Correlation between gene mutation status and molecular subtypes

Ovarian Serous Cystadenocarcinoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1GH9H7B

Overview

Introduction

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

Summary

Testing the association between mutation status of 21 genes and 14 molecular subtypes across 466 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

No gene mutations related to molecuar subtypes.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 21 genes and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	MIR CNMF	MIR 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	Fisher's exact test	Fisher's exact test
TP53	385 (83%)	81	1 (1.00)	0.218 (1.00)	0.894 (1.00)	0.312 (1.00)	0.486 (1.00)	0.214 (1.00)	0.301 (1.00)	0.238 (1.00)	0.502 (1.00)	0.568 (1.00)	0.967 (1.00)	0.913 (1.00)	1 (1.00)
RB1	15 (3%)	451	0.0971 (1.00)	0.285 (1.00)	0.674 (1.00)	0.932 (1.00)	0.118 (1.00)	0.0149 (0.624)	0.817 (1.00)	0.278 (1.00)	0.232 (1.00)	0.769 (1.00)	0.513 (1.00)	0.268 (1.00)
BRCA1	18 (4%)	448	0.0441 (0.77)	0.533 (1.00)	0.756 (1.00)	0.993 (1.00)	0.0463 (0.77)	0.0471 (0.77)	0.207 (1.00)	0.361 (1.00)	0.0673 (0.977)	0.929 (1.00)	0.0698 (0.977)	0.13 (1.00)
NF1	24 (5%)	442	0.622 (1.00)	0.54 (1.00)	0.723 (1.00)	0.729 (1.00)	0.382 (1.00)	0.0329 (0.77)	0.0768 (0.982)	0.00891 (0.624)	0.247 (1.00)	0.233 (1.00)	0.59 (1.00)	0.235 (1.00)	0.357 (1.00)
CDK12	15 (3%)	451	0.0144 (0.624)	0.117 (1.00)	0.221 (1.00)	0.678 (1.00)	0.336 (1.00)	0.0445 (0.77)	0.722 (1.00)	0.331 (1.00)	0.47 (1.00)	0.903 (1.00)	0.697 (1.00)	0.84 (1.00)	1 (1.00)
KRAS	5 (1%)	461	0.26 (1.00)	0.357 (1.00)	0.089 (1.00)	0.397 (1.00)	0.0404 (0.77)	0.74 (1.00)	0.0659 (0.977)	1 (1.00)	0.186 (1.00)	0.418 (1.00)	0.348 (1.00)	0.523 (1.00)
HNF1B	5 (1%)	461	0.549 (1.00)	0.555 (1.00)	0.868 (1.00)	0.601 (1.00)	0.136 (1.00)	0.625 (1.00)	0.00942 (0.624)	0.585 (1.00)	0.355 (1.00)	0.418 (1.00)	0.686 (1.00)	0.589 (1.00)
PTEN	5 (1%)	461	0.65 (1.00)	0.557 (1.00)	0.191 (1.00)	0.145 (1.00)	0.281 (1.00)	0.738 (1.00)	1 (1.00)	0.506 (1.00)	0.786 (1.00)	0.754 (1.00)	0.687 (1.00)	0.829 (1.00)
LARP1	4 (1%)	462	0.192 (1.00)	0.0311 (0.77)	0.312 (1.00)	0.176 (1.00)	1 (1.00)	0.827 (1.00)	0.212 (1.00)	0.24 (1.00)			0.621 (1.00)	0.12 (1.00)	0.357 (1.00)
BRCA2	13 (3%)	453	0.935 (1.00)	0.533 (1.00)	1 (1.00)	0.649 (1.00)	0.357 (1.00)	0.307 (1.00)	0.656 (1.00)	0.466 (1.00)	0.557 (1.00)	0.878 (1.00)	0.817 (1.00)	0.575 (1.00)	0.357 (1.00)
EFEMP1	7 (2%)	459	1 (1.00)	1 (1.00)	0.121 (1.00)	0.749 (1.00)	0.207 (1.00)	0.0327 (0.77)	0.605 (1.00)	0.86 (1.00)			0.709 (1.00)	0.477 (1.00)
NRAS	4 (1%)	462	0.838 (1.00)	0.366 (1.00)	0.566 (1.00)	0.205 (1.00)	0.465 (1.00)	0.567 (1.00)	1 (1.00)	0.862 (1.00)			0.619 (1.00)	0.234 (1.00)
MTA2	4 (1%)	462	0.456 (1.00)	0.367 (1.00)	0.31 (1.00)	0.843 (1.00)	0.403 (1.00)	0.475 (1.00)	0.531 (1.00)	0.656 (1.00)					1 (1.00)
ERCC6	4 (1%)	462	0.839 (1.00)	0.184 (1.00)	0.104 (1.00)	0.279 (1.00)	1 (1.00)	0.107 (1.00)	0.776 (1.00)	1 (1.00)			0.573 (1.00)	0.272 (1.00)
IL21R	8 (2%)	458	0.0451 (0.77)	0.144 (1.00)	0.247 (1.00)	0.0191 (0.702)	0.127 (1.00)	0.15 (1.00)	0.804 (1.00)	0.117 (1.00)	0.267 (1.00)	0.121 (1.00)	0.733 (1.00)	0.555 (1.00)
PKD1L1	6 (1%)	460	1 (1.00)	0.864 (1.00)	0.512 (1.00)	0.47 (1.00)	0.17 (1.00)	0.0362 (0.77)	0.244 (1.00)	0.189 (1.00)	0.828 (1.00)	0.391 (1.00)	0.387 (1.00)	0.352 (1.00)	1 (1.00)
SAMD9L	9 (2%)	457	0.832 (1.00)	0.896 (1.00)	0.691 (1.00)	0.981 (1.00)	0.84 (1.00)	1 (1.00)	0.075 (0.982)	0.397 (1.00)	0.853 (1.00)	0.579 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
AQP2	3 (1%)	463	0.256 (1.00)	0.125 (1.00)	0.373 (1.00)	0.648 (1.00)	0.404 (1.00)	0.384 (1.00)	0.775 (1.00)	1 (1.00)
CREBBP	11 (2%)	455	0.592 (1.00)	0.632 (1.00)	1 (1.00)	0.496 (1.00)	0.747 (1.00)	0.692 (1.00)	0.45 (1.00)	0.833 (1.00)	0.45 (1.00)	0.578 (1.00)	1 (1.00)	0.639 (1.00)
C9ORF171	5 (1%)	461	0.00093 (0.273)	0.00445 (0.624)	0.397 (1.00)	0.255 (1.00)	0.864 (1.00)	0.0141 (0.624)	0.402 (1.00)	0.166 (1.00)			0.3 (1.00)	0.495 (1.00)
NCOA3	5 (1%)	461	0.0939 (1.00)	0.227 (1.00)	0.737 (1.00)	0.645 (1.00)	0.865 (1.00)	0.526 (1.00)					0.177 (1.00)	0.23 (1.00)

