Correlation between gene mutation status and molecular subtypes

Stomach Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1Z89B6R

Overview

Introduction

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

Summary

Testing the association between mutation status of 27 genes and 10 molecular subtypes across 221 patients, 29 significant findings detected with P value < 0.05 and Q value < 0.25.

TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
PIK3CA mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
CBWD1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
ARID1A mutation correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
PGM5 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
APC mutation correlated to 'RPPA_CHIERARCHICAL'.
FBXW7 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.
HLA-B mutation correlated to 'METHLYATION_CNMF'.
CR1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
MLL4 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 27 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, 29 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
TP53	99 (45%)	122	1e-05 (0.00265)	0.0002 (0.0496)	0.21 (1.00)	0.558 (1.00)	0.00033 (0.0815)	0.00033 (0.0815)	0.0104 (1.00)	9e-05 (0.0228)	0.373 (1.00)	0.0001 (0.0252)
CBWD1	28 (13%)	193	3e-05 (0.00774)	1e-05 (0.00265)	6e-05 (0.0154)	0.0215 (1.00)	6e-05 (0.0154)	1e-05 (0.00265)	0.121 (1.00)	0.145 (1.00)	0.0135 (1.00)	0.00466 (1.00)
PIK3CA	48 (22%)	173	1e-05 (0.00265)	0.0004 (0.0972)	0.0154 (1.00)	0.0703 (1.00)	0.00088 (0.209)	1e-05 (0.00265)	0.0173 (1.00)	0.00771 (1.00)	0.00227 (0.522)	0.00351 (0.786)
ARID1A	41 (19%)	180	1e-05 (0.00265)	0.0366 (1.00)	0.0173 (1.00)	0.00079 (0.188)	0.00061 (0.146)	1e-05 (0.00265)	0.164 (1.00)	0.035 (1.00)	0.502 (1.00)	0.107 (1.00)
CR1	20 (9%)	201	0.136 (1.00)	0.00015 (0.0375)	0.0971 (1.00)	0.104 (1.00)	0.00047 (0.113)	7e-05 (0.0178)	0.3 (1.00)	0.0211 (1.00)	0.109 (1.00)	0.222 (1.00)
PGM5	22 (10%)	199	0.00124 (0.29)	0.00015 (0.0375)	0.183 (1.00)	0.0222 (1.00)	0.00044 (0.106)	0.00324 (0.735)	0.451 (1.00)	0.237 (1.00)	0.137 (1.00)	0.0714 (1.00)
MLL4	20 (9%)	201	0.0571 (1.00)	0.00012 (0.0301)	0.444 (1.00)	0.0441 (1.00)	0.0929 (1.00)	0.00036 (0.0882)	0.111 (1.00)	0.0774 (1.00)	0.0698 (1.00)	0.0137 (1.00)
APC	33 (15%)	188	0.643 (1.00)	0.0238 (1.00)	0.0743 (1.00)	0.00059 (0.142)	0.232 (1.00)	0.00326 (0.735)	0.00992 (1.00)	0.02 (1.00)	0.0967 (1.00)	0.087 (1.00)
FBXW7	19 (9%)	202	0.11 (1.00)	0.0106 (1.00)	0.00185 (0.429)	0.0135 (1.00)	0.0145 (1.00)	6e-05 (0.0154)	0.3 (1.00)	0.122 (1.00)	0.00744 (1.00)	0.0174 (1.00)
HLA-B	12 (5%)	209	0.104 (1.00)	0.00039 (0.0952)	0.00508 (1.00)	0.00159 (0.37)	0.0205 (1.00)	0.0403 (1.00)	0.0851 (1.00)	0.0282 (1.00)	0.0421 (1.00)	0.195 (1.00)
KRAS	25 (11%)	196	0.0114 (1.00)	0.696 (1.00)	0.564 (1.00)	0.0721 (1.00)	0.24 (1.00)	0.0517 (1.00)	0.185 (1.00)	0.761 (1.00)	0.0303 (1.00)	0.847 (1.00)
RHOA	13 (6%)	208	0.136 (1.00)	0.389 (1.00)	0.872 (1.00)	0.712 (1.00)	0.541 (1.00)	0.801 (1.00)	0.00991 (1.00)	0.274 (1.00)	0.0326 (1.00)	0.174 (1.00)
SMAD4	19 (9%)	202	0.477 (1.00)	1 (1.00)	0.0666 (1.00)	0.332 (1.00)	0.00206 (0.476)	0.263 (1.00)	0.421 (1.00)	0.546 (1.00)	0.345 (1.00)	0.591 (1.00)
IRF2	14 (6%)	207	0.374 (1.00)	0.231 (1.00)	0.0735 (1.00)	0.351 (1.00)	0.31 (1.00)	0.631 (1.00)	0.0602 (1.00)	0.156 (1.00)	0.0476 (1.00)	0.13 (1.00)
LARP4B	12 (5%)	209	0.14 (1.00)	0.0496 (1.00)	0.00311 (0.709)	0.0227 (1.00)	0.152 (1.00)	0.0843 (1.00)	0.229 (1.00)	0.0359 (1.00)	0.0737 (1.00)	0.132 (1.00)
CDH1	18 (8%)	203	0.0484 (1.00)	0.341 (1.00)	0.612 (1.00)	0.878 (1.00)	0.126 (1.00)	0.0512 (1.00)	0.00485 (1.00)	0.0543 (1.00)	0.0741 (1.00)	0.426 (1.00)
BCOR	16 (7%)	205	0.015 (1.00)	0.0504 (1.00)	0.17 (1.00)	0.0151 (1.00)	0.0191 (1.00)	0.00584 (1.00)	0.033 (1.00)	0.0391 (1.00)	0.354 (1.00)	0.136 (1.00)
C13ORF33	6 (3%)	215	0.155 (1.00)	0.00432 (0.963)	0.0155 (1.00)	0.277 (1.00)	0.122 (1.00)	0.00325 (0.735)	0.429 (1.00)	0.875 (1.00)	0.6 (1.00)	0.353 (1.00)
CIC	14 (6%)	207	0.0294 (1.00)	0.00623 (1.00)	0.0319 (1.00)	0.0133 (1.00)	0.664 (1.00)	0.00514 (1.00)	0.0228 (1.00)	0.0086 (1.00)	0.302 (1.00)	0.117 (1.00)
ACVR1B	10 (5%)	211	0.119 (1.00)	0.299 (1.00)	0.662 (1.00)	0.156 (1.00)	0.00534 (1.00)	0.358 (1.00)	0.391 (1.00)	0.406 (1.00)	1 (1.00)	0.229 (1.00)
ZBTB20	16 (7%)	205	0.0421 (1.00)	0.00108 (0.254)	0.148 (1.00)	0.167 (1.00)	0.0424 (1.00)	0.00441 (0.979)	0.19 (1.00)	0.00246 (0.563)	0.224 (1.00)	0.0343 (1.00)
MVK	8 (4%)	213	0.352 (1.00)	0.0382 (1.00)	0.0434 (1.00)	0.00106 (0.25)	0.553 (1.00)	0.173 (1.00)	0.0348 (1.00)	0.448 (1.00)	0.328 (1.00)	0.658 (1.00)
ERBB2	11 (5%)	210	0.905 (1.00)	0.435 (1.00)	0.261 (1.00)	0.671 (1.00)	0.758 (1.00)	0.648 (1.00)	0.304 (1.00)	0.438 (1.00)	0.738 (1.00)	0.3 (1.00)
C1R	3 (1%)	218	0.6 (1.00)		0.211 (1.00)	0.0406 (1.00)			0.623 (1.00)	0.616 (1.00)
CTNND1	13 (6%)	208	0.0368 (1.00)	0.0634 (1.00)	0.286 (1.00)	0.104 (1.00)	0.0271 (1.00)	0.528 (1.00)	0.507 (1.00)	0.156 (1.00)	0.589 (1.00)	0.273 (1.00)
MLXIPL	13 (6%)	208	0.298 (1.00)	0.345 (1.00)	0.0303 (1.00)	0.0136 (1.00)	0.0758 (1.00)	0.319 (1.00)	0.0875 (1.00)	1 (1.00)	0.396 (1.00)	0.701 (1.00)
NLK	5 (2%)	216	0.781 (1.00)	0.31 (1.00)	0.166 (1.00)	0.24 (1.00)	0.416 (1.00)	0.812 (1.00)	0.39 (1.00)	1 (1.00)	0.469 (1.00)	0.332 (1.00)

