Correlation between gene mutation status and molecular subtypes

Colon Adenocarcinoma (Primary solid tumor)

16 April 2014 | analyses__2014_04_16

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/C1RR1WVT

Overview

Introduction

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

Summary

Testing the association between mutation status of 16 genes and 9 molecular subtypes across 154 patients, 7 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 16 genes and 9 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 7 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN 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	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
BRAF	20 (13%)	134	4.96e-07 (6.65e-05)	1.22e-07 (1.64e-05)	0.000101 (0.0134)	0.722 (1.00)	0.926 (1.00)	0.0103 (1.00)	0.146 (1.00)	0.462 (1.00)	1 (1.00)
TP53	74 (48%)	80	0.00233 (0.3)	0.0127 (1.00)	2.17e-08 (2.95e-06)	0.268 (1.00)	0.38 (1.00)	0.000112 (0.0148)	0.83 (1.00)	0.62 (1.00)	1 (1.00)
KRAS	58 (38%)	96	0.025 (1.00)	0.000725 (0.095)	0.836 (1.00)	0.704 (1.00)	0.752 (1.00)	0.303 (1.00)	0.596 (1.00)	0.626 (1.00)	0.283 (1.00)
FBXW7	29 (19%)	125	0.226 (1.00)	0.093 (1.00)	0.00183 (0.237)	0.0038 (0.486)	0.233 (1.00)	0.132 (1.00)	1 (1.00)	1 (1.00)	0.474 (1.00)
APC	103 (67%)	51	0.171 (1.00)	0.0198 (1.00)	0.0374 (1.00)	0.218 (1.00)	0.388 (1.00)	0.87 (1.00)	0.141 (1.00)	0.601 (1.00)	0.258 (1.00)
PIK3CA	26 (17%)	128	0.335 (1.00)	0.321 (1.00)	0.0338 (1.00)	0.116 (1.00)	0.332 (1.00)	0.0435 (1.00)	1 (1.00)	0.514 (1.00)	0.416 (1.00)
NRAS	15 (10%)	139	0.0773 (1.00)	0.38 (1.00)	0.867 (1.00)	0.465 (1.00)	0.332 (1.00)	0.229 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
SMAD4	18 (12%)	136	0.303 (1.00)	0.587 (1.00)	0.00721 (0.908)	0.852 (1.00)	0.495 (1.00)	0.582 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
FAM123B	19 (12%)	135	0.21 (1.00)	0.00698 (0.886)	0.0249 (1.00)	0.286 (1.00)	0.422 (1.00)	0.214 (1.00)	1 (1.00)	0.425 (1.00)	0.338 (1.00)
SOX9	9 (6%)	145	0.235 (1.00)	0.214 (1.00)	0.398 (1.00)	0.231 (1.00)	0.461 (1.00)	0.668 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
ACVR2A	8 (5%)	146	0.045 (1.00)	0.296 (1.00)	0.0542 (1.00)	0.199 (1.00)	0.668 (1.00)	0.665 (1.00)	1 (1.00)	1 (1.00)	0.162 (1.00)
TNFRSF10C	6 (4%)	148	0.381 (1.00)	0.676 (1.00)	0.119 (1.00)	0.68 (1.00)	0.169 (1.00)	0.0967 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
ACOT4	3 (2%)	151	0.665 (1.00)	0.391 (1.00)	0.75 (1.00)			0.81 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
SMAD2	10 (6%)	144	0.0995 (1.00)	0.19 (1.00)	0.0497 (1.00)	1 (1.00)	0.377 (1.00)	0.126 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
PCBP1	4 (3%)	150	0.33 (1.00)	0.552 (1.00)	0.368 (1.00)			0.852 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
GGT1	3 (2%)	151			0.355 (1.00)			0.81 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)

'APC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.171 (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	34	57	28	22
APC MUTATED	18	42	21	14
APC WILD-TYPE	16	15	7	8