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S1. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
TP53 MUTATED	145	145	94
TP53 WILD-TYPE	31	30	20

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.218 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
TP53 MUTATED	220	106	58
TP53 WILD-TYPE	39	30	12

'TP53 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
TP53 MUTATED	109	115	160
TP53 WILD-TYPE	25	24	32

'TP53 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S4. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
TP53 MUTATED	58	42	41	61	26	51	23	20	31	31
TP53 WILD-TYPE	15	3	8	9	4	13	4	9	8	8

'TP53 MUTATION STATUS' versus 'CN_CNMF'

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

Table S5. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
TP53 MUTATED	109	139	129
TP53 WILD-TYPE	28	26	24

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
TP53 MUTATED	120	113	152
TP53 WILD-TYPE	18	30	32

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
TP53 MUTATED	99	128	48
TP53 WILD-TYPE	28	23	13

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.238 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
TP53 MUTATED	92	37	44	102
TP53 WILD-TYPE	30	6	10	18

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.502 (Fisher's exact test), Q value = 1

Table S9. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
TP53 MUTATED	52	74	86
TP53 WILD-TYPE	12	10	14

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 1

Table S10. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
TP53 MUTATED	104	39	69
TP53 WILD-TYPE	18	4	14

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.967 (Fisher's exact test), Q value = 1

Table S11. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
TP53 MUTATED	83	135	106
TP53 WILD-TYPE	14	24	20

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S12. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
TP53 MUTATED	75	50	118	81
TP53 WILD-TYPE	15	10	19	14

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S13. Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	9	5
TP53 MUTATED	8	5
TP53 WILD-TYPE	1	0

'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0971 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
RB1 MUTATED	9	2	4
RB1 WILD-TYPE	167	173	110

'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.285 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
RB1 MUTATED	6	5	4
RB1 WILD-TYPE	253	131	66

'RB1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
RB1 MUTATED	3	4	8
RB1 WILD-TYPE	131	135	184

'RB1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 1

Table S17. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
RB1 MUTATED	1	3	1	2	1	2	1	1	2	1
RB1 WILD-TYPE	72	42	48	68	29	62	26	28	37	38

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
RB1 MUTATED	5	2	8
RB1 WILD-TYPE	132	163	145

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.62

Table S19. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
RB1 MUTATED	8	6	1
RB1 WILD-TYPE	130	137	183

Figure S1. Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S20. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
RB1 MUTATED	4	7	3
RB1 WILD-TYPE	123	144	58

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S21. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
RB1 MUTATED	4	3	4	3
RB1 WILD-TYPE	118	40	50	117

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S22. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
RB1 MUTATED	0	4	3
RB1 WILD-TYPE	64	80	97

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S23. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
RB1 MUTATED	3	2	2
RB1 WILD-TYPE	119	41	81

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 1

Table S24. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
RB1 MUTATED	3	8	3
RB1 WILD-TYPE	94	151	123

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S25. Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
RB1 MUTATED	3	0	8	3
RB1 WILD-TYPE	87	60	129	92

'BRCA1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.77

Table S26. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
BRCA1 MUTATED	3	12	3
BRCA1 WILD-TYPE	173	163	111

Figure S2. Get High-res Image Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BRCA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S27. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
BRCA1 MUTATED	8	7	3
BRCA1 WILD-TYPE	251	129	67

'BRCA1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S28. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
BRCA1 MUTATED	6	6	6
BRCA1 WILD-TYPE	128	133	186

'BRCA1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.993 (Fisher's exact test), Q value = 1

Table S29. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
BRCA1 MUTATED	4	2	1	3	1	3	0	1	1	2
BRCA1 WILD-TYPE	69	43	48	67	29	61	27	28	38	37

