Correlation between gene mutation status and molecular subtypes
Uveal Melanoma (Primary solid tumor)
13 July 2018 | None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
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 10 molecular subtypes across 80 patients, 33 significant findings detected with P value < 0.05 and Q value < 0.25.

- EIF1AX mutation correlated to 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- BAP1 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- GNAQ mutation correlated to 'CN_CNMF'.

- GNA11 mutation correlated to 'CN_CNMF'.

- SF3B1 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'LINCRNA_CNMF', 'LINCRNA_CHIERARCHICAL', 'MIR_MATURE_CNMF', 'MIR_MATURE_CHIERARCHICAL', 'CN_CNMF', 'CN_THRESHOLDED_CNMF', 'METHYLATION_CNMF', and 'METHYLATION_CHIERARCHICAL'.

- SRSF2 mutation correlated to 'MRNA_CNMF'.

- CYSLTR2 mutation correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 7 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 33 significant findings detected.

|  | Clinical Features | MRNA CNMF | MRNA CHIERARCHICAL | LINCRNA CNMF | LINCRNA CHIERARCHICAL | MIR MATURE CNMF | MIR MATURE CHIERARCHICAL | CN CNMF | CN THRESHOLDED CNMF | METHYLATION CNMF | METHYLATION CHIERARCHICAL
| nMutated (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
BAP1 | 20 (25%) | 60 | 1e-05 (0.000117) | 1e-05 (0.000117) | 0.0036 (0.0133) | 1e-05 (0.000117) | 0.0144 (0.0348) | 0.00165 (0.00877) | 1e-05 (0.000117) | 1e-05 (0.000117) | 9e-05 (0.000787) | 1e-05 (0.000117)
SF3B1 | 18 (22%) | 62 | 0.0431 (0.0915) | 0.00444 (0.0141) | 0.00321 (0.0125) | 0.0193 (0.0451) | 0.00403 (0.0139) | 0.0105 (0.0283) | 0.00299 (0.0123) | 0.00021 (0.00134) | 9e-05 (0.000787) | 0.00188 (0.00877)
EIF1AX | 10 (12%) | 70 | 0.068 (0.126) | 0.00654 (0.0199) | 0.00418 (0.0139) | 0.00184 (0.00877) | 0.0101 (0.0283) | 0.00206 (0.00901) | 0.00938 (0.0274) | 0.00021 (0.00134) | 0.00016 (0.00124) | 0.00073 (0.00426)
GNAQ | 40 (50%) | 40 | 0.557 (0.696) | 0.0851 (0.149) | 0.501 (0.65) | 0.0684 (0.126) | 0.151 (0.24) | 0.0579 (0.116) | 0.0247 (0.0541) | 0.154 (0.24) | 0.517 (0.658) | 0.0778 (0.14)
GNA11 | 35 (44%) | 45 | 0.781 (0.882) | 0.141 (0.231) | 0.332 (0.467) | 0.0672 (0.126) | 0.618 (0.736) | 0.334 (0.467) | 0.0137 (0.0341) | 0.207 (0.315) | 0.592 (0.727) | 0.142 (0.231)
SRSF2 | 3 (4%) | 77 | 0.0234 (0.0529) | 0.05 (0.103) | 0.901 (0.986) | 0.621 (0.736) | 1 (1.00) | 0.671 (0.783) | 1 (1.00) | 0.727 (0.834) | 0.269 (0.4) | 0.434 (0.574)
CYSLTR2 | 3 (4%) | 77 | 0.0939 (0.16) | 0.329 (0.467) | 0.43 (0.574) | 0.423 (0.574) | 0.889 (0.986) | 1 (1.00) | 0.0136 (0.0341) | 1 (1.00) | 1 (1.00) | 1 (1.00)

'EIF1AX MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.068 (Fisher's exact test), Q value = 0.13

Table S1. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
EIF1AX MUTATED | 0 | 1 | 8 | 1 | 0
EIF1AX WILD-TYPE | 11 | 10 | 21 | 20 | 8

'EIF1AX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00654 (Fisher's exact test), Q value = 0.02

Table S2. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
EIF1AX MUTATED | 0 | 3 | 7 | 0
EIF1AX WILD-TYPE | 15 | 12 | 20 | 23

Figure S1. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'LINCRNA_CNMF'

P value = 0.00418 (Fisher's exact test), Q value = 0.014

Table S3. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
EIF1AX MUTATED | 0 | 4 | 2 | 1 | 3
EIF1AX WILD-TYPE | 18 | 3 | 26 | 10 | 13

