Correlation between gene mutation status and molecular subtypes

Stomach Adenocarcinoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_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/C1V1238R

Overview

Introduction

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

Summary

Testing the association between mutation status of 20 genes and 10 molecular subtypes across 220 patients, 19 significant findings detected with P value < 0.05 and Q value < 0.25.

PIK3CA mutation correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
PGM5 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
CBWD1 mutation correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
ARID1A mutation correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
PTEN mutation correlated to 'MRNASEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 20 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 19 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
TP53	99 (45%)	121	7.48e-10 (1.5e-07)	3.37e-05 (0.00656)	0.17 (1.00)	0.855 (1.00)	0.000261 (0.0492)	0.000375 (0.0702)	0.0327 (1.00)	1.29e-05 (0.00254)	0.204 (1.00)	2.33e-05 (0.00456)
PIK3CA	48 (22%)	172	0.00139 (0.251)	3.38e-09 (6.72e-07)	0.0143 (1.00)	0.000338 (0.0636)	0.000924 (0.169)	3.97e-05 (0.0077)	0.00508 (0.843)	0.0171 (1.00)	0.0179 (1.00)	0.00312 (0.539)
CBWD1	28 (13%)	192	0.0029 (0.504)	4.65e-06 (0.000921)	7.85e-05 (0.0151)	0.00466 (0.784)	9.94e-05 (0.019)	0.00371 (0.634)	0.0284 (1.00)	0.00791 (1.00)	0.238 (1.00)	0.00018 (0.0342)
PGM5	22 (10%)	198	0.00946 (1.00)	7.48e-05 (0.0144)	0.153 (1.00)	0.0283 (1.00)	0.000974 (0.177)	0.00238 (0.423)	0.276 (1.00)	0.029 (1.00)	0.117 (1.00)	0.0171 (1.00)
ARID1A	41 (19%)	179	0.0005 (0.093)	0.00711 (1.00)	0.0151 (1.00)	0.0637 (1.00)	0.000738 (0.137)	0.00996 (1.00)	0.0861 (1.00)	0.00608 (1.00)	0.883 (1.00)	0.162 (1.00)
PTEN	14 (6%)	206	0.0495 (1.00)	0.0152 (1.00)	0.00434 (0.734)	0.0101 (1.00)	0.000833 (0.153)	0.0121 (1.00)	0.158 (1.00)	0.012 (1.00)	0.288 (1.00)	0.00607 (1.00)
KRAS	25 (11%)	195	0.0118 (1.00)	0.127 (1.00)	0.557 (1.00)	0.921 (1.00)	0.216 (1.00)	0.0262 (1.00)	0.164 (1.00)	0.505 (1.00)	0.0973 (1.00)	0.912 (1.00)
SMAD4	19 (9%)	201	0.778 (1.00)	0.963 (1.00)	0.064 (1.00)	0.735 (1.00)	0.00387 (0.658)	0.193 (1.00)	0.201 (1.00)	0.157 (1.00)	0.531 (1.00)	0.536 (1.00)
RHOA	13 (6%)	207	0.251 (1.00)	0.189 (1.00)	0.872 (1.00)	0.86 (1.00)	0.558 (1.00)	0.0531 (1.00)	0.0035 (0.602)	0.0848 (1.00)	0.00268 (0.469)	0.038 (1.00)
IRF2	14 (6%)	206	0.67 (1.00)	0.414 (1.00)	0.0641 (1.00)	0.764 (1.00)	0.21 (1.00)	0.632 (1.00)	0.0301 (1.00)	0.0244 (1.00)	0.123 (1.00)	0.0866 (1.00)
CDH1	18 (8%)	202	0.189 (1.00)	0.457 (1.00)	0.574 (1.00)	0.64 (1.00)	0.11 (1.00)	0.0575 (1.00)	0.0261 (1.00)	0.0495 (1.00)	0.0791 (1.00)	0.123 (1.00)
FBXW7	19 (9%)	201	0.12 (1.00)	0.0221 (1.00)	0.00182 (0.326)	0.0142 (1.00)	0.00743 (1.00)	0.323 (1.00)	0.155 (1.00)	0.0696 (1.00)	0.00949 (1.00)	0.00256 (0.45)
B2M	8 (4%)	212	0.0958 (1.00)	0.0232 (1.00)	0.0861 (1.00)	0.695 (1.00)	0.0513 (1.00)	0.3 (1.00)	0.355 (1.00)	0.149 (1.00)	0.598 (1.00)	0.103 (1.00)
FAM46D	6 (3%)	214	0.661 (1.00)	0.708 (1.00)	0.744 (1.00)	0.109 (1.00)	0.103 (1.00)	1 (1.00)	0.775 (1.00)	0.67 (1.00)	1 (1.00)	0.714 (1.00)
RNF43	9 (4%)	211	0.838 (1.00)	0.596 (1.00)	0.577 (1.00)	0.113 (1.00)	0.273 (1.00)	0.798 (1.00)	0.634 (1.00)	0.181 (1.00)	0.878 (1.00)	0.274 (1.00)
APC	33 (15%)	187	0.875 (1.00)	0.0231 (1.00)	0.0755 (1.00)	0.0909 (1.00)	0.302 (1.00)	0.00248 (0.438)	0.0124 (1.00)	0.00499 (0.834)	0.06 (1.00)	0.00989 (1.00)
WSB2	7 (3%)	213	0.417 (1.00)	0.131 (1.00)	0.0861 (1.00)	0.0629 (1.00)	0.126 (1.00)	0.0291 (1.00)	0.00144 (0.259)	0.065 (1.00)	0.132 (1.00)	0.0464 (1.00)
MAP2K7	14 (6%)	206	0.319 (1.00)	0.0984 (1.00)	0.821 (1.00)	0.764 (1.00)	0.0501 (1.00)	0.488 (1.00)	0.158 (1.00)	0.0964 (1.00)	0.791 (1.00)	0.261 (1.00)
TRPS1	30 (14%)	190	0.92 (1.00)	0.0435 (1.00)	0.111 (1.00)	0.118 (1.00)	0.0233 (1.00)	0.235 (1.00)	0.332 (1.00)	0.665 (1.00)	0.516 (1.00)	0.118 (1.00)
C13ORF33	6 (3%)	214	0.344 (1.00)	0.0165 (1.00)	0.0152 (1.00)	0.0861 (1.00)	0.141 (1.00)	0.46 (1.00)	0.515 (1.00)	0.44 (1.00)	0.216 (1.00)	0.274 (1.00)

