Correlation between gene mutation status and molecular subtypes

Kidney Renal Clear Cell Carcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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/C1K35SJZ

Overview

Introduction

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

Summary

Testing the association between mutation status of 29 genes and 12 molecular subtypes across 417 patients, 15 significant findings detected with P value < 0.05 and Q value < 0.25.

SETD2 mutation correlated to 'METHLYATION_CNMF'.
BAP1 mutation correlated to 'MRNA_CHIERARCHICAL', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
PTEN mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
PBRM1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
FAM200A mutation correlated to 'RPPA_CNMF'.
MTOR mutation correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 29 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, 15 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	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
BAP1	41 (10%)	376	0.0322 (1.00)	0.00043 (0.106)	0.0161 (1.00)	0.00015 (0.0372)	0.021 (1.00)	0.0238 (1.00)	0.00014 (0.0349)	6e-05 (0.0151)	3e-05 (0.00759)	1e-05 (0.00257)	0.128 (1.00)	0.351 (1.00)
PBRM1	136 (33%)	281	0.149 (1.00)	0.0595 (1.00)	0.0415 (1.00)	2e-05 (0.00508)	0.0013 (0.315)	0.98 (1.00)	0.00658 (1.00)	1e-05 (0.00257)	0.00369 (0.886)	0.0309 (1.00)	0.00013 (0.0325)	0.0885 (1.00)
PTEN	18 (4%)	399	0.106 (1.00)	0.0328 (1.00)	0.099 (1.00)	0.169 (1.00)	0.119 (1.00)	0.307 (1.00)	3e-05 (0.00759)	0.00043 (0.106)	0.00163 (0.393)	0.114 (1.00)	0.0737 (1.00)	1 (1.00)
MTOR	23 (6%)	394			0.726 (1.00)	0.154 (1.00)	0.00038 (0.0939)	0.00096 (0.233)	0.919 (1.00)	0.759 (1.00)	0.256 (1.00)	0.246 (1.00)	0.876 (1.00)	1 (1.00)
SETD2	44 (11%)	373	1 (1.00)	0.501 (1.00)	0.449 (1.00)	1e-05 (0.00257)	0.664 (1.00)	0.303 (1.00)	0.47 (1.00)	0.0788 (1.00)	0.402 (1.00)	0.236 (1.00)	0.542 (1.00)	0.358 (1.00)
FAM200A	5 (1%)	412			0.719 (1.00)		0.00089 (0.217)	0.254 (1.00)	0.147 (1.00)	0.389 (1.00)	0.207 (1.00)	0.416 (1.00)
KDM5C	26 (6%)	391			0.275 (1.00)	0.0882 (1.00)	0.338 (1.00)	0.114 (1.00)	0.0691 (1.00)	0.102 (1.00)	0.0104 (1.00)	0.0414 (1.00)	1 (1.00)	1 (1.00)
VHL	166 (40%)	251	0.112 (1.00)	0.226 (1.00)	0.423 (1.00)	0.748 (1.00)	0.144 (1.00)	0.333 (1.00)	0.0077 (1.00)	0.0505 (1.00)	0.159 (1.00)	0.133 (1.00)	0.437 (1.00)	0.731 (1.00)
TP53	9 (2%)	408			0.382 (1.00)	0.515 (1.00)	0.445 (1.00)	0.424 (1.00)	0.446 (1.00)	0.172 (1.00)	0.466 (1.00)	0.517 (1.00)	1 (1.00)	1 (1.00)
NEFH	5 (1%)	412			0.858 (1.00)	0.542 (1.00)	0.978 (1.00)	0.177 (1.00)	0.00981 (1.00)	0.272 (1.00)	0.627 (1.00)	0.83 (1.00)	0.447 (1.00)	0.12 (1.00)
CCDC120	4 (1%)	413			0.107 (1.00)		0.442 (1.00)	1 (1.00)	0.668 (1.00)	0.486 (1.00)	0.826 (1.00)	1 (1.00)
GUSB	4 (1%)	413			0.57 (1.00)		0.312 (1.00)	0.627 (1.00)	0.174 (1.00)	0.702 (1.00)	0.455 (1.00)	0.875 (1.00)
PIK3CA	12 (3%)	405			0.523 (1.00)	0.653 (1.00)	0.795 (1.00)	0.284 (1.00)	0.356 (1.00)	0.449 (1.00)	0.751 (1.00)	0.945 (1.00)
PCK1	5 (1%)	412			0.45 (1.00)	0.62 (1.00)	1 (1.00)	0.815 (1.00)	0.85 (1.00)	0.459 (1.00)	0.729 (1.00)	0.386 (1.00)
ARID1A	12 (3%)	405			0.521 (1.00)	0.259 (1.00)	0.904 (1.00)	1 (1.00)	0.328 (1.00)	0.252 (1.00)	0.247 (1.00)	0.00892 (1.00)	0.382 (1.00)	0.193 (1.00)
ATM	11 (3%)	406			0.728 (1.00)	0.474 (1.00)	0.64 (1.00)	1 (1.00)	0.295 (1.00)	0.0306 (1.00)	0.115 (1.00)	0.091 (1.00)
DPCR1	6 (1%)	411			0.205 (1.00)	0.51 (1.00)	0.216 (1.00)	1 (1.00)	0.227 (1.00)	0.335 (1.00)	0.873 (1.00)	0.931 (1.00)
FGFR3	4 (1%)	413			0.692 (1.00)	0.841 (1.00)	0.956 (1.00)	1 (1.00)	0.815 (1.00)	0.292 (1.00)	0.825 (1.00)	0.316 (1.00)
PTCH1	7 (2%)	410			1 (1.00)	0.0548 (1.00)	0.409 (1.00)	0.157 (1.00)	0.876 (1.00)	0.332 (1.00)	0.896 (1.00)	0.609 (1.00)
RBMX	4 (1%)	413			0.694 (1.00)	0.618 (1.00)	0.109 (1.00)	0.457 (1.00)	0.4 (1.00)	0.701 (1.00)	0.336 (1.00)	0.126 (1.00)
ARAP3	3 (1%)	414			0.602 (1.00)		1 (1.00)	1 (1.00)	0.775 (1.00)	1 (1.00)	0.795 (1.00)	0.839 (1.00)
GPR172B	4 (1%)	413			1 (1.00)		0.12 (1.00)	0.796 (1.00)	0.527 (1.00)	1 (1.00)	0.61 (1.00)	1 (1.00)
EGFR	7 (2%)	410			0.696 (1.00)	0.682 (1.00)	0.738 (1.00)	0.496 (1.00)	0.612 (1.00)	0.21 (1.00)	1 (1.00)	0.0948 (1.00)
IL1RAP	4 (1%)	413			0.571 (1.00)	0.617 (1.00)	0.26 (1.00)	0.0918 (1.00)	0.816 (1.00)	0.486 (1.00)	0.558 (1.00)	0.638 (1.00)
BCL6	5 (1%)	412			0.45 (1.00)	0.618 (1.00)	0.812 (1.00)	0.732 (1.00)	1 (1.00)	0.461 (1.00)	0.727 (1.00)	0.484 (1.00)
NFAT5	6 (1%)	411			0.367 (1.00)	0.879 (1.00)	0.254 (1.00)	0.531 (1.00)	0.338 (1.00)	0.567 (1.00)	0.282 (1.00)	0.0957 (1.00)
LARP1	5 (1%)	412			0.449 (1.00)	0.442 (1.00)	0.241 (1.00)	0.528 (1.00)	0.847 (1.00)	1 (1.00)	0.63 (1.00)	0.321 (1.00)
KIAA1751	6 (1%)	411			0.579 (1.00)	0.641 (1.00)	0.614 (1.00)	0.0747 (1.00)	0.323 (1.00)	1 (1.00)	0.386 (1.00)	0.321 (1.00)
INSRR	4 (1%)	413			0.695 (1.00)	0.123 (1.00)	0.298 (1.00)	0.388 (1.00)	0.397 (1.00)	0.386 (1.00)	0.455 (1.00)	0.787 (1.00)

