Correlation between gene mutation status and molecular subtypes

Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1DR2T02

Overview

Introduction

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

Summary

Testing the association between mutation status of 33 genes and 12 molecular subtypes across 248 patients, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

CTNNB1 mutation correlated to 'MRNA_CNMF', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
PIK3R1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
PTEN mutation correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
KRAS mutation correlated to 'MRNA_CHIERARCHICAL' and 'MIRSEQ_CNMF'.
TP53 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
CTCF mutation correlated to 'CN_CNMF'.
ARID1A mutation correlated to 'CN_CNMF'.
RNF43 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 33 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 36 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
TP53	69 (28%)	179	3.76e-05 (0.0131)	2.45e-07 (8.74e-05)	4.35e-30 (1.64e-27)	2.53e-12 (9.2e-10)	2.01e-05 (0.00706)	0.0014 (0.469)	4.09e-24 (1.53e-21)	6.53e-21 (2.44e-18)	3.53e-17 (1.3e-14)	1.52e-13 (5.55e-11)	6.65e-09 (2.38e-06)	1.24e-09 (4.45e-07)
PTEN	161 (65%)	87	0.00442 (1.00)	0.000362 (0.125)	1.82e-20 (6.75e-18)	1.79e-12 (6.52e-10)	0.0257 (1.00)	0.183 (1.00)	4.45e-21 (1.66e-18)	2.86e-17 (1.06e-14)	7.65e-16 (2.81e-13)	1.44e-13 (5.26e-11)	5.35e-09 (1.92e-06)	8.55e-14 (3.14e-11)
CTNNB1	74 (30%)	174	5.68e-07 (0.000202)	0.00115 (0.389)	8.75e-06 (0.00309)	0.00315 (1.00)	1.29e-10 (4.65e-08)	0.112 (1.00)	1.4e-20 (5.2e-18)	3.02e-06 (0.00107)	1.98e-11 (7.16e-09)	0.138 (1.00)	0.0232 (1.00)	0.00379 (1.00)
PIK3R1	83 (33%)	165	0.0669 (1.00)	0.0218 (1.00)	0.000523 (0.18)	3.32e-05 (0.0116)	0.649 (1.00)	0.877 (1.00)	0.000113 (0.0391)	2.24e-05 (0.00787)	0.0133 (1.00)	0.146 (1.00)	0.0126 (1.00)	0.000575 (0.197)
KRAS	53 (21%)	195	0.203 (1.00)	0.000649 (0.221)	0.00606 (1.00)	0.123 (1.00)	0.297 (1.00)	0.855 (1.00)	0.00755 (1.00)	0.0376 (1.00)	0.000628 (0.215)	0.564 (1.00)	0.143 (1.00)	0.457 (1.00)
CTCF	44 (18%)	204	0.149 (1.00)	0.421 (1.00)	0.000441 (0.152)	0.0433 (1.00)	0.0458 (1.00)	1 (1.00)	0.000834 (0.284)	0.00121 (0.411)	0.00949 (1.00)	0.00316 (1.00)	0.00792 (1.00)	0.103 (1.00)
ARID1A	83 (33%)	165	0.266 (1.00)	0.011 (1.00)	7.11e-07 (0.000252)	0.227 (1.00)	0.0271 (1.00)	1 (1.00)	0.00267 (0.888)	0.0452 (1.00)	0.0226 (1.00)	0.053 (1.00)	0.0664 (1.00)	0.0139 (1.00)
RNF43	12 (5%)	236	0.133 (1.00)	0.151 (1.00)	0.443 (1.00)	0.377 (1.00)	0.296 (1.00)	1 (1.00)	0.032 (1.00)	2.55e-05 (0.00892)	0.129 (1.00)	0.445 (1.00)	0.349 (1.00)	0.484 (1.00)
PPP2R1A	27 (11%)	221	0.076 (1.00)	0.0518 (1.00)	0.0121 (1.00)	0.0129 (1.00)	0.141 (1.00)	0.313 (1.00)	0.00577 (1.00)	0.00531 (1.00)	0.0257 (1.00)	0.0356 (1.00)	0.0673 (1.00)	0.0127 (1.00)
PIK3CA	132 (53%)	116	0.834 (1.00)	0.198 (1.00)	0.475 (1.00)	0.677 (1.00)	0.366 (1.00)	0.365 (1.00)	0.148 (1.00)	0.989 (1.00)	0.746 (1.00)	0.32 (1.00)	0.41 (1.00)	0.753 (1.00)
PRKAR1B	4 (2%)	244			0.988 (1.00)	0.509 (1.00)	0.887 (1.00)	1 (1.00)	0.387 (1.00)	0.262 (1.00)	0.482 (1.00)	0.37 (1.00)	0.797 (1.00)	0.155 (1.00)
FBXW7	39 (16%)	209	0.225 (1.00)	0.692 (1.00)	0.343 (1.00)	0.0757 (1.00)	0.106 (1.00)	0.107 (1.00)	0.0237 (1.00)	0.0148 (1.00)	0.135 (1.00)	0.104 (1.00)	0.351 (1.00)	0.0228 (1.00)
SPOP	21 (8%)	227	0.349 (1.00)	1 (1.00)	0.85 (1.00)	0.356 (1.00)	0.834 (1.00)	0.415 (1.00)	0.352 (1.00)	0.362 (1.00)	0.0343 (1.00)	0.462 (1.00)	0.61 (1.00)	0.692 (1.00)
ARID5B	29 (12%)	219	0.961 (1.00)	0.459 (1.00)	0.0427 (1.00)	0.136 (1.00)	0.164 (1.00)	0.182 (1.00)	0.0531 (1.00)	0.0676 (1.00)	0.0452 (1.00)	0.346 (1.00)	0.263 (1.00)	0.724 (1.00)
FGFR2	31 (12%)	217	0.385 (1.00)	0.293 (1.00)	0.611 (1.00)	0.914 (1.00)	0.97 (1.00)	0.829 (1.00)	0.527 (1.00)	0.565 (1.00)	0.876 (1.00)	0.59 (1.00)	0.644 (1.00)	0.82 (1.00)
NFE2L2	15 (6%)	233	0.0905 (1.00)	0.833 (1.00)	0.00636 (1.00)	0.631 (1.00)	0.248 (1.00)	1 (1.00)	0.0134 (1.00)	0.574 (1.00)	0.392 (1.00)	0.775 (1.00)	0.263 (1.00)	0.724 (1.00)
CCND1	14 (6%)	234	0.631 (1.00)	0.833 (1.00)	0.154 (1.00)	0.495 (1.00)	0.514 (1.00)	0.509 (1.00)	0.635 (1.00)	0.269 (1.00)	0.124 (1.00)	0.612 (1.00)	0.439 (1.00)	0.853 (1.00)
CHD4	35 (14%)	213	0.0986 (1.00)	0.284 (1.00)	0.776 (1.00)	0.852 (1.00)	0.97 (1.00)	0.287 (1.00)	0.872 (1.00)	0.479 (1.00)	0.739 (1.00)	0.59 (1.00)	0.405 (1.00)	0.97 (1.00)
FAM9A	14 (6%)	234			0.887 (1.00)	0.27 (1.00)	0.178 (1.00)	0.0227 (1.00)	0.0562 (1.00)	0.065 (1.00)	0.308 (1.00)	0.0424 (1.00)	0.0237 (1.00)	0.149 (1.00)
MORC4	20 (8%)	228	0.583 (1.00)	0.18 (1.00)	0.34 (1.00)	0.28 (1.00)	0.212 (1.00)	0.0332 (1.00)	0.00821 (1.00)	0.266 (1.00)	0.315 (1.00)	0.19 (1.00)	0.322 (1.00)	0.0396 (1.00)
CASP8	17 (7%)	231	0.381 (1.00)	0.0595 (1.00)	0.204 (1.00)	0.626 (1.00)	0.154 (1.00)	0.269 (1.00)	0.375 (1.00)	0.126 (1.00)	0.152 (1.00)	0.189 (1.00)	0.367 (1.00)	0.91 (1.00)
FOXA2	12 (5%)	236			0.304 (1.00)	0.795 (1.00)	0.0719 (1.00)	0.744 (1.00)	0.506 (1.00)	0.589 (1.00)	0.0582 (1.00)	0.8 (1.00)	0.681 (1.00)	0.332 (1.00)
ABI1	4 (2%)	244			0.821 (1.00)		0.64 (1.00)	0.637 (1.00)	0.681 (1.00)	0.262 (1.00)	0.687 (1.00)	0.655 (1.00)
DNER	18 (7%)	230	0.191 (1.00)	0.0515 (1.00)	0.013 (1.00)	0.597 (1.00)	0.0217 (1.00)	0.581 (1.00)	0.126 (1.00)	0.0936 (1.00)	0.785 (1.00)	0.153 (1.00)	0.681 (1.00)	0.91 (1.00)
BCOR	30 (12%)	218	0.687 (1.00)	0.405 (1.00)	0.00577 (1.00)	0.0246 (1.00)	0.512 (1.00)	0.5 (1.00)	0.00134 (0.451)	0.323 (1.00)	0.0495 (1.00)	0.0922 (1.00)	0.866 (1.00)	0.176 (1.00)
BRS3	15 (6%)	233	0.536 (1.00)	0.151 (1.00)	0.339 (1.00)	0.519 (1.00)	0.392 (1.00)	0.54 (1.00)	0.108 (1.00)	0.00295 (0.98)	0.393 (1.00)	0.00527 (1.00)	0.562 (1.00)	0.343 (1.00)
SGK1	15 (6%)	233	0.381 (1.00)	0.0595 (1.00)	0.43 (1.00)	0.625 (1.00)	0.226 (1.00)	0.0954 (1.00)	0.0301 (1.00)	0.893 (1.00)	0.431 (1.00)	1 (1.00)	0.687 (1.00)	0.853 (1.00)
NRAS	9 (4%)	239			0.749 (1.00)		0.316 (1.00)	1 (1.00)	0.56 (1.00)	0.908 (1.00)	0.604 (1.00)	0.213 (1.00)
TIAL1	11 (4%)	237	0.381 (1.00)	0.405 (1.00)	0.362 (1.00)	0.0634 (1.00)	0.564 (1.00)	0.744 (1.00)	0.00545 (1.00)	0.0128 (1.00)	0.812 (1.00)	1 (1.00)	0.477 (1.00)	0.724 (1.00)
SIN3A	21 (8%)	227			0.0266 (1.00)	0.598 (1.00)	0.00607 (1.00)	0.129 (1.00)	0.00261 (0.873)	0.0226 (1.00)	0.16 (1.00)	0.00595 (1.00)	0.517 (1.00)	0.465 (1.00)
SLC48A1	5 (2%)	243			0.736 (1.00)	0.639 (1.00)	0.803 (1.00)	0.372 (1.00)	0.876 (1.00)	0.849 (1.00)	0.726 (1.00)	0.686 (1.00)	0.797 (1.00)	0.458 (1.00)
ZFHX3	44 (18%)	204	0.375 (1.00)	0.0291 (1.00)	0.094 (1.00)	0.0648 (1.00)	0.318 (1.00)	0.179 (1.00)	0.592 (1.00)	0.115 (1.00)	0.207 (1.00)	0.614 (1.00)	0.847 (1.00)	0.526 (1.00)
RB1	20 (8%)	228	0.639 (1.00)	1 (1.00)	0.31 (1.00)	0.626 (1.00)	0.12 (1.00)	0.313 (1.00)	0.583 (1.00)	0.271 (1.00)	0.955 (1.00)	0.00126 (0.425)	0.854 (1.00)	1 (1.00)