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
TP53 MUTATED	22	15	19	4	38
TP53 WILD-TYPE	82	4	19	2	15

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
TP53 MUTATED	28	35	19
TP53 WILD-TYPE	40	14	40

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

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
TP53 MUTATED	33	25	30
TP53 WILD-TYPE	30	43	37

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
TP53 MUTATED	15	26	20	27
TP53 WILD-TYPE	14	33	20	43

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.082

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
TP53 MUTATED	14	12	12	17	30
TP53 WILD-TYPE	34	31	19	13	14

Figure S3. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.082

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
TP53 MUTATED	15	1	9	16	21	18	5
TP53 WILD-TYPE	17	14	25	24	11	10	10

Figure S4. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
TP53 MUTATED	39	23	37
TP53 WILD-TYPE	55	43	24

Figure S5. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.023

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
TP53 MUTATED	41	18	40
TP53 WILD-TYPE	69	35	18

Figure S6. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
TP53 MUTATED	30	30	23
TP53 WILD-TYPE	34	26	34

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.025

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
TP53 MUTATED	46	8	29
TP53 WILD-TYPE	50	31	13

Figure S7. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S11. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
PIK3CA MUTATED	37	4	4	1	2
PIK3CA WILD-TYPE	67	15	34	5	51

Figure S8. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.097

Table S12. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
PIK3CA MUTATED	27	5	10
PIK3CA WILD-TYPE	41	44	49

Figure S9. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
PIK3CA MUTATED	20	8	17
PIK3CA WILD-TYPE	43	60	50

Figure S10. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0703 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
PIK3CA MUTATED	10	11	13	11
PIK3CA WILD-TYPE	19	48	27	59

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.21

Table S15. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
PIK3CA MUTATED	20	8	3	9	4
PIK3CA WILD-TYPE	28	35	28	21	40

Figure S11. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S16. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
PIK3CA MUTATED	4	12	3	10	7	1	7
PIK3CA WILD-TYPE	28	3	31	30	25	27	8

Figure S12. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 1

Table S17. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
PIK3CA MUTATED	29	11	8
PIK3CA WILD-TYPE	65	55	53

Figure S13. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00771 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
PIK3CA MUTATED	33	9	6
PIK3CA WILD-TYPE	77	44	52

Figure S14. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.52

Table S19. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
PIK3CA MUTATED	25	9	8
PIK3CA WILD-TYPE	39	47	49

Figure S15. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00351 (Fisher's exact test), Q value = 0.79

Table S20. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
PIK3CA MUTATED	31	8	3
PIK3CA WILD-TYPE	65	31	39

Figure S16. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CBWD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0077

Table S21. Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
CBWD1 MUTATED	25	0	3	0	0
CBWD1 WILD-TYPE	79	19	35	6	53

Figure S17. Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CBWD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S22. Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
CBWD1 MUTATED	21	0	1
CBWD1 WILD-TYPE	47	49	58

Figure S18. Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CBWD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S23. Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
CBWD1 MUTATED	18	2	7
CBWD1 WILD-TYPE	45	66	60

Figure S19. Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CBWD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
CBWD1 MUTATED	7	7	9	4
CBWD1 WILD-TYPE	22	52	31	66

Figure S20. Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S25. Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
CBWD1 MUTATED	15	4	3	2	0
CBWD1 WILD-TYPE	33	39	28	28	44