'APC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0198 (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
ALL	53	42	46
APC MUTATED	40	21	34
APC WILD-TYPE	13	21	12

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

'APC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0374 (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
ALL	65	67	20
APC MUTATED	49	37	15
APC WILD-TYPE	16	30	5

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

'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 1

Table S4. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
APC MUTATED	19	28	12	9
APC WILD-TYPE	4	19	6	7

'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S5. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
APC MUTATED	4	5	9	50
APC WILD-TYPE	3	3	1	29

'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.87 (Chi-square test), Q value = 1

Table S6. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
APC MUTATED	4	13	3	13	68
APC WILD-TYPE	4	7	1	7	32

'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S7. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
APC MUTATED	99	0	2
APC WILD-TYPE	47	1	3

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
APC MUTATED	2	92
APC WILD-TYPE	2	45

'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.258 (Fisher's exact test), Q value = 1

Table S9. Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
APC MUTATED	1	93	0
APC WILD-TYPE	1	45	1

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S10. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
PIK3CA MUTATED	6	5	6	4
PIK3CA WILD-TYPE	28	52	22	18

'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
PIK3CA MUTATED	9	8	4
PIK3CA WILD-TYPE	44	34	42

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 1

Table S12. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
PIK3CA MUTATED	6	17	2
PIK3CA WILD-TYPE	59	50	18

Figure S3. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
PIK3CA MUTATED	8	8	1	4
PIK3CA WILD-TYPE	15	39	17	12

'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S14. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
PIK3CA MUTATED	1	2	4	14
PIK3CA WILD-TYPE	6	6	6	65

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0435 (Chi-square test), Q value = 1

Table S15. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
PIK3CA MUTATED	2	2	1	8	13
PIK3CA WILD-TYPE	6	18	3	12	87

Figure S4. Get High-res Image Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S16. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
PIK3CA MUTATED	25	0	1
PIK3CA WILD-TYPE	121	1	4

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.514 (Fisher's exact test), Q value = 1

Table S17. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
PIK3CA MUTATED	1	22
PIK3CA WILD-TYPE	3	115

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S18. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
PIK3CA MUTATED	1	22	0
PIK3CA WILD-TYPE	1	116	1

'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 4.96e-07 (Fisher's exact test), Q value = 6.6e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
BRAF MUTATED	14	1	3	0
BRAF WILD-TYPE	20	56	25	22

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

'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.22e-07 (Fisher's exact test), Q value = 1.6e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
BRAF MUTATED	1	16	1
BRAF WILD-TYPE	52	26	45

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

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000101 (Fisher's exact test), Q value = 0.013

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
BRAF MUTATED	1	17	2
BRAF WILD-TYPE	64	50	18

Figure S7. Get High-res Image Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S22. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
BRAF MUTATED	3	4	3	1
BRAF WILD-TYPE	20	43	15	15

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.926 (Fisher's exact test), Q value = 1

Table S23. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
BRAF MUTATED	1	1	1	8
BRAF WILD-TYPE	6	7	9	71

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0103 (Chi-square test), Q value = 1

Table S24. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
BRAF MUTATED	0	0	1	7	12
BRAF WILD-TYPE	8	20	3	13	88

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

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S25. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
BRAF MUTATED	19	1	0
BRAF WILD-TYPE	127	0	5

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
BRAF MUTATED	1	19
BRAF WILD-TYPE	3	118

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S27. Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
BRAF MUTATED	0	20	0
BRAF WILD-TYPE	2	118	1

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
KRAS MUTATED	10	16	17	7
KRAS WILD-TYPE	24	41	11	15

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

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000725 (Fisher's exact test), Q value = 0.095

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
KRAS MUTATED	27	16	7
KRAS WILD-TYPE	26	26	39

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

'KRAS MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
KRAS MUTATED	23	27	7
KRAS WILD-TYPE	42	40	13

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.704 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
KRAS MUTATED	9	22	6	8
KRAS WILD-TYPE	14	25	12	8

