Correlation between gene mutation status and molecular subtypes

Thyroid Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1F47MZ4

Overview

Introduction

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

Summary

Testing the association between mutation status of 11 genes and 10 molecular subtypes across 401 patients, 26 significant findings detected with P value < 0.05 and Q value < 0.25.

BRAF mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
NRAS mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
HRAS mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 11 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, 26 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
BRAF	240 (60%)	161	0.00054 (0.0394)	1e-05 (0.00098)	2e-05 (0.00152)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)
HRAS	14 (3%)	387	2e-05 (0.00152)	1e-05 (0.00098)	9e-05 (0.00666)	0.0087 (0.626)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)
NRAS	34 (8%)	367	0.0111 (0.775)	1e-05 (0.00098)	1 (1.00)	0.01 (0.712)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)	1e-05 (0.00098)
EIF1AX	6 (1%)	395	0.732 (1.00)	0.133 (1.00)	0.324 (1.00)	0.319 (1.00)	0.0584 (1.00)	0.116 (1.00)	0.328 (1.00)	0.385 (1.00)	0.382 (1.00)	0.313 (1.00)
NUP93	4 (1%)	397	1 (1.00)	1 (1.00)			0.59 (1.00)	0.682 (1.00)	1 (1.00)	1 (1.00)	0.843 (1.00)	0.83 (1.00)
PPM1D	5 (1%)	396	1 (1.00)	1 (1.00)	0.112 (1.00)	0.849 (1.00)	0.916 (1.00)	0.0522 (1.00)	0.38 (1.00)	0.18 (1.00)	0.287 (1.00)	0.443 (1.00)
DNMT3A	3 (1%)	398	0.24 (1.00)	0.732 (1.00)			0.738 (1.00)	0.812 (1.00)	0.317 (1.00)	0.116 (1.00)	0.653 (1.00)	0.135 (1.00)
KRAS	4 (1%)	397	1 (1.00)	0.207 (1.00)			0.232 (1.00)	0.305 (1.00)	0.217 (1.00)	0.132 (1.00)	0.33 (1.00)	0.277 (1.00)
DLC1	4 (1%)	397	1 (1.00)	1 (1.00)			0.59 (1.00)	0.685 (1.00)	1 (1.00)	1 (1.00)	0.84 (1.00)	0.83 (1.00)
ITGAL	4 (1%)	397	0.333 (1.00)	0.378 (1.00)			0.333 (1.00)	0.51 (1.00)	0.552 (1.00)	0.576 (1.00)	0.398 (1.00)	0.572 (1.00)
NLRP6	3 (1%)	398	0.52 (1.00)	0.415 (1.00)			0.411 (1.00)	0.299 (1.00)	0.776 (1.00)	0.189 (1.00)	0.532 (1.00)	0.363 (1.00)

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.039

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	313	60
BRAF MUTATED	8	203	29
BRAF WILD-TYPE	18	110	31

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

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	127	61
BRAF MUTATED	185	19	36
BRAF WILD-TYPE	28	108	25

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

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0015

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	76	77
BRAF MUTATED	21	57	43
BRAF WILD-TYPE	39	19	34

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

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	47	27	9
BRAF MUTATED	6	23	29	6	36	12	9
BRAF WILD-TYPE	40	4	2	20	11	15	0

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

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	43	93	133
BRAF MUTATED	13	27	78	122
BRAF WILD-TYPE	117	16	15	11

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

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	107	77	61	92	62
BRAF MUTATED	4	36	59	86	55
BRAF WILD-TYPE	103	41	2	6	7

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

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	140	130
BRAF MUTATED	15	122	102
BRAF WILD-TYPE	115	18	28

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

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	123
BRAF MUTATED	4	137	98
BRAF WILD-TYPE	104	32	25

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

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	131	127
BRAF MUTATED	23	117	99
BRAF WILD-TYPE	119	14	28

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

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	153	81	60
BRAF MUTATED	4	127	52	56
BRAF WILD-TYPE	102	26	29	4

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

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.77

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	313	60
NRAS MUTATED	1	20	11
NRAS WILD-TYPE	25	293	49

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

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	127	61
NRAS MUTATED	0	34	0
NRAS WILD-TYPE	213	93	61

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

'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	76	77
NRAS MUTATED	4	5	5
NRAS WILD-TYPE	56	71	72

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.71

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	47	27	9
NRAS MUTATED	5	1	0	3	0	5	0
NRAS WILD-TYPE	41	26	31	23	47	22	9

