Correlation between gene mutation status and molecular subtypes

Overview

Introduction

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

Summary

Testing the association between mutation status of 25 genes and 12 molecular subtypes across 436 patients, 32 significant findings detected with P value < 0.05 and Q value < 0.25.

SETD2 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
PBRM1 mutation correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
KDM5C mutation correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
VHL mutation correlated to 'MRNA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
MTOR mutation correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.
PTEN mutation correlated to 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
NEFH mutation correlated to 'MRNASEQ_CNMF'.
NF2 mutation correlated to 'RPPA_CHIERARCHICAL'.
GPR50 mutation correlated to 'RPPA_CNMF'.
TFDP2 mutation correlated to 'RPPA_CHIERARCHICAL'.
EMG1 mutation correlated to 'MRNA_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 25 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 32 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	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
PBRM1	131 (30%)	305	0.04 (0.316)	0.00909 (0.13)	0.0244 (0.237)	1e-05 (0.0015)	0.00748 (0.119)	0.275 (0.842)	3e-05 (0.003)	9e-05 (0.0054)	0.00061 (0.0261)	0.00097 (0.0327)	0.00036 (0.018)	0.00112 (0.0336)
VHL	192 (44%)	244	0.0264 (0.248)	0.0656 (0.428)	0.0724 (0.453)	0.196 (0.762)	0.0276 (0.251)	0.851 (1.00)	7e-05 (0.00525)	0.00098 (0.0327)	0.27 (0.842)	0.00753 (0.119)	0.581 (1.00)	0.651 (1.00)
PTEN	15 (3%)	421			0.862 (1.00)	0.134 (0.642)	0.271 (0.842)	0.0162 (0.173)	0.00901 (0.13)	0.00711 (0.119)	1e-05 (0.0015)	0.258 (0.841)
SETD2	43 (10%)	393	0.603 (1.00)	0.141 (0.651)	0.852 (1.00)	0.00172 (0.043)	0.495 (1.00)	0.0433 (0.317)	0.148 (0.663)	0.0141 (0.161)	0.0862 (0.528)	0.484 (1.00)	0.293 (0.872)	0.0245 (0.237)
KDM5C	25 (6%)	411			0.0426 (0.317)	0.233 (0.804)	0.323 (0.889)	0.196 (0.762)	0.0145 (0.161)	0.00276 (0.0637)	0.00171 (0.043)	0.205 (0.762)	0.879 (1.00)	0.662 (1.00)
MTOR	28 (6%)	408			0.488 (1.00)	0.299 (0.872)	0.0133 (0.159)	0.00658 (0.119)	0.319 (0.889)	0.849 (1.00)	0.952 (1.00)	0.177 (0.749)	0.785 (1.00)	0.817 (1.00)
EMG1	4 (1%)	432	0.0102 (0.139)	0.0486 (0.339)	0.131 (0.642)				0.0424 (0.317)	0.0111 (0.145)	0.146 (0.663)	0.0648 (0.428)
NEFH	6 (1%)	430			0.605 (1.00)	0.587 (1.00)	0.896 (1.00)	0.04 (0.316)	0.00398 (0.0853)	0.0295 (0.259)	0.97 (1.00)	0.449 (1.00)	0.878 (1.00)	0.0943 (0.55)
NF2	6 (1%)	430			0.322 (0.889)	0.557 (1.00)	0.223 (0.797)	0.0124 (0.155)	0.384 (0.985)	0.206 (0.762)	0.519 (1.00)	0.248 (0.819)
GPR50	3 (1%)	433			0.829 (1.00)	0.0959 (0.55)	0.00583 (0.117)	0.879 (1.00)	0.717 (1.00)	0.22 (0.794)	0.214 (0.781)	0.353 (0.954)
TFDP2	4 (1%)	432			0.57 (1.00)		0.133 (0.642)	0.0213 (0.22)	0.808 (1.00)	0.697 (1.00)	0.3 (0.872)	0.263 (0.841)
TP53	9 (2%)	427			0.451 (1.00)	0.201 (0.762)	0.122 (0.641)	0.137 (0.642)	0.263 (0.841)	0.116 (0.632)	0.398 (1.00)	0.357 (0.956)	0.504 (1.00)	0.507 (1.00)
ATM	12 (3%)	424			0.0538 (0.367)	0.0971 (0.55)	0.977 (1.00)	0.951 (1.00)	0.289 (0.867)	0.328 (0.895)	0.185 (0.752)	0.134 (0.642)
NUDT11	4 (1%)	432			0.137 (0.642)	0.908 (1.00)	0.395 (1.00)	0.479 (1.00)	0.553 (1.00)	0.504 (1.00)	1 (1.00)	1 (1.00)
PIK3CA	10 (2%)	426			0.182 (0.752)	1 (1.00)	0.159 (0.691)	0.665 (1.00)	0.248 (0.819)	0.789 (1.00)	0.759 (1.00)	1 (1.00)
FAM200A	4 (1%)	432			0.0302 (0.259)				0.102 (0.566)	0.317 (0.889)	0.302 (0.872)	0.0906 (0.544)
DPCR1	6 (1%)	430			0.493 (1.00)	0.437 (1.00)	0.401 (1.00)	0.775 (1.00)	0.229 (0.802)	0.0461 (0.329)	0.245 (0.819)	0.882 (1.00)
EGFR	6 (1%)	430			0.984 (1.00)	0.426 (1.00)	0.97 (1.00)	0.273 (0.842)	0.0716 (0.453)	1 (1.00)	1 (1.00)	0.852 (1.00)
SH3KBP1	3 (1%)	433			0.871 (1.00)		0.875 (1.00)	0.788 (1.00)	0.901 (1.00)	0.874 (1.00)	1 (1.00)	0.478 (1.00)
ARID1A	10 (2%)	426			0.82 (1.00)	0.546 (1.00)	0.7 (1.00)	0.83 (1.00)	0.63 (1.00)	0.987 (1.00)	0.539 (1.00)	0.195 (0.762)	0.426 (1.00)	0.126 (0.642)
ARAP3	3 (1%)	433			0.309 (0.882)		0.875 (1.00)	1 (1.00)	0.535 (1.00)	1 (1.00)	1 (1.00)	0.789 (1.00)
SLC16A9	4 (1%)	432			0.376 (0.98)	0.629 (1.00)	0.569 (1.00)	0.2 (0.762)	0.153 (0.674)	0.0356 (0.297)	0.701 (1.00)	1 (1.00)
PCK1	4 (1%)	432			0.896 (1.00)		0.281 (0.851)	1 (1.00)	0.376 (0.98)	0.74 (1.00)	0.492 (1.00)	0.681 (1.00)
CUL9	7 (2%)	429			0.958 (1.00)	0.118 (0.634)	0.853 (1.00)	0.447 (1.00)	0.23 (0.802)	0.894 (1.00)	0.555 (1.00)	0.384 (0.985)	0.879 (1.00)	0.409 (1.00)
ZDHHC1	4 (1%)	432			0.243 (0.819)		0.42 (1.00)	0.177 (0.749)	0.763 (1.00)	0.185 (0.752)	0.555 (1.00)	0.37 (0.98)

