Correlation between gene mutation status and molecular subtypes

Ovarian Serous Cystadenocarcinoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1JD4VV7

Overview

Introduction

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

Summary

Testing the association between mutation status of 23 genes and 14 molecular subtypes across 466 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.

C9ORF171 mutation correlated to 'MRNA_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 23 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, one 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
C9ORF171	5 (1%)	461	0.00071 (0.229)	0.00403 (0.649)	0.396 (1.00)	0.255 (1.00)	0.866 (1.00)	0.0139 (0.931)	0.196 (1.00)	0.683 (1.00)			0.3 (1.00)	0.496 (1.00)
TP53	383 (82%)	83	0.975 (1.00)	0.2 (1.00)	0.853 (1.00)	0.426 (1.00)	0.421 (1.00)	0.161 (1.00)	0.14 (1.00)	0.423 (1.00)	0.353 (1.00)	0.892 (1.00)	0.935 (1.00)	0.885 (1.00)	1 (1.00)
BRCA1	19 (4%)	447	0.0796 (1.00)	0.413 (1.00)	0.583 (1.00)	0.979 (1.00)	0.0264 (0.931)	0.0401 (0.931)	0.379 (1.00)	0.369 (1.00)	0.455 (1.00)	0.591 (1.00)	0.0692 (1.00)	0.131 (1.00)
NF1	24 (5%)	442	0.622 (1.00)	0.54 (1.00)	0.723 (1.00)	0.729 (1.00)	0.378 (1.00)	0.0342 (0.931)	0.13 (1.00)	0.0947 (1.00)	0.377 (1.00)	0.137 (1.00)	0.592 (1.00)	0.233 (1.00)	0.357 (1.00)
RB1	15 (3%)	451	0.0971 (1.00)	0.285 (1.00)	0.682 (1.00)	0.931 (1.00)	0.119 (1.00)	0.0156 (0.931)	0.774 (1.00)	0.759 (1.00)	0.114 (1.00)	0.543 (1.00)	0.512 (1.00)	0.269 (1.00)
BRCA2	13 (3%)	453	0.936 (1.00)	0.531 (1.00)	1 (1.00)	0.648 (1.00)	0.357 (1.00)	0.306 (1.00)	0.489 (1.00)	0.682 (1.00)	0.555 (1.00)	0.563 (1.00)	0.817 (1.00)	0.576 (1.00)	0.357 (1.00)
IL21R	8 (2%)	458	0.0448 (0.961)	0.147 (1.00)	0.246 (1.00)	0.0184 (0.931)	0.129 (1.00)	0.15 (1.00)	0.295 (1.00)	0.919 (1.00)	0.0894 (1.00)	0.0753 (1.00)	0.734 (1.00)	0.555 (1.00)
KRAS	5 (1%)	461	0.258 (1.00)	0.358 (1.00)	0.0886 (1.00)	0.394 (1.00)	0.0405 (0.931)	0.74 (1.00)	0.091 (1.00)	0.749 (1.00)	0.119 (1.00)	0.188 (1.00)	0.348 (1.00)	0.523 (1.00)
YSK4	10 (2%)	456	1 (1.00)	0.597 (1.00)	1 (1.00)	0.396 (1.00)	0.839 (1.00)	0.196 (1.00)	0.477 (1.00)	0.0537 (1.00)	0.555 (1.00)	0.411 (1.00)	0.544 (1.00)	0.833 (1.00)
ANKRD35	9 (2%)	457	0.435 (1.00)	0.647 (1.00)	0.156 (1.00)	0.342 (1.00)	0.337 (1.00)	0.405 (1.00)	0.863 (1.00)	0.533 (1.00)	0.789 (1.00)	0.747 (1.00)	0.625 (1.00)	0.367 (1.00)
MTA2	4 (1%)	462	0.458 (1.00)	0.369 (1.00)	0.309 (1.00)	0.84 (1.00)	0.402 (1.00)	0.475 (1.00)	0.684 (1.00)	0.913 (1.00)					1 (1.00)
CYP11B1	8 (2%)	458	0.105 (1.00)	0.7 (1.00)	0.498 (1.00)	0.0352 (0.931)	0.297 (1.00)	0.15 (1.00)	0.0648 (1.00)	0.247 (1.00)	0.442 (1.00)	1 (1.00)	0.123 (1.00)	0.649 (1.00)
NRAS	4 (1%)	462	0.84 (1.00)	0.369 (1.00)	0.57 (1.00)	0.202 (1.00)	0.469 (1.00)	0.565 (1.00)	1 (1.00)	0.53 (1.00)			0.618 (1.00)	0.233 (1.00)
ACBD4	3 (1%)	463	0.468 (1.00)	0.023 (0.931)	0.483 (1.00)	0.153 (1.00)	1 (1.00)	0.383 (1.00)
EFEMP1	7 (2%)	459	1 (1.00)	1 (1.00)	0.121 (1.00)	0.748 (1.00)	0.207 (1.00)	0.0342 (0.931)	0.715 (1.00)	1 (1.00)			0.711 (1.00)	0.476 (1.00)
PODN	6 (1%)	460	0.516 (1.00)	0.238 (1.00)	0.776 (1.00)	0.157 (1.00)	0.291 (1.00)	0.26 (1.00)	0.111 (1.00)	0.229 (1.00)			0.482 (1.00)	0.392 (1.00)
TOP2A	8 (2%)	458	0.354 (1.00)	0.699 (1.00)	0.671 (1.00)	0.287 (1.00)	0.8 (1.00)	0.02 (0.931)	0.79 (1.00)	1 (1.00)			0.798 (1.00)	0.685 (1.00)
NCOA3	5 (1%)	461	0.0958 (1.00)	0.224 (1.00)	0.738 (1.00)	0.643 (1.00)	0.863 (1.00)	0.529 (1.00)					0.176 (1.00)	0.229 (1.00)
TP53TG5	3 (1%)	463	0.464 (1.00)	0.557 (1.00)	0.484 (1.00)	0.251 (1.00)	0.0639 (1.00)	0.198 (1.00)
RPGRIP1	7 (2%)	459	1 (1.00)	0.767 (1.00)	0.0349 (0.931)	0.565 (1.00)	0.897 (1.00)	0.348 (1.00)	0.489 (1.00)	0.616 (1.00)	0.555 (1.00)	1 (1.00)	0.711 (1.00)	0.584 (1.00)
PTEN	5 (1%)	461	0.65 (1.00)	0.557 (1.00)	0.193 (1.00)	0.142 (1.00)	0.281 (1.00)	0.739 (1.00)	1 (1.00)	0.119 (1.00)			0.685 (1.00)	0.828 (1.00)
RB1CC1	9 (2%)	457	0.759 (1.00)	0.415 (1.00)	0.294 (1.00)	0.647 (1.00)	0.702 (1.00)	0.403 (1.00)	1 (1.00)	0.207 (1.00)	0.788 (1.00)	0.498 (1.00)	0.43 (1.00)	0.282 (1.00)
LPAR3	4 (1%)	462	0.681 (1.00)	0.366 (1.00)	0.31 (1.00)	0.324 (1.00)	0.839 (1.00)	0.0733 (1.00)	0.816 (1.00)	0.217 (1.00)	0.472 (1.00)	0.747 (1.00)	0.616 (1.00)	0.688 (1.00)