Figure S2. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'EIF1AX MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.0088

Table S4. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
EIF1AX MUTATED | 0 | 7 | 0 | 3
EIF1AX WILD-TYPE | 21 | 17 | 20 | 12

Figure S3. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIR_MATURE_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.028

Table S5. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
EIF1AX MUTATED | 1 | 0 | 5 | 2 | 2
EIF1AX WILD-TYPE | 12 | 21 | 13 | 22 | 2

Figure S4. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'EIF1AX MUTATION STATUS' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.00206 (Fisher's exact test), Q value = 0.009

Table S6. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
EIF1AX MUTATED | 0 | 0 | 3 | 4 | 3
EIF1AX WILD-TYPE | 21 | 20 | 5 | 13 | 11

Figure S5. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00938 (Fisher's exact test), Q value = 0.027

Table S7. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
EIF1AX MUTATED | 0 | 0 | 10 | 0 | 0
EIF1AX WILD-TYPE | 18 | 21 | 27 | 2 | 2

Figure S6. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

'EIF1AX MUTATION STATUS' versus 'CN_THRESHOLDED_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0013

Table S8. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
EIF1AX MUTATED | 0 | 0 | 10 | 0 | 0 | 0 | 0 | 0
EIF1AX WILD-TYPE | 16 | 7 | 12 | 12 | 2 | 14 | 5 | 2

Figure S7. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'EIF1AX MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0012

Table S9. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
EIF1AX MUTATED | 0 | 6 | 0 | 4
EIF1AX WILD-TYPE | 28 | 7 | 16 | 19

Figure S8. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'EIF1AX MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0043

Table S10. Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
EIF1AX MUTATED | 0 | 4 | 6
EIF1AX WILD-TYPE | 40 | 11 | 19

Figure S9. Get High-res Image Gene #1: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S11. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
BAP1 MUTATED | 8 | 1 | 0 | 8 | 3
BAP1 WILD-TYPE | 3 | 10 | 29 | 13 | 5

Figure S10. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S12. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
BAP1 MUTATED | 8 | 1 | 0 | 11
BAP1 WILD-TYPE | 7 | 14 | 27 | 12

Figure S11. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'LINCRNA_CNMF'

P value = 0.0036 (Fisher's exact test), Q value = 0.013

Table S13. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
BAP1 MUTATED | 9 | 0 | 8 | 3 | 0
BAP1 WILD-TYPE | 9 | 7 | 20 | 8 | 16

Figure S12. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'BAP1 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S14. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
BAP1 MUTATED | 11 | 0 | 9 | 0
BAP1 WILD-TYPE | 10 | 24 | 11 | 15

Figure S13. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIR_MATURE_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.035

Table S15. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
BAP1 MUTATED | 5 | 10 | 3 | 2 | 0
BAP1 WILD-TYPE | 8 | 11 | 15 | 22 | 4

Figure S14. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'BAP1 MUTATION STATUS' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.00165 (Fisher's exact test), Q value = 0.0088

Table S16. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
BAP1 MUTATED | 8 | 10 | 0 | 1 | 1
BAP1 WILD-TYPE | 13 | 10 | 8 | 16 | 13

Figure S15. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S17. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
BAP1 MUTATED | 7 | 11 | 0 | 1 | 1
BAP1 WILD-TYPE | 11 | 10 | 37 | 1 | 1

Figure S16. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'CN_THRESHOLDED_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S18. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
BAP1 MUTATED | 5 | 5 | 0 | 0 | 0 | 9 | 1 | 0
BAP1 WILD-TYPE | 11 | 2 | 22 | 12 | 2 | 5 | 4 | 2

Figure S17. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'BAP1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00079

Table S19. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
BAP1 MUTATED | 13 | 1 | 6 | 0
BAP1 WILD-TYPE | 15 | 12 | 10 | 23

Figure S18. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'BAP1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S20. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
BAP1 MUTATED | 20 | 0 | 0
BAP1 WILD-TYPE | 20 | 15 | 25

Figure S19. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'GNAQ MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 0.7

Table S21. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
GNAQ MUTATED | 5 | 4 | 18 | 10 | 3
GNAQ WILD-TYPE | 6 | 7 | 11 | 11 | 5

'GNAQ MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0851 (Fisher's exact test), Q value = 0.15

Table S22. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
GNAQ MUTATED | 6 | 6 | 19 | 9
GNAQ WILD-TYPE | 9 | 9 | 8 | 14

'GNAQ MUTATION STATUS' versus 'LINCRNA_CNMF'