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
KRAS MUTATED	3	2	5	35
KRAS WILD-TYPE	4	6	5	44

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.303 (Chi-square test), Q value = 1

Table S33. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
KRAS MUTATED	2	5	2	11	36
KRAS WILD-TYPE	6	15	2	9	64

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S34. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
KRAS MUTATED	53	0	3
KRAS WILD-TYPE	93	1	2

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S35. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
KRAS MUTATED	2	50
KRAS WILD-TYPE	2	87

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.283 (Fisher's exact test), Q value = 1

Table S36. Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
KRAS MUTATED	0	51	1
KRAS WILD-TYPE	2	87	0

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.3

Table S37. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
TP53 MUTATED	12	39	9	10
TP53 WILD-TYPE	22	18	19	12

Figure S11. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 1

Table S38. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
TP53 MUTATED	29	13	28
TP53 WILD-TYPE	24	29	18

Figure S12. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 2.17e-08 (Fisher's exact test), Q value = 2.9e-06

Table S39. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
TP53 MUTATED	47	15	11
TP53 WILD-TYPE	18	52	9

Figure S13. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S40. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
TP53 MUTATED	8	24	8	4
TP53 WILD-TYPE	15	23	10	12

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
TP53 MUTATED	3	1	4	36
TP53 WILD-TYPE	4	7	6	43

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000112 (Chi-square test), Q value = 0.015

Table S42. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
TP53 MUTATED	3	12	0	1	57
TP53 WILD-TYPE	5	8	4	19	43

Figure S14. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S43. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
TP53 MUTATED	70	0	3
TP53 WILD-TYPE	76	1	2

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S44. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
TP53 MUTATED	1	68
TP53 WILD-TYPE	3	69

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S45. Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
TP53 MUTATED	1	68	0
TP53 WILD-TYPE	1	70	1

'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 1

Table S46. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
FBXW7 MUTATED	10	7	5	3
FBXW7 WILD-TYPE	24	50	23	19

'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.093 (Fisher's exact test), Q value = 1

Table S47. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
FBXW7 MUTATED	8	12	5
FBXW7 WILD-TYPE	45	30	41

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00183 (Fisher's exact test), Q value = 0.24

Table S48. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
FBXW7 MUTATED	5	21	3
FBXW7 WILD-TYPE	60	46	17

Figure S15. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0038 (Fisher's exact test), Q value = 0.49

Table S49. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
FBXW7 MUTATED	4	8	1	9
FBXW7 WILD-TYPE	19	39	17	7

Figure S16. Get High-res Image Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 1

Table S50. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
FBXW7 MUTATED	1	4	2	15
FBXW7 WILD-TYPE	6	4	8	64

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.132 (Chi-square test), Q value = 1

Table S51. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
FBXW7 MUTATED	1	1	0	7	20
FBXW7 WILD-TYPE	7	19	4	13	80

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S52. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
FBXW7 MUTATED	28	0	1
FBXW7 WILD-TYPE	118	1	4

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S53. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
FBXW7 MUTATED	0	27
FBXW7 WILD-TYPE	4	110

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S54. Gene #6: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
FBXW7 MUTATED	1	26	0
FBXW7 WILD-TYPE	1	112	1

'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0773 (Fisher's exact test), Q value = 1

Table S55. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
NRAS MUTATED	0	8	4	2
NRAS WILD-TYPE	34	49	24	20

'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S56. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
NRAS MUTATED	7	2	5
NRAS WILD-TYPE	46	40	41

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S57. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
NRAS MUTATED	7	7	1
NRAS WILD-TYPE	58	60	19

'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.465 (Fisher's exact test), Q value = 1

Table S58. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
NRAS MUTATED	1	8	1	2
NRAS WILD-TYPE	22	39	17	14

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S59. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
NRAS MUTATED	0	2	0	10
NRAS WILD-TYPE	7	6	10	69

