Correlation between gene mutation status and molecular subtypes

Overview

Introduction

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

Summary

Testing the association between mutation status of 24 genes and 10 molecular subtypes across 223 patients, 9 significant findings detected with P value < 0.05 and Q value < 0.25.

FBXW7 mutation correlated to 'CN_CNMF'.
BRAF mutation correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'CN_CNMF'.
KRAS mutation correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.
TP53 mutation correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.
PIK3CA mutation correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 24 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, 9 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	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
BRAF	22 (10%)	201	2.84e-06 (0.000594)	1.41e-07 (2.97e-05)	0.000332 (0.0678)		0.482 (1.00)	0.304 (1.00)	0.473 (1.00)	0.277 (1.00)	1 (1.00)	0.684 (1.00)
KRAS	96 (43%)	127	7.86e-05 (0.0162)	4.23e-05 (0.00877)	0.322 (1.00)	0.107 (1.00)	0.565 (1.00)	1 (1.00)	0.00165 (0.331)	0.716 (1.00)	0.0218 (1.00)	0.0431 (1.00)
TP53	119 (53%)	104	0.00206 (0.412)	0.000493 (0.1)	1.15e-10 (2.42e-08)		0.562 (1.00)	0.755 (1.00)	0.0253 (1.00)	0.736 (1.00)	0.0307 (1.00)	0.567 (1.00)
FBXW7	38 (17%)	185	0.0626 (1.00)	0.0455 (1.00)	2.6e-05 (0.00541)		0.0122 (1.00)	0.0362 (1.00)	0.00143 (0.289)	0.442 (1.00)	0.416 (1.00)	0.156 (1.00)
PIK3CA	33 (15%)	190	0.208 (1.00)	0.569 (1.00)	0.00032 (0.0655)		0.0673 (1.00)	0.129 (1.00)	0.0826 (1.00)	1 (1.00)	0.165 (1.00)	1 (1.00)
APC	160 (72%)	63	0.00773 (1.00)	0.0271 (1.00)	0.119 (1.00)		0.466 (1.00)	0.461 (1.00)	0.381 (1.00)	0.187 (1.00)	0.34 (1.00)	0.837 (1.00)
NRAS	20 (9%)	203	0.0478 (1.00)	0.127 (1.00)	0.199 (1.00)		0.909 (1.00)	0.474 (1.00)	0.191 (1.00)	1 (1.00)	0.268 (1.00)	1 (1.00)
SMAD4	26 (12%)	197	0.0322 (1.00)	0.289 (1.00)	0.0646 (1.00)		0.827 (1.00)	0.339 (1.00)	0.589 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
FAM123B	25 (11%)	198	0.0787 (1.00)	0.0924 (1.00)	0.00912 (1.00)		0.345 (1.00)	0.588 (1.00)	0.0494 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
SMAD2	15 (7%)	208	0.134 (1.00)	0.518 (1.00)	0.161 (1.00)		0.592 (1.00)	0.133 (1.00)	0.71 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
TCF7L2	18 (8%)	205	1 (1.00)	0.416 (1.00)	0.00239 (0.477)		0.836 (1.00)	0.896 (1.00)	0.353 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
ACVR2A	9 (4%)	214	0.00717 (1.00)	0.184 (1.00)	0.0236 (1.00)		0.0952 (1.00)	0.469 (1.00)	1 (1.00)	1 (1.00)	0.173 (1.00)	1 (1.00)
SOX9	10 (4%)	213	0.129 (1.00)	0.123 (1.00)	0.00856 (1.00)		0.189 (1.00)	0.694 (1.00)	0.773 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
ELF3	6 (3%)	217	0.363 (1.00)	0.811 (1.00)	0.273 (1.00)		0.544 (1.00)	0.436 (1.00)	0.0496 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
CRTC1	6 (3%)	217	0.123 (1.00)	0.165 (1.00)	0.273 (1.00)		0.175 (1.00)	0.482 (1.00)	0.775 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
TNFRSF10C	6 (3%)	217	0.317 (1.00)	0.287 (1.00)	0.707 (1.00)		0.278 (1.00)	0.378 (1.00)	0.223 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
KIAA1804	15 (7%)	208	0.271 (1.00)	0.394 (1.00)	0.028 (1.00)		0.506 (1.00)	0.474 (1.00)	0.71 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
KRTAP5-5	4 (2%)	219	0.327 (1.00)	0.482 (1.00)	0.839 (1.00)		0.385 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
PTEN	7 (3%)	216	0.0276 (1.00)	0.337 (1.00)	0.07 (1.00)		0.544 (1.00)	0.436 (1.00)	0.148 (1.00)	1 (1.00)	0.347 (1.00)	0.298 (1.00)
ACOT4	3 (1%)	220	0.255 (1.00)	0.49 (1.00)	0.792 (1.00)				0.523 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
MYO1B	13 (6%)	210	0.00868 (1.00)	0.00887 (1.00)	0.00479 (0.949)		0.0215 (1.00)	0.469 (1.00)	0.175 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
PCBP1	6 (3%)	217	0.234 (1.00)	0.811 (1.00)	0.795 (1.00)		0.648 (1.00)	0.482 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
GGT1	3 (1%)	220			0.162 (1.00)				0.523 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
ACVR1B	14 (6%)	209	0.374 (1.00)	0.316 (1.00)	0.0986 (1.00)		0.735 (1.00)	0.376 (1.00)	0.86 (1.00)	1 (1.00)	0.581 (1.00)	1 (1.00)