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.975 (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	144	93
TP53 WILD-TYPE	31	31	21

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.2 (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	219	105	58
TP53 WILD-TYPE	40	31	12

'TP53 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.853 (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	113	160
TP53 WILD-TYPE	25	26	32

'TP53 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.426 (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	41	41	61	26	50	23	20	31	31
TP53 WILD-TYPE	15	4	8	9	4	14	4	9	8	8

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.421 (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	108	138	129
TP53 WILD-TYPE	29	27	24

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.161 (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	112	151
TP53 WILD-TYPE	18	31	33

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.14 (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	104	161	72
TP53 MUTATED	79	137	56
TP53 WILD-TYPE	25	24	16

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.423 (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	105	81	104	47
TP53 MUTATED	79	67	87	39
TP53 WILD-TYPE	26	14	17	8

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.353 (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	90	55	74
TP53 MUTATED	77	45	67
TP53 WILD-TYPE	13	10	7

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.892 (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	94	97	28
TP53 MUTATED	80	84	25
TP53 WILD-TYPE	14	13	3

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.935 (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	82	135	105
TP53 WILD-TYPE	15	24	21

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.885 (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	49	117	81
TP53 WILD-TYPE	15	11	20	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

'BRCA1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0796 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
BRCA1 MUTATED	4	12	3
BRCA1 WILD-TYPE	172	163	111

'BRCA1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.413 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
BRCA1 MUTATED	8	7	4
BRCA1 WILD-TYPE	251	129	66

'BRCA1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
BRCA1 MUTATED	7	6	6
BRCA1 WILD-TYPE	127	133	186

'BRCA1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.979 (Fisher's exact test), Q value = 1

Table S17. Gene #2: '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	3	1	3	1	3	0	1	1	2
BRCA1 WILD-TYPE	69	42	48	67	29	61	27	28	38	37

'BRCA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.93

Table S18. Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
BRCA1 MUTATED	5	12	2
BRCA1 WILD-TYPE	132	153	151

Figure S1. Get High-res Image Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'BRCA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.93

Table S19. Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
BRCA1 MUTATED	1	8	10
BRCA1 WILD-TYPE	137	135	174

Figure S2. Get High-res Image Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'BRCA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S20. Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
BRCA1 MUTATED	6	4	3
BRCA1 WILD-TYPE	98	157	69

'BRCA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 1

Table S21. Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
BRCA1 MUTATED	3	2	4	4
BRCA1 WILD-TYPE	102	79	100	43

'BRCA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S22. Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
BRCA1 MUTATED	6	4	2
BRCA1 WILD-TYPE	84	51	72

'BRCA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S23. Gene #2: 'BRCA1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
BRCA1 MUTATED	7	4	1
BRCA1 WILD-TYPE	87	93	27

