Correlation between gene mutation status and molecular subtypes
Uveal Melanoma (Primary solid tumor)
21 August 2015 | analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C10K27W7
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/C10K27W7
Overview
Introduction

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

Summary

Testing the association between mutation status of 8 genes and 8 molecular subtypes across 80 patients, 29 significant findings detected with P value < 0.05 and Q value < 0.25.

- GNAQ mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- EIF1AX mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- SF3B1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- CYSLTR2 mutation correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- BAP1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

- SFRS2 mutation correlated to 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 8 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, 29 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
SF3B1 | 18 (22%) | 62 | 0.00081 (0.00942) | 0.00103 (0.00942) | 0.0005 (0.00942) | 0.00173 (0.0123) | 0.00031 (0.00942) | 0.0177 (0.0565) | 0.00072 (0.00942) | 0.0111 (0.0393)
GNAQ | 40 (50%) | 40 | 0.0303 (0.0923) | 0.0405 (0.0996) | 0.0457 (0.101) | 0.0382 (0.0983) | 0.0384 (0.0983) | 0.0895 (0.159) | 0.0536 (0.11) | 0.00737 (0.0337)
EIF1AX | 10 (12%) | 70 | 0.0009 (0.00942) | 0.00193 (0.0124) | 0.00993 (0.0374) | 0.00836 (0.0357) | 0.00359 (0.0191) | 0.00518 (0.0255) | 0.0647 (0.122) | 0.171 (0.255)
BAP1 | 12 (15%) | 68 | 0.00072 (0.00942) | 0.00337 (0.0191) | 0.0153 (0.0515) | 0.00126 (0.0101) | 0.0322 (0.0936) | 0.00924 (0.037) | 0.0551 (0.11) | 0.0524 (0.11)
CYSLTR2 | 3 (4%) | 77 | 0.0374 (0.0983) | 1 (1.00) | 0.0433 (0.101) | 0.107 (0.181) | 0.798 (0.912) | 0.274 (0.358) | 1 (1.00) | 0.572 (0.677)
SFRS2 | 3 (4%) | 77 | 1 (1.00) | 0.169 (0.255) | 0.0444 (0.101) | 0.107 (0.181) | 0.231 (0.322) | 0.382 (0.479) | 1 (1.00) | 0.232 (0.322)
GNA11 | 36 (45%) | 44 | 0.0787 (0.144) | 0.0624 (0.121) | 0.191 (0.277) | 0.135 (0.216) | 0.147 (0.229) | 0.268 (0.357) | 0.237 (0.323) | 0.31 (0.397)
PRMT8 | 5 (6%) | 75 | 0.857 (0.962) | 0.624 (0.726) | 0.497 (0.612) | 0.528 (0.637) | 1 (1.00) | 0.924 (1.00) | 0.127 (0.209) | 1 (1.00)

'GNAQ MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.092

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
GNAQ MUTATED | 8 | 24 | 8
GNAQ WILD-TYPE | 14 | 12 | 14

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

'GNAQ MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.1

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
GNAQ MUTATED | 13 | 7 | 20
GNAQ WILD-TYPE | 20 | 11 | 9

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

'GNAQ MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0457 (Fisher's exact test), Q value = 0.1

Table S3. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
GNAQ MUTATED | 12 | 5 | 23
GNAQ WILD-TYPE | 18 | 10 | 12

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

'GNAQ MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0382 (Fisher's exact test), Q value = 0.098

Table S4. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
GNAQ MUTATED | 10 | 22 | 8
GNAQ WILD-TYPE | 19 | 11 | 10

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

'GNAQ MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.098

Table S5. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
GNAQ MUTATED | 13 | 7 | 20
GNAQ WILD-TYPE | 21 | 10 | 9

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

'GNAQ MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0895 (Fisher's exact test), Q value = 0.16

Table S6. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
GNAQ MUTATED | 5 | 8 | 18 | 9
GNAQ WILD-TYPE | 12 | 5 | 10 | 13

'GNAQ MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0536 (Fisher's exact test), Q value = 0.11

Table S7. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
GNAQ MUTATED | 12 | 19 | 6
GNAQ WILD-TYPE | 20 | 9 | 8

'GNAQ MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00737 (Fisher's exact test), Q value = 0.034

Table S8. Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
GNAQ MUTATED | 1 | 2 | 11 | 12 | 5 | 6
GNAQ WILD-TYPE | 4 | 10 | 5 | 4 | 10 | 4

Figure S6. Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GNA11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0787 (Fisher's exact test), Q value = 0.14

Table S9. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
GNA11 MUTATED | 14 | 12 | 10
GNA11 WILD-TYPE | 8 | 24 | 12

'GNA11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0624 (Fisher's exact test), Q value = 0.12

Table S10. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
GNA11 MUTATED | 18 | 10 | 8
GNA11 WILD-TYPE | 15 | 8 | 21

'GNA11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 0.28

Table S11. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
GNA11 MUTATED | 17 | 7 | 12
GNA11 WILD-TYPE | 13 | 8 | 23