'PPP2R1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.076 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
PPP2R1A MUTATED	3	5	0	0
PPP2R1A WILD-TYPE	9	13	11	10

'PPP2R1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0518 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
PPP2R1A MUTATED	4	0	4
PPP2R1A WILD-TYPE	13	18	12

'PPP2R1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0121 (Chi-square test), Q value = 1

Table S3. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
PPP2R1A MUTATED	11	0	12	2	0	0
PPP2R1A WILD-TYPE	146	12	42	6	10	1

Figure S1. Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PPP2R1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 1

Table S4. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
PPP2R1A MUTATED	10	1	5
PPP2R1A WILD-TYPE	33	40	46

Figure S2. Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PPP2R1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.141 (Chi-square test), Q value = 1

Table S5. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
PPP2R1A MUTATED	3	7	2	0	2	4
PPP2R1A WILD-TYPE	36	29	35	10	38	20

'PPP2R1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
PPP2R1A MUTATED	9	9
PPP2R1A WILD-TYPE	106	62

'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00577 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
PPP2R1A MUTATED	15	2	6	4
PPP2R1A WILD-TYPE	48	34	66	70

Figure S3. Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00531 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
PPP2R1A MUTATED	17	4	6
PPP2R1A WILD-TYPE	68	44	106

Figure S4. Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0257 (Chi-square test), Q value = 1

Table S9. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
PPP2R1A MUTATED	10	4	3	2	6
PPP2R1A WILD-TYPE	32	74	20	24	65

Figure S5. Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 1

Table S10. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
PPP2R1A MUTATED	0	8	17
PPP2R1A WILD-TYPE	4	123	88

Figure S6. Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 1

Table S11. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
PPP2R1A MUTATED	9	3	4
PPP2R1A WILD-TYPE	27	23	50

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 1

Table S12. Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
PPP2R1A MUTATED	6	6	4	0
PPP2R1A WILD-TYPE	17	16	61	6

Figure S7. Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
PIK3CA MUTATED	7	8	6	6
PIK3CA WILD-TYPE	5	10	5	4

'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S14. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
PIK3CA MUTATED	12	8	7
PIK3CA WILD-TYPE	5	10	9

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.475 (Chi-square test), Q value = 1

Table S15. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
PIK3CA MUTATED	86	8	24	3	6	1
PIK3CA WILD-TYPE	71	4	30	5	4	0

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S16. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
PIK3CA MUTATED	22	23	24
PIK3CA WILD-TYPE	21	18	27

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.366 (Chi-square test), Q value = 1

Table S17. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
PIK3CA MUTATED	17	22	19	7	18	15
PIK3CA WILD-TYPE	22	14	18	3	22	9

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S18. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
PIK3CA MUTATED	64	34
PIK3CA WILD-TYPE	51	37

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S19. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
PIK3CA MUTATED	27	24	39	40
PIK3CA WILD-TYPE	36	12	33	34

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.989 (Fisher's exact test), Q value = 1

Table S20. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
PIK3CA MUTATED	45	25	60
PIK3CA WILD-TYPE	40	23	52

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.746 (Chi-square test), Q value = 1

Table S21. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
PIK3CA MUTATED	20	46	11	13	38
PIK3CA WILD-TYPE	22	32	12	13	33

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 1

Table S22. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
PIK3CA MUTATED	3	74	51
PIK3CA WILD-TYPE	1	57	54

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 1

Table S23. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
PIK3CA MUTATED	15	14	30
PIK3CA WILD-TYPE	21	12	24

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S24. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
PIK3CA MUTATED	12	9	35	3
PIK3CA WILD-TYPE	11	13	30	3

'CTNNB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 5.68e-07 (Fisher's exact test), Q value = 2e-04

Table S25. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
CTNNB1 MUTATED	0	3	4	10
CTNNB1 WILD-TYPE	12	15	7	0

Figure S8. Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.39

Table S26. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
CTNNB1 MUTATED	3	12	2
CTNNB1 WILD-TYPE	14	6	14

Figure S9. Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 8.75e-06 (Chi-square test), Q value = 0.0031

Table S27. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
CTNNB1 MUTATED	60	7	1	2	2	0
CTNNB1 WILD-TYPE	97	5	53	6	8	1

Figure S10. Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 1

Table S28. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
CTNNB1 MUTATED	4	15	18
CTNNB1 WILD-TYPE	39	26	33

Figure S11. Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1.29e-10 (Chi-square test), Q value = 4.7e-08

Table S29. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
CTNNB1 MUTATED	6	10	6	0	32	10
CTNNB1 WILD-TYPE	33	26	31	10	8	14

Figure S12. Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S30. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
CTNNB1 MUTATED	45	19
CTNNB1 WILD-TYPE	70	52

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.4e-20 (Fisher's exact test), Q value = 5.2e-18

Table S31. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
CTNNB1 MUTATED	3	4	53	13
CTNNB1 WILD-TYPE	60	32	19	61

Figure S13. Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.02e-06 (Fisher's exact test), Q value = 0.0011

Table S32. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
CTNNB1 MUTATED	9	19	45
CTNNB1 WILD-TYPE	76	29	67

Figure S14. Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.98e-11 (Chi-square test), Q value = 7.2e-09

Table S33. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
CTNNB1 MUTATED	1	13	6	20	31
CTNNB1 WILD-TYPE	41	65	17	6	40

Figure S15. Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 1

Table S34. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
CTNNB1 MUTATED	0	45	26
CTNNB1 WILD-TYPE	4	86	79

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 1

Table S35. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
CTNNB1 MUTATED	3	9	15
CTNNB1 WILD-TYPE	33	17	39

Figure S16. Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00379 (Fisher's exact test), Q value = 1

Table S36. Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
CTNNB1 MUTATED	4	0	22	1
CTNNB1 WILD-TYPE	19	22	43	5

Figure S17. Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0669 (Fisher's exact test), Q value = 1