'BRCA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0692 (Fisher's exact test), Q value = 1

Table S24. Gene #2: '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 = 0.131 (Fisher's exact test), Q value = 1

Table S25. Gene #2: '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 S26. Gene #3: '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 S27. Gene #3: '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 S28. Gene #3: '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 S29. Gene #3: '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 = 0.378 (Fisher's exact test), Q value = 1

Table S30. Gene #3: '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 = 0.0342 (Fisher's exact test), Q value = 0.93

Table S31. Gene #3: '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 S3. Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S32. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
NF1 MUTATED	8	4	4
NF1 WILD-TYPE	96	157	68

'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0947 (Fisher's exact test), Q value = 1

Table S33. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
NF1 MUTATED	9	2	2	3
NF1 WILD-TYPE	96	79	102	44

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 1

Table S34. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
NF1 MUTATED	5	2	1
NF1 WILD-TYPE	85	53	73

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S35. Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
NF1 MUTATED	6	1	1
NF1 WILD-TYPE	88	96	27

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S36. Gene #3: '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 = 0.233 (Fisher's exact test), Q value = 1

Table S37. Gene #3: '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 S38. Gene #3: '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

'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S39. Gene #4: '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 S40. Gene #4: '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 = 0.682 (Fisher's exact test), Q value = 1

Table S41. Gene #4: '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 = 0.931 (Fisher's exact test), Q value = 1

Table S42. Gene #4: '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 = 0.119 (Fisher's exact test), Q value = 1

Table S43. Gene #4: '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 = 0.0156 (Fisher's exact test), Q value = 0.93

Table S44. Gene #4: '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 S4. Get High-res Image Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S45. Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
RB1 MUTATED	4	6	4
RB1 WILD-TYPE	100	155	68

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S46. Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
RB1 MUTATED	4	2	6	2
RB1 WILD-TYPE	101	79	98	45

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S47. Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
RB1 MUTATED	1	0	4
RB1 WILD-TYPE	89	55	70

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.543 (Fisher's exact test), Q value = 1

Table S48. Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
RB1 MUTATED	1	3	1
RB1 WILD-TYPE	93	94	27

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S49. Gene #4: '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 = 0.269 (Fisher's exact test), Q value = 1

Table S50. Gene #4: '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

'BRCA2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.936 (Fisher's exact test), Q value = 1

Table S51. Gene #5: '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 = 0.531 (Fisher's exact test), Q value = 1

Table S52. Gene #5: '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 S53. Gene #5: '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 = 0.648 (Fisher's exact test), Q value = 1

Table S54. Gene #5: '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 S55. Gene #5: '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 = 0.306 (Fisher's exact test), Q value = 1

Table S56. Gene #5: '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 = 0.489 (Fisher's exact test), Q value = 1

Table S57. Gene #5: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
BRCA2 MUTATED	2	4	0
BRCA2 WILD-TYPE	102	157	72

'BRCA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S58. Gene #5: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
BRCA2 MUTATED	1	1	3	1
BRCA2 WILD-TYPE	104	80	101	46

'BRCA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S59. Gene #5: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
BRCA2 MUTATED	4	2	1
BRCA2 WILD-TYPE	86	53	73

'BRCA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.563 (Fisher's exact test), Q value = 1

Table S60. Gene #5: 'BRCA2 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
BRCA2 MUTATED	4	2	1
BRCA2 WILD-TYPE	90	95	27

'BRCA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S61. Gene #5: '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 = 0.576 (Fisher's exact test), Q value = 1

Table S62. Gene #5: '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 S63. Gene #5: '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

'IL21R MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.96

Table S64. Gene #6: '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 S5. Get High-res Image Gene #6: 'IL21R MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'IL21R MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S65. Gene #6: '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 = 0.246 (Fisher's exact test), Q value = 1

Table S66. Gene #6: '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 = 0.0184 (Fisher's exact test), Q value = 0.93

Table S67. Gene #6: '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 S6. Get High-res Image Gene #6: 'IL21R MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'IL21R MUTATION STATUS' versus 'CN_CNMF'

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

Table S68. Gene #6: '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 S69. Gene #6: '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 = 0.295 (Fisher's exact test), Q value = 1

Table S70. Gene #6: 'IL21R MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
IL21R MUTATED	3	2	3
IL21R WILD-TYPE	101	159	69

'IL21R MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S71. Gene #6: 'IL21R MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
IL21R MUTATED	3	1	3	1
IL21R WILD-TYPE	102	80	101	46

'IL21R MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0894 (Fisher's exact test), Q value = 1

Table S72. Gene #6: 'IL21R MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
IL21R MUTATED	4	0	0
IL21R WILD-TYPE	86	55	74

'IL21R MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0753 (Fisher's exact test), Q value = 1

Table S73. Gene #6: 'IL21R MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
IL21R MUTATED	4	0	0
IL21R WILD-TYPE	90	97	28

'IL21R MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.734 (Fisher's exact test), Q value = 1

Table S74. Gene #6: '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 S75. Gene #6: '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