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00139 (Chi-square test), Q value = 0.25

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
PIK3CA MUTATED	35	4	3	2	4	0
PIK3CA WILD-TYPE	68	14	32	5	51	1

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

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.38e-09 (Fisher's exact test), Q value = 6.7e-07

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
PIK3CA MUTATED	19	15	4	4
PIK3CA WILD-TYPE	8	36	40	49

Figure S2. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
PIK3CA MUTATED	20	8	17
PIK3CA WILD-TYPE	42	60	50

Figure S3. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.000338 (Fisher's exact test), Q value = 0.064

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
PIK3CA MUTATED	22	15	8
PIK3CA WILD-TYPE	59	21	72

Figure S4. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000924 (Chi-square test), Q value = 0.17

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
PIK3CA MUTATED	20	8	3	9	4
PIK3CA WILD-TYPE	28	35	27	21	40

Figure S5. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.97e-05 (Fisher's exact test), Q value = 0.0077

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
PIK3CA MUTATED	3	29	12
PIK3CA WILD-TYPE	50	48	53

Figure S6. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00508 (Fisher's exact test), Q value = 0.84

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
PIK3CA MUTATED	27	14	7
PIK3CA WILD-TYPE	57	55	60

Figure S7. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
PIK3CA MUTATED	16	5	27
PIK3CA WILD-TYPE	56	49	67

Figure S8. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
PIK3CA MUTATED	21	13	8
PIK3CA WILD-TYPE	35	56	43

Figure S9. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00312 (Fisher's exact test), Q value = 0.54

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
PIK3CA MUTATED	3	28	11
PIK3CA WILD-TYPE	39	56	39

Figure S10. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PGM5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00946 (Chi-square test), Q value = 1

Table S11. Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
PGM5 MUTATED	16	3	1	2	0	0
PGM5 WILD-TYPE	87	15	34	5	55	1

Figure S11. Get High-res Image Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PGM5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 7.48e-05 (Fisher's exact test), Q value = 0.014

Table S12. Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
PGM5 MUTATED	3	12	1	0
PGM5 WILD-TYPE	24	39	43	53

Figure S12. Get High-res Image Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PGM5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
PGM5 MUTATED	10	4	6
PGM5 WILD-TYPE	52	64	61

'PGM5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
PGM5 MUTATED	11	6	3
PGM5 WILD-TYPE	70	30	77

Figure S13. Get High-res Image Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PGM5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000974 (Chi-square test), Q value = 0.18

Table S15. Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
PGM5 MUTATED	11	2	5	1	0
PGM5 WILD-TYPE	37	41	25	29	44

Figure S14. Get High-res Image Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PGM5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00238 (Fisher's exact test), Q value = 0.42

Table S16. Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
PGM5 MUTATED	0	13	6
PGM5 WILD-TYPE	53	64	59

Figure S15. Get High-res Image Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PGM5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 1

Table S17. Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
PGM5 MUTATED	12	5	5
PGM5 WILD-TYPE	72	64	62

'PGM5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
PGM5 MUTATED	7	1	14
PGM5 WILD-TYPE	65	53	80

Figure S16. Get High-res Image Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PGM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S19. Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
PGM5 MUTATED	4	10	2
PGM5 WILD-TYPE	52	59	49