Table S37. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
PIK3R1 MUTATED	5	2	6	3
PIK3R1 WILD-TYPE	7	16	5	7

'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 1

Table S38. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
PIK3R1 MUTATED	8	7	1
PIK3R1 WILD-TYPE	9	11	15

Figure S18. Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000523 (Chi-square test), Q value = 0.18

Table S39. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
PIK3R1 MUTATED	64	2	6	5	5	0
PIK3R1 WILD-TYPE	93	10	48	3	5	1

Figure S19. Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.32e-05 (Fisher's exact test), Q value = 0.012

Table S40. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
PIK3R1 MUTATED	5	12	28
PIK3R1 WILD-TYPE	38	29	23

Figure S20. Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.649 (Chi-square test), Q value = 1

Table S41. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
PIK3R1 MUTATED	13	11	18	3	16	9
PIK3R1 WILD-TYPE	26	25	19	7	24	15

'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S42. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
PIK3R1 MUTATED	44	26
PIK3R1 WILD-TYPE	71	45

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.039

Table S43. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
PIK3R1 MUTATED	7	15	28	31
PIK3R1 WILD-TYPE	56	21	44	43

Figure S21. Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.0079

Table S44. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
PIK3R1 MUTATED	13	24	44
PIK3R1 WILD-TYPE	72	24	68

Figure S22. Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Chi-square test), Q value = 1

Table S45. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
PIK3R1 MUTATED	5	29	7	9	31
PIK3R1 WILD-TYPE	37	49	16	17	40

Figure S23. Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S46. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
PIK3R1 MUTATED	1	51	29
PIK3R1 WILD-TYPE	3	80	76

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 1

Table S47. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
PIK3R1 MUTATED	5	9	23
PIK3R1 WILD-TYPE	31	17	31

Figure S24. Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000575 (Fisher's exact test), Q value = 0.2

Table S48. Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
PIK3R1 MUTATED	4	1	29	3
PIK3R1 WILD-TYPE	19	21	36	3

Figure S25. Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PRKAR1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.988 (Chi-square test), Q value = 1

Table S49. Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
PRKAR1B MUTATED	3	0	1	0	0	0
PRKAR1B WILD-TYPE	154	12	53	8	10	1

'PRKAR1B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S50. Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
PRKAR1B MUTATED	2	0	1
PRKAR1B WILD-TYPE	41	41	50

'PRKAR1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.887 (Chi-square test), Q value = 1

Table S51. Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
PRKAR1B MUTATED	1	1	1	0	0	1
PRKAR1B WILD-TYPE	38	35	36	10	40	23

'PRKAR1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S52. Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
PRKAR1B MUTATED	3	1
PRKAR1B WILD-TYPE	112	70

'PRKAR1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S53. Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
PRKAR1B MUTATED	2	1	1	0
PRKAR1B WILD-TYPE	61	35	71	74

'PRKAR1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S54. Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
PRKAR1B MUTATED	1	2	1
PRKAR1B WILD-TYPE	84	46	111

'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.482 (Chi-square test), Q value = 1

Table S55. Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
PRKAR1B MUTATED	1	0	1	0	2
PRKAR1B WILD-TYPE	41	78	22	26	69

'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S56. Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
PRKAR1B MUTATED	0	1	3
PRKAR1B WILD-TYPE	4	130	102

'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S57. Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
PRKAR1B MUTATED	1	1	1
PRKAR1B WILD-TYPE	35	25	53

'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 1

Table S58. Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
PRKAR1B MUTATED	1	0	1	1
PRKAR1B WILD-TYPE	22	22	64	5

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00442 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
PTEN MUTATED	11	6	9	7
PTEN WILD-TYPE	1	12	2	3

Figure S26. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000362 (Fisher's exact test), Q value = 0.13

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
PTEN MUTATED	15	14	4
PTEN WILD-TYPE	2	4	12

Figure S27. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 1.82e-20 (Chi-square test), Q value = 6.8e-18

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
PTEN MUTATED	129	7	4	6	9	1
PTEN WILD-TYPE	28	5	50	2	1	0

Figure S28. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.79e-12 (Fisher's exact test), Q value = 6.5e-10

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
PTEN MUTATED	7	30	44
PTEN WILD-TYPE	36	11	7

Figure S29. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0257 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
PTEN MUTATED	26	21	33	9	29	14
PTEN WILD-TYPE	13	15	4	1	11	10

Figure S30. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2
ALL	115	71
PTEN MUTATED	86	46
PTEN WILD-TYPE	29	25

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.45e-21 (Fisher's exact test), Q value = 1.7e-18

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
PTEN MUTATED	10	25	55	68
PTEN WILD-TYPE	53	11	17	6

Figure S31. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.86e-17 (Fisher's exact test), Q value = 1.1e-14

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
PTEN MUTATED	24	38	96
PTEN WILD-TYPE	61	10	16

Figure S32. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7.65e-16 (Chi-square test), Q value = 2.8e-13

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
PTEN MUTATED	6	72	12	17	51
PTEN WILD-TYPE	36	6	11	9	20

Figure S33. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.44e-13 (Fisher's exact test), Q value = 5.3e-11

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
PTEN MUTATED	4	112	42
PTEN WILD-TYPE	0	19	63

Figure S34. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.35e-09 (Fisher's exact test), Q value = 1.9e-06

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
PTEN MUTATED	11	11	48
PTEN WILD-TYPE	25	15	6

Figure S35. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.55e-14 (Fisher's exact test), Q value = 3.1e-11

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
PTEN MUTATED	6	2	58	4
PTEN WILD-TYPE	17	20	7	2

Figure S36. Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S71. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
KRAS MUTATED	5	2	3	1
KRAS WILD-TYPE	7	16	8	9

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000649 (Fisher's exact test), Q value = 0.22

Table S72. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
KRAS MUTATED	9	1	1
KRAS WILD-TYPE	8	17	15

Figure S37. Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00606 (Chi-square test), Q value = 1

Table S73. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
KRAS MUTATED	43	3	2	0	2	0
KRAS WILD-TYPE	114	9	52	8	8	1

Figure S38. Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S74. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
KRAS MUTATED	6	8	16
KRAS WILD-TYPE	37	33	35

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.297 (Chi-square test), Q value = 1

Table S75. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
KRAS MUTATED	6	9	12	3	5	5
KRAS WILD-TYPE	33	27	25	7	35	19

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.855 (Fisher's exact test), Q value = 1

Table S76. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
KRAS MUTATED	24	16
KRAS WILD-TYPE	91	55

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 1

Table S77. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
KRAS MUTATED	7	14	12	19
KRAS WILD-TYPE	56	22	60	55

Figure S39. Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 1

Table S78. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
KRAS MUTATED	12	16	24
KRAS WILD-TYPE	73	32	88

Figure S40. Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000628 (Chi-square test), Q value = 0.21

Table S79. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
KRAS MUTATED	3	19	9	0	21
KRAS WILD-TYPE	39	59	14	26	50

Figure S41. Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S80. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
KRAS MUTATED	0	31	21
KRAS WILD-TYPE	4	100	84

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 1

Table S81. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
KRAS MUTATED	4	8	13
KRAS WILD-TYPE	32	18	41

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S82. Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
KRAS MUTATED	6	3	16	0
KRAS WILD-TYPE	17	19	49	6

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 3.76e-05 (Fisher's exact test), Q value = 0.013

Table S83. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
TP53 MUTATED	2	13	1	0
TP53 WILD-TYPE	10	5	10	10

Figure S42. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 2.45e-07 (Fisher's exact test), Q value = 8.7e-05

Table S84. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
TP53 MUTATED	3	0	13
TP53 WILD-TYPE	14	18	3

Figure S43. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 4.35e-30 (Chi-square test), Q value = 1.6e-27

Table S85. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
TP53 MUTATED	11	2	50	3	2	0
TP53 WILD-TYPE	146	10	4	5	8	1

Figure S44. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.53e-12 (Fisher's exact test), Q value = 9.2e-10

Table S86. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
TP53 MUTATED	31	4	5
TP53 WILD-TYPE	12	37	46

Figure S45. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 2.01e-05 (Chi-square test), Q value = 0.0071

Table S87. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
TP53 MUTATED	9	19	4	2	2	8
TP53 WILD-TYPE	30	17	33	8	38	16

Figure S46. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.47

Table S88. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
TP53 MUTATED	18	26
TP53 WILD-TYPE	97	45

Figure S47. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.09e-24 (Fisher's exact test), Q value = 1.5e-21

Table S89. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
TP53 MUTATED	50	8	8	3
TP53 WILD-TYPE	13	28	64	71

Figure S48. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.53e-21 (Fisher's exact test), Q value = 2.4e-18

Table S90. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
TP53 MUTATED	56	6	7
TP53 WILD-TYPE	29	42	105

Figure S49. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 3.53e-17 (Chi-square test), Q value = 1.3e-14

