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 36 genes and 10 molecular subtypes across 492 patients, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

BRAF mutation correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
NRAS mutation correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
HRAS mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
EIF1AX mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
LMTK2 mutation correlated to 'CN_CNMF'.
TG mutation correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
AKT1 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
ZC3H11A mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 36 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, 36 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	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
HRAS	16 (3%)	476	0.00032 (0.0048)	1e-05 (0.000157)	0.00509 (0.0611)	0.00767 (0.0891)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)
BRAF	290 (59%)	202	0.944 (1.00)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)
NRAS	40 (8%)	452	0.211 (0.987)	1e-05 (0.000157)	0.139 (0.807)	0.0104 (0.116)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)	1e-05 (0.000157)
TG	20 (4%)	472	0.0965 (0.685)	0.0154 (0.154)	0.0135 (0.139)	0.826 (1.00)	0.0415 (0.355)	0.0337 (0.303)	0.0304 (0.28)	0.00043 (0.00619)	0.00129 (0.0172)	0.00121 (0.0168)
EIF1AX	7 (1%)	485	0.136 (0.807)	0.273 (0.987)	0.457 (1.00)	0.3 (1.00)	0.0345 (0.303)	0.0113 (0.12)	0.177 (0.939)	0.136 (0.807)	0.0549 (0.451)	0.029 (0.28)
LMTK2	4 (1%)	488	0.0107 (0.116)	1 (1.00)			0.902 (1.00)	0.72 (1.00)	0.824 (1.00)	0.835 (1.00)	0.506 (1.00)	0.62 (1.00)
AKT1	5 (1%)	487	0.0297 (0.28)	0.161 (0.892)			0.122 (0.771)	0.00241 (0.031)	0.223 (0.987)	0.452 (1.00)	0.538 (1.00)	0.455 (1.00)
ZC3H11A	3 (1%)	489	0.102 (0.695)	0.341 (1.00)			0.101 (0.695)	0.00371 (0.0461)	0.68 (1.00)	0.627 (1.00)	0.504 (1.00)	0.622 (1.00)
NUDT11	10 (2%)	482	0.713 (1.00)	0.826 (1.00)	0.934 (1.00)	0.703 (1.00)	0.438 (1.00)	0.977 (1.00)	0.863 (1.00)	1 (1.00)	1 (1.00)	0.913 (1.00)
RPTN	10 (2%)	482	0.925 (1.00)	0.599 (1.00)	0.486 (1.00)	1 (1.00)	0.549 (1.00)	0.679 (1.00)	0.152 (0.857)	1 (1.00)	0.681 (1.00)	0.849 (1.00)
EMG1	11 (2%)	481	0.308 (1.00)	0.181 (0.943)	0.0753 (0.59)	0.0551 (0.451)	0.282 (0.987)	0.212 (0.987)	0.107 (0.716)	1 (1.00)	1 (1.00)	0.924 (1.00)
FAM47C	14 (3%)	478	0.281 (0.987)	0.923 (1.00)	1 (1.00)	0.454 (1.00)	0.653 (1.00)	0.282 (0.987)	0.097 (0.685)	0.196 (0.982)	0.468 (1.00)	0.31 (1.00)
DLX6	7 (1%)	485	0.796 (1.00)	0.508 (1.00)			0.912 (1.00)	0.924 (1.00)	0.0926 (0.685)	1 (1.00)	0.28 (0.987)	0.0835 (0.64)
GPR44	4 (1%)	488	0.701 (1.00)	0.437 (1.00)			0.808 (1.00)	0.12 (0.771)	0.164 (0.896)	0.379 (1.00)	0.177 (0.939)	0.374 (1.00)
TMEM184A	5 (1%)	487	0.457 (1.00)	0.894 (1.00)			1 (1.00)	0.904 (1.00)	1 (1.00)	0.638 (1.00)	0.907 (1.00)	0.831 (1.00)
NUP93	4 (1%)	488	0.588 (1.00)	0.733 (1.00)			0.458 (1.00)	0.566 (1.00)	0.748 (1.00)	1 (1.00)	0.592 (1.00)	1 (1.00)
GAGE2A	4 (1%)	488	0.814 (1.00)	0.651 (1.00)			1 (1.00)	0.483 (1.00)	0.747 (1.00)	0.305 (1.00)	0.215 (0.987)	0.479 (1.00)
ABL1	5 (1%)	487	0.225 (0.987)	0.687 (1.00)	0.225 (0.987)	0.335 (1.00)	0.442 (1.00)	0.374 (1.00)	0.339 (1.00)	0.744 (1.00)	0.794 (1.00)	0.57 (1.00)
SRPX	4 (1%)	488	0.294 (1.00)	0.853 (1.00)			0.605 (1.00)	0.808 (1.00)	0.905 (1.00)	0.571 (1.00)	0.623 (1.00)	0.355 (1.00)
PPM1D	6 (1%)	486	0.385 (1.00)	0.394 (1.00)	0.272 (0.987)	0.64 (1.00)	0.482 (1.00)	0.251 (0.987)	0.582 (1.00)	0.251 (0.987)	0.489 (1.00)	1 (1.00)
PTCD1	3 (1%)	489	1 (1.00)	1 (1.00)	0.558 (1.00)	0.708 (1.00)	0.746 (1.00)	0.472 (1.00)	0.228 (0.987)	0.362 (1.00)	0.627 (1.00)	0.357 (1.00)
TSC22D1	4 (1%)	488	0.39 (1.00)	0.0961 (0.685)			1 (1.00)	0.664 (1.00)	0.905 (1.00)	0.564 (1.00)	1 (1.00)	1 (1.00)
ZNF878	3 (1%)	489		0.458 (1.00)			0.214 (0.987)	0.28 (0.987)	0.143 (0.819)	1 (1.00)	1 (1.00)	1 (1.00)
RBM10	4 (1%)	488	0.7 (1.00)	0.535 (1.00)			0.81 (1.00)	1 (1.00)	0.745 (1.00)	1 (1.00)	0.738 (1.00)	1 (1.00)
EP400	3 (1%)	489	1 (1.00)	0.071 (0.568)			0.137 (0.807)	0.234 (0.987)	0.676 (1.00)	0.624 (1.00)	0.261 (0.987)	0.626 (1.00)
ABCD1	4 (1%)	488	0.7 (1.00)	0.921 (1.00)			1 (1.00)	0.876 (1.00)	0.269 (0.987)	1 (1.00)	0.219 (0.987)	0.244 (0.987)
MYH10	4 (1%)	488	0.699 (1.00)	0.502 (1.00)			1 (1.00)	1 (1.00)	1 (1.00)	0.138 (0.807)	0.266 (0.987)	0.828 (1.00)
NLRP6	4 (1%)	488	0.7 (1.00)	0.793 (1.00)			0.739 (1.00)	0.481 (1.00)	0.367 (1.00)	0.303 (1.00)	0.541 (1.00)	0.31 (1.00)
IGSF3	4 (1%)	488	0.388 (1.00)	0.921 (1.00)			1 (1.00)	0.665 (1.00)	0.27 (0.987)	0.245 (0.987)	0.239 (0.987)	0.243 (0.987)
PRMT8	3 (1%)	489	0.255 (0.987)	0.885 (1.00)			0.425 (1.00)	0.876 (1.00)	0.859 (1.00)	0.362 (1.00)	0.626 (1.00)	0.357 (1.00)
ARMCX3	3 (1%)	489	0.622 (1.00)	0.885 (1.00)			0.648 (1.00)	0.875 (1.00)	0.111 (0.728)	0.479 (1.00)
RYR1	7 (1%)	485	0.213 (0.987)	0.419 (1.00)			0.953 (1.00)	1 (1.00)	0.834 (1.00)	0.898 (1.00)	0.782 (1.00)	0.801 (1.00)
TNRC18	4 (1%)	488	0.59 (1.00)	0.694 (1.00)			0.603 (1.00)	0.346 (1.00)	0.622 (1.00)	0.834 (1.00)	0.897 (1.00)	0.361 (1.00)
TMEM90B	3 (1%)	489	0.622 (1.00)	0.885 (1.00)			1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.898 (1.00)	1 (1.00)
RANBP9	3 (1%)	489	0.623 (1.00)	0.684 (1.00)			0.494 (1.00)	0.259 (0.987)	0.677 (1.00)	0.626 (1.00)	0.259 (0.987)	0.623 (1.00)
DGCR8	3 (1%)	489		0.776 (1.00)	0.323 (1.00)	0.415 (1.00)	0.645 (1.00)	0.719 (1.00)	0.597 (1.00)	0.187 (0.95)	0.898 (1.00)	0.187 (0.95)