'PGM5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 1

Table S20. Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
PGM5 MUTATED	0	12	4
PGM5 WILD-TYPE	42	72	46

Figure S17. Get High-res Image Gene #2: 'PGM5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0118 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
KRAS MUTATED	17	1	1	3	3	0
KRAS WILD-TYPE	86	17	34	4	52	1

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

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
KRAS MUTATED	2	9	5	2
KRAS WILD-TYPE	25	42	39	51

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
KRAS MUTATED	10	7	7
KRAS WILD-TYPE	52	61	60

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
KRAS MUTATED	11	4	9
KRAS WILD-TYPE	70	32	71

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.216 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
KRAS MUTATED	9	4	2	4	2
KRAS WILD-TYPE	39	39	28	26	42

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0262 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
KRAS MUTATED	1	12	8
KRAS WILD-TYPE	52	65	57

Figure S19. Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
KRAS MUTATED	13	4	8
KRAS WILD-TYPE	71	65	59

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.505 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
KRAS MUTATED	8	4	13
KRAS WILD-TYPE	64	50	81

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0973 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
KRAS MUTATED	5	11	2
KRAS WILD-TYPE	51	58	49

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
KRAS MUTATED	5	8	5
KRAS WILD-TYPE	37	76	45

'CBWD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0029 (Chi-square test), Q value = 0.5

Table S31. Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
CBWD1 MUTATED	23	1	3	1	0	0
CBWD1 WILD-TYPE	80	17	32	6	55	1

Figure S20. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CBWD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.65e-06 (Fisher's exact test), Q value = 0.00092

Table S32. Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
CBWD1 MUTATED	4	16	2	0
CBWD1 WILD-TYPE	23	35	42	53

Figure S21. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CBWD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 7.85e-05 (Fisher's exact test), Q value = 0.015

Table S33. Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
CBWD1 MUTATED	18	2	7
CBWD1 WILD-TYPE	44	66	60

Figure S22. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CBWD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00466 (Fisher's exact test), Q value = 0.78

Table S34. Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
CBWD1 MUTATED	14	9	4
CBWD1 WILD-TYPE	67	27	76

Figure S23. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9.94e-05 (Chi-square test), Q value = 0.019

Table S35. Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
CBWD1 MUTATED	15	4	3	2	0
CBWD1 WILD-TYPE	33	39	27	28	44

Figure S24. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00371 (Fisher's exact test), Q value = 0.63

Table S36. Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
CBWD1 MUTATED	2	17	5
CBWD1 WILD-TYPE	51	60	60

Figure S25. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 1

Table S37. Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
CBWD1 MUTATED	17	7	4
CBWD1 WILD-TYPE	67	62	63

Figure S26. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00791 (Fisher's exact test), Q value = 1

Table S38. Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
CBWD1 MUTATED	10	1	17
CBWD1 WILD-TYPE	62	53	77

Figure S27. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 1

Table S39. Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
CBWD1 MUTATED	8	11	3
CBWD1 WILD-TYPE	48	58	48

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.034

Table S40. Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
CBWD1 MUTATED	0	19	3
CBWD1 WILD-TYPE	42	65	47

Figure S28. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 7.48e-10 (Chi-square test), Q value = 1.5e-07

Table S41. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
TP53 MUTATED	21	14	20	4	39	0
TP53 WILD-TYPE	82	4	15	3	16	1

Figure S29. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.37e-05 (Fisher's exact test), Q value = 0.0066

Table S42. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
TP53 MUTATED	5	25	15	37
TP53 WILD-TYPE	22	26	29	16

Figure S30. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S43. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
TP53 MUTATED	33	25	30
TP53 WILD-TYPE	29	43	37

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.855 (Fisher's exact test), Q value = 1

Table S44. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
TP53 MUTATED	37	17	34
TP53 WILD-TYPE	44	19	46

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000261 (Chi-square test), Q value = 0.049

Table S45. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
TP53 MUTATED	14	12	12	17	30
TP53 WILD-TYPE	34	31	18	13	14

Figure S31. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000375 (Fisher's exact test), Q value = 0.07

Table S46. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
TP53 MUTATED	35	30	20
TP53 WILD-TYPE	18	47	45

Figure S32. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 1

Table S47. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
TP53 MUTATED	34	26	39
TP53 WILD-TYPE	50	43	28

Figure S33. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.0025

Table S48. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
TP53 MUTATED	23	39	37
TP53 WILD-TYPE	49	15	57

Figure S34. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 1

Table S49. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
TP53 MUTATED	25	38	20
TP53 WILD-TYPE	31	31	31

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.33e-05 (Fisher's exact test), Q value = 0.0046

Table S50. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
TP53 MUTATED	31	39	13
TP53 WILD-TYPE	11	45	37

Figure S35. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 5e-04 (Chi-square test), Q value = 0.093