'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	16	10
SETD2 MUTATED	1	2	0
SETD2 WILD-TYPE	16	14	10

'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.141 (Fisher's exact test), Q value = 0.65

Table S2. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	3	5	3	10	10	4	8
SETD2 MUTATED	0	2	0	0	1	0	0
SETD2 WILD-TYPE	3	3	3	10	9	4	8

'SETD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S3. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
SETD2 MUTATED	6	8	12	7	7	3
SETD2 WILD-TYPE	43	60	118	56	62	51

'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.043

Table S4. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
SETD2 MUTATED	2	4	19	5
SETD2 WILD-TYPE	55	55	64	59

Figure S1. Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S5. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
SETD2 MUTATED	5	8	10	10	6	1
SETD2 WILD-TYPE	64	66	68	59	72	28

'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.32

Table S6. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
SETD2 MUTATED	7	16	9	8
SETD2 WILD-TYPE	102	79	63	113

Figure S2. Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 0.66

Table S7. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
SETD2 MUTATED	3	10	9	15	6
SETD2 WILD-TYPE	57	127	63	120	24

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.16

Table S8. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
SETD2 MUTATED	18	3	10	12	0	0
SETD2 WILD-TYPE	81	22	140	103	30	15

Figure S3. Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0862 (Fisher's exact test), Q value = 0.53

Table S9. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
SETD2 MUTATED	3	2	16	12	8
SETD2 WILD-TYPE	68	47	143	92	36

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S10. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
SETD2 MUTATED	11	17	13
SETD2 WILD-TYPE	135	156	95

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.87

Table S11. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	20	39	31
SETD2 MUTATED	0	3	7	3
SETD2 WILD-TYPE	17	17	32	28

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0245 (Fisher's exact test), Q value = 0.24

Table S12. Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	18	44	26	19
SETD2 MUTATED	0	7	6	0
SETD2 WILD-TYPE	18	37	20	19

Figure S4. Get High-res Image Gene #1: 'SETD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.32

Table S13. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	16	10
PBRM1 MUTATED	9	3	1
PBRM1 WILD-TYPE	8	13	9

Figure S5. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00909 (Fisher's exact test), Q value = 0.13

Table S14. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	3	5	3	10	10	4	8
PBRM1 MUTATED	2	3	0	0	4	3	1
PBRM1 WILD-TYPE	1	2	3	10	6	1	7

Figure S6. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.24

Table S15. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
PBRM1 MUTATED	18	12	38	26	25	12
PBRM1 WILD-TYPE	31	56	92	37	44	42

Figure S7. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0015

Table S16. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
PBRM1 MUTATED	8	12	35	36
PBRM1 WILD-TYPE	49	47	48	28

Figure S8. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00748 (Fisher's exact test), Q value = 0.12

Table S17. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
PBRM1 MUTATED	19	36	20	23	19	5
PBRM1 WILD-TYPE	50	38	58	46	59	24

Figure S9. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.84

Table S18. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
PBRM1 MUTATED	30	33	17	42
PBRM1 WILD-TYPE	79	62	55	79

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.003

Table S19. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
PBRM1 MUTATED	5	50	25	34	16
PBRM1 WILD-TYPE	55	87	47	101	14

Figure S10. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0054

Table S20. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
PBRM1 MUTATED	39	5	57	26	2	1
PBRM1 WILD-TYPE	60	20	93	89	28	14

Figure S11. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.026

Table S21. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
PBRM1 MUTATED	18	6	65	24	14
PBRM1 WILD-TYPE	53	43	94	80	30

