Correlation between gene mutation status and molecular subtypes
Pheochromocytoma and Paraganglioma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C19G5KW8
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C19G5KW8
Overview
Introduction

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

Summary

Testing the association between mutation status of 9 genes and 10 molecular subtypes across 178 patients, 32 significant findings detected with P value < 0.05 and Q value < 0.25.

- HRAS mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- EPAS1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- NF1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- RET mutation correlated to 'CN_CNMF'.

- CSDE1 mutation correlated to 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 9 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, 32 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
HRAS | 18 (10%) | 160 | 1e-05 (3e-04) | 6e-05 (0.00103) | 0.0546 (0.149) | 0.00116 (0.00746) | 1e-05 (3e-04) | 1e-05 (3e-04) | 5e-05 (0.00103) | 0.00024 (0.00216) | 8e-05 (0.00103) | 0.00039 (0.00292)
EPAS1 | 8 (4%) | 170 | 0.0112 (0.0337) | 0.0059 (0.0229) | 0.00789 (0.0263) | 0.355 (0.627) | 0.00176 (0.0088) | 0.00134 (0.00793) | 0.00169 (0.0088) | 0.0171 (0.0496) | 0.00038 (0.00292) | 0.00192 (0.00909)
NF1 | 15 (8%) | 163 | 0.00016 (0.0017) | 0.00062 (0.00429) | 0.0422 (0.119) | 0.0886 (0.217) | 0.00973 (0.0306) | 8e-05 (0.00103) | 0.00017 (0.0017) | 0.00673 (0.0242) | 0.00986 (0.0306) | 0.00141 (0.00793)
CSDE1 | 4 (2%) | 174 | 0.283 (0.565) | 0.58 (0.829) |  |  | 0.489 (0.758) | 0.00493 (0.0222) | 0.35 (0.627) | 0.00564 (0.0229) | 0.00763 (0.0263) | 0.00612 (0.0229)
RET | 6 (3%) | 172 | 0.0054 (0.0229) | 0.486 (0.758) | 0.207 (0.454) | 0.324 (0.627) | 0.0892 (0.217) | 0.104 (0.239) | 0.436 (0.728) | 0.0676 (0.174) | 0.258 (0.527) | 0.183 (0.411)
GPR128 | 4 (2%) | 174 | 1 (1.00) | 0.101 (0.239) |  |  | 0.89 (1.00) | 0.888 (1.00) | 0.545 (0.803) | 0.776 (0.995) | 0.527 (0.803) | 0.553 (0.803)
AMMECR1 | 3 (2%) | 175 | 0.788 (0.995) | 1 (1.00) | 0.348 (0.627) | 1 (1.00) | 0.244 (0.511) | 0.628 (0.867) | 0.796 (0.995) | 1 (1.00) | 0.594 (0.835) | 0.79 (0.995)
SHROOM4 | 3 (2%) | 175 |  | 1 (1.00) |  |  | 0.47 (0.755) | 0.538 (0.803) | 1 (1.00) | 0.678 (0.911) | 0.723 (0.958) | 0.636 (0.867)
FAM83D | 3 (2%) | 175 | 0.348 (0.627) | 0.334 (0.627) |  |  | 0.409 (0.708) | 0.462 (0.755) | 0.0579 (0.153) | 0.818 (1.00) | 0.227 (0.486) | 0.437 (0.728)

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-04

Table S1. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 38
HRAS MUTATED | 14 | 0 | 1
HRAS WILD-TYPE | 46 | 63 | 37

Figure S1. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.001

Table S2. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 85 | 49
HRAS MUTATED | 0 | 17 | 1
HRAS WILD-TYPE | 44 | 68 | 48

Figure S2. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0546 (Fisher's exact test), Q value = 0.15

Table S3. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 14 | 9 | 20 | 6 | 17 | 13
HRAS MUTATED | 3 | 2 | 5 | 0 | 0 | 0
HRAS WILD-TYPE | 11 | 7 | 15 | 6 | 17 | 13

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.0075

Table S4. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 28
HRAS MUTATED | 1 | 7 | 2
HRAS WILD-TYPE | 32 | 11 | 26

Figure S3. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-04

Table S5. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 69 | 49 | 21
HRAS MUTATED | 0 | 18 | 0 | 0
HRAS WILD-TYPE | 39 | 51 | 49 | 21

