Correlation between gene mutation status and molecular subtypes

Colorectal Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C16D5RQG

Overview

Introduction

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

Summary

Testing the association between mutation status of 46 genes and 10 molecular subtypes across 223 patients, 16 significant findings detected with P value < 0.05 and Q value < 0.25.

TP53 mutation correlated to 'CN_CNMF'.
KRAS mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
FBXW7 mutation correlated to 'CN_CNMF'.
BRAF mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
CDC27 mutation correlated to 'MRNA_CNMF'.
PCDHA3 mutation correlated to 'MRNA_CHIERARCHICAL'.
CASP8 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
ZFP3 mutation correlated to 'MRNA_CNMF'.
RWDD2B mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 46 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 16 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	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
BRAF	21 (9%)	202	1e-05 (0.00401)	1e-05 (0.00401)	5e-05 (0.0198)		0.397 (1.00)	1 (1.00)	0.372 (1.00)	1e-05 (0.00401)	1 (1.00)	0.148 (1.00)
KRAS	97 (43%)	126	0.00017 (0.0671)	0.00037 (0.145)	0.506 (1.00)	0.107 (1.00)	0.569 (1.00)	0.954 (1.00)	0.00023 (0.0906)	0.00686 (1.00)	0.0227 (1.00)	0.139 (1.00)
CASP8	10 (4%)	213	0.00027 (0.106)	1e-05 (0.00401)	0.00046 (0.178)		0.0443 (1.00)	0.231 (1.00)	1 (1.00)	0.00128 (0.485)	1 (1.00)	0.0564 (1.00)
TP53	117 (52%)	106	0.0025 (0.94)	0.00092 (0.352)	1e-05 (0.00401)		0.753 (1.00)	0.955 (1.00)	0.0181 (1.00)	0.00066 (0.254)	0.033 (1.00)	0.255 (1.00)
FBXW7	38 (17%)	185	0.0605 (1.00)	0.0179 (1.00)	0.00045 (0.175)		0.0112 (1.00)	0.119 (1.00)	0.00268 (1)	0.00101 (0.386)	0.415 (1.00)	0.014 (1.00)
CDC27	13 (6%)	210	0.00026 (0.102)	0.25 (1.00)	0.00072 (0.276)		0.936 (1.00)	0.826 (1.00)	0.441 (1.00)	0.0394 (1.00)	0.459 (1.00)	0.00251 (0.941)
PCDHA3	12 (5%)	211	0.0443 (1.00)	0.00042 (0.164)	0.0886 (1.00)		0.846 (1.00)	1 (1.00)	0.515 (1.00)	0.161 (1.00)	1 (1.00)	0.37 (1.00)
ZFP3	8 (4%)	215	0.00049 (0.19)	0.0575 (1.00)	0.00254 (0.95)		0.289 (1.00)	0.737 (1.00)	0.2 (1.00)	0.00475 (1.00)	1 (1.00)	0.00737 (1.00)
RWDD2B	7 (3%)	216	0.0257 (1.00)	0.733 (1.00)	0.0335 (1.00)		0.86 (1.00)	0.486 (1.00)	1 (1.00)	0.309 (1.00)	1 (1.00)	0.00051 (0.197)
APC	163 (73%)	60	0.00599 (1.00)	0.00127 (0.483)	0.145 (1.00)		0.297 (1.00)	0.154 (1.00)	0.755 (1.00)	0.0555 (1.00)	0.643 (1.00)	0.831 (1.00)
NRAS	20 (9%)	203	0.0471 (1.00)	0.0324 (1.00)	0.269 (1.00)		0.912 (1.00)	0.636 (1.00)	0.332 (1.00)	1 (1.00)	0.267 (1.00)	0.626 (1.00)
SMAD4	26 (12%)	197	0.03 (1.00)	0.0743 (1.00)	0.0625 (1.00)		0.859 (1.00)	1 (1.00)	0.415 (1.00)	0.0141 (1.00)	1 (1.00)	0.366 (1.00)
SMAD2	15 (7%)	208	0.135 (1.00)	0.677 (1.00)	0.437 (1.00)		0.596 (1.00)	0.678 (1.00)	0.567 (1.00)	0.237 (1.00)	1 (1.00)	0.731 (1.00)
FAM123B	24 (11%)	199	0.0867 (1.00)	0.304 (1.00)	0.0266 (1.00)		0.541 (1.00)	1 (1.00)	0.0742 (1.00)	0.0757 (1.00)	1 (1.00)	0.0616 (1.00)
PIK3CA	33 (15%)	190	0.203 (1.00)	0.408 (1.00)	0.00503 (1.00)		0.0615 (1.00)	0.316 (1.00)	0.0276 (1.00)	0.0271 (1.00)	0.164 (1.00)	0.748 (1.00)
TCF7L2	18 (8%)	205	1 (1.00)	0.634 (1.00)	0.209 (1.00)		0.836 (1.00)	0.606 (1.00)	0.335 (1.00)	0.612 (1.00)	1 (1.00)	0.13 (1.00)
ARID1A	20 (9%)	203	0.0234 (1.00)	0.193 (1.00)	0.0155 (1.00)		0.978 (1.00)	0.509 (1.00)	0.912 (1.00)	0.736 (1.00)	1 (1.00)	0.0135 (1.00)
MGC42105	11 (5%)	212	0.00134 (0.507)	0.0584 (1.00)	0.11 (1.00)		0.134 (1.00)	1 (1.00)	1 (1.00)	0.113 (1.00)	1 (1.00)	0.249 (1.00)
ACVR1B	14 (6%)	209	0.375 (1.00)	0.027 (1.00)	0.0439 (1.00)		0.734 (1.00)	0.191 (1.00)	1 (1.00)	0.19 (1.00)	0.582 (1.00)	0.229 (1.00)
KIAA1804	15 (7%)	208	0.27 (1.00)	0.894 (1.00)	0.0876 (1.00)		0.508 (1.00)	0.75 (1.00)	0.568 (1.00)	0.238 (1.00)	1 (1.00)	0.208 (1.00)
PCDHGB1	8 (4%)	215	0.206 (1.00)	0.197 (1.00)	0.19 (1.00)		0.508 (1.00)	0.668 (1.00)	0.526 (1.00)	0.45 (1.00)	1 (1.00)	0.25 (1.00)
PCBP1	5 (2%)	218	0.567 (1.00)	0.728 (1.00)	0.504 (1.00)				1 (1.00)	0.494 (1.00)	1 (1.00)	1 (1.00)
ZHX2	10 (4%)	213	0.118 (1.00)	0.222 (1.00)	0.389 (1.00)		0.238 (1.00)	0.222 (1.00)	0.56 (1.00)	0.518 (1.00)	1 (1.00)	0.205 (1.00)
PCDHA2	12 (5%)	211	0.207 (1.00)	0.785 (1.00)	0.0449 (1.00)		0.906 (1.00)	1 (1.00)	0.755 (1.00)	0.323 (1.00)	0.525 (1.00)	0.0797 (1.00)
ELF3	8 (4%)	215	0.797 (1.00)	0.801 (1.00)	0.09 (1.00)		0.88 (1.00)	0.339 (1.00)	0.022 (1.00)	0.121 (1.00)	1 (1.00)	0.262 (1.00)
CRTC1	4 (2%)	219	0.0644 (1.00)	0.117 (1.00)	0.628 (1.00)				1 (1.00)	0.246 (1.00)	1 (1.00)	1 (1.00)
CACNG3	8 (4%)	215	0.0155 (1.00)	0.204 (1.00)	0.007 (1.00)		0.126 (1.00)	0.334 (1.00)	0.144 (1.00)	0.0633 (1.00)	0.386 (1.00)	0.025 (1.00)
PCDHGA7	5 (2%)	218	0.365 (1.00)	0.492 (1.00)	0.144 (1.00)				0.743 (1.00)	1 (1.00)	1 (1.00)	0.641 (1.00)
CCBP2	10 (4%)	213	0.158 (1.00)	0.0378 (1.00)	0.568 (1.00)		0.072 (1.00)	1 (1.00)	0.373 (1.00)	0.516 (1.00)	1 (1.00)	0.373 (1.00)
MAP2K4	11 (5%)	212	0.458 (1.00)	0.446 (1.00)	0.0874 (1.00)		0.1 (1.00)	0.523 (1.00)	0.426 (1.00)	0.675 (1.00)	1 (1.00)	0.375 (1.00)
PCDHGA9	6 (3%)	217	0.0681 (1.00)	0.0786 (1.00)	0.0107 (1.00)		0.668 (1.00)	0.589 (1.00)	0.378 (1.00)	0.205 (1.00)	1 (1.00)	0.732 (1.00)
RBM10	8 (4%)	215	0.275 (1.00)	0.732 (1.00)	0.726 (1.00)		0.239 (1.00)	0.741 (1.00)	1 (1.00)	0.136 (1.00)	1 (1.00)	1 (1.00)
PTEN	7 (3%)	216	0.0269 (1.00)	0.392 (1.00)	0.0337 (1.00)		0.542 (1.00)	1 (1.00)	0.0987 (1.00)	0.0164 (1.00)	0.348 (1.00)	0.0243 (1.00)
DNMT1	17 (8%)	206	0.0244 (1.00)	0.0657 (1.00)	0.11 (1.00)		0.0541 (1.00)	0.332 (1.00)	0.355 (1.00)	0.0365 (1.00)	1 (1.00)	0.0702 (1.00)
BCOR	9 (4%)	214	0.0193 (1.00)	0.281 (1.00)	0.00635 (1.00)		0.466 (1.00)	1 (1.00)	0.756 (1.00)	0.144 (1.00)	1 (1.00)	0.025 (1.00)
PCDHGB5	7 (3%)	216	0.1 (1.00)	0.0726 (1.00)	0.243 (1.00)		0.882 (1.00)	0.739 (1.00)	0.0697 (1.00)	0.567 (1.00)	1 (1.00)	1 (1.00)
TBC1D10C	3 (1%)	220	0.693 (1.00)	0.24 (1.00)	0.818 (1.00)				1 (1.00)	0.614 (1.00)	1 (1.00)	0.597 (1.00)
ERCC6L	5 (2%)	218	0.005 (1.00)	0.489 (1.00)	0.334 (1.00)				0.743 (1.00)	0.705 (1.00)	1 (1.00)	0.188 (1.00)
ERBB3	14 (6%)	209	0.136 (1.00)	0.0423 (1.00)	0.113 (1.00)		0.663 (1.00)	0.727 (1.00)	0.844 (1.00)	0.199 (1.00)	1 (1.00)	0.0538 (1.00)
KLK2	3 (1%)	220	0.54 (1.00)	0.133 (1.00)	0.82 (1.00)				1 (1.00)	0.611 (1.00)
TAPBP	5 (2%)	218	0.101 (1.00)	0.644 (1.00)	0.332 (1.00)		1 (1.00)	0.174 (1.00)	0.301 (1.00)	0.291 (1.00)	1 (1.00)	0.0131 (1.00)
ERBB2	9 (4%)	214	0.378 (1.00)	0.189 (1.00)	0.35 (1.00)		0.0743 (1.00)	0.283 (1.00)	0.321 (1.00)	0.0789 (1.00)	0.386 (1.00)	0.116 (1.00)
MORC2	5 (2%)	218	0.183 (1.00)	0.642 (1.00)	0.333 (1.00)		0.208 (1.00)	0.484 (1.00)	0.744 (1.00)	0.29 (1.00)	1 (1.00)	0.137 (1.00)
ABCA8	12 (5%)	211	0.00154 (0.581)	0.024 (1.00)	0.0113 (1.00)		0.0306 (1.00)	0.286 (1.00)	0.478 (1.00)	0.162 (1.00)	0.495 (1.00)	0.368 (1.00)
SETD2	13 (6%)	210	0.0345 (1.00)	0.184 (1.00)	0.00106 (0.404)		0.0937 (1.00)	0.74 (1.00)	0.0653 (1.00)	0.0175 (1.00)	1 (1.00)	0.442 (1.00)
ESR1	11 (5%)	212	0.193 (1.00)	0.0103 (1.00)	0.0498 (1.00)		0.718 (1.00)	0.286 (1.00)	0.807 (1.00)	0.194 (1.00)	1 (1.00)	0.179 (1.00)