Figure S12. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.033

Table S22. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
PBRM1 MUTATED	29	67	31
PBRM1 WILD-TYPE	117	106	77

Figure S13. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.018

Table S23. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	20	39	31
PBRM1 MUTATED	4	1	21	6
PBRM1 WILD-TYPE	13	19	18	25

Figure S14. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00112 (Fisher's exact test), Q value = 0.034

Table S24. Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	18	44	26	19
PBRM1 MUTATED	4	8	7	13
PBRM1 WILD-TYPE	14	36	19	6

Figure S15. Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.32

Table S25. Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
KDM5C MUTATED	5	1	10	0	5	4
KDM5C WILD-TYPE	44	67	120	63	64	50

Figure S16. Get High-res Image Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KDM5C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 0.8

Table S26. Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
KDM5C MUTATED	1	5	8	3
KDM5C WILD-TYPE	56	54	75	61

'KDM5C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 0.89

Table S27. Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
KDM5C MUTATED	2	3	7	6	2	2
KDM5C WILD-TYPE	67	71	71	63	76	27

'KDM5C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 0.76

Table S28. Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
KDM5C MUTATED	2	7	5	8
KDM5C WILD-TYPE	107	88	67	113

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.16

Table S29. Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
KDM5C MUTATED	0	5	5	9	5
KDM5C WILD-TYPE	60	132	67	126	25

Figure S17. Get High-res Image Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00276 (Fisher's exact test), Q value = 0.064

Table S30. Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
KDM5C MUTATED	13	1	2	8	0	0
KDM5C WILD-TYPE	86	24	148	107	30	15

Figure S18. Get High-res Image Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.043

Table S31. Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
KDM5C MUTATED	1	1	5	11	7
KDM5C WILD-TYPE	70	48	154	93	37

Figure S19. Get High-res Image Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.205 (Fisher's exact test), Q value = 0.76

Table S32. Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
KDM5C MUTATED	8	7	10
KDM5C WILD-TYPE	138	166	98

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S33. Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	20	39	31
KDM5C MUTATED	0	0	2	1
KDM5C WILD-TYPE	17	20	37	30

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S34. Gene #3: 'KDM5C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	18	44	26	19
KDM5C MUTATED	0	2	0	1
KDM5C WILD-TYPE	18	42	26	18

'VHL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.25

Table S35. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	16	10
VHL MUTATED	10	4	1
VHL WILD-TYPE	7	12	9

Figure S20. Get High-res Image Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'VHL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0656 (Fisher's exact test), Q value = 0.43

Table S36. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	3	5	3	10	10	4	8
VHL MUTATED	1	0	0	4	6	3	1
VHL WILD-TYPE	2	5	3	6	4	1	7

'VHL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0724 (Fisher's exact test), Q value = 0.45

Table S37. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
VHL MUTATED	19	25	52	31	41	24
VHL WILD-TYPE	30	43	78	32	28	30

'VHL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 0.76

Table S38. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
VHL MUTATED	27	20	43	30
VHL WILD-TYPE	30	39	40	34

'VHL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.25

Table S39. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
VHL MUTATED	27	43	31	23	41	13
VHL WILD-TYPE	42	31	47	46	37	16

Figure S21. Get High-res Image Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'VHL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.851 (Fisher's exact test), Q value = 1

Table S40. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
VHL MUTATED	48	42	30	58
VHL WILD-TYPE	61	53	42	63

'VHL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0052

Table S41. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
VHL MUTATED	12	75	37	54	14
VHL WILD-TYPE	48	62	35	81	16

Figure S22. Get High-res Image Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.033

Table S42. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
VHL MUTATED	45	6	81	48	11	1
VHL WILD-TYPE	54	19	69	67	19	14

Figure S23. Get High-res Image Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.84

Table S43. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
VHL MUTATED	33	22	76	36	21
VHL WILD-TYPE	38	27	83	68	23

'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00753 (Fisher's exact test), Q value = 0.12

Table S44. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
VHL MUTATED	60	91	37
VHL WILD-TYPE	86	82	71

Figure S24. Get High-res Image Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S45. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	20	39	31
VHL MUTATED	6	8	17	17
VHL WILD-TYPE	11	12	22	14

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S46. Gene #4: 'VHL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	18	44	26	19
VHL MUTATED	7	23	10	8
VHL WILD-TYPE	11	21	16	11

'MTOR MUTATION STATUS' versus 'CN_CNMF'

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

Table S47. Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
MTOR MUTATED	3	1	9	5	6	4
MTOR WILD-TYPE	46	67	121	58	63	50

'MTOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 0.87

Table S48. Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
MTOR MUTATED	3	3	11	6
MTOR WILD-TYPE	54	56	72	58

'MTOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.16

Table S49. Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
MTOR MUTATED	2	6	10	7	1	0
MTOR WILD-TYPE	67	68	68	62	77	29

Figure S25. Get High-res Image Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MTOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00658 (Fisher's exact test), Q value = 0.12

Table S50. Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
MTOR MUTATED	3	14	3	6
MTOR WILD-TYPE	106	81	69	115

Figure S26. Get High-res Image Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.89

Table S51. Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
MTOR MUTATED	5	11	2	10	0
MTOR WILD-TYPE	55	126	70	125	30

'MTOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S52. Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
MTOR MUTATED	5	2	9	10	1	1
MTOR WILD-TYPE	94	23	141	105	29	14

'MTOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.952 (Fisher's exact test), Q value = 1