'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S1. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
SETD2 MUTATED	2	2	0
SETD2 WILD-TYPE	20	19	3

'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.501 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	4	10	3	10	10	8	1
SETD2 MUTATED	1	2	0	0	1	0	0
SETD2 WILD-TYPE	3	8	3	10	9	8	1

'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
SETD2 MUTATED	17	13	14
SETD2 WILD-TYPE	173	82	116

'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S4. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
SETD2 MUTATED	6	0	22
SETD2 WILD-TYPE	90	53	72

Figure S1. Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.664 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
SETD2 MUTATED	14	6	7	5	7	2
SETD2 WILD-TYPE	79	50	60	59	61	36

'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
SETD2 MUTATED	14	14	13
SETD2 WILD-TYPE	91	160	94

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
SETD2 MUTATED	8	15	21
SETD2 WILD-TYPE	60	162	149

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0788 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
SETD2 MUTATED	6	24	14
SETD2 WILD-TYPE	108	166	97

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 1

Table S9. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
SETD2 MUTATED	7	17	18
SETD2 WILD-TYPE	88	155	122

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 1

Table S10. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
SETD2 MUTATED	7	11	18	6
SETD2 WILD-TYPE	105	90	141	29

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 1

Table S11. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	20	42	28
SETD2 MUTATED	0	3	7	3
SETD2 WILD-TYPE	12	17	35	25

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S12. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	45	43
SETD2 MUTATED	0	7	6
SETD2 WILD-TYPE	14	38	37

'BAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 1

Table S13. Gene #2: '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 S2. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.11

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	4	10	3	10	10	8	1
BAP1 MUTATED	0	0	0	7	1	0	0
BAP1 WILD-TYPE	4	10	3	3	9	8	1

Figure S3. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
BAP1 MUTATED	11	10	20
BAP1 WILD-TYPE	179	85	110

Figure S4. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.037

Table S16. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
BAP1 MUTATED	1	6	16
BAP1 WILD-TYPE	95	47	78

Figure S5. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 1

Table S17. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
BAP1 MUTATED	4	10	8	2	9	2
BAP1 WILD-TYPE	89	46	59	62	59	36

Figure S6. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
BAP1 MUTATED	10	9	16
BAP1 WILD-TYPE	95	165	91

Figure S7. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.035

Table S19. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
BAP1 MUTATED	7	6	28
BAP1 WILD-TYPE	61	171	142

Figure S8. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S20. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
BAP1 MUTATED	19	6	16
BAP1 WILD-TYPE	95	184	95

Figure S9. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

Table S21. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
BAP1 MUTATED	9	5	27
BAP1 WILD-TYPE	86	167	113

Figure S10. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S22. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
BAP1 MUTATED	11	20	4	6
BAP1 WILD-TYPE	101	81	155	29

Figure S11. Get High-res Image Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S23. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	20	42	28
BAP1 MUTATED	2	1	1	4
BAP1 WILD-TYPE	10	19	41	24