'APC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00773 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
APC MUTATED	21	46	50	30
APC WILD-TYPE	21	11	17	9

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

'APC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
APC MUTATED	32	35	35	45
APC WILD-TYPE	8	13	26	11

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

'APC MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
APC MUTATED	54	53	47	3
APC WILD-TYPE	15	32	15	1

'APC MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S4. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
APC MUTATED	32	44	17	18
APC WILD-TYPE	8	23	7	8

'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.461 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
APC MUTATED	16	75	15	5
APC WILD-TYPE	4	34	4	4

'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
APC MUTATED	5	20	7	124
APC WILD-TYPE	3	6	6	45

'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S7. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
APC MUTATED	155	1	0
APC WILD-TYPE	58	1	1

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
APC MUTATED	3	5	141
APC WILD-TYPE	0	4	53

'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S9. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
APC MUTATED	6	1	142
APC WILD-TYPE	2	1	54

'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0626 (Fisher's exact test), Q value = 1

Table S10. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
FBXW7 MUTATED	11	6	7	9
FBXW7 WILD-TYPE	31	51	60	30

'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
FBXW7 MUTATED	4	5	17	7
FBXW7 WILD-TYPE	36	43	44	49

Figure S3. Get High-res Image Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 2.6e-05 (Fisher's exact test), Q value = 0.0054

Table S12. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
FBXW7 MUTATED	2	26	9	1
FBXW7 WILD-TYPE	67	59	53	3

Figure S4. Get High-res Image Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
FBXW7 MUTATED	7	9	2	11
FBXW7 WILD-TYPE	33	58	22	15

Figure S5. Get High-res Image Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
FBXW7 MUTATED	3	18	8	0
FBXW7 WILD-TYPE	17	91	11	9

Figure S6. Get High-res Image Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.29

Table S15. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
FBXW7 MUTATED	0	12	1	25
FBXW7 WILD-TYPE	8	14	12	144

Figure S7. Get High-res Image Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S16. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
FBXW7 MUTATED	37	1	0
FBXW7 WILD-TYPE	176	1	1

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S17. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
FBXW7 MUTATED	0	0	36
FBXW7 WILD-TYPE	3	9	158

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S18. Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
FBXW7 MUTATED	0	1	35
FBXW7 WILD-TYPE	8	1	161

'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 1

Table S19. Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
NRAS MUTATED	0	8	6	5
NRAS WILD-TYPE	42	49	61	34

Figure S8. Get High-res Image Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S20. Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
NRAS MUTATED	1	8	4	6
NRAS WILD-TYPE	39	40	57	50

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
NRAS MUTATED	9	9	2	0
NRAS WILD-TYPE	60	76	60	4

'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.909 (Fisher's exact test), Q value = 1

Table S22. Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
NRAS MUTATED	3	7	1	2
NRAS WILD-TYPE	37	60	23	24

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.474 (Fisher's exact test), Q value = 1

Table S23. Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
NRAS MUTATED	0	10	2	1
NRAS WILD-TYPE	20	99	17	8

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
NRAS MUTATED	0	5	0	14
NRAS WILD-TYPE	8	21	13	155

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S25. Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
NRAS MUTATED	19	0	0
NRAS WILD-TYPE	194	2	1

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
NRAS MUTATED	1	0	17
NRAS WILD-TYPE	2	9	177

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S27. Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
NRAS MUTATED	0	0	18
NRAS WILD-TYPE	8	2	178