Table S53. Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
MTOR MUTATED	5	4	9	7	3
MTOR WILD-TYPE	66	45	150	97	41

'MTOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.177 (Fisher's exact test), Q value = 0.75

Table S54. Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
MTOR MUTATED	11	7	10
MTOR WILD-TYPE	135	166	98

'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S55. Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	20	39	31
MTOR MUTATED	1	1	4	1
MTOR WILD-TYPE	16	19	35	30

'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S56. Gene #5: 'MTOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	18	44	26	19
MTOR MUTATED	1	2	2	2
MTOR WILD-TYPE	17	42	24	17

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 1

Table S57. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
TP53 MUTATED	1	1	3	1	0	3
TP53 WILD-TYPE	48	67	127	62	69	51

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.76

Table S58. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
TP53 MUTATED	3	3	2	0
TP53 WILD-TYPE	54	56	81	64

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.64

Table S59. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
TP53 MUTATED	2	0	4	1	0	0
TP53 WILD-TYPE	67	74	74	68	78	29

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 0.64

Table S60. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
TP53 MUTATED	0	1	3	3
TP53 WILD-TYPE	109	94	69	118

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 0.84

Table S61. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
TP53 MUTATED	3	1	1	3	1
TP53 WILD-TYPE	57	136	71	132	29

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.116 (Fisher's exact test), Q value = 0.63

Table S62. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
TP53 MUTATED	1	0	2	3	1	2
TP53 WILD-TYPE	98	25	148	112	29	13

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 1

Table S63. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
TP53 MUTATED	1	2	2	4	0
TP53 WILD-TYPE	70	47	157	100	44

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.357 (Fisher's exact test), Q value = 0.96

Table S64. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
TP53 MUTATED	3	2	4
TP53 WILD-TYPE	143	171	104

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S65. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	20	39	31
TP53 MUTATED	1	1	2	0
TP53 WILD-TYPE	16	19	37	31

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.507 (Fisher's exact test), Q value = 1

Table S66. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	18	44	26	19
TP53 MUTATED	1	1	2	0
TP53 WILD-TYPE	17	43	24	19

'PTEN MUTATION STATUS' versus 'CN_CNMF'

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

Table S67. Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
PTEN MUTATED	2	1	6	1	2	2
PTEN WILD-TYPE	47	67	124	62	67	52

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.64

Table S68. Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
PTEN MUTATED	1	4	4	0
PTEN WILD-TYPE	56	55	79	64

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.84

Table S69. Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
PTEN MUTATED	2	1	7	2	2	1
PTEN WILD-TYPE	67	73	71	67	76	28

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.17

Table S70. Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
PTEN MUTATED	1	8	4	2
PTEN WILD-TYPE	108	87	68	119

Figure S27. Get High-res Image Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00901 (Fisher's exact test), Q value = 0.13

Table S71. Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
PTEN MUTATED	2	0	6	6	1
PTEN WILD-TYPE	58	137	66	129	29

Figure S28. Get High-res Image Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00711 (Fisher's exact test), Q value = 0.12

Table S72. Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
PTEN MUTATED	5	1	0	8	0	1
PTEN WILD-TYPE	94	24	150	107	30	14

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

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0015

Table S73. Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
PTEN MUTATED	0	1	2	3	9
PTEN WILD-TYPE	71	48	157	101	35

Figure S30. Get High-res Image Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.258 (Fisher's exact test), Q value = 0.84

Table S74. Gene #7: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
PTEN MUTATED	7	3	5
PTEN WILD-TYPE	139	170	103

'NEFH MUTATION STATUS' versus 'CN_CNMF'

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

Table S75. Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
NEFH MUTATED	1	0	1	1	2	1
NEFH WILD-TYPE	48	68	129	62	67	53

'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 1

Table S76. Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
NEFH MUTATED	1	0	3	1
NEFH WILD-TYPE	56	59	80	63

'NEFH MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S77. Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
NEFH MUTATED	1	2	2	0	1	0
NEFH WILD-TYPE	68	72	76	69	77	29

'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.32

Table S78. Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
NEFH MUTATED	2	4	0	0
NEFH WILD-TYPE	107	91	72	121

Figure S31. Get High-res Image Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00398 (Fisher's exact test), Q value = 0.085

Table S79. Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
NEFH MUTATED	3	0	0	1	2
NEFH WILD-TYPE	57	137	72	134	28

Figure S32. Get High-res Image Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.26

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
NEFH MUTATED	2	2	0	1	1	0
NEFH WILD-TYPE	97	23	150	114	29	15

Figure S33. Get High-res Image Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S81. Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
NEFH MUTATED	1	1	3	1	0
NEFH WILD-TYPE	70	48	156	103	44

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S82. Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
NEFH MUTATED	1	2	3
NEFH WILD-TYPE	145	171	105

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S83. Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	20	39	31
NEFH MUTATED	0	0	2	1
NEFH WILD-TYPE	17	20	37	30

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0943 (Fisher's exact test), Q value = 0.55

Table S84. Gene #8: 'NEFH MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	18	44	26	19
NEFH MUTATED	0	0	1	2
NEFH WILD-TYPE	18	44	25	17

'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 0.89

Table S85. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
NF2 MUTATED	0	0	4	0	2	0
NF2 WILD-TYPE	49	68	126	63	67	54

'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S86. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
NF2 MUTATED	0	1	2	0
NF2 WILD-TYPE	57	58	81	64