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S60. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
NRAS MUTATED	2	3	0	3	6
NRAS WILD-TYPE	6	17	4	17	94

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S61. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
NRAS MUTATED	14	0	0
NRAS WILD-TYPE	132	1	5

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S62. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
NRAS MUTATED	0	13
NRAS WILD-TYPE	4	124

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S63. Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
NRAS MUTATED	0	13	0
NRAS WILD-TYPE	2	125	1

'SMAD4 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S64. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
SMAD4 MUTATED	6	4	5	2
SMAD4 WILD-TYPE	28	53	23	20

'SMAD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 1

Table S65. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
SMAD4 MUTATED	5	7	5
SMAD4 WILD-TYPE	48	35	41

'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00721 (Fisher's exact test), Q value = 0.91

Table S66. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
SMAD4 MUTATED	2	12	4
SMAD4 WILD-TYPE	63	55	16

Figure S17. Get High-res Image Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S67. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
SMAD4 MUTATED	3	8	2	1
SMAD4 WILD-TYPE	20	39	16	15

'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 1

Table S68. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
SMAD4 MUTATED	2	0	1	11
SMAD4 WILD-TYPE	5	8	9	68

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.582 (Chi-square test), Q value = 1

Table S69. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
SMAD4 MUTATED	1	1	0	4	11
SMAD4 WILD-TYPE	7	19	4	16	89

'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S70. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
SMAD4 MUTATED	17	0	0
SMAD4 WILD-TYPE	129	1	5

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients	CLUS_2	CLUS_3
ALL	4	137
SMAD4 MUTATED	0	17
SMAD4 WILD-TYPE	4	120

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S72. Gene #8: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
SMAD4 MUTATED	0	17	0
SMAD4 WILD-TYPE	2	121	1

'FAM123B MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S73. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
FAM123B MUTATED	8	6	4	1
FAM123B WILD-TYPE	26	51	24	21

'FAM123B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00698 (Fisher's exact test), Q value = 0.89

Table S74. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
FAM123B MUTATED	8	10	1
FAM123B WILD-TYPE	45	32	45

Figure S18. Get High-res Image Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FAM123B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 1

Table S75. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
FAM123B MUTATED	5	13	0
FAM123B WILD-TYPE	60	54	20

Figure S19. Get High-res Image Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FAM123B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S76. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
FAM123B MUTATED	2	4	1	4
FAM123B WILD-TYPE	21	43	17	12

'FAM123B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.422 (Fisher's exact test), Q value = 1

Table S77. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
FAM123B MUTATED	0	2	1	8
FAM123B WILD-TYPE	7	6	9	71

'FAM123B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.214 (Chi-square test), Q value = 1

Table S78. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
FAM123B MUTATED	0	0	1	2	16
FAM123B WILD-TYPE	8	20	3	18	84

'FAM123B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S79. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
FAM123B MUTATED	19	0	0
FAM123B WILD-TYPE	127	1	5

'FAM123B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S80. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
FAM123B MUTATED	1	17
FAM123B WILD-TYPE	3	120

'FAM123B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 1

Table S81. Gene #9: 'FAM123B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
FAM123B MUTATED	1	17	0
FAM123B WILD-TYPE	1	121	1

'SOX9 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S82. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
SOX9 MUTATED	2	3	0	3
SOX9 WILD-TYPE	32	54	28	19

'SOX9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S83. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
SOX9 MUTATED	2	1	5
SOX9 WILD-TYPE	51	41	41

'SOX9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 1

Table S84. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
SOX9 MUTATED	2	6	1
SOX9 WILD-TYPE	63	61	19

'SOX9 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S85. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
SOX9 MUTATED	0	3	0	2
SOX9 WILD-TYPE	23	44	18	14

'SOX9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S86. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
SOX9 MUTATED	1	0	0	4
SOX9 WILD-TYPE	6	8	10	75

'SOX9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.668 (Chi-square test), Q value = 1