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 1

Table S76. Gene #7: '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 = 0.358 (Fisher's exact test), Q value = 1

Table S77. Gene #7: '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 = 0.0886 (Fisher's exact test), Q value = 1

Table S78. Gene #7: '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 = 0.394 (Fisher's exact test), Q value = 1

Table S79. Gene #7: '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 = 0.0405 (Fisher's exact test), Q value = 0.93

Table S80. Gene #7: '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 S7. Get High-res Image Gene #7: '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 S81. Gene #7: '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 = 0.091 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
KRAS MUTATED	2	0	2
KRAS WILD-TYPE	102	161	70

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
KRAS MUTATED	1	2	1	0
KRAS WILD-TYPE	104	79	103	47

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
KRAS MUTATED	0	2	1
KRAS WILD-TYPE	90	53	73

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.188 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
KRAS MUTATED	0	2	1
KRAS WILD-TYPE	94	95	27

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S86. Gene #7: '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 S87. Gene #7: '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

'YSK4 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S88. Gene #8: 'YSK4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
YSK4 MUTATED	4	4	2
YSK4 WILD-TYPE	172	171	112

'YSK4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S89. Gene #8: 'YSK4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
YSK4 MUTATED	4	4	2
YSK4 WILD-TYPE	255	132	68

'YSK4 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S90. Gene #8: 'YSK4 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
YSK4 MUTATED	3	3	4
YSK4 WILD-TYPE	131	136	188

'YSK4 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.396 (Fisher's exact test), Q value = 1

Table S91. Gene #8: 'YSK4 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
YSK4 MUTATED	2	1	0	3	2	0	0	1	0	1
YSK4 WILD-TYPE	71	44	49	67	28	64	27	28	39	38

'YSK4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S92. Gene #8: 'YSK4 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
YSK4 MUTATED	2	3	4
YSK4 WILD-TYPE	135	162	149

'YSK4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 1

Table S93. Gene #8: 'YSK4 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
YSK4 MUTATED	1	2	7
YSK4 WILD-TYPE	137	141	177

'YSK4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S94. Gene #8: 'YSK4 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
YSK4 MUTATED	3	4	0
YSK4 WILD-TYPE	101	157	72

'YSK4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0537 (Fisher's exact test), Q value = 1

Table S95. Gene #8: 'YSK4 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
YSK4 MUTATED	0	2	5	0
YSK4 WILD-TYPE	105	79	99	47

'YSK4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S96. Gene #8: 'YSK4 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
YSK4 MUTATED	4	2	1
YSK4 WILD-TYPE	86	53	73

'YSK4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 1

Table S97. Gene #8: 'YSK4 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
YSK4 MUTATED	5	2	0
YSK4 WILD-TYPE	89	95	28

'YSK4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S98. Gene #8: 'YSK4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
YSK4 MUTATED	3	2	3
YSK4 WILD-TYPE	94	157	123

'YSK4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S99. Gene #8: 'YSK4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
YSK4 MUTATED	1	2	3	2
YSK4 WILD-TYPE	89	58	134	93

'ANKRD35 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S100. Gene #9: 'ANKRD35 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
ANKRD35 MUTATED	2	5	2
ANKRD35 WILD-TYPE	174	170	112

'ANKRD35 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 1

Table S101. Gene #9: 'ANKRD35 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
ANKRD35 MUTATED	4	4	1
ANKRD35 WILD-TYPE	255	132	69

'ANKRD35 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 1

Table S102. Gene #9: 'ANKRD35 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
ANKRD35 MUTATED	1	1	7
ANKRD35 WILD-TYPE	133	138	185

'ANKRD35 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 1

Table S103. Gene #9: 'ANKRD35 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
ANKRD35 MUTATED	1	0	0	1	0	4	1	1	1	0
ANKRD35 WILD-TYPE	72	45	49	69	30	60	26	28	38	39

'ANKRD35 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 1

Table S104. Gene #9: 'ANKRD35 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
ANKRD35 MUTATED	4	4	1
ANKRD35 WILD-TYPE	133	161	152

'ANKRD35 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 1

Table S105. Gene #9: 'ANKRD35 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
ANKRD35 MUTATED	3	1	5
ANKRD35 WILD-TYPE	135	142	179

'ANKRD35 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S106. Gene #9: 'ANKRD35 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
ANKRD35 MUTATED	1	4	1
ANKRD35 WILD-TYPE	103	157	71

'ANKRD35 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S107. Gene #9: 'ANKRD35 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
ANKRD35 MUTATED	2	3	1	0
ANKRD35 WILD-TYPE	103	78	103	47

'ANKRD35 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S108. Gene #9: 'ANKRD35 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
ANKRD35 MUTATED	2	0	1
ANKRD35 WILD-TYPE	88	55	73

'ANKRD35 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S109. Gene #9: 'ANKRD35 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
ANKRD35 MUTATED	2	1	0
ANKRD35 WILD-TYPE	92	96	28

'ANKRD35 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S110. Gene #9: 'ANKRD35 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
ANKRD35 MUTATED	2	4	1
ANKRD35 WILD-TYPE	95	155	125