'GNA11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 0.22

Table S12. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
GNA11 MUTATED | 17 | 11 | 8
GNA11 WILD-TYPE | 12 | 22 | 10

'GNA11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.23

Table S13. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
GNA11 MUTATED | 17 | 10 | 9
GNA11 WILD-TYPE | 17 | 7 | 20

'GNA11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.268 (Fisher's exact test), Q value = 0.36

Table S14. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
GNA11 MUTATED | 10 | 4 | 10 | 12
GNA11 WILD-TYPE | 7 | 9 | 18 | 10

'GNA11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 0.32

Table S15. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
GNA11 MUTATED | 16 | 9 | 8
GNA11 WILD-TYPE | 16 | 19 | 6

'GNA11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.4

Table S16. Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
GNA11 MUTATED | 4 | 7 | 6 | 5 | 8 | 3
GNA11 WILD-TYPE | 1 | 5 | 10 | 11 | 7 | 7

'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0094

Table S17. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
EIF1AX MUTATED | 0 | 10 | 0
EIF1AX WILD-TYPE | 22 | 26 | 22

Figure S7. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00193 (Fisher's exact test), Q value = 0.012

Table S18. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
EIF1AX MUTATED | 0 | 2 | 8
EIF1AX WILD-TYPE | 33 | 16 | 21

Figure S8. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00993 (Fisher's exact test), Q value = 0.037

Table S19. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
EIF1AX MUTATED | 0 | 2 | 8
EIF1AX WILD-TYPE | 30 | 13 | 27

Figure S9. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00836 (Fisher's exact test), Q value = 0.036

Table S20. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
EIF1AX MUTATED | 0 | 8 | 2
EIF1AX WILD-TYPE | 29 | 25 | 16

Figure S10. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.019

Table S21. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
EIF1AX MUTATED | 0 | 3 | 7
EIF1AX WILD-TYPE | 34 | 14 | 22

Figure S11. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00518 (Fisher's exact test), Q value = 0.026

Table S22. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
EIF1AX MUTATED | 0 | 3 | 7 | 0
EIF1AX WILD-TYPE | 17 | 10 | 21 | 22

Figure S12. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0647 (Fisher's exact test), Q value = 0.12

Table S23. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
EIF1AX MUTATED | 1 | 6 | 1
EIF1AX WILD-TYPE | 31 | 22 | 13

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 0.25

Table S24. Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
EIF1AX MUTATED | 0 | 1 | 4 | 3 | 0 | 0
EIF1AX WILD-TYPE | 5 | 11 | 12 | 13 | 15 | 10

'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0094

Table S25. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
SF3B1 MUTATED | 0 | 14 | 4
SF3B1 WILD-TYPE | 22 | 22 | 18

Figure S13. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0094

Table S26. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
SF3B1 MUTATED | 1 | 6 | 11
SF3B1 WILD-TYPE | 32 | 12 | 18

Figure S14. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0094

Table S27. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
SF3B1 MUTATED | 3 | 0 | 15
SF3B1 WILD-TYPE | 27 | 15 | 20

Figure S15. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.012

Table S28. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
SF3B1 MUTATED | 2 | 14 | 2
SF3B1 WILD-TYPE | 27 | 19 | 16

Figure S16. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0094

Table S29. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
SF3B1 MUTATED | 1 | 5 | 12
SF3B1 WILD-TYPE | 33 | 12 | 17

Figure S17. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.057

Table S30. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
SF3B1 MUTATED | 1 | 5 | 10 | 2
SF3B1 WILD-TYPE | 16 | 8 | 18 | 20

Figure S18. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0094

Table S31. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
SF3B1 MUTATED | 1 | 11 | 5
SF3B1 WILD-TYPE | 31 | 17 | 9

Figure S19. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.039

Table S32. Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
SF3B1 MUTATED | 0 | 1 | 6 | 8 | 2 | 0
SF3B1 WILD-TYPE | 5 | 11 | 10 | 8 | 13 | 10

Figure S20. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PRMT8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.857 (Fisher's exact test), Q value = 0.96

Table S33. Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
PRMT8 MUTATED | 1 | 2 | 2
PRMT8 WILD-TYPE | 21 | 34 | 20

'PRMT8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 0.73

Table S34. Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
PRMT8 MUTATED | 3 | 0 | 2
PRMT8 WILD-TYPE | 30 | 18 | 27

'PRMT8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 0.61

Table S35. Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
PRMT8 MUTATED | 3 | 1 | 1
PRMT8 WILD-TYPE | 27 | 14 | 34

'PRMT8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.528 (Fisher's exact test), Q value = 0.64

Table S36. Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
PRMT8 MUTATED | 3 | 1 | 1
PRMT8 WILD-TYPE | 26 | 32 | 17

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S37. Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
PRMT8 MUTATED | 2 | 1 | 2
PRMT8 WILD-TYPE | 32 | 16 | 27

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S38. Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
PRMT8 MUTATED | 1 | 0 | 2 | 2
PRMT8 WILD-TYPE | 16 | 13 | 26 | 20

