Correlation between gene mutation status and molecular subtypes
Uveal Melanoma (Primary solid tumor)
28 January 2016 | analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1571BH8
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1571BH8
Overview
Introduction

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

Summary

Testing the association between mutation status of 7 genes and 8 molecular subtypes across 80 patients, 27 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

- BAP1 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'.

- SFRS2 mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 7 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, 27 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 | 0.0364 (0.0841) | 0.00011 (0.000684) | 9e-05 (0.00063) | 0.00183 (0.00932) | 0.0325 (0.0829) | 0.0184 (0.0596) | 0.00793 (0.0313) | 0.0166 (0.0582)
BAP1 | 22 (28%) | 58 | 3e-05 (0.00028) | 1e-05 (0.000112) | 1e-05 (0.000112) | 1e-05 (0.000112) | 1e-05 (0.000112) | 1e-05 (0.000112) | 0.00277 (0.0129) | 7e-05 (0.00056)
EIF1AX | 10 (12%) | 70 | 0.221 (0.326) | 0.00022 (0.00123) | 0.0192 (0.0596) | 0.00839 (0.0313) | 0.0253 (0.0746) | 0.00498 (0.0215) | 0.215 (0.325) | 0.036 (0.0841)
GNAQ | 40 (50%) | 40 | 0.373 (0.435) | 0.505 (0.555) | 0.134 (0.215) | 0.0375 (0.0841) | 0.0448 (0.0929) | 0.0899 (0.168) | 0.099 (0.179) | 0.0324 (0.0829)
CYSLTR2 | 3 (4%) | 77 | 0.0275 (0.0771) | 1 (1.00) | 0.0599 (0.116) | 0.107 (0.184) | 0.24 (0.344) | 0.274 (0.357) | 0.6 (0.646) | 0.367 (0.435)
SFRS2 | 3 (4%) | 77 | 0.258 (0.357) | 0.182 (0.283) | 0.0595 (0.116) | 0.109 (0.184) | 0.402 (0.45) | 0.381 (0.435) | 0.818 (0.833) | 0.0416 (0.0896)
GNA11 | 36 (45%) | 44 | 0.269 (0.357) | 0.726 (0.753) | 0.35 (0.426) | 0.134 (0.215) | 0.669 (0.707) | 0.268 (0.357) | 0.324 (0.404) | 0.307 (0.391)

'GNAQ MUTATION STATUS' versus 'CN_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 0.43

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
GNAQ MUTATED | 10 | 2 | 4 | 20 | 3 | 1
GNAQ WILD-TYPE | 12 | 5 | 6 | 11 | 3 | 3

'GNAQ MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 0.55

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
GNAQ MUTATED | 11 | 8 | 7 | 14
GNAQ WILD-TYPE | 17 | 6 | 7 | 10

'GNAQ MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.22

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
GNAQ MUTATED | 8 | 5 | 21 | 6
GNAQ WILD-TYPE | 10 | 10 | 11 | 9

'GNAQ MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.084

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 S1. Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'GNAQ MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.093

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
GNAQ MUTATED | 2 | 1 | 7 | 17 | 10 | 3
GNAQ WILD-TYPE | 6 | 7 | 4 | 8 | 13 | 2

Figure S2. Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'GNAQ MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0899 (Fisher's exact test), Q value = 0.17

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 = 0.099 (Fisher's exact test), Q value = 0.18

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
GNAQ MUTATED | 9 | 0 | 11 | 5 | 4 | 5 | 3
GNAQ WILD-TYPE | 11 | 7 | 6 | 4 | 4 | 2 | 3

'GNAQ MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.083

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
GNAQ MUTATED | 7 | 20 | 5 | 5
GNAQ WILD-TYPE | 11 | 8 | 11 | 7

Figure S3. Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GNA11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.36

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
GNA11 MUTATED | 12 | 5 | 3 | 11 | 2 | 3
GNA11 WILD-TYPE | 10 | 2 | 7 | 20 | 4 | 1

'GNA11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 0.75

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
GNA11 MUTATED | 15 | 6 | 6 | 9
GNA11 WILD-TYPE | 13 | 8 | 8 | 15

'GNA11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.43

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
GNA11 MUTATED | 11 | 7 | 11 | 7
GNA11 WILD-TYPE | 7 | 8 | 21 | 8