'BRCA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.77

Table S30. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
BRCA1 MUTATED	5	11	2
BRCA1 WILD-TYPE	132	154	151

Figure S3. Get High-res Image Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'BRCA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 0.77

Table S31. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
BRCA1 MUTATED	1	7	10
BRCA1 WILD-TYPE	137	136	174

Figure S4. Get High-res Image Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'BRCA1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S32. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
BRCA1 MUTATED	5	3	4
BRCA1 WILD-TYPE	122	148	57

'BRCA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.361 (Fisher's exact test), Q value = 1

Table S33. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
BRCA1 MUTATED	6	0	3	3
BRCA1 WILD-TYPE	116	43	51	117

'BRCA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 0.98

Table S34. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
BRCA1 MUTATED	7	2	4
BRCA1 WILD-TYPE	57	82	96

'BRCA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.929 (Fisher's exact test), Q value = 1

Table S35. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
BRCA1 MUTATED	6	2	5
BRCA1 WILD-TYPE	116	41	78

'BRCA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0698 (Fisher's exact test), Q value = 0.98

Table S36. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
BRCA1 MUTATED	6	2	6
BRCA1 WILD-TYPE	91	157	120

'BRCA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.13 (Fisher's exact test), Q value = 1

Table S37. Gene #3: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
BRCA1 MUTATED	5	1	2	6
BRCA1 WILD-TYPE	85	59	135	89

'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S38. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
NF1 MUTATED	7	11	6
NF1 WILD-TYPE	169	164	108

'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.54 (Fisher's exact test), Q value = 1

Table S39. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
NF1 MUTATED	13	9	2
NF1 WILD-TYPE	246	127	68

'NF1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.723 (Fisher's exact test), Q value = 1

Table S40. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
NF1 MUTATED	8	8	8
NF1 WILD-TYPE	126	131	184

'NF1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S41. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
NF1 MUTATED	4	2	1	3	2	5	0	2	1	4
NF1 WILD-TYPE	69	43	48	67	28	59	27	27	38	35

'NF1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S42. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
NF1 MUTATED	9	10	5
NF1 WILD-TYPE	128	155	148

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.77

Table S43. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
NF1 MUTATED	2	8	14
NF1 WILD-TYPE	136	135	170

Figure S5. Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0768 (Fisher's exact test), Q value = 0.98

Table S44. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
NF1 MUTATED	9	3	4
NF1 WILD-TYPE	118	148	57

'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00891 (Fisher's exact test), Q value = 0.62

Table S45. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
NF1 MUTATED	10	4	0	2
NF1 WILD-TYPE	112	39	54	118

Figure S6. Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S46. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
NF1 MUTATED	3	1	6
NF1 WILD-TYPE	61	83	94

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 1

Table S47. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
NF1 MUTATED	3	1	6
NF1 WILD-TYPE	119	42	77

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S48. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
NF1 MUTATED	3	10	7
NF1 WILD-TYPE	94	149	119

'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S49. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
NF1 MUTATED	7	1	5	7
NF1 WILD-TYPE	83	59	132	88

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S50. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	9	5
NF1 MUTATED	0	1
NF1 WILD-TYPE	9	4

'CDK12 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0144 (Fisher's exact test), Q value = 0.62

Table S51. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
CDK12 MUTATED	5	10	0
CDK12 WILD-TYPE	171	165	114

Figure S7. Get High-res Image Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDK12 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S52. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
CDK12 MUTATED	12	3	0
CDK12 WILD-TYPE	247	133	70

'CDK12 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 1

Table S53. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
CDK12 MUTATED	7	2	6
CDK12 WILD-TYPE	127	137	186

'CDK12 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.678 (Fisher's exact test), Q value = 1

Table S54. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
CDK12 MUTATED	5	0	2	3	0	2	1	1	0	1
CDK12 WILD-TYPE	68	45	47	67	30	62	26	28	39	38

'CDK12 MUTATION STATUS' versus 'CN_CNMF'

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

Table S55. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
CDK12 MUTATED	2	5	7
CDK12 WILD-TYPE	135	160	146

'CDK12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.77

Table S56. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
CDK12 MUTATED	4	1	10
CDK12 WILD-TYPE	134	142	174

Figure S8. Get High-res Image Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'CDK12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S57. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
CDK12 MUTATED	3	6	2
CDK12 WILD-TYPE	124	145	59

'CDK12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S58. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
CDK12 MUTATED	2	3	2	4
CDK12 WILD-TYPE	120	40	52	116

'CDK12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S59. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
CDK12 MUTATED	4	2	3
CDK12 WILD-TYPE	60	82	97

'CDK12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S60. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
CDK12 MUTATED	4	2	3
CDK12 WILD-TYPE	118	41	80

'CDK12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 1

Table S61. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
CDK12 MUTATED	2	7	5
CDK12 WILD-TYPE	95	152	121

'CDK12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.84 (Fisher's exact test), Q value = 1

Table S62. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
CDK12 MUTATED	4	3	4	3
CDK12 WILD-TYPE	86	57	133	92

'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S63. Gene #5: 'CDK12 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	9	5
CDK12 MUTATED	1	0
CDK12 WILD-TYPE	8	5

