Correlation between gene mutation status and molecular subtypes

Kidney Renal Papillary Cell Carcinoma (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/C1V40SVX

Overview

Introduction

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

Summary

Testing the association between mutation status of 7 genes and 8 molecular subtypes across 168 patients, 4 significant findings detected with P value < 0.05 and Q value < 0.25.

NEFH mutation correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
ZNF598 mutation correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 7 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 4 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Chi-square test	Chi-square 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
NEFH	10 (6%)	158	0.423 (1.00)	0.567 (1.00)	0.0614 (1.00)	0.426 (1.00)	0.0235 (1.00)	0.00043 (0.0232)	0.0157 (0.802)	0.003 (0.159)
ZNF598	13 (8%)	155	0.134 (1.00)	0.379 (1.00)	0.0978 (1.00)	0.385 (1.00)	0.675 (1.00)	0.0004 (0.022)	0.452 (1.00)	0.000209 (0.0117)
SKI	6 (4%)	162	0.0954 (1.00)	0.0833 (1.00)	0.127 (1.00)	0.674 (1.00)	0.696 (1.00)	0.38 (1.00)	0.776 (1.00)	0.858 (1.00)
HNRNPM	11 (7%)	157	0.309 (1.00)	0.845 (1.00)	0.828 (1.00)	0.258 (1.00)	0.544 (1.00)	0.345 (1.00)	0.682 (1.00)	0.403 (1.00)
NF2	12 (7%)	156	0.0523 (1.00)	0.0338 (1.00)	0.0768 (1.00)	0.932 (1.00)	0.93 (1.00)	0.609 (1.00)	0.868 (1.00)	1 (1.00)
BMS1	13 (8%)	155	0.906 (1.00)	0.52 (1.00)	0.324 (1.00)	0.876 (1.00)	0.59 (1.00)	0.0991 (1.00)	1 (1.00)	0.323 (1.00)
MUC2	26 (15%)	142	0.164 (1.00)	0.319 (1.00)	0.00856 (0.445)	0.0821 (1.00)	0.712 (1.00)	0.171 (1.00)	0.34 (1.00)	0.317 (1.00)

'SKI MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0954 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	59	34	37	16	22
SKI MUTATED	5	0	0	1	0
SKI WILD-TYPE	54	34	37	15	22

'SKI MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0833 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	23	30	38	29
SKI MUTATED	4	0	0	1	1
SKI WILD-TYPE	29	23	30	37	28

'SKI MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S3. Gene #1: 'SKI MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	64	47	25
SKI MUTATED	1	1	1	3
SKI WILD-TYPE	31	63	46	22

'SKI MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S4. Gene #1: 'SKI MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	63	48
SKI MUTATED	1	3	2
SKI WILD-TYPE	56	60	46

'SKI MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'SKI MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	58	55
SKI MUTATED	3	2	1
SKI WILD-TYPE	52	56	54

'SKI MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S6. Gene #1: 'SKI MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	70	73
SKI MUTATED	2	2	2
SKI WILD-TYPE	23	68	71

'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S7. Gene #1: 'SKI MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	61	55
SKI MUTATED	2	3	1
SKI WILD-TYPE	50	58	54

'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.858 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'SKI MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	82	20
SKI MUTATED	2	3	1
SKI WILD-TYPE	64	79	19

'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.423 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	59	34	37	16	22
NEFH MUTATED	2	1	3	1	3
NEFH WILD-TYPE	57	33	34	15	19

'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.567 (Chi-square test), Q value = 1

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	23	30	38	29
NEFH MUTATED	2	0	3	3	1
NEFH WILD-TYPE	31	23	27	35	28

'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0614 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	64	47	25
NEFH MUTATED	5	2	3	0
NEFH WILD-TYPE	27	62	44	25

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.426 (Fisher's exact test), Q value = 1

Table S12. Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	63	48
NEFH MUTATED	4	5	1
NEFH WILD-TYPE	53	58	47

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	58	55
NEFH MUTATED	6	0	4
NEFH WILD-TYPE	49	58	51

Figure S1. Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.023

Table S14. Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	70	73
NEFH MUTATED	0	0	10
NEFH WILD-TYPE	25	70	63

Figure S2. Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.8

Table S15. Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	61	55
NEFH MUTATED	4	0	6
NEFH WILD-TYPE	48	61	49

Figure S3. Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.003 (Fisher's exact test), Q value = 0.16

Table S16. Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	82	20
NEFH MUTATED	0	10	0
NEFH WILD-TYPE	66	72	20

Figure S4. Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HNRNPM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.309 (Chi-square test), Q value = 1

Table S17. Gene #3: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	59	34	37	16	22
HNRNPM MUTATED	6	0	2	2	1
HNRNPM WILD-TYPE	53	34	35	14	21

'HNRNPM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.845 (Chi-square test), Q value = 1

Table S18. Gene #3: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	23	30	38	29
HNRNPM MUTATED	2	2	2	4	1
HNRNPM WILD-TYPE	31	21	28	34	28

'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S19. Gene #3: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	64	47	25
HNRNPM MUTATED	1	4	4	2
HNRNPM WILD-TYPE	31	60	43	23

'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S20. Gene #3: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	63	48
HNRNPM MUTATED	6	2	3
HNRNPM WILD-TYPE	51	61	45

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S21. Gene #3: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	58	55
HNRNPM MUTATED	2	4	5
HNRNPM WILD-TYPE	53	54	50

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S22. Gene #3: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	70	73
HNRNPM MUTATED	1	7	3
HNRNPM WILD-TYPE	24	63	70

