Correlation between gene mutation status and molecular subtypes

Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

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 (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1RF5SPR

Overview

Introduction

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

Summary

Testing the association between mutation status of 9 genes and 12 molecular subtypes across 417 patients, 13 significant findings detected with P value < 0.05 and Q value < 0.25.

BAP1 mutation correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
VHL mutation correlated to 'MRNASEQ_CNMF'.
SETD2 mutation correlated to 'METHLYATION_CNMF'.
PBRM1 mutation correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
PTEN mutation correlated to 'MRNASEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 9 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 13 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	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	Chi-square 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	Chi-square test
BAP1	42 (10%)	375	0.0318 (1.00)	0.0281 (1.00)	0.0868 (1.00)	0.000133 (0.0115)	0.00121 (0.103)	0.134 (1.00)	1.29e-05 (0.00115)	2.71e-08 (2.55e-06)	8.79e-06 (0.000799)	4e-06 (0.000368)	0.163 (1.00)	0.0719 (1.00)
PBRM1	137 (33%)	280	0.135 (1.00)	0.212 (1.00)	0.0111 (0.858)	9.34e-06 (0.000841)	0.000762 (0.0655)	0.75 (1.00)	0.00465 (0.372)	0.0221 (1.00)	0.00311 (0.252)	0.00265 (0.217)	2.38e-05 (0.00209)	0.0323 (1.00)
VHL	218 (52%)	199	0.0163 (1.00)	0.0188 (1.00)	0.0574 (1.00)	0.806 (1.00)	0.342 (1.00)	0.642 (1.00)	0.0023 (0.191)	0.0103 (0.811)	0.0439 (1.00)	0.274 (1.00)	0.117 (1.00)	0.337 (1.00)
SETD2	48 (12%)	369	0.764 (1.00)	0.787 (1.00)	0.64 (1.00)	3.43e-07 (3.19e-05)	0.329 (1.00)	0.349 (1.00)	0.717 (1.00)	0.798 (1.00)	0.683 (1.00)	0.459 (1.00)	1 (1.00)	0.55 (1.00)
PTEN	18 (4%)	399	0.106 (1.00)	0.0903 (1.00)	0.125 (1.00)	0.154 (1.00)	0.214 (1.00)	0.0552 (1.00)	0.00126 (0.106)	0.0454 (1.00)	0.0425 (1.00)	0.129 (1.00)	0.0128 (0.958)	0.459 (1.00)
KDM5C	27 (6%)	390			0.447 (1.00)	0.172 (1.00)	0.477 (1.00)	0.581 (1.00)	0.15 (1.00)	0.783 (1.00)	0.0114 (0.864)	0.724 (1.00)	0.332 (1.00)	0.466 (1.00)
TSPAN19	5 (1%)	412			0.451 (1.00)		0.0807 (1.00)	0.203 (1.00)	0.724 (1.00)	0.524 (1.00)	0.452 (1.00)	0.289 (1.00)
TCEB1	3 (1%)	414			0.011 (0.856)		0.342 (1.00)	0.797 (1.00)	0.0419 (1.00)	0.099 (1.00)	0.164 (1.00)	0.632 (1.00)
NEFH	6 (1%)	411			0.672 (1.00)	0.371 (1.00)	0.963 (1.00)	0.2 (1.00)	0.108 (1.00)	0.219 (1.00)	0.432 (1.00)	0.26 (1.00)	0.544 (1.00)	0.95 (1.00)

'BAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
BAP1 MUTATED	1	7	0
BAP1 WILD-TYPE	21	14	3

Figure S1. Get High-res Image Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	22	20
BAP1 MUTATED	0	1	7
BAP1 WILD-TYPE	4	21	13

Figure S2. Get High-res Image Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0868 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	185	93
BAP1 MUTATED	20	13	9
BAP1 WILD-TYPE	117	172	84

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000133 (Fisher's exact test), Q value = 0.012

Table S4. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	87	98	58
BAP1 MUTATED	15	1	7
BAP1 WILD-TYPE	72	97	51

Figure S3. Get High-res Image Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00121 (Chi-square test), Q value = 0.1

Table S5. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
BAP1 MUTATED	2	11	10	1	2	10
BAP1 WILD-TYPE	86	64	64	58	36	42

Figure S4. Get High-res Image Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	133	88
BAP1 MUTATED	10	15	11
BAP1 WILD-TYPE	155	118	77

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.0012

Table S7. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
BAP1 MUTATED	5	8	29
BAP1 WILD-TYPE	172	65	136

Figure S5. Get High-res Image Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.71e-08 (Fisher's exact test), Q value = 2.6e-06

Table S8. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	188	180	47
BAP1 MUTATED	5	36	1
BAP1 WILD-TYPE	183	144	46

Figure S6. Get High-res Image Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 8.79e-06 (Fisher's exact test), Q value = 8e-04