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.351 (Fisher's exact test), Q value = 1

Table S24. Gene #2: 'BAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	45	43
BAP1 MUTATED	2	4	2
BAP1 WILD-TYPE	12	41	41

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S25. Gene #3: '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 = 0.0328 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	4	10	3	10	10	8	1
PTEN MUTATED	0	4	0	0	0	0	0
PTEN WILD-TYPE	4	6	3	10	10	8	1

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

'PTEN MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
PTEN MUTATED	4	4	9
PTEN WILD-TYPE	186	91	121

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
PTEN MUTATED	1	3	5
PTEN WILD-TYPE	95	50	89

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
PTEN MUTATED	2	7	2	2	4	1
PTEN WILD-TYPE	91	49	65	62	64	37

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
PTEN MUTATED	3	7	8
PTEN WILD-TYPE	102	167	99

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0076

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
PTEN MUTATED	2	0	16
PTEN WILD-TYPE	66	177	154

Figure S13. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.11

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
PTEN MUTATED	4	2	12
PTEN WILD-TYPE	110	188	99

Figure S14. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.39

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
PTEN MUTATED	7	1	10
PTEN WILD-TYPE	88	171	130

Figure S15. Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
PTEN MUTATED	7	5	3	3
PTEN WILD-TYPE	105	96	156	32

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0737 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	20	42	28
PTEN MUTATED	0	0	0	3
PTEN WILD-TYPE	12	20	42	25

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	45	43
PTEN MUTATED	0	2	1
PTEN WILD-TYPE	14	43	42

'PBRM1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.149 (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 = 0.0595 (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	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	4	10	3	10	10	8	1
PBRM1 MUTATED	2	4	0	0	4	4	1
PBRM1 WILD-TYPE	2	6	3	10	6	4	0

'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
PBRM1 MUTATED	72	22	42
PBRM1 WILD-TYPE	118	73	88

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 = 2e-05 (Fisher's exact test), Q value = 0.0051

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
PBRM1 MUTATED	42	6	42
PBRM1 WILD-TYPE	54	47	52

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 = 0.0013 (Fisher's exact test), Q value = 0.31

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	93	56	67	64	68	38
PBRM1 MUTATED	47	16	21	19	13	10
PBRM1 WILD-TYPE	46	40	46	45	55	28

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 = 0.98 (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	105	174	107
PBRM1 MUTATED	35	57	34
PBRM1 WILD-TYPE	70	117	73

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00658 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
PBRM1 MUTATED	14	71	50
PBRM1 WILD-TYPE	54	106	120

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 = 1e-05 (Fisher's exact test), Q value = 0.0026

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
PBRM1 MUTATED	21	85	29
PBRM1 WILD-TYPE	93	105	82

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 = 0.00369 (Fisher's exact test), Q value = 0.89

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
PBRM1 MUTATED	22	71	39
PBRM1 WILD-TYPE	73	101	101

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 = 0.0309 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
PBRM1 MUTATED	28	30	65	9
PBRM1 WILD-TYPE	84	71	94	26

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 = 0.00013 (Fisher's exact test), Q value = 0.032

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	20	42	28
PBRM1 MUTATED	4	1	22	4
PBRM1 WILD-TYPE	8	19	20	24

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 = 0.0885 (Fisher's exact 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
ALL	14	45	43
PBRM1 MUTATED	4	9	18
PBRM1 WILD-TYPE	10	36	25

'KDM5C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.275 (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	190	95	130
KDM5C MUTATED	12	3	11
KDM5C WILD-TYPE	178	92	119

'KDM5C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0882 (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	96	53	94
KDM5C MUTATED	4	2	11
KDM5C WILD-TYPE	92	51	83

'KDM5C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.338 (Fisher's exact 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	93	56	67	64	68	38
KDM5C MUTATED	5	7	5	2	3	1
KDM5C WILD-TYPE	88	49	62	62	65	37

'KDM5C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.114 (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	105	174	107
KDM5C MUTATED	10	6	7
KDM5C WILD-TYPE	95	168	100

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0691 (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	68	177	170
KDM5C MUTATED	2	7	16
KDM5C WILD-TYPE	66	170	154

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.102 (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	114	190	111
KDM5C MUTATED	11	7	7
KDM5C WILD-TYPE	103	183	104

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
KDM5C MUTATED	2	8	16
KDM5C WILD-TYPE	93	164	124

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 = 0.0414 (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	CLUS_4
ALL	112	101	159	35
KDM5C MUTATED	4	10	7	5
KDM5C WILD-TYPE	108	91	152	30

Figure S25. Get High-res Image Gene #5: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (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	CLUS_4
ALL	12	20	42	28
KDM5C MUTATED	0	0	2	1
KDM5C WILD-TYPE	12	20	40	27

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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	14	45	43
KDM5C MUTATED	0	2	1
KDM5C WILD-TYPE	14	43	42

'VHL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	22	21	3
VHL MUTATED	13	6	1
VHL WILD-TYPE	9	15	2

'VHL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	4	10	3	10	10	8	1
VHL MUTATED	2	2	0	4	6	5	1
VHL WILD-TYPE	2	8	3	6	4	3	0

'VHL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
VHL MUTATED	80	40	46
VHL WILD-TYPE	110	55	84

'VHL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.748 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
VHL MUTATED	46	23	40
VHL WILD-TYPE	50	30	54

'VHL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
VHL MUTATED	47	21	21	22	26	18
VHL WILD-TYPE	46	35	46	42	42	20

