Correlation between gene mutation status and molecular subtypes

Overview

Introduction

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

Summary

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

GNAQ mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
EIF1AX mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
SF3B1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
CYSLTR2 mutation correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
BAP1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
SFRS2 mutation correlated to 'MRNASEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 8 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 29 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
SF3B1	18 (22%)	62	0.00081 (0.00942)	0.00103 (0.00942)	0.0005 (0.00942)	0.00173 (0.0123)	0.00031 (0.00942)	0.0177 (0.0565)	0.00072 (0.00942)	0.0111 (0.0393)
GNAQ	40 (50%)	40	0.0303 (0.0923)	0.0405 (0.0996)	0.0457 (0.101)	0.0382 (0.0983)	0.0384 (0.0983)	0.0895 (0.159)	0.0536 (0.11)	0.00737 (0.0337)
EIF1AX	10 (12%)	70	0.0009 (0.00942)	0.00193 (0.0124)	0.00993 (0.0374)	0.00836 (0.0357)	0.00359 (0.0191)	0.00518 (0.0255)	0.0647 (0.122)	0.171 (0.255)
BAP1	12 (15%)	68	0.00072 (0.00942)	0.00337 (0.0191)	0.0153 (0.0515)	0.00126 (0.0101)	0.0322 (0.0936)	0.00924 (0.037)	0.0551 (0.11)	0.0524 (0.11)
CYSLTR2	3 (4%)	77	0.0374 (0.0983)	1 (1.00)	0.0433 (0.101)	0.107 (0.181)	0.798 (0.912)	0.274 (0.358)	1 (1.00)	0.572 (0.677)
SFRS2	3 (4%)	77	1 (1.00)	0.169 (0.255)	0.0444 (0.101)	0.107 (0.181)	0.231 (0.322)	0.382 (0.479)	1 (1.00)	0.232 (0.322)
GNA11	36 (45%)	44	0.0787 (0.144)	0.0624 (0.121)	0.191 (0.277)	0.135 (0.216)	0.147 (0.229)	0.268 (0.357)	0.237 (0.323)	0.31 (0.397)
PRMT8	5 (6%)	75	0.857 (0.962)	0.624 (0.726)	0.497 (0.612)	0.528 (0.637)	1 (1.00)	0.924 (1.00)	0.127 (0.209)	1 (1.00)

'GNAQ MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

'GNAQ MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

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

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

'GNAQ MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

'GNAQ MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'GNAQ MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

'GNAQ MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

'GNAQ MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

'GNAQ MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'GNA11 MUTATION STATUS' versus 'CN_CNMF'

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

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

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

'GNA11 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

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

'GNA11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

'GNA11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

'GNA11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

'GNA11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

'GNA11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

'GNA11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

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

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

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

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

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

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

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

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

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

'PRMT8 MUTATION STATUS' versus 'CN_CNMF'

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

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

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

'PRMT8 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

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

'PRMT8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

'PRMT8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

'CYSLTR2 MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

'CYSLTR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

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

'CYSLTR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

'CYSLTR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

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

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

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

'SFRS2 MUTATION STATUS' versus 'CN_CNMF'

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

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

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

'SFRS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

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

'SFRS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

'SFRS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

'SFRS2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

'SFRS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

'SFRS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

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

'SFRS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

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

Methods & Data

Input

Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/19894046/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/19785804/UVM-TP.transferedmergedcluster.txt
Number of patients = 80
Number of significantly mutated genes = 8
Number of Molecular subtypes = 8
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Q value calculation

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

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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