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 0.21

Table S39. Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
PRMT8 MUTATED | 3 | 0 | 2
PRMT8 WILD-TYPE | 29 | 28 | 12

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S40. Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
PRMT8 MUTATED | 0 | 1 | 1 | 1 | 1 | 1
PRMT8 WILD-TYPE | 5 | 11 | 15 | 15 | 14 | 9

'CYSLTR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.098

Table S41. Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
CYSLTR2 MUTATED | 0 | 0 | 3
CYSLTR2 WILD-TYPE | 22 | 36 | 19

Figure S21. Get High-res Image Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CYSLTR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S42. Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
CYSLTR2 MUTATED | 1 | 1 | 1
CYSLTR2 WILD-TYPE | 32 | 17 | 28

'CYSLTR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.1

Table S43. Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
CYSLTR2 MUTATED | 1 | 2 | 0
CYSLTR2 WILD-TYPE | 29 | 13 | 35

Figure S22. Get High-res Image Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'CYSLTR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.18

Table S44. Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
CYSLTR2 MUTATED | 1 | 0 | 2
CYSLTR2 WILD-TYPE | 28 | 33 | 16

'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 0.91

Table S45. Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
CYSLTR2 MUTATED | 2 | 0 | 1
CYSLTR2 WILD-TYPE | 32 | 17 | 28

'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.274 (Fisher's exact test), Q value = 0.36

Table S46. Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
CYSLTR2 MUTATED | 2 | 0 | 1 | 0
CYSLTR2 WILD-TYPE | 15 | 13 | 27 | 22

'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S47. Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
CYSLTR2 MUTATED | 2 | 1 | 0
CYSLTR2 WILD-TYPE | 30 | 27 | 14

'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 0.68

Table S48. Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
CYSLTR2 MUTATED | 0 | 1 | 0 | 0 | 1 | 1
CYSLTR2 WILD-TYPE | 5 | 11 | 16 | 16 | 14 | 9

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0094

Table S49. Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
BAP1 MUTATED | 6 | 0 | 6
BAP1 WILD-TYPE | 16 | 36 | 16

Figure S23. Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.019

Table S50. Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
BAP1 MUTATED | 9 | 3 | 0
BAP1 WILD-TYPE | 24 | 15 | 29

Figure S24. Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.051

Table S51. Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
BAP1 MUTATED | 7 | 4 | 1
BAP1 WILD-TYPE | 23 | 11 | 34

Figure S25. Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.01

Table S52. Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
BAP1 MUTATED | 6 | 0 | 6
BAP1 WILD-TYPE | 23 | 33 | 12

Figure S26. Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.094

Table S53. Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
BAP1 MUTATED | 9 | 2 | 1
BAP1 WILD-TYPE | 25 | 15 | 28

Figure S27. Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00924 (Fisher's exact test), Q value = 0.037

Table S54. Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
BAP1 MUTATED | 5 | 0 | 1 | 6
BAP1 WILD-TYPE | 12 | 13 | 27 | 16

Figure S28. Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0551 (Fisher's exact test), Q value = 0.11

Table S55. Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
BAP1 MUTATED | 8 | 1 | 2
BAP1 WILD-TYPE | 24 | 27 | 12

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0524 (Fisher's exact test), Q value = 0.11

Table S56. Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
BAP1 MUTATED | 1 | 3 | 2 | 0 | 1 | 4
BAP1 WILD-TYPE | 4 | 9 | 14 | 16 | 14 | 6

'SFRS2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S57. Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
SFRS2 MUTATED | 1 | 1 | 1
SFRS2 WILD-TYPE | 21 | 35 | 21

'SFRS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.25

Table S58. Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
SFRS2 MUTATED | 1 | 2 | 0
SFRS2 WILD-TYPE | 32 | 16 | 29

'SFRS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.1

Table S59. Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
SFRS2 MUTATED | 1 | 2 | 0
SFRS2 WILD-TYPE | 29 | 13 | 35

Figure S29. Get High-res Image Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'SFRS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.18

Table S60. Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
SFRS2 MUTATED | 1 | 0 | 2
SFRS2 WILD-TYPE | 28 | 33 | 16

'SFRS2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.32

Table S61. Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
SFRS2 MUTATED | 3 | 0 | 0
SFRS2 WILD-TYPE | 31 | 17 | 29

'SFRS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.48

Table S62. Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 17 | 13 | 28 | 22
SFRS2 MUTATED | 1 | 1 | 0 | 1
SFRS2 WILD-TYPE | 16 | 12 | 28 | 21

'SFRS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S63. Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
SFRS2 MUTATED | 2 | 1 | 0
SFRS2 WILD-TYPE | 30 | 27 | 14

'SFRS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.32

Table S64. Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 5 | 12 | 16 | 16 | 15 | 10
SFRS2 MUTATED | 0 | 2 | 0 | 0 | 1 | 0
SFRS2 WILD-TYPE | 5 | 10 | 16 | 16 | 14 | 10

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/UVM-TP/19894046/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/19785804/UVM-TP.transferedmergedcluster.txt

- Number of patients = 80

- Number of significantly mutated genes = 8

- 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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