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.944 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
BRAF MUTATED	79	80	129
BRAF WILD-TYPE	52	57	91

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
BRAF MUTATED	41	14	49	40	146
BRAF WILD-TYPE	5	130	35	0	32

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

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
BRAF MUTATED	20	43	9	46
BRAF WILD-TYPE	43	18	31	5

Figure S2. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
BRAF MUTATED	4	22	29	5	38	12	8
BRAF WILD-TYPE	42	5	2	21	11	15	1

Figure S3. Get High-res Image Gene #1: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
BRAF MUTATED	143	21	34	92
BRAF WILD-TYPE	11	143	24	22

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

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
BRAF MUTATED	100	4	47	73	66
BRAF WILD-TYPE	3	127	38	22	10

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

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
BRAF MUTATED	123	13	100	53
BRAF WILD-TYPE	40	130	19	13

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

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
BRAF MUTATED	136	3	150
BRAF WILD-TYPE	40	122	40

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

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
BRAF MUTATED	95	10	88	84
BRAF WILD-TYPE	34	112	18	21

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

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
BRAF MUTATED	120	3	154
BRAF WILD-TYPE	40	115	30

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

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 0.99

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
NRAS MUTATED	15	9	14
NRAS WILD-TYPE	116	128	206

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
NRAS MUTATED	0	40	0	0	0
NRAS WILD-TYPE	46	104	84	40	178

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

'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.81

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
NRAS MUTATED	5	5	3	0
NRAS WILD-TYPE	58	56	37	51

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.12

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
NRAS MUTATED	4	1	0	3	0	5	0
NRAS WILD-TYPE	42	26	31	23	49	22	9

Figure S11. Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
NRAS MUTATED	0	40	0	0
NRAS WILD-TYPE	154	124	58	114

Figure S12. Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
NRAS MUTATED	0	40	0	0	0
NRAS WILD-TYPE	103	91	85	95	76

Figure S13. Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
NRAS MUTATED	1	38	0	1
NRAS WILD-TYPE	162	105	119	65

Figure S14. Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
NRAS MUTATED	1	39	0
NRAS WILD-TYPE	175	86	190

Figure S15. Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
NRAS MUTATED	2	36	0	0
NRAS WILD-TYPE	127	86	106	105

Figure S16. Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
NRAS MUTATED	1	37	0
NRAS WILD-TYPE	159	81	184

Figure S17. Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0048

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
HRAS MUTATED	11	0	5
HRAS WILD-TYPE	120	137	215

Figure S18. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
HRAS MUTATED	0	16	0	0	0
HRAS WILD-TYPE	46	128	84	40	178

Figure S19. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00509 (Fisher's exact test), Q value = 0.061

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
HRAS MUTATED	8	1	1	0
HRAS WILD-TYPE	55	60	39	51

Figure S20. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00767 (Fisher's exact test), Q value = 0.089

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
HRAS MUTATED	7	0	0	2	0	1	0
HRAS WILD-TYPE	39	27	31	24	49	26	9

Figure S21. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
HRAS MUTATED	0	16	0	0
HRAS WILD-TYPE	154	148	58	114

Figure S22. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
HRAS MUTATED	0	16	0	0	0
HRAS WILD-TYPE	103	115	85	95	76

Figure S23. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
HRAS MUTATED	0	16	0	0
HRAS WILD-TYPE	163	127	119	66

Figure S24. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
HRAS MUTATED	0	16	0
HRAS WILD-TYPE	176	109	190

Figure S25. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
HRAS MUTATED	0	14	0	0
HRAS WILD-TYPE	129	108	106	105

Figure S26. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00016

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
HRAS MUTATED	0	14	0
HRAS WILD-TYPE	160	104	184

Figure S27. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

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

Table S31. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
NUDT11 MUTATED	2	4	4
NUDT11 WILD-TYPE	129	133	216

'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S32. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
NUDT11 MUTATED	1	2	1	1	5
NUDT11 WILD-TYPE	45	142	83	39	173

'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.934 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
NUDT11 MUTATED	1	2	1	1
NUDT11 WILD-TYPE	62	59	39	50

'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S34. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
NUDT11 MUTATED	1	0	1	0	1	2	0
NUDT11 WILD-TYPE	45	27	30	26	48	25	9

'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S35. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
NUDT11 MUTATED	4	2	0	4
NUDT11 WILD-TYPE	150	162	58	110

'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S36. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
NUDT11 MUTATED	2	2	2	2	2
NUDT11 WILD-TYPE	101	129	83	93	74

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S37. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
NUDT11 MUTATED	4	2	2	2
NUDT11 WILD-TYPE	159	141	117	64

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S38. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
NUDT11 MUTATED	4	2	4
NUDT11 WILD-TYPE	172	123	186

