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 10 genes and 10 molecular subtypes across 261 patients, 7 significant findings detected with P value < 0.05 and Q value < 0.25.

SPOP mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
TP53 mutation correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
FOXA1 mutation correlated to 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 10 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, 7 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Chi-square test	Fisher's exact test
SPOP	26 (10%)	235	0.000169 (0.0155)	1.55e-08 (1.49e-06)	0.324 (1.00)	0.743 (1.00)	0.000141 (0.0131)	5.74e-07 (5.4e-05)	0.418 (1.00)	0.915 (1.00)	0.133 (1.00)	0.0934 (1.00)
TP53	23 (9%)	238	3.89e-07 (3.69e-05)	0.271 (1.00)	0.00775 (0.658)	0.0187 (1.00)	0.0181 (1.00)	0.00039 (0.0351)	0.825 (1.00)	0.42 (1.00)	0.355 (1.00)	0.529 (1.00)
FOXA1	12 (5%)	249	0.0228 (1.00)	0.000178 (0.0162)	1 (1.00)	0.714 (1.00)	0.0459 (1.00)	0.0434 (1.00)	0.345 (1.00)	0.0702 (1.00)	0.492 (1.00)	0.187 (1.00)
KIDINS220	3 (1%)	258	0.54 (1.00)	0.389 (1.00)			1 (1.00)	1 (1.00)	0.794 (1.00)	1 (1.00)	0.968 (1.00)	1 (1.00)
CTNNB1	9 (3%)	252	0.0573 (1.00)	0.0426 (1.00)	0.04 (1.00)	0.0379 (1.00)	0.0758 (1.00)	0.306 (1.00)	0.442 (1.00)	0.292 (1.00)	0.772 (1.00)	0.539 (1.00)
PTEN	13 (5%)	248	0.0351 (1.00)	0.287 (1.00)	0.197 (1.00)	0.598 (1.00)	0.151 (1.00)	0.0618 (1.00)	0.252 (1.00)	0.124 (1.00)	0.29 (1.00)	0.519 (1.00)
LMOD2	3 (1%)	258	1 (1.00)	0.638 (1.00)			1 (1.00)	1 (1.00)	0.786 (1.00)	0.778 (1.00)	0.0811 (1.00)	0.596 (1.00)
IDH1	4 (2%)	257	0.114 (1.00)	0.00643 (0.566)	0.0609 (1.00)	0.024 (1.00)	0.0357 (1.00)	0.0102 (0.856)	0.00646 (0.566)	0.00604 (0.537)	0.00649 (0.566)	0.134 (1.00)
NKX3-1	5 (2%)	256	0.358 (1.00)	0.632 (1.00)	0.0286 (1.00)	0.0697 (1.00)	1 (1.00)	0.871 (1.00)	0.0204 (1.00)	0.429 (1.00)	0.0244 (1.00)	0.0113 (0.935)
CDKN1B	4 (2%)	257	0.114 (1.00)	0.104 (1.00)	0.243 (1.00)	0.387 (1.00)	0.329 (1.00)	0.273 (1.00)	0.733 (1.00)	0.0358 (1.00)	0.898 (1.00)	0.102 (1.00)

'KIDINS220 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'KIDINS220 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	144	79
KIDINS220 MUTATED	0	1	2
KIDINS220 WILD-TYPE	35	143	77

'KIDINS220 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S2. Gene #1: 'KIDINS220 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
KIDINS220 MUTATED	1	2	0
KIDINS220 WILD-TYPE	74	87	97

'KIDINS220 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S3. Gene #1: 'KIDINS220 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	81	88
KIDINS220 MUTATED	1	1	1
KIDINS220 WILD-TYPE	88	80	87

'KIDINS220 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S4. Gene #1: 'KIDINS220 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	84	91
KIDINS220 MUTATED	1	1	1
KIDINS220 WILD-TYPE	82	83	90

'KIDINS220 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.794 (Chi-square test), Q value = 1