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S64. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
KRAS MUTATED	4	1	0
KRAS WILD-TYPE	172	174	114

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S65. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
KRAS MUTATED	4	0	1
KRAS WILD-TYPE	255	136	69

'KRAS MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.089 (Fisher's exact test), Q value = 1

Table S66. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
KRAS MUTATED	3	2	0
KRAS WILD-TYPE	131	137	192

'KRAS MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S67. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
KRAS MUTATED	2	1	0	0	0	0	1	0	1	0
KRAS WILD-TYPE	71	44	49	70	30	64	26	29	38	39

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.77

Table S68. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
KRAS MUTATED	4	1	0
KRAS WILD-TYPE	133	164	153

Figure S9. Get High-res Image Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S69. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
KRAS MUTATED	1	1	3
KRAS WILD-TYPE	137	142	181

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0659 (Fisher's exact test), Q value = 0.98

Table S70. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
KRAS MUTATED	2	0	2
KRAS WILD-TYPE	125	151	59

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S71. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
KRAS MUTATED	2	0	0	2
KRAS WILD-TYPE	120	43	54	118

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 1

Table S72. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
KRAS MUTATED	2	1	0
KRAS WILD-TYPE	62	83	100

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 1

Table S73. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
KRAS MUTATED	2	1	0
KRAS WILD-TYPE	120	42	83

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S74. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
KRAS MUTATED	1	0	2
KRAS WILD-TYPE	96	159	124

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S75. Gene #6: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
KRAS MUTATED	0	0	1	2
KRAS WILD-TYPE	90	60	136	93

'HNF1B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

Table S76. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
HNF1B MUTATED	1	2	2
HNF1B WILD-TYPE	175	173	112

'HNF1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.555 (Fisher's exact test), Q value = 1

Table S77. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
HNF1B MUTATED	2	2	1
HNF1B WILD-TYPE	257	134	69

'HNF1B MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S78. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
HNF1B MUTATED	2	1	2
HNF1B WILD-TYPE	132	138	190

'HNF1B MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S79. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
HNF1B MUTATED	1	1	0	1	1	0	1	0	0	0
HNF1B WILD-TYPE	72	44	49	69	29	64	26	29	39	39

'HNF1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 1

Table S80. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
HNF1B MUTATED	0	4	1
HNF1B WILD-TYPE	137	161	152

'HNF1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S81. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
HNF1B MUTATED	2	2	1
HNF1B WILD-TYPE	136	141	183

'HNF1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00942 (Fisher's exact test), Q value = 0.62

Table S82. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
HNF1B MUTATED	1	0	3
HNF1B WILD-TYPE	126	151	58

Figure S10. Get High-res Image Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'HNF1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S83. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
HNF1B MUTATED	3	0	0	1
HNF1B WILD-TYPE	119	43	54	119

'HNF1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 1

Table S84. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
HNF1B MUTATED	1	2	0
HNF1B WILD-TYPE	63	82	100

'HNF1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 1

Table S85. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
HNF1B MUTATED	2	1	0
HNF1B WILD-TYPE	120	42	83

'HNF1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S86. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
HNF1B MUTATED	0	2	2
HNF1B WILD-TYPE	97	157	124

'HNF1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S87. Gene #7: 'HNF1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
HNF1B MUTATED	0	0	2	2
HNF1B WILD-TYPE	90	60	135	93

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.65 (Fisher's exact test), Q value = 1

Table S88. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
PTEN MUTATED	2	1	2
PTEN WILD-TYPE	174	174	112

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S89. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
PTEN MUTATED	2	2	1
PTEN WILD-TYPE	257	134	69

'PTEN MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 1

Table S90. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
PTEN MUTATED	1	0	4
PTEN WILD-TYPE	133	139	188

'PTEN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 1

Table S91. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
PTEN MUTATED	0	0	0	3	0	0	1	0	1	0
PTEN WILD-TYPE	73	45	49	67	30	64	26	29	38	39

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 1

Table S92. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
PTEN MUTATED	2	3	0
PTEN WILD-TYPE	135	162	153

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S93. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
PTEN MUTATED	1	1	3
PTEN WILD-TYPE	137	142	181

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S94. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
PTEN MUTATED	1	2	0
PTEN WILD-TYPE	126	149	61

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 1

Table S95. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
PTEN MUTATED	2	0	1	0
PTEN WILD-TYPE	120	43	53	120

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 1

Table S96. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
PTEN MUTATED	0	1	2
PTEN WILD-TYPE	64	83	98

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 1

Table S97. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
PTEN MUTATED	1	1	1
PTEN WILD-TYPE	121	42	82

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S98. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
PTEN MUTATED	0	2	2
PTEN WILD-TYPE	97	157	124

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.829 (Fisher's exact test), Q value = 1

Table S99. Gene #8: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
PTEN MUTATED	1	0	1	2
PTEN WILD-TYPE	89	60	136	93

'LARP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 1

Table S100. Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
LARP1 MUTATED	2	0	2
LARP1 WILD-TYPE	174	175	112

'LARP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.77

Table S101. Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
LARP1 MUTATED	0	2	2
LARP1 WILD-TYPE	259	134	68

Figure S11. Get High-res Image Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'LARP1 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S102. Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
LARP1 MUTATED	1	0	3
LARP1 WILD-TYPE	133	139	189