'APC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
APC MUTATED	21	45	52	31
APC WILD-TYPE	21	12	15	8

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

'APC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.48

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
APC MUTATED	26	31	51	41
APC WILD-TYPE	22	6	22	6

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

'APC MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
APC MUTATED	50	69	31	10
APC WILD-TYPE	29	21	8	2

'APC MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S4. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
APC MUTATED	33	45	16	20
APC WILD-TYPE	7	22	8	6

'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S5. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
APC MUTATED	10	87	17
APC WILD-TYPE	1	39	3

'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
APC MUTATED	5	22	11	123
APC WILD-TYPE	2	6	6	45

'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0555 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
APC MUTATED	0	3	1	59	98
APC WILD-TYPE	1	2	0	30	26

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
APC MUTATED	3	6	143
APC WILD-TYPE	0	3	51

'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.831 (Fisher's exact test), Q value = 1

Table S9. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
APC MUTATED	6	45	101
APC WILD-TYPE	1	17	36

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.94

Table S10. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
TP53 MUTATED	17	40	37	14
TP53 WILD-TYPE	25	17	30	25

Figure S3. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.35

Table S11. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
TP53 MUTATED	15	25	36	32
TP53 WILD-TYPE	33	12	37	15

Figure S4. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S12. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
TP53 MUTATED	19	68	19	9
TP53 WILD-TYPE	60	22	20	3

Figure S5. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.753 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
TP53 MUTATED	18	34	14	12
TP53 WILD-TYPE	22	33	10	14

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.955 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
TP53 MUTATED	6	62	10
TP53 WILD-TYPE	5	64	10

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
TP53 MUTATED	2	8	11	94
TP53 WILD-TYPE	5	20	6	74

Figure S6. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.25

Table S16. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
TP53 MUTATED	0	4	0	34	77
TP53 WILD-TYPE	1	1	1	55	47

Figure S7. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 1

Table S17. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
TP53 MUTATED	3	2	104
TP53 WILD-TYPE	0	7	90

Figure S8. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S18. Gene #2: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
TP53 MUTATED	5	28	76
TP53 WILD-TYPE	2	34	61

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.067

Table S19. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
KRAS MUTATED	13	15	31	27
KRAS WILD-TYPE	29	42	36	12

Figure S9. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.14

Table S20. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
KRAS MUTATED	20	9	44	13
KRAS WILD-TYPE	28	28	29	34

Figure S10. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

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

Table S21. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
KRAS MUTATED	38	34	19	5
KRAS WILD-TYPE	41	56	20	7

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S22. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	1	5	2
KRAS MUTATED	0	1	2
KRAS WILD-TYPE	1	4	0

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 1

Table S23. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
KRAS MUTATED	16	34	9	13
KRAS WILD-TYPE	24	33	15	13

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.954 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
KRAS MUTATED	5	57	10
KRAS WILD-TYPE	6	69	10

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.091

Table S25. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
KRAS MUTATED	3	21	2	68
KRAS WILD-TYPE	4	7	15	100

Figure S11. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00686 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
KRAS MUTATED	0	3	1	48	42
KRAS WILD-TYPE	1	2	0	41	82

Figure S12. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 1

Table S27. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
KRAS MUTATED	0	7	80
KRAS WILD-TYPE	3	2	114

Figure S13. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 1

Table S28. Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
KRAS MUTATED	3	20	64
KRAS WILD-TYPE	4	42	73

'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0471 (Fisher's exact test), Q value = 1

Table S29. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
NRAS MUTATED	0	8	6	5
NRAS WILD-TYPE	42	49	61	34

Figure S14. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 1

Table S30. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
NRAS MUTATED	2	4	12	1
NRAS WILD-TYPE	46	33	61	46

Figure S15. Get High-res Image Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
NRAS MUTATED	8	11	1	0
NRAS WILD-TYPE	71	79	38	12

'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
NRAS MUTATED	3	7	1	2
NRAS WILD-TYPE	37	60	23	24

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.636 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
NRAS MUTATED	0	11	2
NRAS WILD-TYPE	11	115	18

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S34. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
NRAS MUTATED	0	5	1	13
NRAS WILD-TYPE	7	23	16	155

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S35. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
NRAS MUTATED	0	0	0	8	11
NRAS WILD-TYPE	1	5	1	81	113

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S36. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
NRAS MUTATED	1	0	17
NRAS WILD-TYPE	2	9	177

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S37. Gene #4: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
NRAS MUTATED	1	5	12
NRAS WILD-TYPE	6	57	125

'SMAD4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 1

Table S38. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
SMAD4 MUTATED	7	4	4	9
SMAD4 WILD-TYPE	35	53	63	30

Figure S16. Get High-res Image Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SMAD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0743 (Fisher's exact test), Q value = 1

Table S39. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
SMAD4 MUTATED	9	2	11	2
SMAD4 WILD-TYPE	39	35	62	45

'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0625 (Fisher's exact test), Q value = 1

Table S40. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
SMAD4 MUTATED	14	5	5	2
SMAD4 WILD-TYPE	65	85	34	10

'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.859 (Fisher's exact test), Q value = 1

Table S41. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
SMAD4 MUTATED	4	10	4	3
SMAD4 WILD-TYPE	36	57	20	23

'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S42. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
SMAD4 MUTATED	1	18	2
SMAD4 WILD-TYPE	10	108	18

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S43. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
SMAD4 MUTATED	1	4	0	20
SMAD4 WILD-TYPE	6	24	17	148

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 1

Table S44. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
SMAD4 MUTATED	0	0	0	18	7
SMAD4 WILD-TYPE	1	5	1	71	117

Figure S17. Get High-res Image Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S45. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
SMAD4 MUTATED	0	1	24
SMAD4 WILD-TYPE	3	8	170