Figure S21. Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S26. Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
CBWD1 MUTATED	5	0	1	6	3	0	9
CBWD1 WILD-TYPE	27	15	33	34	29	28	6

Figure S22. Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S27. Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
CBWD1 MUTATED	17	5	6
CBWD1 WILD-TYPE	77	61	55

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 1

Table S28. Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
CBWD1 MUTATED	19	4	5
CBWD1 WILD-TYPE	91	49	53

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 1

Table S29. Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
CBWD1 MUTATED	13	7	2
CBWD1 WILD-TYPE	51	49	55

Figure S23. Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00466 (Fisher's exact test), Q value = 1

Table S30. Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
CBWD1 MUTATED	19	2	1
CBWD1 WILD-TYPE	77	37	41

Figure S24. Get High-res Image Gene #3: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
KRAS MUTATED	16	1	3	3	2
KRAS WILD-TYPE	88	18	35	3	51

Figure S25. Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
KRAS MUTATED	9	4	5
KRAS WILD-TYPE	59	45	54

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
KRAS MUTATED	10	7	7
KRAS WILD-TYPE	53	61	60

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0721 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
KRAS MUTATED	4	3	9	8
KRAS WILD-TYPE	25	56	31	62

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
KRAS MUTATED	9	4	2	4	2
KRAS WILD-TYPE	39	39	29	26	42

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
KRAS MUTATED	6	0	1	4	5	1	4
KRAS WILD-TYPE	26	15	33	36	27	27	11

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
KRAS MUTATED	11	4	10
KRAS WILD-TYPE	83	62	51

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.761 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
KRAS MUTATED	14	6	5
KRAS WILD-TYPE	96	47	53

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
KRAS MUTATED	4	11	3
KRAS WILD-TYPE	60	45	54

Figure S26. Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
KRAS MUTATED	10	3	5
KRAS WILD-TYPE	86	36	37

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S41. Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
ARID1A MUTATED	33	2	6	0	0
ARID1A WILD-TYPE	71	17	32	6	53

Figure S27. Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 1

Table S42. Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
ARID1A MUTATED	18	5	7
ARID1A WILD-TYPE	50	44	52

Figure S28. Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 1

Table S43. Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
ARID1A MUTATED	19	7	13
ARID1A WILD-TYPE	44	61	54

Figure S29. Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.19

Table S44. Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
ARID1A MUTATED	6	6	17	10
ARID1A WILD-TYPE	23	53	23	60

Figure S30. Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.15

Table S45. Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
ARID1A MUTATED	19	9	4	5	2
ARID1A WILD-TYPE	29	34	27	25	42

Figure S31. Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0026

Table S46. Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
ARID1A MUTATED	6	8	3	5	5	2	10
ARID1A WILD-TYPE	26	7	31	35	27	26	5

Figure S32. Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S47. Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
ARID1A MUTATED	23	9	9
ARID1A WILD-TYPE	71	57	52

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 1

Table S48. Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
ARID1A MUTATED	28	6	7
ARID1A WILD-TYPE	82	47	51

Figure S33. Get High-res Image Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S49. Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
ARID1A MUTATED	13	10	7
ARID1A WILD-TYPE	51	46	50

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S50. Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
ARID1A MUTATED	21	6	3
ARID1A WILD-TYPE	75	33	39

'PGM5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.29

Table S51. Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
PGM5 MUTATED	18	2	1	1	0
PGM5 WILD-TYPE	86	17	37	5	53

Figure S34. Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PGM5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.037

Table S52. Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
PGM5 MUTATED	14	1	1
PGM5 WILD-TYPE	54	48	58

Figure S35. Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PGM5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S53. Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
PGM5 MUTATED	10	4	6
PGM5 WILD-TYPE	53	64	61

'PGM5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 1

Table S54. Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
PGM5 MUTATED	5	4	8	3
PGM5 WILD-TYPE	24	55	32	67

Figure S36. Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PGM5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.11

Table S55. Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
PGM5 MUTATED	11	2	5	1	0
PGM5 WILD-TYPE	37	41	26	29	44

Figure S37. Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PGM5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.74

Table S56. Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
PGM5 MUTATED	2	0	2	6	3	0	6
PGM5 WILD-TYPE	30	15	32	34	29	28	9

Figure S38. Get High-res Image Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PGM5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S57. Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
PGM5 MUTATED	11	4	7
PGM5 WILD-TYPE	83	62	54

'PGM5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S58. Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
PGM5 MUTATED	15	3	4
PGM5 WILD-TYPE	95	50	54

'PGM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S59. Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
PGM5 MUTATED	6	8	2
PGM5 WILD-TYPE	58	48	55

'PGM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0714 (Fisher's exact test), Q value = 1

Table S60. Gene #6: 'PGM5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
PGM5 MUTATED	13	2	1
PGM5 WILD-TYPE	83	37	41

'RHOA MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
RHOA MUTATED	10	1	2	0	0
RHOA WILD-TYPE	94	18	36	6	53

'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
RHOA MUTATED	3	2	6
RHOA WILD-TYPE	65	47	53

'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
RHOA MUTATED	3	4	5
RHOA WILD-TYPE	60	64	62

'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.712 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
RHOA MUTATED	2	5	1	4
RHOA WILD-TYPE	27	54	39	66

'RHOA MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
RHOA MUTATED	2	4	2	3	1
RHOA WILD-TYPE	46	39	29	27	43

'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.801 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
RHOA MUTATED	2	0	4	3	2	1	0
RHOA WILD-TYPE	30	15	30	37	30	27	15

'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00991 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
RHOA MUTATED	5	8	0
RHOA WILD-TYPE	89	58	61

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

'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
RHOA MUTATED	8	4	1
RHOA WILD-TYPE	102	49	57

'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
RHOA MUTATED	5	0	6
RHOA WILD-TYPE	59	56	51

Figure S40. Get High-res Image Gene #7: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
RHOA MUTATED	5	5	1
RHOA WILD-TYPE	91	34	41

'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.477 (Fisher's exact test), Q value = 1

Table S71. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
SMAD4 MUTATED	7	2	6	0	4
SMAD4 WILD-TYPE	97	17	32	6	49

