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 35 genes and 10 molecular subtypes across 306 patients, 19 significant findings detected with P value < 0.05 and Q value < 0.25.

HRAS mutation correlated to 'CN_CNMF'.
TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
NFE2L2 mutation correlated to 'METHLYATION_CNMF'.
NOTCH1 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CNMF'.
NSD1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
CASP8 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
CSMD3 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 35 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, 19 significant findings detected.


		Clinical Features	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	Chi-square 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	Chi-square test
TP53	213 (70%)	93	8.22e-13 (2.84e-10)	1.4e-19 (4.84e-17)	0.0858 (1.00)	0.0628 (1.00)	0.00584 (1.00)	0.000164 (0.0548)	0.0511 (1.00)	0.000232 (0.0772)	0.0472 (1.00)	0.00367 (1.00)
CASP8	27 (9%)	279	7.37e-07 (0.000252)	4.67e-11 (1.61e-08)	0.0168 (1.00)	0.311 (1.00)	2.22e-08 (7.65e-06)	2.55e-08 (8.73e-06)	0.052 (1.00)	0.209 (1.00)	0.192 (1.00)	0.126 (1.00)
CSMD3	70 (23%)	236	0.00471 (1.00)	8.17e-05 (0.0275)	0.013 (1.00)	0.15 (1.00)	1.09e-05 (0.00369)	1.04e-05 (0.00354)	0.000372 (0.123)	0.0133 (1.00)	0.00438 (1.00)	0.0045 (1.00)
NSD1	33 (11%)	273	0.0667 (1.00)	2.78e-23 (9.69e-21)	0.0974 (1.00)	0.459 (1.00)	0.000214 (0.0714)	1.09e-05 (0.00369)	0.0807 (1.00)	0.0153 (1.00)	0.0341 (1.00)	0.0482 (1.00)
NOTCH1	57 (19%)	249	0.115 (1.00)	0.00818 (1.00)	0.0577 (1.00)	0.0267 (1.00)	0.00339 (1.00)	0.000549 (0.181)	0.000269 (0.0892)	0.23 (1.00)	0.0337 (1.00)	0.0119 (1.00)
HRAS	10 (3%)	296	0.000127 (0.0427)	0.00165 (0.535)	0.389 (1.00)	0.234 (1.00)	0.00141 (0.462)	0.0012 (0.396)	0.262 (1.00)	0.23 (1.00)	0.626 (1.00)	0.411 (1.00)
NFE2L2	17 (6%)	289	0.916 (1.00)	3.02e-05 (0.0102)	0.348 (1.00)	1 (1.00)	1 (1.00)	0.862 (1.00)	0.724 (1.00)	0.209 (1.00)	0.397 (1.00)	0.419 (1.00)
PIK3CA	64 (21%)	242	0.173 (1.00)	0.0298 (1.00)	0.702 (1.00)	0.881 (1.00)	0.08 (1.00)	0.356 (1.00)	0.0445 (1.00)	0.485 (1.00)	0.789 (1.00)	0.49 (1.00)
CDKN2A	65 (21%)	241	0.142 (1.00)	0.00193 (0.625)	0.0012 (0.396)	0.307 (1.00)	0.214 (1.00)	0.357 (1.00)	0.312 (1.00)	0.166 (1.00)	0.639 (1.00)	0.569 (1.00)
FAT1	69 (23%)	237	0.681 (1.00)	0.13 (1.00)	0.905 (1.00)	1 (1.00)	0.142 (1.00)	0.254 (1.00)	0.0842 (1.00)	0.235 (1.00)	0.93 (1.00)	0.484 (1.00)
JUB	18 (6%)	288	0.275 (1.00)	0.0796 (1.00)	0.397 (1.00)	0.466 (1.00)	0.141 (1.00)	0.503 (1.00)	0.0962 (1.00)	1 (1.00)	0.0779 (1.00)	0.953 (1.00)
MLL2	53 (17%)	253	0.141 (1.00)	0.0405 (1.00)	0.5 (1.00)	0.811 (1.00)	0.112 (1.00)	0.187 (1.00)	0.0677 (1.00)	0.00182 (0.59)	0.499 (1.00)	0.195 (1.00)
FBXW7	15 (5%)	291	0.471 (1.00)	0.125 (1.00)	0.416 (1.00)	0.134 (1.00)	0.653 (1.00)	1 (1.00)	0.81 (1.00)	0.766 (1.00)	0.546 (1.00)	0.0465 (1.00)
ZNF750	13 (4%)	293	1 (1.00)	0.136 (1.00)	0.805 (1.00)	0.526 (1.00)	0.079 (1.00)	0.105 (1.00)	0.708 (1.00)	1 (1.00)	0.425 (1.00)	0.764 (1.00)
EPHA2	13 (4%)	293	0.213 (1.00)	0.00144 (0.469)	0.741 (1.00)	0.902 (1.00)	0.071 (1.00)	0.114 (1.00)	0.101 (1.00)	0.0059 (1.00)	0.138 (1.00)	0.229 (1.00)
FLG	47 (15%)	259	0.919 (1.00)	0.0844 (1.00)	0.548 (1.00)	0.762 (1.00)	0.0493 (1.00)	0.0791 (1.00)	0.0405 (1.00)	0.149 (1.00)	0.4 (1.00)	0.26 (1.00)
B2M	7 (2%)	299	0.219 (1.00)	0.067 (1.00)			0.585 (1.00)	0.45 (1.00)	0.33 (1.00)	0.787 (1.00)	0.658 (1.00)	0.856 (1.00)
EP300	24 (8%)	282	0.419 (1.00)	0.503 (1.00)	0.573 (1.00)	0.278 (1.00)	0.00561 (1.00)	0.0174 (1.00)	0.41 (1.00)	0.847 (1.00)	0.735 (1.00)	0.267 (1.00)
RHOA	4 (1%)	302	0.0599 (1.00)	0.0921 (1.00)	0.138 (1.00)	0.449 (1.00)	0.825 (1.00)	0.212 (1.00)	0.0734 (1.00)	0.431 (1.00)	0.0375 (1.00)	0.0398 (1.00)
HLA-A	9 (3%)	297	0.367 (1.00)	0.186 (1.00)	1 (1.00)	0.453 (1.00)	0.19 (1.00)	0.23 (1.00)	0.612 (1.00)	0.0573 (1.00)	0.695 (1.00)	0.381 (1.00)
CTCF	11 (4%)	295	0.182 (1.00)	0.0296 (1.00)	0.616 (1.00)	0.856 (1.00)	0.425 (1.00)	0.445 (1.00)	0.484 (1.00)	0.534 (1.00)	0.715 (1.00)	0.972 (1.00)
RB1	10 (3%)	296	0.703 (1.00)	0.406 (1.00)	0.327 (1.00)	0.123 (1.00)	0.0459 (1.00)	0.0314 (1.00)	0.161 (1.00)	1 (1.00)	0.532 (1.00)	0.0629 (1.00)
TGFBR2	10 (3%)	296	0.542 (1.00)	0.0274 (1.00)	0.438 (1.00)	1 (1.00)	0.231 (1.00)	0.596 (1.00)	0.918 (1.00)	1 (1.00)	0.897 (1.00)	0.244 (1.00)
NECAB1	6 (2%)	300	0.362 (1.00)	0.157 (1.00)	0.872 (1.00)	0.659 (1.00)	0.0746 (1.00)	0.018 (1.00)	0.581 (1.00)	0.554 (1.00)	0.512 (1.00)	0.167 (1.00)
MAPK1	4 (1%)	302	0.297 (1.00)	0.885 (1.00)	1 (1.00)	0.743 (1.00)	0.688 (1.00)	0.351 (1.00)	0.682 (1.00)	0.197 (1.00)	0.697 (1.00)	0.984 (1.00)
EPB41L3	16 (5%)	290	0.203 (1.00)	0.0296 (1.00)	0.675 (1.00)	0.128 (1.00)	0.0688 (1.00)	0.0154 (1.00)	0.131 (1.00)	0.117 (1.00)	0.326 (1.00)	0.323 (1.00)
RAC1	9 (3%)	297	0.233 (1.00)	0.509 (1.00)	1 (1.00)	0.743 (1.00)	0.19 (1.00)	0.0372 (1.00)	0.28 (1.00)	0.156 (1.00)	0.375 (1.00)	0.137 (1.00)
CUL3	10 (3%)	296	0.277 (1.00)	0.122 (1.00)	0.377 (1.00)	0.199 (1.00)	0.47 (1.00)	0.781 (1.00)	0.649 (1.00)	0.504 (1.00)	0.375 (1.00)	0.686 (1.00)
PRB1	7 (2%)	299	0.0588 (1.00)	0.149 (1.00)	0.357 (1.00)	0.659 (1.00)	0.889 (1.00)	0.485 (1.00)	0.242 (1.00)	0.304 (1.00)	0.00226 (0.728)	0.987 (1.00)
TRPV4	7 (2%)	299	0.847 (1.00)	0.91 (1.00)	1 (1.00)	1 (1.00)	0.496 (1.00)	0.261 (1.00)	0.113 (1.00)	0.459 (1.00)	0.714 (1.00)	0.0778 (1.00)
EPDR1	6 (2%)	300	0.544 (1.00)	0.302 (1.00)	0.714 (1.00)	0.773 (1.00)	0.33 (1.00)	0.655 (1.00)	1 (1.00)	0.772 (1.00)	0.0556 (1.00)	0.697 (1.00)
SLC26A7	8 (3%)	298	0.643 (1.00)	0.403 (1.00)	0.394 (1.00)	0.289 (1.00)	0.128 (1.00)	0.0795 (1.00)	0.573 (1.00)	0.642 (1.00)	0.297 (1.00)	0.571 (1.00)
KCNA3	8 (3%)	298	0.869 (1.00)	0.842 (1.00)	0.0452 (1.00)	0.592 (1.00)	0.549 (1.00)	0.215 (1.00)	0.811 (1.00)	0.642 (1.00)	0.568 (1.00)	0.21 (1.00)
HIST1H1B	7 (2%)	299	0.605 (1.00)	0.284 (1.00)	0.945 (1.00)	0.648 (1.00)	0.721 (1.00)	0.435 (1.00)	0.611 (1.00)	0.0188 (1.00)	0.714 (1.00)	0.0789 (1.00)
STEAP4	10 (3%)	296	0.147 (1.00)	0.595 (1.00)	0.171 (1.00)	0.12 (1.00)	0.0993 (1.00)	0.215 (1.00)	0.285 (1.00)	0.584 (1.00)	0.715 (1.00)	0.381 (1.00)