Table S51. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
ARID1A MUTATED	32	2	5	1	1	0
ARID1A WILD-TYPE	71	16	30	6	54	1

Figure S36. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00711 (Fisher's exact test), Q value = 1

Table S52. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
ARID1A MUTATED	9	12	6	3
ARID1A WILD-TYPE	18	39	38	50

Figure S37. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S53. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
ARID1A MUTATED	19	7	13
ARID1A WILD-TYPE	43	61	54

Figure S38. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0637 (Fisher's exact test), Q value = 1

Table S54. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
ARID1A MUTATED	22	7	10
ARID1A WILD-TYPE	59	29	70

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000738 (Chi-square test), Q value = 0.14

Table S55. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
ARID1A MUTATED	19	9	4	5	2
ARID1A WILD-TYPE	29	34	26	25	42

Figure S39. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00996 (Fisher's exact test), Q value = 1

Table S56. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
ARID1A MUTATED	4	22	13
ARID1A WILD-TYPE	49	55	52

Figure S40. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0861 (Fisher's exact test), Q value = 1

Table S57. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
ARID1A MUTATED	22	10	9
ARID1A WILD-TYPE	62	59	58

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00608 (Fisher's exact test), Q value = 1

Table S58. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
ARID1A MUTATED	11	4	26
ARID1A WILD-TYPE	61	50	68

Figure S41. Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S59. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
ARID1A MUTATED	9	13	8
ARID1A WILD-TYPE	47	56	43

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S60. Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
ARID1A MUTATED	4	19	7
ARID1A WILD-TYPE	38	65	43

'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.778 (Chi-square test), Q value = 1

Table S61. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
SMAD4 MUTATED	8	1	5	0	5	0
SMAD4 WILD-TYPE	95	17	30	7	50	1

'SMAD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.963 (Fisher's exact test), Q value = 1

Table S62. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
SMAD4 MUTATED	2	5	3	5
SMAD4 WILD-TYPE	25	46	41	48

'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.064 (Fisher's exact test), Q value = 1

Table S63. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
SMAD4 MUTATED	9	5	2
SMAD4 WILD-TYPE	53	63	65

'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S64. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
SMAD4 MUTATED	6	4	6
SMAD4 WILD-TYPE	75	32	74

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00387 (Chi-square test), Q value = 0.66

Table S65. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
SMAD4 MUTATED	5	1	7	4	0
SMAD4 WILD-TYPE	43	42	23	26	44

Figure S42. Get High-res Image Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S66. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
SMAD4 MUTATED	2	10	5
SMAD4 WILD-TYPE	51	67	60

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 1

Table S67. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
SMAD4 MUTATED	11	4	4
SMAD4 WILD-TYPE	73	65	63

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 1

Table S68. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
SMAD4 MUTATED	5	2	12
SMAD4 WILD-TYPE	67	52	82

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S69. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
SMAD4 MUTATED	4	8	3
SMAD4 WILD-TYPE	52	61	48

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.536 (Fisher's exact test), Q value = 1

Table S70. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
SMAD4 MUTATED	2	9	4
SMAD4 WILD-TYPE	40	75	46

'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.251 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
RHOA MUTATED	10	1	2	0	0	0
RHOA WILD-TYPE	93	17	33	7	55	1

'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
RHOA MUTATED	1	2	6	2
RHOA WILD-TYPE	26	49	38	51

'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
RHOA MUTATED	3	4	5
RHOA WILD-TYPE	59	64	62

'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
RHOA MUTATED	4	2	6
RHOA WILD-TYPE	77	34	74

'RHOA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.558 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
RHOA MUTATED	2	4	2	3	1
RHOA WILD-TYPE	46	39	28	27	43

'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0531 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
RHOA MUTATED	1	3	8
RHOA WILD-TYPE	52	74	57

'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.6

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
RHOA MUTATED	4	9	0
RHOA WILD-TYPE	80	60	67

Figure S43. Get High-res Image Gene #8: 'RHOA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0848 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
RHOA MUTATED	8	1	4
RHOA WILD-TYPE	64	53	90

'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.47

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
RHOA MUTATED	4	0	7
RHOA WILD-TYPE	52	69	44

Figure S44. Get High-res Image Gene #8: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
RHOA MUTATED	1	3	7
RHOA WILD-TYPE	41	81	43

Figure S45. Get High-res Image Gene #8: 'RHOA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'IRF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.67 (Chi-square 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	CLUS_6
ALL	103	18	35	7	55	1
IRF2 MUTATED	9	1	1	1	2	0
IRF2 WILD-TYPE	94	17	34	6	53	1

'IRF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.414 (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	CLUS_4
ALL	27	51	44	53
IRF2 MUTATED	1	5	1	2
IRF2 WILD-TYPE	26	46	43	51

'IRF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0641 (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	62	68	67
IRF2 MUTATED	8	2	3
IRF2 WILD-TYPE	54	66	64