'LARP1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 1

Table S103. Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
LARP1 MUTATED	0	0	0	0	1	1	1	0	1	0
LARP1 WILD-TYPE	73	45	49	70	29	63	26	29	38	39

'LARP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S104. Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
LARP1 MUTATED	1	2	1
LARP1 WILD-TYPE	136	163	152

'LARP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S105. Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
LARP1 MUTATED	1	2	1
LARP1 WILD-TYPE	137	141	183

'LARP1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S106. Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
LARP1 MUTATED	2	0	1
LARP1 WILD-TYPE	125	151	60

'LARP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 1

Table S107. Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
LARP1 MUTATED	1	1	1	0
LARP1 WILD-TYPE	121	42	53	120

'LARP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S108. Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
LARP1 MUTATED	0	1	2
LARP1 WILD-TYPE	97	158	124

'LARP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S109. Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
LARP1 MUTATED	0	2	1	0
LARP1 WILD-TYPE	90	58	136	95

'LARP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S110. Gene #9: 'LARP1 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	9	5
LARP1 MUTATED	0	1
LARP1 WILD-TYPE	9	4

'BRCA2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.935 (Fisher's exact test), Q value = 1

Table S111. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
BRCA2 MUTATED	6	4	3
BRCA2 WILD-TYPE	170	171	111

'BRCA2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S112. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
BRCA2 MUTATED	9	2	2
BRCA2 WILD-TYPE	250	134	68

'BRCA2 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S113. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
BRCA2 MUTATED	4	4	5
BRCA2 WILD-TYPE	130	135	187

'BRCA2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.649 (Fisher's exact test), Q value = 1

Table S114. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
BRCA2 MUTATED	2	1	0	1	1	2	2	2	1	1
BRCA2 WILD-TYPE	71	44	49	69	29	62	25	27	38	38

'BRCA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S115. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
BRCA2 MUTATED	5	6	2
BRCA2 WILD-TYPE	132	159	151

'BRCA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S116. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
BRCA2 MUTATED	6	2	5
BRCA2 WILD-TYPE	132	141	179

'BRCA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.656 (Fisher's exact test), Q value = 1

Table S117. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
BRCA2 MUTATED	2	4	0
BRCA2 WILD-TYPE	125	147	61

'BRCA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S118. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
BRCA2 MUTATED	1	0	1	4
BRCA2 WILD-TYPE	121	43	53	116

'BRCA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S119. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
BRCA2 MUTATED	2	1	4
BRCA2 WILD-TYPE	62	83	96

'BRCA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S120. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
BRCA2 MUTATED	3	1	3
BRCA2 WILD-TYPE	119	42	80

'BRCA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S121. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
BRCA2 MUTATED	3	4	5
BRCA2 WILD-TYPE	94	155	121

'BRCA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.575 (Fisher's exact test), Q value = 1

Table S122. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
BRCA2 MUTATED	4	3	3	2
BRCA2 WILD-TYPE	86	57	134	93

'BRCA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S123. Gene #10: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	9	5
BRCA2 MUTATED	0	1
BRCA2 WILD-TYPE	9	4

'EFEMP1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S124. Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
EFEMP1 MUTATED	3	3	1
EFEMP1 WILD-TYPE	173	172	113

'EFEMP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S125. Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
EFEMP1 MUTATED	4	2	1
EFEMP1 WILD-TYPE	255	134	69

'EFEMP1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 1

Table S126. Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
EFEMP1 MUTATED	0	4	3
EFEMP1 WILD-TYPE	134	135	189

'EFEMP1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.749 (Fisher's exact test), Q value = 1

Table S127. Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
EFEMP1 MUTATED	0	1	2	2	0	1	0	0	1	0
EFEMP1 WILD-TYPE	73	44	47	68	30	63	27	29	38	39

'EFEMP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S128. Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
EFEMP1 MUTATED	0	4	3
EFEMP1 WILD-TYPE	137	161	150

'EFEMP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.77

Table S129. Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
EFEMP1 MUTATED	1	0	6
EFEMP1 WILD-TYPE	137	143	178

Figure S12. Get High-res Image Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'EFEMP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 1

Table S130. Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
EFEMP1 MUTATED	3	2	0
EFEMP1 WILD-TYPE	124	149	61

'EFEMP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S131. Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
EFEMP1 MUTATED	3	0	0	2
EFEMP1 WILD-TYPE	119	43	54	118

'EFEMP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.709 (Fisher's exact test), Q value = 1

Table S132. Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
EFEMP1 MUTATED	2	2	3
EFEMP1 WILD-TYPE	95	157	123

'EFEMP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.477 (Fisher's exact test), Q value = 1

Table S133. Gene #11: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
EFEMP1 MUTATED	3	1	1	2
EFEMP1 WILD-TYPE	87	59	136	93

'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S134. Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
NRAS MUTATED	1	2	1
NRAS WILD-TYPE	175	173	113

'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.366 (Fisher's exact test), Q value = 1

Table S135. Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
NRAS MUTATED	4	0	0
NRAS WILD-TYPE	255	136	70

'NRAS MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S136. Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
NRAS MUTATED	0	2	2
NRAS WILD-TYPE	134	137	190

'NRAS MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S137. Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
NRAS MUTATED	0	0	1	0	0	0	0	1	1	1
NRAS WILD-TYPE	73	45	48	70	30	64	27	28	38	38

