Correlation between gene mutation status and molecular subtypes

Glioblastoma Multiforme (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1DZ0744

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 10 molecular subtypes across 283 patients, 20 significant findings detected with P value < 0.05 and Q value < 0.25.

TP53 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
NF1 mutation correlated to 'MRNA_CHIERARCHICAL'.
IDH1 mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
ATRX mutation correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
EGFR mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 33 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 20 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	MIR CNMF	MIR CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
IDH1	14 (5%)	269	0.00011 (0.0298)	1e-05 (0.00283)	6e-05 (0.0164)	0.00311 (0.799)	3e-05 (0.00825)	1e-05 (0.00283)	0.00369 (0.941)	0.00125 (0.329)	0.00082 (0.217)	2e-05 (0.00554)
TP53	79 (28%)	204	0.00066 (0.176)	1e-05 (0.00283)	0.00149 (0.39)	0.149 (1.00)	1e-05 (0.00283)	0.00085 (0.224)	0.0376 (1.00)	0.00875 (1.00)	0.00174 (0.452)	0.00164 (0.428)
ATRX	16 (6%)	267	0.00206 (0.534)	1e-05 (0.00283)	0.00689 (1.00)	0.0183 (1.00)	2e-05 (0.00554)	4e-05 (0.011)	0.0059 (1.00)	0.0515 (1.00)	0.00207 (0.534)	0.00022 (0.0594)
EGFR	74 (26%)	209	0.00695 (1.00)	0.0557 (1.00)	0.51 (1.00)	0.14 (1.00)	1e-05 (0.00283)	0.00031 (0.0831)	7e-05 (0.019)	0.00025 (0.0672)	0.0421 (1.00)	0.00607 (1.00)
NF1	29 (10%)	254	0.0796 (1.00)	0.00041 (0.109)	0.0263 (1.00)	0.933 (1.00)	0.00869 (1.00)	0.0683 (1.00)	0.229 (1.00)	0.00596 (1.00)	0.566 (1.00)	0.452 (1.00)
PIK3R1	32 (11%)	251	0.756 (1.00)	0.193 (1.00)	0.198 (1.00)	0.531 (1.00)	0.636 (1.00)	0.247 (1.00)	0.989 (1.00)	0.679 (1.00)	0.408 (1.00)	0.223 (1.00)
RB1	24 (8%)	259	0.0334 (1.00)	0.0176 (1.00)	0.13 (1.00)	0.921 (1.00)	0.108 (1.00)	0.0108 (1.00)	0.492 (1.00)	0.227 (1.00)	0.0813 (1.00)	0.58 (1.00)
PTEN	87 (31%)	196	0.116 (1.00)	0.0754 (1.00)	0.0279 (1.00)	0.643 (1.00)	0.431 (1.00)	0.223 (1.00)	0.378 (1.00)	0.144 (1.00)	0.273 (1.00)	0.647 (1.00)
PIK3CA	29 (10%)	254	0.792 (1.00)	0.162 (1.00)	0.571 (1.00)	1 (1.00)	0.817 (1.00)	0.821 (1.00)	0.756 (1.00)	0.312 (1.00)	0.262 (1.00)	0.237 (1.00)
STAG2	12 (4%)	271	0.392 (1.00)	0.699 (1.00)	0.716 (1.00)	0.589 (1.00)	0.751 (1.00)	0.0432 (1.00)	0.00702 (1.00)	0.395 (1.00)	0.476 (1.00)	0.103 (1.00)
SEMG1	8 (3%)	275	0.68 (1.00)	0.177 (1.00)	0.888 (1.00)	1 (1.00)	0.163 (1.00)	0.168 (1.00)			1 (1.00)	0.337 (1.00)
RPL5	7 (2%)	276	0.381 (1.00)	0.508 (1.00)	0.868 (1.00)	0.468 (1.00)	1 (1.00)		0.844 (1.00)	0.686 (1.00)	0.465 (1.00)	1 (1.00)
SLC26A3	7 (2%)	276	0.94 (1.00)	0.767 (1.00)	0.465 (1.00)	0.364 (1.00)	0.648 (1.00)	0.183 (1.00)	0.166 (1.00)	0.155 (1.00)	0.155 (1.00)	0.164 (1.00)
MAP3K1	6 (2%)	277	1 (1.00)	0.73 (1.00)	0.808 (1.00)	0.647 (1.00)	1 (1.00)				0.575 (1.00)	1 (1.00)
BRAF	6 (2%)	277	0.769 (1.00)	0.713 (1.00)	0.318 (1.00)	0.0295 (1.00)	0.59 (1.00)		1 (1.00)	0.641 (1.00)	0.792 (1.00)	1 (1.00)
PDGFRA	11 (4%)	272	0.0125 (1.00)	0.146 (1.00)	0.905 (1.00)	0.137 (1.00)	0.195 (1.00)	0.73 (1.00)	1 (1.00)	1 (1.00)	0.0263 (1.00)	0.00453 (1.00)
KDR	8 (3%)	275	0.205 (1.00)	0.654 (1.00)	0.279 (1.00)	0.513 (1.00)	0.732 (1.00)	0.346 (1.00)	0.143 (1.00)	0.526 (1.00)
TMPRSS6	6 (2%)	277	0.668 (1.00)	0.702 (1.00)	0.664 (1.00)	0.264 (1.00)	0.881 (1.00)	0.349 (1.00)	0.254 (1.00)	0.327 (1.00)	0.572 (1.00)	1 (1.00)
CHD8	9 (3%)	274	0.701 (1.00)	0.531 (1.00)	0.133 (1.00)	0.644 (1.00)	0.188 (1.00)		0.624 (1.00)	0.758 (1.00)	0.274 (1.00)	0.611 (1.00)
SEMA3C	11 (4%)	272	0.485 (1.00)	0.174 (1.00)	0.121 (1.00)	0.85 (1.00)	0.543 (1.00)	0.414 (1.00)	0.339 (1.00)	0.683 (1.00)	0.103 (1.00)	0.166 (1.00)
ZDHHC4	3 (1%)	280			0.165 (1.00)	1 (1.00)	0.0517 (1.00)
MMP13	5 (2%)	278	0.911 (1.00)	0.218 (1.00)	0.766 (1.00)	0.0503 (1.00)	0.152 (1.00)
PRKCD	3 (1%)	280	0.175 (1.00)	0.0835 (1.00)	0.164 (1.00)	1 (1.00)	0.38 (1.00)
REN	5 (2%)	278	0.48 (1.00)	0.416 (1.00)	0.0736 (1.00)	0.516 (1.00)	0.62 (1.00)		1 (1.00)	0.834 (1.00)
LRRC55	6 (2%)	277	0.373 (1.00)	0.537 (1.00)	0.336 (1.00)	0.868 (1.00)	0.332 (1.00)
MUC17	22 (8%)	261	0.0121 (1.00)	0.191 (1.00)	0.706 (1.00)	0.703 (1.00)	0.924 (1.00)	0.841 (1.00)	0.243 (1.00)	0.326 (1.00)	0.861 (1.00)	1 (1.00)
CD209	5 (2%)	278	0.911 (1.00)	1 (1.00)	0.0672 (1.00)	0.608 (1.00)	0.691 (1.00)		0.488 (1.00)	1 (1.00)
DDX5	4 (1%)	279	0.218 (1.00)	1 (1.00)	0.537 (1.00)	0.445 (1.00)	0.143 (1.00)
TP63	6 (2%)	277	1 (1.00)	0.73 (1.00)	0.409 (1.00)	0.647 (1.00)	0.775 (1.00)		0.0681 (1.00)	0.208 (1.00)	0.254 (1.00)	0.11 (1.00)
CD1D	4 (1%)	279	0.88 (1.00)	1 (1.00)	0.643 (1.00)	0.123 (1.00)	0.825 (1.00)		0.891 (1.00)	1 (1.00)
LZTR1	10 (4%)	273	1 (1.00)	0.518 (1.00)	0.36 (1.00)	0.703 (1.00)	0.443 (1.00)	0.13 (1.00)	0.84 (1.00)	0.894 (1.00)	0.174 (1.00)	0.751 (1.00)
TEX15	8 (3%)	275	0.309 (1.00)	0.243 (1.00)	0.3 (1.00)	0.72 (1.00)	0.547 (1.00)	0.823 (1.00)	0.868 (1.00)	0.275 (1.00)	0.00346 (0.886)	0.824 (1.00)
FBN3	11 (4%)	272	0.191 (1.00)	0.308 (1.00)	0.905 (1.00)	0.922 (1.00)	0.106 (1.00)	1 (1.00)	0.279 (1.00)	0.373 (1.00)	0.857 (1.00)	1 (1.00)