Table S5. Gene #1: 'KIDINS220 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	63	39	80	16	61
KIDINS220 MUTATED	1	1	1	0	0
KIDINS220 WILD-TYPE	62	38	79	16	61

'KIDINS220 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S6. Gene #1: 'KIDINS220 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	54	89	73
KIDINS220 MUTATED	0	1	1	1
KIDINS220 WILD-TYPE	43	53	88	72

'KIDINS220 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.968 (Chi-square test), Q value = 1

Table S7. Gene #1: 'KIDINS220 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	16	85	59	18
KIDINS220 MUTATED	1	0	1	1	0
KIDINS220 WILD-TYPE	80	16	84	58	18

'KIDINS220 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S8. Gene #1: 'KIDINS220 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	32	78	82
KIDINS220 MUTATED	1	0	1	1
KIDINS220 WILD-TYPE	66	32	77	81

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0573 (Fisher's exact test), Q value = 1

Table S9. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	144	79
CTNNB1 MUTATED	3	2	4
CTNNB1 WILD-TYPE	32	142	75

'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 1

Table S10. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
CTNNB1 MUTATED	3	0	6
CTNNB1 WILD-TYPE	72	89	91

Figure S1. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
CTNNB1 MUTATED	0	0	4
CTNNB1 WILD-TYPE	42	59	59

Figure S2. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 1

Table S12. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	64	48
CTNNB1 MUTATED	0	4	0
CTNNB1 WILD-TYPE	52	60	48

Figure S3. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0758 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	81	88
CTNNB1 MUTATED	4	0	5
CTNNB1 WILD-TYPE	85	81	83

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.306 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	84	91
CTNNB1 MUTATED	3	1	5
CTNNB1 WILD-TYPE	80	83	86

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.442 (Chi-square test), Q value = 1

Table S15. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	63	39	80	16	61
CTNNB1 MUTATED	2	0	3	0	4
CTNNB1 WILD-TYPE	61	39	77	16	57

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	54	89	73
CTNNB1 MUTATED	0	4	3	2
CTNNB1 WILD-TYPE	43	50	86	71

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.772 (Chi-square test), Q value = 1

Table S17. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	16	85	59	18
CTNNB1 MUTATED	3	1	2	3	0
CTNNB1 WILD-TYPE	78	15	83	56	18

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	32	78	82
CTNNB1 MUTATED	2	0	2	5
CTNNB1 WILD-TYPE	65	32	76	77

'SPOP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000169 (Fisher's exact test), Q value = 0.016

Table S19. Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	144	79
SPOP MUTATED	10	6	9
SPOP WILD-TYPE	25	138	70

Figure S4. Get High-res Image Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SPOP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.55e-08 (Fisher's exact test), Q value = 1.5e-06

Table S20. Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
SPOP MUTATED	21	4	1
SPOP WILD-TYPE	54	85	96

Figure S5. Get High-res Image Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SPOP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S21. Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
SPOP MUTATED	4	3	8
SPOP WILD-TYPE	38	56	55

'SPOP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.743 (Fisher's exact test), Q value = 1

Table S22. Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	64	48
SPOP MUTATED	5	7	3
SPOP WILD-TYPE	47	57	45

'SPOP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000141 (Fisher's exact test), Q value = 0.013

Table S23. Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	81	88
SPOP MUTATED	17	7	1
SPOP WILD-TYPE	72	74	87

Figure S6. Get High-res Image Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SPOP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.74e-07 (Fisher's exact test), Q value = 5.4e-05

Table S24. Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	84	91
SPOP MUTATED	20	4	1
SPOP WILD-TYPE	63	80	90

Figure S7. Get High-res Image Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SPOP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.418 (Chi-square test), Q value = 1

Table S25. Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	63	39	80	16	61
SPOP MUTATED	4	4	10	0	8
SPOP WILD-TYPE	59	35	70	16	53

'SPOP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S26. Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	54	89	73
SPOP MUTATED	3	6	9	8
SPOP WILD-TYPE	40	48	80	65

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.133 (Chi-square test), Q value = 1

Table S27. Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	16	85	59	18
SPOP MUTATED	4	0	10	9	3
SPOP WILD-TYPE	77	16	75	50	15