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.465 (Fisher's exact test), Q value = 1

Table S138. Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
NRAS MUTATED	2	2	0
NRAS WILD-TYPE	135	163	153

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S139. Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
NRAS MUTATED	0	2	2
NRAS WILD-TYPE	138	141	182

'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S140. Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
NRAS MUTATED	1	2	0
NRAS WILD-TYPE	126	149	61

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.862 (Fisher's exact test), Q value = 1

Table S141. Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
NRAS MUTATED	1	0	0	2
NRAS WILD-TYPE	121	43	54	118

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 1

Table S142. Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
NRAS MUTATED	0	1	2
NRAS WILD-TYPE	97	158	124

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 1

Table S143. Gene #12: 'NRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
NRAS MUTATED	1	0	0	2
NRAS WILD-TYPE	89	60	137	93

'MTA2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.456 (Fisher's exact test), Q value = 1

Table S144. Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
MTA2 MUTATED	3	1	0
MTA2 WILD-TYPE	173	174	114

'MTA2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S145. Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
MTA2 MUTATED	4	0	0
MTA2 WILD-TYPE	255	136	70

'MTA2 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 1

Table S146. Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
MTA2 MUTATED	1	0	3
MTA2 WILD-TYPE	133	139	189

'MTA2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S147. Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
MTA2 MUTATED	0	0	1	2	0	1	0	0	0	0
MTA2 WILD-TYPE	73	45	48	68	30	63	27	29	39	39

'MTA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 1

Table S148. Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
MTA2 MUTATED	1	0	2
MTA2 WILD-TYPE	136	165	151

'MTA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 1

Table S149. Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
MTA2 MUTATED	2	0	2
MTA2 WILD-TYPE	136	143	182

'MTA2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S150. Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
MTA2 MUTATED	1	3	0
MTA2 WILD-TYPE	126	148	61

'MTA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.656 (Fisher's exact test), Q value = 1

Table S151. Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
MTA2 MUTATED	1	1	0	2
MTA2 WILD-TYPE	121	42	54	118

'MTA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S152. Gene #13: 'MTA2 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	9	5
MTA2 MUTATED	1	0
MTA2 WILD-TYPE	8	5

'ERCC6 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S153. Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
ERCC6 MUTATED	1	2	1
ERCC6 WILD-TYPE	175	173	113

'ERCC6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.184 (Fisher's exact test), Q value = 1

Table S154. Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
ERCC6 MUTATED	1	3	0
ERCC6 WILD-TYPE	258	133	70

'ERCC6 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 1

Table S155. Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
ERCC6 MUTATED	1	3	0
ERCC6 WILD-TYPE	133	136	192

'ERCC6 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 1

Table S156. Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
ERCC6 MUTATED	0	1	1	0	1	0	0	0	0	1
ERCC6 WILD-TYPE	73	44	48	70	29	64	27	29	39	38

'ERCC6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S157. Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
ERCC6 MUTATED	1	2	1
ERCC6 WILD-TYPE	136	163	152

'ERCC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S158. Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
ERCC6 MUTATED	1	3	0
ERCC6 WILD-TYPE	137	140	184

'ERCC6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.776 (Fisher's exact test), Q value = 1

Table S159. Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
ERCC6 MUTATED	2	1	0
ERCC6 WILD-TYPE	125	150	61

'ERCC6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S160. Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
ERCC6 MUTATED	2	0	0	1
ERCC6 WILD-TYPE	120	43	54	119

'ERCC6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 1

Table S161. Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
ERCC6 MUTATED	2	1	1
ERCC6 WILD-TYPE	95	158	125

'ERCC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S162. Gene #14: 'ERCC6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
ERCC6 MUTATED	0	2	1	1
ERCC6 WILD-TYPE	90	58	136	94

'IL21R MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.77

Table S163. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
IL21R MUTATED	0	5	3
IL21R WILD-TYPE	176	170	111

Figure S13. Get High-res Image Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'IL21R MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S164. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
IL21R MUTATED	3	5	0
IL21R WILD-TYPE	256	131	70

'IL21R MUTATION STATUS' versus 'MIR_CNMF'

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

Table S165. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
IL21R MUTATED	3	4	1
IL21R WILD-TYPE	131	135	191

'IL21R MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.7

Table S166. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
IL21R MUTATED	0	1	1	0	0	3	0	3	0	0
IL21R WILD-TYPE	73	44	48	70	30	61	27	26	39	39

Figure S14. Get High-res Image Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'IL21R MUTATION STATUS' versus 'CN_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S167. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
IL21R MUTATED	0	5	3
IL21R WILD-TYPE	137	160	150

'IL21R MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S168. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
IL21R MUTATED	0	3	5
IL21R WILD-TYPE	138	140	179

'IL21R MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S169. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
IL21R MUTATED	3	3	2
IL21R WILD-TYPE	124	148	59

'IL21R MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S170. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
IL21R MUTATED	2	2	3	1
IL21R WILD-TYPE	120	41	51	119

'IL21R MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 1

Table S171. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
IL21R MUTATED	0	1	4
IL21R WILD-TYPE	64	83	96

'IL21R MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 1

Table S172. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
IL21R MUTATED	1	0	4
IL21R WILD-TYPE	121	43	79

'IL21R MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S173. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
IL21R MUTATED	2	2	1
IL21R WILD-TYPE	95	157	125