Table S9. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	180	136
BAP1 MUTATED	9	6	27
BAP1 WILD-TYPE	82	174	109

Figure S7. Get High-res Image Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-06 (Fisher's exact test), Q value = 0.00037

Table S10. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	233	152
BAP1 MUTATED	9	12	21
BAP1 WILD-TYPE	13	221	131

Figure S8. Get High-res Image Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 1

Table S11. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	79	65
BAP1 MUTATED	3	3	8
BAP1 WILD-TYPE	36	76	57

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0719 (Chi-square test), Q value = 1

Table S12. Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	2	39	69	9	64
BAP1 MUTATED	0	2	10	1	1
BAP1 WILD-TYPE	2	37	59	8	63

'VHL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
VHL MUTATED	16	7	1
VHL WILD-TYPE	6	14	2

Figure S9. Get High-res Image Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'VHL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	22	20
VHL MUTATED	1	16	7
VHL WILD-TYPE	3	6	13

Figure S10. Get High-res Image Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0574 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	185	93
VHL MUTATED	63	109	46
VHL WILD-TYPE	74	76	47

'VHL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.806 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	87	98	58
VHL MUTATED	51	54	31
VHL WILD-TYPE	36	44	27

'VHL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.342 (Chi-square test), Q value = 1

Table S17. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
VHL MUTATED	53	41	34	26	21	25
VHL WILD-TYPE	35	34	40	33	17	27

'VHL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	133	88
VHL MUTATED	90	66	44
VHL WILD-TYPE	75	67	44

'VHL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0023 (Fisher's exact test), Q value = 0.19

Table S19. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
VHL MUTATED	110	32	75
VHL WILD-TYPE	67	41	90

Figure S11. Get High-res Image Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.81

Table S20. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	188	180	47
VHL MUTATED	113	85	19
VHL WILD-TYPE	75	95	28

Figure S12. Get High-res Image Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 1

Table S21. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	180	136
VHL MUTATED	46	106	61
VHL WILD-TYPE	45	74	75

Figure S13. Get High-res Image Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.274 (Fisher's exact test), Q value = 1

Table S22. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	233	152
VHL MUTATED	9	129	75
VHL WILD-TYPE	13	104	77

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 1

Table S23. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	79	65
VHL MUTATED	18	50	32
VHL WILD-TYPE	21	29	33

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.337 (Chi-square test), Q value = 1

Table S24. Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	2	39	69	9	64
VHL MUTATED	1	18	35	7	39
VHL WILD-TYPE	1	21	34	2	25

'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.764 (Fisher's exact test), Q value = 1

Table S25. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
SETD2 MUTATED	2	3	0
SETD2 WILD-TYPE	20	18	3

'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.787 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	22	20
SETD2 MUTATED	0	2	3
SETD2 WILD-TYPE	4	20	17

'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S27. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	185	93
SETD2 MUTATED	16	19	13
SETD2 WILD-TYPE	121	166	80

'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.43e-07 (Fisher's exact test), Q value = 3.2e-05

Table S28. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	87	98	58
SETD2 MUTATED	24	7	0
SETD2 WILD-TYPE	63	91	58

Figure S14. Get High-res Image Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.329 (Chi-square test), Q value = 1

Table S29. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
SETD2 MUTATED	16	6	7	6	3	7
SETD2 WILD-TYPE	72	69	67	53	35	45

'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 1

Table S30. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	133	88
SETD2 MUTATED	15	19	11
SETD2 WILD-TYPE	150	114	77

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.717 (Fisher's exact test), Q value = 1

Table S31. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
SETD2 MUTATED	18	9	21
SETD2 WILD-TYPE	159	64	144

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S32. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	188	180	47
SETD2 MUTATED	20	23	5
SETD2 WILD-TYPE	168	157	42

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 1

Table S33. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	180	136
SETD2 MUTATED	8	21	17
SETD2 WILD-TYPE	83	159	119

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 1

Table S34. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	233	152
SETD2 MUTATED	1	30	15
SETD2 WILD-TYPE	21	203	137

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S35. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	79	65
SETD2 MUTATED	4	10	8
SETD2 WILD-TYPE	35	69	57

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.55 (Chi-square test), Q value = 1

Table S36. Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	2	39	69	9	64
SETD2 MUTATED	0	2	11	1	8
SETD2 WILD-TYPE	2	37	58	8	56

'PBRM1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S37. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
PBRM1 MUTATED	10	4	1
PBRM1 WILD-TYPE	12	17	2

'PBRM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S38. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	22	20
PBRM1 MUTATED	1	10	4
PBRM1 WILD-TYPE	3	12	16

'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.86

Table S39. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	185	93
PBRM1 MUTATED	49	69	19
PBRM1 WILD-TYPE	88	116	74