'IRF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.764 (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
ALL	81	36	80
IRF2 MUTATED	6	3	4
IRF2 WILD-TYPE	75	33	76

'IRF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.21 (Chi-square 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	30	30	44
IRF2 MUTATED	6	2	1	1	1
IRF2 WILD-TYPE	42	41	29	29	43

'IRF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.632 (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
ALL	53	77	65
IRF2 MUTATED	2	6	3
IRF2 WILD-TYPE	51	71	62

'IRF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0301 (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	84	69	67
IRF2 MUTATED	10	1	3
IRF2 WILD-TYPE	74	68	64

Figure S46. Get High-res Image Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'IRF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0244 (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	72	54	94
IRF2 MUTATED	4	0	10
IRF2 WILD-TYPE	68	54	84

Figure S47. Get High-res Image Gene #9: 'IRF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IRF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.123 (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	56	69	51
IRF2 MUTATED	4	5	0
IRF2 WILD-TYPE	52	64	51

'IRF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0866 (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	42	84	50
IRF2 MUTATED	2	7	0
IRF2 WILD-TYPE	40	77	50

'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.189 (Chi-square test), Q value = 1

Table S91. Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
CDH1 MUTATED	12	1	3	1	0	0
CDH1 WILD-TYPE	91	17	32	6	55	1

'CDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S92. Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
CDH1 MUTATED	1	4	6	3
CDH1 WILD-TYPE	26	47	38	50

'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S93. Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
CDH1 MUTATED	4	8	6
CDH1 WILD-TYPE	58	60	61

'CDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S94. Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
CDH1 MUTATED	7	2	9
CDH1 WILD-TYPE	74	34	71

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.11 (Chi-square test), Q value = 1

Table S95. Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
CDH1 MUTATED	2	7	1	4	2
CDH1 WILD-TYPE	46	36	29	26	42

'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0575 (Fisher's exact test), Q value = 1

Table S96. Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
CDH1 MUTATED	1	6	9
CDH1 WILD-TYPE	52	71	56

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 1

Table S97. Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
CDH1 MUTATED	8	9	1
CDH1 WILD-TYPE	76	60	66

Figure S48. Get High-res Image Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0495 (Fisher's exact test), Q value = 1

Table S98. Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
CDH1 MUTATED	10	1	7
CDH1 WILD-TYPE	62	53	87

Figure S49. Get High-res Image Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S99. Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
CDH1 MUTATED	5	2	7
CDH1 WILD-TYPE	51	67	44

'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S100. Gene #10: 'CDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
CDH1 MUTATED	1	6	7
CDH1 WILD-TYPE	41	78	43

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0495 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
PTEN MUTATED	12	0	0	1	1	0
PTEN WILD-TYPE	91	18	35	6	54	1

Figure S50. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
PTEN MUTATED	4	4	0	1
PTEN WILD-TYPE	23	47	44	52

Figure S51. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.73

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
PTEN MUTATED	8	0	5
PTEN WILD-TYPE	54	68	62

Figure S52. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
PTEN MUTATED	10	2	1
PTEN WILD-TYPE	71	34	79

Figure S53. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000833 (Chi-square test), Q value = 0.15

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
PTEN MUTATED	10	1	0	2	1
PTEN WILD-TYPE	38	42	30	28	43

Figure S54. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
PTEN MUTATED	1	11	2
PTEN WILD-TYPE	52	66	63

Figure S55. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
PTEN MUTATED	9	2	3
PTEN WILD-TYPE	75	67	64

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
PTEN MUTATED	3	0	11
PTEN WILD-TYPE	69	54	83

Figure S56. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
PTEN MUTATED	5	3	1
PTEN WILD-TYPE	51	66	50

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
PTEN MUTATED	0	9	0
PTEN WILD-TYPE	42	75	50

Figure S57. Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.12 (Chi-square 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	CLUS_6
ALL	103	18	35	7	55	1
FBXW7 MUTATED	15	1	1	0	2	0
FBXW7 WILD-TYPE	88	17	34	7	53	1

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0221 (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	CLUS_4
ALL	27	51	44	53
FBXW7 MUTATED	1	10	2	2
FBXW7 WILD-TYPE	26	41	42	51

Figure S58. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.33

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
FBXW7 MUTATED	12	1	5
FBXW7 WILD-TYPE	50	67	62

Figure S59. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
FBXW7 MUTATED	11	5	2
FBXW7 WILD-TYPE	70	31	78

Figure S60. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00743 (Chi-square 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	30	30	44
FBXW7 MUTATED	10	1	1	2	2
FBXW7 WILD-TYPE	38	42	29	28	42

Figure S61. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
FBXW7 MUTATED	4	9	3
FBXW7 WILD-TYPE	49	68	62

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.155 (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	84	69	67
FBXW7 MUTATED	11	3	5
FBXW7 WILD-TYPE	73	66	62