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.18

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
TP53 MUTATED	16	19	11	22
TP53 WILD-TYPE	53	24	63	32

Figure S1. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0028

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
TP53 MUTATED	15	30	7	16
TP53 WILD-TYPE	48	20	41	63

Figure S2. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.39

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
TP53 MUTATED	12	39	10	18
TP53 WILD-TYPE	65	54	35	42

Figure S3. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'TP53 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
TP53 MUTATED	47	15	17
TP53 WILD-TYPE	91	46	59

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0028

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
TP53 MUTATED	35	14	29
TP53 WILD-TYPE	48	96	51

Figure S4. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.22

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
TP53 MUTATED	9	13	19
TP53 WILD-TYPE	34	39	13

Figure S5. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
TP53 MUTATED	12	17	4	10
TP53 WILD-TYPE	29	21	27	23

Figure S6. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00875 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
TP53 MUTATED	15	22	6
TP53 WILD-TYPE	33	30	37

Figure S7. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.45

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
TP53 MUTATED	23	13	8
TP53 WILD-TYPE	21	49	27

Figure S8. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00164 (Fisher's exact test), Q value = 0.43

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
TP53 MUTATED	18	21	5
TP53 WILD-TYPE	13	65	19

Figure S9. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S11. Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
PIK3R1 MUTATED	7	2	8	5
PIK3R1 WILD-TYPE	62	41	66	49

'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S12. Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
PIK3R1 MUTATED	7	6	6	3
PIK3R1 WILD-TYPE	56	44	42	76

'PIK3R1 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S13. Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
PIK3R1 MUTATED	12	13	4	3
PIK3R1 WILD-TYPE	65	80	41	57

'PIK3R1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S14. Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
PIK3R1 MUTATED	16	5	11
PIK3R1 WILD-TYPE	122	56	65

'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S15. Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
PIK3R1 MUTATED	7	14	10
PIK3R1 WILD-TYPE	76	96	70

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S16. Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
PIK3R1 MUTATED	2	5	5
PIK3R1 WILD-TYPE	41	47	27

'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S17. Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
PIK3R1 MUTATED	7	6	4	5
PIK3R1 WILD-TYPE	34	32	27	28

'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
PIK3R1 MUTATED	9	8	5
PIK3R1 WILD-TYPE	39	44	38

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S19. Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
PIK3R1 MUTATED	5	6	1
PIK3R1 WILD-TYPE	39	56	34

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 1

Table S20. Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
PIK3R1 MUTATED	4	8	0
PIK3R1 WILD-TYPE	27	78	24

'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 1

Table S21. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
RB1 MUTATED	11	2	3	2
RB1 WILD-TYPE	58	41	71	52

Figure S10. Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 1

Table S22. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
RB1 MUTATED	5	2	0	11
RB1 WILD-TYPE	58	48	48	68

Figure S11. Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S23. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
RB1 MUTATED	11	4	3	6
RB1 WILD-TYPE	66	89	42	54

'RB1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.921 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
RB1 MUTATED	12	6	6
RB1 WILD-TYPE	126	55	70

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S25. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
RB1 MUTATED	9	5	10
RB1 WILD-TYPE	74	105	70

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
RB1 MUTATED	9	2	1
RB1 WILD-TYPE	34	50	31

Figure S12. Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S27. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
RB1 MUTATED	3	1	2	4
RB1 WILD-TYPE	38	37	29	29

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S28. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
RB1 MUTATED	6	2	2
RB1 WILD-TYPE	42	50	41

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0813 (Fisher's exact test), Q value = 1

Table S29. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
RB1 MUTATED	1	8	1
RB1 WILD-TYPE	43	54	34

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.58 (Fisher's exact test), Q value = 1

Table S30. Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
RB1 MUTATED	1	8	1
RB1 WILD-TYPE	30	78	23

'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S31. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
NF1 MUTATED	11	4	4	2
NF1 WILD-TYPE	58	39	70	52

'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.11

Table S32. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
NF1 MUTATED	14	1	1	5
NF1 WILD-TYPE	49	49	47	74

Figure S13. Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
NF1 MUTATED	12	3	5	8
NF1 WILD-TYPE	65	90	40	52

Figure S14. Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'NF1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S34. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
NF1 MUTATED	14	7	7
NF1 WILD-TYPE	124	54	69

'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00869 (Fisher's exact test), Q value = 1

Table S35. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
NF1 MUTATED	5	8	16
NF1 WILD-TYPE	78	102	64

Figure S15. Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0683 (Fisher's exact test), Q value = 1

Table S36. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
NF1 MUTATED	8	2	3
NF1 WILD-TYPE	35	50	29