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
PIK3CA MUTATED	27	29	6
PIK3CA WILD-TYPE	135	84	21

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0298 (Chi-square test), Q value = 1

Table S2. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
PIK3CA MUTATED	5	6	17	16	9	10	1
PIK3CA WILD-TYPE	38	46	46	28	32	41	11

Figure S1. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S3. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
PIK3CA MUTATED	12	9	8	10
PIK3CA WILD-TYPE	43	43	27	56

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S4. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
PIK3CA MUTATED	2	14	23
PIK3CA WILD-TYPE	15	59	95

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.08 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
PIK3CA MUTATED	31	13	20
PIK3CA WILD-TYPE	91	83	66

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S6. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
PIK3CA MUTATED	28	16	20
PIK3CA WILD-TYPE	93	49	98

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
PIK3CA MUTATED	17	33	14
PIK3CA WILD-TYPE	46	103	91

Figure S2. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S8. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
PIK3CA MUTATED	2	22	40
PIK3CA WILD-TYPE	12	99	129

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S9. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
PIK3CA MUTATED	8	15	23	11
PIK3CA WILD-TYPE	27	47	84	53

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.49 (Chi-square test), Q value = 1

Table S10. Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
PIK3CA MUTATED	2	2	7	11	19	16
PIK3CA WILD-TYPE	2	5	39	33	83	49

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
CDKN2A MUTATED	39	18	8
CDKN2A WILD-TYPE	123	95	19

'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00193 (Chi-square test), Q value = 0.62

Table S12. Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
CDKN2A MUTATED	5	17	19	1	11	11	1
CDKN2A WILD-TYPE	38	35	44	43	30	40	11

Figure S3. Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.4

Table S13. Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
CDKN2A MUTATED	11	6	17	19
CDKN2A WILD-TYPE	44	46	18	47

Figure S4. Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
CDKN2A MUTATED	2	22	29
CDKN2A WILD-TYPE	15	51	89

'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
CDKN2A MUTATED	22	19	24
CDKN2A WILD-TYPE	100	77	62

'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
CDKN2A MUTATED	21	16	28
CDKN2A WILD-TYPE	100	49	90

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S17. Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
CDKN2A MUTATED	13	24	27
CDKN2A WILD-TYPE	50	112	78

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S18. Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
CDKN2A MUTATED	3	32	29
CDKN2A WILD-TYPE	11	89	140

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S19. Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
CDKN2A MUTATED	10	11	24	13
CDKN2A WILD-TYPE	25	51	83	51

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.569 (Chi-square test), Q value = 1

Table S20. Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
CDKN2A MUTATED	2	1	7	10	25	13
CDKN2A WILD-TYPE	2	6	39	34	77	52

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000127 (Fisher's exact test), Q value = 0.043

Table S21. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
HRAS MUTATED	0	10	0
HRAS WILD-TYPE	162	103	27

Figure S5. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00165 (Chi-square test), Q value = 0.53

Table S22. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
HRAS MUTATED	1	1	0	0	6	2	0
HRAS WILD-TYPE	42	51	63	44	35	49	12

Figure S6. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
HRAS MUTATED	1	1	3	2
HRAS WILD-TYPE	54	51	32	64

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
HRAS MUTATED	1	4	2
HRAS WILD-TYPE	16	69	116

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00141 (Fisher's exact test), Q value = 0.46

Table S25. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
HRAS MUTATED	1	1	8
HRAS WILD-TYPE	121	95	78

Figure S7. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.4

Table S26. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
HRAS MUTATED	1	7	2
HRAS WILD-TYPE	120	58	116

Figure S8. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S27. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
HRAS MUTATED	3	2	5
HRAS WILD-TYPE	60	134	100

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 1

Table S28. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
HRAS MUTATED	1	2	7
HRAS WILD-TYPE	13	119	162

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S29. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
HRAS MUTATED	2	2	5	1
HRAS WILD-TYPE	33	60	102	63

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.411 (Chi-square test), Q value = 1

Table S30. Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
HRAS MUTATED	0	0	2	4	3	1
HRAS WILD-TYPE	4	7	44	40	99	64

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 8.22e-13 (Fisher's exact test), Q value = 2.8e-10

Table S31. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
TP53 MUTATED	142	54	15
TP53 WILD-TYPE	20	59	12

Figure S9. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.4e-19 (Chi-square test), Q value = 4.8e-17

Table S32. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
TP53 MUTATED	35	48	54	4	26	36	10
TP53 WILD-TYPE	8	4	9	40	15	15	2

Figure S10. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0858 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
TP53 MUTATED	45	33	28	54
TP53 WILD-TYPE	10	19	7	12

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0628 (Fisher's exact test), Q value = 1

Table S34. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
TP53 MUTATED	9	57	94
TP53 WILD-TYPE	8	16	24

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00584 (Fisher's exact test), Q value = 1

Table S35. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
TP53 MUTATED	75	78	59
TP53 WILD-TYPE	47	18	27

Figure S11. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000164 (Fisher's exact test), Q value = 0.055

Table S36. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
TP53 MUTATED	72	42	98
TP53 WILD-TYPE	49	23	20

Figure S12. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0511 (Fisher's exact test), Q value = 1

Table S37. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
TP53 MUTATED	39	91	82
TP53 WILD-TYPE	24	45	23

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000232 (Fisher's exact test), Q value = 0.077