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0934 (Fisher's exact test), Q value = 1

Table S28. Gene #3: 'SPOP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	32	78	82
SPOP MUTATED	3	1	11	11
SPOP WILD-TYPE	64	31	67	71

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 3.89e-07 (Fisher's exact test), Q value = 3.7e-05

Table S29. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	144	79
TP53 MUTATED	0	4	19
TP53 WILD-TYPE	35	140	60

Figure S8. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S30. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
TP53 MUTATED	6	5	12
TP53 WILD-TYPE	69	84	85

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00775 (Fisher's exact test), Q value = 0.66

Table S31. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
TP53 MUTATED	0	3	10
TP53 WILD-TYPE	42	56	53

Figure S9. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 1

Table S32. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	64	48
TP53 MUTATED	1	10	2
TP53 WILD-TYPE	51	54	46

Figure S10. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	81	88
TP53 MUTATED	6	3	14
TP53 WILD-TYPE	83	78	74

Figure S11. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.035

Table S34. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	84	91
TP53 MUTATED	4	2	17
TP53 WILD-TYPE	79	82	74

Figure S12. Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.825 (Chi-square test), Q value = 1

Table S35. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	63	39	80	16	61
TP53 MUTATED	5	2	9	1	6
TP53 WILD-TYPE	58	37	71	15	55

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.42 (Fisher's exact test), Q value = 1

Table S36. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	54	89	73
TP53 MUTATED	2	7	6	8
TP53 WILD-TYPE	41	47	83	65

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.355 (Chi-square test), Q value = 1

Table S37. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	16	85	59	18
TP53 MUTATED	5	0	11	6	1
TP53 WILD-TYPE	76	16	74	53	17

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.529 (Fisher's exact test), Q value = 1

Table S38. Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	32	78	82
TP53 MUTATED	4	2	10	7
TP53 WILD-TYPE	63	30	68	75

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 1

Table S39. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	144	79
PTEN MUTATED	3	3	7
PTEN WILD-TYPE	32	141	72

Figure S13. Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S40. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
PTEN MUTATED	4	2	7
PTEN WILD-TYPE	71	87	90

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 1

Table S41. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
PTEN MUTATED	4	1	3
PTEN WILD-TYPE	38	58	60

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S42. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	64	48
PTEN MUTATED	4	2	2
PTEN WILD-TYPE	48	62	46

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	81	88
PTEN MUTATED	6	1	6
PTEN WILD-TYPE	83	80	82

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0618 (Fisher's exact test), Q value = 1

Table S44. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	84	91
PTEN MUTATED	4	1	8
PTEN WILD-TYPE	79	83	83

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.252 (Chi-square test), Q value = 1

Table S45. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	63	39	80	16	61
PTEN MUTATED	3	0	3	1	6
PTEN WILD-TYPE	60	39	77	15	55

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 1

Table S46. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	54	89	73
PTEN MUTATED	1	6	2	4
PTEN WILD-TYPE	42	48	87	69

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.29 (Chi-square test), Q value = 1

Table S47. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	16	85	59	18
PTEN MUTATED	3	1	3	6	0
PTEN WILD-TYPE	78	15	82	53	18

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.519 (Fisher's exact test), Q value = 1

Table S48. Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	32	78	82
PTEN MUTATED	3	0	4	6
PTEN WILD-TYPE	64	32	74	76

'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S49. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	144	79
FOXA1 MUTATED	5	4	3
FOXA1 WILD-TYPE	30	140	76

Figure S14. Get High-res Image Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000178 (Fisher's exact test), Q value = 0.016

Table S50. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
FOXA1 MUTATED	10	1	1
FOXA1 WILD-TYPE	65	88	96

Figure S15. Get High-res Image Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S51. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
FOXA1 MUTATED	2	2	3
FOXA1 WILD-TYPE	40	57	60

'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S52. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	64	48
FOXA1 MUTATED	3	3	1
FOXA1 WILD-TYPE	49	61	47