'VHL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.333 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
VHL MUTATED	39	77	39
VHL WILD-TYPE	66	97	68

'VHL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0077 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
VHL MUTATED	21	86	59
VHL WILD-TYPE	47	91	111

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

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0505 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
VHL MUTATED	38	88	40
VHL WILD-TYPE	76	102	71

'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
VHL MUTATED	39	76	47
VHL WILD-TYPE	56	96	93

'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
VHL MUTATED	45	33	73	11
VHL WILD-TYPE	67	68	86	24

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.437 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	20	42	28
VHL MUTATED	5	6	17	15
VHL WILD-TYPE	7	14	25	13

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.731 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	45	43
VHL MUTATED	5	21	17
VHL WILD-TYPE	9	24	26

'FAM200A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S71. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
FAM200A MUTATED	2	2	1
FAM200A WILD-TYPE	188	93	129

'FAM200A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.22

Table S72. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
FAM200A MUTATED	0	0	0	0	0	3
FAM200A WILD-TYPE	93	56	67	64	68	35

Figure S27. Get High-res Image Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FAM200A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 1

Table S73. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
FAM200A MUTATED	0	3	0
FAM200A WILD-TYPE	105	171	107

'FAM200A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 1

Table S74. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
FAM200A MUTATED	1	4	0
FAM200A WILD-TYPE	67	173	170

'FAM200A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 1

Table S75. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
FAM200A MUTATED	1	4	0
FAM200A WILD-TYPE	113	186	111

'FAM200A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 1

Table S76. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
FAM200A MUTATED	1	4	0
FAM200A WILD-TYPE	94	168	140

'FAM200A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 1

Table S77. Gene #7: 'FAM200A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
FAM200A MUTATED	1	0	4	0
FAM200A WILD-TYPE	111	101	155	35

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S78. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
TP53 MUTATED	3	1	5
TP53 WILD-TYPE	187	94	125

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 1

Table S79. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
TP53 MUTATED	1	2	3
TP53 WILD-TYPE	95	51	91

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 1

Table S80. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
TP53 MUTATED	0	2	2	1	2	1
TP53 WILD-TYPE	93	54	65	63	66	37

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.424 (Fisher's exact test), Q value = 1

Table S81. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
TP53 MUTATED	1	3	4
TP53 WILD-TYPE	104	171	103

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 1

Table S82. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
TP53 MUTATED	2	2	5
TP53 WILD-TYPE	66	175	165

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S83. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
TP53 MUTATED	2	2	5
TP53 WILD-TYPE	112	188	106

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 1

Table S84. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
TP53 MUTATED	3	2	4
TP53 WILD-TYPE	92	170	136

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.517 (Fisher's exact test), Q value = 1

Table S85. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
TP53 MUTATED	4	2	2	1
TP53 WILD-TYPE	108	99	157	34

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S86. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	20	42	28
TP53 MUTATED	0	1	2	1
TP53 WILD-TYPE	12	19	40	27

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S87. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	45	43
TP53 MUTATED	0	2	2
TP53 WILD-TYPE	14	43	41

'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.858 (Fisher's exact test), Q value = 1

Table S88. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
NEFH MUTATED	3	1	1
NEFH WILD-TYPE	187	94	129

'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 1

Table S89. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
NEFH MUTATED	3	0	1
NEFH WILD-TYPE	93	53	93

'NEFH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.978 (Fisher's exact test), Q value = 1

Table S90. 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	93	56	67	64	68	38
NEFH MUTATED	2	0	1	1	1	0
NEFH WILD-TYPE	91	56	66	63	67	38

'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.177 (Fisher's exact test), Q value = 1

Table S91. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
NEFH MUTATED	0	2	3
NEFH WILD-TYPE	105	172	104

'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00981 (Fisher's exact test), Q value = 1

Table S92. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
NEFH MUTATED	3	0	2
NEFH WILD-TYPE	65	177	168

Figure S28. Get High-res Image Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.272 (Fisher's exact test), Q value = 1

Table S93. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
NEFH MUTATED	3	1	1
NEFH WILD-TYPE	111	189	110

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
NEFH MUTATED	0	3	2
NEFH WILD-TYPE	95	169	138

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S95. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
NEFH MUTATED	1	2	2	0
NEFH WILD-TYPE	111	99	157	35

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S96. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	20	42	28
NEFH MUTATED	0	0	3	0
NEFH WILD-TYPE	12	20	39	28

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 1

Table S97. Gene #9: 'NEFH MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	45	43
NEFH MUTATED	0	0	3
NEFH WILD-TYPE	14	45	40

'CCDC120 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 1

Table S98. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
CCDC120 MUTATED	0	2	2
CCDC120 WILD-TYPE	190	93	128

'CCDC120 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S99. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
CCDC120 MUTATED	1	0	2	0	0	0
CCDC120 WILD-TYPE	92	56	65	64	68	38

'CCDC120 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S100. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
CCDC120 MUTATED	1	1	1
CCDC120 WILD-TYPE	104	173	106

'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S101. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
CCDC120 MUTATED	1	1	2
CCDC120 WILD-TYPE	67	176	168

'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 1

Table S102. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
CCDC120 MUTATED	0	3	1
CCDC120 WILD-TYPE	114	187	110

'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S103. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
CCDC120 MUTATED	1	1	2
CCDC120 WILD-TYPE	94	171	138

'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S104. Gene #10: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
CCDC120 MUTATED	1	1	2	0
CCDC120 WILD-TYPE	111	100	157	35

'MTOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 1

Table S105. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
MTOR MUTATED	9	5	9
MTOR WILD-TYPE	181	90	121

'MTOR MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S106. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
MTOR MUTATED	5	2	11
MTOR WILD-TYPE	91	51	83

'MTOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.094

Table S107. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
MTOR MUTATED	4	8	8	0	1	0
MTOR WILD-TYPE	89	48	59	64	67	38

Figure S29. Get High-res Image Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MTOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.23

Table S108. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
MTOR MUTATED	8	2	11
MTOR WILD-TYPE	97	172	96

Figure S30. Get High-res Image Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.919 (Fisher's exact test), Q value = 1

Table S109. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
MTOR MUTATED	4	9	10
MTOR WILD-TYPE	64	168	160

'MTOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S110. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
MTOR MUTATED	7	9	7
MTOR WILD-TYPE	107	181	104

'MTOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 1

Table S111. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
MTOR MUTATED	6	6	11
MTOR WILD-TYPE	89	166	129

'MTOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.246 (Fisher's exact test), Q value = 1

Table S112. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
MTOR MUTATED	7	8	5	3
MTOR WILD-TYPE	105	93	154	32

'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S113. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	20	42	28
MTOR MUTATED	1	1	3	1
MTOR WILD-TYPE	11	19	39	27

'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S114. Gene #11: 'MTOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	45	43
MTOR MUTATED	1	3	2
MTOR WILD-TYPE	13	42	41

'GUSB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 1

Table S115. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
GUSB MUTATED	3	0	1
GUSB WILD-TYPE	187	95	129

'GUSB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 1

Table S116. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
GUSB MUTATED	0	0	1	0	2	0
GUSB WILD-TYPE	93	56	66	64	66	38

'GUSB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S117. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
GUSB MUTATED	1	2	0
GUSB WILD-TYPE	104	172	107

'GUSB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 1

Table S118. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
GUSB MUTATED	1	0	3
GUSB WILD-TYPE	67	177	167

'GUSB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S119. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
GUSB MUTATED	1	1	2
GUSB WILD-TYPE	113	189	109

'GUSB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.455 (Fisher's exact test), Q value = 1

Table S120. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
GUSB MUTATED	2	1	1
GUSB WILD-TYPE	93	171	139

'GUSB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S121. Gene #12: 'GUSB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
GUSB MUTATED	2	1	1	0
GUSB WILD-TYPE	110	100	158	35

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 1

Table S122. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
PIK3CA MUTATED	7	1	4
PIK3CA WILD-TYPE	183	94	126

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S123. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
PIK3CA MUTATED	3	0	3
PIK3CA WILD-TYPE	93	53	91

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S124. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
PIK3CA MUTATED	4	1	1	2	3	0
PIK3CA WILD-TYPE	89	55	66	62	65	38

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 1

Table S125. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
PIK3CA MUTATED	5	3	3
PIK3CA WILD-TYPE	100	171	104

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.356 (Fisher's exact test), Q value = 1

Table S126. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
PIK3CA MUTATED	0	6	6
PIK3CA WILD-TYPE	68	171	164

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S127. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
PIK3CA MUTATED	2	5	5
PIK3CA WILD-TYPE	112	185	106

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.751 (Fisher's exact test), Q value = 1

Table S128. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
PIK3CA MUTATED	3	4	5
PIK3CA WILD-TYPE	92	168	135

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S129. Gene #13: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
PIK3CA MUTATED	4	2	5	1
PIK3CA WILD-TYPE	108	99	154	34

'PCK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 1

Table S130. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
PCK1 MUTATED	4	0	1
PCK1 WILD-TYPE	186	95	129

'PCK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S131. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
PCK1 MUTATED	1	0	2
PCK1 WILD-TYPE	95	53	92

'PCK1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S132. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
PCK1 MUTATED	1	0	1	1	1	0
PCK1 WILD-TYPE	92	56	66	63	67	38

'PCK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.815 (Fisher's exact test), Q value = 1

Table S133. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
PCK1 MUTATED	1	1	2
PCK1 WILD-TYPE	104	173	105

'PCK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S134. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
PCK1 MUTATED	0	3	2
PCK1 WILD-TYPE	68	174	168

'PCK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S135. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
PCK1 MUTATED	0	3	2
PCK1 WILD-TYPE	114	187	109

'PCK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 1

Table S136. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
PCK1 MUTATED	2	2	1
PCK1 WILD-TYPE	93	170	139

'PCK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S137. Gene #14: 'PCK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
PCK1 MUTATED	3	0	2	0
PCK1 WILD-TYPE	109	101	157	35

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.521 (Fisher's exact test), Q value = 1

Table S138. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
ARID1A MUTATED	7	1	4
ARID1A WILD-TYPE	183	94	126

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 1

Table S139. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
ARID1A MUTATED	5	1	1
ARID1A WILD-TYPE	91	52	93

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S140. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
ARID1A MUTATED	4	1	1	3	2	1
ARID1A WILD-TYPE	89	55	66	61	66	37

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S141. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
ARID1A MUTATED	3	6	3
ARID1A WILD-TYPE	102	168	104

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 1

Table S142. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
ARID1A MUTATED	1	8	3
ARID1A WILD-TYPE	67	169	167

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 1

Table S143. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
ARID1A MUTATED	1	8	3
ARID1A WILD-TYPE	113	182	108

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 1

Table S144. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
ARID1A MUTATED	1	8	3
ARID1A WILD-TYPE	94	164	137

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00892 (Fisher's exact test), Q value = 1