Table S38. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
TP53 MUTATED	11	99	102
TP53 WILD-TYPE	3	22	67

Figure S13. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 1

Table S39. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
TP53 MUTATED	21	38	76	52
TP53 WILD-TYPE	14	24	31	12

Figure S14. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00367 (Chi-square test), Q value = 1

Table S40. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
TP53 MUTATED	2	4	22	30	82	47
TP53 WILD-TYPE	2	3	24	14	20	18

Figure S15. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S41. Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
NFE2L2 MUTATED	9	7	1
NFE2L2 WILD-TYPE	153	106	26

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.02e-05 (Chi-square test), Q value = 0.01

Table S42. Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
NFE2L2 MUTATED	0	0	11	0	5	1	0
NFE2L2 WILD-TYPE	43	52	52	44	36	50	12

Figure S16. Get High-res Image Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S43. Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
NFE2L2 MUTATED	4	6	2	2
NFE2L2 WILD-TYPE	51	46	33	64

'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S44. Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
NFE2L2 MUTATED	1	5	8
NFE2L2 WILD-TYPE	16	68	110

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S45. Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
NFE2L2 MUTATED	7	5	5
NFE2L2 WILD-TYPE	115	91	81

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S46. Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
NFE2L2 MUTATED	6	4	7
NFE2L2 WILD-TYPE	115	61	111

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S47. Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
NFE2L2 MUTATED	2	9	6
NFE2L2 WILD-TYPE	61	127	99

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S48. Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
NFE2L2 MUTATED	2	5	10
NFE2L2 WILD-TYPE	12	116	159

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S49. Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
NFE2L2 MUTATED	0	3	8	5
NFE2L2 WILD-TYPE	35	59	99	59

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.419 (Chi-square test), Q value = 1

Table S50. Gene #5: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
NFE2L2 MUTATED	1	0	1	4	6	4
NFE2L2 WILD-TYPE	3	7	45	40	96	61

'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
NOTCH1 MUTATED	24	24	8
NOTCH1 WILD-TYPE	138	89	19

'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00818 (Chi-square test), Q value = 1

Table S52. Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
NOTCH1 MUTATED	3	13	10	2	12	14	3
NOTCH1 WILD-TYPE	40	39	53	42	29	37	9

Figure S17. Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0577 (Fisher's exact test), Q value = 1

Table S53. Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
NOTCH1 MUTATED	15	4	6	14
NOTCH1 WILD-TYPE	40	48	29	52

'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 1

Table S54. Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
NOTCH1 MUTATED	2	21	16
NOTCH1 WILD-TYPE	15	52	102

Figure S18. Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00339 (Fisher's exact test), Q value = 1

Table S55. Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
NOTCH1 MUTATED	12	23	22
NOTCH1 WILD-TYPE	110	73	64

Figure S19. Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000549 (Fisher's exact test), Q value = 0.18

Table S56. Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
NOTCH1 MUTATED	11	20	26
NOTCH1 WILD-TYPE	110	45	92

Figure S20. Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000269 (Fisher's exact test), Q value = 0.089

Table S57. Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
NOTCH1 MUTATED	15	12	29
NOTCH1 WILD-TYPE	48	124	76

Figure S21. Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 1

Table S58. Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
NOTCH1 MUTATED	4	26	26
NOTCH1 WILD-TYPE	10	95	143

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 1

Table S59. Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
NOTCH1 MUTATED	8	4	21	15
NOTCH1 WILD-TYPE	27	58	86	49

Figure S22. Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0119 (Chi-square test), Q value = 1

Table S60. Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
NOTCH1 MUTATED	1	2	4	14	22	5
NOTCH1 WILD-TYPE	3	5	42	30	80	60

Figure S23. Get High-res Image Gene #6: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0667 (Fisher's exact test), Q value = 1

Table S61. Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
NSD1 MUTATED	24	7	2
NSD1 WILD-TYPE	138	106	25

'NSD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.78e-23 (Chi-square test), Q value = 9.7e-21

Table S62. Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
NSD1 MUTATED	25	1	0	3	3	1	0
NSD1 WILD-TYPE	18	51	63	41	38	50	12

Figure S24. Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NSD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0974 (Fisher's exact test), Q value = 1

Table S63. Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
NSD1 MUTATED	7	7	5	2
NSD1 WILD-TYPE	48	45	30	64

'NSD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S64. Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
NSD1 MUTATED	0	8	13
NSD1 WILD-TYPE	17	65	105

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000214 (Fisher's exact test), Q value = 0.071

Table S65. Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
NSD1 MUTATED	24	3	6
NSD1 WILD-TYPE	98	93	80

Figure S25. Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0037

Table S66. Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
NSD1 MUTATED	26	2	5
NSD1 WILD-TYPE	95	63	113

Figure S26. Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0807 (Fisher's exact test), Q value = 1

Table S67. Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
NSD1 MUTATED	7	20	6
NSD1 WILD-TYPE	56	116	99

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 1

Table S68. Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
NSD1 MUTATED	2	6	25
NSD1 WILD-TYPE	12	115	144

Figure S27. Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 1

Table S69. Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
NSD1 MUTATED	3	13	10	3
NSD1 WILD-TYPE	32	49	97	61

Figure S28. Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0482 (Chi-square test), Q value = 1

Table S70. Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
NSD1 MUTATED	0	0	8	4	5	12
NSD1 WILD-TYPE	4	7	38	40	97	53

Figure S29. Get High-res Image Gene #7: 'NSD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S71. Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
FAT1 MUTATED	38	26	4
FAT1 WILD-TYPE	124	87	23

'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.13 (Chi-square test), Q value = 1

Table S72. Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
FAT1 MUTATED	11	10	16	3	13	12	4
FAT1 WILD-TYPE	32	42	47	41	28	39	8

'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S73. Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
FAT1 MUTATED	12	11	7	17
FAT1 WILD-TYPE	43	41	28	49

'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S74. Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
FAT1 MUTATED	4	16	27
FAT1 WILD-TYPE	13	57	91

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 1

Table S75. Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
FAT1 MUTATED	21	27	21
FAT1 WILD-TYPE	101	69	65

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S76. Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
FAT1 MUTATED	22	15	32
FAT1 WILD-TYPE	99	50	86

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0842 (Fisher's exact test), Q value = 1

Table S77. Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
FAT1 MUTATED	10	27	31
FAT1 WILD-TYPE	53	109	74

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S78. Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
FAT1 MUTATED	4	32	32
FAT1 WILD-TYPE	10	89	137

'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S79. Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
FAT1 MUTATED	8	13	27	16
FAT1 WILD-TYPE	27	49	80	48

'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.484 (Chi-square test), Q value = 1

Table S80. Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
FAT1 MUTATED	1	1	8	12	30	12
FAT1 WILD-TYPE	3	6	38	32	72	53

'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 7.37e-07 (Fisher's exact test), Q value = 0.00025

Table S81. Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
CASP8 MUTATED	2	21	3
CASP8 WILD-TYPE	160	92	24

Figure S30. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.67e-11 (Chi-square test), Q value = 1.6e-08

Table S82. Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
CASP8 MUTATED	2	2	0	0	16	6	1
CASP8 WILD-TYPE	41	50	63	44	25	45	11

Figure S31. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 1

Table S83. Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
CASP8 MUTATED	5	1	8	8
CASP8 WILD-TYPE	50	51	27	58

Figure S32. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 1

Table S84. Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
CASP8 MUTATED	1	11	10
CASP8 WILD-TYPE	16	62	108

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.22e-08 (Fisher's exact test), Q value = 7.6e-06

Table S85. Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
CASP8 MUTATED	1	5	21
CASP8 WILD-TYPE	121	91	65

Figure S33. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.55e-08 (Fisher's exact test), Q value = 8.7e-06

Table S86. Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
CASP8 MUTATED	1	18	8
CASP8 WILD-TYPE	120	47	110

Figure S34. Get High-res Image Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.052 (Fisher's exact test), Q value = 1

Table S87. Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
CASP8 MUTATED	7	6	13
CASP8 WILD-TYPE	56	130	92

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S88. Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
CASP8 MUTATED	3	10	13
CASP8 WILD-TYPE	11	111	156