Figure S15. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9.34e-06 (Fisher's exact test), Q value = 0.00084

Table S40. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	87	98	58
PBRM1 MUTATED	40	44	7
PBRM1 WILD-TYPE	47	54	51

Figure S16. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.000762 (Chi-square test), Q value = 0.066

Table S41. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
PBRM1 MUTATED	46	16	22	17	10	16
PBRM1 WILD-TYPE	42	59	52	42	28	36

Figure S17. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.75 (Fisher's exact test), Q value = 1

Table S42. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	133	88
PBRM1 MUTATED	53	47	27
PBRM1 WILD-TYPE	112	86	61

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00465 (Fisher's exact test), Q value = 0.37

Table S43. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
PBRM1 MUTATED	72	15	49
PBRM1 WILD-TYPE	105	58	116

Figure S18. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 1

Table S44. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	188	180	47
PBRM1 MUTATED	74	52	10
PBRM1 WILD-TYPE	114	128	37

Figure S19. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.25

Table S45. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	180	136
PBRM1 MUTATED	20	74	39
PBRM1 WILD-TYPE	71	106	97

Figure S20. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00265 (Fisher's exact test), Q value = 0.22

Table S46. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	233	152
PBRM1 MUTATED	4	92	37
PBRM1 WILD-TYPE	18	141	115

Figure S21. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.38e-05 (Fisher's exact test), Q value = 0.0021

Table S47. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	79	65
PBRM1 MUTATED	3	38	20
PBRM1 WILD-TYPE	36	41	45

Figure S22. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0323 (Chi-square test), Q value = 1

Table S48. Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	2	39	69	9	64
PBRM1 MUTATED	1	7	23	1	29
PBRM1 WILD-TYPE	1	32	46	8	35

Figure S23. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 1

Table S49. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	185	93
KDM5C MUTATED	12	10	5
KDM5C WILD-TYPE	125	175	88

'KDM5C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 1

Table S50. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	87	98	58
KDM5C MUTATED	10	4	4
KDM5C WILD-TYPE	77	94	54

'KDM5C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.477 (Chi-square test), Q value = 1

Table S51. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
KDM5C MUTATED	5	3	6	2	2	6
KDM5C WILD-TYPE	83	72	68	57	36	46

'KDM5C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S52. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	133	88
KDM5C MUTATED	8	10	6
KDM5C WILD-TYPE	157	123	82

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 1

Table S53. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
KDM5C MUTATED	9	2	15
KDM5C WILD-TYPE	168	71	150

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.783 (Fisher's exact test), Q value = 1

Table S54. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	188	180	47
KDM5C MUTATED	11	13	2
KDM5C WILD-TYPE	177	167	45

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.86

Table S55. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	180	136
KDM5C MUTATED	2	9	16
KDM5C WILD-TYPE	89	171	120

Figure S24. Get High-res Image Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S56. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	233	152
KDM5C MUTATED	2	16	9
KDM5C WILD-TYPE	20	217	143

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 1

Table S57. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	79	65
KDM5C MUTATED	0	5	4
KDM5C WILD-TYPE	39	74	61

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.466 (Chi-square test), Q value = 1

Table S58. Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	2	39	69	9	64
KDM5C MUTATED	0	1	6	0	2
KDM5C WILD-TYPE	2	38	63	9	62

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 1

Table S59. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
PTEN MUTATED	0	4	0
PTEN WILD-TYPE	22	17	3

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0903 (Fisher's exact test), Q value = 1

Table S60. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	22	20
PTEN MUTATED	0	0	4
PTEN WILD-TYPE	4	22	16

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 1

Table S61. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	185	93
PTEN MUTATED	9	4	4
PTEN WILD-TYPE	128	181	89

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 1

Table S62. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	87	98	58
PTEN MUTATED	5	1	3
PTEN WILD-TYPE	82	97	55

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.214 (Chi-square test), Q value = 1

Table S63. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
PTEN MUTATED	2	6	2	2	1	5
PTEN WILD-TYPE	86	69	72	57	37	47

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0552 (Fisher's exact test), Q value = 1

Table S64. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	133	88
PTEN MUTATED	9	2	7
PTEN WILD-TYPE	156	131	81

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.11

Table S65. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
PTEN MUTATED	1	4	13
PTEN WILD-TYPE	176	69	152

Figure S25. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 1

Table S66. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	188	180	47
PTEN MUTATED	4	13	1
PTEN WILD-TYPE	184	167	46

Figure S26. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 1

Table S67. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	180	136
PTEN MUTATED	6	3	9
PTEN WILD-TYPE	85	177	127

Figure S27. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 1

Table S68. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	233	152
PTEN MUTATED	0	7	11
PTEN WILD-TYPE	22	226	141

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.96

Table S69. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	79	65
PTEN MUTATED	0	0	5
PTEN WILD-TYPE	39	79	60