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S46. Gene #5: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
SMAD4 MUTATED	0	5	20
SMAD4 WILD-TYPE	7	57	117

'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0605 (Fisher's exact test), Q value = 1

Table S47. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
FBXW7 MUTATED	11	6	7	9
FBXW7 WILD-TYPE	31	51	60	30

'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 1

Table S48. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
FBXW7 MUTATED	15	4	10	4
FBXW7 WILD-TYPE	33	33	63	43

Figure S18. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.18

Table S49. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
FBXW7 MUTATED	24	6	6	2
FBXW7 WILD-TYPE	55	84	33	10

Figure S19. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 1

Table S50. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
FBXW7 MUTATED	7	9	2	11
FBXW7 WILD-TYPE	33	58	22	15

Figure S20. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S51. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
FBXW7 MUTATED	1	21	7
FBXW7 WILD-TYPE	10	105	13

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 1

Table S52. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
FBXW7 MUTATED	0	12	1	25
FBXW7 WILD-TYPE	7	16	16	143

Figure S21. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.39

Table S53. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
FBXW7 MUTATED	0	1	0	26	11
FBXW7 WILD-TYPE	1	4	1	63	113

Figure S22. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S54. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
FBXW7 MUTATED	0	0	36
FBXW7 WILD-TYPE	3	9	158

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 1

Table S55. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
FBXW7 MUTATED	3	5	28
FBXW7 WILD-TYPE	4	57	109

Figure S23. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SMAD2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S56. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
SMAD2 MUTATED	4	2	2	5
SMAD2 WILD-TYPE	38	55	65	34

'SMAD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 1

Table S57. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
SMAD2 MUTATED	5	2	4	2
SMAD2 WILD-TYPE	43	35	69	45

'SMAD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S58. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
SMAD2 MUTATED	8	4	2	1
SMAD2 WILD-TYPE	71	86	37	11

'SMAD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.596 (Fisher's exact test), Q value = 1

Table S59. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
SMAD2 MUTATED	2	3	2	3
SMAD2 WILD-TYPE	38	64	22	23

'SMAD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S60. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
SMAD2 MUTATED	0	8	2
SMAD2 WILD-TYPE	11	118	18

'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S61. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
SMAD2 MUTATED	0	3	0	12
SMAD2 WILD-TYPE	7	25	17	156

'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.237 (Fisher's exact test), Q value = 1

Table S62. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
SMAD2 MUTATED	0	0	0	10	5
SMAD2 WILD-TYPE	1	5	1	79	119

'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S63. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
SMAD2 MUTATED	0	0	14
SMAD2 WILD-TYPE	3	9	180

'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S64. Gene #7: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
SMAD2 MUTATED	0	3	11
SMAD2 WILD-TYPE	7	59	126

'FAM123B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0867 (Fisher's exact test), Q value = 1

Table S65. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
FAM123B MUTATED	9	5	4	5
FAM123B WILD-TYPE	33	52	63	34

'FAM123B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 1

Table S66. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
FAM123B MUTATED	9	4	7	3
FAM123B WILD-TYPE	39	33	66	44

'FAM123B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 1

Table S67. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
FAM123B MUTATED	15	5	3	0
FAM123B WILD-TYPE	64	85	36	12

Figure S24. Get High-res Image Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FAM123B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S68. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
FAM123B MUTATED	2	7	2	4
FAM123B WILD-TYPE	38	60	22	22

'FAM123B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S69. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
FAM123B MUTATED	1	12	2
FAM123B WILD-TYPE	10	114	18

'FAM123B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0742 (Fisher's exact test), Q value = 1

Table S70. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
FAM123B MUTATED	1	7	1	15
FAM123B WILD-TYPE	6	21	16	153

'FAM123B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0757 (Fisher's exact test), Q value = 1

Table S71. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
FAM123B MUTATED	0	0	0	16	8
FAM123B WILD-TYPE	1	5	1	73	116

'FAM123B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S72. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
FAM123B MUTATED	0	1	22
FAM123B WILD-TYPE	3	8	172

'FAM123B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0616 (Fisher's exact test), Q value = 1

Table S73. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
FAM123B MUTATED	2	3	18
FAM123B WILD-TYPE	5	59	119

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S74. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PIK3CA MUTATED	8	4	7	7
PIK3CA WILD-TYPE	34	53	60	32

'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.408 (Fisher's exact test), Q value = 1

Table S75. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
PIK3CA MUTATED	9	3	10	4
PIK3CA WILD-TYPE	39	34	63	43

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 1

Table S76. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
PIK3CA MUTATED	20	6	4	2
PIK3CA WILD-TYPE	59	84	35	10

Figure S25. Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0615 (Fisher's exact test), Q value = 1

Table S77. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
PIK3CA MUTATED	11	9	1	6
PIK3CA WILD-TYPE	29	58	23	20

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S78. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
PIK3CA MUTATED	3	19	5
PIK3CA WILD-TYPE	8	107	15

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 1

Table S79. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
PIK3CA MUTATED	2	8	0	23
PIK3CA WILD-TYPE	5	20	17	145

Figure S26. Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 1

Table S80. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
PIK3CA MUTATED	0	1	0	21	11
PIK3CA WILD-TYPE	1	4	1	68	113

Figure S27. Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S81. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PIK3CA MUTATED	0	3	26
PIK3CA WILD-TYPE	3	6	168

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S82. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
PIK3CA MUTATED	1	7	21
PIK3CA WILD-TYPE	6	55	116

'TCF7L2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S83. Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
TCF7L2 MUTATED	3	4	5	3
TCF7L2 WILD-TYPE	39	53	62	36

'TCF7L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S84. Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
TCF7L2 MUTATED	2	4	5	4
TCF7L2 WILD-TYPE	46	33	68	43

'TCF7L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 1

Table S85. Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
TCF7L2 MUTATED	6	7	2	3
TCF7L2 WILD-TYPE	73	83	37	9

'TCF7L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S86. Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
TCF7L2 MUTATED	3	5	1	3
TCF7L2 WILD-TYPE	37	62	23	23

'TCF7L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S87. Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
TCF7L2 MUTATED	1	9	2
TCF7L2 WILD-TYPE	10	117	18

'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S88. Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
TCF7L2 MUTATED	0	0	1	16
TCF7L2 WILD-TYPE	7	28	16	152

'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S89. Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
TCF7L2 MUTATED	0	0	0	5	12
TCF7L2 WILD-TYPE	1	5	1	84	112

'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S90. Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
TCF7L2 MUTATED	0	0	15
TCF7L2 WILD-TYPE	3	9	179

'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S91. Gene #10: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
TCF7L2 MUTATED	2	4	9
TCF7L2 WILD-TYPE	5	58	128

'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 1

Table S92. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ARID1A MUTATED	9	3	3	4
ARID1A WILD-TYPE	33	54	64	35

Figure S28. Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S93. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
ARID1A MUTATED	8	4	4	3
ARID1A WILD-TYPE	40	33	69	44

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 1

Table S94. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
ARID1A MUTATED	14	4	2	0
ARID1A WILD-TYPE	65	86	37	12

Figure S29. Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S95. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ARID1A MUTATED	4	6	2	3
ARID1A WILD-TYPE	36	61	22	23

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.509 (Fisher's exact test), Q value = 1

Table S96. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
ARID1A MUTATED	0	12	3
ARID1A WILD-TYPE	11	114	17

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S97. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
ARID1A MUTATED	0	2	2	16
ARID1A WILD-TYPE	7	26	15	152

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.736 (Fisher's exact test), Q value = 1

Table S98. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
ARID1A MUTATED	0	0	0	10	10
ARID1A WILD-TYPE	1	5	1	79	114

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S99. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ARID1A MUTATED	0	0	16
ARID1A WILD-TYPE	3	9	178

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 1

Table S100. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
ARID1A MUTATED	2	8	6
ARID1A WILD-TYPE	5	54	131

Figure S30. Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S101. Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
BRAF MUTATED	13	1	1	4
BRAF WILD-TYPE	29	56	66	35

Figure S31. Get High-res Image Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S102. Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
BRAF MUTATED	15	1	3	0
BRAF WILD-TYPE	33	36	70	47

Figure S32. Get High-res Image Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.02

Table S103. Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
BRAF MUTATED	17	1	3	0
BRAF WILD-TYPE	62	89	36	12

Figure S33. Get High-res Image Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S104. Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
BRAF MUTATED	3	4	4	1
BRAF WILD-TYPE	37	63	20	25

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S105. Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
BRAF MUTATED	1	10	1
BRAF WILD-TYPE	10	116	19

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 1

Table S106. Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
BRAF MUTATED	1	4	0	16
BRAF WILD-TYPE	6	24	17	152

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S107. Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
BRAF MUTATED	1	0	0	18	2
BRAF WILD-TYPE	0	5	1	71	122

Figure S34. Get High-res Image Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S108. Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
BRAF MUTATED	0	1	20
BRAF WILD-TYPE	3	8	174

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 1

Table S109. Gene #12: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
BRAF MUTATED	0	3	18
BRAF WILD-TYPE	7	59	119