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S39. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
NUDT11 MUTATED	3	2	2	2
NUDT11 WILD-TYPE	126	120	104	103

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S40. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
NUDT11 MUTATED	4	2	3
NUDT11 WILD-TYPE	156	116	181

'RPTN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.925 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
RPTN MUTATED	3	3	4
RPTN WILD-TYPE	128	134	216

'RPTN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.599 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
RPTN MUTATED	1	3	1	2	3
RPTN WILD-TYPE	45	141	83	38	175

'RPTN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.486 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
RPTN MUTATED	2	0	0	1
RPTN WILD-TYPE	61	61	40	50

'RPTN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
RPTN MUTATED	1	0	1	0	1	0	0
RPTN WILD-TYPE	45	27	30	26	48	27	9

'RPTN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
RPTN MUTATED	3	2	1	4
RPTN WILD-TYPE	151	162	57	110

'RPTN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
RPTN MUTATED	2	2	1	4	1
RPTN WILD-TYPE	101	129	84	91	75

'RPTN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 0.86

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
RPTN MUTATED	2	1	4	3
RPTN WILD-TYPE	161	142	115	63

'RPTN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
RPTN MUTATED	4	2	4
RPTN WILD-TYPE	172	123	186

'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
RPTN MUTATED	2	2	2	4
RPTN WILD-TYPE	127	120	104	101

'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
RPTN MUTATED	3	2	5
RPTN WILD-TYPE	157	116	179

'EMG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.308 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
EMG1 MUTATED	3	1	7
EMG1 WILD-TYPE	128	136	213

'EMG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.94

Table S52. Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
EMG1 MUTATED	3	3	0	1	4
EMG1 WILD-TYPE	43	141	84	39	174

'EMG1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0753 (Fisher's exact test), Q value = 0.59

Table S53. Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
EMG1 MUTATED	0	3	0	3
EMG1 WILD-TYPE	63	58	40	48

'EMG1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0551 (Fisher's exact test), Q value = 0.45

Table S54. Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
EMG1 MUTATED	0	0	3	0	2	0	1
EMG1 WILD-TYPE	46	27	28	26	47	27	8

'EMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.99

Table S55. Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
EMG1 MUTATED	6	3	0	1
EMG1 WILD-TYPE	148	161	58	113

'EMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.99

Table S56. Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
EMG1 MUTATED	5	3	0	1	1
EMG1 WILD-TYPE	98	128	85	94	75

'EMG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.72

Table S57. Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
EMG1 MUTATED	2	4	1	4
EMG1 WILD-TYPE	161	139	118	62

'EMG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S58. Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
EMG1 MUTATED	4	3	4
EMG1 WILD-TYPE	172	122	186

'EMG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S59. Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
EMG1 MUTATED	3	3	2	2
EMG1 WILD-TYPE	126	119	104	103

'EMG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S60. Gene #6: 'EMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
EMG1 MUTATED	3	3	4
EMG1 WILD-TYPE	157	115	180

'FAM47C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 0.99

Table S61. Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
FAM47C MUTATED	6	4	4
FAM47C WILD-TYPE	125	133	216

'FAM47C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S62. Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
FAM47C MUTATED	1	5	1	1	6
FAM47C WILD-TYPE	45	139	83	39	172

'FAM47C MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S63. Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
FAM47C MUTATED	2	1	1	1
FAM47C WILD-TYPE	61	60	39	50

'FAM47C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 1

Table S64. Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
FAM47C MUTATED	1	1	0	1	1	0	1
FAM47C WILD-TYPE	45	26	31	25	48	27	8

'FAM47C MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S65. Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
FAM47C MUTATED	5	5	0	4
FAM47C WILD-TYPE	149	159	58	110

'FAM47C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 0.99

Table S66. Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
FAM47C MUTATED	4	5	0	4	1
FAM47C WILD-TYPE	99	126	85	91	75

'FAM47C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.097 (Fisher's exact test), Q value = 0.68

Table S67. Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
FAM47C MUTATED	1	5	6	2
FAM47C WILD-TYPE	162	138	113	64

'FAM47C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 0.98

Table S68. Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
FAM47C MUTATED	2	5	7
FAM47C WILD-TYPE	174	120	183

'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S69. Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
FAM47C MUTATED	2	4	2	5
FAM47C WILD-TYPE	127	118	104	100

'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 1

Table S70. Gene #7: 'FAM47C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
FAM47C MUTATED	2	4	7
FAM47C WILD-TYPE	158	114	177

'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.81

Table S71. Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
EIF1AX MUTATED	0	4	3
EIF1AX WILD-TYPE	131	133	217

'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.99

Table S72. Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
EIF1AX MUTATED	0	5	1	0	1
EIF1AX WILD-TYPE	46	139	83	40	177

'EIF1AX MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S73. Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
EIF1AX MUTATED	2	1	2	0
EIF1AX WILD-TYPE	61	60	38	51

'EIF1AX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.3 (Fisher's exact test), Q value = 1

Table S74. Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
EIF1AX MUTATED	3	0	0	1	0	1	0
EIF1AX WILD-TYPE	43	27	31	25	49	26	9

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.3

Table S75. Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
EIF1AX MUTATED	0	6	0	1
EIF1AX WILD-TYPE	154	158	58	113

Figure S28. Get High-res Image Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.12

Table S76. Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
EIF1AX MUTATED	0	6	1	0	0
EIF1AX WILD-TYPE	103	125	84	95	76

Figure S29. Get High-res Image Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.94

Table S77. Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
EIF1AX MUTATED	1	5	1	0
EIF1AX WILD-TYPE	162	138	118	66

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 0.81

Table S78. Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
EIF1AX MUTATED	2	4	1
EIF1AX WILD-TYPE	174	121	189

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0549 (Fisher's exact test), Q value = 0.45

Table S79. Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
EIF1AX MUTATED	1	5	0	1
EIF1AX WILD-TYPE	128	117	106	104

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.28

Table S80. Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
EIF1AX MUTATED	1	5	1
EIF1AX WILD-TYPE	159	113	183

Figure S30. Get High-res Image Gene #8: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'DLX6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S81. Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
DLX6 MUTATED	2	1	4
DLX6 WILD-TYPE	129	136	216

'DLX6 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S82. Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
DLX6 MUTATED	0	2	0	0	5
DLX6 WILD-TYPE	46	142	84	40	173

'DLX6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S83. Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
DLX6 MUTATED	2	3	0	2
DLX6 WILD-TYPE	152	161	58	112

'DLX6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S84. Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
DLX6 MUTATED	1	2	1	1	2
DLX6 WILD-TYPE	102	129	84	94	74

'DLX6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0926 (Fisher's exact test), Q value = 0.68

Table S85. Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
DLX6 MUTATED	0	2	3	2
DLX6 WILD-TYPE	163	141	116	64