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S37. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
NF1 MUTATED	7	3	1	5
NF1 WILD-TYPE	34	35	30	28

'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00596 (Fisher's exact test), Q value = 1

Table S38. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
NF1 MUTATED	11	4	1
NF1 WILD-TYPE	37	48	42

Figure S16. Get High-res Image Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S39. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
NF1 MUTATED	2	5	4
NF1 WILD-TYPE	42	57	31

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S40. Gene #4: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
NF1 MUTATED	1	7	3
NF1 WILD-TYPE	30	79	21

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 1

Table S41. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
PTEN MUTATED	25	10	18	22
PTEN WILD-TYPE	44	33	56	32

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0754 (Fisher's exact test), Q value = 1

Table S42. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
PTEN MUTATED	18	16	9	32
PTEN WILD-TYPE	45	34	39	47

'PTEN MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 1

Table S43. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
PTEN MUTATED	30	19	18	20
PTEN WILD-TYPE	47	74	27	40

Figure S17. Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'PTEN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S44. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
PTEN MUTATED	45	21	21
PTEN WILD-TYPE	93	40	55

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.431 (Fisher's exact test), Q value = 1

Table S45. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
PTEN MUTATED	30	30	25
PTEN WILD-TYPE	53	80	55

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 1

Table S46. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
PTEN MUTATED	17	12	11
PTEN WILD-TYPE	26	40	21

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S47. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
PTEN MUTATED	12	14	6	12
PTEN WILD-TYPE	29	24	25	21

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S48. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
PTEN MUTATED	20	13	11
PTEN WILD-TYPE	28	39	32

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 1

Table S49. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
PTEN MUTATED	10	23	12
PTEN WILD-TYPE	34	39	23

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S50. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
PTEN MUTATED	8	28	9
PTEN WILD-TYPE	23	58	15

'IDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.03

Table S51. Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
IDH1 MUTATED	1	3	0	9
IDH1 WILD-TYPE	68	40	74	45

Figure S18. Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0028

Table S52. Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
IDH1 MUTATED	0	13	0	0
IDH1 WILD-TYPE	63	37	48	79

Figure S19. Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.016

Table S53. Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
IDH1 MUTATED	0	13	1	0
IDH1 WILD-TYPE	77	80	44	60

Figure S20. Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'IDH1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.00311 (Fisher's exact test), Q value = 0.8

Table S54. Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
IDH1 MUTATED	13	0	1
IDH1 WILD-TYPE	125	61	75

Figure S21. Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0082

Table S55. Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
IDH1 MUTATED	2	0	11
IDH1 WILD-TYPE	81	110	69

Figure S22. Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0028

Table S56. Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
IDH1 MUTATED	0	0	9
IDH1 WILD-TYPE	43	52	23

Figure S23. Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00369 (Fisher's exact test), Q value = 0.94

Table S57. Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
IDH1 MUTATED	1	6	0	0
IDH1 WILD-TYPE	40	32	31	33

Figure S24. Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.33

Table S58. Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
IDH1 MUTATED	0	7	0
IDH1 WILD-TYPE	48	45	43

Figure S25. Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.22

Table S59. Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
IDH1 MUTATED	7	0	1
IDH1 WILD-TYPE	37	62	34

Figure S26. Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0055

Table S60. Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
IDH1 MUTATED	8	0	0
IDH1 WILD-TYPE	23	86	24

Figure S27. Get High-res Image Gene #6: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S61. Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
PIK3CA MUTATED	6	6	9	5
PIK3CA WILD-TYPE	63	37	65	49

'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S62. Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
PIK3CA MUTATED	8	6	8	4
PIK3CA WILD-TYPE	55	44	40	75

'PIK3CA MUTATION STATUS' versus 'MIR_CNMF'

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

Table S63. Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
PIK3CA MUTATED	9	11	2	6
PIK3CA WILD-TYPE	68	82	43	54

'PIK3CA MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S64. Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
PIK3CA MUTATED	14	6	8
PIK3CA WILD-TYPE	124	55	68

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

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

Table S65. Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
PIK3CA MUTATED	7	11	9
PIK3CA WILD-TYPE	76	99	71

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S66. Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
PIK3CA MUTATED	4	7	3
PIK3CA WILD-TYPE	39	45	29

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S67. Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
PIK3CA MUTATED	3	5	2	4
PIK3CA WILD-TYPE	38	33	29	29

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S68. Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
PIK3CA MUTATED	7	5	2
PIK3CA WILD-TYPE	41	47	41

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S69. Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
PIK3CA MUTATED	6	3	2
PIK3CA WILD-TYPE	38	59	33

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S70. Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
PIK3CA MUTATED	4	7	0
PIK3CA WILD-TYPE	27	79	24

'STAG2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S71. Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
STAG2 MUTATED	4	3	1	2
STAG2 WILD-TYPE	65	40	73	52

'STAG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S72. Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
STAG2 MUTATED	2	1	3	4
STAG2 WILD-TYPE	61	49	45	75

'STAG2 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.716 (Fisher's exact test), Q value = 1

Table S73. Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
STAG2 MUTATED	4	5	2	1
STAG2 WILD-TYPE	73	88	43	59

'STAG2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S74. Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
STAG2 MUTATED	5	2	5
STAG2 WILD-TYPE	133	59	71

'STAG2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S75. Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
STAG2 MUTATED	5	4	3
STAG2 WILD-TYPE	78	106	77

'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 1

Table S76. Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
STAG2 MUTATED	4	0	1
STAG2 WILD-TYPE	39	52	31

Figure S28. Get High-res Image Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00702 (Fisher's exact test), Q value = 1

Table S77. Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
STAG2 MUTATED	0	2	0	5
STAG2 WILD-TYPE	41	36	31	28

Figure S29. Get High-res Image Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 1

Table S78. Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
STAG2 MUTATED	4	2	1
STAG2 WILD-TYPE	44	50	42

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 1

Table S79. Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
STAG2 MUTATED	1	3	3
STAG2 WILD-TYPE	43	59	32

'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S80. Gene #8: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
STAG2 MUTATED	0	4	3
STAG2 WILD-TYPE	31	82	21

'SEMG1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S81. Gene #9: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
SEMG1 MUTATED	1	1	4	2
SEMG1 WILD-TYPE	68	42	70	52

'SEMG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S82. Gene #9: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
SEMG1 MUTATED	0	2	1	5
SEMG1 WILD-TYPE	63	48	47	74

'SEMG1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S83. Gene #9: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
SEMG1 MUTATED	2	4	1	1
SEMG1 WILD-TYPE	75	89	44	59

'SEMG1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S84. Gene #9: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
SEMG1 MUTATED	4	2	2
SEMG1 WILD-TYPE	134	59	74

'SEMG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 1

Table S85. Gene #9: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
SEMG1 MUTATED	3	5	0
SEMG1 WILD-TYPE	80	105	80

'SEMG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 1

Table S86. Gene #9: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
SEMG1 MUTATED	2	0	2
SEMG1 WILD-TYPE	41	52	30

'SEMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S87. Gene #9: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
SEMG1 MUTATED	1	1	1
SEMG1 WILD-TYPE	43	61	34

'SEMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S88. Gene #9: 'SEMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
SEMG1 MUTATED	1	1	1
SEMG1 WILD-TYPE	30	85	23

'RPL5 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S89. Gene #10: 'RPL5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
RPL5 MUTATED	1	2	3	0
RPL5 WILD-TYPE	68	41	71	54

'RPL5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S90. Gene #10: 'RPL5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
RPL5 MUTATED	3	0	1	2
RPL5 WILD-TYPE	60	50	47	77

'RPL5 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S91. Gene #10: 'RPL5 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
RPL5 MUTATED	1	3	1	2
RPL5 WILD-TYPE	76	90	44	58

'RPL5 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S92. Gene #10: 'RPL5 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
RPL5 MUTATED	3	3	1
RPL5 WILD-TYPE	135	58	75

'RPL5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S93. Gene #10: 'RPL5 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
RPL5 MUTATED	2	3	2
RPL5 WILD-TYPE	81	107	78

'RPL5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.844 (Fisher's exact test), Q value = 1

Table S94. Gene #10: 'RPL5 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
RPL5 MUTATED	2	1	1	0
RPL5 WILD-TYPE	39	37	30	33

'RPL5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S95. Gene #10: 'RPL5 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
RPL5 MUTATED	1	1	2
RPL5 WILD-TYPE	47	51	41

'RPL5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S96. Gene #10: 'RPL5 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
RPL5 MUTATED	2	1	0
RPL5 WILD-TYPE	42	61	35

'RPL5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S97. Gene #10: 'RPL5 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
RPL5 MUTATED	1	2	0
RPL5 WILD-TYPE	30	84	24

'SLC26A3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.94 (Fisher's exact test), Q value = 1

Table S98. Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
SLC26A3 MUTATED	1	1	2	2
SLC26A3 WILD-TYPE	68	42	72	52

'SLC26A3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S99. Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
SLC26A3 MUTATED	2	1	2	1
SLC26A3 WILD-TYPE	61	49	46	78

'SLC26A3 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S100. Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
SLC26A3 MUTATED	1	4	0	2
SLC26A3 WILD-TYPE	76	89	45	58

'SLC26A3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S101. Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
SLC26A3 MUTATED	4	0	3
SLC26A3 WILD-TYPE	134	61	73

'SLC26A3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S102. Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
SLC26A3 MUTATED	2	4	1
SLC26A3 WILD-TYPE	81	106	79

'SLC26A3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S103. Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
SLC26A3 MUTATED	0	3	0
SLC26A3 WILD-TYPE	43	49	32

'SLC26A3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S104. Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
SLC26A3 MUTATED	3	0	1	0
SLC26A3 WILD-TYPE	38	38	30	33

'SLC26A3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S105. Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
SLC26A3 MUTATED	3	0	1
SLC26A3 WILD-TYPE	45	52	42

'SLC26A3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S106. Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
SLC26A3 MUTATED	2	0	2
SLC26A3 WILD-TYPE	42	62	33

'SLC26A3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S107. Gene #11: 'SLC26A3 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
SLC26A3 MUTATED	2	1	1
SLC26A3 WILD-TYPE	29	85	23

'MAP3K1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S108. Gene #12: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
MAP3K1 MUTATED	1	1	2	1
MAP3K1 WILD-TYPE	68	42	72	53

'MAP3K1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S109. Gene #12: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
MAP3K1 MUTATED	1	1	2	1
MAP3K1 WILD-TYPE	62	49	46	78

'MAP3K1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 1

Table S110. Gene #12: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
MAP3K1 MUTATED	2	2	0	2
MAP3K1 WILD-TYPE	75	91	45	58

'MAP3K1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S111. Gene #12: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
MAP3K1 MUTATED	2	2	2
MAP3K1 WILD-TYPE	136	59	74

'MAP3K1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S112. Gene #12: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
MAP3K1 MUTATED	2	2	2
MAP3K1 WILD-TYPE	81	108	78

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S113. Gene #12: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
MAP3K1 MUTATED	1	3	0
MAP3K1 WILD-TYPE	43	59	35

'MAP3K1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S114. Gene #12: 'MAP3K1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
MAP3K1 MUTATED	1	3	0
MAP3K1 WILD-TYPE	30	83	24

'ATRX MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.53

Table S115. Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
ATRX MUTATED	2	4	0	7
ATRX WILD-TYPE	67	39	74	47

Figure S30. Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ATRX MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0028

Table S116. Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
ATRX MUTATED	0	11	0	2
ATRX WILD-TYPE	63	39	48	77

Figure S31. Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 1

Table S117. Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
ATRX MUTATED	2	11	3	0
ATRX WILD-TYPE	75	82	42	60

Figure S32. Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'ATRX MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 1

Table S118. Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
ATRX MUTATED	13	0	3
ATRX WILD-TYPE	125	61	73

Figure S33. Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'ATRX MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0055

Table S119. Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
ATRX MUTATED	1	1	13
ATRX WILD-TYPE	82	109	67

Figure S34. Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'ATRX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.011

Table S120. Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
ATRX MUTATED	0	0	8
ATRX WILD-TYPE	43	52	24

Figure S35. Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'ATRX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0059 (Fisher's exact test), Q value = 1

Table S121. Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
ATRX MUTATED	0	6	0	2
ATRX WILD-TYPE	41	32	31	31

Figure S36. Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'ATRX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0515 (Fisher's exact test), Q value = 1

Table S122. Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
ATRX MUTATED	2	6	0
ATRX WILD-TYPE	46	46	43

'ATRX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.53

Table S123. Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
ATRX MUTATED	7	1	0
ATRX WILD-TYPE	37	61	35

Figure S37. Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'ATRX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.059

Table S124. Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
ATRX MUTATED	7	1	0
ATRX WILD-TYPE	24	85	24

Figure S38. Get High-res Image Gene #13: 'ATRX MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S125. Gene #14: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
BRAF MUTATED	1	1	2	0
BRAF WILD-TYPE	68	42	72	54

'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.713 (Fisher's exact test), Q value = 1

Table S126. Gene #14: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
BRAF MUTATED	2	0	1	1
BRAF WILD-TYPE	61	50	47	78

'BRAF MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 1

Table S127. Gene #14: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
BRAF MUTATED	2	1	0	3
BRAF WILD-TYPE	75	92	45	57