Table S145. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
ARID1A MUTATED	0	1	10	1
ARID1A WILD-TYPE	112	100	149	34

Figure S31. Get High-res Image Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S146. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	20	42	28
ARID1A MUTATED	1	0	2	0
ARID1A WILD-TYPE	11	20	40	28

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 1

Table S147. Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	45	43
ARID1A MUTATED	1	0	2
ARID1A WILD-TYPE	13	45	41

'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.728 (Fisher's exact test), Q value = 1

Table S148. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
ATM MUTATED	6	3	2
ATM WILD-TYPE	184	92	128

'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 1

Table S149. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
ATM MUTATED	5	1	2
ATM WILD-TYPE	91	52	92

'ATM MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S150. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
ATM MUTATED	3	1	0	3	2	1
ATM WILD-TYPE	90	55	67	61	66	37

'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S151. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
ATM MUTATED	3	4	3
ATM WILD-TYPE	102	170	104

'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 1

Table S152. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
ATM MUTATED	0	7	4
ATM WILD-TYPE	68	170	166

'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0306 (Fisher's exact test), Q value = 1

Table S153. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
ATM MUTATED	0	9	2
ATM WILD-TYPE	114	181	109

Figure S32. Get High-res Image Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S154. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
ATM MUTATED	0	7	3
ATM WILD-TYPE	95	165	137

'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.091 (Fisher's exact test), Q value = 1

Table S155. Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
ATM MUTATED	0	3	5	2
ATM WILD-TYPE	112	98	154	33

'DPCR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 1

Table S156. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
DPCR1 MUTATED	1	3	2
DPCR1 WILD-TYPE	189	92	128

'DPCR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.51 (Fisher's exact test), Q value = 1

Table S157. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
DPCR1 MUTATED	1	2	3
DPCR1 WILD-TYPE	95	51	91

'DPCR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 1

Table S158. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
DPCR1 MUTATED	0	2	2	0	1	1
DPCR1 WILD-TYPE	93	54	65	64	67	37

'DPCR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S159. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
DPCR1 MUTATED	1	3	2
DPCR1 WILD-TYPE	104	171	105

'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 1

Table S160. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
DPCR1 MUTATED	2	1	3
DPCR1 WILD-TYPE	66	176	167

'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.335 (Fisher's exact test), Q value = 1

Table S161. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
DPCR1 MUTATED	3	1	2
DPCR1 WILD-TYPE	111	189	109

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.873 (Fisher's exact test), Q value = 1

Table S162. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
DPCR1 MUTATED	2	2	2
DPCR1 WILD-TYPE	93	170	138

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S163. Gene #17: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
DPCR1 MUTATED	2	2	2	0
DPCR1 WILD-TYPE	110	99	157	35

'FGFR3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 1

Table S164. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
FGFR3 MUTATED	2	0	2
FGFR3 WILD-TYPE	188	95	128

'FGFR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 1

Table S165. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
FGFR3 MUTATED	1	1	2
FGFR3 WILD-TYPE	95	52	92

'FGFR3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.956 (Fisher's exact test), Q value = 1

Table S166. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
FGFR3 MUTATED	1	0	0	1	1	0
FGFR3 WILD-TYPE	92	56	67	63	67	38

'FGFR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S167. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
FGFR3 MUTATED	1	1	1
FGFR3 WILD-TYPE	104	173	106

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.815 (Fisher's exact test), Q value = 1

Table S168. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
FGFR3 MUTATED	1	2	1
FGFR3 WILD-TYPE	67	175	169

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 1

Table S169. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
FGFR3 MUTATED	0	2	2
FGFR3 WILD-TYPE	114	188	109

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 1

Table S170. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
FGFR3 MUTATED	1	1	2
FGFR3 WILD-TYPE	94	171	138

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 1

Table S171. Gene #18: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
FGFR3 MUTATED	3	0	1	0
FGFR3 WILD-TYPE	109	101	158	35

'PTCH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S172. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
PTCH1 MUTATED	3	2	2
PTCH1 WILD-TYPE	187	93	128

'PTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0548 (Fisher's exact test), Q value = 1

Table S173. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
PTCH1 MUTATED	0	0	4
PTCH1 WILD-TYPE	96	53	90

'PTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S174. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
PTCH1 MUTATED	2	3	0	1	1	0
PTCH1 WILD-TYPE	91	53	67	63	67	38

'PTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 1

Table S175. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
PTCH1 MUTATED	2	1	4
PTCH1 WILD-TYPE	103	173	103

'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S176. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
PTCH1 MUTATED	1	4	2
PTCH1 WILD-TYPE	67	173	168

'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S177. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
PTCH1 MUTATED	3	4	0
PTCH1 WILD-TYPE	111	186	111

'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.896 (Fisher's exact test), Q value = 1

Table S178. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
PTCH1 MUTATED	1	3	3
PTCH1 WILD-TYPE	94	169	137

'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S179. Gene #19: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
PTCH1 MUTATED	1	3	3	0
PTCH1 WILD-TYPE	111	98	156	35

'RBMX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S180. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
RBMX MUTATED	2	0	2
RBMX WILD-TYPE	188	95	128

'RBMX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 1

Table S181. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
RBMX MUTATED	1	0	2
RBMX WILD-TYPE	95	53	92

'RBMX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 1

Table S182. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
RBMX MUTATED	0	2	0	0	1	0
RBMX WILD-TYPE	93	54	67	64	67	38

'RBMX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.457 (Fisher's exact test), Q value = 1