'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.00059

Table S28. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
BRAF MUTATED	13	1	1	5
BRAF WILD-TYPE	29	56	66	34

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

'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.41e-07 (Fisher's exact test), Q value = 3e-05

Table S29. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
BRAF MUTATED	1	0	18	1
BRAF WILD-TYPE	39	48	43	55

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

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000332 (Fisher's exact test), Q value = 0.068

Table S30. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
BRAF MUTATED	1	18	3	0
BRAF WILD-TYPE	68	67	59	4

Figure S11. Get High-res Image Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S31. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
BRAF MUTATED	3	4	4	2
BRAF WILD-TYPE	37	63	20	24

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S32. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
BRAF MUTATED	1	8	2	2
BRAF WILD-TYPE	19	101	17	7

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.473 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
BRAF MUTATED	1	4	0	17
BRAF WILD-TYPE	7	22	13	152

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S34. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
BRAF MUTATED	21	1	0
BRAF WILD-TYPE	192	1	1

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S35. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
BRAF MUTATED	0	1	21
BRAF WILD-TYPE	3	8	173

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.684 (Fisher's exact test), Q value = 1

Table S36. Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
BRAF MUTATED	0	0	22
BRAF WILD-TYPE	8	2	174

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 7.86e-05 (Fisher's exact test), Q value = 0.016

Table S37. Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
KRAS MUTATED	13	14	31	27
KRAS WILD-TYPE	29	43	36	12

Figure S12. Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 4.23e-05 (Fisher's exact test), Q value = 0.0088

Table S38. Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
KRAS MUTATED	10	33	26	16
KRAS WILD-TYPE	30	15	35	40

Figure S13. Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S39. Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
KRAS MUTATED	25	40	27	3
KRAS WILD-TYPE	44	45	35	1

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S40. Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	5	2	1
KRAS MUTATED	1	2	0
KRAS WILD-TYPE	4	0	1

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S41. Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
KRAS MUTATED	16	34	9	13
KRAS WILD-TYPE	24	33	15	13

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S42. Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
KRAS MUTATED	9	50	9	4
KRAS WILD-TYPE	11	59	10	5

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.33

Table S43. Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
KRAS MUTATED	4	19	2	66
KRAS WILD-TYPE	4	7	11	103

Figure S14. Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.716 (Fisher's exact test), Q value = 1

Table S44. Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
KRAS MUTATED	89	1	1
KRAS WILD-TYPE	124	1	0

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 1

Table S45. Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
KRAS MUTATED	0	7	79
KRAS WILD-TYPE	3	2	115

Figure S15. Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0431 (Fisher's exact test), Q value = 1

Table S46. Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
KRAS MUTATED	1	2	83
KRAS WILD-TYPE	7	0	113

Figure S16. Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.41

Table S47. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
TP53 MUTATED	17	40	39	14
TP53 WILD-TYPE	25	17	28	25

Figure S17. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000493 (Fisher's exact test), Q value = 0.1

Table S48. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
TP53 MUTATED	30	19	25	36
TP53 WILD-TYPE	10	29	36	20

Figure S18. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.15e-10 (Fisher's exact test), Q value = 2.4e-08

Table S49. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
TP53 MUTATED	55	23	38	1
TP53 WILD-TYPE	14	62	24	3

Figure S19. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S50. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
TP53 MUTATED	18	34	15	12
TP53 WILD-TYPE	22	33	9	14

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
TP53 MUTATED	8	57	9	5
TP53 WILD-TYPE	12	52	10	4

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 1

Table S52. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
TP53 MUTATED	3	7	8	96
TP53 WILD-TYPE	5	19	5	73

Figure S20. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.736 (Fisher's exact test), Q value = 1

Table S53. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
TP53 MUTATED	113	1	0
TP53 WILD-TYPE	100	1	1

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 1

Table S54. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
TP53 MUTATED	3	2	106
TP53 WILD-TYPE	0	7	88

Figure S21. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S55. Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
TP53 MUTATED	6	1	104
TP53 WILD-TYPE	2	1	92

'SMAD4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 1

Table S56. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
SMAD4 MUTATED	7	4	4	9
SMAD4 WILD-TYPE	35	53	63	30

Figure S22. Get High-res Image Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SMAD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 1

Table S57. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
SMAD4 MUTATED	5	6	10	3
SMAD4 WILD-TYPE	35	42	51	53

'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0646 (Fisher's exact test), Q value = 1