'DLX6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S86. Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
DLX6 MUTATED	2	2	3
DLX6 WILD-TYPE	174	123	187

'DLX6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.99

Table S87. Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
DLX6 MUTATED	0	2	2	3
DLX6 WILD-TYPE	129	120	104	102

'DLX6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0835 (Fisher's exact test), Q value = 0.64

Table S88. Gene #9: 'DLX6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
DLX6 MUTATED	0	2	5
DLX6 WILD-TYPE	160	116	179

'GPR44 MUTATION STATUS' versus 'CN_CNMF'

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

Table S89. Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
GPR44 MUTATED	2	1	1
GPR44 WILD-TYPE	129	136	219

'GPR44 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S90. Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
GPR44 MUTATED	0	2	0	1	1
GPR44 WILD-TYPE	46	142	84	39	177

'GPR44 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S91. Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
GPR44 MUTATED	1	1	1	1
GPR44 WILD-TYPE	153	163	57	113

'GPR44 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 0.77

Table S92. Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
GPR44 MUTATED	0	0	1	1	2
GPR44 WILD-TYPE	103	131	84	94	74

'GPR44 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.9

Table S93. Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
GPR44 MUTATED	3	0	0	1
GPR44 WILD-TYPE	160	143	119	65

'GPR44 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S94. Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
GPR44 MUTATED	3	0	1
GPR44 WILD-TYPE	173	125	189

'GPR44 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.94

Table S95. Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
GPR44 MUTATED	3	0	1	0
GPR44 WILD-TYPE	126	122	105	105

'GPR44 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 1

Table S96. Gene #10: 'GPR44 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
GPR44 MUTATED	3	0	1
GPR44 WILD-TYPE	157	118	183

'TMEM184A MUTATION STATUS' versus 'CN_CNMF'

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

Table S97. Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
TMEM184A MUTATED	2	0	3
TMEM184A WILD-TYPE	129	137	217

'TMEM184A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S98. Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
TMEM184A MUTATED	0	2	0	0	3
TMEM184A WILD-TYPE	46	142	84	40	175

'TMEM184A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S99. Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
TMEM184A MUTATED	2	2	0	1
TMEM184A WILD-TYPE	152	162	58	113

'TMEM184A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S100. Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
TMEM184A MUTATED	1	2	1	0	1
TMEM184A WILD-TYPE	102	129	84	95	75

'TMEM184A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S101. Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
TMEM184A MUTATED	2	2	1	0
TMEM184A WILD-TYPE	161	141	118	66

'TMEM184A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S102. Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
TMEM184A MUTATED	2	2	1
TMEM184A WILD-TYPE	174	123	189

'TMEM184A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 1

Table S103. Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
TMEM184A MUTATED	2	1	1	0
TMEM184A WILD-TYPE	127	121	105	105

'TMEM184A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S104. Gene #11: 'TMEM184A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
TMEM184A MUTATED	2	1	1
TMEM184A WILD-TYPE	158	117	183

'NUP93 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S105. Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
NUP93 MUTATED	0	1	3
NUP93 WILD-TYPE	131	136	217

'NUP93 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S106. Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
NUP93 MUTATED	1	1	0	0	2
NUP93 WILD-TYPE	45	143	84	40	176

'NUP93 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S107. Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
NUP93 MUTATED	3	1	0	0
NUP93 WILD-TYPE	151	163	58	114

'NUP93 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S108. Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
NUP93 MUTATED	2	1	0	0	1
NUP93 WILD-TYPE	101	130	85	95	75

'NUP93 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S109. Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
NUP93 MUTATED	1	1	2	0
NUP93 WILD-TYPE	162	142	117	66

'NUP93 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S110. Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
NUP93 MUTATED	1	1	2
NUP93 WILD-TYPE	175	124	188

'NUP93 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 1

Table S111. Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
NUP93 MUTATED	1	1	0	2
NUP93 WILD-TYPE	128	121	106	103

'NUP93 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S112. Gene #12: 'NUP93 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
NUP93 MUTATED	1	1	2
NUP93 WILD-TYPE	159	117	182

'GAGE2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.814 (Fisher's exact test), Q value = 1

Table S113. Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
GAGE2A MUTATED	1	2	1
GAGE2A WILD-TYPE	130	135	219

'GAGE2A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S114. Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
GAGE2A MUTATED	0	1	0	1	2
GAGE2A WILD-TYPE	46	143	84	39	176

'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S115. Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
GAGE2A MUTATED	1	2	0	1
GAGE2A WILD-TYPE	153	162	58	113

'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S116. Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
GAGE2A MUTATED	0	1	0	2	1
GAGE2A WILD-TYPE	103	130	85	93	75

'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.747 (Fisher's exact test), Q value = 1

Table S117. Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
GAGE2A MUTATED	1	1	2	0
GAGE2A WILD-TYPE	162	142	117	66

'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S118. Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
GAGE2A MUTATED	0	1	3
GAGE2A WILD-TYPE	176	124	187

'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.99

Table S119. Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
GAGE2A MUTATED	0	1	2	0
GAGE2A WILD-TYPE	129	121	104	105

'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S120. Gene #13: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
GAGE2A MUTATED	0	1	2
GAGE2A WILD-TYPE	160	117	182

'ABL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 0.99

Table S121. Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
ABL1 MUTATED	3	1	1
ABL1 WILD-TYPE	128	136	219

'ABL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S122. Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
ABL1 MUTATED	0	3	1	0	1
ABL1 WILD-TYPE	46	141	83	40	177

'ABL1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 0.99

Table S123. Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
ABL1 MUTATED	0	2	1	0
ABL1 WILD-TYPE	63	59	39	51

'ABL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S124. Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
ABL1 MUTATED	0	0	1	1	0	1	0
ABL1 WILD-TYPE	46	27	30	25	49	26	9

'ABL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S125. Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
ABL1 MUTATED	1	3	1	0
ABL1 WILD-TYPE	153	161	57	114

'ABL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 1

Table S126. Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
ABL1 MUTATED	0	3	1	0	1
ABL1 WILD-TYPE	103	128	84	95	75

'ABL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S127. Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
ABL1 MUTATED	1	3	0	1
ABL1 WILD-TYPE	162	140	119	65

'ABL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S128. Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
ABL1 MUTATED	1	2	2
ABL1 WILD-TYPE	175	123	188

'ABL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S129. Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
ABL1 MUTATED	1	2	1	0
ABL1 WILD-TYPE	128	120	105	105

'ABL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S130. Gene #14: 'ABL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
ABL1 MUTATED	1	2	1
ABL1 WILD-TYPE	159	116	183

'LMTK2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.12

Table S131. Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
LMTK2 MUTATED	0	4	0
LMTK2 WILD-TYPE	131	133	220

Figure S31. Get High-res Image Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'LMTK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S132. Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
LMTK2 MUTATED	0	1	1	0	2
LMTK2 WILD-TYPE	46	143	83	40	176

