 | 79 | 72 |
P value = 0.651 (Fisher's exact test), Q value = 1
Table S40. Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 77 | 93 | 77 |
PCDHAC2 MUTATED | 9 | 11 | 6 |
PCDHAC2 WILD-TYPE | 68 | 82 | 71 |
P value = 0.156 (Fisher's exact test), Q value = 1
Table S41. Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 130 | 74 |
FOXA1 MUTATED | 3 | 3 | 5 |
FOXA1 WILD-TYPE | 39 | 127 | 69 |
P value = 0.000691 (Fisher's exact test), Q value = 0.045
Table S42. Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 73 | 84 | 92 |
FOXA1 MUTATED | 9 | 1 | 1 |
FOXA1 WILD-TYPE | 64 | 83 | 91 |
Figure S12. Get High-res Image Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

P value = 1 (Fisher's exact test), Q value = 1
Table S43. Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 57 | 56 |
FOXA1 MUTATED | 2 | 2 | 2 |
FOXA1 WILD-TYPE | 39 | 55 | 54 |
P value = 0.68 (Fisher's exact test), Q value = 1
Table S44. Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 57 | 47 |
FOXA1 MUTATED | 3 | 2 | 1 |
FOXA1 WILD-TYPE | 47 | 55 | 46 |
P value = 0.0768 (Fisher's exact test), Q value = 1
Table S45. Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 63 | 68 | 50 |
FOXA1 MUTATED | 7 | 2 | 1 | 1 |
FOXA1 WILD-TYPE | 59 | 61 | 67 | 49 |
P value = 0.00255 (Fisher's exact test), Q value = 0.16
Table S46. Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 76 | 62 | 33 |
FOXA1 MUTATED | 2 | 0 | 4 | 5 |
FOXA1 WILD-TYPE | 74 | 76 | 58 | 28 |
Figure S13. Get High-res Image Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.299 (Chi-square test), Q value = 1
Table S47. Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 62 | 23 | 15 | 70 | 77 |
FOXA1 MUTATED | 1 | 0 | 0 | 5 | 5 |
FOXA1 WILD-TYPE | 61 | 23 | 15 | 65 | 72 |
P value = 0.0728 (Fisher's exact test), Q value = 1
Table S48. Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 111 | 69 |
FOXA1 MUTATED | 0 | 6 | 5 |
FOXA1 WILD-TYPE | 67 | 105 | 64 |
P value = 0.212 (Fisher's exact test), Q value = 1
Table S49. Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 89 | 78 |
FOXA1 MUTATED | 1 | 5 | 5 |
FOXA1 WILD-TYPE | 79 | 84 | 73 |
P value = 0.235 (Fisher's exact test), Q value = 1
Table S50. Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 77 | 93 | 77 |
FOXA1 MUTATED | 1 | 5 | 5 |
FOXA1 WILD-TYPE | 76 | 88 | 72 |
P value = 3.88e-08 (Fisher's exact test), Q value = 2.7e-06
Table S51. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 130 | 74 |
TP53 MUTATED | 0 | 2 | 18 |
TP53 WILD-TYPE | 42 | 128 | 56 |
Figure S14. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 1
Table S52. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 73 | 84 | 92 |
TP53 MUTATED | 6 | 4 | 10 |
TP53 WILD-TYPE | 67 | 80 | 82 |
P value = 0.0102 (Fisher's exact test), Q value = 0.62
Table S53. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 57 | 56 |
TP53 MUTATED | 0 | 3 | 9 |
TP53 WILD-TYPE | 41 | 54 | 47 |
Figure S15. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 1
Table S54. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 57 | 47 |
TP53 MUTATED | 1 | 9 | 2 |
TP53 WILD-TYPE | 49 | 48 | 45 |
Figure S16. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.17
Table S55. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 63 | 68 | 50 |
TP53 MUTATED | 2 | 4 | 13 | 1 |
TP53 WILD-TYPE | 64 | 59 | 55 | 49 |
Figure S17. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

P value = 0.00309 (Fisher's exact test), Q value = 0.19
Table S56. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 76 | 62 | 33 |
TP53 MUTATED | 1 | 13 | 5 | 1 |
TP53 WILD-TYPE | 75 | 63 | 57 | 32 |
Figure S18. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