'NF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 0.8

Table S87. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
NF2 MUTATED	1	1	3	0	0	1
NF2 WILD-TYPE	68	73	75	69	78	28

'NF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.15

Table S88. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
NF2 MUTATED	0	3	3	0
NF2 WILD-TYPE	109	92	69	121

Figure S34. Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.99

Table S89. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
NF2 MUTATED	2	1	0	3	0
NF2 WILD-TYPE	58	136	72	132	30

'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.76

Table S90. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
NF2 MUTATED	0	0	1	4	1	0
NF2 WILD-TYPE	99	25	149	111	29	15

'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 1

Table S91. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
NF2 MUTATED	1	1	1	3	0
NF2 WILD-TYPE	70	48	158	101	44

'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.82

Table S92. Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
NF2 MUTATED	4	1	1
NF2 WILD-TYPE	142	172	107

'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0538 (Fisher's exact test), Q value = 0.37

Table S93. Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
ATM MUTATED	4	0	2	1	4	1
ATM WILD-TYPE	45	68	128	62	65	53

'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0971 (Fisher's exact test), Q value = 0.55

Table S94. Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
ATM MUTATED	0	1	2	5
ATM WILD-TYPE	57	58	81	59

'ATM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.977 (Fisher's exact test), Q value = 1

Table S95. Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
ATM MUTATED	2	2	2	1	3	1
ATM WILD-TYPE	67	72	76	68	75	28

'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.951 (Fisher's exact test), Q value = 1

Table S96. Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
ATM MUTATED	4	2	2	3
ATM WILD-TYPE	105	93	70	118

'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.87

Table S97. Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
ATM MUTATED	0	7	1	3	1
ATM WILD-TYPE	60	130	71	132	29

'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.328 (Fisher's exact test), Q value = 0.9

Table S98. Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
ATM MUTATED	2	0	8	1	1	0
ATM WILD-TYPE	97	25	142	114	29	15

'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.75

Table S99. Gene #10: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
ATM MUTATED	0	1	8	2	0
ATM WILD-TYPE	71	48	151	102	44

'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.64

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
ATM MUTATED	1	5	5
ATM WILD-TYPE	145	168	103

'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.64

Table S101. Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
NUDT11 MUTATED	0	0	1	0	3	0
NUDT11 WILD-TYPE	49	68	129	63	66	54

'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S102. Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
NUDT11 MUTATED	0	1	2	1
NUDT11 WILD-TYPE	57	58	81	63

'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S103. Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
NUDT11 MUTATED	0	1	1	1	0	1
NUDT11 WILD-TYPE	69	73	77	68	78	28

'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S104. Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
NUDT11 MUTATED	0	2	1	1
NUDT11 WILD-TYPE	109	93	71	120

'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S105. Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
NUDT11 MUTATED	1	2	1	0	0
NUDT11 WILD-TYPE	59	135	71	135	30

'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S106. Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
NUDT11 MUTATED	1	0	2	0	1	0
NUDT11 WILD-TYPE	98	25	148	115	29	15

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S107. Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
NUDT11 MUTATED	1	0	2	1	0
NUDT11 WILD-TYPE	70	49	157	103	44

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S108. Gene #11: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
NUDT11 MUTATED	1	2	1
NUDT11 WILD-TYPE	145	171	107

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.75

Table S109. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
PIK3CA MUTATED	4	1	3	1	1	0
PIK3CA WILD-TYPE	45	67	127	62	68	54

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S110. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
PIK3CA MUTATED	1	1	2	1
PIK3CA WILD-TYPE	56	58	81	63

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.69

Table S111. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
PIK3CA MUTATED	3	0	3	2	0	1
PIK3CA WILD-TYPE	66	74	75	67	78	28

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.665 (Fisher's exact test), Q value = 1

Table S112. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
PIK3CA MUTATED	1	2	2	4
PIK3CA WILD-TYPE	108	93	70	117

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 0.82

Table S113. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
PIK3CA MUTATED	0	5	0	5	0
PIK3CA WILD-TYPE	60	132	72	130	30

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S114. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
PIK3CA MUTATED	1	0	4	4	1	0
PIK3CA WILD-TYPE	98	25	146	111	29	15

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S115. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
PIK3CA MUTATED	2	1	3	4	0
PIK3CA WILD-TYPE	69	48	156	100	44

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S116. Gene #12: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
PIK3CA MUTATED	4	4	2
PIK3CA WILD-TYPE	142	169	106

'GPR50 MUTATION STATUS' versus 'CN_CNMF'

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

Table S117. Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
GPR50 MUTATED	0	1	1	1	0	0
GPR50 WILD-TYPE	49	67	129	62	69	54

'GPR50 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0959 (Fisher's exact test), Q value = 0.55

Table S118. Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
GPR50 MUTATED	2	1	0	0
GPR50 WILD-TYPE	55	58	83	64

'GPR50 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00583 (Fisher's exact test), Q value = 0.12

Table S119. Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
GPR50 MUTATED	1	0	0	0	0	2
GPR50 WILD-TYPE	68	74	78	69	78	27

Figure S35. Get High-res Image Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'GPR50 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S120. Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
GPR50 MUTATED	1	0	1	1
GPR50 WILD-TYPE	108	95	71	120

'GPR50 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.717 (Fisher's exact test), Q value = 1

Table S121. Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
GPR50 MUTATED	1	1	0	1	0
GPR50 WILD-TYPE	59	136	72	134	30