'IL21R MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.555 (Fisher's exact test), Q value = 1

Table S174. Gene #15: 'IL21R MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
IL21R MUTATED	1	1	3	0
IL21R WILD-TYPE	89	59	134	95

'PKD1L1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S175. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
PKD1L1 MUTATED	3	2	1
PKD1L1 WILD-TYPE	173	173	113

'PKD1L1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.864 (Fisher's exact test), Q value = 1

Table S176. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
PKD1L1 MUTATED	4	1	1
PKD1L1 WILD-TYPE	255	135	69

'PKD1L1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.512 (Fisher's exact test), Q value = 1

Table S177. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
PKD1L1 MUTATED	3	1	2
PKD1L1 WILD-TYPE	131	138	190

'PKD1L1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S178. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
PKD1L1 MUTATED	3	0	2	1	0	0	0	0	0	0
PKD1L1 WILD-TYPE	70	45	47	69	30	64	27	29	39	39

'PKD1L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 1

Table S179. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
PKD1L1 MUTATED	0	2	4
PKD1L1 WILD-TYPE	137	163	149

'PKD1L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.77

Table S180. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
PKD1L1 MUTATED	4	2	0
PKD1L1 WILD-TYPE	134	141	184

Figure S15. Get High-res Image Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'PKD1L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 1

Table S181. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
PKD1L1 MUTATED	0	3	1
PKD1L1 WILD-TYPE	127	148	60

'PKD1L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 1

Table S182. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
PKD1L1 MUTATED	0	1	0	3
PKD1L1 WILD-TYPE	122	42	54	117

'PKD1L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S183. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
PKD1L1 MUTATED	1	2	1
PKD1L1 WILD-TYPE	63	82	99

'PKD1L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 1

Table S184. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
PKD1L1 MUTATED	3	1	0
PKD1L1 WILD-TYPE	119	42	83

'PKD1L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 1

Table S185. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
PKD1L1 MUTATED	0	3	3
PKD1L1 WILD-TYPE	97	156	123

'PKD1L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S186. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
PKD1L1 MUTATED	0	2	2	2
PKD1L1 WILD-TYPE	90	58	135	93

'PKD1L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S187. Gene #16: 'PKD1L1 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	9	5
PKD1L1 MUTATED	1	0
PKD1L1 WILD-TYPE	8	5

'SAMD9L MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S188. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
SAMD9L MUTATED	3	3	3
SAMD9L WILD-TYPE	173	172	111

'SAMD9L MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S189. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
SAMD9L MUTATED	6	2	1
SAMD9L WILD-TYPE	253	134	69

'SAMD9L MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.691 (Fisher's exact test), Q value = 1

Table S190. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
SAMD9L MUTATED	2	4	3
SAMD9L WILD-TYPE	132	135	189

'SAMD9L MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.981 (Fisher's exact test), Q value = 1

Table S191. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
SAMD9L MUTATED	1	1	2	1	0	2	0	0	1	1
SAMD9L WILD-TYPE	72	44	47	69	30	62	27	29	38	38

'SAMD9L MUTATION STATUS' versus 'CN_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 1

Table S192. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
SAMD9L MUTATED	2	3	4
SAMD9L WILD-TYPE	135	162	149

'SAMD9L MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S193. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
SAMD9L MUTATED	3	3	3
SAMD9L WILD-TYPE	135	140	181

'SAMD9L MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.075 (Fisher's exact test), Q value = 0.98

Table S194. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
SAMD9L MUTATED	2	2	4
SAMD9L WILD-TYPE	125	149	57

'SAMD9L MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S195. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
SAMD9L MUTATED	5	1	1	1
SAMD9L WILD-TYPE	117	42	53	119

'SAMD9L MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S196. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
SAMD9L MUTATED	1	1	3
SAMD9L WILD-TYPE	63	83	97

'SAMD9L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S197. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
SAMD9L MUTATED	4	0	1
SAMD9L WILD-TYPE	118	43	82

'SAMD9L MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S198. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
SAMD9L MUTATED	2	3	2
SAMD9L WILD-TYPE	95	156	124

'SAMD9L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S199. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
SAMD9L MUTATED	1	1	3	2
SAMD9L WILD-TYPE	89	59	134	93

'SAMD9L MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S200. Gene #17: 'SAMD9L MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	9	5
SAMD9L MUTATED	1	0
SAMD9L WILD-TYPE	8	5

'AQP2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S201. Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
AQP2 MUTATED	1	0	2
AQP2 WILD-TYPE	175	175	112

'AQP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S202. Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
AQP2 MUTATED	0	2	1
AQP2 WILD-TYPE	259	134	69

'AQP2 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 1

Table S203. Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
AQP2 MUTATED	2	0	1
AQP2 WILD-TYPE	132	139	191

'AQP2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S204. Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
AQP2 MUTATED	1	1	0	0	0	0	0	0	1	0
AQP2 WILD-TYPE	72	44	49	70	30	64	27	29	38	39

'AQP2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.404 (Fisher's exact test), Q value = 1

Table S205. Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
AQP2 MUTATED	1	0	2
AQP2 WILD-TYPE	136	165	151

'AQP2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 1

Table S206. Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
AQP2 MUTATED	2	0	1
AQP2 WILD-TYPE	136	143	183

'AQP2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S207. Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
AQP2 MUTATED	2	1	0
AQP2 WILD-TYPE	125	150	61