'LMTK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S133. Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
LMTK2 MUTATED	2	1	0	1
LMTK2 WILD-TYPE	152	163	58	113

'LMTK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.72 (Fisher's exact test), Q value = 1

Table S134. Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
LMTK2 MUTATED	2	1	0	1	0
LMTK2 WILD-TYPE	101	130	85	94	76

'LMTK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S135. Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
LMTK2 MUTATED	1	1	1	1
LMTK2 WILD-TYPE	162	142	118	65

'LMTK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S136. Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
LMTK2 MUTATED	2	1	1
LMTK2 WILD-TYPE	174	124	189

'LMTK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S137. Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
LMTK2 MUTATED	2	0	1	0
LMTK2 WILD-TYPE	127	122	105	105

'LMTK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S138. Gene #15: 'LMTK2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
LMTK2 MUTATED	2	0	1
LMTK2 WILD-TYPE	158	118	183

'SRPX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 1

Table S139. Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
SRPX MUTATED	2	0	2
SRPX WILD-TYPE	129	137	218

'SRPX MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S140. Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
SRPX MUTATED	0	2	1	0	1
SRPX WILD-TYPE	46	142	83	40	177

'SRPX MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S141. Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
SRPX MUTATED	1	2	1	0
SRPX WILD-TYPE	153	162	57	114

'SRPX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S142. Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
SRPX MUTATED	1	2	1	0	0
SRPX WILD-TYPE	102	129	84	95	76

'SRPX MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S143. Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
SRPX MUTATED	1	2	1	0
SRPX WILD-TYPE	162	141	118	66

'SRPX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S144. Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
SRPX MUTATED	1	2	1
SRPX WILD-TYPE	175	123	189

'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 1

Table S145. Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
SRPX MUTATED	2	1	0	0
SRPX WILD-TYPE	127	121	106	105

'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.355 (Fisher's exact test), Q value = 1

Table S146. Gene #16: 'SRPX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
SRPX MUTATED	2	1	0
SRPX WILD-TYPE	158	117	184

'PPM1D MUTATION STATUS' versus 'CN_CNMF'

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

Table S147. Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
PPM1D MUTATED	2	0	4
PPM1D WILD-TYPE	129	137	216

'PPM1D MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S148. Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
PPM1D MUTATED	0	1	0	1	4
PPM1D WILD-TYPE	46	143	84	39	174

'PPM1D MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.99

Table S149. Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
PPM1D MUTATED	0	1	0	2
PPM1D WILD-TYPE	63	60	40	49

'PPM1D MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S150. Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
PPM1D MUTATED	0	0	1	0	2	0	0
PPM1D WILD-TYPE	46	27	30	26	47	27	9

'PPM1D MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 1

Table S151. Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
PPM1D MUTATED	2	1	0	3
PPM1D WILD-TYPE	152	163	58	111

'PPM1D MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.99

Table S152. Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
PPM1D MUTATED	1	0	1	3	1
PPM1D WILD-TYPE	102	131	84	92	75

'PPM1D MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S153. Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
PPM1D MUTATED	2	1	3	0
PPM1D WILD-TYPE	161	142	116	66

'PPM1D MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.99

Table S154. Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
PPM1D MUTATED	2	0	4
PPM1D WILD-TYPE	174	125	186

'PPM1D MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S155. Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
PPM1D MUTATED	2	0	2	2
PPM1D WILD-TYPE	127	122	104	103

'PPM1D MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S156. Gene #17: 'PPM1D MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
PPM1D MUTATED	2	1	3
PPM1D WILD-TYPE	158	117	181

'TG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0965 (Fisher's exact test), Q value = 0.68

Table S157. Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
TG MUTATED	4	10	6
TG WILD-TYPE	127	127	214

'TG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.15

Table S158. Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
TG MUTATED	1	12	0	0	7
TG WILD-TYPE	45	132	84	40	171

Figure S32. Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.14

Table S159. Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
TG MUTATED	1	4	5	0
TG WILD-TYPE	62	57	35	51

Figure S33. Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S160. Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
TG MUTATED	2	0	2	2	2	2	0
TG WILD-TYPE	44	27	29	24	47	25	9

'TG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.36

Table S161. Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
TG MUTATED	4	13	1	2
TG WILD-TYPE	150	151	57	112

Figure S34. Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.3

Table S162. Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
TG MUTATED	3	12	1	2	2
TG WILD-TYPE	100	119	84	93	74

Figure S35. Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.28

Table S163. Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
TG MUTATED	2	11	4	3
TG WILD-TYPE	161	132	115	63

Figure S36. Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0062

Table S164. Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
TG MUTATED	1	12	7
TG WILD-TYPE	175	113	183

Figure S37. Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.017

Table S165. Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
TG MUTATED	0	11	4	3
TG WILD-TYPE	129	111	102	102

Figure S38. Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.017

Table S166. Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
TG MUTATED	1	11	6
TG WILD-TYPE	159	107	178

Figure S39. Get High-res Image Gene #18: 'TG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTCD1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S167. Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
PTCD1 MUTATED	1	1	1
PTCD1 WILD-TYPE	130	136	219

'PTCD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S168. Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
PTCD1 MUTATED	0	1	0	0	2
PTCD1 WILD-TYPE	46	143	84	40	176

'PTCD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 1

Table S169. Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
PTCD1 MUTATED	1	2	0	0
PTCD1 WILD-TYPE	62	59	40	51

'PTCD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S170. Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
PTCD1 MUTATED	1	0	1	0	0	1	0
PTCD1 WILD-TYPE	45	27	30	26	49	26	9

'PTCD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S171. Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
PTCD1 MUTATED	2	1	0	0
PTCD1 WILD-TYPE	152	163	58	114

'PTCD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.472 (Fisher's exact test), Q value = 1

Table S172. Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
PTCD1 MUTATED	2	1	0	0	0
PTCD1 WILD-TYPE	101	130	85	95	76

'PTCD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.228 (Fisher's exact test), Q value = 0.99

Table S173. Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
PTCD1 MUTATED	2	0	0	1
PTCD1 WILD-TYPE	161	143	119	65

'PTCD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S174. Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
PTCD1 MUTATED	2	1	0
PTCD1 WILD-TYPE	174	124	190

'PTCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S175. Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
PTCD1 MUTATED	2	1	0	0
PTCD1 WILD-TYPE	127	121	106	105

'PTCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S176. Gene #19: 'PTCD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
PTCD1 MUTATED	2	1	0
PTCD1 WILD-TYPE	158	117	184

'TSC22D1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 1

Table S177. Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
TSC22D1 MUTATED	0	2	2
TSC22D1 WILD-TYPE	131	135	218

'TSC22D1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0961 (Fisher's exact test), Q value = 0.68