'GPR50 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 0.79

Table S122. Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
GPR50 MUTATED	0	0	1	1	0	1
GPR50 WILD-TYPE	99	25	149	114	30	14

'GPR50 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.78

Table S123. Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
GPR50 MUTATED	1	0	0	1	1
GPR50 WILD-TYPE	70	49	159	103	43

'GPR50 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.353 (Fisher's exact test), Q value = 0.95

Table S124. Gene #13: 'GPR50 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
GPR50 MUTATED	2	0	1
GPR50 WILD-TYPE	144	173	107

'TFDP2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 1

Table S125. Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
TFDP2 MUTATED	1	0	2	0	0	1
TFDP2 WILD-TYPE	48	68	128	63	69	53

'TFDP2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.64

Table S126. Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
TFDP2 MUTATED	1	0	3	0	0	0
TFDP2 WILD-TYPE	68	74	75	69	78	29

'TFDP2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.22

Table S127. Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
TFDP2 MUTATED	1	0	3	0
TFDP2 WILD-TYPE	108	95	69	121

Figure S36. Get High-res Image Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TFDP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S128. Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
TFDP2 MUTATED	0	1	0	2	0
TFDP2 WILD-TYPE	60	136	72	133	30

'TFDP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S129. Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
TFDP2 MUTATED	0	0	1	2	0	0
TFDP2 WILD-TYPE	99	25	149	113	30	15

'TFDP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 0.87

Table S130. Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
TFDP2 MUTATED	1	0	0	2	0
TFDP2 WILD-TYPE	70	49	159	102	44

'TFDP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.84

Table S131. Gene #14: 'TFDP2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
TFDP2 MUTATED	0	1	2
TFDP2 WILD-TYPE	146	172	106

'FAM200A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.26

Table S132. Gene #15: 'FAM200A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
FAM200A MUTATED	2	0	0	0	2	0
FAM200A WILD-TYPE	47	68	130	63	67	54

Figure S37. Get High-res Image Gene #15: 'FAM200A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FAM200A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.57

Table S133. Gene #15: 'FAM200A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
FAM200A MUTATED	0	3	0	0	1
FAM200A WILD-TYPE	60	134	72	135	29

'FAM200A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 0.89

Table S134. Gene #15: 'FAM200A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
FAM200A MUTATED	0	0	4	0	0	0
FAM200A WILD-TYPE	99	25	146	115	30	15

'FAM200A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.87

Table S135. Gene #15: 'FAM200A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
FAM200A MUTATED	0	0	4	0	0
FAM200A WILD-TYPE	71	49	155	104	44

'FAM200A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0906 (Fisher's exact test), Q value = 0.54

Table S136. Gene #15: 'FAM200A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
FAM200A MUTATED	0	4	0
FAM200A WILD-TYPE	146	169	108

'DPCR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 1

Table S137. Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
DPCR1 MUTATED	0	1	1	2	2	0
DPCR1 WILD-TYPE	49	67	129	61	67	54

'DPCR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S138. Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
DPCR1 MUTATED	2	1	3	0
DPCR1 WILD-TYPE	55	58	80	64

'DPCR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S139. Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
DPCR1 MUTATED	0	0	2	2	1	1
DPCR1 WILD-TYPE	69	74	76	67	77	28

'DPCR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S140. Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
DPCR1 MUTATED	2	2	0	2
DPCR1 WILD-TYPE	107	93	72	119

'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.8

Table S141. Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
DPCR1 MUTATED	2	0	1	3	0
DPCR1 WILD-TYPE	58	137	71	132	30

'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0461 (Fisher's exact test), Q value = 0.33

Table S142. Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
DPCR1 MUTATED	1	1	0	2	1	1
DPCR1 WILD-TYPE	98	24	150	113	29	14

Figure S38. Get High-res Image Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.82

Table S143. Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
DPCR1 MUTATED	1	1	1	1	2
DPCR1 WILD-TYPE	70	48	158	103	42

'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S144. Gene #16: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
DPCR1 MUTATED	2	2	2
DPCR1 WILD-TYPE	144	171	106

'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.984 (Fisher's exact test), Q value = 1

Table S145. Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
EGFR MUTATED	1	1	2	1	1	0
EGFR WILD-TYPE	48	67	128	62	68	54

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S146. Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
EGFR MUTATED	0	0	1	2
EGFR WILD-TYPE	57	59	82	62

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S147. Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
EGFR MUTATED	1	2	1	1	1	0
EGFR WILD-TYPE	68	72	77	68	77	29

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.273 (Fisher's exact test), Q value = 0.84

Table S148. Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
EGFR MUTATED	1	0	1	4
EGFR WILD-TYPE	108	95	71	117

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0716 (Fisher's exact test), Q value = 0.45

Table S149. Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
EGFR MUTATED	0	1	2	1	2
EGFR WILD-TYPE	60	136	70	134	28

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S150. Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
EGFR MUTATED	1	0	3	2	0	0
EGFR WILD-TYPE	98	25	147	113	30	15

'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S151. Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
EGFR MUTATED	1	0	3	1	0
EGFR WILD-TYPE	70	49	156	103	44

'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S152. Gene #17: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
EGFR MUTATED	1	3	1
EGFR WILD-TYPE	145	170	107

'SH3KBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.871 (Fisher's exact test), Q value = 1

Table S153. Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
SH3KBP1 MUTATED	0	0	1	1	1	0
SH3KBP1 WILD-TYPE	49	68	129	62	68	54