P value = 0.501 (Fisher's exact test), Q value = 0.65

Table S23. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
GNAQ MUTATED | 8 | 3 | 14 | 4 | 11
GNAQ WILD-TYPE | 10 | 4 | 14 | 7 | 5

'GNAQ MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0684 (Fisher's exact test), Q value = 0.13

Table S24. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
GNAQ MUTATED | 6 | 15 | 9 | 10
GNAQ WILD-TYPE | 15 | 9 | 11 | 5

'GNAQ MUTATION STATUS' versus 'MIR_MATURE_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.24

Table S25. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
GNAQ MUTATED | 3 | 9 | 11 | 15 | 2
GNAQ WILD-TYPE | 10 | 12 | 7 | 9 | 2

'GNAQ MUTATION STATUS' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0579 (Fisher's exact test), Q value = 0.12

Table S26. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
GNAQ MUTATED | 6 | 8 | 5 | 11 | 10
GNAQ WILD-TYPE | 15 | 12 | 3 | 6 | 4

'GNAQ MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.054

Table S27. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
GNAQ MUTATED | 7 | 7 | 25 | 1 | 0
GNAQ WILD-TYPE | 11 | 14 | 12 | 1 | 2

Figure S20. Get High-res Image Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

'GNAQ MUTATION STATUS' versus 'CN_THRESHOLDED_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.24

Table S28. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
GNAQ MUTATED | 6 | 2 | 15 | 7 | 1 | 4 | 3 | 2
GNAQ WILD-TYPE | 10 | 5 | 7 | 5 | 1 | 10 | 2 | 0

'GNAQ MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 0.66

Table S29. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
GNAQ MUTATED | 11 | 8 | 8 | 13
GNAQ WILD-TYPE | 17 | 5 | 8 | 10

'GNAQ MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.0778 (Fisher's exact test), Q value = 0.14

Table S30. Gene #3: 'GNAQ MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
GNAQ MUTATED | 15 | 10 | 15
GNAQ WILD-TYPE | 25 | 5 | 10

'GNA11 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 0.88

Table S31. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
GNA11 MUTATED | 6 | 5 | 10 | 10 | 4
GNA11 WILD-TYPE | 5 | 6 | 19 | 11 | 4

'GNA11 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.141 (Fisher's exact test), Q value = 0.23

Table S32. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
GNA11 MUTATED | 8 | 8 | 7 | 12
GNA11 WILD-TYPE | 7 | 7 | 20 | 11

'GNA11 MUTATION STATUS' versus 'LINCRNA_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 0.47

Table S33. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
GNA11 MUTATED | 10 | 4 | 11 | 6 | 4
GNA11 WILD-TYPE | 8 | 3 | 17 | 5 | 12

'GNA11 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0672 (Fisher's exact test), Q value = 0.13

Table S34. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
GNA11 MUTATED | 14 | 8 | 9 | 4
GNA11 WILD-TYPE | 7 | 16 | 11 | 11

'GNA11 MUTATION STATUS' versus 'MIR_MATURE_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 0.74

Table S35. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
GNA11 MUTATED | 7 | 11 | 8 | 8 | 1
GNA11 WILD-TYPE | 6 | 10 | 10 | 16 | 3

'GNA11 MUTATION STATUS' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 0.47

Table S36. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
GNA11 MUTATED | 13 | 9 | 3 | 5 | 5
GNA11 WILD-TYPE | 8 | 11 | 5 | 12 | 9

'GNA11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.034

Table S37. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
GNA11 MUTATED | 8 | 14 | 11 | 0 | 2
GNA11 WILD-TYPE | 10 | 7 | 26 | 2 | 0

Figure S21. Get High-res Image Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

'GNA11 MUTATION STATUS' versus 'CN_THRESHOLDED_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 0.32

Table S38. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
GNA11 MUTATED | 8 | 5 | 6 | 4 | 1 | 9 | 2 | 0
GNA11 WILD-TYPE | 8 | 2 | 16 | 8 | 1 | 5 | 3 | 2

'GNA11 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 0.73

Table S39. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
GNA11 MUTATED | 15 | 5 | 7 | 8
GNA11 WILD-TYPE | 13 | 8 | 9 | 15

'GNA11 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 0.23

Table S40. Gene #4: 'GNA11 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
GNA11 MUTATED | 22 | 5 | 8
GNA11 WILD-TYPE | 18 | 10 | 17

'SF3B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.092

Table S41. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
SF3B1 MUTATED | 2 | 0 | 11 | 5 | 0
SF3B1 WILD-TYPE | 9 | 11 | 18 | 16 | 8