Table S183. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
RBMX MUTATED	0	1	2
RBMX WILD-TYPE	105	173	105

'RBMX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S184. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
RBMX MUTATED	0	1	3
RBMX WILD-TYPE	68	176	167

'RBMX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.701 (Fisher's exact test), Q value = 1

Table S185. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
RBMX MUTATED	1	1	2
RBMX WILD-TYPE	113	189	109

'RBMX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 1

Table S186. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
RBMX MUTATED	1	0	2
RBMX WILD-TYPE	94	172	138

'RBMX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 1

Table S187. Gene #20: 'RBMX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
RBMX MUTATED	1	1	0	1
RBMX WILD-TYPE	111	100	159	34

'ARAP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S188. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
ARAP3 MUTATED	2	1	0
ARAP3 WILD-TYPE	188	94	130

'ARAP3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S189. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
ARAP3 MUTATED	1	0	1	0	1	0
ARAP3 WILD-TYPE	92	56	66	64	67	38

'ARAP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S190. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
ARAP3 MUTATED	1	1	1
ARAP3 WILD-TYPE	104	173	106

'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S191. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
ARAP3 MUTATED	0	1	2
ARAP3 WILD-TYPE	68	176	168

'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S192. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
ARAP3 MUTATED	1	1	1
ARAP3 WILD-TYPE	113	189	110

'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S193. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
ARAP3 MUTATED	0	2	1
ARAP3 WILD-TYPE	95	170	139

'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S194. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
ARAP3 MUTATED	1	0	2	0
ARAP3 WILD-TYPE	111	101	157	35

'GPR172B MUTATION STATUS' versus 'CN_CNMF'

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

Table S195. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
GPR172B MUTATED	2	1	1
GPR172B WILD-TYPE	188	94	129

'GPR172B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 1

Table S196. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
GPR172B MUTATED	0	1	0	2	0	0
GPR172B WILD-TYPE	93	55	67	62	68	38

'GPR172B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S197. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
GPR172B MUTATED	0	2	1
GPR172B WILD-TYPE	105	172	106

'GPR172B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 1

Table S198. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
GPR172B MUTATED	0	3	1
GPR172B WILD-TYPE	68	174	169

'GPR172B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S199. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
GPR172B MUTATED	1	2	1
GPR172B WILD-TYPE	113	188	110

'GPR172B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S200. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
GPR172B MUTATED	0	1	2
GPR172B WILD-TYPE	95	171	138

'GPR172B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S201. Gene #22: 'GPR172B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
GPR172B MUTATED	1	1	1	0
GPR172B WILD-TYPE	111	100	158	35

'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S202. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
EGFR MUTATED	4	2	1
EGFR WILD-TYPE	186	93	129

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S203. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
EGFR MUTATED	2	0	2
EGFR WILD-TYPE	94	53	92

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S204. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
EGFR MUTATED	2	2	0	1	1	1
EGFR WILD-TYPE	91	54	67	63	67	37

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.496 (Fisher's exact test), Q value = 1

Table S205. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
EGFR MUTATED	3	2	2
EGFR WILD-TYPE	102	172	105

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.612 (Fisher's exact test), Q value = 1

Table S206. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
EGFR MUTATED	0	3	4
EGFR WILD-TYPE	68	174	166

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 1

Table S207. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
EGFR MUTATED	0	4	3
EGFR WILD-TYPE	114	186	108

'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S208. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
EGFR MUTATED	1	3	2
EGFR WILD-TYPE	94	169	138

'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0948 (Fisher's exact test), Q value = 1

Table S209. Gene #23: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
EGFR MUTATED	0	1	3	2
EGFR WILD-TYPE	112	100	156	33

'IL1RAP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.571 (Fisher's exact test), Q value = 1

Table S210. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
IL1RAP MUTATED	3	0	1
IL1RAP WILD-TYPE	187	95	129

'IL1RAP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S211. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
IL1RAP MUTATED	1	0	2
IL1RAP WILD-TYPE	95	53	92

'IL1RAP MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S212. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
IL1RAP MUTATED	3	1	0	0	0	0
IL1RAP WILD-TYPE	90	55	67	64	68	38

'IL1RAP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0918 (Fisher's exact test), Q value = 1

Table S213. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
IL1RAP MUTATED	2	0	2
IL1RAP WILD-TYPE	103	174	105

'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.816 (Fisher's exact test), Q value = 1

Table S214. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
IL1RAP MUTATED	1	2	1
IL1RAP WILD-TYPE	67	175	169

'IL1RAP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 1

Table S215. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
IL1RAP MUTATED	0	3	1
IL1RAP WILD-TYPE	114	187	110

'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 1

Table S216. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
IL1RAP MUTATED	0	3	1
IL1RAP WILD-TYPE	95	169	139

'IL1RAP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S217. Gene #24: 'IL1RAP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
IL1RAP MUTATED	1	0	3	0
IL1RAP WILD-TYPE	111	101	156	35

'BCL6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 1

Table S218. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
BCL6 MUTATED	4	0	1
BCL6 WILD-TYPE	186	95	129

'BCL6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 1

Table S219. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
BCL6 MUTATED	1	0	2
BCL6 WILD-TYPE	95	53	92

'BCL6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.812 (Fisher's exact test), Q value = 1

Table S220. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
BCL6 MUTATED	1	1	2	0	1	0
BCL6 WILD-TYPE	92	55	65	64	67	38

'BCL6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S221. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
BCL6 MUTATED	2	2	1
BCL6 WILD-TYPE	103	172	106