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0696 (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	72	54	94
FBXW7 MUTATED	4	2	13
FBXW7 WILD-TYPE	68	52	81

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00949 (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	56	69	51
FBXW7 MUTATED	5	10	0
FBXW7 WILD-TYPE	51	59	51

Figure S62. 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 = 0.00256 (Fisher's exact test), Q value = 0.45

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
FBXW7 MUTATED	2	13	0
FBXW7 WILD-TYPE	40	71	50

Figure S63. Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'B2M MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0958 (Chi-square test), Q value = 1

Table S121. Gene #13: 'B2M MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
B2M MUTATED	8	0	0	0	0	0
B2M WILD-TYPE	95	18	35	7	55	1

'B2M MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 1

Table S122. Gene #13: 'B2M MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
B2M MUTATED	1	6	1	0
B2M WILD-TYPE	26	45	43	53

Figure S64. Get High-res Image Gene #13: 'B2M MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'B2M MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0861 (Fisher's exact test), Q value = 1

Table S123. Gene #13: 'B2M MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
B2M MUTATED	4	0	3
B2M WILD-TYPE	58	68	64

'B2M MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S124. Gene #13: 'B2M MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
B2M MUTATED	3	2	2
B2M WILD-TYPE	78	34	78

'B2M MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0513 (Chi-square test), Q value = 1

Table S125. Gene #13: 'B2M MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
B2M MUTATED	5	1	0	1	0
B2M WILD-TYPE	43	42	30	29	44

'B2M MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S126. Gene #13: 'B2M MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
B2M MUTATED	1	5	1
B2M WILD-TYPE	52	72	64

'B2M MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S127. Gene #13: 'B2M MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
B2M MUTATED	5	2	1
B2M WILD-TYPE	79	67	66

'B2M MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S128. Gene #13: 'B2M MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
B2M MUTATED	2	0	6
B2M WILD-TYPE	70	54	88

'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S129. Gene #13: 'B2M MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
B2M MUTATED	4	2	2
B2M WILD-TYPE	52	67	49

'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S130. Gene #13: 'B2M MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
B2M MUTATED	0	7	1
B2M WILD-TYPE	42	77	49

'FAM46D MUTATION STATUS' versus 'CN_CNMF'

P value = 0.661 (Chi-square test), Q value = 1

Table S131. Gene #14: 'FAM46D MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
FAM46D MUTATED	3	0	0	0	3	0
FAM46D WILD-TYPE	100	18	35	7	52	1

'FAM46D MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S132. Gene #14: 'FAM46D MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
FAM46D MUTATED	0	2	2	1
FAM46D WILD-TYPE	27	49	42	52

'FAM46D MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S133. Gene #14: 'FAM46D MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
FAM46D MUTATED	2	1	2
FAM46D WILD-TYPE	60	67	65

'FAM46D MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S134. Gene #14: 'FAM46D MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
FAM46D MUTATED	3	2	0
FAM46D WILD-TYPE	78	34	80

'FAM46D MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.103 (Chi-square test), Q value = 1

Table S135. Gene #14: 'FAM46D MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
FAM46D MUTATED	0	1	0	3	2
FAM46D WILD-TYPE	48	42	30	27	42

'FAM46D MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S136. Gene #14: 'FAM46D MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
FAM46D MUTATED	2	2	2
FAM46D WILD-TYPE	51	75	63

'FAM46D MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S137. Gene #14: 'FAM46D MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
FAM46D MUTATED	3	1	2
FAM46D WILD-TYPE	81	68	65

'FAM46D MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S138. Gene #14: 'FAM46D MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
FAM46D MUTATED	1	2	3
FAM46D WILD-TYPE	71	52	91

'FAM46D MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S139. Gene #14: 'FAM46D MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
FAM46D MUTATED	2	2	1
FAM46D WILD-TYPE	54	67	50

'FAM46D MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S140. Gene #14: 'FAM46D MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
FAM46D MUTATED	2	2	1
FAM46D WILD-TYPE	40	82	49

'RNF43 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.838 (Chi-square test), Q value = 1

Table S141. Gene #15: 'RNF43 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
RNF43 MUTATED	6	1	1	0	1	0
RNF43 WILD-TYPE	97	17	34	7	54	1

'RNF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S142. Gene #15: 'RNF43 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
RNF43 MUTATED	0	3	2	1
RNF43 WILD-TYPE	27	48	42	52

'RNF43 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.577 (Fisher's exact test), Q value = 1

Table S143. Gene #15: 'RNF43 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
RNF43 MUTATED	4	2	3
RNF43 WILD-TYPE	58	66	64

'RNF43 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.113 (Fisher's exact test), Q value = 1

Table S144. Gene #15: 'RNF43 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
RNF43 MUTATED	5	3	1
RNF43 WILD-TYPE	76	33	79

'RNF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.273 (Chi-square test), Q value = 1