'SH3KBP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S154. Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
SH3KBP1 MUTATED	0	1	1	1	0	0
SH3KBP1 WILD-TYPE	69	73	77	68	78	29

'SH3KBP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S155. Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
SH3KBP1 MUTATED	0	1	1	1
SH3KBP1 WILD-TYPE	109	94	71	120

'SH3KBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.901 (Fisher's exact test), Q value = 1

Table S156. Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
SH3KBP1 MUTATED	0	2	0	1	0
SH3KBP1 WILD-TYPE	60	135	72	134	30

'SH3KBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.874 (Fisher's exact test), Q value = 1

Table S157. Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
SH3KBP1 MUTATED	0	0	2	1	0	0
SH3KBP1 WILD-TYPE	99	25	148	114	30	15

'SH3KBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S158. Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
SH3KBP1 MUTATED	0	0	2	1	0
SH3KBP1 WILD-TYPE	71	49	157	103	44

'SH3KBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.478 (Fisher's exact test), Q value = 1

Table S159. Gene #18: 'SH3KBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
SH3KBP1 MUTATED	0	2	1
SH3KBP1 WILD-TYPE	146	171	107

'EMG1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.14

Table S160. Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	16	10
EMG1 MUTATED	0	0	3
EMG1 WILD-TYPE	17	16	7

Figure S39. Get High-res Image Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'EMG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.34

Table S161. Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	3	5	3	10	10	4	8
EMG1 MUTATED	0	0	0	0	0	0	3
EMG1 WILD-TYPE	3	5	3	10	10	4	5

Figure S40. Get High-res Image Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'EMG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 0.64

Table S162. Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
EMG1 MUTATED	0	1	0	0	1	2
EMG1 WILD-TYPE	49	67	130	63	68	52

'EMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0424 (Fisher's exact test), Q value = 0.32

Table S163. Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
EMG1 MUTATED	3	1	0	0	0
EMG1 WILD-TYPE	57	136	72	135	30

Figure S41. Get High-res Image Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.14

Table S164. Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
EMG1 MUTATED	0	0	2	0	0	2
EMG1 WILD-TYPE	99	25	148	115	30	13

Figure S42. Get High-res Image Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'EMG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.66

Table S165. Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
EMG1 MUTATED	1	0	0	3	0
EMG1 WILD-TYPE	70	49	159	101	44

'EMG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0648 (Fisher's exact test), Q value = 0.43

Table S166. Gene #19: 'EMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
EMG1 MUTATED	0	1	3
EMG1 WILD-TYPE	146	172	105

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S167. Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
ARID1A MUTATED	1	1	2	3	2	1
ARID1A WILD-TYPE	48	67	128	60	67	53

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.546 (Fisher's exact test), Q value = 1

Table S168. Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
ARID1A MUTATED	3	2	1	2
ARID1A WILD-TYPE	54	57	82	62

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S169. Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
ARID1A MUTATED	2	1	4	2	1	0
ARID1A WILD-TYPE	67	73	74	67	77	29

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S170. Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
ARID1A MUTATED	2	3	1	4
ARID1A WILD-TYPE	107	92	71	117

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S171. Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
ARID1A MUTATED	0	5	1	4	0
ARID1A WILD-TYPE	60	132	71	131	30

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.987 (Fisher's exact test), Q value = 1

Table S172. Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
ARID1A MUTATED	2	0	4	3	1	0
ARID1A WILD-TYPE	97	25	146	112	29	15

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S173. Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
ARID1A MUTATED	0	1	6	2	1
ARID1A WILD-TYPE	71	48	153	102	43

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.76

Table S174. Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
ARID1A MUTATED	2	7	1
ARID1A WILD-TYPE	144	166	107

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S175. Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	20	39	31
ARID1A MUTATED	1	0	2	0
ARID1A WILD-TYPE	16	20	37	31

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 0.64

Table S176. Gene #20: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	18	44	26	19
ARID1A MUTATED	1	0	2	0
ARID1A WILD-TYPE	17	44	24	19

'ARAP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.88

Table S177. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
ARAP3 MUTATED	0	1	0	1	0	1
ARAP3 WILD-TYPE	49	67	130	62	69	53

'ARAP3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S178. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
ARAP3 MUTATED	0	1	0	1	1	0
ARAP3 WILD-TYPE	69	73	78	68	77	29

'ARAP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S179. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
ARAP3 MUTATED	1	1	0	1
ARAP3 WILD-TYPE	108	94	72	120

'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S180. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
ARAP3 MUTATED	1	1	1	0	0
ARAP3 WILD-TYPE	59	136	71	135	30

'ARAP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S181. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
ARAP3 MUTATED	1	0	1	1	0	0
ARAP3 WILD-TYPE	98	25	149	114	30	15

'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S182. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
ARAP3 MUTATED	0	0	2	1	0
ARAP3 WILD-TYPE	71	49	157	103	44

'ARAP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S183. Gene #21: 'ARAP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
ARAP3 MUTATED	1	2	0
ARAP3 WILD-TYPE	145	171	108

'SLC16A9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.98

Table S184. Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
SLC16A9 MUTATED	0	1	0	1	1	1
SLC16A9 WILD-TYPE	49	67	130	62	68	53

'SLC16A9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 1

Table S185. Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
SLC16A9 MUTATED	1	1	0	1
SLC16A9 WILD-TYPE	56	58	83	63

'SLC16A9 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S186. Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
SLC16A9 MUTATED	2	1	0	0	1	0
SLC16A9 WILD-TYPE	67	73	78	69	77	29