Figure S22. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SF3B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.014

Table S42. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
SF3B1 MUTATED | 0 | 3 | 12 | 3
SF3B1 WILD-TYPE | 15 | 12 | 15 | 20

Figure S23. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'LINCRNA_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.012

Table S43. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
SF3B1 MUTATED | 0 | 0 | 7 | 3 | 8
SF3B1 WILD-TYPE | 18 | 7 | 21 | 8 | 8

Figure S24. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

'SF3B1 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.045

Table S44. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
SF3B1 MUTATED | 3 | 7 | 1 | 7
SF3B1 WILD-TYPE | 18 | 17 | 19 | 8

Figure S25. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'MIR_MATURE_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.014

Table S45. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
SF3B1 MUTATED | 0 | 1 | 6 | 10 | 1
SF3B1 WILD-TYPE | 13 | 20 | 12 | 14 | 3

Figure S26. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

'SF3B1 MUTATION STATUS' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.028

Table S46. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
SF3B1 MUTATED | 2 | 1 | 2 | 7 | 6
SF3B1 WILD-TYPE | 19 | 19 | 6 | 10 | 8

Figure S27. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00299 (Fisher's exact test), Q value = 0.012

Table S47. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
SF3B1 MUTATED | 3 | 0 | 14 | 0 | 1
SF3B1 WILD-TYPE | 15 | 21 | 23 | 2 | 1

Figure S28. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

'SF3B1 MUTATION STATUS' versus 'CN_THRESHOLDED_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.0013

Table S48. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
SF3B1 MUTATED | 4 | 0 | 2 | 8 | 1 | 1 | 0 | 2
SF3B1 WILD-TYPE | 12 | 7 | 20 | 4 | 1 | 13 | 5 | 0

Figure S29. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

'SF3B1 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00079

Table S49. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
SF3B1 MUTATED | 0 | 2 | 5 | 11
SF3B1 WILD-TYPE | 28 | 11 | 11 | 12

Figure S30. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

'SF3B1 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.00188 (Fisher's exact test), Q value = 0.0088

Table S50. Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
SF3B1 MUTATED | 3 | 4 | 11
SF3B1 WILD-TYPE | 37 | 11 | 14

Figure S31. Get High-res Image Gene #5: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

'SRSF2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.053

Table S51. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
SRSF2 MUTATED | 0 | 2 | 0 | 0 | 1
SRSF2 WILD-TYPE | 11 | 9 | 29 | 21 | 7

Figure S32. Get High-res Image Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SRSF2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.1

Table S52. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
SRSF2 MUTATED | 1 | 2 | 0 | 0
SRSF2 WILD-TYPE | 14 | 13 | 27 | 23

'SRSF2 MUTATION STATUS' versus 'LINCRNA_CNMF'

P value = 0.901 (Fisher's exact test), Q value = 0.99

Table S53. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
SRSF2 MUTATED | 1 | 0 | 2 | 0 | 0
SRSF2 WILD-TYPE | 17 | 7 | 26 | 11 | 16

'SRSF2 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.621 (Fisher's exact test), Q value = 0.74

Table S54. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
SRSF2 MUTATED | 1 | 2 | 0 | 0
SRSF2 WILD-TYPE | 20 | 22 | 20 | 15

'SRSF2 MUTATION STATUS' versus 'MIR_MATURE_CNMF'

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

Table S55. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
SRSF2 MUTATED | 0 | 1 | 1 | 1 | 0
SRSF2 WILD-TYPE | 13 | 20 | 17 | 23 | 4

'SRSF2 MUTATION STATUS' versus 'MIR_MATURE_CHIERARCHICAL'

P value = 0.671 (Fisher's exact test), Q value = 0.78

Table S56. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
SRSF2 MUTATED | 1 | 2 | 0 | 0 | 0
SRSF2 WILD-TYPE | 20 | 18 | 8 | 17 | 14

'SRSF2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S57. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
SRSF2 MUTATED | 1 | 1 | 1 | 0 | 0
SRSF2 WILD-TYPE | 17 | 20 | 36 | 2 | 2

'SRSF2 MUTATION STATUS' versus 'CN_THRESHOLDED_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 0.83

Table S58. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
SRSF2 MUTATED | 1 | 0 | 0 | 1 | 0 | 1 | 0 | 0
SRSF2 WILD-TYPE | 15 | 7 | 22 | 11 | 2 | 13 | 5 | 2

'SRSF2 MUTATION STATUS' versus 'METHYLATION_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.4