Table S145. Gene #15: 'RNF43 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
RNF43 MUTATED	2	1	0	3	1
RNF43 WILD-TYPE	46	42	30	27	43

'RNF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S146. Gene #15: 'RNF43 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
RNF43 MUTATED	1	3	3
RNF43 WILD-TYPE	52	74	62

'RNF43 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S147. Gene #15: 'RNF43 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
RNF43 MUTATED	5	2	2
RNF43 WILD-TYPE	79	67	65

'RNF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 1

Table S148. Gene #15: 'RNF43 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
RNF43 MUTATED	3	0	6
RNF43 WILD-TYPE	69	54	88

'RNF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S149. Gene #15: 'RNF43 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
RNF43 MUTATED	2	3	1
RNF43 WILD-TYPE	54	66	50

'RNF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S150. Gene #15: 'RNF43 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
RNF43 MUTATED	0	5	1
RNF43 WILD-TYPE	42	79	49

'APC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.875 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
APC MUTATED	16	3	3	1	10	0
APC WILD-TYPE	87	15	32	6	45	1

'APC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
APC MUTATED	1	12	2	7
APC WILD-TYPE	26	39	42	46

Figure S65. Get High-res Image Gene #16: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0755 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
APC MUTATED	13	5	11
APC WILD-TYPE	49	63	56

'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0909 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
APC MUTATED	17	5	7
APC WILD-TYPE	64	31	73

'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.302 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
APC MUTATED	9	2	5	6	7
APC WILD-TYPE	39	41	25	24	37

'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.44

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
APC MUTATED	5	20	4
APC WILD-TYPE	48	57	61

Figure S66. Get High-res Image Gene #16: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
APC MUTATED	19	4	10
APC WILD-TYPE	65	65	57

Figure S67. Get High-res Image Gene #16: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00499 (Fisher's exact test), Q value = 0.83

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
APC MUTATED	4	7	22
APC WILD-TYPE	68	47	72

Figure S68. Get High-res Image Gene #16: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.06 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
APC MUTATED	8	12	2
APC WILD-TYPE	48	57	49

'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00989 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
APC MUTATED	5	16	1
APC WILD-TYPE	37	68	49

Figure S69. Get High-res Image Gene #16: 'APC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'WSB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.417 (Chi-square test), Q value = 1

Table S161. Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
WSB2 MUTATED	6	0	1	0	0	0
WSB2 WILD-TYPE	97	18	34	7	55	1

'WSB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 1

Table S162. Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
WSB2 MUTATED	1	4	1	0
WSB2 WILD-TYPE	26	47	43	53

'WSB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0861 (Fisher's exact test), Q value = 1

Table S163. Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
WSB2 MUTATED	4	0	3
WSB2 WILD-TYPE	58	68	64

'WSB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0629 (Fisher's exact test), Q value = 1

Table S164. Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
WSB2 MUTATED	5	2	0
WSB2 WILD-TYPE	76	34	80

'WSB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S165. Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
WSB2 MUTATED	4	0	1	2	0
WSB2 WILD-TYPE	44	43	29	28	44

'WSB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 1

Table S166. Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
WSB2 MUTATED	1	6	0
WSB2 WILD-TYPE	52	71	65

Figure S70. Get High-res Image Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'WSB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.26

Table S167. Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
WSB2 MUTATED	7	0	0
WSB2 WILD-TYPE	77	69	67

Figure S71. Get High-res Image Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'WSB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.065 (Fisher's exact test), Q value = 1

Table S168. Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
WSB2 MUTATED	1	0	6
WSB2 WILD-TYPE	71	54	88

'WSB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S169. Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
WSB2 MUTATED	4	2	0
WSB2 WILD-TYPE	52	67	51

'WSB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0464 (Fisher's exact test), Q value = 1

Table S170. Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
WSB2 MUTATED	0	6	0
WSB2 WILD-TYPE	42	78	50

Figure S72. Get High-res Image Gene #17: 'WSB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MAP2K7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.319 (Chi-square test), Q value = 1

Table S171. Gene #18: 'MAP2K7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
MAP2K7 MUTATED	10	0	2	1	1	0
MAP2K7 WILD-TYPE	93	18	33	6	54	1

'MAP2K7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0984 (Fisher's exact test), Q value = 1

Table S172. Gene #18: 'MAP2K7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
MAP2K7 MUTATED	1	7	2	1
MAP2K7 WILD-TYPE	26	44	42	52

'MAP2K7 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S173. Gene #18: 'MAP2K7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
MAP2K7 MUTATED	3	5	5
MAP2K7 WILD-TYPE	59	63	62

'MAP2K7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.764 (Fisher's exact test), Q value = 1

Table S174. Gene #18: 'MAP2K7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
MAP2K7 MUTATED	6	3	4
MAP2K7 WILD-TYPE	75	33	76

'MAP2K7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0501 (Chi-square test), Q value = 1