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

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	43	93	133
NRAS MUTATED	34	0	0	0
NRAS WILD-TYPE	96	43	93	133

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

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	107	77	61	92	62
NRAS MUTATED	33	1	0	0	0
NRAS WILD-TYPE	74	76	61	92	62

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

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	140	130
NRAS MUTATED	33	0	1
NRAS WILD-TYPE	97	140	129

Figure S16. Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	123
NRAS MUTATED	33	0	1
NRAS WILD-TYPE	75	169	122

Figure S17. Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	131	127
NRAS MUTATED	33	0	1
NRAS WILD-TYPE	109	131	126

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

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	153	81	60
NRAS MUTATED	32	0	2	0
NRAS WILD-TYPE	74	153	79	60

Figure S19. Get High-res Image Gene #2: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0015

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	313	60
HRAS MUTATED	0	4	10
HRAS WILD-TYPE	26	309	50

Figure S20. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	127	61
HRAS MUTATED	0	14	0
HRAS WILD-TYPE	213	113	61

Figure S21. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0067

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	76	77
HRAS MUTATED	9	1	0
HRAS WILD-TYPE	51	75	77

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

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0087 (Fisher's exact test), Q value = 0.63

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	47	27	9
HRAS MUTATED	7	0	0	2	0	1	0
HRAS WILD-TYPE	39	27	31	24	47	26	9

Figure S23. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	43	93	133
HRAS MUTATED	14	0	0	0
HRAS WILD-TYPE	116	43	93	133

Figure S24. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	107	77	61	92	62
HRAS MUTATED	14	0	0	0	0
HRAS WILD-TYPE	93	77	61	92	62

Figure S25. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	140	130
HRAS MUTATED	14	0	0
HRAS WILD-TYPE	116	140	130

Figure S26. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	123
HRAS MUTATED	14	0	0
HRAS WILD-TYPE	94	169	123

Figure S27. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	131	127
HRAS MUTATED	14	0	0
HRAS WILD-TYPE	128	131	127

Figure S28. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	153	81	60
HRAS MUTATED	14	0	0	0
HRAS WILD-TYPE	92	153	81	60

Figure S29. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	313	60
EIF1AX MUTATED	0	6	0
EIF1AX WILD-TYPE	26	307	60

'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S32. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	127	61
EIF1AX MUTATED	1	4	1
EIF1AX WILD-TYPE	212	123	60

'EIF1AX MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S33. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	76	77
EIF1AX MUTATED	3	1	1
EIF1AX WILD-TYPE	57	75	76

'EIF1AX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 1

Table S34. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	47	27	9
EIF1AX MUTATED	3	0	0	1	0	1	0
EIF1AX WILD-TYPE	43	27	31	25	47	26	9

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0584 (Fisher's exact test), Q value = 1

Table S35. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	43	93	133
EIF1AX MUTATED	5	0	1	0
EIF1AX WILD-TYPE	125	43	92	133

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S36. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	107	77	61	92	62
EIF1AX MUTATED	4	2	0	0	0
EIF1AX WILD-TYPE	103	75	61	92	62

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S37. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	140	130
EIF1AX MUTATED	4	1	1
EIF1AX WILD-TYPE	126	139	129

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S38. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	123
EIF1AX MUTATED	3	1	2
EIF1AX WILD-TYPE	105	168	121

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S39. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	131	127
EIF1AX MUTATED	4	1	1
EIF1AX WILD-TYPE	138	130	126

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S40. Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	153	81	60
EIF1AX MUTATED	3	1	2	0
EIF1AX WILD-TYPE	103	152	79	60

'NUP93 MUTATION STATUS' versus 'CN_CNMF'

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

Table S41. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	313	60
NUP93 MUTATED	0	4	0
NUP93 WILD-TYPE	26	309	60

'NUP93 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S42. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	127	61
NUP93 MUTATED	3	1	0
NUP93 WILD-TYPE	210	126	61

'NUP93 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S43. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	43	93	133
NUP93 MUTATED	1	0	0	3
NUP93 WILD-TYPE	129	43	93	130

'NUP93 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S44. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	107	77	61	92	62
NUP93 MUTATED	1	0	0	2	1
NUP93 WILD-TYPE	106	77	61	90	61

'NUP93 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S45. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	140	130
NUP93 MUTATED	1	2	1
NUP93 WILD-TYPE	129	138	129

'NUP93 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S46. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	123
NUP93 MUTATED	1	2	1
NUP93 WILD-TYPE	107	167	122