'GNA11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.134 (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 = 0.669 (Fisher's exact test), Q value = 0.71

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
GNA11 MUTATED | 5 | 5 | 4 | 9 | 11 | 2
GNA11 WILD-TYPE | 3 | 3 | 7 | 16 | 12 | 3

'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 = 0.324 (Fisher's exact test), Q value = 0.4

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
GNA11 MUTATED | 10 | 6 | 6 | 3 | 4 | 2 | 2
GNA11 WILD-TYPE | 10 | 1 | 11 | 6 | 4 | 5 | 4

'GNA11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.39

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
GNA11 MUTATED | 10 | 9 | 9 | 5
GNA11 WILD-TYPE | 8 | 19 | 7 | 7

'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 0.33

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
EIF1AX MUTATED | 2 | 0 | 0 | 8 | 0 | 0
EIF1AX WILD-TYPE | 20 | 7 | 10 | 23 | 6 | 4

'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0012

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
EIF1AX MUTATED | 0 | 6 | 0 | 4
EIF1AX WILD-TYPE | 28 | 8 | 14 | 20

Figure S4. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.06

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
EIF1AX MUTATED | 0 | 2 | 8 | 0
EIF1AX WILD-TYPE | 18 | 13 | 24 | 15

Figure S5. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00839 (Fisher's exact test), Q value = 0.031

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 S6. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.075

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
EIF1AX MUTATED | 0 | 0 | 3 | 6 | 0 | 1
EIF1AX WILD-TYPE | 8 | 8 | 8 | 19 | 23 | 4

Figure S7. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00498 (Fisher's exact test), Q value = 0.021

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 S8. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.33

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
EIF1AX MUTATED | 0 | 1 | 4 | 1 | 1 | 0 | 1
EIF1AX WILD-TYPE | 20 | 6 | 13 | 8 | 7 | 7 | 5

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.084

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
EIF1AX MUTATED | 0 | 6 | 0 | 2
EIF1AX WILD-TYPE | 18 | 22 | 16 | 10

Figure S9. Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.084

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
SF3B1 MUTATED | 3 | 0 | 1 | 13 | 0 | 1
SF3B1 WILD-TYPE | 19 | 7 | 9 | 18 | 6 | 3

Figure S10. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00068

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
SF3B1 MUTATED | 0 | 2 | 5 | 11
SF3B1 WILD-TYPE | 28 | 12 | 9 | 13

Figure S11. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00063

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
SF3B1 MUTATED | 3 | 0 | 15 | 0
SF3B1 WILD-TYPE | 15 | 15 | 17 | 15

Figure S12. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.0093

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

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.083

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
SF3B1 MUTATED | 1 | 1 | 3 | 10 | 1 | 2
SF3B1 WILD-TYPE | 7 | 7 | 8 | 15 | 22 | 3

Figure S14. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.06

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 S15. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00793 (Fisher's exact test), Q value = 0.031

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
SF3B1 MUTATED | 0 | 0 | 7 | 3 | 3 | 2 | 2
SF3B1 WILD-TYPE | 20 | 7 | 10 | 6 | 5 | 5 | 4

Figure S16. 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 = 0.0166 (Fisher's exact test), Q value = 0.058

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
SF3B1 MUTATED | 1 | 12 | 2 | 2
SF3B1 WILD-TYPE | 17 | 16 | 14 | 10

Figure S17. Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00028

Table S33. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
BAP1 MUTATED | 8 | 5 | 5 | 0 | 3 | 1
BAP1 WILD-TYPE | 14 | 2 | 5 | 31 | 3 | 3

Figure S18. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S34. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
BAP1 MUTATED | 14 | 1 | 7 | 0
BAP1 WILD-TYPE | 14 | 13 | 7 | 24

Figure S19. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S35. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
BAP1 MUTATED | 11 | 6 | 0 | 5
BAP1 WILD-TYPE | 7 | 9 | 32 | 10

Figure S20. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S36. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 29 | 33 | 18
BAP1 MUTATED | 14 | 0 | 8
BAP1 WILD-TYPE | 15 | 33 | 10

