Correlation between gene mutation status and molecular subtypes

Uveal Melanoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

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.

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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