'BRAF MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 1

Table S128. Gene #14: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
BRAF MUTATED	2	4	0
BRAF WILD-TYPE	136	57	76

Figure S39. Get High-res Image Gene #14: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

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

Table S129. Gene #14: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
BRAF MUTATED	1	2	3
BRAF WILD-TYPE	82	108	77

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S130. Gene #14: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
BRAF MUTATED	1	1	0	1
BRAF WILD-TYPE	40	37	31	32

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S131. Gene #14: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
BRAF MUTATED	2	1	0
BRAF WILD-TYPE	46	51	43

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S132. Gene #14: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
BRAF MUTATED	1	2	0
BRAF WILD-TYPE	43	60	35

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S133. Gene #14: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
BRAF MUTATED	1	2	0
BRAF WILD-TYPE	30	84	24

'EGFR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00695 (Fisher's exact test), Q value = 1

Table S134. Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
EGFR MUTATED	20	7	31	10
EGFR WILD-TYPE	49	36	43	44

Figure S40. Get High-res Image Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'EGFR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0557 (Fisher's exact test), Q value = 1

Table S135. Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
EGFR MUTATED	18	7	17	26
EGFR WILD-TYPE	45	43	31	53

'EGFR MUTATION STATUS' versus 'MIR_CNMF'

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

Table S136. Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
EGFR MUTATED	22	27	8	17
EGFR WILD-TYPE	55	66	37	43

'EGFR MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 1

Table S137. Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
EGFR MUTATED	30	19	25
EGFR WILD-TYPE	108	42	51

'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0028

Table S138. Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
EGFR MUTATED	15	48	9
EGFR WILD-TYPE	68	62	71

Figure S41. Get High-res Image Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.083

Table S139. Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
EGFR MUTATED	13	24	2
EGFR WILD-TYPE	30	28	30

Figure S42. Get High-res Image Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.019

Table S140. Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
EGFR MUTATED	13	5	16	2
EGFR WILD-TYPE	28	33	15	31

Figure S43. Get High-res Image Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.067

Table S141. Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
EGFR MUTATED	8	7	21
EGFR WILD-TYPE	40	45	22

Figure S44. Get High-res Image Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 1

Table S142. Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
EGFR MUTATED	8	22	15
EGFR WILD-TYPE	36	40	20

Figure S45. Get High-res Image Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00607 (Fisher's exact test), Q value = 1

Table S143. Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
EGFR MUTATED	3	32	10
EGFR WILD-TYPE	28	54	14

Figure S46. Get High-res Image Gene #15: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'PDGFRA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 1

Table S144. Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
PDGFRA MUTATED	1	6	2	1
PDGFRA WILD-TYPE	68	37	72	53

Figure S47. Get High-res Image Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PDGFRA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S145. Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
PDGFRA MUTATED	1	5	2	2
PDGFRA WILD-TYPE	62	45	46	77

'PDGFRA MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S146. Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
PDGFRA MUTATED	4	3	2	2
PDGFRA WILD-TYPE	73	90	43	58

'PDGFRA MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S147. Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
PDGFRA MUTATED	9	1	1
PDGFRA WILD-TYPE	129	60	75

'PDGFRA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S148. Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
PDGFRA MUTATED	2	3	6
PDGFRA WILD-TYPE	81	107	74

'PDGFRA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S149. Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
PDGFRA MUTATED	1	2	2
PDGFRA WILD-TYPE	42	50	30

'PDGFRA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S150. Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
PDGFRA MUTATED	2	1	1	1
PDGFRA WILD-TYPE	39	37	30	32

'PDGFRA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S151. Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
PDGFRA MUTATED	2	2	1
PDGFRA WILD-TYPE	46	50	42

'PDGFRA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 1

Table S152. Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
PDGFRA MUTATED	5	1	0
PDGFRA WILD-TYPE	39	61	35

Figure S48. Get High-res Image Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'PDGFRA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00453 (Fisher's exact test), Q value = 1

Table S153. Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
PDGFRA MUTATED	5	1	0
PDGFRA WILD-TYPE	26	85	24

Figure S49. Get High-res Image Gene #16: 'PDGFRA MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'KDR MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S154. Gene #17: 'KDR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
KDR MUTATED	1	2	1	4
KDR WILD-TYPE	68	41	73	50

'KDR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 1

Table S155. Gene #17: 'KDR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
KDR MUTATED	1	3	1	3
KDR WILD-TYPE	62	47	47	76

'KDR MUTATION STATUS' versus 'MIR_CNMF'

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

Table S156. Gene #17: 'KDR MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
KDR MUTATED	2	1	3	2
KDR WILD-TYPE	75	92	42	58

'KDR MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S157. Gene #17: 'KDR MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
KDR MUTATED	6	1	1
KDR WILD-TYPE	132	60	75

'KDR MUTATION STATUS' versus 'CN_CNMF'

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

Table S158. Gene #17: 'KDR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
KDR MUTATED	3	2	3
KDR WILD-TYPE	80	108	77

'KDR MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S159. Gene #17: 'KDR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
KDR MUTATED	2	0	1
KDR WILD-TYPE	41	52	31

'KDR MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S160. Gene #17: 'KDR MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
KDR MUTATED	3	0	0	2
KDR WILD-TYPE	38	38	31	31

'KDR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S161. Gene #17: 'KDR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
KDR MUTATED	3	1	1
KDR WILD-TYPE	45	51	42

'TMPRSS6 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S162. Gene #18: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
TMPRSS6 MUTATED	2	0	3	1
TMPRSS6 WILD-TYPE	67	43	71	53

'TMPRSS6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S163. Gene #18: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
TMPRSS6 MUTATED	3	1	1	1
TMPRSS6 WILD-TYPE	60	49	47	78

'TMPRSS6 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S164. Gene #18: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
TMPRSS6 MUTATED	3	1	1	1
TMPRSS6 WILD-TYPE	74	92	44	59

'TMPRSS6 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.264 (Fisher's exact test), Q value = 1

Table S165. Gene #18: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
TMPRSS6 MUTATED	2	3	1
TMPRSS6 WILD-TYPE	136	58	75

'TMPRSS6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.881 (Fisher's exact test), Q value = 1

Table S166. Gene #18: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
TMPRSS6 MUTATED	2	3	1
TMPRSS6 WILD-TYPE	81	107	79

'TMPRSS6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S167. Gene #18: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
TMPRSS6 MUTATED	2	0	1
TMPRSS6 WILD-TYPE	41	52	31

'TMPRSS6 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S168. Gene #18: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
TMPRSS6 MUTATED	2	0	2	0
TMPRSS6 WILD-TYPE	39	38	29	33

'TMPRSS6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.327 (Fisher's exact test), Q value = 1