'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 1

Table S89. Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
CASP8 MUTATED	5	2	12	5
CASP8 WILD-TYPE	30	60	95	59

'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.126 (Chi-square test), Q value = 1

Table S90. Gene #9: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
CASP8 MUTATED	1	1	4	7	10	1
CASP8 WILD-TYPE	3	6	42	37	92	64

'JUB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 1

Table S91. Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
JUB MUTATED	13	4	1
JUB WILD-TYPE	149	109	26

'JUB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0796 (Chi-square test), Q value = 1

Table S92. Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
JUB MUTATED	0	6	5	1	3	1	2
JUB WILD-TYPE	43	46	58	43	38	50	10

'JUB MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S93. Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
JUB MUTATED	5	2	3	2
JUB WILD-TYPE	50	50	32	64

'JUB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.466 (Fisher's exact test), Q value = 1

Table S94. Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
JUB MUTATED	1	6	5
JUB WILD-TYPE	16	67	113

'JUB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 1

Table S95. Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
JUB MUTATED	5	4	9
JUB WILD-TYPE	117	92	77

'JUB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.503 (Fisher's exact test), Q value = 1

Table S96. Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
JUB MUTATED	5	5	8
JUB WILD-TYPE	116	60	110

'JUB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0962 (Fisher's exact test), Q value = 1

Table S97. Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
JUB MUTATED	7	8	3
JUB WILD-TYPE	56	128	102

'JUB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S98. Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
JUB MUTATED	0	7	11
JUB WILD-TYPE	14	114	158

'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0779 (Fisher's exact test), Q value = 1

Table S99. Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
JUB MUTATED	6	3	7	2
JUB WILD-TYPE	29	59	100	62

'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.953 (Chi-square test), Q value = 1

Table S100. Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
JUB MUTATED	0	0	4	3	7	4
JUB WILD-TYPE	4	7	42	41	95	61

'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 1

Table S101. Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
MLL2 MUTATED	35	14	4
MLL2 WILD-TYPE	127	99	23

'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0405 (Chi-square test), Q value = 1

Table S102. Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
MLL2 MUTATED	11	7	17	9	4	5	0
MLL2 WILD-TYPE	32	45	46	35	37	46	12

Figure S35. Get High-res Image Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 1

Table S103. Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
MLL2 MUTATED	7	11	8	10
MLL2 WILD-TYPE	48	41	27	56

'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S104. Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
MLL2 MUTATED	3	14	19
MLL2 WILD-TYPE	14	59	99

'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S105. Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
MLL2 MUTATED	28	12	13
MLL2 WILD-TYPE	94	84	73

'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 1

Table S106. Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
MLL2 MUTATED	26	12	15
MLL2 WILD-TYPE	95	53	103

'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0677 (Fisher's exact test), Q value = 1

Table S107. Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
MLL2 MUTATED	12	29	11
MLL2 WILD-TYPE	51	107	94

'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00182 (Fisher's exact test), Q value = 0.59

Table S108. Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
MLL2 MUTATED	0	12	40
MLL2 WILD-TYPE	14	109	129

Figure S36. Get High-res Image Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.499 (Fisher's exact test), Q value = 1

Table S109. Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
MLL2 MUTATED	5	14	18	8
MLL2 WILD-TYPE	30	48	89	56

'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.195 (Chi-square test), Q value = 1

Table S110. Gene #11: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
MLL2 MUTATED	0	1	10	10	10	14
MLL2 WILD-TYPE	4	6	36	34	92	51

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 1

Table S111. Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
FBXW7 MUTATED	10	5	0
FBXW7 WILD-TYPE	152	108	27

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.125 (Chi-square test), Q value = 1

Table S112. Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
FBXW7 MUTATED	3	0	5	1	3	1	2
FBXW7 WILD-TYPE	40	52	58	43	38	50	10

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S113. Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
FBXW7 MUTATED	1	4	1	5
FBXW7 WILD-TYPE	54	48	34	61

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S114. Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
FBXW7 MUTATED	1	1	9
FBXW7 WILD-TYPE	16	72	109

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S115. Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
FBXW7 MUTATED	7	3	5
FBXW7 WILD-TYPE	115	93	81

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S116. Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
FBXW7 MUTATED	6	3	6
FBXW7 WILD-TYPE	115	62	112

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.81 (Fisher's exact test), Q value = 1

Table S117. Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
FBXW7 MUTATED	4	6	5
FBXW7 WILD-TYPE	59	130	100

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118. Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
FBXW7 MUTATED	0	5	10
FBXW7 WILD-TYPE	14	116	159

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S119. Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
FBXW7 MUTATED	1	5	4	2
FBXW7 WILD-TYPE	34	57	103	62

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0465 (Chi-square test), Q value = 1

Table S120. Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
FBXW7 MUTATED	0	2	1	1	4	4
FBXW7 WILD-TYPE	4	5	45	43	98	61

Figure S37. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

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

Table S121. Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
ZNF750 MUTATED	7	5	1
ZNF750 WILD-TYPE	155	108	26

'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.136 (Chi-square test), Q value = 1

Table S122. Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
ZNF750 MUTATED	1	0	4	5	1	2	0
ZNF750 WILD-TYPE	42	52	59	39	40	49	12

'ZNF750 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S123. Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
ZNF750 MUTATED	2	2	0	2
ZNF750 WILD-TYPE	53	50	35	64

'ZNF750 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S124. Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
ZNF750 MUTATED	1	2	3
ZNF750 WILD-TYPE	16	71	115

'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.079 (Fisher's exact test), Q value = 1

Table S125. Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
ZNF750 MUTATED	9	3	1
ZNF750 WILD-TYPE	113	93	85

'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S126. Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
ZNF750 MUTATED	9	1	3
ZNF750 WILD-TYPE	112	64	115

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.708 (Fisher's exact test), Q value = 1

Table S127. Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
ZNF750 MUTATED	3	7	3
ZNF750 WILD-TYPE	60	129	102

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S128. Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
ZNF750 MUTATED	0	5	8
ZNF750 WILD-TYPE	14	116	161

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S129. Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
ZNF750 MUTATED	0	4	4	4
ZNF750 WILD-TYPE	35	58	103	60

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.764 (Chi-square test), Q value = 1

Table S130. Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
ZNF750 MUTATED	0	1	3	2	4	2
ZNF750 WILD-TYPE	4	6	43	42	98	63

'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 1

Table S131. Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
EPHA2 MUTATED	4	6	2
EPHA2 WILD-TYPE	158	107	25

'EPHA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00144 (Chi-square test), Q value = 0.47

Table S132. Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
EPHA2 MUTATED	1	3	0	1	6	0	2
EPHA2 WILD-TYPE	42	49	63	43	35	51	10

Figure S38. Get High-res Image Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S133. Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
EPHA2 MUTATED	4	2	1	5
EPHA2 WILD-TYPE	51	50	34	61

'EPHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S134. Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
EPHA2 MUTATED	1	5	6
EPHA2 WILD-TYPE	16	68	112

'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.071 (Fisher's exact test), Q value = 1

Table S135. Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
EPHA2 MUTATED	2	4	7
EPHA2 WILD-TYPE	120	92	79

'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S136. Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
EPHA2 MUTATED	2	5	6
EPHA2 WILD-TYPE	119	60	112

'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 1

Table S137. Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
EPHA2 MUTATED	4	2	6
EPHA2 WILD-TYPE	59	134	99

'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S138. Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
EPHA2 MUTATED	3	6	3
EPHA2 WILD-TYPE	11	115	166

Figure S39. Get High-res Image Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S139. Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
EPHA2 MUTATED	2	0	6	1
EPHA2 WILD-TYPE	33	62	101	63

'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.229 (Chi-square test), Q value = 1

Table S140. Gene #14: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
EPHA2 MUTATED	0	1	1	3	4	0
EPHA2 WILD-TYPE	4	6	45	41	98	65

'FLG MUTATION STATUS' versus 'CN_CNMF'

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

Table S141. Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
FLG MUTATED	24	19	4
FLG WILD-TYPE	138	94	23