P value = 0.456 (Chi-square test), Q value = 1
Table S57. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 62 | 23 | 15 | 70 | 77 |
TP53 MUTATED | 4 | 0 | 1 | 6 | 9 |
TP53 WILD-TYPE | 58 | 23 | 14 | 64 | 68 |
P value = 0.802 (Fisher's exact test), Q value = 1
Table S58. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 111 | 69 |
TP53 MUTATED | 4 | 10 | 6 |
TP53 WILD-TYPE | 63 | 101 | 63 |
P value = 0.644 (Fisher's exact test), Q value = 1
Table S59. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 89 | 78 |
TP53 MUTATED | 5 | 9 | 6 |
TP53 WILD-TYPE | 75 | 80 | 72 |
P value = 0.749 (Fisher's exact test), Q value = 1
Table S60. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 77 | 93 | 77 |
TP53 MUTATED | 5 | 9 | 6 |
TP53 WILD-TYPE | 72 | 84 | 71 |
P value = 1 (Fisher's exact test), Q value = 1
Table S61. Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 42 | 130 | 74 |
TMEM216 MUTATED | 0 | 3 | 1 |
TMEM216 WILD-TYPE | 42 | 127 | 73 |
P value = 0.836 (Fisher's exact test), Q value = 1
Table S62. Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 73 | 84 | 92 |
TMEM216 MUTATED | 1 | 2 | 1 |
TMEM216 WILD-TYPE | 72 | 82 | 91 |
P value = 0.781 (Fisher's exact test), Q value = 1
Table S63. Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 41 | 57 | 56 |
TMEM216 MUTATED | 0 | 2 | 1 |
TMEM216 WILD-TYPE | 41 | 55 | 55 |
P value = 0.0272 (Fisher's exact test), Q value = 1
Table S64. Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 50 | 57 | 47 |
TMEM216 MUTATED | 0 | 0 | 3 |
TMEM216 WILD-TYPE | 50 | 57 | 44 |
Figure S19. Get High-res Image Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1
Table S65. Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 66 | 63 | 68 | 50 |
TMEM216 MUTATED | 1 | 1 | 1 | 1 |
TMEM216 WILD-TYPE | 65 | 62 | 67 | 49 |
P value = 1 (Fisher's exact test), Q value = 1
Table S66. Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
---|---|---|---|---|
ALL | 76 | 76 | 62 | 33 |
TMEM216 MUTATED | 1 | 2 | 1 | 0 |
TMEM216 WILD-TYPE | 75 | 74 | 61 | 33 |
P value = 0.792 (Chi-square test), Q value = 1
Table S67. Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 |
---|---|---|---|---|---|
ALL | 62 | 23 | 15 | 70 | 77 |
TMEM216 MUTATED | 2 | 0 | 0 | 1 | 1 |
TMEM216 WILD-TYPE | 60 | 23 | 15 | 69 | 76 |
P value = 1 (Fisher's exact test), Q value = 1
Table S68. Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 67 | 111 | 69 |
TMEM216 MUTATED | 1 | 2 | 1 |
TMEM216 WILD-TYPE | 66 | 109 | 68 |
P value = 0.839 (Fisher's exact test), Q value = 1
Table S69. Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 80 | 89 | 78 |
TMEM216 MUTATED | 2 | 1 | 1 |
TMEM216 WILD-TYPE | 78 | 88 | 77 |
P value = 0.832 (Fisher's exact test), Q value = 1
Table S70. Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'
nPatients | CLUS_1 | CLUS_2 | CLUS_3 |
---|---|---|---|
ALL | 77 | 93 | 77 |
TMEM216 MUTATED | 2 | 1 | 1 |
TMEM216 WILD-TYPE | 75 | 92 | 76 |
-
Mutation data file = transformed.cor.cli.txt
-
Molecular subtypes file = PRAD-TP.transferedmergedcluster.txt
-
Number of patients = 249
-
Number of significantly mutated genes = 7
-
Number of Molecular subtypes = 10
-
Exclude genes that fewer than K tumors have mutations, K = 3
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For 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.