'SMAD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S72. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
SMAD4 MUTATED	6	4	5
SMAD4 WILD-TYPE	62	45	54

'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0666 (Fisher's exact test), Q value = 1

Table S73. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
SMAD4 MUTATED	9	5	2
SMAD4 WILD-TYPE	54	63	65

'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S74. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
SMAD4 MUTATED	3	2	5	6
SMAD4 WILD-TYPE	26	57	35	64

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.48

Table S75. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
SMAD4 MUTATED	5	1	7	4	0
SMAD4 WILD-TYPE	43	42	24	26	44

Figure S41. Get High-res Image Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S76. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
SMAD4 MUTATED	4	1	1	5	4	0	2
SMAD4 WILD-TYPE	28	14	33	35	28	28	13

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S77. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
SMAD4 MUTATED	11	4	4
SMAD4 WILD-TYPE	83	62	57

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S78. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
SMAD4 MUTATED	12	3	4
SMAD4 WILD-TYPE	98	50	54

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 1

Table S79. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
SMAD4 MUTATED	8	4	3
SMAD4 WILD-TYPE	56	52	54

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S80. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
SMAD4 MUTATED	10	3	2
SMAD4 WILD-TYPE	86	36	40

'IRF2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S81. Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
IRF2 MUTATED	9	1	1	1	2
IRF2 WILD-TYPE	95	18	37	5	51

'IRF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S82. Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
IRF2 MUTATED	6	2	1
IRF2 WILD-TYPE	62	47	58

'IRF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0735 (Fisher's exact test), Q value = 1

Table S83. Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
IRF2 MUTATED	8	2	3
IRF2 WILD-TYPE	55	66	64

'IRF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S84. Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
IRF2 MUTATED	2	2	5	4
IRF2 WILD-TYPE	27	57	35	66

'IRF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S85. Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
IRF2 MUTATED	6	2	1	1	1
IRF2 WILD-TYPE	42	41	30	29	43

'IRF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S86. Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
IRF2 MUTATED	3	0	1	3	1	1	2
IRF2 WILD-TYPE	29	15	33	37	31	27	13

'IRF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0602 (Fisher's exact test), Q value = 1

Table S87. Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
IRF2 MUTATED	10	1	3
IRF2 WILD-TYPE	84	65	58

'IRF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 1

Table S88. Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
IRF2 MUTATED	10	3	1
IRF2 WILD-TYPE	100	50	57

'IRF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 1

Table S89. Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
IRF2 MUTATED	6	3	0
IRF2 WILD-TYPE	58	53	57

Figure S42. Get High-res Image Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'IRF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S90. Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
IRF2 MUTATED	8	0	1
IRF2 WILD-TYPE	88	39	41

'LARP4B MUTATION STATUS' versus 'CN_CNMF'

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

Table S91. Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
LARP4B MUTATED	10	1	0	0	1
LARP4B WILD-TYPE	94	18	38	6	52

'LARP4B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 1

Table S92. Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
LARP4B MUTATED	6	3	0
LARP4B WILD-TYPE	62	46	59

Figure S43. Get High-res Image Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'LARP4B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.71

Table S93. Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
LARP4B MUTATED	8	0	3
LARP4B WILD-TYPE	55	68	64

Figure S44. Get High-res Image Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'LARP4B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S94. Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
LARP4B MUTATED	2	2	6	1
LARP4B WILD-TYPE	27	57	34	69

Figure S45. Get High-res Image Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'LARP4B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S95. Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
LARP4B MUTATED	4	0	2	3	1
LARP4B WILD-TYPE	44	43	29	27	43

'LARP4B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0843 (Fisher's exact test), Q value = 1

Table S96. Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
LARP4B MUTATED	2	0	0	1	3	1	3
LARP4B WILD-TYPE	30	15	34	39	29	27	12

'LARP4B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S97. Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
LARP4B MUTATED	7	1	4
LARP4B WILD-TYPE	87	65	57

'LARP4B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 1

Table S98. Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
LARP4B MUTATED	10	0	2
LARP4B WILD-TYPE	100	53	56

Figure S46. Get High-res Image Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'LARP4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0737 (Fisher's exact test), Q value = 1

Table S99. Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
LARP4B MUTATED	5	4	0
LARP4B WILD-TYPE	59	52	57

'LARP4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 1

Table S100. Gene #10: 'LARP4B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
LARP4B MUTATED	8	0	1
LARP4B WILD-TYPE	88	39	41

'APC MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
APC MUTATED	16	3	3	1	10
APC WILD-TYPE	88	16	35	5	43

'APC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
APC MUTATED	12	8	2
APC WILD-TYPE	56	41	57

Figure S47. Get High-res Image Gene #11: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0743 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
APC MUTATED	13	5	11
APC WILD-TYPE	50	63	56

'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.14

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
APC MUTATED	5	6	14	4
APC WILD-TYPE	24	53	26	66

Figure S48. Get High-res Image Gene #11: 'APC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
APC MUTATED	9	2	5	6	7
APC WILD-TYPE	39	41	26	24	37

'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00326 (Fisher's exact test), Q value = 0.74

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
APC MUTATED	1	0	2	8	8	4	6
APC WILD-TYPE	31	15	32	32	24	24	9

Figure S49. Get High-res Image Gene #11: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00992 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
APC MUTATED	19	3	11
APC WILD-TYPE	75	63	50

Figure S50. Get High-res Image Gene #11: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.02 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
APC MUTATED	21	2	10
APC WILD-TYPE	89	51	48

Figure S51. Get High-res Image Gene #11: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0967 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
APC MUTATED	9	10	3
APC WILD-TYPE	55	46	54

'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.087 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
APC MUTATED	15	1	6
APC WILD-TYPE	81	38	36

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
FBXW7 MUTATED	15	1	1	0	2
FBXW7 WILD-TYPE	89	18	37	6	51

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
FBXW7 MUTATED	11	3	1
FBXW7 WILD-TYPE	57	46	58