Table S87. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
SOX9 MUTATED	1	0	0	1	7
SOX9 WILD-TYPE	7	20	4	19	93

'SOX9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S88. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
SOX9 MUTATED	9	0	0
SOX9 WILD-TYPE	137	1	5

'SOX9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S89. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
SOX9 MUTATED	0	9
SOX9 WILD-TYPE	4	128

'SOX9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S90. Gene #10: 'SOX9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
SOX9 MUTATED	0	9	0
SOX9 WILD-TYPE	2	129	1

'ACVR2A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 1

Table S91. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
ACVR2A MUTATED	5	1	1	0
ACVR2A WILD-TYPE	29	56	27	22

Figure S20. Get High-res Image Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ACVR2A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.296 (Fisher's exact test), Q value = 1

Table S92. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
ACVR2A MUTATED	2	4	1
ACVR2A WILD-TYPE	51	38	45

'ACVR2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0542 (Fisher's exact test), Q value = 1

Table S93. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
ACVR2A MUTATED	1	7	0
ACVR2A WILD-TYPE	64	60	20

'ACVR2A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S94. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
ACVR2A MUTATED	0	4	0	2
ACVR2A WILD-TYPE	23	43	18	14

'ACVR2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S95. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
ACVR2A MUTATED	0	1	0	5
ACVR2A WILD-TYPE	7	7	10	74

'ACVR2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.665 (Chi-square test), Q value = 1

Table S96. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
ACVR2A MUTATED	0	1	0	0	7
ACVR2A WILD-TYPE	8	19	4	20	93

'ACVR2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S97. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
ACVR2A MUTATED	8	0	0
ACVR2A WILD-TYPE	138	1	5

'ACVR2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S98. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
ACVR2A MUTATED	0	8
ACVR2A WILD-TYPE	4	129

'ACVR2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S99. Gene #11: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
ACVR2A MUTATED	1	7	0
ACVR2A WILD-TYPE	1	131	1

'TNFRSF10C MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S100. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
TNFRSF10C MUTATED	2	2	0	2
TNFRSF10C WILD-TYPE	32	55	28	20

'TNFRSF10C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S101. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
TNFRSF10C MUTATED	2	1	3
TNFRSF10C WILD-TYPE	51	41	43

'TNFRSF10C MUTATION STATUS' versus 'CN_CNMF'

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

Table S102. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
TNFRSF10C MUTATED	5	1	0
TNFRSF10C WILD-TYPE	60	66	20

'TNFRSF10C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S103. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
TNFRSF10C MUTATED	2	2	0	1
TNFRSF10C WILD-TYPE	21	45	18	15

'TNFRSF10C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 1

Table S104. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
TNFRSF10C MUTATED	0	0	2	3
TNFRSF10C WILD-TYPE	7	8	8	76

'TNFRSF10C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0967 (Chi-square test), Q value = 1

Table S105. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
TNFRSF10C MUTATED	1	0	1	0	4
TNFRSF10C WILD-TYPE	7	20	3	20	96

'TNFRSF10C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S106. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
TNFRSF10C MUTATED	6	0	0
TNFRSF10C WILD-TYPE	140	1	5

'TNFRSF10C MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S107. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
TNFRSF10C MUTATED	0	6
TNFRSF10C WILD-TYPE	4	131

'TNFRSF10C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S108. Gene #12: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
TNFRSF10C MUTATED	0	6	0
TNFRSF10C WILD-TYPE	2	132	1

'ACOT4 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S109. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
ACOT4 MUTATED	1	1	0	1
ACOT4 WILD-TYPE	33	56	28	21

'ACOT4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S110. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
ACOT4 MUTATED	1	2	0
ACOT4 WILD-TYPE	52	40	46

'ACOT4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.75 (Fisher's exact test), Q value = 1

Table S111. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
ACOT4 MUTATED	2	1	0
ACOT4 WILD-TYPE	63	66	20

'ACOT4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.81 (Chi-square test), Q value = 1