Table S58. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
SMAD4 MUTATED	3	15	8	0
SMAD4 WILD-TYPE	66	70	54	4

'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S59. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
SMAD4 MUTATED	4	10	4	3
SMAD4 WILD-TYPE	36	57	20	23

'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S60. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
SMAD4 MUTATED	2	14	2	3
SMAD4 WILD-TYPE	18	95	17	6

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.589 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
SMAD4 MUTATED	1	4	0	20
SMAD4 WILD-TYPE	7	22	13	149

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S62. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
SMAD4 MUTATED	25	0	0
SMAD4 WILD-TYPE	188	2	1

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S63. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
SMAD4 MUTATED	0	1	24
SMAD4 WILD-TYPE	3	8	170

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S64. Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
SMAD4 MUTATED	1	0	24
SMAD4 WILD-TYPE	7	2	172

'FAM123B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0787 (Fisher's exact test), Q value = 1

Table S65. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
FAM123B MUTATED	9	5	4	6
FAM123B WILD-TYPE	33	52	63	33

'FAM123B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0924 (Fisher's exact test), Q value = 1

Table S66. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
FAM123B MUTATED	2	3	12	7
FAM123B WILD-TYPE	38	45	49	49

'FAM123B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00912 (Fisher's exact test), Q value = 1

Table S67. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
FAM123B MUTATED	5	17	2	0
FAM123B WILD-TYPE	64	68	60	4

Figure S23. Get High-res Image Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FAM123B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S68. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
FAM123B MUTATED	2	7	2	5
FAM123B WILD-TYPE	38	60	22	21

'FAM123B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S69. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
FAM123B MUTATED	1	12	3	0
FAM123B WILD-TYPE	19	97	16	9

'FAM123B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 1

Table S70. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
FAM123B MUTATED	1	7	0	17
FAM123B WILD-TYPE	7	19	13	152

Figure S24. Get High-res Image Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FAM123B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S71. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
FAM123B MUTATED	25	0	0
FAM123B WILD-TYPE	188	2	1

'FAM123B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S72. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
FAM123B MUTATED	0	1	23
FAM123B WILD-TYPE	3	8	171

'FAM123B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S73. Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
FAM123B MUTATED	1	0	23
FAM123B WILD-TYPE	7	2	173

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S74. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PIK3CA MUTATED	8	4	7	7
PIK3CA WILD-TYPE	34	53	60	32

'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S75. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
PIK3CA MUTATED	3	7	10	6
PIK3CA WILD-TYPE	37	41	51	50

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.066

Table S76. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
PIK3CA MUTATED	4	23	4	1
PIK3CA WILD-TYPE	65	62	58	3

Figure S25. Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 1

Table S77. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
PIK3CA MUTATED	11	9	1	6
PIK3CA WILD-TYPE	29	58	23	20

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 1

Table S78. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
PIK3CA MUTATED	6	16	5	0
PIK3CA WILD-TYPE	14	93	14	9

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0826 (Fisher's exact test), Q value = 1

Table S79. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
PIK3CA MUTATED	2	7	0	23
PIK3CA WILD-TYPE	6	19	13	146

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S80. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
PIK3CA MUTATED	32	0	0
PIK3CA WILD-TYPE	181	2	1

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 1

Table S81. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PIK3CA MUTATED	0	3	26
PIK3CA WILD-TYPE	3	6	168

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S82. Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
PIK3CA MUTATED	1	0	28
PIK3CA WILD-TYPE	7	2	168

'SMAD2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S83. Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
SMAD2 MUTATED	4	2	2	5
SMAD2 WILD-TYPE	38	55	65	34

'SMAD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S84. Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
SMAD2 MUTATED	3	2	6	2
SMAD2 WILD-TYPE	37	46	55	54

'SMAD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S85. Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
SMAD2 MUTATED	2	10	3	0
SMAD2 WILD-TYPE	67	75	59	4

'SMAD2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S86. Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
SMAD2 MUTATED	2	3	2	3
SMAD2 WILD-TYPE	38	64	22	23

'SMAD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 1

Table S87. Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
SMAD2 MUTATED	0	6	3	1
SMAD2 WILD-TYPE	20	103	16	8

'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 1

Table S88. Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
SMAD2 MUTATED	0	3	0	12
SMAD2 WILD-TYPE	8	23	13	157

'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S89. Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
SMAD2 MUTATED	15	0	0
SMAD2 WILD-TYPE	198	2	1

'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S90. Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
SMAD2 MUTATED	0	0	14
SMAD2 WILD-TYPE	3	9	180