Figure S52. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.43

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
FBXW7 MUTATED	12	1	5
FBXW7 WILD-TYPE	51	67	62

Figure S53. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
FBXW7 MUTATED	4	4	8	2
FBXW7 WILD-TYPE	25	55	32	68

Figure S54. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
FBXW7 MUTATED	10	1	1	2	2
FBXW7 WILD-TYPE	38	42	30	28	42

Figure S55. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
FBXW7 MUTATED	4	0	0	1	2	2	7
FBXW7 WILD-TYPE	28	15	34	39	30	26	8

Figure S56. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
FBXW7 MUTATED	11	3	5
FBXW7 WILD-TYPE	83	63	56

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.122 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
FBXW7 MUTATED	14	2	3
FBXW7 WILD-TYPE	96	51	55

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00744 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
FBXW7 MUTATED	8	7	0
FBXW7 WILD-TYPE	56	49	57

Figure S57. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
FBXW7 MUTATED	13	0	2
FBXW7 WILD-TYPE	83	39	40

Figure S58. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 1

Table S121. Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
CDH1 MUTATED	13	1	3	0	0
CDH1 WILD-TYPE	91	18	35	6	53

Figure S59. Get High-res Image Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 1

Table S122. Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
CDH1 MUTATED	5	2	7
CDH1 WILD-TYPE	63	47	52

'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S123. Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
CDH1 MUTATED	4	8	6
CDH1 WILD-TYPE	59	60	61

'CDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S124. Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
CDH1 MUTATED	2	7	3	6
CDH1 WILD-TYPE	27	52	37	64

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S125. Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
CDH1 MUTATED	2	7	1	4	2
CDH1 WILD-TYPE	46	36	30	26	42

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0512 (Fisher's exact test), Q value = 1

Table S126. Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
CDH1 MUTATED	1	0	8	3	3	1	0
CDH1 WILD-TYPE	31	15	26	37	29	27	15

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00485 (Fisher's exact test), Q value = 1

Table S127. Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
CDH1 MUTATED	9	9	0
CDH1 WILD-TYPE	85	57	61

Figure S60. Get High-res Image Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0543 (Fisher's exact test), Q value = 1

Table S128. Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
CDH1 MUTATED	10	7	1
CDH1 WILD-TYPE	100	46	57

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0741 (Fisher's exact test), Q value = 1

Table S129. Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
CDH1 MUTATED	6	1	7
CDH1 WILD-TYPE	58	55	50

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S130. Gene #13: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
CDH1 MUTATED	7	5	2
CDH1 WILD-TYPE	89	34	40

'HLA-B MUTATION STATUS' versus 'CN_CNMF'

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

Table S131. Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
HLA-B MUTATED	10	1	1	0	0
HLA-B WILD-TYPE	94	18	37	6	53

'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.095

Table S132. Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
HLA-B MUTATED	9	0	0
HLA-B WILD-TYPE	59	49	59

Figure S61. Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00508 (Fisher's exact test), Q value = 1

Table S133. Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
HLA-B MUTATED	9	1	2
HLA-B WILD-TYPE	54	67	65

Figure S62. Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.37

Table S134. Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
HLA-B MUTATED	3	1	7	1
HLA-B WILD-TYPE	26	58	33	69

Figure S63. Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 1

Table S135. Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
HLA-B MUTATED	5	0	2	3	0
HLA-B WILD-TYPE	43	43	29	27	44

Figure S64. Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 1

Table S136. Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
HLA-B MUTATED	3	1	0	1	2	0	3
HLA-B WILD-TYPE	29	14	34	39	30	28	12

Figure S65. Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0851 (Fisher's exact test), Q value = 1

Table S137. Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
HLA-B MUTATED	9	2	1
HLA-B WILD-TYPE	85	64	60

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 1

Table S138. Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
HLA-B MUTATED	10	2	0
HLA-B WILD-TYPE	100	51	58

Figure S66. Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S139. Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
HLA-B MUTATED	7	1	1
HLA-B WILD-TYPE	57	55	56

Figure S67. Get High-res Image Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S140. Gene #14: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
HLA-B MUTATED	7	2	0
HLA-B WILD-TYPE	89	37	42

'BCOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
BCOR MUTATED	14	0	2	0	0
BCOR WILD-TYPE	90	19	36	6	53

Figure S68. Get High-res Image Gene #15: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'BCOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0504 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
BCOR MUTATED	7	0	3
BCOR WILD-TYPE	61	49	56

'BCOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
BCOR MUTATED	7	2	5
BCOR WILD-TYPE	56	66	62

'BCOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
BCOR MUTATED	2	4	7	1
BCOR WILD-TYPE	27	55	33	69

Figure S69. Get High-res Image Gene #15: 'BCOR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'BCOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
BCOR MUTATED	8	2	1	2	0
BCOR WILD-TYPE	40	41	30	28	44

Figure S70. Get High-res Image Gene #15: 'BCOR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
BCOR MUTATED	4	3	0	1	2	0	3
BCOR WILD-TYPE	28	12	34	39	30	28	12

Figure S71. Get High-res Image Gene #15: 'BCOR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
BCOR MUTATED	12	2	2
BCOR WILD-TYPE	82	64	59

Figure S72. Get High-res Image Gene #15: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
BCOR MUTATED	13	2	1
BCOR WILD-TYPE	97	51	57

Figure S73. Get High-res Image Gene #15: 'BCOR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
BCOR MUTATED	6	2	2
BCOR WILD-TYPE	58	54	55

'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
BCOR MUTATED	8	2	0
BCOR WILD-TYPE	88	37	42

'C13ORF33 MUTATION STATUS' versus 'CN_CNMF'

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

Table S151. Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
C13ORF33 MUTATED	4	0	1	1	0
C13ORF33 WILD-TYPE	100	19	37	5	53

'C13ORF33 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00432 (Fisher's exact test), Q value = 0.96

Table S152. Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
C13ORF33 MUTATED	6	0	0
C13ORF33 WILD-TYPE	62	49	59

Figure S74. Get High-res Image Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'C13ORF33 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 1

