Correlation between gene mutation status and molecular subtypes

Stomach Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

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 (2013): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1D21VP5

Overview

Introduction

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

Summary

Testing the association between mutation status of 25 genes and 8 molecular subtypes across 220 patients, 26 significant findings detected with P value < 0.05 and Q value < 0.25.

PGM5 mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
CBWD1 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
TP53 mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
PIK3CA mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
ARID1A mutation correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
RHOA mutation correlated to 'MIRSEQ_MATURE_CNMF'.
IRF2 mutation correlated to 'MIRSEQ_CNMF'.
APC mutation correlated to 'MIRSEQ_CNMF'.
BCOR mutation correlated to 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 25 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, 26 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	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
CBWD1	28 (13%)	192	0.000149 (0.027)	1.79e-06 (0.000348)	0.000857 (0.15)	7.48e-05 (0.0139)	2.36e-05 (0.0045)	0.000274 (0.049)	0.078 (1.00)	0.0267 (1.00)
TP53	99 (45%)	121	4.33e-09 (8.49e-07)	3.18e-05 (0.00605)	7.74e-05 (0.0143)	0.00381 (0.641)	6.4e-06 (0.00124)	9.12e-06 (0.00175)	0.0704 (1.00)	9.4e-05 (0.0173)
PIK3CA	48 (22%)	172	0.000108 (0.0198)	1.83e-09 (3.6e-07)	0.00058 (0.103)	1.37e-07 (2.68e-05)	0.0245 (1.00)	0.0119 (1.00)	0.000367 (0.0654)	0.00471 (0.777)
ARID1A	41 (19%)	179	0.000215 (0.0387)	0.00656 (1.00)	3.52e-05 (0.00665)	0.000131 (0.0238)	0.0198 (1.00)	0.0128 (1.00)	0.761 (1.00)	0.312 (1.00)
PGM5	22 (10%)	198	0.00138 (0.237)	4.28e-05 (0.00804)	0.00635 (1.00)	0.00164 (0.279)	0.0126 (1.00)	0.00398 (0.665)	0.208 (1.00)	0.168 (1.00)
RHOA	13 (6%)	207	0.142 (1.00)	0.189 (1.00)	0.829 (1.00)	0.604 (1.00)	0.106 (1.00)	0.283 (1.00)	0.000594 (0.105)	0.297 (1.00)
IRF2	15 (7%)	205	0.0906 (1.00)	0.233 (1.00)	0.434 (1.00)	0.0297 (1.00)	0.00102 (0.176)	0.0125 (1.00)	0.135 (1.00)	0.249 (1.00)
APC	33 (15%)	187	0.97 (1.00)	0.0207 (1.00)	0.102 (1.00)	0.0318 (1.00)	0.000956 (0.166)	0.0129 (1.00)	0.0272 (1.00)	0.0049 (0.803)
BCOR	16 (7%)	204	0.0156 (1.00)	6.67e-05 (0.0125)	0.0045 (0.747)	0.0561 (1.00)	0.00821 (1.00)	0.00336 (0.567)	0.183 (1.00)	0.0259 (1.00)
TRIM48	14 (6%)	206	0.252 (1.00)	0.322 (1.00)	0.41 (1.00)	0.109 (1.00)	0.126 (1.00)	0.192 (1.00)	0.0907 (1.00)	1 (1.00)
KRAS	25 (11%)	195	0.00873 (1.00)	0.127 (1.00)	0.351 (1.00)	0.128 (1.00)	0.85 (1.00)	0.96 (1.00)	0.179 (1.00)	0.674 (1.00)
SMAD4	19 (9%)	201	0.648 (1.00)	0.963 (1.00)	0.0524 (1.00)	0.226 (1.00)	0.258 (1.00)	0.16 (1.00)	0.94 (1.00)	0.462 (1.00)
MXRA8	11 (5%)	209	0.118 (1.00)	0.0232 (1.00)	0.0909 (1.00)	0.0394 (1.00)	0.153 (1.00)	0.00949 (1.00)	0.428 (1.00)	0.0635 (1.00)
CDH1	18 (8%)	202	0.252 (1.00)	0.458 (1.00)	0.0314 (1.00)	0.00564 (0.92)	0.11 (1.00)	0.0876 (1.00)	0.278 (1.00)	0.114 (1.00)
PTEN	14 (6%)	206	0.0057 (0.924)	0.0152 (1.00)	0.00155 (0.265)	0.0452 (1.00)	0.027 (1.00)	0.0397 (1.00)	0.1 (1.00)	0.0575 (1.00)
B2M	8 (4%)	212	0.0258 (1.00)	0.0232 (1.00)	0.0329 (1.00)	0.0968 (1.00)	0.108 (1.00)	0.287 (1.00)	0.428 (1.00)	0.0635 (1.00)
FBXW7	19 (9%)	201	0.0833 (1.00)	0.022 (1.00)	0.0157 (1.00)	0.292 (1.00)	0.102 (1.00)	0.0169 (1.00)	0.0238 (1.00)	0.0812 (1.00)
PTH2	4 (2%)	216	1 (1.00)	0.687 (1.00)	0.281 (1.00)	0.472 (1.00)	0.672 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
FAM46D	6 (3%)	214	1 (1.00)	0.708 (1.00)	0.222 (1.00)	0.636 (1.00)	0.56 (1.00)	0.767 (1.00)	1 (1.00)	0.731 (1.00)
RNF43	9 (4%)	211	0.175 (1.00)	0.596 (1.00)	0.202 (1.00)	0.525 (1.00)	0.338 (1.00)	0.167 (1.00)	0.521 (1.00)	0.45 (1.00)
MAP2K7	14 (6%)	206	0.00583 (0.938)	0.0984 (1.00)	0.41 (1.00)	0.51 (1.00)	0.133 (1.00)	0.171 (1.00)	0.33 (1.00)	0.052 (1.00)
WSB2	7 (3%)	213	0.341 (1.00)	0.131 (1.00)	0.215 (1.00)	0.0394 (1.00)	0.103 (1.00)	0.0913 (1.00)	0.0244 (1.00)	0.00941 (1.00)
C13ORF33	6 (3%)	214	0.364 (1.00)	0.0165 (1.00)	0.243 (1.00)	0.407 (1.00)	0.0768 (1.00)	0.324 (1.00)	0.274 (1.00)	0.45 (1.00)
TRPS1	30 (14%)	190	0.64 (1.00)	0.0397 (1.00)	0.0233 (1.00)	0.24 (1.00)	0.0327 (1.00)	0.866 (1.00)	0.378 (1.00)	0.583 (1.00)
IAPP	4 (2%)	216	0.84 (1.00)		0.763 (1.00)	0.257 (1.00)	0.449 (1.00)	0.816 (1.00)