'ANKRD35 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S111. Gene #9: 'ANKRD35 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
ANKRD35 MUTATED	2	2	3	0
ANKRD35 WILD-TYPE	88	58	134	95

'C9ORF171 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.23

Table S112. Gene #10: '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 S8. Get High-res Image Gene #10: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'C9ORF171 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00403 (Fisher's exact test), Q value = 0.65

Table S113. Gene #10: '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 S9. Get High-res Image Gene #10: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'C9ORF171 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 1

Table S114. Gene #10: '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 S115. Gene #10: '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 = 0.866 (Fisher's exact test), Q value = 1

Table S116. Gene #10: '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 = 0.0139 (Fisher's exact test), Q value = 0.93

Table S117. Gene #10: '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 S10. Get High-res Image Gene #10: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'C9ORF171 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 1

Table S118. Gene #10: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
C9ORF171 MUTATED	3	1	0
C9ORF171 WILD-TYPE	101	160	72

'C9ORF171 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S119. Gene #10: 'C9ORF171 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
C9ORF171 MUTATED	2	0	2	0
C9ORF171 WILD-TYPE	103	81	102	47

'C9ORF171 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S120. Gene #10: '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 = 0.496 (Fisher's exact test), Q value = 1

Table S121. Gene #10: '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

'MTA2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 1

Table S122. Gene #11: '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 = 0.369 (Fisher's exact test), Q value = 1

Table S123. Gene #11: '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 = 0.309 (Fisher's exact test), Q value = 1

Table S124. Gene #11: '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 = 0.84 (Fisher's exact test), Q value = 1

Table S125. Gene #11: '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 = 0.402 (Fisher's exact test), Q value = 1

Table S126. Gene #11: '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 S127. Gene #11: '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 = 0.684 (Fisher's exact test), Q value = 1

Table S128. Gene #11: 'MTA2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
MTA2 MUTATED	2	2	0
MTA2 WILD-TYPE	102	159	72

'MTA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S129. Gene #11: 'MTA2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
MTA2 MUTATED	1	1	2	0
MTA2 WILD-TYPE	104	80	102	47

'MTA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S130. Gene #11: '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

'CYP11B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S131. Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
CYP11B1 MUTATED	1	6	1
CYP11B1 WILD-TYPE	175	169	113

'CYP11B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.7 (Fisher's exact test), Q value = 1

Table S132. Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
CYP11B1 MUTATED	5	3	0
CYP11B1 WILD-TYPE	254	133	70

'CYP11B1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S133. Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
CYP11B1 MUTATED	2	1	5
CYP11B1 WILD-TYPE	132	138	187

'CYP11B1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0352 (Fisher's exact test), Q value = 0.93

Table S134. Gene #12: 'CYP11B1 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
CYP11B1 MUTATED	0	0	0	1	0	2	0	2	0	3
CYP11B1 WILD-TYPE	73	45	49	69	30	62	27	27	39	36

Figure S11. Get High-res Image Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'CYP11B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 1

Table S135. Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
CYP11B1 MUTATED	2	5	1
CYP11B1 WILD-TYPE	135	160	152

'CYP11B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S136. Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
CYP11B1 MUTATED	0	3	5
CYP11B1 WILD-TYPE	138	140	179

'CYP11B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0648 (Fisher's exact test), Q value = 1

Table S137. Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
CYP11B1 MUTATED	3	0	1
CYP11B1 WILD-TYPE	101	161	71

'CYP11B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S138. Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
CYP11B1 MUTATED	3	1	0	0
CYP11B1 WILD-TYPE	102	80	104	47

'CYP11B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S139. Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
CYP11B1 MUTATED	2	3	1
CYP11B1 WILD-TYPE	88	52	73

'CYP11B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S140. Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
CYP11B1 MUTATED	3	3	0
CYP11B1 WILD-TYPE	91	94	28

'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S141. Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
CYP11B1 MUTATED	0	6	2
CYP11B1 WILD-TYPE	97	153	124

'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S142. Gene #12: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
CYP11B1 MUTATED	3	0	3	2
CYP11B1 WILD-TYPE	87	60	134	93

'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S143. Gene #13: '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 = 0.369 (Fisher's exact test), Q value = 1

Table S144. Gene #13: '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 = 0.57 (Fisher's exact test), Q value = 1

Table S145. Gene #13: '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 = 0.202 (Fisher's exact test), Q value = 1

Table S146. Gene #13: '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 = 0.469 (Fisher's exact test), Q value = 1

Table S147. Gene #13: '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 = 0.565 (Fisher's exact test), Q value = 1

Table S148. Gene #13: '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 S149. Gene #13: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
NRAS MUTATED	1	2	0
NRAS WILD-TYPE	103	159	72

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.53 (Fisher's exact test), Q value = 1

Table S150. Gene #13: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
NRAS MUTATED	0	1	2	0
NRAS WILD-TYPE	105	80	102	47

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S151. Gene #13: '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 = 0.233 (Fisher's exact test), Q value = 1