Figure S28. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.459 (Chi-square test), Q value = 1

Table S70. Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	2	39	69	9	64
PTEN MUTATED	0	2	3	0	0
PTEN WILD-TYPE	2	37	66	9	64

'TSPAN19 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 1

Table S71. Gene #7: 'TSPAN19 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	185	93
TSPAN19 MUTATED	3	1	1
TSPAN19 WILD-TYPE	134	184	92

'TSPAN19 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0807 (Chi-square test), Q value = 1

Table S72. Gene #7: 'TSPAN19 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
TSPAN19 MUTATED	1	0	0	3	1	0
TSPAN19 WILD-TYPE	87	75	74	56	37	52

'TSPAN19 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S73. Gene #7: 'TSPAN19 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	133	88
TSPAN19 MUTATED	4	0	1
TSPAN19 WILD-TYPE	161	133	87

'TSPAN19 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S74. Gene #7: 'TSPAN19 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
TSPAN19 MUTATED	2	0	3
TSPAN19 WILD-TYPE	175	73	162

'TSPAN19 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.524 (Fisher's exact test), Q value = 1

Table S75. Gene #7: 'TSPAN19 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	188	180	47
TSPAN19 MUTATED	3	1	1
TSPAN19 WILD-TYPE	185	179	46

'TSPAN19 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S76. Gene #7: 'TSPAN19 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	180	136
TSPAN19 MUTATED	1	1	3
TSPAN19 WILD-TYPE	90	179	133

'TSPAN19 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 1

Table S77. Gene #7: 'TSPAN19 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	233	152
TSPAN19 MUTATED	1	2	2
TSPAN19 WILD-TYPE	21	231	150

'TCEB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.86

Table S78. Gene #8: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	185	93
TCEB1 MUTATED	0	0	3
TCEB1 WILD-TYPE	137	185	90

Figure S29. Get High-res Image Gene #8: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TCEB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.342 (Chi-square test), Q value = 1

Table S79. Gene #8: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
TCEB1 MUTATED	0	2	1	0	0	0
TCEB1 WILD-TYPE	88	73	73	59	38	52

'TCEB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S80. Gene #8: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	133	88
TCEB1 MUTATED	2	1	0
TCEB1 WILD-TYPE	163	132	88

'TCEB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 1

Table S81. Gene #8: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
TCEB1 MUTATED	0	2	1
TCEB1 WILD-TYPE	177	71	164

Figure S30. Get High-res Image Gene #8: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TCEB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.099 (Fisher's exact test), Q value = 1

Table S82. Gene #8: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	188	180	47
TCEB1 MUTATED	0	2	1
TCEB1 WILD-TYPE	188	178	46

'TCEB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 1

Table S83. Gene #8: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	180	136
TCEB1 MUTATED	2	1	0
TCEB1 WILD-TYPE	89	179	136

'TCEB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.632 (Fisher's exact test), Q value = 1

Table S84. Gene #8: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	233	152
TCEB1 MUTATED	0	1	2
TCEB1 WILD-TYPE	22	232	150

'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.672 (Fisher's exact test), Q value = 1

Table S85. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	185	93
NEFH MUTATED	1	3	2
NEFH WILD-TYPE	136	182	91

'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 1

Table S86. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	87	98	58
NEFH MUTATED	3	2	0
NEFH WILD-TYPE	84	96	58

'NEFH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.963 (Chi-square test), Q value = 1

Table S87. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	75	74	59	38	52
NEFH MUTATED	2	1	1	1	0	1
NEFH WILD-TYPE	86	74	73	58	38	51

'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.2 (Fisher's exact test), Q value = 1

Table S88. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	133	88
NEFH MUTATED	1	2	3
NEFH WILD-TYPE	164	131	85

'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S89. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	177	73	165
NEFH MUTATED	1	3	2
NEFH WILD-TYPE	176	70	163

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 1

Table S90. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	188	180	47
NEFH MUTATED	2	2	2
NEFH WILD-TYPE	186	178	45

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.432 (Fisher's exact test), Q value = 1

Table S91. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	91	180	136
NEFH MUTATED	0	4	2
NEFH WILD-TYPE	91	176	134

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S92. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	233	152
NEFH MUTATED	1	4	1
NEFH WILD-TYPE	21	229	151

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S93. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	39	79	65
NEFH MUTATED	0	3	1
NEFH WILD-TYPE	39	76	64

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.95 (Chi-square test), Q value = 1

Table S94. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	2	39	69	9	64
NEFH MUTATED	0	1	1	0	2
NEFH WILD-TYPE	2	38	68	9	62

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = KIRC-TP.transferedmergedcluster.txt
Number of patients = 417
Number of significantly mutated genes = 9
Number of Molecular subtypes = 12
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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] 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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