'MGC42105 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.51

Table S110. Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
MGC42105 MUTATED	6	0	1	4
MGC42105 WILD-TYPE	36	57	66	35

Figure S35. Get High-res Image Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MGC42105 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0584 (Fisher's exact test), Q value = 1

Table S111. Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
MGC42105 MUTATED	6	0	4	1
MGC42105 WILD-TYPE	42	37	69	46

'MGC42105 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 1

Table S112. Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
MGC42105 MUTATED	8	2	1	0
MGC42105 WILD-TYPE	71	88	38	12

'MGC42105 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S113. Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
MGC42105 MUTATED	0	3	1	3
MGC42105 WILD-TYPE	40	64	23	23

'MGC42105 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S114. Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
MGC42105 MUTATED	0	6	1
MGC42105 WILD-TYPE	11	120	19

'MGC42105 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S115. Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
MGC42105 MUTATED	0	1	0	9
MGC42105 WILD-TYPE	7	27	17	159

'MGC42105 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.113 (Fisher's exact test), Q value = 1

Table S116. Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
MGC42105 MUTATED	0	0	0	8	2
MGC42105 WILD-TYPE	1	5	1	81	122

'MGC42105 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117. Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
MGC42105 MUTATED	0	0	11
MGC42105 WILD-TYPE	3	9	183

'MGC42105 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 1

Table S118. Gene #13: 'MGC42105 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
MGC42105 MUTATED	0	1	10
MGC42105 WILD-TYPE	7	61	127

'ACVR1B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 1

Table S119. Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ACVR1B MUTATED	3	2	2	4
ACVR1B WILD-TYPE	39	55	65	35

'ACVR1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 1

Table S120. Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
ACVR1B MUTATED	5	4	2	0
ACVR1B WILD-TYPE	43	33	71	47

Figure S36. Get High-res Image Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ACVR1B MUTATION STATUS' versus 'CN_CNMF'

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

Table S121. Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
ACVR1B MUTATED	10	2	2	0
ACVR1B WILD-TYPE	69	88	37	12

Figure S37. Get High-res Image Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ACVR1B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S122. Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ACVR1B MUTATED	2	5	1	3
ACVR1B WILD-TYPE	38	62	23	23

'ACVR1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S123. Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
ACVR1B MUTATED	1	7	3
ACVR1B WILD-TYPE	10	119	17

'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S124. Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
ACVR1B MUTATED	0	2	1	11
ACVR1B WILD-TYPE	7	26	16	157

'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S125. Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
ACVR1B MUTATED	0	0	0	10	4
ACVR1B WILD-TYPE	1	5	1	79	120

'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 1

Table S126. Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ACVR1B MUTATED	0	1	13
ACVR1B WILD-TYPE	3	8	181

'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S127. Gene #14: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
ACVR1B MUTATED	1	2	11
ACVR1B WILD-TYPE	6	60	126

'CDC27 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S128. Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
CDC27 MUTATED	4	0	1	7
CDC27 WILD-TYPE	38	57	66	32

Figure S38. Get High-res Image Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDC27 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.25 (Fisher's exact test), Q value = 1

Table S129. Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
CDC27 MUTATED	6	1	3	2
CDC27 WILD-TYPE	42	36	70	45

'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.28

Table S130. Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
CDC27 MUTATED	11	0	2	0
CDC27 WILD-TYPE	68	90	37	12

Figure S39. Get High-res Image Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDC27 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S131. Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
CDC27 MUTATED	2	5	1	2
CDC27 WILD-TYPE	38	62	23	24

'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S132. Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
CDC27 MUTATED	1	8	1
CDC27 WILD-TYPE	10	118	19

'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 1

Table S133. Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
CDC27 MUTATED	1	1	0	11
CDC27 WILD-TYPE	6	27	17	157

'CDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 1

Table S134. Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
CDC27 MUTATED	1	0	0	8	4
CDC27 WILD-TYPE	0	5	1	81	120

Figure S40. Get High-res Image Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S135. Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
CDC27 MUTATED	0	1	9
CDC27 WILD-TYPE	3	8	185

'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.94

Table S136. Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
CDC27 MUTATED	3	3	4
CDC27 WILD-TYPE	4	59	133

Figure S41. Get High-res Image Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KIAA1804 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 1

Table S137. Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
KIAA1804 MUTATED	3	1	6	4
KIAA1804 WILD-TYPE	39	56	61	35

'KIAA1804 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S138. Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
KIAA1804 MUTATED	4	2	4	4
KIAA1804 WILD-TYPE	44	35	69	43

'KIAA1804 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0876 (Fisher's exact test), Q value = 1

Table S139. Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
KIAA1804 MUTATED	9	5	0	1
KIAA1804 WILD-TYPE	70	85	39	11

'KIAA1804 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S140. Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
KIAA1804 MUTATED	2	6	1	4
KIAA1804 WILD-TYPE	38	61	23	22

'KIAA1804 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S141. Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
KIAA1804 MUTATED	0	12	1
KIAA1804 WILD-TYPE	11	114	19

'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S142. Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
KIAA1804 MUTATED	0	3	0	12
KIAA1804 WILD-TYPE	7	25	17	156

'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S143. Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
KIAA1804 MUTATED	0	0	0	10	5
KIAA1804 WILD-TYPE	1	5	1	79	119

'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S144. Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
KIAA1804 MUTATED	0	0	15
KIAA1804 WILD-TYPE	3	9	179

'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S145. Gene #16: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
KIAA1804 MUTATED	1	2	12
KIAA1804 WILD-TYPE	6	60	125

'PCDHGB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 1

Table S146. Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PCDHGB1 MUTATED	3	1	1	3
PCDHGB1 WILD-TYPE	39	56	66	36

'PCDHGB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 1

Table S147. Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
PCDHGB1 MUTATED	4	2	1	1
PCDHGB1 WILD-TYPE	44	35	72	46

'PCDHGB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S148. Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
PCDHGB1 MUTATED	6	2	0	0
PCDHGB1 WILD-TYPE	73	88	39	12

'PCDHGB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S149. Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
PCDHGB1 MUTATED	1	2	0	2
PCDHGB1 WILD-TYPE	39	65	24	24

'PCDHGB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S150. Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
PCDHGB1 MUTATED	0	4	1
PCDHGB1 WILD-TYPE	11	122	19

'PCDHGB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S151. Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
PCDHGB1 MUTATED	0	2	0	6
PCDHGB1 WILD-TYPE	7	26	17	162

'PCDHGB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S152. Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
PCDHGB1 MUTATED	0	0	0	5	3
PCDHGB1 WILD-TYPE	1	5	1	84	121

'PCDHGB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S153. Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PCDHGB1 MUTATED	0	0	6
PCDHGB1 WILD-TYPE	3	9	188

'PCDHGB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.25 (Fisher's exact test), Q value = 1

Table S154. Gene #17: 'PCDHGB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
PCDHGB1 MUTATED	1	1	4
PCDHGB1 WILD-TYPE	6	61	133

'PCBP1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S155. Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PCBP1 MUTATED	0	1	2	2
PCBP1 WILD-TYPE	42	56	65	37

'PCBP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S156. Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
PCBP1 MUTATED	1	0	2	2
PCBP1 WILD-TYPE	47	37	71	45

'PCBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 1

Table S157. Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
PCBP1 MUTATED	2	1	2	0
PCBP1 WILD-TYPE	77	89	37	12

'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S158. Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
PCBP1 MUTATED	0	0	0	5
PCBP1 WILD-TYPE	7	28	17	163

'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 1

Table S159. Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
PCBP1 MUTATED	0	0	0	1	4
PCBP1 WILD-TYPE	1	5	1	88	120

'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S160. Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PCBP1 MUTATED	0	0	4
PCBP1 WILD-TYPE	3	9	190

'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S161. Gene #18: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
PCBP1 MUTATED	0	1	3
PCBP1 WILD-TYPE	7	61	134

'ZHX2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S162. Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ZHX2 MUTATED	5	1	2	1
ZHX2 WILD-TYPE	37	56	65	38

'ZHX2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 1

Table S163. Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
ZHX2 MUTATED	4	1	1	3
ZHX2 WILD-TYPE	44	36	72	44

'ZHX2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S164. Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
ZHX2 MUTATED	6	2	2	0
ZHX2 WILD-TYPE	73	88	37	12

'ZHX2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S165. Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ZHX2 MUTATED	0	4	0	2
ZHX2 WILD-TYPE	40	63	24	24

'ZHX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 1

Table S166. Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
ZHX2 MUTATED	0	4	2
ZHX2 WILD-TYPE	11	122	18

'ZHX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S167. Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
ZHX2 MUTATED	0	0	0	10
ZHX2 WILD-TYPE	7	28	17	158

'ZHX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S168. Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
ZHX2 MUTATED	0	0	0	6	4
ZHX2 WILD-TYPE	1	5	1	83	120

'ZHX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S169. Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ZHX2 MUTATED	0	0	8
ZHX2 WILD-TYPE	3	9	186

'ZHX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S170. Gene #19: 'ZHX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
ZHX2 MUTATED	1	1	6
ZHX2 WILD-TYPE	6	61	131