'PGM5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.24

Table S1. Gene #2: 'PGM5 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	99	22	19	79
PGM5 MUTATED	13	4	4	1
PGM5 WILD-TYPE	86	18	15	78

Figure S1. Get High-res Image Gene #2: 'PGM5 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'PGM5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.28e-05 (Fisher's exact test), Q value = 0.008

Table S2. Gene #2: 'PGM5 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
PGM5 MUTATED	3	12	1	0
PGM5 WILD-TYPE	24	39	43	53

Figure S2. Get High-res Image Gene #2: 'PGM5 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'CBWD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000149 (Fisher's exact test), Q value = 0.027

Table S3. Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	99	22	19	79
CBWD1 MUTATED	20	3	4	1
CBWD1 WILD-TYPE	79	19	15	78

Figure S3. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'CBWD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.00035

Table S4. Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
CBWD1 MUTATED	4	16	2	0
CBWD1 WILD-TYPE	23	35	42	53

Figure S4. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000857 (Chi-square test), Q value = 0.15

Table S5. Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	35	28	33	39
CBWD1 MUTATED	11	2	3	4	0
CBWD1 WILD-TYPE	25	33	25	29	39

Figure S5. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.48e-05 (Fisher's exact test), Q value = 0.014

Table S6. Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	33	46	57
CBWD1 MUTATED	2	1	1	16
CBWD1 WILD-TYPE	33	32	45	41

Figure S6. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.36e-05 (Fisher's exact test), Q value = 0.0045

Table S7. Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	50	61	43
CBWD1 MUTATED	14	1	11	0
CBWD1 WILD-TYPE	44	49	50	43

Figure S7. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000274 (Fisher's exact test), Q value = 0.049

Table S8. Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	65	94
CBWD1 MUTATED	0	7	19
CBWD1 WILD-TYPE	53	58	75

Figure S8. Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 4.33e-09 (Fisher's exact test), Q value = 8.5e-07

Table S9. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	99	22	19	79
TP53 MUTATED	22	15	9	52
TP53 WILD-TYPE	77	7	10	27

Figure S9. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.006

Table S10. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
TP53 MUTATED	5	25	15	37
TP53 WILD-TYPE	22	26	29	16

Figure S10. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 7.74e-05 (Chi-square test), Q value = 0.014

Table S11. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	35	28	33	39
TP53 MUTATED	9	10	10	19	28
TP53 WILD-TYPE	27	25	18	14	11

Figure S11. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 6.4e-06 (Fisher's exact test), Q value = 0.0012

Table S12. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	50	61	43
TP53 MUTATED	20	16	26	34
TP53 WILD-TYPE	38	34	35	9

Figure S12. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.12e-06 (Fisher's exact test), Q value = 0.0018

Table S13. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	53	65	94
TP53 MUTATED	39	22	35
TP53 WILD-TYPE	14	43	59

Figure S13. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.4e-05 (Fisher's exact test), Q value = 0.017

Table S14. Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	42	57	69
TP53 MUTATED	30	16	34
TP53 WILD-TYPE	12	41	35

Figure S14. Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.02

Table S15. Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	99	22	19	79
PIK3CA MUTATED	30	7	6	5
PIK3CA WILD-TYPE	69	15	13	74

Figure S15. Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.83e-09 (Fisher's exact test), Q value = 3.6e-07

Table S16. Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
PIK3CA MUTATED	19	15	4	4
PIK3CA WILD-TYPE	8	36	40	49

Figure S16. Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Chi-square test), Q value = 0.1

Table S17. Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	35	28	33	39
PIK3CA MUTATED	16	6	4	10	2
PIK3CA WILD-TYPE	20	29	24	23	37

Figure S17. Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-07 (Fisher's exact test), Q value = 2.7e-05

Table S18. Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	33	46	57
PIK3CA MUTATED	1	14	2	21
PIK3CA WILD-TYPE	34	19	44	36

Figure S18. Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000367 (Fisher's exact test), Q value = 0.065

Table S19. Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	66
PIK3CA MUTATED	23	6	10
PIK3CA WILD-TYPE	31	42	56

Figure S19. Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_MATURE_CNMF'

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000215 (Fisher's exact test), Q value = 0.039

Table S20. Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	99	22	19	79
ARID1A MUTATED	30	2	4	5
ARID1A WILD-TYPE	69	20	15	74

Figure S20. Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.52e-05 (Chi-square test), Q value = 0.0066

Table S21. Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	36	35	28	33	39
ARID1A MUTATED	17	7	3	6	1
ARID1A WILD-TYPE	19	28	25	27	38

Figure S21. Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000131 (Fisher's exact test), Q value = 0.024

Table S22. Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	35	33	46	57
ARID1A MUTATED	3	9	2	20
ARID1A WILD-TYPE	32	24	44	37

Figure S22. Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000594 (Fisher's exact test), Q value = 0.1

Table S23. Gene #9: 'RHOA MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	54	48	66
RHOA MUTATED	3	8	0
RHOA WILD-TYPE	51	40	66

Figure S23. Get High-res Image Gene #9: 'RHOA MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_MATURE_CNMF'

'IRF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.18

Table S24. Gene #11: 'IRF2 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	50	61	43
IRF2 MUTATED	9	0	5	0
IRF2 WILD-TYPE	49	50	56	43

Figure S24. Get High-res Image Gene #11: 'IRF2 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000956 (Fisher's exact test), Q value = 0.17

Table S25. Gene #19: 'APC MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	50	61	43
APC MUTATED	16	1	10	4
APC WILD-TYPE	42	49	51	39

Figure S25. Get High-res Image Gene #19: 'APC MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'BCOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.67e-05 (Fisher's exact test), Q value = 0.012

Table S26. Gene #22: 'BCOR MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	27	51	44	53
BCOR MUTATED	7	2	1	0
BCOR WILD-TYPE	20	49	43	53

Figure S26. Get High-res Image Gene #22: 'BCOR MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

Methods & Data

Input

Mutation data file = STAD-TP.mutsig.cluster.txt
Molecular subtypes file = STAD-TP.transferedmergedcluster.txt
Number of patients = 220
Number of significantly mutated genes = 25
Number of Molecular subtypes = 8
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Chi-square test

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

Q value calculation

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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