Table S178. Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
TSC22D1 MUTATED	1	2	0	1	0
TSC22D1 WILD-TYPE	45	142	84	39	178

'TSC22D1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S179. Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
TSC22D1 MUTATED	1	2	0	1
TSC22D1 WILD-TYPE	153	162	58	113

'TSC22D1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S180. Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
TSC22D1 MUTATED	0	2	0	1	1
TSC22D1 WILD-TYPE	103	129	85	94	75

'TSC22D1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S181. Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
TSC22D1 MUTATED	1	2	1	0
TSC22D1 WILD-TYPE	162	141	118	66

'TSC22D1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S182. Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
TSC22D1 MUTATED	1	2	1
TSC22D1 WILD-TYPE	175	123	189

'TSC22D1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S183. Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
TSC22D1 MUTATED	1	1	1	0
TSC22D1 WILD-TYPE	128	121	105	105

'TSC22D1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S184. Gene #20: 'TSC22D1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
TSC22D1 MUTATED	1	1	1
TSC22D1 WILD-TYPE	159	117	183

'AKT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.28

Table S185. Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
AKT1 MUTATED	4	0	1
AKT1 WILD-TYPE	127	137	219

Figure S40. Get High-res Image Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'AKT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 0.89

Table S186. Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
AKT1 MUTATED	0	0	0	1	4
AKT1 WILD-TYPE	46	144	84	39	174

'AKT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.77

Table S187. Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
AKT1 MUTATED	4	0	0	1
AKT1 WILD-TYPE	150	164	58	113

'AKT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00241 (Fisher's exact test), Q value = 0.031

Table S188. Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
AKT1 MUTATED	1	0	0	0	4
AKT1 WILD-TYPE	102	131	85	95	72

Figure S41. Get High-res Image Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'AKT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 0.99

Table S189. Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
AKT1 MUTATED	2	0	3	0
AKT1 WILD-TYPE	161	143	116	66

'AKT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S190. Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
AKT1 MUTATED	2	0	3
AKT1 WILD-TYPE	174	125	187

'AKT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S191. Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
AKT1 MUTATED	2	0	1	2
AKT1 WILD-TYPE	127	122	105	103

'AKT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 1

Table S192. Gene #21: 'AKT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
AKT1 MUTATED	2	0	3
AKT1 WILD-TYPE	158	118	181

'ZNF878 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S193. Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
ZNF878 MUTATED	0	2	1	0	0
ZNF878 WILD-TYPE	46	142	83	40	178

'ZNF878 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.99

Table S194. Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
ZNF878 MUTATED	0	2	1	0
ZNF878 WILD-TYPE	154	162	57	114

'ZNF878 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 0.99

Table S195. Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
ZNF878 MUTATED	0	1	2	0	0
ZNF878 WILD-TYPE	103	130	83	95	76

'ZNF878 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 0.82

Table S196. Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
ZNF878 MUTATED	0	2	0	1
ZNF878 WILD-TYPE	163	141	119	65

'ZNF878 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S197. Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
ZNF878 MUTATED	1	1	1
ZNF878 WILD-TYPE	175	124	189

'ZNF878 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S198. Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
ZNF878 MUTATED	1	1	1	0
ZNF878 WILD-TYPE	128	121	105	105

'ZNF878 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S199. Gene #22: 'ZNF878 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
ZNF878 MUTATED	1	1	1
ZNF878 WILD-TYPE	159	117	183

'RBM10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S200. Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
RBM10 MUTATED	2	1	1
RBM10 WILD-TYPE	129	136	219

'RBM10 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S201. Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
RBM10 MUTATED	0	1	1	1	1
RBM10 WILD-TYPE	46	143	83	39	177

'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S202. Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
RBM10 MUTATED	1	1	1	1
RBM10 WILD-TYPE	153	163	57	113

'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S203. Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
RBM10 MUTATED	1	1	1	1	0
RBM10 WILD-TYPE	102	130	84	94	76

'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S204. Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
RBM10 MUTATED	1	1	2	0
RBM10 WILD-TYPE	162	142	117	66

'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S205. Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
RBM10 MUTATED	1	1	2
RBM10 WILD-TYPE	175	124	188

'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S206. Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
RBM10 MUTATED	1	2	0	1
RBM10 WILD-TYPE	128	120	106	104

'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S207. Gene #23: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
RBM10 MUTATED	1	1	2
RBM10 WILD-TYPE	159	117	182

'EP400 MUTATION STATUS' versus 'CN_CNMF'

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

Table S208. Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
EP400 MUTATED	1	1	1
EP400 WILD-TYPE	130	136	219

'EP400 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.071 (Fisher's exact test), Q value = 0.57

Table S209. Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
EP400 MUTATED	2	0	0	0	1
EP400 WILD-TYPE	44	144	84	40	177

'EP400 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.81

Table S210. Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
EP400 MUTATED	2	0	1	0
EP400 WILD-TYPE	152	164	57	114

'EP400 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 0.99

Table S211. Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
EP400 MUTATED	2	0	1	0	0
EP400 WILD-TYPE	101	131	84	95	76

'EP400 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 1

Table S212. Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
EP400 MUTATED	2	0	1	0
EP400 WILD-TYPE	161	143	118	66

'EP400 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S213. Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
EP400 MUTATED	2	0	1
EP400 WILD-TYPE	174	125	189

'EP400 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 0.99

Table S214. Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
EP400 MUTATED	1	0	0	2
EP400 WILD-TYPE	128	122	106	103

'EP400 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S215. Gene #24: 'EP400 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
EP400 MUTATED	2	0	1
EP400 WILD-TYPE	158	118	183

'ABCD1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S216. Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
ABCD1 MUTATED	2	1	1
ABCD1 WILD-TYPE	129	136	219

'ABCD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S217. Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
ABCD1 MUTATED	0	2	0	0	2
ABCD1 WILD-TYPE	46	142	84	40	176

'ABCD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S218. Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
ABCD1 MUTATED	1	2	0	1
ABCD1 WILD-TYPE	153	162	58	113

'ABCD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S219. Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
ABCD1 MUTATED	1	2	0	1	0
ABCD1 WILD-TYPE	102	129	85	94	76

'ABCD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.99

Table S220. Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
ABCD1 MUTATED	0	2	2	0
ABCD1 WILD-TYPE	163	141	117	66

'ABCD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S221. Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
ABCD1 MUTATED	1	1	2
ABCD1 WILD-TYPE	175	124	188

'ABCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.99

Table S222. Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
ABCD1 MUTATED	0	2	0	2
ABCD1 WILD-TYPE	129	120	106	103

'ABCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.244 (Fisher's exact test), Q value = 0.99

Table S223. Gene #25: 'ABCD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
ABCD1 MUTATED	0	2	2
ABCD1 WILD-TYPE	160	116	182

'MYH10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S224. Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
MYH10 MUTATED	2	1	1
MYH10 WILD-TYPE	129	136	219