'PCDHA3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 1

Table S171. Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PCDHA3 MUTATED	4	3	0	3
PCDHA3 WILD-TYPE	38	54	67	36

Figure S42. Get High-res Image Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PCDHA3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.16

Table S172. Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
PCDHA3 MUTATED	6	4	0	0
PCDHA3 WILD-TYPE	42	33	73	47

Figure S43. Get High-res Image Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PCDHA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0886 (Fisher's exact test), Q value = 1

Table S173. Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
PCDHA3 MUTATED	8	2	1	1
PCDHA3 WILD-TYPE	71	88	38	11

'PCDHA3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.846 (Fisher's exact test), Q value = 1

Table S174. Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
PCDHA3 MUTATED	2	4	2	2
PCDHA3 WILD-TYPE	38	63	22	24

'PCDHA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S175. Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
PCDHA3 MUTATED	0	9	1
PCDHA3 WILD-TYPE	11	117	19

'PCDHA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S176. Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
PCDHA3 MUTATED	0	3	1	8
PCDHA3 WILD-TYPE	7	25	16	160

'PCDHA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 1

Table S177. Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
PCDHA3 MUTATED	0	0	0	9	3
PCDHA3 WILD-TYPE	1	5	1	80	121

'PCDHA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S178. Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PCDHA3 MUTATED	0	0	11
PCDHA3 WILD-TYPE	3	9	183

'PCDHA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.37 (Fisher's exact test), Q value = 1

Table S179. Gene #20: 'PCDHA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
PCDHA3 MUTATED	1	2	8
PCDHA3 WILD-TYPE	6	60	129

'PCDHA2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S180. Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PCDHA2 MUTATED	3	3	1	4
PCDHA2 WILD-TYPE	39	54	66	35

'PCDHA2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S181. Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
PCDHA2 MUTATED	4	2	3	2
PCDHA2 WILD-TYPE	44	35	70	45

'PCDHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 1

Table S182. Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
PCDHA2 MUTATED	9	3	0	0
PCDHA2 WILD-TYPE	70	87	39	12

Figure S44. Get High-res Image Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PCDHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S183. Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
PCDHA2 MUTATED	1	2	1	0
PCDHA2 WILD-TYPE	39	65	23	26

'PCDHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S184. Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
PCDHA2 MUTATED	0	4	0
PCDHA2 WILD-TYPE	11	122	20

'PCDHA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S185. Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
PCDHA2 MUTATED	0	2	0	10
PCDHA2 WILD-TYPE	7	26	17	158

'PCDHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S186. Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
PCDHA2 MUTATED	0	0	0	8	4
PCDHA2 WILD-TYPE	1	5	1	81	120

'PCDHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.525 (Fisher's exact test), Q value = 1

Table S187. Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PCDHA2 MUTATED	0	1	11
PCDHA2 WILD-TYPE	3	8	183

'PCDHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0797 (Fisher's exact test), Q value = 1

Table S188. Gene #21: 'PCDHA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
PCDHA2 MUTATED	2	3	7
PCDHA2 WILD-TYPE	5	59	130

'ELF3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S189. Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ELF3 MUTATED	1	1	3	2
ELF3 WILD-TYPE	41	56	64	37

'ELF3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.801 (Fisher's exact test), Q value = 1

Table S190. Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
ELF3 MUTATED	1	1	4	1
ELF3 WILD-TYPE	47	36	69	46

'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.09 (Fisher's exact test), Q value = 1

Table S191. Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
ELF3 MUTATED	3	1	4	0
ELF3 WILD-TYPE	76	89	35	12

'ELF3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S192. Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ELF3 MUTATED	2	3	0	1
ELF3 WILD-TYPE	38	64	24	25

'ELF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 1

Table S193. Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
ELF3 MUTATED	1	4	1
ELF3 WILD-TYPE	10	122	19

'ELF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 1

Table S194. Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
ELF3 MUTATED	1	3	1	3
ELF3 WILD-TYPE	6	25	16	165

Figure S45. Get High-res Image Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S195. Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
ELF3 MUTATED	0	1	0	5	2
ELF3 WILD-TYPE	1	4	1	84	122

'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S196. Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ELF3 MUTATED	0	0	8
ELF3 WILD-TYPE	3	9	186

'ELF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S197. Gene #22: 'ELF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
ELF3 MUTATED	1	3	4
ELF3 WILD-TYPE	6	59	133

'CRTC1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0644 (Fisher's exact test), Q value = 1

Table S198. Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
CRTC1 MUTATED	0	0	4	0
CRTC1 WILD-TYPE	42	57	63	39

'CRTC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S199. Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
CRTC1 MUTATED	0	0	1	3
CRTC1 WILD-TYPE	48	37	72	44

'CRTC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.628 (Fisher's exact test), Q value = 1

Table S200. Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
CRTC1 MUTATED	1	3	0	0
CRTC1 WILD-TYPE	78	87	39	12

'CRTC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S201. Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
CRTC1 MUTATED	0	0	0	4
CRTC1 WILD-TYPE	7	28	17	164

'CRTC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S202. Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
CRTC1 MUTATED	0	0	0	0	4
CRTC1 WILD-TYPE	1	5	1	89	120

'CRTC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S203. Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
CRTC1 MUTATED	0	0	4
CRTC1 WILD-TYPE	3	9	190

'CRTC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S204. Gene #23: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
CRTC1 MUTATED	0	1	3
CRTC1 WILD-TYPE	7	61	134

'CASP8 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.11

Table S205. Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
CASP8 MUTATED	6	0	0	3
CASP8 WILD-TYPE	36	57	67	36

Figure S46. Get High-res Image Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.004

Table S206. Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
CASP8 MUTATED	9	0	0	0
CASP8 WILD-TYPE	39	37	73	47

Figure S47. Get High-res Image Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.18

Table S207. Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
CASP8 MUTATED	10	0	0	0
CASP8 WILD-TYPE	69	90	39	12

Figure S48. Get High-res Image Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 1

Table S208. Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
CASP8 MUTATED	4	1	0	3
CASP8 WILD-TYPE	36	66	24	23

Figure S49. Get High-res Image Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 1

Table S209. Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
CASP8 MUTATED	1	5	2
CASP8 WILD-TYPE	10	121	18

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S210. Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
CASP8 MUTATED	0	1	0	9
CASP8 WILD-TYPE	7	27	17	159

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.49

Table S211. Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
CASP8 MUTATED	0	0	0	10	0
CASP8 WILD-TYPE	1	5	1	79	124

Figure S50. Get High-res Image Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S212. Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
CASP8 MUTATED	0	0	8
CASP8 WILD-TYPE	3	9	186

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0564 (Fisher's exact test), Q value = 1

Table S213. Gene #24: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
CASP8 MUTATED	1	0	7
CASP8 WILD-TYPE	6	62	130

'CACNG3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 1

Table S214. Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
CACNG3 MUTATED	4	1	0	3
CACNG3 WILD-TYPE	38	56	67	36

Figure S51. Get High-res Image Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CACNG3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 1

Table S215. Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
CACNG3 MUTATED	4	1	3	0
CACNG3 WILD-TYPE	44	36	70	47

'CACNG3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.007 (Fisher's exact test), Q value = 1

Table S216. Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
CACNG3 MUTATED	7	0	0	0
CACNG3 WILD-TYPE	72	90	39	12

Figure S52. Get High-res Image Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CACNG3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S217. Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
CACNG3 MUTATED	1	1	1	3
CACNG3 WILD-TYPE	39	66	23	23

'CACNG3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 1

Table S218. Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
CACNG3 MUTATED	1	4	1
CACNG3 WILD-TYPE	10	122	19

'CACNG3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S219. Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
CACNG3 MUTATED	1	2	0	5
CACNG3 WILD-TYPE	6	26	17	163

'CACNG3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0633 (Fisher's exact test), Q value = 1

Table S220. Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
CACNG3 MUTATED	0	0	0	7	1
CACNG3 WILD-TYPE	1	5	1	82	123

'CACNG3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S221. Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
CACNG3 MUTATED	0	1	7
CACNG3 WILD-TYPE	3	8	187

'CACNG3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 1

Table S222. Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
CACNG3 MUTATED	2	1	5
CACNG3 WILD-TYPE	5	61	132

Figure S53. Get High-res Image Gene #25: 'CACNG3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PCDHGA7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 1

Table S223. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PCDHGA7 MUTATED	2	0	2	1
PCDHGA7 WILD-TYPE	40	57	65	38

'PCDHGA7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.492 (Fisher's exact test), Q value = 1

Table S224. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
PCDHGA7 MUTATED	2	0	1	2
PCDHGA7 WILD-TYPE	46	37	72	45

'PCDHGA7 MUTATION STATUS' versus 'CN_CNMF'

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

Table S225. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
PCDHGA7 MUTATED	3	0	2	0
PCDHGA7 WILD-TYPE	76	90	37	12

'PCDHGA7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 1

Table S226. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
PCDHGA7 MUTATED	0	1	0	4
PCDHGA7 WILD-TYPE	7	27	17	164