Table S152. Gene #13: '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

'ACBD4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 1

Table S153. Gene #14: 'ACBD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
ACBD4 MUTATED	2	0	1
ACBD4 WILD-TYPE	174	175	113

'ACBD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.93

Table S154. Gene #14: 'ACBD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
ACBD4 MUTATED	0	1	2
ACBD4 WILD-TYPE	259	135	68

Figure S12. Get High-res Image Gene #14: 'ACBD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ACBD4 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S155. Gene #14: 'ACBD4 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
ACBD4 MUTATED	0	2	1
ACBD4 WILD-TYPE	134	137	191

'ACBD4 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.153 (Fisher's exact test), Q value = 1

Table S156. Gene #14: 'ACBD4 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
ACBD4 MUTATED	0	0	0	1	0	0	0	0	2	0
ACBD4 WILD-TYPE	73	45	49	69	30	64	27	29	37	39

'ACBD4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S157. Gene #14: 'ACBD4 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
ACBD4 MUTATED	1	1	1
ACBD4 WILD-TYPE	136	164	152

'ACBD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 1

Table S158. Gene #14: 'ACBD4 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
ACBD4 MUTATED	2	0	1
ACBD4 WILD-TYPE	136	143	183

'EFEMP1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S159. Gene #15: '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 S160. Gene #15: '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 S161. Gene #15: '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 = 0.748 (Fisher's exact test), Q value = 1

Table S162. Gene #15: '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 S163. Gene #15: '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 = 0.0342 (Fisher's exact test), Q value = 0.93

Table S164. Gene #15: '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 S13. Get High-res Image Gene #15: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'EFEMP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 1

Table S165. Gene #15: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
EFEMP1 MUTATED	2	3	0
EFEMP1 WILD-TYPE	102	158	72

'EFEMP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S166. Gene #15: 'EFEMP1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
EFEMP1 MUTATED	2	1	2	0
EFEMP1 WILD-TYPE	103	80	102	47

'EFEMP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.711 (Fisher's exact test), Q value = 1

Table S167. Gene #15: '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 = 0.476 (Fisher's exact test), Q value = 1

Table S168. Gene #15: '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

'PODN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.516 (Fisher's exact test), Q value = 1

Table S169. Gene #16: 'PODN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
PODN MUTATED	3	3	0
PODN WILD-TYPE	173	172	114

'PODN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S170. Gene #16: 'PODN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
PODN MUTATED	5	0	1
PODN WILD-TYPE	254	136	69

'PODN MUTATION STATUS' versus 'MIR_CNMF'

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

Table S171. Gene #16: 'PODN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
PODN MUTATED	2	1	3
PODN WILD-TYPE	132	138	189

'PODN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S172. Gene #16: 'PODN 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
PODN MUTATED	0	1	0	1	0	0	0	2	1	1
PODN WILD-TYPE	73	44	49	69	30	64	27	27	38	38

'PODN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 1

Table S173. Gene #16: 'PODN MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
PODN MUTATED	0	3	3
PODN WILD-TYPE	137	162	150

'PODN MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S174. Gene #16: 'PODN MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
PODN MUTATED	3	0	3
PODN WILD-TYPE	135	143	181

'PODN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 1

Table S175. Gene #16: 'PODN MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
PODN MUTATED	0	5	0
PODN WILD-TYPE	104	156	72

'PODN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 1

Table S176. Gene #16: 'PODN MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
PODN MUTATED	0	2	3	0
PODN WILD-TYPE	105	79	101	47

'PODN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 1

Table S177. Gene #16: 'PODN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
PODN MUTATED	1	2	0
PODN WILD-TYPE	96	157	126

'PODN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 1

Table S178. Gene #16: 'PODN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
PODN MUTATED	2	0	1	0
PODN WILD-TYPE	88	60	136	95

'TOP2A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 1

Table S179. Gene #17: 'TOP2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
TOP2A MUTATED	1	4	3
TOP2A WILD-TYPE	175	171	111

'TOP2A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S180. Gene #17: 'TOP2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
TOP2A MUTATED	5	3	0
TOP2A WILD-TYPE	254	133	70

'TOP2A MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.671 (Fisher's exact test), Q value = 1

Table S181. Gene #17: 'TOP2A MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
TOP2A MUTATED	3	3	2
TOP2A WILD-TYPE	131	136	190

'TOP2A MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 1

Table S182. Gene #17: 'TOP2A 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
TOP2A MUTATED	3	0	0	0	0	3	0	1	0	1
TOP2A WILD-TYPE	70	45	49	70	30	61	27	28	39	38

'TOP2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.8 (Fisher's exact test), Q value = 1

Table S183. Gene #17: 'TOP2A MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
TOP2A MUTATED	3	2	2
TOP2A WILD-TYPE	134	163	151

'TOP2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.93

Table S184. Gene #17: 'TOP2A MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
TOP2A MUTATED	0	1	7
TOP2A WILD-TYPE	138	142	177

Figure S14. Get High-res Image Gene #17: 'TOP2A MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'TOP2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S185. Gene #17: 'TOP2A MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
TOP2A MUTATED	1	1	1
TOP2A WILD-TYPE	103	160	71