Figure S21. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S37. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
BAP1 MUTATED | 6 | 2 | 0 | 1 | 12 | 1
BAP1 WILD-TYPE | 2 | 6 | 11 | 24 | 11 | 4

Figure S22. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S38. Gene #5: '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 | 9 | 0 | 1 | 12
BAP1 WILD-TYPE | 8 | 13 | 27 | 10

Figure S23. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.013

Table S39. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
BAP1 MUTATED | 10 | 3 | 0 | 4 | 3 | 1 | 0
BAP1 WILD-TYPE | 10 | 4 | 17 | 5 | 5 | 6 | 6

Figure S24. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00056

Table S40. Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
BAP1 MUTATED | 11 | 1 | 6 | 3
BAP1 WILD-TYPE | 7 | 27 | 10 | 9

Figure S25. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CYSLTR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.077

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
CYSLTR2 MUTATED | 0 | 0 | 2 | 0 | 1 | 0
CYSLTR2 WILD-TYPE | 22 | 7 | 8 | 31 | 5 | 4

Figure S26. 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 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
CYSLTR2 MUTATED | 1 | 0 | 1 | 1
CYSLTR2 WILD-TYPE | 27 | 14 | 13 | 23

'CYSLTR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0599 (Fisher's exact test), Q value = 0.12

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
CYSLTR2 MUTATED | 0 | 2 | 0 | 1
CYSLTR2 WILD-TYPE | 18 | 13 | 32 | 14

'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 = 0.24 (Fisher's exact test), Q value = 0.34

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
CYSLTR2 MUTATED | 1 | 1 | 0 | 0 | 1 | 0
CYSLTR2 WILD-TYPE | 7 | 7 | 11 | 25 | 22 | 5

'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 = 0.6 (Fisher's exact test), Q value = 0.65

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
CYSLTR2 MUTATED | 1 | 0 | 0 | 1 | 0 | 1 | 0
CYSLTR2 WILD-TYPE | 19 | 7 | 17 | 8 | 8 | 6 | 6

'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.43

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
CYSLTR2 MUTATED | 1 | 0 | 1 | 1
CYSLTR2 WILD-TYPE | 17 | 28 | 15 | 11

'SFRS2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.36

Table S49. Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 22 | 7 | 10 | 31 | 6 | 4
SFRS2 MUTATED | 3 | 0 | 0 | 0 | 0 | 0
SFRS2 WILD-TYPE | 19 | 7 | 10 | 31 | 6 | 4

'SFRS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.28

Table S50. Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 14 | 14 | 24
SFRS2 MUTATED | 1 | 2 | 0 | 0
SFRS2 WILD-TYPE | 27 | 12 | 14 | 24

'SFRS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0595 (Fisher's exact test), Q value = 0.12

Table S51. Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 15 | 32 | 15
SFRS2 MUTATED | 0 | 2 | 0 | 1
SFRS2 WILD-TYPE | 18 | 13 | 32 | 14

'SFRS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.18

Table S52. Gene #7: '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 = 0.402 (Fisher's exact test), Q value = 0.45

Table S53. Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6
--- | --- | --- | --- | --- | --- | ---
ALL | 8 | 8 | 11 | 25 | 23 | 5
SFRS2 MUTATED | 1 | 0 | 1 | 0 | 1 | 0
SFRS2 WILD-TYPE | 7 | 8 | 10 | 25 | 22 | 5

'SFRS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.381 (Fisher's exact test), Q value = 0.44

Table S54. Gene #7: '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 = 0.818 (Fisher's exact test), Q value = 0.83

Table S55. Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 20 | 7 | 17 | 9 | 8 | 7 | 6
SFRS2 MUTATED | 1 | 1 | 1 | 0 | 0 | 0 | 0
SFRS2 WILD-TYPE | 19 | 6 | 16 | 9 | 8 | 7 | 6

'SFRS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0416 (Fisher's exact test), Q value = 0.09

Table S56. Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 18 | 28 | 16 | 12
SFRS2 MUTATED | 0 | 0 | 1 | 2
SFRS2 WILD-TYPE | 18 | 28 | 15 | 10

Figure S27. Get High-res Image Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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/22572046/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/22542449/UVM-TP.transferedmergedcluster.txt

- Number of patients = 80

- Number of significantly mutated genes = 7

- 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)
Copyright © 2016 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle