Correlation between gene mutation status and molecular subtypes

Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

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/C1KK997G

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, 16 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 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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, 16 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	Fisher's exact test
PBRM1	137 (33%)	280	0.135 (1.00)	0.212 (1.00)	0.00179 (0.147)	9.34e-06 (0.00085)	0.000762 (0.0647)	0.75 (1.00)	0.00534 (0.401)	0.0021 (0.17)	0.00437 (0.336)	0.00216 (0.173)	3.61e-06 (0.000332)	0.00223 (0.176)
BAP1	42 (10%)	375	0.0318 (1.00)	0.0281 (1.00)	0.063 (1.00)	0.000133 (0.0114)	0.00121 (0.1)	0.134 (1.00)	2.45e-05 (0.00218)	8.33e-08 (7.83e-06)	3.25e-05 (0.00283)	2.8e-05 (0.00246)	0.376 (1.00)	0.0297 (1.00)
VHL	218 (52%)	199	0.0163 (1.00)	0.0188 (1.00)	0.0541 (1.00)	0.806 (1.00)	0.342 (1.00)	0.642 (1.00)	0.00102 (0.0854)	0.00444 (0.337)	0.027 (1.00)	0.273 (1.00)	0.213 (1.00)	0.133 (1.00)
SETD2	48 (12%)	369	0.764 (1.00)	0.787 (1.00)	0.579 (1.00)	3.43e-07 (3.19e-05)	0.329 (1.00)	0.349 (1.00)	0.597 (1.00)	0.456 (1.00)	0.748 (1.00)	0.487 (1.00)	0.756 (1.00)	0.106 (1.00)
PTEN	18 (4%)	399	0.106 (1.00)	0.0903 (1.00)	0.151 (1.00)	0.154 (1.00)	0.214 (1.00)	0.0552 (1.00)	2.17e-05 (0.00195)	0.0166 (1.00)	0.00806 (0.589)	0.0791 (1.00)	0.00427 (0.333)	0.0473 (1.00)
KDM5C	27 (6%)	390			0.173 (1.00)	0.172 (1.00)	0.477 (1.00)	0.581 (1.00)	0.0914 (1.00)	0.708 (1.00)	0.00597 (0.442)	0.851 (1.00)	0.224 (1.00)	0.758 (1.00)
TSPAN19	5 (1%)	412			0.444 (1.00)		0.0807 (1.00)	0.203 (1.00)	0.408 (1.00)	0.442 (1.00)	0.45 (1.00)	0.0358 (1.00)
TCEB1	3 (1%)	414			0.00865 (0.623)		0.342 (1.00)	0.797 (1.00)	0.0409 (1.00)	0.0311 (1.00)	0.251 (1.00)	0.63 (1.00)
NEFH	6 (1%)	411			0.583 (1.00)	0.371 (1.00)	0.963 (1.00)	0.2 (1.00)	0.104 (1.00)	0.164 (1.00)	0.495 (1.00)	0.252 (1.00)	0.559 (1.00)	1 (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 = 0.063 (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	147	182	86
BAP1 MUTATED	22	13	7
BAP1 WILD-TYPE	125	169	79

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000133 (Fisher's exact test), Q value = 0.011

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 = 2.45e-05 (Fisher's exact test), Q value = 0.0022

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	169	71
BAP1 MUTATED	5	29	8
BAP1 WILD-TYPE	168	140	63

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 = 8.33e-08 (Fisher's exact test), Q value = 7.8e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	185	44
BAP1 MUTATED	5	36	1
BAP1 WILD-TYPE	179	149	43

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 = 3.25e-05 (Fisher's exact test), Q value = 0.0028

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	179	130
BAP1 MUTATED	9	7	26
BAP1 WILD-TYPE	89	172	104

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 = 2.8e-05 (Fisher's exact test), Q value = 0.0025

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	232	21	154
BAP1 MUTATED	11	6	25
BAP1 WILD-TYPE	221	15	129

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 = 0.376 (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	43	79	61
BAP1 MUTATED	3	4	7
BAP1 WILD-TYPE	40	75	54

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact 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
ALL	74	59	50
BAP1 MUTATED	2	9	3
BAP1 WILD-TYPE	72	50	47

Figure S9. Get High-res Image Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'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 S10. 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 S11. Get High-res Image Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0541 (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	147	182	86
VHL MUTATED	66	106	46
VHL WILD-TYPE	81	76	40

'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 = 0.00102 (Fisher's exact test), Q value = 0.085

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	169	71
VHL MUTATED	109	76	31
VHL WILD-TYPE	64	93	40

Figure S12. Get High-res Image Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.34

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	185	44
VHL MUTATED	112	87	17
VHL WILD-TYPE	72	98	27

Figure S13. Get High-res Image Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.027 (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	98	179	130
VHL MUTATED	50	106	57
VHL WILD-TYPE	48	73	73

Figure S14. Get High-res Image Gene #2: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.273 (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	232	21	154
VHL MUTATED	129	9	75
VHL WILD-TYPE	103	12	79

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.213 (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	43	79	61
VHL MUTATED	21	49	30
VHL WILD-TYPE	22	30	31

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.133 (Fisher's exact 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
ALL	74	59	50
VHL MUTATED	47	28	25
VHL WILD-TYPE	27	31	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 = 0.579 (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	147	182	86
SETD2 MUTATED	18	18	12
SETD2 WILD-TYPE	129	164	74

'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 S15. 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 = 0.597 (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	173	169	71
SETD2 MUTATED	17	22	9
SETD2 WILD-TYPE	156	147	62

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.456 (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	184	185	44
SETD2 MUTATED	20	25	3
SETD2 WILD-TYPE	164	160	41

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.748 (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	98	179	130
SETD2 MUTATED	9	22	15
SETD2 WILD-TYPE	89	157	115

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.487 (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	232	21	154
SETD2 MUTATED	30	1	15
SETD2 WILD-TYPE	202	20	139

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.756 (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	43	79	61
SETD2 MUTATED	4	11	7
SETD2 WILD-TYPE	39	68	54

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.106 (Fisher's exact 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
ALL	74	59	50
SETD2 MUTATED	11	9	2
SETD2 WILD-TYPE	63	50	48

'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 = 0.00179 (Fisher's exact test), Q value = 0.15

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	182	86
PBRM1 MUTATED	54	68	15
PBRM1 WILD-TYPE	93	114	71

Figure S16. 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 = 0.00085

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 S17. 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 = 0.065

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 S18. 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 = 0.00534 (Fisher's exact test), Q value = 0.4

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	169	71
PBRM1 MUTATED	71	50	15
PBRM1 WILD-TYPE	102	119	56

Figure S19. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0021 (Fisher's exact test), Q value = 0.17

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	184	185	44
PBRM1 MUTATED	75	54	7
PBRM1 WILD-TYPE	109	131	37

Figure S20. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00437 (Fisher's exact test), Q value = 0.34

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	179	130
PBRM1 MUTATED	24	74	35
PBRM1 WILD-TYPE	74	105	95

Figure S21. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00216 (Fisher's exact test), Q value = 0.17

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	232	21	154
PBRM1 MUTATED	92	4	37
PBRM1 WILD-TYPE	140	17	117

Figure S22. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.61e-06 (Fisher's exact test), Q value = 0.00033

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	79	61
PBRM1 MUTATED	3	39	19
PBRM1 WILD-TYPE	40	40	42

Figure S23. 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 = 0.00223 (Fisher's exact test), Q value = 0.18

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	74	59	50
PBRM1 MUTATED	35	17	9
PBRM1 WILD-TYPE	39	42	41

Figure S24. Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.173 (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	147	182	86
KDM5C MUTATED	14	8	5
KDM5C WILD-TYPE	133	174	81

'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 = 0.0914 (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	173	169	71
KDM5C MUTATED	8	16	2
KDM5C WILD-TYPE	165	153	69

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.708 (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	184	185	44
KDM5C MUTATED	10	14	2
KDM5C WILD-TYPE	174	171	42

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00597 (Fisher's exact test), Q value = 0.44

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	179	130
KDM5C MUTATED	2	9	16
KDM5C WILD-TYPE	96	170	114

Figure S25. Get High-res Image Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.851 (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	232	21	154
KDM5C MUTATED	17	1	9
KDM5C WILD-TYPE	215	20	145

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.224 (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	43	79	61
KDM5C MUTATED	0	5	4
KDM5C WILD-TYPE	43	74	57

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.758 (Fisher's exact 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
ALL	74	59	50
KDM5C MUTATED	3	4	2
KDM5C WILD-TYPE	71	55	48

'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 = 0.151 (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	147	182	86
PTEN MUTATED	10	5	2
PTEN WILD-TYPE	137	177	84

'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 = 2.17e-05 (Fisher's exact test), Q value = 0.002

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	173	169	71
PTEN MUTATED	0	16	2
PTEN WILD-TYPE	173	153	69

Figure S26. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0166 (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	184	185	44
PTEN MUTATED	3	14	1
PTEN WILD-TYPE	181	171	43

Figure S27. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00806 (Fisher's exact test), Q value = 0.59

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	98	179	130
PTEN MUTATED	7	2	9
PTEN WILD-TYPE	91	177	121

Figure S28. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0791 (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	232	21	154
PTEN MUTATED	6	1	11
PTEN WILD-TYPE	226	20	143

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00427 (Fisher's exact test), Q value = 0.33

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	79	61
PTEN MUTATED	0	0	5
PTEN WILD-TYPE	43	79	56

Figure S29. 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 = 0.0473 (Fisher's exact 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
ALL	74	59	50
PTEN MUTATED	0	4	1
PTEN WILD-TYPE	74	55	49

Figure S30. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TSPAN19 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.444 (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	147	182	86
TSPAN19 MUTATED	3	1	1
TSPAN19 WILD-TYPE	144	181	85

'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 = 0.408 (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	173	169	71
TSPAN19 MUTATED	1	3	0
TSPAN19 WILD-TYPE	172	166	71

'TSPAN19 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.442 (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	184	185	44
TSPAN19 MUTATED	1	2	1
TSPAN19 WILD-TYPE	183	183	43

'TSPAN19 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.45 (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	98	179	130
TSPAN19 MUTATED	1	1	3
TSPAN19 WILD-TYPE	97	178	127

'TSPAN19 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0358 (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	232	21	154
TSPAN19 MUTATED	2	2	1
TSPAN19 WILD-TYPE	230	19	153

Figure S31. Get High-res Image Gene #7: 'TSPAN19 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TCEB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.62

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	182	86
TCEB1 MUTATED	0	0	3
TCEB1 WILD-TYPE	147	182	83

Figure S32. 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 = 0.0409 (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	173	169	71
TCEB1 MUTATED	0	1	2
TCEB1 WILD-TYPE	173	168	69

Figure S33. Get High-res Image Gene #8: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TCEB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0311 (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	184	185	44
TCEB1 MUTATED	0	1	2
TCEB1 WILD-TYPE	184	184	42

Figure S34. Get High-res Image Gene #8: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TCEB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.251 (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	98	179	130
TCEB1 MUTATED	2	1	0
TCEB1 WILD-TYPE	96	178	130

'TCEB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.63 (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	232	21	154
TCEB1 MUTATED	1	0	2
TCEB1 WILD-TYPE	231	21	152

'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.583 (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	147	182	86
NEFH MUTATED	1	3	2
NEFH WILD-TYPE	146	179	84

'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 = 0.104 (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	173	169	71
NEFH MUTATED	1	2	3
NEFH WILD-TYPE	172	167	68

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.164 (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	184	185	44
NEFH MUTATED	2	2	2
NEFH WILD-TYPE	182	183	42

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.495 (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	98	179	130
NEFH MUTATED	0	4	2
NEFH WILD-TYPE	98	175	128

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.252 (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	232	21	154
NEFH MUTATED	4	1	1
NEFH WILD-TYPE	228	20	153

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.559 (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	43	79	61
NEFH MUTATED	0	3	1
NEFH WILD-TYPE	43	76	60

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (Fisher's exact 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
ALL	74	59	50
NEFH MUTATED	2	1	1
NEFH WILD-TYPE	72	58	49

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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