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S23. Gene #3: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	61	55
HNRNPM MUTATED	2	5	4
HNRNPM WILD-TYPE	50	56	51

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.403 (Fisher's exact test), Q value = 1

Table S24. Gene #3: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	82	20
HNRNPM MUTATED	6	5	0
HNRNPM WILD-TYPE	60	77	20

'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0523 (Chi-square test), Q value = 1

Table S25. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	59	34	37	16	22
NF2 MUTATED	2	1	6	0	3
NF2 WILD-TYPE	57	33	31	16	19

'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0338 (Chi-square test), Q value = 1

Table S26. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	23	30	38	29
NF2 MUTATED	0	4	2	5	0
NF2 WILD-TYPE	33	19	28	33	29

Figure S5. Get High-res Image Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0768 (Fisher's exact test), Q value = 1

Table S27. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	64	47	25
NF2 MUTATED	0	7	5	0
NF2 WILD-TYPE	32	57	42	25

'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 1

Table S28. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	63	48
NF2 MUTATED	4	4	4
NF2 WILD-TYPE	53	59	44

'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S29. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	58	55
NF2 MUTATED	4	5	3
NF2 WILD-TYPE	51	53	52

'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S30. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	70	73
NF2 MUTATED	1	4	7
NF2 WILD-TYPE	24	66	66

'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	61	55
NF2 MUTATED	4	5	3
NF2 WILD-TYPE	48	56	52

'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S32. Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	82	20
NF2 MUTATED	5	6	1
NF2 WILD-TYPE	61	76	19

'ZNF598 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.134 (Chi-square test), Q value = 1

Table S33. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	59	34	37	16	22
ZNF598 MUTATED	5	0	5	0	3
ZNF598 WILD-TYPE	54	34	32	16	19

'ZNF598 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.379 (Chi-square test), Q value = 1

Table S34. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	23	30	38	29
ZNF598 MUTATED	3	4	1	2	2
ZNF598 WILD-TYPE	30	19	29	36	27

'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0978 (Fisher's exact test), Q value = 1

Table S35. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	64	47	25
ZNF598 MUTATED	1	5	2	5
ZNF598 WILD-TYPE	31	59	45	20

'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S36. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	63	48
ZNF598 MUTATED	3	4	6
ZNF598 WILD-TYPE	54	59	42

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S37. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	58	55
ZNF598 MUTATED	3	6	4
ZNF598 WILD-TYPE	52	52	51

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.022

Table S38. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	70	73
ZNF598 MUTATED	5	8	0
ZNF598 WILD-TYPE	20	62	73

Figure S6. Get High-res Image Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S39. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	61	55
ZNF598 MUTATED	3	7	3
ZNF598 WILD-TYPE	49	54	52

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000209 (Fisher's exact test), Q value = 0.012

Table S40. Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	82	20
ZNF598 MUTATED	10	0	3
ZNF598 WILD-TYPE	56	82	17

Figure S7. Get High-res Image Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BMS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.906 (Chi-square test), Q value = 1

Table S41. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	59	34	37	16	22
BMS1 MUTATED	6	2	3	1	1
BMS1 WILD-TYPE	53	32	34	15	21

'BMS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.52 (Chi-square test), Q value = 1

Table S42. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	23	30	38	29
BMS1 MUTATED	3	1	1	2	4
BMS1 WILD-TYPE	30	22	29	36	25

'BMS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S43. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	64	47	25
BMS1 MUTATED	3	3	3	4
BMS1 WILD-TYPE	29	61	44	21

'BMS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S44. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	63	48
BMS1 MUTATED	5	4	4
BMS1 WILD-TYPE	52	59	44

'BMS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S45. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	58	55
BMS1 MUTATED	6	4	3
BMS1 WILD-TYPE	49	54	52

'BMS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0991 (Fisher's exact test), Q value = 1

Table S46. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	70	73
BMS1 MUTATED	3	2	8
BMS1 WILD-TYPE	22	68	65

'BMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S47. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	61	55
BMS1 MUTATED	4	5	4
BMS1 WILD-TYPE	48	56	51

'BMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S48. Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	82	20
BMS1 MUTATED	3	9	1
BMS1 WILD-TYPE	63	73	19

'MUC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.164 (Chi-square test), Q value = 1

Table S49. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	59	34	37	16	22
MUC2 MUTATED	8	2	10	3	3
MUC2 WILD-TYPE	51	32	27	13	19

'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S50. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	33	23	30	38	29
MUC2 MUTATED	7	5	5	6	1
MUC2 WILD-TYPE	26	18	25	32	28

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 0.45

Table S51. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	32	64	47	25
MUC2 MUTATED	11	10	4	1
MUC2 WILD-TYPE	21	54	43	24

Figure S8. Get High-res Image Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0821 (Fisher's exact test), Q value = 1

Table S52. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	57	63	48
MUC2 MUTATED	6	15	5
MUC2 WILD-TYPE	51	48	43

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 1

Table S53. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	55	58	55
MUC2 MUTATED	10	9	7
MUC2 WILD-TYPE	45	49	48

'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 1

Table S54. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	25	70	73
MUC2 MUTATED	6	7	13
MUC2 WILD-TYPE	19	63	60

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S55. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	52	61	55
MUC2 MUTATED	11	9	6
MUC2 WILD-TYPE	41	52	49

'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S56. Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	66	82	20
MUC2 MUTATED	7	15	4
MUC2 WILD-TYPE	59	67	16

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = KIRP-TP.transferedmergedcluster.txt
Number of patients = 168
Number of significantly mutated genes = 7
Number of Molecular subtypes = 8
Exclude genes that fewer than K tumors have mutations, K = 3

Chi-square test

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

References

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

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

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

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