Table S112. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
ACOT4 MUTATED	0	0	0	1	2
ACOT4 WILD-TYPE	8	20	4	19	98

'ACOT4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S113. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
ACOT4 MUTATED	3	0	0
ACOT4 WILD-TYPE	143	1	5

'ACOT4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S114. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
ACOT4 MUTATED	0	3
ACOT4 WILD-TYPE	4	134

'ACOT4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S115. Gene #13: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
ACOT4 MUTATED	0	3	0
ACOT4 WILD-TYPE	2	135	1

'SMAD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0995 (Fisher's exact test), Q value = 1

Table S116. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
SMAD2 MUTATED	3	1	4	1
SMAD2 WILD-TYPE	31	56	24	21

'SMAD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S117. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
SMAD2 MUTATED	3	5	1
SMAD2 WILD-TYPE	50	37	45

'SMAD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 1

Table S118. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
SMAD2 MUTATED	1	8	1
SMAD2 WILD-TYPE	64	59	19

Figure S21. Get High-res Image Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SMAD2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S119. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	23	47	18	16
SMAD2 MUTATED	2	3	1	1
SMAD2 WILD-TYPE	21	44	17	15

'SMAD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 1

Table S120. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	7	8	10	79
SMAD2 MUTATED	1	1	0	5
SMAD2 WILD-TYPE	6	7	10	74

'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S121. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
SMAD2 MUTATED	0	1	0	4	5
SMAD2 WILD-TYPE	8	19	4	16	95

'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S122. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
SMAD2 MUTATED	10	0	0
SMAD2 WILD-TYPE	136	1	5

'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S123. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
SMAD2 MUTATED	0	9
SMAD2 WILD-TYPE	4	128

'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S124. Gene #14: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
SMAD2 MUTATED	0	9	0
SMAD2 WILD-TYPE	2	129	1

'PCBP1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S125. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	57	28	22
PCBP1 MUTATED	0	2	2	0
PCBP1 WILD-TYPE	34	55	26	22

'PCBP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.552 (Fisher's exact test), Q value = 1

Table S126. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	42	46
PCBP1 MUTATED	2	0	2
PCBP1 WILD-TYPE	51	42	44

'PCBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 1

Table S127. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
PCBP1 MUTATED	2	1	1
PCBP1 WILD-TYPE	63	66	19

'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.852 (Chi-square test), Q value = 1

Table S128. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
PCBP1 MUTATED	0	1	0	0	3
PCBP1 WILD-TYPE	8	19	4	20	97

'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S129. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
PCBP1 MUTATED	4	0	0
PCBP1 WILD-TYPE	142	1	5

'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S130. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
PCBP1 MUTATED	0	3
PCBP1 WILD-TYPE	4	134

'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S131. Gene #15: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
PCBP1 MUTATED	0	3	0
PCBP1 WILD-TYPE	2	135	1

'GGT1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S132. Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	65	67	20
GGT1 MUTATED	0	3	0
GGT1 WILD-TYPE	65	64	20

'GGT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.81 (Chi-square test), Q value = 1

Table S133. Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	8	20	4	20	100
GGT1 MUTATED	0	0	0	0	3
GGT1 WILD-TYPE	8	20	4	20	97

'GGT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S134. Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	146	1	5
GGT1 MUTATED	3	0	0
GGT1 WILD-TYPE	143	1	5

'GGT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S135. Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CNMF'

nPatients	CLUS_2	CLUS_3
ALL	4	137
GGT1 MUTATED	0	3
GGT1 WILD-TYPE	4	134

'GGT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S136. Gene #16: 'GGT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	2	138	1
GGT1 MUTATED	0	3	0
GGT1 WILD-TYPE	2	135	1

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = COAD-TP.transferedmergedcluster.txt
Number of patients = 154
Number of significantly mutated genes = 16
Number of Molecular subtypes = 9
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Chi-square test

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

Q value calculation

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

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

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

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

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