Correlation between gene mutation status and molecular subtypes
Uveal Melanoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1V123X8
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/C1V123X8
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, 30 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'.

- 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' and 'MRNASEQ_CNMF'.

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, 30 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 | 0.00084 (0.00433) | 0.00082 (0.00433) | 0.00045 (0.0042) | 0.00201 (0.00804) | 0.0004 (0.0042) | 0.0188 (0.0457) | 0.00085 (0.00433) | 0.0108 (0.0275)
BAP1 | 16 (20%) | 64 | 4e-05 (0.00224) | 0.00018 (0.00336) | 0.00083 (0.00433) | 0.00017 (0.00336) | 0.00135 (0.0063) | 0.0004 (0.0042) | 0.00298 (0.0111) | 0.0107 (0.0275)
GNAQ | 40 (50%) | 40 | 0.0306 (0.0714) | 0.0415 (0.083) | 0.0462 (0.0862) | 0.0378 (0.0814) | 0.0393 (0.0815) | 0.093 (0.149) | 0.0523 (0.0945) | 0.00743 (0.0231)
EIF1AX | 10 (12%) | 70 | 0.00079 (0.00433) | 0.00159 (0.00685) | 0.00967 (0.0271) | 0.00847 (0.025) | 0.00345 (0.0121) | 0.00479 (0.0158) | 0.0648 (0.11) | 0.171 (0.239)
CYSLTR2 | 3 (4%) | 77 | 0.0375 (0.0814) | 1 (1.00) | 0.0443 (0.0856) | 0.107 (0.167) | 0.795 (0.89) | 0.272 (0.346) | 1 (1.00) | 0.574 (0.67)
GNA11 | 36 (45%) | 44 | 0.0767 (0.126) | 0.0625 (0.109) | 0.188 (0.257) | 0.135 (0.2) | 0.146 (0.209) | 0.27 (0.346) | 0.235 (0.313) | 0.31 (0.386)
PRMT8 | 5 (6%) | 75 | 0.857 (0.941) | 0.626 (0.715) | 0.499 (0.608) | 0.531 (0.633) | 1 (1.00) | 0.924 (0.995) | 0.126 (0.191) | 1 (1.00)

'GNAQ MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.071

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 = 0.0415 (Fisher's exact test), Q value = 0.083

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 = 0.0462 (Fisher's exact test), Q value = 0.086

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 = 0.0378 (Fisher's exact test), Q value = 0.081

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 = 0.0393 (Fisher's exact test), Q value = 0.082

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 = 0.093 (Fisher's exact test), Q value = 0.15

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 = 0.0523 (Fisher's exact test), Q value = 0.094

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 = 0.00743 (Fisher's exact test), Q value = 0.023

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 = 0.0767 (Fisher's exact test), Q value = 0.13

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 = 0.0625 (Fisher's exact test), Q value = 0.11

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 = 0.188 (Fisher's exact test), Q value = 0.26

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 = 0.2

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 = 0.146 (Fisher's exact test), Q value = 0.21

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 = 0.27 (Fisher's exact test), Q value = 0.35

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 = 0.235 (Fisher's exact test), Q value = 0.31

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 = 0.39

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 = 0.00079 (Fisher's exact test), Q value = 0.0043

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 = 0.00159 (Fisher's exact test), Q value = 0.0068

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 = 0.00967 (Fisher's exact test), Q value = 0.027

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 = 0.00847 (Fisher's exact test), Q value = 0.025

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 = 0.00345 (Fisher's exact test), Q value = 0.012

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 = 0.00479 (Fisher's exact test), Q value = 0.016

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 = 0.0648 (Fisher's exact test), Q value = 0.11

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 = 0.24

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 = 0.00084 (Fisher's exact test), Q value = 0.0043

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 = 0.00082 (Fisher's exact test), Q value = 0.0043

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 = 0.00045 (Fisher's exact test), Q value = 0.0042

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 = 0.00201 (Fisher's exact test), Q value = 0.008

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 = 4e-04 (Fisher's exact test), Q value = 0.0042

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 = 0.0188 (Fisher's exact test), Q value = 0.046

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 = 0.00085 (Fisher's exact test), Q value = 0.0043

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 = 0.0108 (Fisher's exact test), Q value = 0.028

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'

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0022

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 22 | 36 | 22
BAP1 MUTATED | 9 | 0 | 7
BAP1 WILD-TYPE | 13 | 36 | 15

Figure S21. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0034

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 33 | 18 | 29
BAP1 MUTATED | 13 | 3 | 0
BAP1 WILD-TYPE | 20 | 15 | 29

Figure S22. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0043

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 30 | 15 | 35
BAP1 MUTATED | 11 | 4 | 1
BAP1 WILD-TYPE | 19 | 11 | 34

Figure S23. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0034

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 | 10 | 0 | 6
BAP1 WILD-TYPE | 19 | 33 | 12

Figure S24. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0063

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 34 | 17 | 29
BAP1 MUTATED | 13 | 2 | 1
BAP1 WILD-TYPE | 21 | 15 | 28

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

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.0042

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 | 7 | 0 | 1 | 8
BAP1 WILD-TYPE | 10 | 13 | 27 | 14

Figure S26. Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00298 (Fisher's exact test), Q value = 0.011

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

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 32 | 28 | 14
BAP1 MUTATED | 12 | 1 | 2
BAP1 WILD-TYPE | 20 | 27 | 12

Figure S27. 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 = 0.0107 (Fisher's exact test), Q value = 0.028

Table S40. Gene #5: '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 | 2 | 4 | 2 | 0 | 2 | 5
BAP1 WILD-TYPE | 3 | 8 | 14 | 16 | 13 | 5

Figure S28. Get High-res Image Gene #5: 'BAP1 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 = 0.94

Table S41. Gene #6: '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 = 0.626 (Fisher's exact test), Q value = 0.72

Table S42. Gene #6: '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 = 0.499 (Fisher's exact test), Q value = 0.61

Table S43. Gene #6: '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 = 0.531 (Fisher's exact test), Q value = 0.63

Table S44. Gene #6: '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 S45. Gene #6: '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 S46. Gene #6: '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 = 0.126 (Fisher's exact test), Q value = 0.19

Table S47. Gene #6: '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 S48. Gene #6: '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 = 0.0375 (Fisher's exact test), Q value = 0.081

Table S49. Gene #7: '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 S29. Get High-res Image Gene #7: '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 S50. Gene #7: '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 = 0.0443 (Fisher's exact test), Q value = 0.086

Table S51. Gene #7: '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 S30. Get High-res Image Gene #7: '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 = 0.17

Table S52. Gene #7: '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 = 0.795 (Fisher's exact test), Q value = 0.89

Table S53. Gene #7: '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 = 0.272 (Fisher's exact test), Q value = 0.35

Table S54. Gene #7: '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 S55. Gene #7: '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 = 0.574 (Fisher's exact test), Q value = 0.67

Table S56. Gene #7: '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

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/15890468/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/15952300/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 © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle