Correlation between gene mutation status and molecular subtypes
Pheochromocytoma and Paraganglioma (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1K35SKD
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/C1K35SKD
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 8 molecular subtypes across 178 patients, 18 significant findings detected with P value < 0.05 and Q value < 0.25.

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

- EPAS1 mutation correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- NF1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_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 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 18 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
HRAS | 18 (10%) | 160 | 2e-05 (0.0014) | 6e-05 (0.00402) | 1e-05 (0.00071) | 2e-05 (0.0014) | 6e-05 (0.00402) | 0.00019 (0.0116) | 0.00012 (0.00768) | 0.00041 (0.0246)
EPAS1 | 8 (4%) | 170 | 0.0109 (0.48) | 0.00676 (0.324) | 0.00133 (0.0771) | 0.00166 (0.0913) | 0.00162 (0.0907) | 0.0165 (0.709) | 0.00018 (0.0112) | 0.00191 (0.103)
NF1 | 15 (8%) | 163 | 0.00013 (0.00819) | 0.00057 (0.0336) | 0.00942 (0.433) | 5e-05 (0.0034) | 0.00011 (0.00715) | 0.00637 (0.312) | 0.00991 (0.446) | 0.00134 (0.0771)
RET | 6 (3%) | 172 | 0.00522 (0.277) | 0.486 (1.00) | 0.0898 (1.00) | 0.105 (1.00) | 0.436 (1.00) | 0.0681 (1.00) | 0.258 (1.00) | 0.184 (1.00)
CSDE1 | 4 (2%) | 174 | 0.285 (1.00) | 0.583 (1.00) | 0.49 (1.00) | 0.00541 (0.281) | 0.35 (1.00) | 0.00578 (0.295) | 0.00744 (0.35) | 0.00601 (0.3)
GPR128 | 4 (2%) | 174 | 1 (1.00) | 0.101 (1.00) | 0.891 (1.00) | 0.888 (1.00) | 0.543 (1.00) | 0.774 (1.00) | 0.53 (1.00) | 0.559 (1.00)
AMMECR1 | 3 (2%) | 175 | 0.79 (1.00) | 1 (1.00) | 0.244 (1.00) | 0.628 (1.00) | 0.796 (1.00) | 1 (1.00) | 0.594 (1.00) | 0.793 (1.00)
SHROOM4 | 3 (2%) | 175 |  | 1 (1.00) | 0.467 (1.00) | 0.541 (1.00) | 1 (1.00) | 0.679 (1.00) | 0.724 (1.00) | 0.638 (1.00)
FAM83D | 3 (2%) | 175 | 0.344 (1.00) | 0.334 (1.00) | 0.409 (1.00) | 0.463 (1.00) | 0.0576 (1.00) | 0.815 (1.00) | 0.228 (1.00) | 0.439 (1.00)

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

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 = 0.004

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 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

Table S3. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: '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 S3. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S4. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: '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 S4. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.004

Table S5. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: '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 S5. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.012

Table S6. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: '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 S6. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0077

Table S7. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: '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 S7. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.025

Table S8. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: '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 S8. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.48

Table S9. 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 S9. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'EPAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00676 (Fisher's exact test), Q value = 0.32

Table S10. 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 S10. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.077

Table S11. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: '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 S11. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.091

Table S12. Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: '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 S12. Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.091

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

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.71

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

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.011

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

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00191 (Fisher's exact test), Q value = 0.1

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

'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0082

Table S17. 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 S17. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.034

Table S18. 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 S18. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00942 (Fisher's exact test), Q value = 0.43

Table S19. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: '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 S19. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0034

Table S20. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: '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 S20. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0071

Table S21. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: '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 S21. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.31

Table S22. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: '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 S22. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00991 (Fisher's exact test), Q value = 0.45

Table S23. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: '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 S23. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00134 (Fisher's exact test), Q value = 0.077

Table S24. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: '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 S24. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00522 (Fisher's exact test), Q value = 0.28

Table S25. 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 S25. 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 = 1

Table S26. 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 'MRNASEQ_CNMF'

P value = 0.0898 (Fisher's exact test), Q value = 1

Table S27. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #3: '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 = 0.105 (Fisher's exact test), Q value = 1

Table S28. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #4: '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 = 1

Table S29. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.0681 (Fisher's exact test), Q value = 1

Table S30. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #6: '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 = 1

Table S31. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.184 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.285 (Fisher's exact test), Q value = 1

Table S33. 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 = 0.583 (Fisher's exact test), Q value = 1

Table S34. 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 = 0.49 (Fisher's exact test), Q value = 1

Table S35. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #3: '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 = 0.00541 (Fisher's exact test), Q value = 0.28

Table S36. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #4: '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 S26. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 1

Table S37. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.00578 (Fisher's exact test), Q value = 0.29

Table S38. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #6: '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 S27. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00744 (Fisher's exact test), Q value = 0.35

Table S39. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #7: '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 S28. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00601 (Fisher's exact test), Q value = 0.3

Table S40. Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #8: '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 S29. Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GPR128 MUTATION STATUS' versus 'CN_CNMF'

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

Table S41. 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 = 1

Table S42. 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 = 0.891 (Fisher's exact test), Q value = 1

Table S43. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #3: '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 S44. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #4: '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 = 0.543 (Fisher's exact test), Q value = 1

Table S45. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.774 (Fisher's exact test), Q value = 1

Table S46. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.53 (Fisher's exact test), Q value = 1

Table S47. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.559 (Fisher's exact test), Q value = 1

Table S48. Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.79 (Fisher's exact test), Q value = 1

Table S49. 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 S50. 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 'MRNASEQ_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 1

Table S51. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #3: '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 = 1

Table S52. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #4: '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 S53. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #5: '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 S54. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 1

Table S55. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.793 (Fisher's exact test), Q value = 1

Table S56. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #8: '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 S57. 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 = 0.467 (Fisher's exact test), Q value = 1

Table S58. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #3: '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 = 0.541 (Fisher's exact test), Q value = 1

Table S59. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #4: '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 S60. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.679 (Fisher's exact test), Q value = 1

Table S61. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.724 (Fisher's exact test), Q value = 1

Table S62. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.638 (Fisher's exact test), Q value = 1

Table S63. Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.344 (Fisher's exact test), Q value = 1

Table S64. 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 = 1

Table S65. 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 = 1

Table S66. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #3: '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 = 0.463 (Fisher's exact test), Q value = 1

Table S67. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #4: '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 = 0.0576 (Fisher's exact test), Q value = 1

Table S68. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.815 (Fisher's exact test), Q value = 1

Table S69. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.228 (Fisher's exact test), Q value = 1

Table S70. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.439 (Fisher's exact test), Q value = 1

Table S71. Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #8: '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 = transformed.cor.cli.txt

- Molecular subtypes file = PCPG-TP.transferedmergedcluster.txt

- Number of patients = 178

- Number of significantly mutated genes = 9

- Number of Molecular subtypes = 8

- 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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