Correlation between gene mutation status and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1VM49R4
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1VM49R4
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

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'.

Results
Overview of the results

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)

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

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

'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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'

'CTNNB1 MUTATION STATUS' versus 'RPPA_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'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

'SPOP MUTATION STATUS' versus 'CN_CNMF'

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'

'SPOP MUTATION STATUS' versus 'METHLYATION_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'

'SPOP MUTATION STATUS' versus 'RPPA_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

'SPOP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

'SPOP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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'

'SPOP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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'

'SPOP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

'SPOP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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'

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

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

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

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

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

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'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

'PCDHAC2 MUTATION STATUS' versus 'CN_CNMF'

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

'PCDHAC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

'PCDHAC2 MUTATION STATUS' versus 'RPPA_CNMF'

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

'PCDHAC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

'PCDHAC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

'PCDHAC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

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

'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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'

'FOXA1 MUTATION STATUS' versus 'RPPA_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

'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

'TP53 MUTATION STATUS' versus 'CN_CNMF'

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'

'TP53 MUTATION STATUS' versus 'METHLYATION_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

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

'TMEM216 MUTATION STATUS' versus 'CN_CNMF'

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

'TMEM216 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

'TMEM216 MUTATION STATUS' versus 'RPPA_CNMF'

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

'TMEM216 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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'

'TMEM216 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

'TMEM216 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Methods & Data
Input

- 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

Fisher's exact test

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

Chi-square test

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

Q value calculation

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.

Download Results

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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