Table S91. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
TP53 MUTATED	34	5	7	4	14
TP53 WILD-TYPE	8	73	16	22	57

Figure S50. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.52e-13 (Fisher's exact test), Q value = 5.5e-11

Table S92. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
TP53 MUTATED	2	10	52
TP53 WILD-TYPE	2	121	53

Figure S51. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.65e-09 (Fisher's exact test), Q value = 2.4e-06

Table S93. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
TP53 MUTATED	25	6	5
TP53 WILD-TYPE	11	20	49

Figure S52. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.24e-09 (Fisher's exact test), Q value = 4.4e-07

Table S94. Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
TP53 MUTATED	9	18	6	3
TP53 WILD-TYPE	14	4	59	3

Figure S53. Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 1

Table S95. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
FBXW7 MUTATED	3	4	4	0
FBXW7 WILD-TYPE	9	14	7	10

'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S96. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
FBXW7 MUTATED	5	3	3
FBXW7 WILD-TYPE	12	15	13

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.343 (Chi-square test), Q value = 1

Table S97. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
FBXW7 MUTATED	25	0	12	0	2	0
FBXW7 WILD-TYPE	132	12	42	8	8	1

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S98. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
FBXW7 MUTATED	11	3	8
FBXW7 WILD-TYPE	32	38	43

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.106 (Chi-square test), Q value = 1

Table S99. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
FBXW7 MUTATED	10	5	5	4	3	4
FBXW7 WILD-TYPE	29	31	32	6	37	20

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S100. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
FBXW7 MUTATED	15	16
FBXW7 WILD-TYPE	100	55

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 1

Table S101. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
FBXW7 MUTATED	14	10	6	9
FBXW7 WILD-TYPE	49	26	66	65

Figure S54. Get High-res Image Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 1

Table S102. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
FBXW7 MUTATED	20	9	10
FBXW7 WILD-TYPE	65	39	102

Figure S55. Get High-res Image Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.135 (Chi-square test), Q value = 1

Table S103. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
FBXW7 MUTATED	9	9	6	1	10
FBXW7 WILD-TYPE	33	69	17	25	61

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S104. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
FBXW7 MUTATED	1	14	20
FBXW7 WILD-TYPE	3	117	85

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S105. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
FBXW7 MUTATED	8	4	6
FBXW7 WILD-TYPE	28	22	48

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 1

Table S106. Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
FBXW7 MUTATED	4	8	6	0
FBXW7 WILD-TYPE	19	14	59	6

Figure S56. Get High-res Image Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 1

Table S107. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
CTCF MUTATED	3	1	4	1
CTCF WILD-TYPE	9	17	7	9

'CTCF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 1

Table S108. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
CTCF MUTATED	4	4	1
CTCF WILD-TYPE	13	14	15

'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000441 (Chi-square test), Q value = 0.15

Table S109. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
CTCF MUTATED	38	0	0	0	3	0
CTCF WILD-TYPE	119	12	54	8	7	1

Figure S57. Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 1

Table S110. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
CTCF MUTATED	3	11	7
CTCF WILD-TYPE	40	30	44

Figure S58. Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0458 (Chi-square test), Q value = 1

Table S111. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
CTCF MUTATED	9	3	5	5	9	3
CTCF WILD-TYPE	30	33	32	5	31	21

Figure S59. Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S112. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
CTCF MUTATED	21	13
CTCF WILD-TYPE	94	58

'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000834 (Fisher's exact test), Q value = 0.28

Table S113. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
CTCF MUTATED	2	7	15	20
CTCF WILD-TYPE	61	29	57	54

Figure S60. Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.41

Table S114. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
CTCF MUTATED	6	8	30
CTCF WILD-TYPE	79	40	82

Figure S61. Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00949 (Chi-square test), Q value = 1

Table S115. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
CTCF MUTATED	1	21	2	4	16
CTCF WILD-TYPE	41	57	21	22	55

Figure S62. Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00316 (Fisher's exact test), Q value = 1

Table S116. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
CTCF MUTATED	0	34	10
CTCF WILD-TYPE	4	97	95

Figure S63. Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00792 (Fisher's exact test), Q value = 1

Table S117. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
CTCF MUTATED	1	1	12
CTCF WILD-TYPE	35	25	42

Figure S64. Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 1

Table S118. Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
CTCF MUTATED	2	0	12	0
CTCF WILD-TYPE	21	22	53	6

'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 1

Table S119. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
ARID1A MUTATED	5	3	4	5
ARID1A WILD-TYPE	7	15	7	5

'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 1

Table S120. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
ARID1A MUTATED	9	7	1
ARID1A WILD-TYPE	8	11	15

Figure S65. Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 7.11e-07 (Chi-square test), Q value = 0.00025

Table S121. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
ARID1A MUTATED	68	2	3	0	6	1
ARID1A WILD-TYPE	89	10	51	8	4	0

Figure S66. Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S122. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
ARID1A MUTATED	10	16	19
ARID1A WILD-TYPE	33	25	32

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0271 (Chi-square test), Q value = 1

Table S123. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
ARID1A MUTATED	12	13	18	3	18	2
ARID1A WILD-TYPE	27	23	19	7	22	22

Figure S67. Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S124. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
ARID1A MUTATED	41	25
ARID1A WILD-TYPE	74	46

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00267 (Fisher's exact test), Q value = 0.89

Table S125. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
ARID1A MUTATED	10	11	30	31
ARID1A WILD-TYPE	53	25	42	43

Figure S68. Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 1

Table S126. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
ARID1A MUTATED	20	20	42
ARID1A WILD-TYPE	65	28	70

Figure S69. Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0226 (Chi-square test), Q value = 1

Table S127. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
ARID1A MUTATED	6	34	9	7	24
ARID1A WILD-TYPE	36	44	14	19	47

Figure S70. Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.053 (Fisher's exact test), Q value = 1

Table S128. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
ARID1A MUTATED	2	51	27
ARID1A WILD-TYPE	2	80	78

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0664 (Fisher's exact test), Q value = 1

Table S129. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
ARID1A MUTATED	7	10	23
ARID1A WILD-TYPE	29	16	31

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 1

Table S130. Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
ARID1A MUTATED	8	3	29	0
ARID1A WILD-TYPE	15	19	36	6

Figure S71. Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SPOP MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.349 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
SPOP MUTATED	2	1	0	2
SPOP WILD-TYPE	10	17	11	8

'SPOP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
SPOP MUTATED	2	2	1
SPOP WILD-TYPE	15	16	15

'SPOP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.85 (Chi-square test), Q value = 1

Table S133. Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
SPOP MUTATED	16	1	3	0	1	0
SPOP WILD-TYPE	141	11	51	8	9	1

'SPOP MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S134. Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
SPOP MUTATED	4	1	5
SPOP WILD-TYPE	39	40	46

'SPOP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.834 (Chi-square test), Q value = 1

Table S135. Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
SPOP MUTATED	5	3	2	1	3	1
SPOP WILD-TYPE	34	33	35	9	37	23

'SPOP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S136. Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
SPOP MUTATED	11	4
SPOP WILD-TYPE	104	67

'SPOP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S137. Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
SPOP MUTATED	4	5	8	4
SPOP WILD-TYPE	59	31	64	70

'SPOP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 1

Table S138. Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
SPOP MUTATED	8	6	7
SPOP WILD-TYPE	77	42	105

'SPOP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0343 (Chi-square test), Q value = 1

Table S139. Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
SPOP MUTATED	1	4	4	1	11
SPOP WILD-TYPE	41	74	19	25	60

Figure S72. Get High-res Image Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SPOP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.462 (Fisher's exact test), Q value = 1

Table S140. Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
SPOP MUTATED	0	9	12
SPOP WILD-TYPE	4	122	93

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S141. Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
SPOP MUTATED	4	2	3
SPOP WILD-TYPE	32	24	51

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S142. Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
SPOP MUTATED	3	2	4	0
SPOP WILD-TYPE	20	20	61	6

'ARID5B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.961 (Fisher's exact test), Q value = 1

Table S143. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
ARID5B MUTATED	3	3	2	2
ARID5B WILD-TYPE	9	15	9	8

'ARID5B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S144. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
ARID5B MUTATED	5	3	2
ARID5B WILD-TYPE	12	15	14

'ARID5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0427 (Chi-square test), Q value = 1

Table S145. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
ARID5B MUTATED	25	2	0	0	1	0
ARID5B WILD-TYPE	132	10	54	8	9	1

Figure S73. Get High-res Image Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ARID5B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S146. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
ARID5B MUTATED	1	1	6
ARID5B WILD-TYPE	42	40	45

'ARID5B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.164 (Chi-square test), Q value = 1

Table S147. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
ARID5B MUTATED	4	5	5	4	3	3
ARID5B WILD-TYPE	35	31	32	6	37	21