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 1

Table S53. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	81	88
FOXA1 MUTATED	8	3	1
FOXA1 WILD-TYPE	81	78	87

Figure S16. Get High-res Image Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S54. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	84	91
FOXA1 MUTATED	8	2	2
FOXA1 WILD-TYPE	75	82	89

Figure S17. Get High-res Image Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.345 (Chi-square test), Q value = 1

Table S55. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	63	39	80	16	61
FOXA1 MUTATED	1	1	6	0	4
FOXA1 WILD-TYPE	62	38	74	16	57

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0702 (Fisher's exact test), Q value = 1

Table S56. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	54	89	73
FOXA1 MUTATED	1	5	1	5
FOXA1 WILD-TYPE	42	49	88	68

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.492 (Chi-square test), Q value = 1

Table S57. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	16	85	59	18
FOXA1 MUTATED	1	1	6	3	1
FOXA1 WILD-TYPE	80	15	79	56	17

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S58. Gene #6: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	32	78	82
FOXA1 MUTATED	1	0	5	6
FOXA1 WILD-TYPE	66	32	73	76

'LMOD2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S59. Gene #7: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	144	79
LMOD2 MUTATED	0	2	1
LMOD2 WILD-TYPE	35	142	78

'LMOD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S60. Gene #7: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
LMOD2 MUTATED	0	2	1
LMOD2 WILD-TYPE	75	87	96

'LMOD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S61. Gene #7: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	81	88
LMOD2 MUTATED	1	1	1
LMOD2 WILD-TYPE	88	80	87

'LMOD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S62. Gene #7: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	84	91
LMOD2 MUTATED	1	1	1
LMOD2 WILD-TYPE	82	83	90

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.786 (Chi-square test), Q value = 1

Table S63. Gene #7: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	63	39	80	16	61
LMOD2 MUTATED	0	1	1	0	1
LMOD2 WILD-TYPE	63	38	79	16	60

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.778 (Fisher's exact test), Q value = 1

Table S64. Gene #7: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	54	89	73
LMOD2 MUTATED	1	0	1	1
LMOD2 WILD-TYPE	42	54	88	72

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0811 (Chi-square test), Q value = 1

Table S65. Gene #7: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	16	85	59	18
LMOD2 MUTATED	0	1	1	0	1
LMOD2 WILD-TYPE	81	15	84	59	17

'LMOD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S66. Gene #7: 'LMOD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	32	78	82
LMOD2 MUTATED	0	1	1	1
LMOD2 WILD-TYPE	67	31	77	81

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 1

Table S67. Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	144	79
IDH1 MUTATED	2	1	1
IDH1 WILD-TYPE	33	143	78

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00643 (Fisher's exact test), Q value = 0.57

Table S68. Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
IDH1 MUTATED	4	0	0
IDH1 WILD-TYPE	71	89	97

Figure S18. Get High-res Image Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0609 (Fisher's exact test), Q value = 1

Table S69. Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
IDH1 MUTATED	0	3	0
IDH1 WILD-TYPE	42	56	63

'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 1

Table S70. Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	64	48
IDH1 MUTATED	0	0	3
IDH1 WILD-TYPE	52	64	45

Figure S19. Get High-res Image Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 1

Table S71. Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	81	88
IDH1 MUTATED	4	0	0
IDH1 WILD-TYPE	85	81	88

Figure S20. Get High-res Image Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.86

Table S72. Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	84	91
IDH1 MUTATED	4	0	0
IDH1 WILD-TYPE	79	84	91

Figure S21. Get High-res Image Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00646 (Chi-square test), Q value = 0.57

Table S73. Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	63	39	80	16	61
IDH1 MUTATED	0	0	1	2	1
IDH1 WILD-TYPE	63	39	79	14	60

Figure S22. Get High-res Image Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00604 (Fisher's exact test), Q value = 0.54

Table S74. Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	54	89	73
IDH1 MUTATED	3	1	0	0
IDH1 WILD-TYPE	40	53	89	73

Figure S23. Get High-res Image Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00649 (Chi-square test), Q value = 0.57