'FLG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0844 (Chi-square test), Q value = 1

Table S142. Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
FLG MUTATED	6	4	15	7	10	4	1
FLG WILD-TYPE	37	48	48	37	31	47	11

'FLG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 1

Table S143. Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
FLG MUTATED	9	9	7	7
FLG WILD-TYPE	46	43	28	59

'FLG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S144. Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
FLG MUTATED	2	13	17
FLG WILD-TYPE	15	60	101

'FLG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 1

Table S145. Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
FLG MUTATED	26	9	12
FLG WILD-TYPE	96	87	74

Figure S40. Get High-res Image Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FLG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0791 (Fisher's exact test), Q value = 1

Table S146. Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
FLG MUTATED	25	10	12
FLG WILD-TYPE	96	55	106

'FLG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 1

Table S147. Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
FLG MUTATED	11	27	9
FLG WILD-TYPE	52	109	96

Figure S41. Get High-res Image Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'FLG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S148. Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
FLG MUTATED	2	13	32
FLG WILD-TYPE	12	108	137

'FLG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S149. Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
FLG MUTATED	3	13	16	8
FLG WILD-TYPE	32	49	91	56

'FLG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.26 (Chi-square test), Q value = 1

Table S150. Gene #15: 'FLG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
FLG MUTATED	0	0	9	8	10	13
FLG WILD-TYPE	4	7	37	36	92	52

'B2M MUTATION STATUS' versus 'CN_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 1

Table S151. Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
B2M MUTATED	2	5	0
B2M WILD-TYPE	160	108	27

'B2M MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.067 (Chi-square test), Q value = 1

Table S152. Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
B2M MUTATED	0	0	1	4	1	1	0
B2M WILD-TYPE	43	52	62	40	40	50	12

'B2M MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S153. Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
B2M MUTATED	4	1	1
B2M WILD-TYPE	118	95	85

'B2M MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S154. Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
B2M MUTATED	4	1	1
B2M WILD-TYPE	117	64	117

'B2M MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 1

Table S155. Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
B2M MUTATED	0	5	2
B2M WILD-TYPE	63	131	103

'B2M MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.787 (Fisher's exact test), Q value = 1

Table S156. Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
B2M MUTATED	0	2	5
B2M WILD-TYPE	14	119	164

'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S157. Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
B2M MUTATED	0	3	3	1
B2M WILD-TYPE	35	59	104	63

'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.856 (Chi-square test), Q value = 1

Table S158. Gene #16: 'B2M MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
B2M MUTATED	0	0	2	2	2	1
B2M WILD-TYPE	4	7	44	42	100	64

'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 1

Table S159. Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
EP300 MUTATED	10	12	2
EP300 WILD-TYPE	152	101	25

'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.503 (Chi-square test), Q value = 1

Table S160. Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
EP300 MUTATED	2	2	4	5	6	4	1
EP300 WILD-TYPE	41	50	59	39	35	47	11

'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 1

Table S161. Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
EP300 MUTATED	3	2	4	4
EP300 WILD-TYPE	52	50	31	62

'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S162. Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
EP300 MUTATED	1	7	5
EP300 WILD-TYPE	16	66	113

'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00561 (Fisher's exact test), Q value = 1

Table S163. Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
EP300 MUTATED	5	5	14
EP300 WILD-TYPE	117	91	72

Figure S42. Get High-res Image Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 1

Table S164. Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
EP300 MUTATED	6	11	7
EP300 WILD-TYPE	115	54	111

Figure S43. Get High-res Image Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S165. Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
EP300 MUTATED	7	8	8
EP300 WILD-TYPE	56	128	97

'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S166. Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
EP300 MUTATED	1	8	14
EP300 WILD-TYPE	13	113	155

'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.735 (Fisher's exact test), Q value = 1

Table S167. Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
EP300 MUTATED	3	3	10	6
EP300 WILD-TYPE	32	59	97	58

'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.267 (Chi-square test), Q value = 1

Table S168. Gene #17: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
EP300 MUTATED	1	0	6	5	8	2
EP300 WILD-TYPE	3	7	40	39	94	63

'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0599 (Fisher's exact test), Q value = 1

Table S169. Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
RHOA MUTATED	1	1	2
RHOA WILD-TYPE	161	112	25

'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0921 (Chi-square test), Q value = 1

Table S170. Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
RHOA MUTATED	0	3	0	0	0	1	0
RHOA WILD-TYPE	43	49	63	44	41	50	12

'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S171. Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
RHOA MUTATED	0	0	0	3
RHOA WILD-TYPE	55	52	35	63

'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S172. Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
RHOA MUTATED	0	0	3
RHOA WILD-TYPE	17	73	115

'RHOA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 1

Table S173. Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
RHOA MUTATED	1	2	1
RHOA WILD-TYPE	121	94	85

'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S174. Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
RHOA MUTATED	0	1	3
RHOA WILD-TYPE	121	64	115

'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0734 (Fisher's exact test), Q value = 1

Table S175. Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
RHOA MUTATED	2	0	2
RHOA WILD-TYPE	61	136	103

'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S176. Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
RHOA MUTATED	0	3	1
RHOA WILD-TYPE	14	118	168

'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 1

Table S177. Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
RHOA MUTATED	1	0	0	3
RHOA WILD-TYPE	34	62	107	61

Figure S44. Get High-res Image Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0398 (Chi-square test), Q value = 1

Table S178. Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
RHOA MUTATED	0	1	0	0	3	0
RHOA WILD-TYPE	4	6	46	44	99	65

Figure S45. Get High-res Image Gene #18: 'RHOA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'CN_CNMF'

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

Table S179. Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
HLA-A MUTATED	3	5	1
HLA-A WILD-TYPE	159	108	26

'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.186 (Chi-square test), Q value = 1

Table S180. Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
HLA-A MUTATED	0	1	2	1	4	1	0
HLA-A WILD-TYPE	43	51	61	43	37	50	12

'HLA-A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S181. Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
HLA-A MUTATED	1	1	1	2
HLA-A WILD-TYPE	54	51	34	64

'HLA-A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 1

Table S182. Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
HLA-A MUTATED	1	1	3
HLA-A WILD-TYPE	16	72	115

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S183. Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
HLA-A MUTATED	3	1	5
HLA-A WILD-TYPE	119	95	81

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 1

Table S184. Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
HLA-A MUTATED	2	4	3
HLA-A WILD-TYPE	119	61	115

'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S185. Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
HLA-A MUTATED	3	3	3
HLA-A WILD-TYPE	60	133	102

'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0573 (Fisher's exact test), Q value = 1

Table S186. Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
HLA-A MUTATED	2	2	5
HLA-A WILD-TYPE	12	119	164

'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.695 (Fisher's exact test), Q value = 1

Table S187. Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
HLA-A MUTATED	2	1	4	2
HLA-A WILD-TYPE	33	61	103	62

'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.381 (Chi-square test), Q value = 1

Table S188. Gene #19: 'HLA-A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
HLA-A MUTATED	0	0	4	1	3	1
HLA-A WILD-TYPE	4	7	42	43	99	64

'CTCF MUTATION STATUS' versus 'CN_CNMF'

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

Table S189. Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
CTCF MUTATED	4	7	0
CTCF WILD-TYPE	158	106	27

'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0296 (Chi-square test), Q value = 1

Table S190. Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
CTCF MUTATED	3	1	0	1	5	1	0
CTCF WILD-TYPE	40	51	63	43	36	50	12

Figure S46. Get High-res Image Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S191. Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
CTCF MUTATED	2	2	0	4
CTCF WILD-TYPE	53	50	35	62

'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S192. Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
CTCF MUTATED	0	2	6
CTCF WILD-TYPE	17	71	112

'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S193. Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
CTCF MUTATED	4	2	5
CTCF WILD-TYPE	118	94	81

'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S194. Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
CTCF MUTATED	4	4	3
CTCF WILD-TYPE	117	61	115

'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S195. Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
CTCF MUTATED	3	3	5
CTCF WILD-TYPE	60	133	100

'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.534 (Fisher's exact test), Q value = 1

Table S196. Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
CTCF MUTATED	1	4	6
CTCF WILD-TYPE	13	117	163