'MYH10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.502 (Fisher's exact test), Q value = 1

Table S225. Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
MYH10 MUTATED	1	2	0	0	1
MYH10 WILD-TYPE	45	142	84	40	177

'MYH10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S226. Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
MYH10 MUTATED	1	2	0	1
MYH10 WILD-TYPE	153	162	58	113

'MYH10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S227. Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
MYH10 MUTATED	1	1	1	1	0
MYH10 WILD-TYPE	102	130	84	94	76

'MYH10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S228. Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
MYH10 MUTATED	2	1	1	0
MYH10 WILD-TYPE	161	142	118	66

'MYH10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.81

Table S229. Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
MYH10 MUTATED	3	1	0
MYH10 WILD-TYPE	173	124	190

'MYH10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.99

Table S230. Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
MYH10 MUTATED	3	1	0	0
MYH10 WILD-TYPE	126	121	106	105

'MYH10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S231. Gene #26: 'MYH10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
MYH10 MUTATED	2	1	1
MYH10 WILD-TYPE	158	117	183

'NLRP6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S232. Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
NLRP6 MUTATED	2	1	1
NLRP6 WILD-TYPE	129	136	219

'NLRP6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S233. Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
NLRP6 MUTATED	0	1	0	0	3
NLRP6 WILD-TYPE	46	143	84	40	175

'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.739 (Fisher's exact test), Q value = 1

Table S234. Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
NLRP6 MUTATED	1	1	0	2
NLRP6 WILD-TYPE	153	163	58	112

'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S235. Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
NLRP6 MUTATED	0	1	0	2	1
NLRP6 WILD-TYPE	103	130	85	93	75

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S236. Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
NLRP6 MUTATED	0	2	1	1
NLRP6 WILD-TYPE	163	141	118	65

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 1

Table S237. Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
NLRP6 MUTATED	0	1	3
NLRP6 WILD-TYPE	176	124	187

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S238. Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
NLRP6 MUTATED	0	2	1	1
NLRP6 WILD-TYPE	129	120	105	104

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 1

Table S239. Gene #27: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
NLRP6 MUTATED	0	1	3
NLRP6 WILD-TYPE	160	117	181

'IGSF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 1

Table S240. Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
IGSF3 MUTATED	0	2	2
IGSF3 WILD-TYPE	131	135	218

'IGSF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S241. Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
IGSF3 MUTATED	0	2	0	0	2
IGSF3 WILD-TYPE	46	142	84	40	176

'IGSF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S242. Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
IGSF3 MUTATED	1	2	0	1
IGSF3 WILD-TYPE	153	162	58	113

'IGSF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S243. Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
IGSF3 MUTATED	0	2	0	1	1
IGSF3 WILD-TYPE	103	129	85	94	75

'IGSF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.99

Table S244. Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
IGSF3 MUTATED	0	2	2	0
IGSF3 WILD-TYPE	163	141	117	66

'IGSF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.245 (Fisher's exact test), Q value = 0.99

Table S245. Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
IGSF3 MUTATED	0	2	2
IGSF3 WILD-TYPE	176	123	188

'IGSF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.99

Table S246. Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
IGSF3 MUTATED	0	2	2	0
IGSF3 WILD-TYPE	129	120	104	105

'IGSF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.243 (Fisher's exact test), Q value = 0.99

Table S247. Gene #28: 'IGSF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
IGSF3 MUTATED	0	2	2
IGSF3 WILD-TYPE	160	116	182

'PRMT8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.99

Table S248. Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
PRMT8 MUTATED	0	0	3
PRMT8 WILD-TYPE	131	137	217

'PRMT8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.885 (Fisher's exact test), Q value = 1

Table S249. Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
PRMT8 MUTATED	0	1	1	0	1
PRMT8 WILD-TYPE	46	143	83	40	177

'PRMT8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S250. Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
PRMT8 MUTATED	0	1	1	1
PRMT8 WILD-TYPE	154	163	57	113

'PRMT8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S251. Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
PRMT8 MUTATED	0	1	1	1	0
PRMT8 WILD-TYPE	103	130	84	94	76

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S252. Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
PRMT8 MUTATED	2	1	0	0
PRMT8 WILD-TYPE	161	142	119	66

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S253. Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
PRMT8 MUTATED	2	1	0
PRMT8 WILD-TYPE	174	124	190

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S254. Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
PRMT8 MUTATED	2	1	0	0
PRMT8 WILD-TYPE	127	121	106	105

'PRMT8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S255. Gene #29: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
PRMT8 MUTATED	2	1	0
PRMT8 WILD-TYPE	158	117	184

'ARMCX3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S256. Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
ARMCX3 MUTATED	1	0	2
ARMCX3 WILD-TYPE	130	137	218

'ARMCX3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.885 (Fisher's exact test), Q value = 1

Table S257. Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
ARMCX3 MUTATED	0	1	1	0	1
ARMCX3 WILD-TYPE	46	143	83	40	177

'ARMCX3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S258. Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
ARMCX3 MUTATED	0	2	0	1
ARMCX3 WILD-TYPE	154	162	58	113

'ARMCX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S259. Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
ARMCX3 MUTATED	0	1	1	1	0
ARMCX3 WILD-TYPE	103	130	84	94	76

'ARMCX3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.73

Table S260. Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
ARMCX3 MUTATED	0	3	0	0
ARMCX3 WILD-TYPE	163	140	119	66

'ARMCX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S261. Gene #30: 'ARMCX3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
ARMCX3 MUTATED	0	1	2
ARMCX3 WILD-TYPE	176	124	188

'RYR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.99

Table S262. Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
RYR1 MUTATED	3	0	4
RYR1 WILD-TYPE	128	137	216

'RYR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S263. Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
RYR1 MUTATED	1	2	2	1	1
RYR1 WILD-TYPE	45	142	82	39	177

'RYR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.953 (Fisher's exact test), Q value = 1

Table S264. Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
RYR1 MUTATED	2	3	1	1
RYR1 WILD-TYPE	152	161	57	113

'RYR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S265. Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
RYR1 MUTATED	2	2	1	1	1
RYR1 WILD-TYPE	101	129	84	94	75

'RYR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S266. Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
RYR1 MUTATED	3	1	2	1
RYR1 WILD-TYPE	160	142	117	65

'RYR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.898 (Fisher's exact test), Q value = 1

Table S267. Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
RYR1 MUTATED	3	1	3
RYR1 WILD-TYPE	173	124	187

'RYR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S268. Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
RYR1 MUTATED	3	1	2	1
RYR1 WILD-TYPE	126	121	104	104

'RYR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S269. Gene #31: 'RYR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
RYR1 MUTATED	3	2	2
RYR1 WILD-TYPE	157	116	182

'TNRC18 MUTATION STATUS' versus 'CN_CNMF'