'TOP2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S186. Gene #17: 'TOP2A MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
TOP2A MUTATED	1	1	1	0
TOP2A WILD-TYPE	104	80	103	47

'TOP2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S187. Gene #17: 'TOP2A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
TOP2A MUTATED	1	4	2
TOP2A WILD-TYPE	96	155	124

'TOP2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.685 (Fisher's exact test), Q value = 1

Table S188. Gene #17: 'TOP2A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
TOP2A MUTATED	3	1	2	1
TOP2A WILD-TYPE	87	59	135	94

'NCOA3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0958 (Fisher's exact test), Q value = 1

Table S189. Gene #18: '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 = 0.224 (Fisher's exact test), Q value = 1

Table S190. Gene #18: '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 = 0.738 (Fisher's exact test), Q value = 1

Table S191. Gene #18: '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 = 0.643 (Fisher's exact test), Q value = 1

Table S192. Gene #18: '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 = 0.863 (Fisher's exact test), Q value = 1

Table S193. Gene #18: '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 = 0.529 (Fisher's exact test), Q value = 1

Table S194. Gene #18: '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 = 0.176 (Fisher's exact test), Q value = 1

Table S195. Gene #18: '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 = 0.229 (Fisher's exact test), Q value = 1

Table S196. Gene #18: '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

'TP53TG5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S197. Gene #19: 'TP53TG5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
TP53TG5 MUTATED	2	0	1
TP53TG5 WILD-TYPE	174	175	113

'TP53TG5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S198. Gene #19: 'TP53TG5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
TP53TG5 MUTATED	1	1	1
TP53TG5 WILD-TYPE	258	135	69

'TP53TG5 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S199. Gene #19: 'TP53TG5 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
TP53TG5 MUTATED	0	2	1
TP53TG5 WILD-TYPE	134	137	191

'TP53TG5 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 1

Table S200. Gene #19: 'TP53TG5 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
TP53TG5 MUTATED	0	0	0	0	0	1	1	0	1	0
TP53TG5 WILD-TYPE	73	45	49	70	30	63	26	29	38	39

'TP53TG5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0639 (Fisher's exact test), Q value = 1

Table S201. Gene #19: 'TP53TG5 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
TP53TG5 MUTATED	0	0	3
TP53TG5 WILD-TYPE	137	165	150

'TP53TG5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 1

Table S202. Gene #19: 'TP53TG5 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
TP53TG5 MUTATED	2	1	0
TP53TG5 WILD-TYPE	136	142	184

'RPGRIP1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S203. Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
RPGRIP1 MUTATED	3	3	1
RPGRIP1 WILD-TYPE	173	172	113

'RPGRIP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S204. Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
RPGRIP1 MUTATED	5	2	0
RPGRIP1 WILD-TYPE	254	134	70

'RPGRIP1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.93

Table S205. Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
RPGRIP1 MUTATED	5	0	2
RPGRIP1 WILD-TYPE	129	139	190

Figure S15. Get High-res Image Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'RPGRIP1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S206. Gene #20: 'RPGRIP1 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
RPGRIP1 MUTATED	2	2	0	1	0	0	0	1	1	0
RPGRIP1 WILD-TYPE	71	43	49	69	30	64	27	28	38	39

'RPGRIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.897 (Fisher's exact test), Q value = 1

Table S207. Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
RPGRIP1 MUTATED	2	2	3
RPGRIP1 WILD-TYPE	135	163	150

'RPGRIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S208. Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
RPGRIP1 MUTATED	4	1	2
RPGRIP1 WILD-TYPE	134	142	182

'RPGRIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S209. Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
RPGRIP1 MUTATED	2	4	0
RPGRIP1 WILD-TYPE	102	157	72

'RPGRIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.616 (Fisher's exact test), Q value = 1

Table S210. Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
RPGRIP1 MUTATED	1	2	3	0
RPGRIP1 WILD-TYPE	104	79	101	47

'RPGRIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S211. Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
RPGRIP1 MUTATED	4	2	1
RPGRIP1 WILD-TYPE	86	53	73

'RPGRIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S212. Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
RPGRIP1 MUTATED	3	3	1
RPGRIP1 WILD-TYPE	91	94	27

'RPGRIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.711 (Fisher's exact test), Q value = 1

Table S213. Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
RPGRIP1 MUTATED	2	2	3
RPGRIP1 WILD-TYPE	95	157	123

'RPGRIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S214. Gene #20: 'RPGRIP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
RPGRIP1 MUTATED	2	0	2	3
RPGRIP1 WILD-TYPE	88	60	135	92

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S215. Gene #21: '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 S216. Gene #21: '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 = 0.193 (Fisher's exact test), Q value = 1

Table S217. Gene #21: '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 = 0.142 (Fisher's exact test), Q value = 1

Table S218. Gene #21: '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 S219. Gene #21: '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 = 0.739 (Fisher's exact test), Q value = 1