Table S169. Gene #18: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
TMPRSS6 MUTATED	2	0	2
TMPRSS6 WILD-TYPE	46	52	41

'TMPRSS6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S170. Gene #18: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
TMPRSS6 MUTATED	1	4	1
TMPRSS6 WILD-TYPE	43	58	34

'TMPRSS6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S171. Gene #18: 'TMPRSS6 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
TMPRSS6 MUTATED	1	4	1
TMPRSS6 WILD-TYPE	30	82	23

'CHD8 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S172. Gene #19: 'CHD8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
CHD8 MUTATED	3	2	1	2
CHD8 WILD-TYPE	66	41	73	52

'CHD8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S173. Gene #19: 'CHD8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
CHD8 MUTATED	2	2	0	4
CHD8 WILD-TYPE	61	48	48	75

'CHD8 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S174. Gene #19: 'CHD8 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
CHD8 MUTATED	0	3	3	2
CHD8 WILD-TYPE	77	90	42	58

'CHD8 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S175. Gene #19: 'CHD8 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
CHD8 MUTATED	5	2	1
CHD8 WILD-TYPE	133	59	75

'CHD8 MUTATION STATUS' versus 'CN_CNMF'

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

Table S176. Gene #19: 'CHD8 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
CHD8 MUTATED	1	3	5
CHD8 WILD-TYPE	82	107	75

'CHD8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 1

Table S177. Gene #19: 'CHD8 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
CHD8 MUTATED	2	4	2	1
CHD8 WILD-TYPE	39	34	29	32

'CHD8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.758 (Fisher's exact test), Q value = 1

Table S178. Gene #19: 'CHD8 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
CHD8 MUTATED	2	4	3
CHD8 WILD-TYPE	46	48	40

'CHD8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 1

Table S179. Gene #19: 'CHD8 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
CHD8 MUTATED	2	1	3
CHD8 WILD-TYPE	42	61	32

'CHD8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.611 (Fisher's exact test), Q value = 1

Table S180. Gene #19: 'CHD8 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
CHD8 MUTATED	2	4	0
CHD8 WILD-TYPE	29	82	24

'SEMA3C MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 1

Table S181. Gene #20: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
SEMA3C MUTATED	3	4	2	2
SEMA3C WILD-TYPE	66	39	72	52

'SEMA3C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S182. Gene #20: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
SEMA3C MUTATED	1	5	1	4
SEMA3C WILD-TYPE	62	45	47	75

'SEMA3C MUTATION STATUS' versus 'MIR_CNMF'

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

Table S183. Gene #20: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
SEMA3C MUTATED	3	7	1	0
SEMA3C WILD-TYPE	74	86	44	60

'SEMA3C MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S184. Gene #20: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
SEMA3C MUTATED	5	2	4
SEMA3C WILD-TYPE	133	59	72

'SEMA3C MUTATION STATUS' versus 'CN_CNMF'

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

Table S185. Gene #20: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
SEMA3C MUTATED	5	4	2
SEMA3C WILD-TYPE	78	106	78

'SEMA3C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 1

Table S186. Gene #20: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
SEMA3C MUTATED	1	4	3
SEMA3C WILD-TYPE	42	48	29

'SEMA3C MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S187. Gene #20: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
SEMA3C MUTATED	2	2	0	0
SEMA3C WILD-TYPE	39	36	31	33

'SEMA3C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S188. Gene #20: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
SEMA3C MUTATED	1	1	2
SEMA3C WILD-TYPE	47	51	41

'SEMA3C MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S189. Gene #20: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
SEMA3C MUTATED	6	2	1
SEMA3C WILD-TYPE	38	60	34

'SEMA3C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S190. Gene #20: 'SEMA3C MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
SEMA3C MUTATED	4	5	0
SEMA3C WILD-TYPE	27	81	24

'ZDHHC4 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 1

Table S191. Gene #21: 'ZDHHC4 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
ZDHHC4 MUTATED	0	3	0	0
ZDHHC4 WILD-TYPE	77	90	45	60

'ZDHHC4 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S192. Gene #21: 'ZDHHC4 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
ZDHHC4 MUTATED	2	0	1
ZDHHC4 WILD-TYPE	136	61	75

'ZDHHC4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0517 (Fisher's exact test), Q value = 1

Table S193. Gene #21: 'ZDHHC4 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
ZDHHC4 MUTATED	3	0	0
ZDHHC4 WILD-TYPE	80	110	80

'MMP13 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S194. Gene #22: 'MMP13 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
MMP13 MUTATED	1	0	2	1
MMP13 WILD-TYPE	68	43	72	53

'MMP13 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S195. Gene #22: 'MMP13 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
MMP13 MUTATED	1	1	2	0
MMP13 WILD-TYPE	62	49	46	79

'MMP13 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 1

Table S196. Gene #22: 'MMP13 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
MMP13 MUTATED	1	2	0	2
MMP13 WILD-TYPE	76	91	45	58

'MMP13 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0503 (Fisher's exact test), Q value = 1

Table S197. Gene #22: 'MMP13 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
MMP13 MUTATED	1	0	4
MMP13 WILD-TYPE	137	61	72

'MMP13 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 1

Table S198. Gene #22: 'MMP13 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
MMP13 MUTATED	0	4	1
MMP13 WILD-TYPE	83	106	79

'PRKCD MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 1

Table S199. Gene #23: 'PRKCD MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
PRKCD MUTATED	0	2	1	0
PRKCD WILD-TYPE	69	41	73	54

'PRKCD MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0835 (Fisher's exact test), Q value = 1

Table S200. Gene #23: 'PRKCD MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
PRKCD MUTATED	0	2	1	0
PRKCD WILD-TYPE	63	48	47	79

'PRKCD MUTATION STATUS' versus 'MIR_CNMF'

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

Table S201. Gene #23: 'PRKCD MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
PRKCD MUTATED	0	3	0	0
PRKCD WILD-TYPE	77	90	45	60

'PRKCD MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S202. Gene #23: 'PRKCD MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
PRKCD MUTATED	2	0	1
PRKCD WILD-TYPE	136	61	75

'PRKCD MUTATION STATUS' versus 'CN_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S203. Gene #23: 'PRKCD MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
PRKCD MUTATED	0	1	2
PRKCD WILD-TYPE	83	109	78

'REN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 1

Table S204. Gene #24: 'REN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
REN MUTATED	0	0	2	1
REN WILD-TYPE	69	43	72	53

'REN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S205. Gene #24: 'REN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
REN MUTATED	0	0	1	2
REN WILD-TYPE	63	50	47	77

'REN MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0736 (Fisher's exact test), Q value = 1

Table S206. Gene #24: 'REN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
REN MUTATED	1	1	3	0
REN WILD-TYPE	76	92	42	60