'ARID5B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S148. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
ARID5B MUTATED	18	6
ARID5B WILD-TYPE	97	65

'ARID5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0531 (Fisher's exact test), Q value = 1

Table S149. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
ARID5B MUTATED	3	8	7	11
ARID5B WILD-TYPE	60	28	65	63

'ARID5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0676 (Fisher's exact test), Q value = 1

Table S150. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
ARID5B MUTATED	6	10	13
ARID5B WILD-TYPE	79	38	99

'ARID5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0452 (Chi-square test), Q value = 1

Table S151. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
ARID5B MUTATED	0	11	3	1	12
ARID5B WILD-TYPE	42	67	20	25	59

Figure S74. Get High-res Image Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ARID5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S152. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
ARID5B MUTATED	1	16	10
ARID5B WILD-TYPE	3	115	95

'ARID5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 1

Table S153. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
ARID5B MUTATED	1	0	5
ARID5B WILD-TYPE	35	26	49

'ARID5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S154. Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
ARID5B MUTATED	1	0	5	0
ARID5B WILD-TYPE	22	22	60	6

'FGFR2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S155. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
FGFR2 MUTATED	3	2	1	0
FGFR2 WILD-TYPE	9	16	10	10

'FGFR2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.293 (Fisher's exact test), Q value = 1

Table S156. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
FGFR2 MUTATED	4	1	1
FGFR2 WILD-TYPE	13	17	15

'FGFR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.611 (Chi-square test), Q value = 1

Table S157. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
FGFR2 MUTATED	22	2	3	1	2	0
FGFR2 WILD-TYPE	135	10	51	7	8	1

'FGFR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.914 (Fisher's exact test), Q value = 1

Table S158. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
FGFR2 MUTATED	5	6	6
FGFR2 WILD-TYPE	38	35	45

'FGFR2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.97 (Chi-square test), Q value = 1

Table S159. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
FGFR2 MUTATED	6	5	6	1	4	3
FGFR2 WILD-TYPE	33	31	31	9	36	21

'FGFR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S160. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
FGFR2 MUTATED	15	10
FGFR2 WILD-TYPE	100	61

'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S161. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
FGFR2 MUTATED	6	7	8	9
FGFR2 WILD-TYPE	57	29	64	65

'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S162. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
FGFR2 MUTATED	9	8	13
FGFR2 WILD-TYPE	76	40	99

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.876 (Chi-square test), Q value = 1

Table S163. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
FGFR2 MUTATED	5	11	2	2	10
FGFR2 WILD-TYPE	37	67	21	24	61

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S164. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
FGFR2 MUTATED	1	16	13
FGFR2 WILD-TYPE	3	115	92

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S165. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
FGFR2 MUTATED	6	2	8
FGFR2 WILD-TYPE	30	24	46

'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S166. Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
FGFR2 MUTATED	3	4	8	1
FGFR2 WILD-TYPE	20	18	57	5

'NFE2L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0905 (Fisher's exact test), Q value = 1

Table S167. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
NFE2L2 MUTATED	0	1	3	0
NFE2L2 WILD-TYPE	12	17	8	10

'NFE2L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S168. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
NFE2L2 MUTATED	2	1	1
NFE2L2 WILD-TYPE	15	17	15

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00636 (Chi-square test), Q value = 1

Table S169. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
NFE2L2 MUTATED	10	2	0	0	3	0
NFE2L2 WILD-TYPE	147	10	54	8	7	1

Figure S75. Get High-res Image Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S170. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
NFE2L2 MUTATED	1	3	3
NFE2L2 WILD-TYPE	42	38	48

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.248 (Chi-square test), Q value = 1

Table S171. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
NFE2L2 MUTATED	3	2	4	2	0	2
NFE2L2 WILD-TYPE	36	34	33	8	40	22

'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S172. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
NFE2L2 MUTATED	8	5
NFE2L2 WILD-TYPE	107	66

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 1

Table S173. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
NFE2L2 MUTATED	1	4	1	8
NFE2L2 WILD-TYPE	62	32	71	66

Figure S76. Get High-res Image Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S174. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
NFE2L2 MUTATED	3	3	8
NFE2L2 WILD-TYPE	82	45	104

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.392 (Chi-square test), Q value = 1

Table S175. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
NFE2L2 MUTATED	1	7	2	0	5
NFE2L2 WILD-TYPE	41	71	21	26	66

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S176. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
NFE2L2 MUTATED	0	9	6
NFE2L2 WILD-TYPE	4	122	99

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 1

Table S177. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
NFE2L2 MUTATED	1	0	5
NFE2L2 WILD-TYPE	35	26	49

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S178. Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
NFE2L2 MUTATED	1	0	5	0
NFE2L2 WILD-TYPE	22	22	60	6

'CCND1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S179. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
CCND1 MUTATED	2	1	0	1
CCND1 WILD-TYPE	10	17	11	9

'CCND1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S180. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
CCND1 MUTATED	2	1	1
CCND1 WILD-TYPE	15	17	15

'CCND1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.154 (Chi-square test), Q value = 1

Table S181. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
CCND1 MUTATED	14	0	0	0	0	0
CCND1 WILD-TYPE	143	12	54	8	10	1

'CCND1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S182. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
CCND1 MUTATED	1	2	4
CCND1 WILD-TYPE	42	39	47

'CCND1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.514 (Chi-square test), Q value = 1

Table S183. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
CCND1 MUTATED	4	3	1	0	1	1
CCND1 WILD-TYPE	35	33	36	10	39	23

'CCND1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S184. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
CCND1 MUTATED	5	5
CCND1 WILD-TYPE	110	66

'CCND1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.635 (Fisher's exact test), Q value = 1

Table S185. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
CCND1 MUTATED	2	2	6	4
CCND1 WILD-TYPE	61	34	66	70

'CCND1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S186. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
CCND1 MUTATED	3	5	6
CCND1 WILD-TYPE	82	43	106

'CCND1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.124 (Chi-square test), Q value = 1

Table S187. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
CCND1 MUTATED	0	3	1	2	8
CCND1 WILD-TYPE	42	75	22	24	63

'CCND1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S188. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
CCND1 MUTATED	0	9	5
CCND1 WILD-TYPE	4	122	100

'CCND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S189. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
CCND1 MUTATED	0	1	3
CCND1 WILD-TYPE	36	25	51

'CCND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S190. Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
CCND1 MUTATED	1	0	3	0
CCND1 WILD-TYPE	22	22	62	6

'CHD4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0986 (Fisher's exact test), Q value = 1

Table S191. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
CHD4 MUTATED	1	6	0	2
CHD4 WILD-TYPE	11	12	11	8

'CHD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S192. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
CHD4 MUTATED	2	2	5
CHD4 WILD-TYPE	15	16	11

'CHD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.776 (Chi-square test), Q value = 1

Table S193. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
CHD4 MUTATED	25	1	7	0	2	0
CHD4 WILD-TYPE	132	11	47	8	8	1

'CHD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S194. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
CHD4 MUTATED	7	5	7
CHD4 WILD-TYPE	36	36	44

'CHD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.97 (Chi-square test), Q value = 1

Table S195. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
CHD4 MUTATED	7	6	5	1	5	3
CHD4 WILD-TYPE	32	30	32	9	35	21

'CHD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S196. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
CHD4 MUTATED	14	13
CHD4 WILD-TYPE	101	58

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S197. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
CHD4 MUTATED	10	6	10	9
CHD4 WILD-TYPE	53	30	62	65

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 1

Table S198. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
CHD4 MUTATED	15	7	13
CHD4 WILD-TYPE	70	41	99

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.739 (Chi-square test), Q value = 1

Table S199. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
CHD4 MUTATED	4	8	3	3	12
CHD4 WILD-TYPE	38	70	20	23	59

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S200. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
CHD4 MUTATED	1	16	13
CHD4 WILD-TYPE	3	115	92

'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S201. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
CHD4 MUTATED	4	2	10
CHD4 WILD-TYPE	32	24	44

'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.97 (Fisher's exact test), Q value = 1

Table S202. Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
CHD4 MUTATED	3	3	10	0
CHD4 WILD-TYPE	20	19	55	6

'FAM9A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.887 (Chi-square test), Q value = 1

Table S203. Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
FAM9A MUTATED	10	0	3	0	1	0
FAM9A WILD-TYPE	147	12	51	8	9	1

'FAM9A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S204. Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
FAM9A MUTATED	5	1	4
FAM9A WILD-TYPE	38	40	47

'FAM9A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.178 (Chi-square test), Q value = 1

Table S205. Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
FAM9A MUTATED	3	5	2	0	0	1
FAM9A WILD-TYPE	36	31	35	10	40	23

'FAM9A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S206. Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
FAM9A MUTATED	3	8
FAM9A WILD-TYPE	112	63