'AQP2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S208. Gene #18: 'AQP2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
AQP2 MUTATED	2	0	0	1
AQP2 WILD-TYPE	120	43	54	119

'CREBBP MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 1

Table S209. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
CREBBP MUTATED	6	3	2
CREBBP WILD-TYPE	170	172	112

'CREBBP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S210. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
CREBBP MUTATED	8	2	1
CREBBP WILD-TYPE	251	134	69

'CREBBP MUTATION STATUS' versus 'MIR_CNMF'

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

Table S211. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
CREBBP MUTATED	3	3	5
CREBBP WILD-TYPE	131	136	187

'CREBBP MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S212. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
CREBBP MUTATED	1	3	1	2	1	0	1	1	0	1
CREBBP WILD-TYPE	72	42	48	68	29	64	26	28	39	38

'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.747 (Fisher's exact test), Q value = 1

Table S213. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
CREBBP MUTATED	3	3	5
CREBBP WILD-TYPE	134	162	148

'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S214. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
CREBBP MUTATED	4	2	5
CREBBP WILD-TYPE	134	141	179

'CREBBP MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S215. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
CREBBP MUTATED	4	5	0
CREBBP WILD-TYPE	123	146	61

'CREBBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S216. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
CREBBP MUTATED	4	1	2	2
CREBBP WILD-TYPE	118	42	52	118

'CREBBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S217. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	84	100
CREBBP MUTATED	0	2	3
CREBBP WILD-TYPE	64	82	97

'CREBBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.578 (Fisher's exact test), Q value = 1

Table S218. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	43	83
CREBBP MUTATED	4	0	1
CREBBP WILD-TYPE	118	43	82

'CREBBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S219. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
CREBBP MUTATED	2	4	3
CREBBP WILD-TYPE	95	155	123

'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S220. Gene #19: 'CREBBP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
CREBBP MUTATED	2	0	4	3
CREBBP WILD-TYPE	88	60	133	92

'C9ORF171 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.27

Table S221. Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
C9ORF171 MUTATED	0	0	5
C9ORF171 WILD-TYPE	176	175	109

Figure S16. Get High-res Image Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'C9ORF171 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00445 (Fisher's exact test), Q value = 0.62

Table S222. Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
C9ORF171 MUTATED	0	5	0
C9ORF171 WILD-TYPE	259	131	70

Figure S17. Get High-res Image Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'C9ORF171 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S223. Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
C9ORF171 MUTATED	3	1	1
C9ORF171 WILD-TYPE	131	138	191

'C9ORF171 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 1

Table S224. Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
C9ORF171 MUTATED	1	0	0	1	2	0	0	0	0	1
C9ORF171 WILD-TYPE	72	45	49	69	28	64	27	29	39	38

'C9ORF171 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 1

Table S225. Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
C9ORF171 MUTATED	2	2	1
C9ORF171 WILD-TYPE	135	163	152

'C9ORF171 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.62

Table S226. Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
C9ORF171 MUTATED	0	0	5
C9ORF171 WILD-TYPE	138	143	179

Figure S18. Get High-res Image Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'C9ORF171 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S227. Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	151	61
C9ORF171 MUTATED	3	1	0
C9ORF171 WILD-TYPE	124	150	61

'C9ORF171 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 1

Table S228. Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	122	43	54	120
C9ORF171 MUTATED	2	0	2	0
C9ORF171 WILD-TYPE	120	43	52	120

'C9ORF171 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 1

Table S229. Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
C9ORF171 MUTATED	2	2	0
C9ORF171 WILD-TYPE	95	157	126

'C9ORF171 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 1

Table S230. Gene #20: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
C9ORF171 MUTATED	1	0	3	0
C9ORF171 WILD-TYPE	89	60	134	95

'NCOA3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0939 (Fisher's exact test), Q value = 1

Table S231. Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
NCOA3 MUTATED	0	4	1
NCOA3 WILD-TYPE	176	171	113

'NCOA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S232. Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
NCOA3 MUTATED	5	0	0
NCOA3 WILD-TYPE	254	136	70

'NCOA3 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 1

Table S233. Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
NCOA3 MUTATED	1	1	3
NCOA3 WILD-TYPE	133	138	189

'NCOA3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S234. Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_10	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	73	45	49	70	30	64	27	29	39	39
NCOA3 MUTATED	0	0	1	2	0	1	1	0	0	0
NCOA3 WILD-TYPE	73	45	48	68	30	63	26	29	39	39

'NCOA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.865 (Fisher's exact test), Q value = 1

Table S235. Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
NCOA3 MUTATED	2	2	1
NCOA3 WILD-TYPE	135	163	152

'NCOA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 1

Table S236. Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
NCOA3 MUTATED	1	3	1
NCOA3 WILD-TYPE	137	140	183

'NCOA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S237. Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
NCOA3 MUTATED	1	4	0
NCOA3 WILD-TYPE	96	155	126

'NCOA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 1

Table S238. Gene #21: 'NCOA3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
NCOA3 MUTATED	3	0	2	0
NCOA3 WILD-TYPE	87	60	135	95

Methods & Data

Input

Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/20020407/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/20141012/OV-TP.transferedmergedcluster.txt
Number of patients = 466
Number of significantly mutated genes = 21
Number of Molecular subtypes = 14
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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