Table S59. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
SRSF2 MUTATED | 1 | 0 | 2 | 0
SRSF2 WILD-TYPE | 27 | 13 | 14 | 23

'SRSF2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

P value = 0.434 (Fisher's exact test), Q value = 0.57

Table S60. Gene #6: 'SRSF2 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
SRSF2 MUTATED | 2 | 1 | 0
SRSF2 WILD-TYPE | 38 | 14 | 25

'CYSLTR2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0939 (Fisher's exact test), Q value = 0.16

Table S61. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 11 | 11 | 29 | 21 | 8
CYSLTR2 MUTATED | 0 | 2 | 0 | 1 | 0
CYSLTR2 WILD-TYPE | 11 | 9 | 29 | 20 | 8

'CYSLTR2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 0.47

Table S62. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 15 | 15 | 27 | 23
CYSLTR2 MUTATED | 0 | 1 | 0 | 2
CYSLTR2 WILD-TYPE | 15 | 14 | 27 | 21

'CYSLTR2 MUTATION STATUS' versus 'LINCRNA_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 0.57

Table S63. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #3: 'LINCRNA_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 7 | 28 | 11 | 16
CYSLTR2 MUTATED | 0 | 0 | 3 | 0 | 0
CYSLTR2 WILD-TYPE | 18 | 7 | 25 | 11 | 16

'CYSLTR2 MUTATION STATUS' versus 'LINCRNA_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 0.57

Table S64. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #4: 'LINCRNA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 21 | 24 | 20 | 15
CYSLTR2 MUTATED | 0 | 1 | 2 | 0
CYSLTR2 WILD-TYPE | 21 | 23 | 18 | 15

'CYSLTR2 MUTATION STATUS' versus 'MIR_MATURE_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 0.99

Table S65. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #5: 'MIR_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 13 | 21 | 18 | 24 | 4
CYSLTR2 MUTATED | 1 | 1 | 0 | 1 | 0
CYSLTR2 WILD-TYPE | 12 | 20 | 18 | 23 | 4

'CYSLTR2 MUTATION STATUS' versus 'MIR_MATURE_CHIERARCHICAL'

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

Table S66. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #6: 'MIR_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 21 | 20 | 8 | 17 | 14
CYSLTR2 MUTATED | 1 | 1 | 0 | 1 | 0
CYSLTR2 WILD-TYPE | 20 | 19 | 8 | 16 | 14

'CYSLTR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.034

Table S67. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 21 | 37 | 2 | 2
CYSLTR2 MUTATED | 2 | 0 | 0 | 1 | 0
CYSLTR2 WILD-TYPE | 16 | 21 | 37 | 1 | 2

Figure S33. Get High-res Image Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #7: 'CN_CNMF'

'CYSLTR2 MUTATION STATUS' versus 'CN_THRESHOLDED_CNMF'

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

Table S68. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #8: 'CN_THRESHOLDED_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 16 | 7 | 22 | 12 | 2 | 14 | 5 | 2
CYSLTR2 MUTATED | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 0
CYSLTR2 WILD-TYPE | 15 | 7 | 21 | 12 | 2 | 13 | 5 | 2

'CYSLTR2 MUTATION STATUS' versus 'METHYLATION_CNMF'

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

Table S69. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #9: 'METHYLATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 28 | 13 | 16 | 23
CYSLTR2 MUTATED | 1 | 0 | 1 | 1
CYSLTR2 WILD-TYPE | 27 | 13 | 15 | 22

'CYSLTR2 MUTATION STATUS' versus 'METHYLATION_CHIERARCHICAL'

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

Table S70. Gene #7: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #10: 'METHYLATION_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 40 | 15 | 25
CYSLTR2 MUTATED | 2 | 0 | 1
CYSLTR2 WILD-TYPE | 38 | 15 | 24

Methods & Data
Input

- Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

- Processed Mutation data file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/5947d552-214f-400c-a2a3-61737bb767b7/correlate_genomic_events_all/4e4e215a-e17e-44fb-bf9c-509dde44b76c/call-preprocess_genomic_event/transformed.cor.cli.txt

- Molecular subtypes file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/9d897bdb-7a9a-423a-ad17-06f28ae98803/aggregate_clusters_workflow/1d8bac82-5a1d-4cd2-aeb1-8ddd0e1e7a20/call-aggregate_clusters/TCGA-UVM-TP.transposedmergedcluster.txt

- Number of patients = 80

- Number of significantly mutated genes = 7

- Number of Molecular subtypes = 10

- Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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