Figure S77. Get High-res Image Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'FAM9A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0562 (Fisher's exact test), Q value = 1

Table S207. Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
FAM9A MUTATED	3	5	5	1
FAM9A WILD-TYPE	60	31	67	73

'FAM9A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.065 (Fisher's exact test), Q value = 1

Table S208. Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
FAM9A MUTATED	9	2	3
FAM9A WILD-TYPE	76	46	109

'FAM9A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.308 (Chi-square test), Q value = 1

Table S209. Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
FAM9A MUTATED	5	2	1	1	5
FAM9A WILD-TYPE	37	76	22	25	66

'FAM9A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 1

Table S210. Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
FAM9A MUTATED	1	4	9
FAM9A WILD-TYPE	3	127	96

Figure S78. Get High-res Image Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FAM9A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 1

Table S211. Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
FAM9A MUTATED	6	0	2
FAM9A WILD-TYPE	30	26	52

Figure S79. Get High-res Image Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'FAM9A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 1

Table S212. Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
FAM9A MUTATED	3	3	2	0
FAM9A WILD-TYPE	20	19	63	6

'MORC4 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S213. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
MORC4 MUTATED	1	3	0	1
MORC4 WILD-TYPE	11	15	11	9

'MORC4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 1

Table S214. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
MORC4 MUTATED	3	0	2
MORC4 WILD-TYPE	14	18	14

'MORC4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.34 (Chi-square test), Q value = 1

Table S215. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
MORC4 MUTATED	16	2	1	0	1	0
MORC4 WILD-TYPE	141	10	53	8	9	1

'MORC4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 1

Table S216. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
MORC4 MUTATED	2	6	4
MORC4 WILD-TYPE	41	35	47

'MORC4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.212 (Chi-square test), Q value = 1

Table S217. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
MORC4 MUTATED	6	5	1	1	4	0
MORC4 WILD-TYPE	33	31	36	9	36	24

'MORC4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 1

Table S218. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
MORC4 MUTATED	6	11
MORC4 WILD-TYPE	109	60

Figure S80. Get High-res Image Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MORC4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00821 (Fisher's exact test), Q value = 1

Table S219. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
MORC4 MUTATED	2	6	10	2
MORC4 WILD-TYPE	61	30	62	72

Figure S81. Get High-res Image Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MORC4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.266 (Fisher's exact test), Q value = 1

Table S220. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
MORC4 MUTATED	8	6	6
MORC4 WILD-TYPE	77	42	106

'MORC4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.315 (Chi-square test), Q value = 1

Table S221. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
MORC4 MUTATED	2	3	3	3	8
MORC4 WILD-TYPE	40	75	20	23	63

'MORC4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S222. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
MORC4 MUTATED	0	7	12
MORC4 WILD-TYPE	4	124	93

'MORC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S223. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
MORC4 MUTATED	2	4	3
MORC4 WILD-TYPE	34	22	51

'MORC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 1

Table S224. Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
MORC4 MUTATED	5	0	4	0
MORC4 WILD-TYPE	18	22	61	6

Figure S82. Get High-res Image Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S225. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
CASP8 MUTATED	2	1	0	0
CASP8 WILD-TYPE	10	17	11	10

'CASP8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0595 (Fisher's exact test), Q value = 1

Table S226. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
CASP8 MUTATED	3	0	0
CASP8 WILD-TYPE	14	18	16

'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.204 (Chi-square test), Q value = 1

Table S227. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
CASP8 MUTATED	14	0	1	0	2	0
CASP8 WILD-TYPE	143	12	53	8	8	1

'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S228. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
CASP8 MUTATED	2	2	5
CASP8 WILD-TYPE	41	39	46

'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.154 (Chi-square test), Q value = 1

Table S229. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
CASP8 MUTATED	3	6	2	2	1	1
CASP8 WILD-TYPE	36	30	35	8	39	23

'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S230. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
CASP8 MUTATED	7	8
CASP8 WILD-TYPE	108	63

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S231. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
CASP8 MUTATED	3	5	5	4
CASP8 WILD-TYPE	60	31	67	70

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S232. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
CASP8 MUTATED	9	4	4
CASP8 WILD-TYPE	76	44	108

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.152 (Chi-square test), Q value = 1

Table S233. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
CASP8 MUTATED	2	4	1	0	9
CASP8 WILD-TYPE	40	74	22	26	62

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S234. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
CASP8 MUTATED	1	7	8
CASP8 WILD-TYPE	3	124	97

'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S235. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
CASP8 MUTATED	3	0	4
CASP8 WILD-TYPE	33	26	50

'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S236. Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
CASP8 MUTATED	2	1	4	0
CASP8 WILD-TYPE	21	21	61	6

'FOXA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.304 (Chi-square test), Q value = 1

Table S237. Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
FOXA2 MUTATED	7	0	3	0	2	0
FOXA2 WILD-TYPE	150	12	51	8	8	1

'FOXA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S238. Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
FOXA2 MUTATED	2	3	2
FOXA2 WILD-TYPE	41	38	49

'FOXA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0719 (Chi-square test), Q value = 1

Table S239. Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
FOXA2 MUTATED	0	4	2	2	2	0
FOXA2 WILD-TYPE	39	32	35	8	38	24

'FOXA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S240. Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
FOXA2 MUTATED	7	3
FOXA2 WILD-TYPE	108	68

'FOXA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S241. Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
FOXA2 MUTATED	3	0	4	5
FOXA2 WILD-TYPE	60	36	68	69

'FOXA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S242. Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
FOXA2 MUTATED	4	1	7
FOXA2 WILD-TYPE	81	47	105

'FOXA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0582 (Chi-square test), Q value = 1

Table S243. Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
FOXA2 MUTATED	2	6	0	3	0
FOXA2 WILD-TYPE	40	72	23	23	71

'FOXA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S244. Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
FOXA2 MUTATED	0	7	4
FOXA2 WILD-TYPE	4	124	101

'FOXA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S245. Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
FOXA2 MUTATED	1	2	4
FOXA2 WILD-TYPE	35	24	50

'FOXA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S246. Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
FOXA2 MUTATED	1	0	5	1
FOXA2 WILD-TYPE	22	22	60	5

'ABI1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.821 (Chi-square test), Q value = 1

Table S247. Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
ABI1 MUTATED	4	0	0	0	0	0
ABI1 WILD-TYPE	153	12	54	8	10	1

'ABI1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.64 (Chi-square test), Q value = 1

Table S248. Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
ABI1 MUTATED	2	1	1	0	0	0
ABI1 WILD-TYPE	37	35	36	10	40	24

'ABI1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 1

Table S249. Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
ABI1 MUTATED	2	2
ABI1 WILD-TYPE	113	69

'ABI1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S250. Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
ABI1 MUTATED	0	1	1	2
ABI1 WILD-TYPE	63	35	71	72

'ABI1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S251. Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
ABI1 MUTATED	1	2	1
ABI1 WILD-TYPE	84	46	111

'ABI1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.687 (Chi-square test), Q value = 1

Table S252. Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
ABI1 MUTATED	0	2	0	1	1
ABI1 WILD-TYPE	42	76	23	25	70

'ABI1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S253. Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
ABI1 MUTATED	0	3	1
ABI1 WILD-TYPE	4	128	104

'DNER MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S254. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
DNER MUTATED	3	2	0	0
DNER WILD-TYPE	9	16	11	10

'DNER MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0515 (Fisher's exact test), Q value = 1

Table S255. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
DNER MUTATED	4	0	1
DNER WILD-TYPE	13	18	15

'DNER MUTATION STATUS' versus 'CN_CNMF'

P value = 0.013 (Chi-square test), Q value = 1

Table S256. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
DNER MUTATED	15	0	0	0	3	0
DNER WILD-TYPE	142	12	54	8	7	1

Figure S83. Get High-res Image Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'DNER MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S257. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
DNER MUTATED	3	1	4
DNER WILD-TYPE	40	40	47

'DNER MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0217 (Chi-square test), Q value = 1

Table S258. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
DNER MUTATED	4	4	4	3	0	0
DNER WILD-TYPE	35	32	33	7	40	24

Figure S84. Get High-res Image Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'DNER MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S259. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
DNER MUTATED	8	7
DNER WILD-TYPE	107	64

'DNER MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S260. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
DNER MUTATED	2	6	5	5
DNER WILD-TYPE	61	30	67	69

'DNER MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0936 (Fisher's exact test), Q value = 1

Table S261. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
DNER MUTATED	6	7	5
DNER WILD-TYPE	79	41	107

'DNER MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.785 (Chi-square test), Q value = 1

Table S262. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
DNER MUTATED	2	5	2	1	7
DNER WILD-TYPE	40	73	21	25	64

'DNER MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S263. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
DNER MUTATED	1	7	9
DNER WILD-TYPE	3	124	96