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S197. Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
CTCF MUTATED	0	3	5	2
CTCF WILD-TYPE	35	59	102	62

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.972 (Chi-square test), Q value = 1

Table S198. Gene #20: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
CTCF MUTATED	0	0	2	2	3	3
CTCF WILD-TYPE	4	7	44	42	99	62

'RB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S199. Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
RB1 MUTATED	5	5	0
RB1 WILD-TYPE	157	108	27

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.406 (Chi-square test), Q value = 1

Table S200. Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
RB1 MUTATED	3	0	2	3	1	1	0
RB1 WILD-TYPE	40	52	61	41	40	50	12

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S201. Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
RB1 MUTATED	0	1	0	3
RB1 WILD-TYPE	55	51	35	63

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S202. Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
RB1 MUTATED	1	0	3
RB1 WILD-TYPE	16	73	115

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 1

Table S203. Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
RB1 MUTATED	8	1	1
RB1 WILD-TYPE	114	95	85

Figure S47. Get High-res Image Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0314 (Fisher's exact test), Q value = 1

Table S204. Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
RB1 MUTATED	8	0	2
RB1 WILD-TYPE	113	65	116

Figure S48. Get High-res Image Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S205. Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
RB1 MUTATED	0	7	3
RB1 WILD-TYPE	63	129	102

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S206. Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
RB1 MUTATED	0	4	6
RB1 WILD-TYPE	14	117	163

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S207. Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
RB1 MUTATED	0	3	5	1
RB1 WILD-TYPE	35	59	102	63

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0629 (Chi-square test), Q value = 1

Table S208. Gene #21: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
RB1 MUTATED	0	0	0	0	3	6
RB1 WILD-TYPE	4	7	46	44	99	59

'CSMD3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 1

Table S209. Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
CSMD3 MUTATED	48	15	7
CSMD3 WILD-TYPE	114	98	20

Figure S49. Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CSMD3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 8.17e-05 (Chi-square test), Q value = 0.028

Table S210. Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
CSMD3 MUTATED	21	8	18	11	4	5	3
CSMD3 WILD-TYPE	22	44	45	33	37	46	9

Figure S50. Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CSMD3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 1

Table S211. Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
CSMD3 MUTATED	15	18	8	7
CSMD3 WILD-TYPE	40	34	27	59

Figure S51. Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CSMD3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S212. Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
CSMD3 MUTATED	6	20	22
CSMD3 WILD-TYPE	11	53	96

'CSMD3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0037

Table S213. Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
CSMD3 MUTATED	44	9	17
CSMD3 WILD-TYPE	78	87	69

Figure S52. Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CSMD3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.04e-05 (Fisher's exact test), Q value = 0.0035

Table S214. Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
CSMD3 MUTATED	45	11	14
CSMD3 WILD-TYPE	76	54	104

Figure S53. Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000372 (Fisher's exact test), Q value = 0.12

Table S215. Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
CSMD3 MUTATED	17	42	11
CSMD3 WILD-TYPE	46	94	94

Figure S54. Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 1

Table S216. Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
CSMD3 MUTATED	5	18	47
CSMD3 WILD-TYPE	9	103	122

Figure S55. Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00438 (Fisher's exact test), Q value = 1

Table S217. Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
CSMD3 MUTATED	6	20	26	5
CSMD3 WILD-TYPE	29	42	81	59

Figure S56. Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CSMD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0045 (Chi-square test), Q value = 1

Table S218. Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
CSMD3 MUTATED	1	0	10	10	12	24
CSMD3 WILD-TYPE	3	7	36	34	90	41

Figure S57. Get High-res Image Gene #22: 'CSMD3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TGFBR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 1

Table S219. Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
TGFBR2 MUTATED	4	5	1
TGFBR2 WILD-TYPE	158	108	26

'TGFBR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0274 (Chi-square test), Q value = 1

Table S220. Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
TGFBR2 MUTATED	3	0	0	0	4	3	0
TGFBR2 WILD-TYPE	40	52	63	44	37	48	12

Figure S58. Get High-res Image Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TGFBR2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 1

Table S221. Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
TGFBR2 MUTATED	3	1	0	4
TGFBR2 WILD-TYPE	52	51	35	62

'TGFBR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S222. Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
TGFBR2 MUTATED	0	3	5
TGFBR2 WILD-TYPE	17	70	113

'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S223. Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
TGFBR2 MUTATED	2	3	5
TGFBR2 WILD-TYPE	120	93	81

'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S224. Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
TGFBR2 MUTATED	3	3	4
TGFBR2 WILD-TYPE	118	62	114

'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S225. Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
TGFBR2 MUTATED	2	4	4
TGFBR2 WILD-TYPE	61	132	101

'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S226. Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
TGFBR2 MUTATED	0	4	6
TGFBR2 WILD-TYPE	14	117	163

'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S227. Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
TGFBR2 MUTATED	1	1	4	3
TGFBR2 WILD-TYPE	34	61	103	61

'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.244 (Chi-square test), Q value = 1

Table S228. Gene #23: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
TGFBR2 MUTATED	0	1	0	3	4	1
TGFBR2 WILD-TYPE	4	6	46	41	98	64

'NECAB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S229. Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
NECAB1 MUTATED	2	4	0
NECAB1 WILD-TYPE	160	109	27

'NECAB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.157 (Chi-square test), Q value = 1

Table S230. Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
NECAB1 MUTATED	2	0	0	1	2	0	1
NECAB1 WILD-TYPE	41	52	63	43	39	51	11

'NECAB1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S231. Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
NECAB1 MUTATED	1	0	1	1
NECAB1 WILD-TYPE	54	52	34	65

'NECAB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.659 (Fisher's exact test), Q value = 1

Table S232. Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
NECAB1 MUTATED	0	2	1
NECAB1 WILD-TYPE	17	71	117

'NECAB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0746 (Fisher's exact test), Q value = 1

Table S233. Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
NECAB1 MUTATED	2	0	4
NECAB1 WILD-TYPE	120	96	82

'NECAB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 1

Table S234. Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
NECAB1 MUTATED	2	4	0
NECAB1 WILD-TYPE	119	61	118

Figure S59. Get High-res Image Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NECAB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S235. Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
NECAB1 MUTATED	2	3	1
NECAB1 WILD-TYPE	61	133	104

'NECAB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.554 (Fisher's exact test), Q value = 1

Table S236. Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
NECAB1 MUTATED	0	1	5
NECAB1 WILD-TYPE	14	120	164

'NECAB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S237. Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
NECAB1 MUTATED	1	2	3	0
NECAB1 WILD-TYPE	34	60	104	64

'NECAB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.167 (Chi-square test), Q value = 1

Table S238. Gene #24: 'NECAB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
NECAB1 MUTATED	0	1	0	2	1	2
NECAB1 WILD-TYPE	4	6	46	42	101	63

'MAPK1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S239. Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
MAPK1 MUTATED	1	2	1
MAPK1 WILD-TYPE	161	111	26

'MAPK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.885 (Chi-square test), Q value = 1

Table S240. Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
MAPK1 MUTATED	0	0	1	1	1	1	0
MAPK1 WILD-TYPE	43	52	62	43	40	50	12

'MAPK1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S241. Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
MAPK1 MUTATED	1	1	1	1
MAPK1 WILD-TYPE	54	51	34	65

'MAPK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S242. Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
MAPK1 MUTATED	0	2	2
MAPK1 WILD-TYPE	17	71	116

'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S243. Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
MAPK1 MUTATED	1	1	2
MAPK1 WILD-TYPE	121	95	84

'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S244. Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
MAPK1 MUTATED	1	2	1
MAPK1 WILD-TYPE	120	63	117

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S245. Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
MAPK1 MUTATED	1	1	2
MAPK1 WILD-TYPE	62	135	103

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S246. Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
MAPK1 MUTATED	1	1	2
MAPK1 WILD-TYPE	13	120	167

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S247. Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
MAPK1 MUTATED	1	0	2	1
MAPK1 WILD-TYPE	34	62	105	63

'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.984 (Chi-square test), Q value = 1