'PCDHGA7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S227. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
PCDHGA7 MUTATED	0	0	0	2	3
PCDHGA7 WILD-TYPE	1	5	1	87	121

'PCDHGA7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S228. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PCDHGA7 MUTATED	0	0	4
PCDHGA7 WILD-TYPE	3	9	190

'PCDHGA7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S229. Gene #26: 'PCDHGA7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
PCDHGA7 MUTATED	0	2	2
PCDHGA7 WILD-TYPE	7	60	135

'CCBP2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 1

Table S230. Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
CCBP2 MUTATED	3	2	1	4
CCBP2 WILD-TYPE	39	55	66	35

'CCBP2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 1

Table S231. Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
CCBP2 MUTATED	3	0	7	0
CCBP2 WILD-TYPE	45	37	66	47

Figure S54. Get High-res Image Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CCBP2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S232. Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
CCBP2 MUTATED	6	3	1	0
CCBP2 WILD-TYPE	73	87	38	12

'CCBP2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.072 (Fisher's exact test), Q value = 1

Table S233. Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
CCBP2 MUTATED	2	2	0	4
CCBP2 WILD-TYPE	38	65	24	22

'CCBP2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S234. Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
CCBP2 MUTATED	0	7	1
CCBP2 WILD-TYPE	11	119	19

'CCBP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S235. Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
CCBP2 MUTATED	0	3	0	7
CCBP2 WILD-TYPE	7	25	17	161

'CCBP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S236. Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
CCBP2 MUTATED	0	0	0	6	4
CCBP2 WILD-TYPE	1	5	1	83	120

'CCBP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S237. Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
CCBP2 MUTATED	0	0	9
CCBP2 WILD-TYPE	3	9	185

'CCBP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S238. Gene #27: 'CCBP2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
CCBP2 MUTATED	1	2	6
CCBP2 WILD-TYPE	6	60	131

'MAP2K4 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S239. Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
MAP2K4 MUTATED	3	1	4	3
MAP2K4 WILD-TYPE	39	56	63	36

'MAP2K4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S240. Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
MAP2K4 MUTATED	5	1	3	2
MAP2K4 WILD-TYPE	43	36	70	45

'MAP2K4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0874 (Fisher's exact test), Q value = 1

Table S241. Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
MAP2K4 MUTATED	8	3	0	0
MAP2K4 WILD-TYPE	71	87	39	12

'MAP2K4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.1 (Fisher's exact test), Q value = 1

Table S242. Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
MAP2K4 MUTATED	1	4	0	4
MAP2K4 WILD-TYPE	39	63	24	22

'MAP2K4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S243. Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
MAP2K4 MUTATED	0	7	2
MAP2K4 WILD-TYPE	11	119	18

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.426 (Fisher's exact test), Q value = 1

Table S244. Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
MAP2K4 MUTATED	0	3	0	8
MAP2K4 WILD-TYPE	7	25	17	160

'MAP2K4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S245. Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
MAP2K4 MUTATED	0	0	0	6	5
MAP2K4 WILD-TYPE	1	5	1	83	119

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S246. Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
MAP2K4 MUTATED	0	0	9
MAP2K4 WILD-TYPE	3	9	185

'MAP2K4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 1

Table S247. Gene #28: 'MAP2K4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
MAP2K4 MUTATED	1	2	6
MAP2K4 WILD-TYPE	6	60	131

'PCDHGA9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0681 (Fisher's exact test), Q value = 1

Table S248. Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PCDHGA9 MUTATED	2	1	0	3
PCDHGA9 WILD-TYPE	40	56	67	36

'PCDHGA9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0786 (Fisher's exact test), Q value = 1

Table S249. Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
PCDHGA9 MUTATED	4	1	1	0
PCDHGA9 WILD-TYPE	44	36	72	47

'PCDHGA9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 1

Table S250. Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
PCDHGA9 MUTATED	3	0	1	2
PCDHGA9 WILD-TYPE	76	90	38	10

Figure S55. Get High-res Image Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PCDHGA9 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S251. Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
PCDHGA9 MUTATED	1	1	1	1
PCDHGA9 WILD-TYPE	39	66	23	25

'PCDHGA9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S252. Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
PCDHGA9 MUTATED	0	3	1
PCDHGA9 WILD-TYPE	11	123	19

'PCDHGA9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S253. Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
PCDHGA9 MUTATED	0	2	0	4
PCDHGA9 WILD-TYPE	7	26	17	164

'PCDHGA9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S254. Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
PCDHGA9 MUTATED	0	0	0	5	1
PCDHGA9 WILD-TYPE	1	5	1	84	123

'PCDHGA9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S255. Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PCDHGA9 MUTATED	0	0	6
PCDHGA9 WILD-TYPE	3	9	188

'PCDHGA9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S256. Gene #29: 'PCDHGA9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
PCDHGA9 MUTATED	0	1	5
PCDHGA9 WILD-TYPE	7	61	132

'RBM10 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 1

Table S257. Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
RBM10 MUTATED	2	1	1	3
RBM10 WILD-TYPE	40	56	66	36

'RBM10 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S258. Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
RBM10 MUTATED	3	1	2	1
RBM10 WILD-TYPE	45	36	71	46

'RBM10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S259. Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
RBM10 MUTATED	4	2	2	0
RBM10 WILD-TYPE	75	88	37	12

'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 1

Table S260. Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
RBM10 MUTATED	0	4	0	2
RBM10 WILD-TYPE	40	63	24	24

'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S261. Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
RBM10 MUTATED	0	5	1
RBM10 WILD-TYPE	11	121	19

'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S262. Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
RBM10 MUTATED	0	1	0	6
RBM10 WILD-TYPE	7	27	17	162

'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S263. Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
RBM10 MUTATED	0	1	0	4	2
RBM10 WILD-TYPE	1	4	1	85	122

'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S264. Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
RBM10 MUTATED	0	0	8
RBM10 WILD-TYPE	3	9	186

'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S265. Gene #30: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
RBM10 MUTATED	0	2	6
RBM10 WILD-TYPE	7	60	131

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 1

Table S266. Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PTEN MUTATED	2	0	1	4
PTEN WILD-TYPE	40	57	66	35

Figure S56. Get High-res Image Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S267. Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
PTEN MUTATED	3	1	3	0
PTEN WILD-TYPE	45	36	70	47

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 1

Table S268. Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
PTEN MUTATED	6	0	1	0
PTEN WILD-TYPE	73	90	38	12

Figure S57. Get High-res Image Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S269. Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
PTEN MUTATED	2	1	0	1
PTEN WILD-TYPE	38	66	24	25

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S270. Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
PTEN MUTATED	0	4	0
PTEN WILD-TYPE	11	122	20

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0987 (Fisher's exact test), Q value = 1

Table S271. Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
PTEN MUTATED	1	2	0	4
PTEN WILD-TYPE	6	26	17	164

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 1

Table S272. Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
PTEN MUTATED	0	0	0	7	0
PTEN WILD-TYPE	1	5	1	82	124

Figure S58. Get High-res Image Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S273. Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PTEN MUTATED	0	1	6
PTEN WILD-TYPE	3	8	188

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 1

Table S274. Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
PTEN MUTATED	2	1	4
PTEN WILD-TYPE	5	61	133

Figure S59. Get High-res Image Gene #31: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'DNMT1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 1

Table S275. Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
DNMT1 MUTATED	4	2	2	7
DNMT1 WILD-TYPE	38	55	65	32

Figure S60. Get High-res Image Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'DNMT1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0657 (Fisher's exact test), Q value = 1

Table S276. Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
DNMT1 MUTATED	8	1	3	3
DNMT1 WILD-TYPE	40	36	70	44

'DNMT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 1

Table S277. Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
DNMT1 MUTATED	11	5	1	0
DNMT1 WILD-TYPE	68	85	38	12

'DNMT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0541 (Fisher's exact test), Q value = 1

Table S278. Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
DNMT1 MUTATED	2	4	1	6
DNMT1 WILD-TYPE	38	63	23	20

'DNMT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S279. Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
DNMT1 MUTATED	1	9	3
DNMT1 WILD-TYPE	10	117	17

'DNMT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S280. Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
DNMT1 MUTATED	0	4	0	12
DNMT1 WILD-TYPE	7	24	17	156

'DNMT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0365 (Fisher's exact test), Q value = 1

Table S281. Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
DNMT1 MUTATED	0	1	0	11	4
DNMT1 WILD-TYPE	1	4	1	78	120

Figure S61. Get High-res Image Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'DNMT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S282. Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
DNMT1 MUTATED	0	0	15
DNMT1 WILD-TYPE	3	9	179

'DNMT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0702 (Fisher's exact test), Q value = 1

Table S283. Gene #32: 'DNMT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
DNMT1 MUTATED	1	1	13
DNMT1 WILD-TYPE	6	61	124

'BCOR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 1

Table S284. Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
BCOR MUTATED	3	0	1	4
BCOR WILD-TYPE	39	57	66	35

Figure S62. Get High-res Image Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BCOR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S285. Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
BCOR MUTATED	4	1	1	2
BCOR WILD-TYPE	44	36	72	45

'BCOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00635 (Fisher's exact test), Q value = 1