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

Table S270. Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
TNRC18 MUTATED	0	1	3
TNRC18 WILD-TYPE	131	136	217

'TNRC18 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S271. Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
TNRC18 MUTATED	1	1	1	0	1
TNRC18 WILD-TYPE	45	143	83	40	177

'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S272. Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
TNRC18 MUTATED	1	2	1	0
TNRC18 WILD-TYPE	153	162	57	114

'TNRC18 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S273. Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
TNRC18 MUTATED	0	1	2	0	1
TNRC18 WILD-TYPE	103	130	83	95	75

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S274. Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
TNRC18 MUTATED	2	1	0	1
TNRC18 WILD-TYPE	161	142	119	65

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S275. Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
TNRC18 MUTATED	2	1	1
TNRC18 WILD-TYPE	174	124	189

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S276. Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
TNRC18 MUTATED	1	1	0	1
TNRC18 WILD-TYPE	128	121	106	104

'TNRC18 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.361 (Fisher's exact test), Q value = 1

Table S277. Gene #32: 'TNRC18 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
TNRC18 MUTATED	2	1	0
TNRC18 WILD-TYPE	158	117	184

'TMEM90B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S278. Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
TMEM90B MUTATED	1	0	2
TMEM90B WILD-TYPE	130	137	218

'TMEM90B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.885 (Fisher's exact test), Q value = 1

Table S279. Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
TMEM90B MUTATED	0	1	1	0	1
TMEM90B WILD-TYPE	46	143	83	40	177

'TMEM90B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S280. Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
TMEM90B MUTATED	1	1	0	1
TMEM90B WILD-TYPE	153	163	58	113

'TMEM90B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S281. Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
TMEM90B MUTATED	1	1	0	1	0
TMEM90B WILD-TYPE	102	130	85	94	76

'TMEM90B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S282. Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
TMEM90B MUTATED	1	1	1	0
TMEM90B WILD-TYPE	162	142	118	66

'TMEM90B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S283. Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
TMEM90B MUTATED	1	1	1
TMEM90B WILD-TYPE	175	124	189

'TMEM90B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.898 (Fisher's exact test), Q value = 1

Table S284. Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
TMEM90B MUTATED	1	1	0	1
TMEM90B WILD-TYPE	128	121	106	104

'TMEM90B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S285. Gene #33: 'TMEM90B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
TMEM90B MUTATED	1	1	1
TMEM90B WILD-TYPE	159	117	183

'ZC3H11A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.69

Table S286. Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
ZC3H11A MUTATED	2	1	0
ZC3H11A WILD-TYPE	129	136	220

'ZC3H11A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 1

Table S287. Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
ZC3H11A MUTATED	0	0	0	1	2
ZC3H11A WILD-TYPE	46	144	84	39	176

'ZC3H11A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.69

Table S288. Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
ZC3H11A MUTATED	3	0	0	0
ZC3H11A WILD-TYPE	151	164	58	114

'ZC3H11A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00371 (Fisher's exact test), Q value = 0.046

Table S289. Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
ZC3H11A MUTATED	0	0	0	0	3
ZC3H11A WILD-TYPE	103	131	85	95	73

Figure S42. Get High-res Image Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S290. Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
ZC3H11A MUTATED	2	0	1	0
ZC3H11A WILD-TYPE	161	143	118	66

'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S291. Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
ZC3H11A MUTATED	2	0	1
ZC3H11A WILD-TYPE	174	125	189

'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S292. Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
ZC3H11A MUTATED	2	0	1	0
ZC3H11A WILD-TYPE	127	122	105	105

'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S293. Gene #34: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
ZC3H11A MUTATED	2	0	1
ZC3H11A WILD-TYPE	158	118	183

'RANBP9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 1

Table S294. Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	131	137	220
RANBP9 MUTATED	1	0	2
RANBP9 WILD-TYPE	130	137	218

'RANBP9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.684 (Fisher's exact test), Q value = 1

Table S295. Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
RANBP9 MUTATED	0	0	1	0	2
RANBP9 WILD-TYPE	46	144	83	40	176

'RANBP9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S296. Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
RANBP9 MUTATED	2	0	0	1
RANBP9 WILD-TYPE	152	164	58	113

'RANBP9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.259 (Fisher's exact test), Q value = 0.99

Table S297. Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
RANBP9 MUTATED	1	0	0	2	0
RANBP9 WILD-TYPE	102	131	85	93	76

'RANBP9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S298. Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
RANBP9 MUTATED	2	0	1	0
RANBP9 WILD-TYPE	161	143	118	66

'RANBP9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S299. Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
RANBP9 MUTATED	2	0	1
RANBP9 WILD-TYPE	174	125	189

'RANBP9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.99

Table S300. Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
RANBP9 MUTATED	1	0	0	2
RANBP9 WILD-TYPE	128	122	106	103

'RANBP9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.623 (Fisher's exact test), Q value = 1

Table S301. Gene #35: 'RANBP9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
RANBP9 MUTATED	2	0	1
RANBP9 WILD-TYPE	158	118	183

'DGCR8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.776 (Fisher's exact test), Q value = 1

Table S302. Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	144	84	40	178
DGCR8 MUTATED	0	2	0	0	1
DGCR8 WILD-TYPE	46	142	84	40	177

'DGCR8 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S303. Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	63	61	40	51
DGCR8 MUTATED	2	0	1	0
DGCR8 WILD-TYPE	61	61	39	51

'DGCR8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S304. Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	49	27	9
DGCR8 MUTATED	2	1	0	0	0	0	0
DGCR8 WILD-TYPE	44	26	31	26	49	27	9

'DGCR8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S305. Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	154	164	58	114
DGCR8 MUTATED	0	2	0	1
DGCR8 WILD-TYPE	154	162	58	113

'DGCR8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S306. Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	131	85	95	76
DGCR8 MUTATED	1	2	0	0	0
DGCR8 WILD-TYPE	102	129	85	95	76

'DGCR8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S307. Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	163	143	119	66
DGCR8 MUTATED	1	1	0	1
DGCR8 WILD-TYPE	162	142	119	65

'DGCR8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 0.95

Table S308. Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	176	125	190
DGCR8 MUTATED	1	2	0
DGCR8 WILD-TYPE	175	123	190

'DGCR8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.898 (Fisher's exact test), Q value = 1

Table S309. Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	129	122	106	105
DGCR8 MUTATED	1	1	0	1
DGCR8 WILD-TYPE	128	121	106	104

'DGCR8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 0.95

Table S310. Gene #36: 'DGCR8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	160	118	184
DGCR8 MUTATED	1	2	0
DGCR8 WILD-TYPE	159	116	184

Methods & Data

Input

Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/22815543/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/22542946/THCA-TP.transferedmergedcluster.txt
Number of patients = 492
Number of significantly mutated genes = 36
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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