Table S75. Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	16	85	59	18
IDH1 MUTATED	0	2	1	1	0
IDH1 WILD-TYPE	81	14	84	58	18

Figure S24. Get High-res Image Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S76. Gene #8: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	32	78	82
IDH1 MUTATED	0	2	1	1
IDH1 WILD-TYPE	67	30	77	81

'NKX3-1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S77. Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	144	79
NKX3-1 MUTATED	1	3	0
NKX3-1 WILD-TYPE	34	141	79

'NKX3-1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 1

Table S78. Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
NKX3-1 MUTATED	1	1	3
NKX3-1 WILD-TYPE	74	88	94

'NKX3-1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 1

Table S79. Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
NKX3-1 MUTATED	4	0	1
NKX3-1 WILD-TYPE	38	59	62

Figure S25. Get High-res Image Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NKX3-1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0697 (Fisher's exact test), Q value = 1

Table S80. Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	64	48
NKX3-1 MUTATED	4	1	0
NKX3-1 WILD-TYPE	48	63	48

'NKX3-1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S81. Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	81	88
NKX3-1 MUTATED	2	1	2
NKX3-1 WILD-TYPE	87	80	86

'NKX3-1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.871 (Fisher's exact test), Q value = 1

Table S82. Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	84	91
NKX3-1 MUTATED	2	1	2
NKX3-1 WILD-TYPE	81	83	89

'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0204 (Chi-square test), Q value = 1

Table S83. Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	63	39	80	16	61
NKX3-1 MUTATED	4	0	0	1	0
NKX3-1 WILD-TYPE	59	39	80	15	61

Figure S26. Get High-res Image Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S84. Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	54	89	73
NKX3-1 MUTATED	2	0	2	1
NKX3-1 WILD-TYPE	41	54	87	72

'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0244 (Chi-square test), Q value = 1

Table S85. Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	16	85	59	18
NKX3-1 MUTATED	5	0	0	0	0
NKX3-1 WILD-TYPE	76	16	85	59	18

Figure S27. Get High-res Image Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NKX3-1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.93

Table S86. Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	32	78	82
NKX3-1 MUTATED	3	2	0	0
NKX3-1 WILD-TYPE	64	30	78	82

Figure S28. Get High-res Image Gene #9: 'NKX3-1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDKN1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 1

Table S87. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	35	144	79
CDKN1B MUTATED	2	1	1
CDKN1B WILD-TYPE	33	143	78

'CDKN1B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S88. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	75	89	97
CDKN1B MUTATED	3	0	1
CDKN1B WILD-TYPE	72	89	96

'CDKN1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S89. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	59	63
CDKN1B MUTATED	1	0	3
CDKN1B WILD-TYPE	41	59	60

'CDKN1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.387 (Fisher's exact test), Q value = 1

Table S90. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	64	48
CDKN1B MUTATED	1	3	0
CDKN1B WILD-TYPE	51	61	48

'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 1

Table S91. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	89	81	88
CDKN1B MUTATED	3	0	1
CDKN1B WILD-TYPE	86	81	87

'CDKN1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S92. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	84	91
CDKN1B MUTATED	1	0	3
CDKN1B WILD-TYPE	82	84	88

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.733 (Chi-square test), Q value = 1

Table S93. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	63	39	80	16	61
CDKN1B MUTATED	2	0	1	0	1
CDKN1B WILD-TYPE	61	39	79	16	60

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 1

Table S94. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	43	54	89	73
CDKN1B MUTATED	2	2	0	0
CDKN1B WILD-TYPE	41	52	89	73

Figure S29. Get High-res Image Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.898 (Chi-square test), Q value = 1

Table S95. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	81	16	85	59	18
CDKN1B MUTATED	2	0	1	1	0
CDKN1B WILD-TYPE	79	16	84	58	18

'CDKN1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 1

Table S96. Gene #10: 'CDKN1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	32	78	82
CDKN1B MUTATED	1	2	0	1
CDKN1B WILD-TYPE	66	30	78	81

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = PRAD-TP.transferedmergedcluster.txt
Number of patients = 261
Number of significantly mutated genes = 10
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

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.

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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