'DNER MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S264. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
DNER MUTATED	1	2	4
DNER WILD-TYPE	35	24	50

'DNER MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S265. Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
DNER MUTATED	2	1	4	0
DNER WILD-TYPE	21	21	61	6

'BCOR MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S266. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
BCOR MUTATED	1	2	0	0
BCOR WILD-TYPE	11	16	11	10

'BCOR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S267. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
BCOR MUTATED	2	0	1
BCOR WILD-TYPE	15	18	15

'BCOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00577 (Chi-square test), Q value = 1

Table S268. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
BCOR MUTATED	26	0	0	0	3	0
BCOR WILD-TYPE	131	12	54	8	7	1

Figure S85. Get High-res Image Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BCOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 1

Table S269. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
BCOR MUTATED	1	4	10
BCOR WILD-TYPE	42	37	41

Figure S86. Get High-res Image Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'BCOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.512 (Chi-square test), Q value = 1

Table S270. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
BCOR MUTATED	5	6	3	3	5	2
BCOR WILD-TYPE	34	30	34	7	35	22

'BCOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.5 (Fisher's exact test), Q value = 1

Table S271. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
BCOR MUTATED	13	11
BCOR WILD-TYPE	102	60

'BCOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.45

Table S272. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
BCOR MUTATED	2	8	15	5
BCOR WILD-TYPE	61	28	57	69

Figure S87. Get High-res Image Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S273. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
BCOR MUTATED	9	9	12
BCOR WILD-TYPE	76	39	100

'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0495 (Chi-square test), Q value = 1

Table S274. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
BCOR MUTATED	2	8	3	1	15
BCOR WILD-TYPE	40	70	20	25	56

Figure S88. Get High-res Image Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0922 (Fisher's exact test), Q value = 1

Table S275. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
BCOR MUTATED	2	14	13
BCOR WILD-TYPE	2	117	92

'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.866 (Fisher's exact test), Q value = 1

Table S276. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
BCOR MUTATED	3	3	7
BCOR WILD-TYPE	33	23	47

'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S277. Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
BCOR MUTATED	2	0	10	1
BCOR WILD-TYPE	21	22	55	5

'BRS3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.536 (Fisher's exact test), Q value = 1

Table S278. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
BRS3 MUTATED	2	2	0	0
BRS3 WILD-TYPE	10	16	11	10

'BRS3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 1

Table S279. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
BRS3 MUTATED	3	0	1
BRS3 WILD-TYPE	14	18	15

'BRS3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.339 (Chi-square test), Q value = 1

Table S280. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
BRS3 MUTATED	13	1	0	0	1	0
BRS3 WILD-TYPE	144	11	54	8	9	1

'BRS3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 1

Table S281. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
BRS3 MUTATED	3	1	1
BRS3 WILD-TYPE	40	40	50

'BRS3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.392 (Chi-square test), Q value = 1

Table S282. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
BRS3 MUTATED	4	4	2	1	1	0
BRS3 WILD-TYPE	35	32	35	9	39	24

'BRS3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S283. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
BRS3 MUTATED	6	6
BRS3 WILD-TYPE	109	65

'BRS3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S284. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
BRS3 MUTATED	3	3	7	1
BRS3 WILD-TYPE	60	33	65	73

'BRS3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00295 (Fisher's exact test), Q value = 0.98

Table S285. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
BRS3 MUTATED	7	6	1
BRS3 WILD-TYPE	78	42	111

Figure S89. Get High-res Image Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'BRS3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.393 (Chi-square test), Q value = 1

Table S286. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
BRS3 MUTATED	1	3	2	1	7
BRS3 WILD-TYPE	41	75	21	25	64

'BRS3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00527 (Fisher's exact test), Q value = 1

Table S287. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
BRS3 MUTATED	2	4	8
BRS3 WILD-TYPE	2	127	97

Figure S90. Get High-res Image Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BRS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S288. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
BRS3 MUTATED	2	1	1
BRS3 WILD-TYPE	34	25	53

'BRS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.343 (Fisher's exact test), Q value = 1

Table S289. Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
BRS3 MUTATED	2	1	1	0
BRS3 WILD-TYPE	21	21	64	6

'SGK1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S290. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
SGK1 MUTATED	2	1	0	0
SGK1 WILD-TYPE	10	17	11	10

'SGK1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0595 (Fisher's exact test), Q value = 1

Table S291. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
SGK1 MUTATED	3	0	0
SGK1 WILD-TYPE	14	18	16

'SGK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.43 (Chi-square test), Q value = 1

Table S292. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
SGK1 MUTATED	10	2	1	1	1	0
SGK1 WILD-TYPE	147	10	53	7	9	1

'SGK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S293. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
SGK1 MUTATED	1	1	3
SGK1 WILD-TYPE	42	40	48

'SGK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.226 (Chi-square test), Q value = 1

Table S294. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
SGK1 MUTATED	4	5	1	2	1	2
SGK1 WILD-TYPE	35	31	36	8	39	22

'SGK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0954 (Fisher's exact test), Q value = 1

Table S295. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
SGK1 MUTATED	6	9
SGK1 WILD-TYPE	109	62

'SGK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 1

Table S296. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
SGK1 MUTATED	1	6	5	3
SGK1 WILD-TYPE	62	30	67	71

Figure S91. Get High-res Image Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SGK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S297. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
SGK1 MUTATED	6	3	6
SGK1 WILD-TYPE	79	45	106

'SGK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.431 (Chi-square test), Q value = 1

Table S298. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
SGK1 MUTATED	1	3	1	2	7
SGK1 WILD-TYPE	41	75	22	24	64

'SGK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S299. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
SGK1 MUTATED	0	8	6
SGK1 WILD-TYPE	4	123	99

'SGK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S300. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
SGK1 MUTATED	1	0	3
SGK1 WILD-TYPE	35	26	51

'SGK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S301. Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
SGK1 MUTATED	1	0	3	0
SGK1 WILD-TYPE	22	22	62	6

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.749 (Chi-square test), Q value = 1

Table S302. Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
NRAS MUTATED	7	0	1	0	1	0
NRAS WILD-TYPE	150	12	53	8	9	1

'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.316 (Chi-square test), Q value = 1

Table S303. Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
NRAS MUTATED	0	2	0	0	2	2
NRAS WILD-TYPE	39	34	37	10	38	22

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S304. Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
NRAS MUTATED	4	2
NRAS WILD-TYPE	111	69

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S305. Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
NRAS MUTATED	3	0	4	2
NRAS WILD-TYPE	60	36	68	72

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S306. Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
NRAS MUTATED	3	1	5
NRAS WILD-TYPE	82	47	107

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.604 (Chi-square test), Q value = 1

Table S307. Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
NRAS MUTATED	2	3	0	0	4
NRAS WILD-TYPE	40	75	23	26	67

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 1

Table S308. Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
NRAS MUTATED	1	4	4
NRAS WILD-TYPE	3	127	101

'TIAL1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S309. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
TIAL1 MUTATED	2	1	0	0
TIAL1 WILD-TYPE	10	17	11	10

'TIAL1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S310. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
TIAL1 MUTATED	2	0	1
TIAL1 WILD-TYPE	15	18	15

'TIAL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.362 (Chi-square test), Q value = 1

Table S311. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
TIAL1 MUTATED	10	0	0	0	1	0
TIAL1 WILD-TYPE	147	12	54	8	9	1

'TIAL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0634 (Fisher's exact test), Q value = 1

Table S312. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
TIAL1 MUTATED	1	0	5
TIAL1 WILD-TYPE	42	41	46

'TIAL1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.564 (Chi-square test), Q value = 1

Table S313. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
TIAL1 MUTATED	1	2	4	1	1	1
TIAL1 WILD-TYPE	38	34	33	9	39	23

'TIAL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S314. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
TIAL1 MUTATED	7	3
TIAL1 WILD-TYPE	108	68

'TIAL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00545 (Fisher's exact test), Q value = 1

Table S315. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
TIAL1 MUTATED	0	4	6	1
TIAL1 WILD-TYPE	63	32	66	73

Figure S92. Get High-res Image Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TIAL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 1

Table S316. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
TIAL1 MUTATED	5	5	1
TIAL1 WILD-TYPE	80	43	111

Figure S93. Get High-res Image Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TIAL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.812 (Chi-square test), Q value = 1

Table S317. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
TIAL1 MUTATED	1	3	1	1	5
TIAL1 WILD-TYPE	41	75	22	25	66

'TIAL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S318. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
TIAL1 MUTATED	0	6	5
TIAL1 WILD-TYPE	4	125	100

'TIAL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S319. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
TIAL1 MUTATED	2	0	4
TIAL1 WILD-TYPE	34	26	50

'TIAL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S320. Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
TIAL1 MUTATED	1	0	5	0
TIAL1 WILD-TYPE	22	22	60	6