Table S175. Gene #18: 'MAP2K7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
MAP2K7 MUTATED	7	3	1	0	1
MAP2K7 WILD-TYPE	41	40	29	30	43

'MAP2K7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S176. Gene #18: 'MAP2K7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
MAP2K7 MUTATED	2	7	3
MAP2K7 WILD-TYPE	51	70	62

'MAP2K7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 1

Table S177. Gene #18: 'MAP2K7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
MAP2K7 MUTATED	9	2	3
MAP2K7 WILD-TYPE	75	67	64

'MAP2K7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0964 (Fisher's exact test), Q value = 1

Table S178. Gene #18: 'MAP2K7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
MAP2K7 MUTATED	3	1	10
MAP2K7 WILD-TYPE	69	53	84

'MAP2K7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S179. Gene #18: 'MAP2K7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
MAP2K7 MUTATED	4	5	2
MAP2K7 WILD-TYPE	52	64	49

'MAP2K7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S180. Gene #18: 'MAP2K7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
MAP2K7 MUTATED	1	8	2
MAP2K7 WILD-TYPE	41	76	48

'TRPS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.92 (Chi-square test), Q value = 1

Table S181. Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
TRPS1 MUTATED	15	2	3	1	9	0
TRPS1 WILD-TYPE	88	16	32	6	46	1

'TRPS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0435 (Fisher's exact test), Q value = 1

Table S182. Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
TRPS1 MUTATED	2	12	2	6
TRPS1 WILD-TYPE	25	39	42	47

Figure S73. Get High-res Image Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TRPS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 1

Table S183. Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
TRPS1 MUTATED	12	5	11
TRPS1 WILD-TYPE	50	63	56

'TRPS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.118 (Fisher's exact test), Q value = 1

Table S184. Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
TRPS1 MUTATED	13	8	7
TRPS1 WILD-TYPE	68	28	73

'TRPS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0233 (Chi-square test), Q value = 1

Table S185. Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
TRPS1 MUTATED	12	2	1	4	7
TRPS1 WILD-TYPE	36	41	29	26	37

Figure S74. Get High-res Image Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TRPS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S186. Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
TRPS1 MUTATED	9	12	5
TRPS1 WILD-TYPE	44	65	60

'TRPS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S187. Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
TRPS1 MUTATED	13	6	11
TRPS1 WILD-TYPE	71	63	56

'TRPS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S188. Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
TRPS1 MUTATED	8	7	15
TRPS1 WILD-TYPE	64	47	79

'TRPS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S189. Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
TRPS1 MUTATED	8	10	4
TRPS1 WILD-TYPE	48	59	47

'TRPS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.118 (Fisher's exact test), Q value = 1

Table S190. Gene #19: 'TRPS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
TRPS1 MUTATED	4	15	3
TRPS1 WILD-TYPE	38	69	47

'C13ORF33 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.344 (Chi-square test), Q value = 1

Table S191. Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	103	18	35	7	55	1
C13ORF33 MUTATED	3	1	1	1	0	0
C13ORF33 WILD-TYPE	100	17	34	6	55	1

'C13ORF33 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 1

Table S192. Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
C13ORF33 MUTATED	1	5	0	0
C13ORF33 WILD-TYPE	26	46	44	53

Figure S75. Get High-res Image Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'C13ORF33 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 1

Table S193. Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	62	68	67
C13ORF33 MUTATED	5	1	0
C13ORF33 WILD-TYPE	57	67	67

Figure S76. Get High-res Image Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'C13ORF33 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0861 (Fisher's exact test), Q value = 1

Table S194. Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	81	36	80
C13ORF33 MUTATED	4	2	0
C13ORF33 WILD-TYPE	77	34	80

'C13ORF33 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.141 (Chi-square test), Q value = 1

Table S195. Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	48	43	30	30	44
C13ORF33 MUTATED	3	0	1	0	0
C13ORF33 WILD-TYPE	45	43	29	30	44

'C13ORF33 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.46 (Fisher's exact test), Q value = 1

Table S196. Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	77	65
C13ORF33 MUTATED	0	3	1
C13ORF33 WILD-TYPE	53	74	64

'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 1

Table S197. Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	84	69	67
C13ORF33 MUTATED	1	3	2
C13ORF33 WILD-TYPE	83	66	65

'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.44 (Fisher's exact test), Q value = 1

Table S198. Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	54	94
C13ORF33 MUTATED	3	0	3
C13ORF33 WILD-TYPE	69	54	91

'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 1

Table S199. Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	69	51
C13ORF33 MUTATED	0	4	2
C13ORF33 WILD-TYPE	56	65	49

'C13ORF33 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S200. Gene #20: 'C13ORF33 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	84	50
C13ORF33 MUTATED	0	5	1
C13ORF33 WILD-TYPE	42	79	49

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = STAD-TP.transferedmergedcluster.txt
Number of patients = 220
Number of significantly mutated genes = 20
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[2] 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)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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