Table S153. Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
C13ORF33 MUTATED	5	1	0
C13ORF33 WILD-TYPE	58	67	67

Figure S75. Get High-res Image Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'C13ORF33 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S154. Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
C13ORF33 MUTATED	1	1	3	1
C13ORF33 WILD-TYPE	28	58	37	69

'C13ORF33 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 1

Table S155. Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
C13ORF33 MUTATED	3	0	1	0	0
C13ORF33 WILD-TYPE	45	43	30	30	44

'C13ORF33 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00325 (Fisher's exact test), Q value = 0.74

Table S156. Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
C13ORF33 MUTATED	0	0	0	1	0	0	3
C13ORF33 WILD-TYPE	32	15	34	39	32	28	12

Figure S76. Get High-res Image Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.429 (Fisher's exact test), Q value = 1

Table S157. Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
C13ORF33 MUTATED	1	3	2
C13ORF33 WILD-TYPE	93	63	59

'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S158. Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
C13ORF33 MUTATED	4	1	1
C13ORF33 WILD-TYPE	106	52	57

'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.6 (Fisher's exact test), Q value = 1

Table S159. Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
C13ORF33 MUTATED	2	3	1
C13ORF33 WILD-TYPE	62	53	56

'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.353 (Fisher's exact test), Q value = 1

Table S160. Gene #16: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
C13ORF33 MUTATED	5	1	0
C13ORF33 WILD-TYPE	91	38	42

'CIC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 1

Table S161. Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
CIC MUTATED	11	0	2	1	0
CIC WILD-TYPE	93	19	36	5	53

Figure S77. Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CIC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00623 (Fisher's exact test), Q value = 1

Table S162. Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
CIC MUTATED	8	0	1
CIC WILD-TYPE	60	49	58

Figure S78. Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CIC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 1

Table S163. Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
CIC MUTATED	9	2	3
CIC WILD-TYPE	54	66	64

Figure S79. Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CIC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S164. Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
CIC MUTATED	4	3	6	1
CIC WILD-TYPE	25	56	34	69

Figure S80. Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S165. Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
CIC MUTATED	3	2	1	3	1
CIC WILD-TYPE	45	41	30	27	43

'CIC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00514 (Fisher's exact test), Q value = 1

Table S166. Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
CIC MUTATED	4	0	0	0	4	0	2
CIC WILD-TYPE	28	15	34	40	28	28	13

Figure S81. Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S167. Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
CIC MUTATED	11	1	2
CIC WILD-TYPE	83	65	59

Figure S82. Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CIC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0086 (Fisher's exact test), Q value = 1

Table S168. Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
CIC MUTATED	12	2	0
CIC WILD-TYPE	98	51	58

Figure S83. Get High-res Image Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 1

Table S169. Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
CIC MUTATED	5	3	1
CIC WILD-TYPE	59	53	56

'CIC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 1

Table S170. Gene #17: 'CIC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
CIC MUTATED	8	1	0
CIC WILD-TYPE	88	38	42

'ACVR1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 1

Table S171. Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
ACVR1B MUTATED	9	0	1	0	0
ACVR1B WILD-TYPE	95	19	37	6	53

'ACVR1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 1

Table S172. Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
ACVR1B MUTATED	5	1	1
ACVR1B WILD-TYPE	63	48	58

'ACVR1B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S173. Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
ACVR1B MUTATED	4	2	4
ACVR1B WILD-TYPE	59	66	63

'ACVR1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 1

Table S174. Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
ACVR1B MUTATED	1	2	5	2
ACVR1B WILD-TYPE	28	57	35	68

'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00534 (Fisher's exact test), Q value = 1

Table S175. Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
ACVR1B MUTATED	3	0	0	4	0
ACVR1B WILD-TYPE	45	43	31	26	44

Figure S84. Get High-res Image Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S176. Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
ACVR1B MUTATED	2	0	0	2	3	0	0
ACVR1B WILD-TYPE	30	15	34	38	29	28	15

'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 1

Table S177. Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
ACVR1B MUTATED	6	1	3
ACVR1B WILD-TYPE	88	65	58

'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.406 (Fisher's exact test), Q value = 1

Table S178. Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
ACVR1B MUTATED	7	2	1
ACVR1B WILD-TYPE	103	51	57

'ACVR1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S179. Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
ACVR1B MUTATED	3	2	2
ACVR1B WILD-TYPE	61	54	55

'ACVR1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S180. Gene #18: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
ACVR1B MUTATED	6	1	0
ACVR1B WILD-TYPE	90	38	42

'ZBTB20 MUTATION STATUS' versus 'CN_CNMF'

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

Table S181. Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
ZBTB20 MUTATED	13	1	2	0	0
ZBTB20 WILD-TYPE	91	18	36	6	53

Figure S85. Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ZBTB20 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.25

Table S182. Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
ZBTB20 MUTATED	10	0	1
ZBTB20 WILD-TYPE	58	49	58

Figure S86. Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ZBTB20 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S183. Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
ZBTB20 MUTATED	7	2	6
ZBTB20 WILD-TYPE	56	66	61

'ZBTB20 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 1

Table S184. Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
ZBTB20 MUTATED	3	3	6	3
ZBTB20 WILD-TYPE	26	56	34	67

'ZBTB20 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S185. Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
ZBTB20 MUTATED	6	1	1	5	1
ZBTB20 WILD-TYPE	42	42	30	25	43

Figure S87. Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZBTB20 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00441 (Fisher's exact test), Q value = 0.98

Table S186. Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
ZBTB20 MUTATED	3	0	0	2	5	0	4
ZBTB20 WILD-TYPE	29	15	34	38	27	28	11

Figure S88. Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S187. Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
ZBTB20 MUTATED	10	2	4
ZBTB20 WILD-TYPE	84	64	57

'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.56

Table S188. Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
ZBTB20 MUTATED	14	2	0
ZBTB20 WILD-TYPE	96	51	58

Figure S89. Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 1

Table S189. Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
ZBTB20 MUTATED	5	5	1
ZBTB20 WILD-TYPE	59	51	56

'ZBTB20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 1

Table S190. Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
ZBTB20 MUTATED	10	1	0
ZBTB20 WILD-TYPE	86	38	42

Figure S90. Get High-res Image Gene #19: 'ZBTB20 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MVK MUTATION STATUS' versus 'CN_CNMF'

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

Table S191. Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
MVK MUTATED	6	0	2	0	0
MVK WILD-TYPE	98	19	36	6	53

'MVK MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 1

Table S192. Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
MVK MUTATED	4	0	0
MVK WILD-TYPE	64	49	59

Figure S91. Get High-res Image Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MVK MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 1

Table S193. Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
MVK MUTATED	5	0	3
MVK WILD-TYPE	58	68	64

Figure S92. Get High-res Image Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'MVK MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.25

Table S194. Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
MVK MUTATED	1	1	6	0
MVK WILD-TYPE	28	58	34	70

Figure S93. Get High-res Image Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MVK MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S195. Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
MVK MUTATED	3	1	1	1	0
MVK WILD-TYPE	45	42	30	29	44

'MVK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S196. Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
MVK MUTATED	1	1	0	1	1	0	2
MVK WILD-TYPE	31	14	34	39	31	28	13

'MVK MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 1

Table S197. Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
MVK MUTATED	7	1	0
MVK WILD-TYPE	87	65	61

Figure S94. Get High-res Image Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MVK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.448 (Fisher's exact test), Q value = 1

Table S198. Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
MVK MUTATED	6	1	1
MVK WILD-TYPE	104	52	57

'MVK MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 1

Table S199. Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
MVK MUTATED	3	0	1
MVK WILD-TYPE	61	56	56

'MVK MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S200. Gene #20: 'MVK MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
MVK MUTATED	3	1	0
MVK WILD-TYPE	93	38	42

'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S201. Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
ERBB2 MUTATED	7	1	1	0	2
ERBB2 WILD-TYPE	97	18	37	6	51

'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S202. Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
ERBB2 MUTATED	5	1	2
ERBB2 WILD-TYPE	63	48	57

'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 1

Table S203. Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
ERBB2 MUTATED	6	2	3
ERBB2 WILD-TYPE	57	66	64

'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.671 (Fisher's exact test), Q value = 1

Table S204. Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
ERBB2 MUTATED	3	3	2	3
ERBB2 WILD-TYPE	26	56	38	67

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S205. Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
ERBB2 MUTATED	4	2	1	2	1
ERBB2 WILD-TYPE	44	41	30	28	43

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S206. Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
ERBB2 MUTATED	2	0	1	3	3	0	1
ERBB2 WILD-TYPE	30	15	33	37	29	28	14

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 1

Table S207. Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
ERBB2 MUTATED	7	3	1
ERBB2 WILD-TYPE	87	63	60

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S208. Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
ERBB2 MUTATED	7	3	1
ERBB2 WILD-TYPE	103	50	57

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S209. Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
ERBB2 MUTATED	4	2	2
ERBB2 WILD-TYPE	60	54	55

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S210. Gene #21: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
ERBB2 MUTATED	6	2	0
ERBB2 WILD-TYPE	90	37	42

'CR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S211. Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
CR1 MUTATED	14	0	3	1	2
CR1 WILD-TYPE	90	19	35	5	51

'CR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.037

Table S212. Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
CR1 MUTATED	12	1	0
CR1 WILD-TYPE	56	48	59

Figure S95. Get High-res Image Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0971 (Fisher's exact test), Q value = 1

Table S213. Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
CR1 MUTATED	10	3	6
CR1 WILD-TYPE	53	65	61

'CR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S214. Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
CR1 MUTATED	5	5	6	3
CR1 WILD-TYPE	24	54	34	67

'CR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.11

Table S215. Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
CR1 MUTATED	11	1	2	4	0
CR1 WILD-TYPE	37	42	29	26	44

Figure S96. Get High-res Image Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.018

Table S216. Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
CR1 MUTATED	2	1	0	6	2	0	7
CR1 WILD-TYPE	30	14	34	34	30	28	8

Figure S97. Get High-res Image Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S217. Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
CR1 MUTATED	12	4	4
CR1 WILD-TYPE	82	62	57

'CR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 1

Table S218. Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
CR1 MUTATED	16	2	2
CR1 WILD-TYPE	94	51	56

Figure S98. Get High-res Image Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 1

Table S219. Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
CR1 MUTATED	7	5	1
CR1 WILD-TYPE	57	51	56

'CR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 1

Table S220. Gene #22: 'CR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
CR1 MUTATED	10	2	1
CR1 WILD-TYPE	86	37	41

'C1R MUTATION STATUS' versus 'CN_CNMF'

P value = 0.6 (Fisher's exact test), Q value = 1

Table S221. Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
C1R MUTATED	3	0	0	0	0
C1R WILD-TYPE	101	19	38	6	53

'C1R MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 1

Table S222. Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
C1R MUTATED	2	0	1
C1R WILD-TYPE	61	68	66

'C1R MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0406 (Fisher's exact test), Q value = 1

Table S223. Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
C1R MUTATED	1	0	2	0
C1R WILD-TYPE	28	59	38	70

Figure S99. Get High-res Image Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'C1R MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S224. Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
C1R MUTATED	2	0	1
C1R WILD-TYPE	92	66	60

'C1R MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S225. Gene #23: 'C1R MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
C1R MUTATED	2	1	0
C1R WILD-TYPE	108	52	58

'CTNND1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 1

Table S226. Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
CTNND1 MUTATED	12	0	0	0	1
CTNND1 WILD-TYPE	92	19	38	6	52

Figure S100. Get High-res Image Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CTNND1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0634 (Fisher's exact test), Q value = 1

Table S227. Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
CTNND1 MUTATED	8	2	1
CTNND1 WILD-TYPE	60	47	58

'CTNND1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S228. Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
CTNND1 MUTATED	6	2	5
CTNND1 WILD-TYPE	57	66	62

'CTNND1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S229. Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
CTNND1 MUTATED	2	3	6	2
CTNND1 WILD-TYPE	27	56	34	68