'SLC16A9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.2 (Fisher's exact test), Q value = 0.76

Table S187. Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
SLC16A9 MUTATED	3	0	0	1
SLC16A9 WILD-TYPE	106	95	72	120

'SLC16A9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 0.67

Table S188. Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
SLC16A9 MUTATED	2	2	0	0	0
SLC16A9 WILD-TYPE	58	135	72	135	30

'SLC16A9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 0.3

Table S189. Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
SLC16A9 MUTATED	0	2	2	0	0	0
SLC16A9 WILD-TYPE	99	23	148	115	30	15

Figure S43. Get High-res Image Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SLC16A9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S190. Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
SLC16A9 MUTATED	0	0	2	1	1
SLC16A9 WILD-TYPE	71	49	157	103	43

'SLC16A9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S191. Gene #22: 'SLC16A9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
SLC16A9 MUTATED	1	2	1
SLC16A9 WILD-TYPE	145	171	107

'PCK1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S192. Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
PCK1 MUTATED	0	1	1	0	1	1
PCK1 WILD-TYPE	49	67	129	63	68	53

'PCK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 0.85

Table S193. Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
PCK1 MUTATED	2	1	0	0	0	0
PCK1 WILD-TYPE	67	73	78	69	78	29

'PCK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S194. Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
PCK1 MUTATED	1	1	0	1
PCK1 WILD-TYPE	108	94	72	120

'PCK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.98

Table S195. Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
PCK1 MUTATED	0	3	1	0	0
PCK1 WILD-TYPE	60	134	71	135	30

'PCK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S196. Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
PCK1 MUTATED	0	0	3	1	0	0
PCK1 WILD-TYPE	99	25	147	114	30	15

'PCK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S197. Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
PCK1 MUTATED	1	0	2	0	1
PCK1 WILD-TYPE	70	49	157	104	43

'PCK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S198. Gene #23: 'PCK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
PCK1 MUTATED	2	2	0
PCK1 WILD-TYPE	144	171	108

'CUL9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.958 (Fisher's exact test), Q value = 1

Table S199. Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
CUL9 MUTATED	0	2	2	1	1	1
CUL9 WILD-TYPE	49	66	128	62	68	53

'CUL9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 0.63

Table S200. Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	57	59	83	64
CUL9 MUTATED	0	1	1	4
CUL9 WILD-TYPE	57	58	82	60

'CUL9 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S201. Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
CUL9 MUTATED	2	1	1	0	2	0
CUL9 WILD-TYPE	67	73	77	69	76	29

'CUL9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.447 (Fisher's exact test), Q value = 1

Table S202. Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
CUL9 MUTATED	2	0	2	2
CUL9 WILD-TYPE	107	95	70	119

'CUL9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.8

Table S203. Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
CUL9 MUTATED	1	2	0	2	2
CUL9 WILD-TYPE	59	135	72	133	28

'CUL9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S204. Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
CUL9 MUTATED	3	0	2	2	0	0
CUL9 WILD-TYPE	96	25	148	113	30	15

'CUL9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S205. Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
CUL9 MUTATED	0	0	4	3	0
CUL9 WILD-TYPE	71	49	155	101	44

'CUL9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 0.99

Table S206. Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
CUL9 MUTATED	1	5	1
CUL9 WILD-TYPE	145	168	107

'CUL9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S207. Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	20	39	31
CUL9 MUTATED	0	0	2	1
CUL9 WILD-TYPE	17	20	37	30

'CUL9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S208. Gene #24: 'CUL9 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	18	44	26	19
CUL9 MUTATED	0	1	2	0
CUL9 WILD-TYPE	18	43	24	19

'ZDHHC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 0.82

Table S209. Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	49	68	130	63	69	54
ZDHHC1 MUTATED	2	1	1	0	0	0
ZDHHC1 WILD-TYPE	47	67	129	63	69	54

'ZDHHC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.42 (Fisher's exact test), Q value = 1

Table S210. Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	69	74	78	69	78	29
ZDHHC1 MUTATED	2	1	0	1	0	0
ZDHHC1 WILD-TYPE	67	73	78	68	78	29

'ZDHHC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.177 (Fisher's exact test), Q value = 0.75

Table S211. Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	95	72	121
ZDHHC1 MUTATED	0	0	1	3
ZDHHC1 WILD-TYPE	109	95	71	118

'ZDHHC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.763 (Fisher's exact test), Q value = 1

Table S212. Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	60	137	72	135	30
ZDHHC1 MUTATED	1	2	0	1	0
ZDHHC1 WILD-TYPE	59	135	72	134	30

'ZDHHC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.75

Table S213. Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	99	25	150	115	30	15
ZDHHC1 MUTATED	0	1	3	0	0	0
ZDHHC1 WILD-TYPE	99	24	147	115	30	15

'ZDHHC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S214. Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	71	49	159	104	44
ZDHHC1 MUTATED	0	1	1	2	0
ZDHHC1 WILD-TYPE	71	48	158	102	44

'ZDHHC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.37 (Fisher's exact test), Q value = 0.98

Table S215. Gene #25: 'ZDHHC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	173	108
ZDHHC1 MUTATED	0	3	1
ZDHHC1 WILD-TYPE	146	170	107

Methods & Data

Input

Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/22815440/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/22555002/KIRC-TP.transferedmergedcluster.txt
Number of patients = 436
Number of significantly mutated genes = 25
Number of Molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

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.

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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