'REN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S207. Gene #24: 'REN MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
REN MUTATED	4	0	1
REN WILD-TYPE	134	61	75

'REN MUTATION STATUS' versus 'CN_CNMF'

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

Table S208. Gene #24: 'REN MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
REN MUTATED	2	1	2
REN WILD-TYPE	81	109	78

'REN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S209. Gene #24: 'REN MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
REN MUTATED	1	1	1	1
REN WILD-TYPE	40	37	30	32

'REN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S210. Gene #24: 'REN MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
REN MUTATED	2	1	1
REN WILD-TYPE	46	51	42

'LRRC55 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S211. Gene #25: 'LRRC55 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
LRRC55 MUTATED	0	1	3	1
LRRC55 WILD-TYPE	69	42	71	53

'LRRC55 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.537 (Fisher's exact test), Q value = 1

Table S212. Gene #25: 'LRRC55 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
LRRC55 MUTATED	0	1	1	3
LRRC55 WILD-TYPE	63	49	47	76

'LRRC55 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S213. Gene #25: 'LRRC55 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
LRRC55 MUTATED	3	3	0	0
LRRC55 WILD-TYPE	74	90	45	60

'LRRC55 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S214. Gene #25: 'LRRC55 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
LRRC55 MUTATED	4	1	1
LRRC55 WILD-TYPE	134	60	75

'LRRC55 MUTATION STATUS' versus 'CN_CNMF'

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

Table S215. Gene #25: 'LRRC55 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
LRRC55 MUTATED	3	3	0
LRRC55 WILD-TYPE	80	107	80

'MUC17 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 1

Table S216. Gene #26: 'MUC17 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
MUC17 MUTATED	10	5	1	3
MUC17 WILD-TYPE	59	38	73	51

Figure S50. Get High-res Image Gene #26: 'MUC17 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MUC17 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S217. Gene #26: 'MUC17 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
MUC17 MUTATED	8	1	3	7
MUC17 WILD-TYPE	55	49	45	72

'MUC17 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.706 (Fisher's exact test), Q value = 1

Table S218. Gene #26: 'MUC17 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
MUC17 MUTATED	5	7	3	7
MUC17 WILD-TYPE	72	86	42	53

'MUC17 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.703 (Fisher's exact test), Q value = 1

Table S219. Gene #26: 'MUC17 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
MUC17 MUTATED	10	4	8
MUC17 WILD-TYPE	128	57	68

'MUC17 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S220. Gene #26: 'MUC17 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
MUC17 MUTATED	7	8	7
MUC17 WILD-TYPE	76	102	73

'MUC17 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S221. Gene #26: 'MUC17 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
MUC17 MUTATED	3	5	2
MUC17 WILD-TYPE	40	47	30

'MUC17 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S222. Gene #26: 'MUC17 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
MUC17 MUTATED	5	1	1	4
MUC17 WILD-TYPE	36	37	30	29

'MUC17 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 1

Table S223. Gene #26: 'MUC17 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
MUC17 MUTATED	6	3	2
MUC17 WILD-TYPE	42	49	41

'MUC17 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.861 (Fisher's exact test), Q value = 1

Table S224. Gene #26: 'MUC17 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
MUC17 MUTATED	4	6	2
MUC17 WILD-TYPE	40	56	33

'MUC17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S225. Gene #26: 'MUC17 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
MUC17 MUTATED	2	8	2
MUC17 WILD-TYPE	29	78	22

'CD209 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S226. Gene #27: 'CD209 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
CD209 MUTATED	1	0	2	1
CD209 WILD-TYPE	68	43	72	53

'CD209 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S227. Gene #27: 'CD209 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
CD209 MUTATED	1	1	1	1
CD209 WILD-TYPE	62	49	47	78

'CD209 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0672 (Fisher's exact test), Q value = 1

Table S228. Gene #27: 'CD209 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
CD209 MUTATED	2	0	0	3
CD209 WILD-TYPE	75	93	45	57

'CD209 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S229. Gene #27: 'CD209 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
CD209 MUTATED	3	0	2
CD209 WILD-TYPE	135	61	74

'CD209 MUTATION STATUS' versus 'CN_CNMF'

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

Table S230. Gene #27: 'CD209 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
CD209 MUTATED	1	1	2
CD209 WILD-TYPE	82	109	78

'CD209 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 1

Table S231. Gene #27: 'CD209 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
CD209 MUTATED	1	0	1	2
CD209 WILD-TYPE	40	38	30	31

'CD209 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S232. Gene #27: 'CD209 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
CD209 MUTATED	1	2	1
CD209 WILD-TYPE	47	50	42

'DDX5 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S233. Gene #28: 'DDX5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
DDX5 MUTATED	1	0	0	2
DDX5 WILD-TYPE	68	43	74	52

'DDX5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S234. Gene #28: 'DDX5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
DDX5 MUTATED	1	1	0	1
DDX5 WILD-TYPE	62	49	48	78

'DDX5 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.537 (Fisher's exact test), Q value = 1

Table S235. Gene #28: 'DDX5 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
DDX5 MUTATED	0	2	1	1
DDX5 WILD-TYPE	77	91	44	59

'DDX5 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S236. Gene #28: 'DDX5 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
DDX5 MUTATED	1	1	2
DDX5 WILD-TYPE	137	60	74

'DDX5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S237. Gene #28: 'DDX5 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
DDX5 MUTATED	0	1	3
DDX5 WILD-TYPE	83	109	77

'TP63 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S238. Gene #29: 'TP63 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
TP63 MUTATED	1	1	2	1
TP63 WILD-TYPE	68	42	72	53

'TP63 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S239. Gene #29: 'TP63 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
TP63 MUTATED	1	1	2	1
TP63 WILD-TYPE	62	49	46	78

'TP63 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S240. Gene #29: 'TP63 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
TP63 MUTATED	1	1	1	3
TP63 WILD-TYPE	76	92	44	57

'TP63 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S241. Gene #29: 'TP63 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
TP63 MUTATED	2	2	2
TP63 WILD-TYPE	136	59	74

'TP63 MUTATION STATUS' versus 'CN_CNMF'

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

Table S242. Gene #29: 'TP63 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
TP63 MUTATED	1	3	2
TP63 WILD-TYPE	82	107	78

'TP63 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0681 (Fisher's exact test), Q value = 1

Table S243. Gene #29: 'TP63 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
TP63 MUTATED	0	1	0	3
TP63 WILD-TYPE	41	37	31	30

'TP63 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S244. Gene #29: 'TP63 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
TP63 MUTATED	3	1	0
TP63 WILD-TYPE	45	51	43

'TP63 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S245. Gene #29: 'TP63 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
TP63 MUTATED	0	1	2
TP63 WILD-TYPE	44	61	33

'TP63 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S246. Gene #29: 'TP63 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
TP63 MUTATED	0	1	2
TP63 WILD-TYPE	31	85	22

'CD1D MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S247. Gene #30: 'CD1D MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
CD1D MUTATED	1	1	1	0
CD1D WILD-TYPE	68	42	73	54

'CD1D MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S248. Gene #30: 'CD1D MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
CD1D MUTATED	1	1	0	1
CD1D WILD-TYPE	62	49	48	78

'CD1D MUTATION STATUS' versus 'MIR_CNMF'

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

Table S249. Gene #30: 'CD1D MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
CD1D MUTATED	2	2	0	0
CD1D WILD-TYPE	75	91	45	60

'CD1D MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

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

Table S250. Gene #30: 'CD1D MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
CD1D MUTATED	1	0	3
CD1D WILD-TYPE	137	61	73

'CD1D MUTATION STATUS' versus 'CN_CNMF'

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

Table S251. Gene #30: 'CD1D MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
CD1D MUTATED	2	1	1
CD1D WILD-TYPE	81	109	79

'CD1D MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S252. Gene #30: 'CD1D MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
CD1D MUTATED	1	1	1	0
CD1D WILD-TYPE	40	37	30	33

'CD1D MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S253. Gene #30: 'CD1D MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
CD1D MUTATED	1	1	1
CD1D WILD-TYPE	47	51	42

'LZTR1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S254. Gene #31: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
LZTR1 MUTATED	2	1	2	2
LZTR1 WILD-TYPE	67	42	72	52

'LZTR1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S255. Gene #31: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
LZTR1 MUTATED	3	2	0	2
LZTR1 WILD-TYPE	60	48	48	77

'LZTR1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.36 (Fisher's exact test), Q value = 1

Table S256. Gene #31: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
LZTR1 MUTATED	5	3	0	2
LZTR1 WILD-TYPE	72	90	45	58

'LZTR1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.703 (Fisher's exact test), Q value = 1

Table S257. Gene #31: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
LZTR1 MUTATED	4	3	3
LZTR1 WILD-TYPE	134	58	73

'LZTR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.443 (Fisher's exact test), Q value = 1

Table S258. Gene #31: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
LZTR1 MUTATED	4	4	1
LZTR1 WILD-TYPE	79	106	79

'LZTR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S259. Gene #31: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
LZTR1 MUTATED	3	0	1
LZTR1 WILD-TYPE	40	52	31

'LZTR1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S260. Gene #31: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
LZTR1 MUTATED	1	2	2	2
LZTR1 WILD-TYPE	40	36	29	31

'LZTR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S261. Gene #31: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
LZTR1 MUTATED	3	2	2
LZTR1 WILD-TYPE	45	50	41

'LZTR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S262. Gene #31: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
LZTR1 MUTATED	2	0	1
LZTR1 WILD-TYPE	42	62	34

'LZTR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S263. Gene #31: 'LZTR1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
LZTR1 MUTATED	0	3	0
LZTR1 WILD-TYPE	31	83	24

'TEX15 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 1

Table S264. Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
TEX15 MUTATED	2	1	1	4
TEX15 WILD-TYPE	67	42	73	50

'TEX15 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S265. Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
TEX15 MUTATED	1	2	0	5
TEX15 WILD-TYPE	62	48	48	74

'TEX15 MUTATION STATUS' versus 'MIR_CNMF'

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

Table S266. Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
TEX15 MUTATED	1	5	0	2
TEX15 WILD-TYPE	76	88	45	58

'TEX15 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.72 (Fisher's exact test), Q value = 1

Table S267. Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
TEX15 MUTATED	3	2	3
TEX15 WILD-TYPE	135	59	73

'TEX15 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.547 (Fisher's exact test), Q value = 1

Table S268. Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
TEX15 MUTATED	4	2	2
TEX15 WILD-TYPE	79	108	78

'TEX15 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.823 (Fisher's exact test), Q value = 1

Table S269. Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
TEX15 MUTATED	2	1	1
TEX15 WILD-TYPE	41	51	31

'TEX15 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S270. Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
TEX15 MUTATED	1	1	1	2
TEX15 WILD-TYPE	40	37	30	31

'TEX15 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 1

Table S271. Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
TEX15 MUTATED	0	3	2
TEX15 WILD-TYPE	48	49	41

'TEX15 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00346 (Fisher's exact test), Q value = 0.89

Table S272. Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
TEX15 MUTATED	5	0	0
TEX15 WILD-TYPE	39	62	35

Figure S51. Get High-res Image Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'TEX15 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S273. Gene #32: 'TEX15 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
TEX15 MUTATED	1	4	0
TEX15 WILD-TYPE	30	82	24

'FBN3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S274. Gene #33: 'FBN3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	43	74	54
FBN3 MUTATED	1	1	6	1
FBN3 WILD-TYPE	68	42	68	53

'FBN3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 1

Table S275. Gene #33: 'FBN3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	50	48	79
FBN3 MUTATED	1	2	4	2
FBN3 WILD-TYPE	62	48	44	77

'FBN3 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S276. Gene #33: 'FBN3 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	93	45	60
FBN3 MUTATED	4	3	2	2
FBN3 WILD-TYPE	73	90	43	58

'FBN3 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.922 (Fisher's exact test), Q value = 1

Table S277. Gene #33: 'FBN3 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	138	61	76
FBN3 MUTATED	5	3	3
FBN3 WILD-TYPE	133	58	73

'FBN3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S278. Gene #33: 'FBN3 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	110	80
FBN3 MUTATED	2	8	1
FBN3 WILD-TYPE	81	102	79

'FBN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S279. Gene #33: 'FBN3 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	43	52	32
FBN3 MUTATED	2	3	1
FBN3 WILD-TYPE	41	49	31

'FBN3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S280. Gene #33: 'FBN3 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	38	31	33
FBN3 MUTATED	0	3	1	2
FBN3 WILD-TYPE	41	35	30	31

'FBN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S281. Gene #33: 'FBN3 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	52	43
FBN3 MUTATED	1	4	1
FBN3 WILD-TYPE	47	48	42

'FBN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S282. Gene #33: 'FBN3 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	62	35
FBN3 MUTATED	1	3	1
FBN3 WILD-TYPE	43	59	34

'FBN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S283. Gene #33: 'FBN3 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	86	24
FBN3 MUTATED	1	3	1
FBN3 WILD-TYPE	30	83	23

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = GBM-TP.transferedmergedcluster.txt
Number of patients = 283
Number of significantly mutated genes = 33
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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