'BCL6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S222. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
BCL6 MUTATED	1	2	2
BCL6 WILD-TYPE	67	175	168

'BCL6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.461 (Fisher's exact test), Q value = 1

Table S223. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
BCL6 MUTATED	0	3	2
BCL6 WILD-TYPE	114	187	109

'BCL6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S224. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
BCL6 MUTATED	2	2	1
BCL6 WILD-TYPE	93	170	139

'BCL6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S225. Gene #25: 'BCL6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
BCL6 MUTATED	1	2	1	1
BCL6 WILD-TYPE	111	99	158	34

'NFAT5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 1

Table S226. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
NFAT5 MUTATED	2	3	1
NFAT5 WILD-TYPE	188	92	129

'NFAT5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S227. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
NFAT5 MUTATED	2	1	3
NFAT5 WILD-TYPE	94	52	91

'NFAT5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.254 (Fisher's exact test), Q value = 1

Table S228. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
NFAT5 MUTATED	0	2	1	0	1	1
NFAT5 WILD-TYPE	93	54	66	64	67	37

'NFAT5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.531 (Fisher's exact test), Q value = 1

Table S229. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
NFAT5 MUTATED	0	3	2
NFAT5 WILD-TYPE	105	171	105

'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 1

Table S230. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
NFAT5 MUTATED	1	1	4
NFAT5 WILD-TYPE	67	176	166

'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S231. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
NFAT5 MUTATED	3	2	1
NFAT5 WILD-TYPE	111	188	110

'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 1

Table S232. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
NFAT5 MUTATED	1	1	4
NFAT5 WILD-TYPE	94	171	136

'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0957 (Fisher's exact test), Q value = 1

Table S233. Gene #26: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
NFAT5 MUTATED	0	1	3	2
NFAT5 WILD-TYPE	112	100	156	33

'LARP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S234. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
LARP1 MUTATED	4	0	1
LARP1 WILD-TYPE	186	95	129

'LARP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S235. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
LARP1 MUTATED	2	1	0
LARP1 WILD-TYPE	94	52	94

'LARP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.241 (Fisher's exact test), Q value = 1

Table S236. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
LARP1 MUTATED	1	0	1	3	0	0
LARP1 WILD-TYPE	92	56	66	61	68	38

'LARP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.528 (Fisher's exact test), Q value = 1

Table S237. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
LARP1 MUTATED	0	3	2
LARP1 WILD-TYPE	105	171	105

'LARP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S238. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
LARP1 MUTATED	0	3	2
LARP1 WILD-TYPE	68	174	168

'LARP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S239. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
LARP1 MUTATED	1	3	1
LARP1 WILD-TYPE	113	187	110

'LARP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S240. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
LARP1 MUTATED	0	3	2
LARP1 WILD-TYPE	95	169	138

'LARP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 1

Table S241. Gene #27: 'LARP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
LARP1 MUTATED	0	1	4	0
LARP1 WILD-TYPE	112	100	155	35

'KIAA1751 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.579 (Fisher's exact test), Q value = 1

Table S242. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
KIAA1751 MUTATED	2	1	3
KIAA1751 WILD-TYPE	188	94	127

'KIAA1751 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S243. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
KIAA1751 MUTATED	3	0	2
KIAA1751 WILD-TYPE	93	53	92

'KIAA1751 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S244. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
KIAA1751 MUTATED	2	0	1	2	0	0
KIAA1751 WILD-TYPE	91	56	66	62	68	38

'KIAA1751 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0747 (Fisher's exact test), Q value = 1

Table S245. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
KIAA1751 MUTATED	2	0	3
KIAA1751 WILD-TYPE	103	174	104

'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 1

Table S246. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
KIAA1751 MUTATED	2	2	1
KIAA1751 WILD-TYPE	66	175	169

'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S247. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
KIAA1751 MUTATED	1	3	1
KIAA1751 WILD-TYPE	113	187	110

'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S248. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
KIAA1751 MUTATED	0	4	2
KIAA1751 WILD-TYPE	95	168	138

'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 1

Table S249. Gene #28: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
KIAA1751 MUTATED	0	3	3	0
KIAA1751 WILD-TYPE	112	98	156	35

'INSRR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.695 (Fisher's exact test), Q value = 1

Table S250. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	190	95	130
INSRR MUTATED	2	0	2
INSRR WILD-TYPE	188	95	128

'INSRR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 1

Table S251. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	53	94
INSRR MUTATED	0	2	2
INSRR WILD-TYPE	96	51	92

'INSRR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.298 (Fisher's exact test), Q value = 1

Table S252. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	93	56	67	64	68	38
INSRR MUTATED	0	1	2	1	0	0
INSRR WILD-TYPE	93	55	65	63	68	38

'INSRR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.388 (Fisher's exact test), Q value = 1

Table S253. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	105	174	107
INSRR MUTATED	0	2	2
INSRR WILD-TYPE	105	172	105

'INSRR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 1

Table S254. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	177	170
INSRR MUTATED	0	1	3
INSRR WILD-TYPE	68	176	167

'INSRR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S255. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	114	190	111
INSRR MUTATED	2	2	0
INSRR WILD-TYPE	112	188	111

'INSRR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.455 (Fisher's exact test), Q value = 1

Table S256. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	95	172	140
INSRR MUTATED	2	1	1
INSRR WILD-TYPE	93	171	139

'INSRR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S257. Gene #29: 'INSRR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	101	159	35
INSRR MUTATED	1	2	1	0
INSRR WILD-TYPE	111	99	158	35

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 = 29
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

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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