Figure S4. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-04

Table S6. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 71 | 48 | 21
HRAS MUTATED | 0 | 18 | 0 | 0
HRAS WILD-TYPE | 38 | 53 | 48 | 21

Figure S5. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S7. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 65 | 39
HRAS MUTATED | 1 | 15 | 2
HRAS WILD-TYPE | 73 | 50 | 37

Figure S6. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0022

Table S8. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 59 | 18 | 25
HRAS MUTATED | 1 | 14 | 1 | 2
HRAS WILD-TYPE | 75 | 45 | 17 | 23

Figure S7. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.001

Table S9. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 36 | 64 | 12 | 41 | 24
HRAS MUTATED | 1 | 15 | 2 | 0 | 0
HRAS WILD-TYPE | 35 | 49 | 10 | 41 | 24

Figure S8. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0029

Table S10. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 80 | 60 | 18 | 19
HRAS MUTATED | 16 | 0 | 1 | 1
HRAS WILD-TYPE | 64 | 60 | 17 | 18

Figure S9. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.034

Table S11. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 38
EPAS1 MUTATED | 0 | 7 | 1
EPAS1 WILD-TYPE | 60 | 56 | 37

Figure S10. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'EPAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 0.023

Table S12. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 85 | 49
EPAS1 MUTATED | 4 | 0 | 4
EPAS1 WILD-TYPE | 40 | 85 | 45

Figure S11. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPAS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00789 (Fisher's exact test), Q value = 0.026

Table S13. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 14 | 9 | 20 | 6 | 17 | 13
EPAS1 MUTATED | 1 | 0 | 0 | 0 | 0 | 4
EPAS1 WILD-TYPE | 13 | 9 | 20 | 6 | 17 | 9

Figure S12. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'EPAS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.355 (Fisher's exact test), Q value = 0.63

Table S14. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 28
EPAS1 MUTATED | 2 | 0 | 3
EPAS1 WILD-TYPE | 31 | 18 | 25

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.0088

Table S15. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 69 | 49 | 21
EPAS1 MUTATED | 1 | 0 | 7 | 0
EPAS1 WILD-TYPE | 38 | 69 | 42 | 21

Figure S13. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.0079

Table S16. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 71 | 48 | 21
EPAS1 MUTATED | 1 | 0 | 7 | 0
EPAS1 WILD-TYPE | 37 | 71 | 41 | 21

Figure S14. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00169 (Fisher's exact test), Q value = 0.0088

Table S17. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 65 | 39
EPAS1 MUTATED | 8 | 0 | 0
EPAS1 WILD-TYPE | 66 | 65 | 39

Figure S15. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.05

Table S18. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 59 | 18 | 25
EPAS1 MUTATED | 8 | 0 | 0 | 0
EPAS1 WILD-TYPE | 68 | 59 | 18 | 25

Figure S16. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0029

Table S19. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 36 | 64 | 12 | 41 | 24
EPAS1 MUTATED | 0 | 0 | 1 | 7 | 0
EPAS1 WILD-TYPE | 36 | 64 | 11 | 34 | 24

Figure S17. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00192 (Fisher's exact test), Q value = 0.0091

Table S20. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 80 | 60 | 18 | 19
EPAS1 MUTATED | 0 | 8 | 0 | 0
EPAS1 WILD-TYPE | 80 | 52 | 18 | 19

Figure S18. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0017

Table S21. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 38
NF1 MUTATED | 3 | 1 | 10
NF1 WILD-TYPE | 57 | 62 | 28

Figure S19. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0043

Table S22. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 85 | 49
NF1 MUTATED | 0 | 14 | 1
NF1 WILD-TYPE | 44 | 71 | 48

Figure S20. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.12

Table S23. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 14 | 9 | 20 | 6 | 17 | 13
NF1 MUTATED | 2 | 1 | 6 | 0 | 0 | 0
NF1 WILD-TYPE | 12 | 8 | 14 | 6 | 17 | 13

Figure S21. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0886 (Fisher's exact test), Q value = 0.22

Table S24. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 28
NF1 MUTATED | 1 | 4 | 4
NF1 WILD-TYPE | 32 | 14 | 24

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00973 (Fisher's exact test), Q value = 0.031

Table S25. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 69 | 49 | 21
NF1 MUTATED | 3 | 11 | 0 | 1
NF1 WILD-TYPE | 36 | 58 | 49 | 20

Figure S22. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.001

Table S26. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 71 | 48 | 21
NF1 MUTATED | 0 | 14 | 0 | 1
NF1 WILD-TYPE | 38 | 57 | 48 | 20

Figure S23. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0017

Table S27. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 65 | 39
NF1 MUTATED | 1 | 13 | 1
NF1 WILD-TYPE | 73 | 52 | 38

Figure S24. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00673 (Fisher's exact test), Q value = 0.024

Table S28. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 59 | 18 | 25
NF1 MUTATED | 2 | 11 | 0 | 2
NF1 WILD-TYPE | 74 | 48 | 18 | 23

Figure S25. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00986 (Fisher's exact test), Q value = 0.031

Table S29. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 36 | 64 | 12 | 41 | 24
NF1 MUTATED | 3 | 10 | 2 | 0 | 0
NF1 WILD-TYPE | 33 | 54 | 10 | 41 | 24

Figure S26. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.0079

Table S30. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 80 | 60 | 18 | 19
NF1 MUTATED | 13 | 0 | 0 | 2
NF1 WILD-TYPE | 67 | 60 | 18 | 17

Figure S27. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0054 (Fisher's exact test), Q value = 0.023

Table S31. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 38
RET MUTATED | 6 | 0 | 0
RET WILD-TYPE | 54 | 63 | 38

Figure S28. Get High-res Image Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.486 (Fisher's exact test), Q value = 0.76

Table S32. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 85 | 49
RET MUTATED | 0 | 4 | 2
RET WILD-TYPE | 44 | 81 | 47

'RET MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 0.45

Table S33. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 14 | 9 | 20 | 6 | 17 | 13
RET MUTATED | 0 | 0 | 3 | 0 | 0 | 0
RET WILD-TYPE | 14 | 9 | 17 | 6 | 17 | 13

'RET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 0.63

Table S34. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 28
RET MUTATED | 0 | 1 | 2
RET WILD-TYPE | 33 | 17 | 26

'RET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0892 (Fisher's exact test), Q value = 0.22

Table S35. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 69 | 49 | 21
RET MUTATED | 0 | 5 | 0 | 1
RET WILD-TYPE | 39 | 64 | 49 | 20

'RET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 0.24

Table S36. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 71 | 48 | 21
RET MUTATED | 0 | 5 | 0 | 1
RET WILD-TYPE | 38 | 66 | 48 | 20

'RET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.73

Table S37. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 65 | 39
RET MUTATED | 1 | 3 | 2
RET WILD-TYPE | 73 | 62 | 37

'RET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0676 (Fisher's exact test), Q value = 0.17

Table S38. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 59 | 18 | 25
RET MUTATED | 0 | 4 | 1 | 1
RET WILD-TYPE | 76 | 55 | 17 | 24

'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.53

Table S39. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 36 | 64 | 12 | 41 | 24
RET MUTATED | 1 | 4 | 1 | 0 | 0
RET WILD-TYPE | 35 | 60 | 11 | 41 | 24

'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 0.41

Table S40. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 80 | 60 | 18 | 19
RET MUTATED | 4 | 0 | 1 | 1
RET WILD-TYPE | 76 | 60 | 17 | 18

'CSDE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.283 (Fisher's exact test), Q value = 0.57

Table S41. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 38
CSDE1 MUTATED | 0 | 3 | 1
CSDE1 WILD-TYPE | 60 | 60 | 37

'CSDE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.58 (Fisher's exact test), Q value = 0.83

Table S42. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 85 | 49
CSDE1 MUTATED | 1 | 3 | 0
CSDE1 WILD-TYPE | 43 | 82 | 49

'CSDE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 0.76

Table S43. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 69 | 49 | 21
CSDE1 MUTATED | 1 | 3 | 0 | 0
CSDE1 WILD-TYPE | 38 | 66 | 49 | 21

'CSDE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00493 (Fisher's exact test), Q value = 0.022

Table S44. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 71 | 48 | 21
CSDE1 MUTATED | 4 | 0 | 0 | 0
CSDE1 WILD-TYPE | 34 | 71 | 48 | 21

Figure S29. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.63

Table S45. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 65 | 39
CSDE1 MUTATED | 1 | 3 | 0
CSDE1 WILD-TYPE | 73 | 62 | 39

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00564 (Fisher's exact test), Q value = 0.023

Table S46. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 59 | 18 | 25
CSDE1 MUTATED | 1 | 0 | 3 | 0
CSDE1 WILD-TYPE | 75 | 59 | 15 | 25

Figure S30. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00763 (Fisher's exact test), Q value = 0.026

Table S47. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 36 | 64 | 12 | 41 | 24
CSDE1 MUTATED | 4 | 0 | 0 | 0 | 0
CSDE1 WILD-TYPE | 32 | 64 | 12 | 41 | 24

Figure S31. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00612 (Fisher's exact test), Q value = 0.023

Table S48. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 80 | 60 | 18 | 19
CSDE1 MUTATED | 1 | 0 | 3 | 0
CSDE1 WILD-TYPE | 79 | 60 | 15 | 19

Figure S32. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GPR128 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S49. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 38
GPR128 MUTATED | 1 | 1 | 1
GPR128 WILD-TYPE | 59 | 62 | 37

'GPR128 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.24

Table S50. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 85 | 49
GPR128 MUTATED | 3 | 1 | 0
GPR128 WILD-TYPE | 41 | 84 | 49

'GPR128 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.89 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 69 | 49 | 21
GPR128 MUTATED | 1 | 1 | 2 | 0
GPR128 WILD-TYPE | 38 | 68 | 47 | 21

'GPR128 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S52. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 71 | 48 | 21
GPR128 MUTATED | 1 | 1 | 2 | 0
GPR128 WILD-TYPE | 37 | 70 | 46 | 21

'GPR128 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 0.8

Table S53. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 65 | 39
GPR128 MUTATED | 3 | 1 | 0
GPR128 WILD-TYPE | 71 | 64 | 39

'GPR128 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.776 (Fisher's exact test), Q value = 1

Table S54. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 59 | 18 | 25
GPR128 MUTATED | 3 | 1 | 0 | 0
GPR128 WILD-TYPE | 73 | 58 | 18 | 25

'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 0.8

Table S55. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 36 | 64 | 12 | 41 | 24
GPR128 MUTATED | 0 | 1 | 0 | 2 | 1
GPR128 WILD-TYPE | 36 | 63 | 12 | 39 | 23

'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.553 (Fisher's exact test), Q value = 0.8

Table S56. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 80 | 60 | 18 | 19
GPR128 MUTATED | 1 | 3 | 0 | 0
GPR128 WILD-TYPE | 79 | 57 | 18 | 19

'AMMECR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S57. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 38
AMMECR1 MUTATED | 1 | 2 | 0
AMMECR1 WILD-TYPE | 59 | 61 | 38

'AMMECR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S58. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 85 | 49
AMMECR1 MUTATED | 1 | 1 | 1
AMMECR1 WILD-TYPE | 43 | 84 | 48

'AMMECR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.63

Table S59. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 14 | 9 | 20 | 6 | 17 | 13
AMMECR1 MUTATED | 0 | 0 | 1 | 1 | 0 | 1
AMMECR1 WILD-TYPE | 14 | 9 | 19 | 5 | 17 | 12

'AMMECR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S60. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 28
AMMECR1 MUTATED | 1 | 1 | 1
AMMECR1 WILD-TYPE | 32 | 17 | 27

'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 0.51

Table S61. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 69 | 49 | 21
AMMECR1 MUTATED | 1 | 0 | 2 | 0
AMMECR1 WILD-TYPE | 38 | 69 | 47 | 21

'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.628 (Fisher's exact test), Q value = 0.87

Table S62. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 71 | 48 | 21
AMMECR1 MUTATED | 0 | 1 | 2 | 0
AMMECR1 WILD-TYPE | 38 | 70 | 46 | 21

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S63. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 65 | 39
AMMECR1 MUTATED | 2 | 1 | 0
AMMECR1 WILD-TYPE | 72 | 64 | 39

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S64. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 59 | 18 | 25
AMMECR1 MUTATED | 2 | 1 | 0 | 0
AMMECR1 WILD-TYPE | 74 | 58 | 18 | 25