'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S91. Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
SMAD2 MUTATED	0	0	14
SMAD2 WILD-TYPE	8	2	182

'TCF7L2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S92. Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
TCF7L2 MUTATED	3	4	5	3
TCF7L2 WILD-TYPE	39	53	62	36

'TCF7L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S93. Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
TCF7L2 MUTATED	4	5	2	4
TCF7L2 WILD-TYPE	36	43	59	52

'TCF7L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.48

Table S94. Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
TCF7L2 MUTATED	7	6	2	3
TCF7L2 WILD-TYPE	62	79	60	1

Figure S26. Get High-res Image Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TCF7L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S95. Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
TCF7L2 MUTATED	3	5	1	3
TCF7L2 WILD-TYPE	37	62	23	23

'TCF7L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S96. Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
TCF7L2 MUTATED	1	9	2	0
TCF7L2 WILD-TYPE	19	100	17	9

'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S97. Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
TCF7L2 MUTATED	0	0	1	16
TCF7L2 WILD-TYPE	8	26	12	153

'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S98. Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
TCF7L2 MUTATED	17	0	0
TCF7L2 WILD-TYPE	196	2	1

'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S99. Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
TCF7L2 MUTATED	0	0	15
TCF7L2 WILD-TYPE	3	9	179

'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S100. Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
TCF7L2 MUTATED	0	0	15
TCF7L2 WILD-TYPE	8	2	181

'ACVR2A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00717 (Fisher's exact test), Q value = 1

Table S101. Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ACVR2A MUTATED	5	1	0	2
ACVR2A WILD-TYPE	37	56	67	37

Figure S27. Get High-res Image Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ACVR2A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.184 (Fisher's exact test), Q value = 1

Table S102. Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
ACVR2A MUTATED	1	0	5	2
ACVR2A WILD-TYPE	39	48	56	54

'ACVR2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 1

Table S103. Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
ACVR2A MUTATED	1	8	0	0
ACVR2A WILD-TYPE	68	77	62	4

Figure S28. Get High-res Image Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ACVR2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0952 (Fisher's exact test), Q value = 1

Table S104. Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ACVR2A MUTATED	0	4	0	3
ACVR2A WILD-TYPE	40	63	24	23

'ACVR2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S105. Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
ACVR2A MUTATED	0	5	2	0
ACVR2A WILD-TYPE	20	104	17	9

'ACVR2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S106. Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
ACVR2A MUTATED	0	1	0	8
ACVR2A WILD-TYPE	8	25	13	161

'ACVR2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S107. Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
ACVR2A MUTATED	9	0	0
ACVR2A WILD-TYPE	204	2	1

'ACVR2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S108. Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ACVR2A MUTATED	1	0	8
ACVR2A WILD-TYPE	2	9	186

'ACVR2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S109. Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
ACVR2A MUTATED	0	0	9
ACVR2A WILD-TYPE	8	2	187

'SOX9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 1

Table S110. Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
SOX9 MUTATED	2	1	6	0
SOX9 WILD-TYPE	40	56	61	39

'SOX9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S111. Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
SOX9 MUTATED	2	5	1	1
SOX9 WILD-TYPE	38	43	60	55

'SOX9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 1

Table S112. Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
SOX9 MUTATED	0	9	1	0
SOX9 WILD-TYPE	69	76	61	4

Figure S29. Get High-res Image Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SOX9 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S113. Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
SOX9 MUTATED	0	3	0	2
SOX9 WILD-TYPE	40	64	24	24

'SOX9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S114. Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
SOX9 MUTATED	0	4	1	0
SOX9 WILD-TYPE	20	105	18	9

'SOX9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.773 (Fisher's exact test), Q value = 1

Table S115. Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
SOX9 MUTATED	0	2	0	8
SOX9 WILD-TYPE	8	24	13	161

'SOX9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S116. Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
SOX9 MUTATED	10	0	0
SOX9 WILD-TYPE	203	2	1

'SOX9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117. Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
SOX9 MUTATED	0	0	10
SOX9 WILD-TYPE	3	9	184

'SOX9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118. Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
SOX9 MUTATED	0	0	10
SOX9 WILD-TYPE	8	2	186

'ELF3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 1

Table S119. Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ELF3 MUTATED	1	0	3	2
ELF3 WILD-TYPE	41	57	64	37

'ELF3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S120. Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
ELF3 MUTATED	2	1	2	1
ELF3 WILD-TYPE	38	47	59	55

'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 1

Table S121. Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
ELF3 MUTATED	0	3	3	0
ELF3 WILD-TYPE	69	82	59	4

'ELF3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S122. Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ELF3 MUTATED	2	1	0	1
ELF3 WILD-TYPE	38	66	24	25

'ELF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S123. Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
ELF3 MUTATED	1	2	1	0
ELF3 WILD-TYPE	19	107	18	9

'ELF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S124. Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
ELF3 MUTATED	1	2	0	2
ELF3 WILD-TYPE	7	24	13	167

Figure S30. Get High-res Image Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S125. Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
ELF3 MUTATED	5	0	0
ELF3 WILD-TYPE	208	2	1

'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S126. Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ELF3 MUTATED	0	0	6
ELF3 WILD-TYPE	3	9	188

'ELF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S127. Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
ELF3 MUTATED	0	0	6
ELF3 WILD-TYPE	8	2	190

'CRTC1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S128. Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
CRTC1 MUTATED	2	0	4	0
CRTC1 WILD-TYPE	40	57	63	39

'CRTC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.165 (Fisher's exact test), Q value = 1

Table S129. Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
CRTC1 MUTATED	3	1	2	0
CRTC1 WILD-TYPE	37	47	59	56

'CRTC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 1

Table S130. Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
CRTC1 MUTATED	0	3	3	0
CRTC1 WILD-TYPE	69	82	59	4

'CRTC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 1

Table S131. Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
CRTC1 MUTATED	2	0	0	1
CRTC1 WILD-TYPE	38	67	24	25

'CRTC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S132. Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
CRTC1 MUTATED	0	2	1	0
CRTC1 WILD-TYPE	20	107	18	9

'CRTC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S133. Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
CRTC1 MUTATED	0	1	0	5
CRTC1 WILD-TYPE	8	25	13	164

'CRTC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S134. Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
CRTC1 MUTATED	6	0	0
CRTC1 WILD-TYPE	207	2	1

'CRTC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S135. Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
CRTC1 MUTATED	0	0	6
CRTC1 WILD-TYPE	3	9	188

'CRTC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S136. Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
CRTC1 MUTATED	0	0	6
CRTC1 WILD-TYPE	8	2	190

'TNFRSF10C MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S137. Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
TNFRSF10C MUTATED	3	1	2	0
TNFRSF10C WILD-TYPE	39	56	65	39

'TNFRSF10C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 1

Table S138. Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
TNFRSF10C MUTATED	1	3	2	0
TNFRSF10C WILD-TYPE	39	45	59	56

'TNFRSF10C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.707 (Fisher's exact test), Q value = 1

Table S139. Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
TNFRSF10C MUTATED	3	2	1	0
TNFRSF10C WILD-TYPE	66	83	61	4

'TNFRSF10C MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S140. Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
TNFRSF10C MUTATED	3	1	0	1
TNFRSF10C WILD-TYPE	37	66	24	25

'TNFRSF10C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S141. Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
TNFRSF10C MUTATED	2	3	0	0
TNFRSF10C WILD-TYPE	18	106	19	9

'TNFRSF10C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 1

Table S142. Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
TNFRSF10C MUTATED	1	1	0	4
TNFRSF10C WILD-TYPE	7	25	13	165

'TNFRSF10C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S143. Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
TNFRSF10C MUTATED	6	0	0
TNFRSF10C WILD-TYPE	207	2	1

'TNFRSF10C MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S144. Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
TNFRSF10C MUTATED	0	0	6
TNFRSF10C WILD-TYPE	3	9	188

'TNFRSF10C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S145. Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
TNFRSF10C MUTATED	0	0	6
TNFRSF10C WILD-TYPE	8	2	190

'KIAA1804 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 1

Table S146. Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
KIAA1804 MUTATED	3	1	6	4
KIAA1804 WILD-TYPE	39	56	61	35

'KIAA1804 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S147. Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
KIAA1804 MUTATED	4	2	6	2
KIAA1804 WILD-TYPE	36	46	55	54

'KIAA1804 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 1

Table S148. Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
KIAA1804 MUTATED	3	10	1	1
KIAA1804 WILD-TYPE	66	75	61	3

Figure S31. Get High-res Image Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KIAA1804 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S149. Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
KIAA1804 MUTATED	2	6	1	4
KIAA1804 WILD-TYPE	38	61	23	22

'KIAA1804 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.474 (Fisher's exact test), Q value = 1

Table S150. Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
KIAA1804 MUTATED	0	11	2	0
KIAA1804 WILD-TYPE	20	98	17	9

'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 1

Table S151. Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
KIAA1804 MUTATED	0	3	0	12
KIAA1804 WILD-TYPE	8	23	13	157

'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S152. Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
KIAA1804 MUTATED	15	0	0
KIAA1804 WILD-TYPE	198	2	1

'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S153. Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
KIAA1804 MUTATED	0	0	15
KIAA1804 WILD-TYPE	3	9	179

'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S154. Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
KIAA1804 MUTATED	0	0	15
KIAA1804 WILD-TYPE	8	2	181

'KRTAP5-5 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S155. Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
KRTAP5-5 MUTATED	1	0	3	0
KRTAP5-5 WILD-TYPE	41	57	64	39

'KRTAP5-5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S156. Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
KRTAP5-5 MUTATED	1	2	1	0
KRTAP5-5 WILD-TYPE	39	46	60	56

'KRTAP5-5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S157. Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
KRTAP5-5 MUTATED	2	1	1	0
KRTAP5-5 WILD-TYPE	67	84	61	4

'KRTAP5-5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S158. Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
KRTAP5-5 MUTATED	0	3	1	0
KRTAP5-5 WILD-TYPE	40	64	23	26

'KRTAP5-5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S159. Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
KRTAP5-5 MUTATED	0	4	0	0
KRTAP5-5 WILD-TYPE	20	105	19	9

'KRTAP5-5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S160. Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
KRTAP5-5 MUTATED	0	0	0	4
KRTAP5-5 WILD-TYPE	8	26	13	165

'KRTAP5-5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S161. Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
KRTAP5-5 MUTATED	4	0	0
KRTAP5-5 WILD-TYPE	209	2	1

'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S162. Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
KRTAP5-5 MUTATED	0	0	3
KRTAP5-5 WILD-TYPE	3	9	191

'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S163. Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
KRTAP5-5 MUTATED	0	0	3
KRTAP5-5 WILD-TYPE	8	2	193

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 1

Table S164. Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PTEN MUTATED	2	0	1	4
PTEN WILD-TYPE	40	57	66	35

Figure S32. Get High-res Image Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 1

Table S165. Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
PTEN MUTATED	1	0	4	2
PTEN WILD-TYPE	39	48	57	54

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.07 (Fisher's exact test), Q value = 1

Table S166. Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
PTEN MUTATED	0	6	1	0
PTEN WILD-TYPE	69	79	61	4

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S167. Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
PTEN MUTATED	2	1	0	1
PTEN WILD-TYPE	38	66	24	25

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S168. Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
PTEN MUTATED	1	2	1	0
PTEN WILD-TYPE	19	107	18	9

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S169. Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
PTEN MUTATED	1	2	0	4
PTEN WILD-TYPE	7	24	13	165

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S170. Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
PTEN MUTATED	7	0	0
PTEN WILD-TYPE	206	2	1

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 1

Table S171. Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PTEN MUTATED	0	1	6
PTEN WILD-TYPE	3	8	188

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 1

Table S172. Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
PTEN MUTATED	1	0	6
PTEN WILD-TYPE	7	2	190

'ACOT4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 1

Table S173. Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ACOT4 MUTATED	2	0	1	0
ACOT4 WILD-TYPE	40	57	66	39

'ACOT4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S174. Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
ACOT4 MUTATED	0	1	2	0
ACOT4 WILD-TYPE	40	47	59	56

'ACOT4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S175. Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
ACOT4 MUTATED	1	2	0	0
ACOT4 WILD-TYPE	68	83	62	4

'ACOT4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 1

Table S176. Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
ACOT4 MUTATED	0	1	0	2
ACOT4 WILD-TYPE	8	25	13	167

'ACOT4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S177. Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
ACOT4 MUTATED	3	0	0
ACOT4 WILD-TYPE	210	2	1

'ACOT4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S178. Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ACOT4 MUTATED	0	0	3
ACOT4 WILD-TYPE	3	9	191

'ACOT4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S179. Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
ACOT4 MUTATED	0	0	3
ACOT4 WILD-TYPE	8	2	193

'MYO1B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00868 (Fisher's exact test), Q value = 1

Table S180. Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
MYO1B MUTATED	6	1	1	4
MYO1B WILD-TYPE	36	56	66	35

Figure S33. Get High-res Image Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MYO1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00887 (Fisher's exact test), Q value = 1

Table S181. Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
MYO1B MUTATED	3	0	8	1
MYO1B WILD-TYPE	37	48	53	55

Figure S34. Get High-res Image Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'MYO1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00479 (Fisher's exact test), Q value = 0.95

Table S182. Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
MYO1B MUTATED	2	11	0	0
MYO1B WILD-TYPE	67	74	62	4

Figure S35. Get High-res Image Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MYO1B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S183. Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
MYO1B MUTATED	3	0	1	3
MYO1B WILD-TYPE	37	67	23	23

Figure S36. Get High-res Image Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MYO1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S184. Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
MYO1B MUTATED	0	5	2	0
MYO1B WILD-TYPE	20	104	17	9

'MYO1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 1

Table S185. Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
MYO1B MUTATED	0	4	0	8
MYO1B WILD-TYPE	8	22	13	161

'MYO1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S186. Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
MYO1B MUTATED	12	0	0
MYO1B WILD-TYPE	201	2	1

'MYO1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S187. Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
MYO1B MUTATED	0	0	12
MYO1B WILD-TYPE	3	9	182

'MYO1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S188. Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
MYO1B MUTATED	0	0	12
MYO1B WILD-TYPE	8	2	184

'PCBP1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S189. Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
PCBP1 MUTATED	0	1	2	3
PCBP1 WILD-TYPE	42	56	65	36

'PCBP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S190. Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
PCBP1 MUTATED	2	1	2	1
PCBP1 WILD-TYPE	38	47	59	55

'PCBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S191. Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
PCBP1 MUTATED	1	3	2	0
PCBP1 WILD-TYPE	68	82	60	4

'PCBP1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S192. Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
PCBP1 MUTATED	0	2	0	1
PCBP1 WILD-TYPE	40	65	24	25

'PCBP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S193. Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
PCBP1 MUTATED	0	2	1	0
PCBP1 WILD-TYPE	20	107	18	9

'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S194. Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
PCBP1 MUTATED	0	0	0	6
PCBP1 WILD-TYPE	8	26	13	163

'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S195. Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
PCBP1 MUTATED	6	0	0
PCBP1 WILD-TYPE	207	2	1

'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S196. Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
PCBP1 MUTATED	0	0	5
PCBP1 WILD-TYPE	3	9	189

'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S197. Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
PCBP1 MUTATED	0	0	5
PCBP1 WILD-TYPE	8	2	191

'GGT1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S198. Gene #23: 'GGT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
GGT1 MUTATED	0	3	0	0
GGT1 WILD-TYPE	69	82	62	4

'GGT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 1

Table S199. Gene #23: 'GGT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
GGT1 MUTATED	0	1	0	2
GGT1 WILD-TYPE	8	25	13	167

'GGT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S200. Gene #23: 'GGT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
GGT1 MUTATED	3	0	0
GGT1 WILD-TYPE	210	2	1

'GGT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S201. Gene #23: 'GGT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
GGT1 MUTATED	0	0	3
GGT1 WILD-TYPE	3	9	191

'GGT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S202. Gene #23: 'GGT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
GGT1 MUTATED	0	0	3
GGT1 WILD-TYPE	8	2	193

'ACVR1B MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S203. Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	42	57	67	39
ACVR1B MUTATED	3	2	2	4
ACVR1B WILD-TYPE	39	55	65	35

'ACVR1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 1

Table S204. Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	48	61	56
ACVR1B MUTATED	0	3	5	3
ACVR1B WILD-TYPE	40	45	56	53

'ACVR1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0986 (Fisher's exact test), Q value = 1

Table S205. Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	69	85	62	4
ACVR1B MUTATED	2	10	2	0
ACVR1B WILD-TYPE	67	75	60	4

'ACVR1B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S206. Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	40	67	24	26
ACVR1B MUTATED	2	5	1	3
ACVR1B WILD-TYPE	38	62	23	23

'ACVR1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S207. Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	20	109	19	9
ACVR1B MUTATED	1	7	3	0
ACVR1B WILD-TYPE	19	102	16	9

'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S208. Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	8	26	13	169
ACVR1B MUTATED	0	2	1	11
ACVR1B WILD-TYPE	8	24	12	158

'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S209. Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	2	1
ACVR1B MUTATED	14	0	0
ACVR1B WILD-TYPE	199	2	1

'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S210. Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	3	9	194
ACVR1B MUTATED	0	1	13
ACVR1B WILD-TYPE	3	8	181

'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S211. Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	8	2	196
ACVR1B MUTATED	0	0	14
ACVR1B WILD-TYPE	8	2	182

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = COADREAD-TP.transferedmergedcluster.txt
Number of patients = 223
Number of significantly mutated genes = 24
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

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

Made with Nozzle