'SIN3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0266 (Chi-square test), Q value = 1

Table S321. Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
SIN3A MUTATED	16	1	0	0	3	0
SIN3A WILD-TYPE	141	11	54	8	7	1

Figure S94. Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SIN3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S322. Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
SIN3A MUTATED	4	3	7
SIN3A WILD-TYPE	39	38	44

'SIN3A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00607 (Chi-square test), Q value = 1

Table S323. Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
SIN3A MUTATED	3	9	3	2	0	1
SIN3A WILD-TYPE	36	27	34	8	40	23

Figure S95. Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'SIN3A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S324. Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
SIN3A MUTATED	8	10
SIN3A WILD-TYPE	107	61

'SIN3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.87

Table S325. Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
SIN3A MUTATED	3	5	12	1
SIN3A WILD-TYPE	60	31	60	73

Figure S96. Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SIN3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 1

Table S326. Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
SIN3A MUTATED	10	7	4
SIN3A WILD-TYPE	75	41	108

Figure S97. Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SIN3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.16 (Chi-square test), Q value = 1

Table S327. Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
SIN3A MUTATED	4	2	2	4	9
SIN3A WILD-TYPE	38	76	21	22	62

'SIN3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00595 (Fisher's exact test), Q value = 1

Table S328. Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
SIN3A MUTATED	1	5	15
SIN3A WILD-TYPE	3	126	90

Figure S98. Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SIN3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S329. Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
SIN3A MUTATED	4	3	3
SIN3A WILD-TYPE	32	23	51

'SIN3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S330. Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
SIN3A MUTATED	3	2	4	1
SIN3A WILD-TYPE	20	20	61	5

'SLC48A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.736 (Chi-square test), Q value = 1

Table S331. Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
SLC48A1 MUTATED	5	0	0	0	0	0
SLC48A1 WILD-TYPE	152	12	54	8	10	1

'SLC48A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S332. Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
SLC48A1 MUTATED	0	1	2
SLC48A1 WILD-TYPE	43	40	49

'SLC48A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.803 (Chi-square test), Q value = 1

Table S333. Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
SLC48A1 MUTATED	1	1	0	0	2	1
SLC48A1 WILD-TYPE	38	35	37	10	38	23

'SLC48A1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S334. Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
SLC48A1 MUTATED	2	3
SLC48A1 WILD-TYPE	113	68

'SLC48A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S335. Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
SLC48A1 MUTATED	1	1	2	1
SLC48A1 WILD-TYPE	62	35	70	73

'SLC48A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S336. Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
SLC48A1 MUTATED	1	1	3
SLC48A1 WILD-TYPE	84	47	109

'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.726 (Chi-square test), Q value = 1

Table S337. Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
SLC48A1 MUTATED	0	2	0	1	2
SLC48A1 WILD-TYPE	42	76	23	25	69

'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S338. Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
SLC48A1 MUTATED	0	2	3
SLC48A1 WILD-TYPE	4	129	102

'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S339. Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
SLC48A1 MUTATED	1	1	1
SLC48A1 WILD-TYPE	35	25	53

'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S340. Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
SLC48A1 MUTATED	1	1	1	0
SLC48A1 WILD-TYPE	22	21	64	6

'RNF43 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S341. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
RNF43 MUTATED	3	1	0	0
RNF43 WILD-TYPE	9	17	11	10

'RNF43 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 1

Table S342. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
RNF43 MUTATED	3	0	1
RNF43 WILD-TYPE	14	18	15

'RNF43 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.443 (Chi-square test), Q value = 1

Table S343. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
RNF43 MUTATED	10	1	0	0	1	0
RNF43 WILD-TYPE	147	11	54	8	9	1

'RNF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S344. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
RNF43 MUTATED	2	0	3
RNF43 WILD-TYPE	41	41	48

'RNF43 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.296 (Chi-square test), Q value = 1

Table S345. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
RNF43 MUTATED	3	2	5	1	1	0
RNF43 WILD-TYPE	36	34	32	9	39	24

'RNF43 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S346. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
RNF43 MUTATED	8	4
RNF43 WILD-TYPE	107	67

'RNF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 1

Table S347. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
RNF43 MUTATED	1	4	6	1
RNF43 WILD-TYPE	62	32	66	73

Figure S99. Get High-res Image Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RNF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.55e-05 (Fisher's exact test), Q value = 0.0089

Table S348. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
RNF43 MUTATED	2	9	1
RNF43 WILD-TYPE	83	39	111

Figure S100. Get High-res Image Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RNF43 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.129 (Chi-square test), Q value = 1

Table S349. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
RNF43 MUTATED	1	1	2	1	7
RNF43 WILD-TYPE	41	77	21	25	64

'RNF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S350. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
RNF43 MUTATED	0	5	7
RNF43 WILD-TYPE	4	126	98

'RNF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.349 (Fisher's exact test), Q value = 1

Table S351. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
RNF43 MUTATED	1	2	1
RNF43 WILD-TYPE	35	24	53

'RNF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S352. Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
RNF43 MUTATED	2	0	2	0
RNF43 WILD-TYPE	21	22	63	6

'ZFHX3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S353. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
ZFHX3 MUTATED	6	6	2	2
ZFHX3 WILD-TYPE	6	12	9	8

'ZFHX3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 1

Table S354. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
ZFHX3 MUTATED	9	2	5
ZFHX3 WILD-TYPE	8	16	11

Figure S101. Get High-res Image Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ZFHX3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.094 (Chi-square test), Q value = 1

Table S355. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
ZFHX3 MUTATED	34	1	3	1	3	0
ZFHX3 WILD-TYPE	123	11	51	7	7	1

'ZFHX3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S356. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
ZFHX3 MUTATED	5	2	11
ZFHX3 WILD-TYPE	38	39	40

'ZFHX3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.318 (Chi-square test), Q value = 1

Table S357. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
ZFHX3 MUTATED	7	11	5	3	5	4
ZFHX3 WILD-TYPE	32	25	32	7	35	20

'ZFHX3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 1

Table S358. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
ZFHX3 MUTATED	18	17
ZFHX3 WILD-TYPE	97	54

'ZFHX3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S359. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
ZFHX3 MUTATED	9	9	12	13
ZFHX3 WILD-TYPE	54	27	60	61

'ZFHX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S360. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
ZFHX3 MUTATED	15	13	15
ZFHX3 WILD-TYPE	70	35	97

'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.207 (Chi-square test), Q value = 1

Table S361. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
ZFHX3 MUTATED	3	14	4	3	17
ZFHX3 WILD-TYPE	39	64	19	23	54

'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S362. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
ZFHX3 MUTATED	1	21	19
ZFHX3 WILD-TYPE	3	110	86

'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S363. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
ZFHX3 MUTATED	4	4	8
ZFHX3 WILD-TYPE	32	22	46

'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S364. Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
ZFHX3 MUTATED	4	1	10	1
ZFHX3 WILD-TYPE	19	21	55	5

'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S365. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	18	11	10
RB1 MUTATED	1	3	2	0
RB1 WILD-TYPE	11	15	9	10

'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S366. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	18	16
RB1 MUTATED	2	2	2
RB1 WILD-TYPE	15	16	14

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.31 (Chi-square test), Q value = 1

Table S367. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	157	12	54	8	10	1
RB1 MUTATED	16	0	2	0	2	0
RB1 WILD-TYPE	141	12	52	8	8	1

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S368. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	41	51
RB1 MUTATED	2	2	5
RB1 WILD-TYPE	41	39	46

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.12 (Chi-square test), Q value = 1

Table S369. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	39	36	37	10	40	24
RB1 MUTATED	3	6	2	3	3	1
RB1 WILD-TYPE	36	30	35	7	37	23

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S370. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	115	71
RB1 MUTATED	9	9
RB1 WILD-TYPE	106	62

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S371. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	36	72	74
RB1 MUTATED	6	2	8	4
RB1 WILD-TYPE	57	34	64	70

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.271 (Fisher's exact test), Q value = 1

Table S372. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	85	48	112
RB1 MUTATED	10	4	6
RB1 WILD-TYPE	75	44	106

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.955 (Chi-square test), Q value = 1

Table S373. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	42	78	23	26	71
RB1 MUTATED	3	5	2	2	7
RB1 WILD-TYPE	39	73	21	24	64

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.43

Table S374. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	4	131	105
RB1 MUTATED	3	7	9
RB1 WILD-TYPE	1	124	96

Figure S102. Get High-res Image Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S375. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	36	26	54
RB1 MUTATED	1	1	3
RB1 WILD-TYPE	35	25	51

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S376. Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	22	65	6
RB1 MUTATED	1	1	3	0
RB1 WILD-TYPE	22	21	62	6

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = UCEC-TP.transferedmergedcluster.txt
Number of patients = 248
Number of significantly mutated genes = 33
Number of Molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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