Table S286. Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
BCOR MUTATED	8	0	1	0
BCOR WILD-TYPE	71	90	38	12

Figure S63. Get High-res Image Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BCOR MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S287. Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
BCOR MUTATED	1	5	0	2
BCOR WILD-TYPE	39	62	24	24

'BCOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S288. Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
BCOR MUTATED	0	7	1
BCOR WILD-TYPE	11	119	19

'BCOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S289. Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
BCOR MUTATED	0	2	0	7
BCOR WILD-TYPE	7	26	17	161

'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S290. Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
BCOR MUTATED	0	0	0	7	2
BCOR WILD-TYPE	1	5	1	82	122

'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S291. Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
BCOR MUTATED	0	0	8
BCOR WILD-TYPE	3	9	186

'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 1

Table S292. Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
BCOR MUTATED	2	1	5
BCOR WILD-TYPE	5	61	132

Figure S64. Get High-res Image Gene #33: 'BCOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PCDHGB5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.1 (Fisher's exact test), Q value = 1

Table S293. Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PCDHGB5 MUTATED	2	2	0	3
PCDHGB5 WILD-TYPE	40	55	67	36

'PCDHGB5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0726 (Fisher's exact test), Q value = 1

Table S294. Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
PCDHGB5 MUTATED	4	2	1	0
PCDHGB5 WILD-TYPE	44	35	72	47

'PCDHGB5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S295. Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
PCDHGB5 MUTATED	5	1	1	0
PCDHGB5 WILD-TYPE	74	89	38	12

'PCDHGB5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S296. Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
PCDHGB5 MUTATED	2	3	0	1
PCDHGB5 WILD-TYPE	38	64	24	25

'PCDHGB5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.739 (Fisher's exact test), Q value = 1

Table S297. Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
PCDHGB5 MUTATED	0	5	1
PCDHGB5 WILD-TYPE	11	121	19

'PCDHGB5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0697 (Fisher's exact test), Q value = 1

Table S298. Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
PCDHGB5 MUTATED	0	2	2	3
PCDHGB5 WILD-TYPE	7	26	15	165

'PCDHGB5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S299. Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
PCDHGB5 MUTATED	0	0	0	4	3
PCDHGB5 WILD-TYPE	1	5	1	85	121

'PCDHGB5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S300. Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PCDHGB5 MUTATED	0	0	5
PCDHGB5 WILD-TYPE	3	9	189

'PCDHGB5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S301. Gene #34: 'PCDHGB5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
PCDHGB5 MUTATED	0	1	4
PCDHGB5 WILD-TYPE	7	61	133

'ZFP3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.19

Table S302. Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ZFP3 MUTATED	3	0	0	5
ZFP3 WILD-TYPE	39	57	67	34

Figure S65. Get High-res Image Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ZFP3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0575 (Fisher's exact test), Q value = 1

Table S303. Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
ZFP3 MUTATED	5	1	2	0
ZFP3 WILD-TYPE	43	36	71	47

'ZFP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00254 (Fisher's exact test), Q value = 0.95

Table S304. Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
ZFP3 MUTATED	8	0	0	0
ZFP3 WILD-TYPE	71	90	39	12

Figure S66. Get High-res Image Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZFP3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S305. Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ZFP3 MUTATED	0	3	1	2
ZFP3 WILD-TYPE	40	64	23	24

'ZFP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S306. Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
ZFP3 MUTATED	0	5	1
ZFP3 WILD-TYPE	11	121	19

'ZFP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S307. Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
ZFP3 MUTATED	0	3	0	5
ZFP3 WILD-TYPE	7	25	17	163

'ZFP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00475 (Fisher's exact test), Q value = 1

Table S308. Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
ZFP3 MUTATED	0	0	0	8	0
ZFP3 WILD-TYPE	1	5	1	81	124

Figure S67. Get High-res Image Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ZFP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S309. Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ZFP3 MUTATED	0	0	8
ZFP3 WILD-TYPE	3	9	186

'ZFP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00737 (Fisher's exact test), Q value = 1

Table S310. Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
ZFP3 MUTATED	2	0	6
ZFP3 WILD-TYPE	5	62	131

Figure S68. Get High-res Image Gene #35: 'ZFP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RWDD2B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 1

Table S311. Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
RWDD2B MUTATED	4	1	0	2
RWDD2B WILD-TYPE	38	56	67	37

Figure S69. Get High-res Image Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'RWDD2B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S312. Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
RWDD2B MUTATED	3	1	2	1
RWDD2B WILD-TYPE	45	36	71	46

'RWDD2B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 1

Table S313. Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
RWDD2B MUTATED	6	0	1	0
RWDD2B WILD-TYPE	73	90	38	12

Figure S70. Get High-res Image Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'RWDD2B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S314. Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
RWDD2B MUTATED	1	1	0	1
RWDD2B WILD-TYPE	39	66	24	25

'RWDD2B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S315. Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
RWDD2B MUTATED	0	2	1
RWDD2B WILD-TYPE	11	124	19

'RWDD2B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S316. Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
RWDD2B MUTATED	0	1	0	6
RWDD2B WILD-TYPE	7	27	17	162

'RWDD2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 1

Table S317. Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
RWDD2B MUTATED	0	0	0	5	2
RWDD2B WILD-TYPE	1	5	1	84	122

'RWDD2B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S318. Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
RWDD2B MUTATED	0	0	6
RWDD2B WILD-TYPE	3	9	188

'RWDD2B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.2

Table S319. Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
RWDD2B MUTATED	3	1	2
RWDD2B WILD-TYPE	4	61	135

Figure S71. Get High-res Image Gene #36: 'RWDD2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TBC1D10C MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S320. Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
TBC1D10C MUTATED	1	0	1	1
TBC1D10C WILD-TYPE	41	57	66	38

'TBC1D10C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S321. Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
TBC1D10C MUTATED	2	0	0	1
TBC1D10C WILD-TYPE	46	37	73	46

'TBC1D10C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S322. Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
TBC1D10C MUTATED	2	1	0	0
TBC1D10C WILD-TYPE	77	89	39	12

'TBC1D10C MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S323. Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
TBC1D10C MUTATED	0	0	0	3
TBC1D10C WILD-TYPE	7	28	17	165

'TBC1D10C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S324. Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
TBC1D10C MUTATED	0	0	0	2	1
TBC1D10C WILD-TYPE	1	5	1	87	123

'TBC1D10C MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S325. Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
TBC1D10C MUTATED	0	0	3
TBC1D10C WILD-TYPE	3	9	191

'TBC1D10C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S326. Gene #37: 'TBC1D10C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
TBC1D10C MUTATED	0	0	3
TBC1D10C WILD-TYPE	7	62	134

'ERCC6L MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.005 (Fisher's exact test), Q value = 1

Table S327. Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ERCC6L MUTATED	4	0	0	1
ERCC6L WILD-TYPE	38	57	67	38

Figure S72. Get High-res Image Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ERCC6L MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S328. Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
ERCC6L MUTATED	2	0	1	2
ERCC6L WILD-TYPE	46	37	72	45

'ERCC6L MUTATION STATUS' versus 'CN_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 1

Table S329. Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
ERCC6L MUTATED	4	1	0	0
ERCC6L WILD-TYPE	75	89	39	12

'ERCC6L MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 1

Table S330. Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
ERCC6L MUTATED	0	1	0	4
ERCC6L WILD-TYPE	7	27	17	164

'ERCC6L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S331. Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
ERCC6L MUTATED	0	0	0	3	2
ERCC6L WILD-TYPE	1	5	1	86	122

'ERCC6L MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S332. Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ERCC6L MUTATED	0	0	5
ERCC6L WILD-TYPE	3	9	189

'ERCC6L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S333. Gene #38: 'ERCC6L MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
ERCC6L MUTATED	1	1	3
ERCC6L WILD-TYPE	6	61	134

'ERBB3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S334. Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ERBB3 MUTATED	5	3	1	2
ERBB3 WILD-TYPE	37	54	66	37

'ERBB3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 1

Table S335. Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
ERBB3 MUTATED	6	1	4	0
ERBB3 WILD-TYPE	42	36	69	47

Figure S73. Get High-res Image Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 1

Table S336. Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
ERBB3 MUTATED	9	3	1	1
ERBB3 WILD-TYPE	70	87	38	11

'ERBB3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 1

Table S337. Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ERBB3 MUTATED	2	6	1	3
ERBB3 WILD-TYPE	38	61	23	23

'ERBB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S338. Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
ERBB3 MUTATED	0	10	2
ERBB3 WILD-TYPE	11	116	18

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.844 (Fisher's exact test), Q value = 1

Table S339. Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
ERBB3 MUTATED	0	2	0	11
ERBB3 WILD-TYPE	7	26	17	157

'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S340. Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
ERBB3 MUTATED	0	0	0	9	4
ERBB3 WILD-TYPE	1	5	1	80	120

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S341. Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ERBB3 MUTATED	0	0	12
ERBB3 WILD-TYPE	3	9	182

'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0538 (Fisher's exact test), Q value = 1

Table S342. Gene #39: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
ERBB3 MUTATED	2	4	6
ERBB3 WILD-TYPE	5	58	131