Table S248. Gene #25: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
MAPK1 MUTATED	0	0	1	1	1	1
MAPK1 WILD-TYPE	4	7	45	43	101	64

'EPB41L3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S249. Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
EPB41L3 MUTATED	11	3	2
EPB41L3 WILD-TYPE	151	110	25

'EPB41L3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0296 (Chi-square test), Q value = 1

Table S250. Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
EPB41L3 MUTATED	6	1	6	0	1	2	0
EPB41L3 WILD-TYPE	37	51	57	44	40	49	12

Figure S60. Get High-res Image Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPB41L3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S251. Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
EPB41L3 MUTATED	1	3	2	4
EPB41L3 WILD-TYPE	54	49	33	62

'EPB41L3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S252. Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
EPB41L3 MUTATED	0	1	9
EPB41L3 WILD-TYPE	17	72	109

'EPB41L3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0688 (Fisher's exact test), Q value = 1

Table S253. Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
EPB41L3 MUTATED	11	2	3
EPB41L3 WILD-TYPE	111	94	83

'EPB41L3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 1

Table S254. Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
EPB41L3 MUTATED	12	1	3
EPB41L3 WILD-TYPE	109	64	115

Figure S61. Get High-res Image Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EPB41L3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 1

Table S255. Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
EPB41L3 MUTATED	4	10	2
EPB41L3 WILD-TYPE	59	126	103

'EPB41L3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S256. Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
EPB41L3 MUTATED	0	3	13
EPB41L3 WILD-TYPE	14	118	156

'EPB41L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S257. Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
EPB41L3 MUTATED	2	6	4	2
EPB41L3 WILD-TYPE	33	56	103	62

'EPB41L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.323 (Chi-square test), Q value = 1

Table S258. Gene #26: 'EPB41L3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
EPB41L3 MUTATED	0	0	2	2	3	7
EPB41L3 WILD-TYPE	4	7	44	42	99	58

'RAC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 1

Table S259. Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
RAC1 MUTATED	3	6	0
RAC1 WILD-TYPE	159	107	27

'RAC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.509 (Chi-square test), Q value = 1

Table S260. Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
RAC1 MUTATED	0	1	1	1	2	3	1
RAC1 WILD-TYPE	43	51	62	43	39	48	11

'RAC1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S261. Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
RAC1 MUTATED	1	1	1	1
RAC1 WILD-TYPE	54	51	34	65

'RAC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S262. Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
RAC1 MUTATED	0	2	2
RAC1 WILD-TYPE	17	71	116

'RAC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S263. Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
RAC1 MUTATED	3	1	5
RAC1 WILD-TYPE	119	95	81

'RAC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 1

Table S264. Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
RAC1 MUTATED	3	5	1
RAC1 WILD-TYPE	118	60	117

Figure S62. Get High-res Image Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RAC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S265. Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
RAC1 MUTATED	3	5	1
RAC1 WILD-TYPE	60	131	104

'RAC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S266. Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
RAC1 MUTATED	0	1	8
RAC1 WILD-TYPE	14	120	161

'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S267. Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
RAC1 MUTATED	1	3	3	0
RAC1 WILD-TYPE	34	59	104	64

'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.137 (Chi-square test), Q value = 1

Table S268. Gene #27: 'RAC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
RAC1 MUTATED	0	0	4	1	1	1
RAC1 WILD-TYPE	4	7	42	43	101	64

'CUL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S269. Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
CUL3 MUTATED	8	2	0
CUL3 WILD-TYPE	154	111	27

'CUL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.122 (Chi-square test), Q value = 1

Table S270. Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
CUL3 MUTATED	3	1	5	0	0	1	0
CUL3 WILD-TYPE	40	51	58	44	41	50	12

'CUL3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S271. Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
CUL3 MUTATED	2	4	0	2
CUL3 WILD-TYPE	53	48	35	64

'CUL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S272. Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
CUL3 MUTATED	2	2	4
CUL3 WILD-TYPE	15	71	114

'CUL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 1

Table S273. Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
CUL3 MUTATED	5	4	1
CUL3 WILD-TYPE	117	92	85

'CUL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S274. Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
CUL3 MUTATED	5	1	4
CUL3 WILD-TYPE	116	64	114

'CUL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S275. Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
CUL3 MUTATED	2	6	2
CUL3 WILD-TYPE	61	130	103

'CUL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S276. Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
CUL3 MUTATED	0	6	4
CUL3 WILD-TYPE	14	115	165

'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S277. Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
CUL3 MUTATED	1	4	2	1
CUL3 WILD-TYPE	34	58	105	63

'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.686 (Chi-square test), Q value = 1

Table S278. Gene #28: 'CUL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
CUL3 MUTATED	0	0	1	0	5	2
CUL3 WILD-TYPE	4	7	45	44	97	63

'PRB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0588 (Fisher's exact test), Q value = 1

Table S279. Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
PRB1 MUTATED	7	0	0
PRB1 WILD-TYPE	155	113	27

'PRB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.149 (Chi-square test), Q value = 1

Table S280. Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
PRB1 MUTATED	3	0	3	0	0	1	0
PRB1 WILD-TYPE	40	52	60	44	41	50	12

'PRB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 1

Table S281. Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
PRB1 MUTATED	2	1	0	0
PRB1 WILD-TYPE	53	51	35	66

'PRB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.659 (Fisher's exact test), Q value = 1

Table S282. Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
PRB1 MUTATED	0	2	1
PRB1 WILD-TYPE	17	71	117

'PRB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S283. Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
PRB1 MUTATED	2	3	2
PRB1 WILD-TYPE	120	93	84

'PRB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S284. Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
PRB1 MUTATED	3	0	4
PRB1 WILD-TYPE	118	65	114

'PRB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 1

Table S285. Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
PRB1 MUTATED	3	3	1
PRB1 WILD-TYPE	60	133	104

'PRB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S286. Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
PRB1 MUTATED	1	3	3
PRB1 WILD-TYPE	13	118	166

'PRB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.73

Table S287. Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
PRB1 MUTATED	3	3	0	0
PRB1 WILD-TYPE	32	59	107	64

Figure S63. Get High-res Image Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PRB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.987 (Chi-square test), Q value = 1

Table S288. Gene #29: 'PRB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
PRB1 MUTATED	0	0	1	1	3	1
PRB1 WILD-TYPE	4	7	45	43	99	64

'TRPV4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S289. Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
TRPV4 MUTATED	5	2	0
TRPV4 WILD-TYPE	157	111	27

'TRPV4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.91 (Chi-square test), Q value = 1

Table S290. Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
TRPV4 MUTATED	0	2	2	1	1	1	0
TRPV4 WILD-TYPE	43	50	61	43	40	50	12

'TRPV4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S291. Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
TRPV4 MUTATED	2	1	1	2
TRPV4 WILD-TYPE	53	51	34	64

'TRPV4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S292. Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
TRPV4 MUTATED	0	2	4
TRPV4 WILD-TYPE	17	71	114

'TRPV4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 1

Table S293. Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
TRPV4 MUTATED	3	1	3
TRPV4 WILD-TYPE	119	95	83

'TRPV4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 1

Table S294. Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
TRPV4 MUTATED	3	3	1
TRPV4 WILD-TYPE	118	62	117

'TRPV4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S295. Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
TRPV4 MUTATED	0	6	1
TRPV4 WILD-TYPE	63	130	104

'TRPV4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S296. Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
TRPV4 MUTATED	0	1	6
TRPV4 WILD-TYPE	14	120	163

'TRPV4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S297. Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
TRPV4 MUTATED	0	1	3	3
TRPV4 WILD-TYPE	35	61	104	61

'TRPV4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0778 (Chi-square test), Q value = 1

Table S298. Gene #30: 'TRPV4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
TRPV4 MUTATED	0	0	0	4	1	2
TRPV4 WILD-TYPE	4	7	46	40	101	63

'EPDR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S299. Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
EPDR1 MUTATED	5	1	0
EPDR1 WILD-TYPE	157	112	27

'EPDR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.302 (Chi-square test), Q value = 1

Table S300. Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
EPDR1 MUTATED	0	3	2	0	0	1	0
EPDR1 WILD-TYPE	43	49	61	44	41	50	12