'NUP93 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S47. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	131	127
NUP93 MUTATED	1	2	1
NUP93 WILD-TYPE	141	129	126

'NUP93 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S48. Gene #5: 'NUP93 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	153	81	60
NUP93 MUTATED	1	2	0	1
NUP93 WILD-TYPE	105	151	81	59

'PPM1D MUTATION STATUS' versus 'CN_CNMF'

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

Table S49. Gene #6: 'PPM1D MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	313	60
PPM1D MUTATED	0	5	0
PPM1D WILD-TYPE	26	308	60

'PPM1D MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S50. Gene #6: 'PPM1D MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	127	61
PPM1D MUTATED	3	2	0
PPM1D WILD-TYPE	210	125	61

'PPM1D MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'PPM1D MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	60	76	77
PPM1D MUTATED	0	0	3
PPM1D WILD-TYPE	60	76	74

'PPM1D MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S52. Gene #6: 'PPM1D MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	46	27	31	26	47	27	9
PPM1D MUTATED	1	0	0	0	2	0	0
PPM1D WILD-TYPE	45	27	31	26	45	27	9

'PPM1D MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S53. Gene #6: 'PPM1D MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	43	93	133
PPM1D MUTATED	1	0	2	2
PPM1D WILD-TYPE	129	43	91	131

'PPM1D MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0522 (Fisher's exact test), Q value = 1

Table S54. Gene #6: 'PPM1D MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	107	77	61	92	62
PPM1D MUTATED	1	0	3	0	1
PPM1D WILD-TYPE	106	77	58	92	61

'PPM1D MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S55. Gene #6: 'PPM1D MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	140	130
PPM1D MUTATED	2	3	0
PPM1D WILD-TYPE	128	137	130

'PPM1D MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 1

Table S56. Gene #6: 'PPM1D MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	123
PPM1D MUTATED	1	4	0
PPM1D WILD-TYPE	107	165	123

'PPM1D MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S57. Gene #6: 'PPM1D MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	131	127
PPM1D MUTATED	2	3	0
PPM1D WILD-TYPE	140	128	127

'PPM1D MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 1

Table S58. Gene #6: 'PPM1D MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	153	81	60
PPM1D MUTATED	1	4	0	0
PPM1D WILD-TYPE	105	149	81	60

'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

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

Table S59. Gene #7: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	313	60
DNMT3A MUTATED	1	2	0
DNMT3A WILD-TYPE	25	311	60

'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S60. Gene #7: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	127	61
DNMT3A MUTATED	1	2	0
DNMT3A WILD-TYPE	212	125	61

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S61. Gene #7: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	43	93	133
DNMT3A MUTATED	2	0	0	1
DNMT3A WILD-TYPE	128	43	93	132

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.812 (Fisher's exact test), Q value = 1

Table S62. Gene #7: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	107	77	61	92	62
DNMT3A MUTATED	2	0	0	1	0
DNMT3A WILD-TYPE	105	77	61	91	62

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S63. Gene #7: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	140	130
DNMT3A MUTATED	2	0	1
DNMT3A WILD-TYPE	128	140	129

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S64. Gene #7: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	123
DNMT3A MUTATED	2	0	1
DNMT3A WILD-TYPE	106	169	122

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S65. Gene #7: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	131	127
DNMT3A MUTATED	2	0	1
DNMT3A WILD-TYPE	140	131	126

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S66. Gene #7: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	153	81	60
DNMT3A MUTATED	2	0	0	1
DNMT3A WILD-TYPE	104	153	81	59

'KRAS MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	313	60
KRAS MUTATED	0	4	0
KRAS WILD-TYPE	26	309	60

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	127	61
KRAS MUTATED	1	3	0
KRAS WILD-TYPE	212	124	61

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S69. Gene #8: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	43	93	133
KRAS MUTATED	3	0	1	0
KRAS WILD-TYPE	127	43	92	133

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S70. Gene #8: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	107	77	61	92	62
KRAS MUTATED	3	1	0	0	0
KRAS WILD-TYPE	104	76	61	92	62

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 1

Table S71. Gene #8: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	140	130
KRAS MUTATED	3	1	0
KRAS WILD-TYPE	127	139	130

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	123
KRAS MUTATED	3	1	0
KRAS WILD-TYPE	105	168	123

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S73. Gene #8: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	131	127
KRAS MUTATED	3	1	0
KRAS WILD-TYPE	139	130	127