'CTNND1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 1

Table S230. Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
CTNND1 MUTATED	7	1	0	3	1
CTNND1 WILD-TYPE	41	42	31	27	43

Figure S101. Get High-res Image Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CTNND1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.528 (Fisher's exact test), Q value = 1

Table S231. Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
CTNND1 MUTATED	1	1	1	2	4	1	2
CTNND1 WILD-TYPE	31	14	33	38	28	27	13

'CTNND1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S232. Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
CTNND1 MUTATED	7	2	4
CTNND1 WILD-TYPE	87	64	57

'CTNND1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 1

Table S233. Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
CTNND1 MUTATED	10	1	2
CTNND1 WILD-TYPE	100	52	56

'CTNND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S234. Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
CTNND1 MUTATED	5	4	2
CTNND1 WILD-TYPE	59	52	55

'CTNND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S235. Gene #24: 'CTNND1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
CTNND1 MUTATED	9	1	1
CTNND1 WILD-TYPE	87	38	41

'MLXIPL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.298 (Fisher's exact test), Q value = 1

Table S236. Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
MLXIPL MUTATED	10	0	2	0	1
MLXIPL WILD-TYPE	94	19	36	6	52

'MLXIPL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 1

Table S237. Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
MLXIPL MUTATED	5	2	1
MLXIPL WILD-TYPE	63	47	58

'MLXIPL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 1

Table S238. Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
MLXIPL MUTATED	8	1	4
MLXIPL WILD-TYPE	55	67	63

Figure S102. Get High-res Image Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'MLXIPL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 1

Table S239. Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
MLXIPL MUTATED	2	3	7	1
MLXIPL WILD-TYPE	27	56	33	69

Figure S103. Get High-res Image Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MLXIPL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0758 (Fisher's exact test), Q value = 1

Table S240. Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
MLXIPL MUTATED	7	1	2	0	2
MLXIPL WILD-TYPE	41	42	29	30	42

'MLXIPL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 1

Table S241. Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
MLXIPL MUTATED	3	0	0	4	2	1	2
MLXIPL WILD-TYPE	29	15	34	36	30	27	13

'MLXIPL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0875 (Fisher's exact test), Q value = 1

Table S242. Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
MLXIPL MUTATED	9	1	3
MLXIPL WILD-TYPE	85	65	58

'MLXIPL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S243. Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
MLXIPL MUTATED	7	3	3
MLXIPL WILD-TYPE	103	50	55

'MLXIPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 1

Table S244. Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
MLXIPL MUTATED	3	4	1
MLXIPL WILD-TYPE	61	52	56

'MLXIPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S245. Gene #25: 'MLXIPL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
MLXIPL MUTATED	6	1	1
MLXIPL WILD-TYPE	90	38	41

'MLL4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0571 (Fisher's exact test), Q value = 1

Table S246. Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
MLL4 MUTATED	15	1	2	1	1
MLL4 WILD-TYPE	89	18	36	5	52

'MLL4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.03

Table S247. Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
MLL4 MUTATED	12	0	1
MLL4 WILD-TYPE	56	49	58

Figure S104. Get High-res Image Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MLL4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S248. Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
MLL4 MUTATED	9	6	5
MLL4 WILD-TYPE	54	62	62

'MLL4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 1

Table S249. Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
MLL4 MUTATED	3	3	9	5
MLL4 WILD-TYPE	26	56	31	65

Figure S105. Get High-res Image Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MLL4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0929 (Fisher's exact test), Q value = 1

Table S250. Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
MLL4 MUTATED	8	2	2	4	1
MLL4 WILD-TYPE	40	41	29	26	43

'MLL4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.088

Table S251. Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
MLL4 MUTATED	2	1	0	3	3	1	7
MLL4 WILD-TYPE	30	14	34	37	29	27	8

Figure S106. Get High-res Image Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MLL4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 1

Table S252. Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
MLL4 MUTATED	13	3	4
MLL4 WILD-TYPE	81	63	57

'MLL4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0774 (Fisher's exact test), Q value = 1

Table S253. Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
MLL4 MUTATED	15	2	3
MLL4 WILD-TYPE	95	51	55

'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0698 (Fisher's exact test), Q value = 1

Table S254. Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
MLL4 MUTATED	8	4	1
MLL4 WILD-TYPE	56	52	56

'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 1

Table S255. Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
MLL4 MUTATED	12	0	1
MLL4 WILD-TYPE	84	39	41

Figure S107. Get High-res Image Gene #26: 'MLL4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NLK MUTATION STATUS' versus 'CN_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S256. Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	104	19	38	6	53
NLK MUTATED	4	0	0	0	1
NLK WILD-TYPE	100	19	38	6	52

'NLK MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S257. Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	49	59
NLK MUTATED	3	1	0
NLK WILD-TYPE	65	48	59

'NLK MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S258. Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	63	68	67
NLK MUTATED	3	0	2
NLK WILD-TYPE	60	68	65

'NLK MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 1

Table S259. Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	29	59	40	70
NLK MUTATED	0	1	3	1
NLK WILD-TYPE	29	58	37	69

'NLK MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S260. Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	31	30	44
NLK MUTATED	3	0	1	0	1
NLK WILD-TYPE	45	43	30	30	43

'NLK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.812 (Fisher's exact test), Q value = 1

Table S261. Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	32	15	34	40	32	28	15
NLK MUTATED	1	0	0	1	1	1	1
NLK WILD-TYPE	31	15	34	39	31	27	14

'NLK MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S262. Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	94	66	61
NLK MUTATED	3	0	2
NLK WILD-TYPE	91	66	59

'NLK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S263. Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	53	58
NLK MUTATED	3	1	1
NLK WILD-TYPE	107	52	57

'NLK MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S264. Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	56	57
NLK MUTATED	2	2	0
NLK WILD-TYPE	62	54	57

'NLK MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S265. Gene #27: 'NLK MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	96	39	42
NLK MUTATED	4	0	0
NLK WILD-TYPE	92	39	42

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = STAD-TP.transferedmergedcluster.txt
Number of patients = 221
Number of significantly mutated genes = 27
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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