'EPDR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S301. Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
EPDR1 MUTATED	1	1	0	3
EPDR1 WILD-TYPE	54	51	35	63

'EPDR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.773 (Fisher's exact test), Q value = 1

Table S302. Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
EPDR1 MUTATED	0	1	4
EPDR1 WILD-TYPE	17	72	114

'EPDR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 1

Table S303. Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
EPDR1 MUTATED	3	3	0
EPDR1 WILD-TYPE	119	93	86

'EPDR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S304. Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
EPDR1 MUTATED	3	0	3
EPDR1 WILD-TYPE	118	65	115

'EPDR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S305. Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
EPDR1 MUTATED	1	3	2
EPDR1 WILD-TYPE	62	133	103

'EPDR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S306. Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
EPDR1 MUTATED	0	3	3
EPDR1 WILD-TYPE	14	118	166

'EPDR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0556 (Fisher's exact test), Q value = 1

Table S307. Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
EPDR1 MUTATED	2	2	0	2
EPDR1 WILD-TYPE	33	60	107	62

'EPDR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.697 (Chi-square test), Q value = 1

Table S308. Gene #31: 'EPDR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
EPDR1 MUTATED	0	0	0	1	2	3
EPDR1 WILD-TYPE	4	7	46	43	100	62

'SLC26A7 MUTATION STATUS' versus 'CN_CNMF'

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

Table S309. Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
SLC26A7 MUTATED	5	2	1
SLC26A7 WILD-TYPE	157	111	26

'SLC26A7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.403 (Chi-square test), Q value = 1

Table S310. Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
SLC26A7 MUTATED	1	0	3	0	2	1	1
SLC26A7 WILD-TYPE	42	52	60	44	39	50	11

'SLC26A7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S311. Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
SLC26A7 MUTATED	1	2	1	0
SLC26A7 WILD-TYPE	54	50	34	66

'SLC26A7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 1

Table S312. Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
SLC26A7 MUTATED	0	3	1
SLC26A7 WILD-TYPE	17	70	117

'SLC26A7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S313. Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
SLC26A7 MUTATED	2	1	5
SLC26A7 WILD-TYPE	120	95	81

'SLC26A7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0795 (Fisher's exact test), Q value = 1

Table S314. Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
SLC26A7 MUTATED	3	4	1
SLC26A7 WILD-TYPE	118	61	117

'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 1

Table S315. Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
SLC26A7 MUTATED	3	3	2
SLC26A7 WILD-TYPE	60	133	103

'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S316. Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
SLC26A7 MUTATED	0	2	6
SLC26A7 WILD-TYPE	14	119	163

'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S317. Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
SLC26A7 MUTATED	2	2	3	0
SLC26A7 WILD-TYPE	33	60	104	64

'SLC26A7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.571 (Chi-square test), Q value = 1

Table S318. Gene #32: 'SLC26A7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
SLC26A7 MUTATED	0	0	1	3	2	1
SLC26A7 WILD-TYPE	4	7	45	41	100	64

'KCNA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S319. Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
KCNA3 MUTATED	4	4	0
KCNA3 WILD-TYPE	158	109	27

'KCNA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.842 (Chi-square test), Q value = 1

Table S320. Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
KCNA3 MUTATED	2	1	2	0	1	2	0
KCNA3 WILD-TYPE	41	51	61	44	40	49	12

'KCNA3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S321. Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
KCNA3 MUTATED	4	1	0	0
KCNA3 WILD-TYPE	51	51	35	66

Figure S64. Get High-res Image Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KCNA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S322. Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
KCNA3 MUTATED	0	3	2
KCNA3 WILD-TYPE	17	70	116

'KCNA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

Table S323. Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
KCNA3 MUTATED	4	1	3
KCNA3 WILD-TYPE	118	95	83

'KCNA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 1

Table S324. Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
KCNA3 MUTATED	4	3	1
KCNA3 WILD-TYPE	117	62	117

'KCNA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S325. Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
KCNA3 MUTATED	2	4	2
KCNA3 WILD-TYPE	61	132	103

'KCNA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S326. Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
KCNA3 MUTATED	0	2	6
KCNA3 WILD-TYPE	14	119	163

'KCNA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S327. Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
KCNA3 MUTATED	0	3	2	1
KCNA3 WILD-TYPE	35	59	105	63

'KCNA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.21 (Chi-square test), Q value = 1

Table S328. Gene #33: 'KCNA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
KCNA3 MUTATED	0	0	1	1	0	4
KCNA3 WILD-TYPE	4	7	45	43	102	61

'HIST1H1B MUTATION STATUS' versus 'CN_CNMF'

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

Table S329. Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
HIST1H1B MUTATED	3	4	0
HIST1H1B WILD-TYPE	159	109	27

'HIST1H1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.284 (Chi-square test), Q value = 1

Table S330. Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
HIST1H1B MUTATED	1	0	2	0	3	1	0
HIST1H1B WILD-TYPE	42	52	61	44	38	50	12

'HIST1H1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S331. Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
HIST1H1B MUTATED	1	2	1	2
HIST1H1B WILD-TYPE	54	50	34	64

'HIST1H1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S332. Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
HIST1H1B MUTATED	0	1	5
HIST1H1B WILD-TYPE	17	72	113

'HIST1H1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S333. Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
HIST1H1B MUTATED	2	2	3
HIST1H1B WILD-TYPE	120	94	83

'HIST1H1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S334. Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
HIST1H1B MUTATED	2	3	2
HIST1H1B WILD-TYPE	119	62	116

'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S335. Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
HIST1H1B MUTATED	2	4	1
HIST1H1B WILD-TYPE	61	132	104

'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 1

Table S336. Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
HIST1H1B MUTATED	2	1	4
HIST1H1B WILD-TYPE	12	120	165

Figure S65. Get High-res Image Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S337. Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
HIST1H1B MUTATED	1	1	2	3
HIST1H1B WILD-TYPE	34	61	105	61

'HIST1H1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0789 (Chi-square test), Q value = 1

Table S338. Gene #34: 'HIST1H1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
HIST1H1B MUTATED	1	0	1	2	1	2
HIST1H1B WILD-TYPE	3	7	45	42	101	63

'STEAP4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S339. Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	162	113	27
STEAP4 MUTATED	8	1	1
STEAP4 WILD-TYPE	154	112	26

'STEAP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.595 (Chi-square test), Q value = 1

Table S340. Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	52	63	44	41	51	12
STEAP4 MUTATED	3	1	3	1	0	2	0
STEAP4 WILD-TYPE	40	51	60	43	41	49	12

'STEAP4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 1

Table S341. Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	52	35	66
STEAP4 MUTATED	1	4	0	1
STEAP4 WILD-TYPE	54	48	35	65

'STEAP4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 1

Table S342. Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	17	73	118
STEAP4 MUTATED	2	1	3
STEAP4 WILD-TYPE	15	72	115

'STEAP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0993 (Fisher's exact test), Q value = 1

Table S343. Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	96	86
STEAP4 MUTATED	6	4	0
STEAP4 WILD-TYPE	116	92	86

'STEAP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 1

Table S344. Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	65	118
STEAP4 MUTATED	6	0	4
STEAP4 WILD-TYPE	115	65	114

'STEAP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 1

Table S345. Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	136	105
STEAP4 MUTATED	0	6	4
STEAP4 WILD-TYPE	63	130	101

'STEAP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S346. Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	121	169
STEAP4 MUTATED	1	4	5
STEAP4 WILD-TYPE	13	117	164

'STEAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S347. Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	62	107	64
STEAP4 MUTATED	0	3	5	2
STEAP4 WILD-TYPE	35	59	102	62

'STEAP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.381 (Chi-square test), Q value = 1

Table S348. Gene #35: 'STEAP4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	4	7	46	44	102	65
STEAP4 MUTATED	0	0	1	0	4	5
STEAP4 WILD-TYPE	4	7	45	44	98	60

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = HNSC-TP.transferedmergedcluster.txt
Number of patients = 306
Number of significantly mutated genes = 35
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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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