'KLK2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S343. Gene #40: 'KLK2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
KLK2 MUTATED	1	1	0	1
KLK2 WILD-TYPE	41	56	67	38

'KLK2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S344. Gene #40: 'KLK2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
KLK2 MUTATED	2	1	0	0
KLK2 WILD-TYPE	46	36	73	47

'KLK2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S345. Gene #40: 'KLK2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
KLK2 MUTATED	2	1	0	0
KLK2 WILD-TYPE	77	89	39	12

'KLK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S346. Gene #40: 'KLK2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
KLK2 MUTATED	0	0	0	3
KLK2 WILD-TYPE	7	28	17	165

'KLK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.611 (Fisher's exact test), Q value = 1

Table S347. Gene #40: 'KLK2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
KLK2 MUTATED	0	0	0	2	1
KLK2 WILD-TYPE	1	5	1	87	123

'TAPBP MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 1

Table S348. Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
TAPBP MUTATED	1	0	1	3
TAPBP WILD-TYPE	41	57	66	36

'TAPBP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S349. Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
TAPBP MUTATED	2	1	2	0
TAPBP WILD-TYPE	46	36	71	47

'TAPBP MUTATION STATUS' versus 'CN_CNMF'

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

Table S350. Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
TAPBP MUTATED	4	1	0	0
TAPBP WILD-TYPE	75	89	39	12

'TAPBP MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S351. Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
TAPBP MUTATED	1	2	0	1
TAPBP WILD-TYPE	39	65	24	25

'TAPBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S352. Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
TAPBP MUTATED	1	2	1
TAPBP WILD-TYPE	10	124	19

'TAPBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S353. Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
TAPBP MUTATED	0	2	0	3
TAPBP WILD-TYPE	7	26	17	165

'TAPBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S354. Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
TAPBP MUTATED	0	0	0	4	1
TAPBP WILD-TYPE	1	5	1	85	123

'TAPBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S355. Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
TAPBP MUTATED	0	0	5
TAPBP WILD-TYPE	3	9	189

'TAPBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 1

Table S356. Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
TAPBP MUTATED	2	1	2
TAPBP WILD-TYPE	5	61	135

Figure S74. Get High-res Image Gene #41: 'TAPBP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ERBB2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S357. Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ERBB2 MUTATED	3	1	2	3
ERBB2 WILD-TYPE	39	56	65	36

'ERBB2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S358. Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
ERBB2 MUTATED	4	1	4	0
ERBB2 WILD-TYPE	44	36	69	47

'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 1

Table S359. Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
ERBB2 MUTATED	5	2	1	1
ERBB2 WILD-TYPE	74	88	38	11

'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0743 (Fisher's exact test), Q value = 1

Table S360. Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ERBB2 MUTATED	3	1	0	3
ERBB2 WILD-TYPE	37	66	24	23

'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.283 (Fisher's exact test), Q value = 1

Table S361. Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
ERBB2 MUTATED	0	5	2
ERBB2 WILD-TYPE	11	121	18

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S362. Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
ERBB2 MUTATED	0	3	0	6
ERBB2 WILD-TYPE	7	25	17	162

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0789 (Fisher's exact test), Q value = 1

Table S363. Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
ERBB2 MUTATED	0	1	0	6	2
ERBB2 WILD-TYPE	1	4	1	83	122

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S364. Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ERBB2 MUTATED	0	1	7
ERBB2 WILD-TYPE	3	8	187

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.116 (Fisher's exact test), Q value = 1

Table S365. Gene #42: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
ERBB2 MUTATED	0	0	8
ERBB2 WILD-TYPE	7	62	129

'MORC2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 1

Table S366. Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
MORC2 MUTATED	2	1	0	2
MORC2 WILD-TYPE	40	56	67	37

'MORC2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S367. Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
MORC2 MUTATED	2	1	2	0
MORC2 WILD-TYPE	46	36	71	47

'MORC2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S368. Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
MORC2 MUTATED	4	1	0	0
MORC2 WILD-TYPE	75	89	39	12

'MORC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S369. Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
MORC2 MUTATED	0	1	0	2
MORC2 WILD-TYPE	40	66	24	24

'MORC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S370. Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
MORC2 MUTATED	0	2	1
MORC2 WILD-TYPE	11	124	19

'MORC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S371. Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
MORC2 MUTATED	0	1	0	4
MORC2 WILD-TYPE	7	27	17	164

'MORC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 1

Table S372. Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
MORC2 MUTATED	0	0	0	4	1
MORC2 WILD-TYPE	1	5	1	85	123

'MORC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S373. Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
MORC2 MUTATED	0	0	4
MORC2 WILD-TYPE	3	9	190

'MORC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S374. Gene #43: 'MORC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
MORC2 MUTATED	1	1	2
MORC2 WILD-TYPE	6	61	135

'ABCA8 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.58

Table S375. Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ABCA8 MUTATED	7	2	0	3
ABCA8 WILD-TYPE	35	55	67	36

Figure S75. Get High-res Image Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ABCA8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 1

Table S376. Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
ABCA8 MUTATED	7	2	1	2
ABCA8 WILD-TYPE	41	35	72	45

Figure S76. Get High-res Image Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ABCA8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 1

Table S377. Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
ABCA8 MUTATED	10	2	0	0
ABCA8 WILD-TYPE	69	88	39	12

Figure S77. Get High-res Image Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ABCA8 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S378. Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ABCA8 MUTATED	2	1	0	4
ABCA8 WILD-TYPE	38	66	24	22

Figure S78. Get High-res Image Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'ABCA8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S379. Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
ABCA8 MUTATED	0	5	2
ABCA8 WILD-TYPE	11	121	18

'ABCA8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 1

Table S380. Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
ABCA8 MUTATED	1	1	0	10
ABCA8 WILD-TYPE	6	27	17	158

'ABCA8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S381. Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
ABCA8 MUTATED	0	0	0	9	3
ABCA8 WILD-TYPE	1	5	1	80	121

'ABCA8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S382. Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ABCA8 MUTATED	0	1	10
ABCA8 WILD-TYPE	3	8	184

'ABCA8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 1

Table S383. Gene #44: 'ABCA8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
ABCA8 MUTATED	1	2	8
ABCA8 WILD-TYPE	6	60	129

'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 1

Table S384. Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
SETD2 MUTATED	5	1	2	5
SETD2 WILD-TYPE	37	56	65	34

Figure S79. Get High-res Image Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S385. Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
SETD2 MUTATED	6	1	5	1
SETD2 WILD-TYPE	42	36	68	46

'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.4

Table S386. Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
SETD2 MUTATED	11	1	0	1
SETD2 WILD-TYPE	68	89	39	11

Figure S80. Get High-res Image Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0937 (Fisher's exact test), Q value = 1

Table S387. Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
SETD2 MUTATED	0	2	1	3
SETD2 WILD-TYPE	40	65	23	23

'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S388. Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
SETD2 MUTATED	0	5	1
SETD2 WILD-TYPE	11	121	19

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0653 (Fisher's exact test), Q value = 1

Table S389. Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
SETD2 MUTATED	0	5	0	8
SETD2 WILD-TYPE	7	23	17	160

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0175 (Fisher's exact test), Q value = 1

Table S390. Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
SETD2 MUTATED	0	0	0	11	2
SETD2 WILD-TYPE	1	5	1	78	122

Figure S81. Get High-res Image Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S391. Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
SETD2 MUTATED	0	0	11
SETD2 WILD-TYPE	3	9	183

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S392. Gene #45: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
SETD2 MUTATED	1	3	7
SETD2 WILD-TYPE	6	59	130

'ESR1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S393. Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ESR1 MUTATED	3	1	2	4
ESR1 WILD-TYPE	39	56	65	35

'ESR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 1

Table S394. Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	48	37	73	47
ESR1 MUTATED	6	2	0	2
ESR1 WILD-TYPE	42	35	73	45

Figure S82. Get High-res Image Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ESR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 1

Table S395. Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	90	39	12
ESR1 MUTATED	8	1	2	0
ESR1 WILD-TYPE	71	89	37	12

Figure S83. Get High-res Image Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ESR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S396. Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ESR1 MUTATED	2	2	1	2
ESR1 WILD-TYPE	38	65	23	24

'ESR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S397. Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	126	20
ESR1 MUTATED	0	5	2
ESR1 WILD-TYPE	11	121	18

'ESR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S398. Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	28	17	168
ESR1 MUTATED	0	2	0	9
ESR1 WILD-TYPE	7	26	17	159

'ESR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 1

Table S399. Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_5	CLUS_6	CLUS_7
ALL	1	5	1	89	124
ESR1 MUTATED	0	0	0	8	3
ESR1 WILD-TYPE	1	5	1	81	121

'ESR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S400. Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ESR1 MUTATED	0	0	9
ESR1 WILD-TYPE	3	9	185

'ESR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 1

Table S401. Gene #46: 'ESR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	7	62	137
ESR1 MUTATED	1	1	7
ESR1 WILD-TYPE	6	61	130

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = COADREAD-TP.transferedmergedcluster.txt
Number of patients = 223
Number of significantly mutated genes = 46
Number of Molecular subtypes = 10
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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