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S74. Gene #8: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	153	81	60
KRAS MUTATED	3	1	0	0
KRAS WILD-TYPE	103	152	81	60

'DLC1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S75. Gene #9: 'DLC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	313	60
DLC1 MUTATED	0	4	0
DLC1 WILD-TYPE	26	309	60

'DLC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S76. Gene #9: 'DLC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	127	61
DLC1 MUTATED	3	1	0
DLC1 WILD-TYPE	210	126	61

'DLC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S77. Gene #9: 'DLC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	43	93	133
DLC1 MUTATED	1	0	0	3
DLC1 WILD-TYPE	129	43	93	130

'DLC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.685 (Fisher's exact test), Q value = 1

Table S78. Gene #9: 'DLC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	107	77	61	92	62
DLC1 MUTATED	1	0	0	2	1
DLC1 WILD-TYPE	106	77	61	90	61

'DLC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S79. Gene #9: 'DLC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	140	130
DLC1 MUTATED	1	2	1
DLC1 WILD-TYPE	129	138	129

'DLC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S80. Gene #9: 'DLC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	123
DLC1 MUTATED	1	2	1
DLC1 WILD-TYPE	107	167	122

'DLC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 1

Table S81. Gene #9: 'DLC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	131	127
DLC1 MUTATED	1	2	1
DLC1 WILD-TYPE	141	129	126

'DLC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S82. Gene #9: 'DLC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	153	81	60
DLC1 MUTATED	1	2	0	1
DLC1 WILD-TYPE	105	151	81	59

'ITGAL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 1

Table S83. Gene #10: 'ITGAL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	313	60
ITGAL MUTATED	1	3	0
ITGAL WILD-TYPE	25	310	60

'ITGAL MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S84. Gene #10: 'ITGAL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	127	61
ITGAL MUTATED	3	0	1
ITGAL WILD-TYPE	210	127	60

'ITGAL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 1

Table S85. Gene #10: 'ITGAL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	43	93	133
ITGAL MUTATED	0	0	1	3
ITGAL WILD-TYPE	130	43	92	130

'ITGAL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.51 (Fisher's exact test), Q value = 1

Table S86. Gene #10: 'ITGAL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	107	77	61	92	62
ITGAL MUTATED	0	1	0	2	1
ITGAL WILD-TYPE	107	76	61	90	61

'ITGAL MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S87. Gene #10: 'ITGAL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	140	130
ITGAL MUTATED	0	2	2
ITGAL WILD-TYPE	130	138	128

'ITGAL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.576 (Fisher's exact test), Q value = 1

Table S88. Gene #10: 'ITGAL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	123
ITGAL MUTATED	0	2	2
ITGAL WILD-TYPE	108	167	121

'ITGAL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S89. Gene #10: 'ITGAL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	131	127
ITGAL MUTATED	0	2	2
ITGAL WILD-TYPE	142	129	125

'ITGAL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	153	81	60
ITGAL MUTATED	0	2	1	1
ITGAL WILD-TYPE	106	151	80	59

'NLRP6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.52 (Fisher's exact test), Q value = 1

Table S91. Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	26	313	60
NLRP6 MUTATED	0	2	1
NLRP6 WILD-TYPE	26	311	59

'NLRP6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.415 (Fisher's exact test), Q value = 1

Table S92. Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	213	127	61
NLRP6 MUTATED	3	0	0
NLRP6 WILD-TYPE	210	127	61

'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 1

Table S93. Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	130	43	93	133
NLRP6 MUTATED	0	0	2	1
NLRP6 WILD-TYPE	130	43	91	132

'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S94. Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	107	77	61	92	62
NLRP6 MUTATED	0	1	1	0	1
NLRP6 WILD-TYPE	107	76	60	92	61

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.776 (Fisher's exact test), Q value = 1

Table S95. Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	130	140	130
NLRP6 MUTATED	1	2	0
NLRP6 WILD-TYPE	129	138	130

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S96. Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	108	169	123
NLRP6 MUTATED	0	3	0
NLRP6 WILD-TYPE	108	166	123

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S97. Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	142	131	127
NLRP6 MUTATED	1	2	0
NLRP6 WILD-TYPE	141	129	127

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S98. Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	153	81	60
NLRP6 MUTATED	0	3	0	0
NLRP6 WILD-TYPE	106	150	81	60

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = THCA-TP.transferedmergedcluster.txt
Number of patients = 401
Number of significantly mutated genes = 11
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Q value calculation

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

Download Results

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

References

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

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

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