Table S220. Gene #21: '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 S221. Gene #21: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
PTEN MUTATED	1	2	0
PTEN WILD-TYPE	103	159	72

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S222. Gene #21: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
PTEN MUTATED	0	0	3	0
PTEN WILD-TYPE	105	81	101	47

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 1

Table S223. Gene #21: '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 = 0.828 (Fisher's exact test), Q value = 1

Table S224. Gene #21: '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

'RB1CC1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S225. Gene #22: 'RB1CC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
RB1CC1 MUTATED	4	4	1
RB1CC1 WILD-TYPE	172	171	113

'RB1CC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.415 (Fisher's exact test), Q value = 1

Table S226. Gene #22: 'RB1CC1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
RB1CC1 MUTATED	6	1	2
RB1CC1 WILD-TYPE	253	135	68

'RB1CC1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 1

Table S227. Gene #22: 'RB1CC1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
RB1CC1 MUTATED	2	1	6
RB1CC1 WILD-TYPE	132	138	186

'RB1CC1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 1

Table S228. Gene #22: 'RB1CC1 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
RB1CC1 MUTATED	0	1	1	3	0	1	1	1	1	0
RB1CC1 WILD-TYPE	73	44	48	67	30	63	26	28	38	39

'RB1CC1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S229. Gene #22: 'RB1CC1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
RB1CC1 MUTATED	3	2	4
RB1CC1 WILD-TYPE	134	163	149

'RB1CC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S230. Gene #22: 'RB1CC1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
RB1CC1 MUTATED	3	1	5
RB1CC1 WILD-TYPE	135	142	179

'RB1CC1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S231. Gene #22: 'RB1CC1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
RB1CC1 MUTATED	2	4	1
RB1CC1 WILD-TYPE	102	157	71

'RB1CC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S232. Gene #22: 'RB1CC1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
RB1CC1 MUTATED	1	1	2	3
RB1CC1 WILD-TYPE	104	80	102	44

'RB1CC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S233. Gene #22: 'RB1CC1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
RB1CC1 MUTATED	2	0	1
RB1CC1 WILD-TYPE	88	55	73

'RB1CC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S234. Gene #22: 'RB1CC1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
RB1CC1 MUTATED	1	1	1
RB1CC1 WILD-TYPE	93	96	27

'RB1CC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 1

Table S235. Gene #22: 'RB1CC1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
RB1CC1 MUTATED	3	4	1
RB1CC1 WILD-TYPE	94	155	125

'RB1CC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S236. Gene #22: 'RB1CC1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
RB1CC1 MUTATED	2	2	4	0
RB1CC1 WILD-TYPE	88	58	133	95

'LPAR3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S237. Gene #23: 'LPAR3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	175	114
LPAR3 MUTATED	2	2	0
LPAR3 WILD-TYPE	174	173	114

'LPAR3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S238. Gene #23: 'LPAR3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	259	136	70
LPAR3 MUTATED	4	0	0
LPAR3 WILD-TYPE	255	136	70

'LPAR3 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S239. Gene #23: 'LPAR3 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	134	139	192
LPAR3 MUTATED	1	0	3
LPAR3 WILD-TYPE	133	139	189

'LPAR3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S240. Gene #23: 'LPAR3 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
LPAR3 MUTATED	0	1	0	2	0	0	1	0	0	0
LPAR3 WILD-TYPE	73	44	49	68	30	64	26	29	39	39

'LPAR3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S241. Gene #23: 'LPAR3 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	137	165	153
LPAR3 MUTATED	1	1	2
LPAR3 WILD-TYPE	136	164	151

'LPAR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0733 (Fisher's exact test), Q value = 1

Table S242. Gene #23: 'LPAR3 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	143	184
LPAR3 MUTATED	3	1	0
LPAR3 WILD-TYPE	135	142	184

'LPAR3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S243. Gene #23: 'LPAR3 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	104	161	72
LPAR3 MUTATED	1	3	0
LPAR3 WILD-TYPE	103	158	72

'LPAR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 1

Table S244. Gene #23: 'LPAR3 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	81	104	47
LPAR3 MUTATED	0	1	3	0
LPAR3 WILD-TYPE	105	80	101	47

'LPAR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 1

Table S245. Gene #23: 'LPAR3 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	90	55	74
LPAR3 MUTATED	2	1	0
LPAR3 WILD-TYPE	88	54	74

'LPAR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S246. Gene #23: 'LPAR3 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	97	28
LPAR3 MUTATED	2	1	0
LPAR3 WILD-TYPE	92	96	28

'LPAR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 1

Table S247. Gene #23: 'LPAR3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	97	159	126
LPAR3 MUTATED	0	1	2
LPAR3 WILD-TYPE	97	158	124

'LPAR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.688 (Fisher's exact test), Q value = 1

Table S248. Gene #23: 'LPAR3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	60	137	95
LPAR3 MUTATED	0	1	1	1
LPAR3 WILD-TYPE	90	59	136	94

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/15650400/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/OV-TP/15120653/OV-TP.transferedmergedcluster.txt
Number of patients = 466
Number of significantly mutated genes = 23
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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