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.594 (Fisher's exact test), Q value = 0.84

Table S65. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 36 | 64 | 12 | 41 | 24
AMMECR1 MUTATED | 0 | 1 | 0 | 2 | 0
AMMECR1 WILD-TYPE | 36 | 63 | 12 | 39 | 24

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S66. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 80 | 60 | 18 | 19
AMMECR1 MUTATED | 1 | 2 | 0 | 0
AMMECR1 WILD-TYPE | 79 | 58 | 18 | 19

'SHROOM4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S67. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 85 | 49
SHROOM4 MUTATED | 1 | 1 | 1
SHROOM4 WILD-TYPE | 43 | 84 | 48

'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.76

Table S68. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 69 | 49 | 21
SHROOM4 MUTATED | 1 | 1 | 0 | 1
SHROOM4 WILD-TYPE | 38 | 68 | 49 | 20

'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.538 (Fisher's exact test), Q value = 0.8

Table S69. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 71 | 48 | 21
SHROOM4 MUTATED | 0 | 1 | 1 | 1
SHROOM4 WILD-TYPE | 38 | 70 | 47 | 20

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S70. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 65 | 39
SHROOM4 MUTATED | 1 | 1 | 1
SHROOM4 WILD-TYPE | 73 | 64 | 38

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.678 (Fisher's exact test), Q value = 0.91

Table S71. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 59 | 18 | 25
SHROOM4 MUTATED | 1 | 1 | 0 | 1
SHROOM4 WILD-TYPE | 75 | 58 | 18 | 24

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.723 (Fisher's exact test), Q value = 0.96

Table S72. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 36 | 64 | 12 | 41 | 24
SHROOM4 MUTATED | 0 | 1 | 0 | 1 | 1
SHROOM4 WILD-TYPE | 36 | 63 | 12 | 40 | 23

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.636 (Fisher's exact test), Q value = 0.87

Table S73. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 80 | 60 | 18 | 19
SHROOM4 MUTATED | 1 | 1 | 0 | 1
SHROOM4 WILD-TYPE | 79 | 59 | 18 | 18

'FAM83D MUTATION STATUS' versus 'CN_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.63

Table S74. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 60 | 63 | 38
FAM83D MUTATED | 2 | 0 | 1
FAM83D WILD-TYPE | 58 | 63 | 37

'FAM83D MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 0.63

Table S75. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 44 | 85 | 49
FAM83D MUTATED | 0 | 3 | 0
FAM83D WILD-TYPE | 44 | 82 | 49

'FAM83D MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.409 (Fisher's exact test), Q value = 0.71

Table S76. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 39 | 69 | 49 | 21
FAM83D MUTATED | 0 | 3 | 0 | 0
FAM83D WILD-TYPE | 39 | 66 | 49 | 21

'FAM83D MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.462 (Fisher's exact test), Q value = 0.76

Table S77. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 38 | 71 | 48 | 21
FAM83D MUTATED | 0 | 3 | 0 | 0
FAM83D WILD-TYPE | 38 | 68 | 48 | 21

'FAM83D MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0579 (Fisher's exact test), Q value = 0.15

Table S78. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 74 | 65 | 39
FAM83D MUTATED | 0 | 3 | 0
FAM83D WILD-TYPE | 74 | 62 | 39

'FAM83D MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S79. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 76 | 59 | 18 | 25
FAM83D MUTATED | 1 | 2 | 0 | 0
FAM83D WILD-TYPE | 75 | 57 | 18 | 25

'FAM83D MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 0.49

Table S80. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 36 | 64 | 12 | 41 | 24
FAM83D MUTATED | 0 | 2 | 1 | 0 | 0
FAM83D WILD-TYPE | 36 | 62 | 11 | 41 | 24

'FAM83D MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.437 (Fisher's exact test), Q value = 0.73

Table S81. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 80 | 60 | 18 | 19
FAM83D MUTATED | 3 | 0 | 0 | 0
FAM83D WILD-TYPE | 77 | 60 | 18 | 19

Methods & Data
Input

- 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/PCPG-TP/15165019/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/15107813/PCPG-TP.transferedmergedcluster.txt

- Number of patients = 178

- Number of significantly mutated genes = 9

- 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

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] 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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