Correlation between gene mutation status and molecular subtypes

Thyroid Adenocarcinoma (Primary solid tumor)

Due to issues with GAF 3.0, we strongly advise caution in the use of these results.

23 September 2013 | analyses__2013_09_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/C1H130DK

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 10 molecular subtypes across 401 patients, 30 significant findings detected with P value < 0.05 and Q value < 0.25.

NRAS mutation correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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'.
HRAS 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'.
OTUD4 mutation correlated to 'MRNASEQ_CNMF'.
EIF1AX mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 7 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, 30 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	0.000423 (0.0161)	1.56e-41 (9.04e-40)	1.51e-05 (0.000618)	6.5e-10 (3.25e-08)	8.11e-54 (5.19e-52)	1.54e-51 (9.73e-50)	9.16e-45 (5.5e-43)	2.33e-49 (1.44e-47)	6.03e-42 (3.56e-40)	9.72e-48 (5.93e-46)
HRAS	14 (3%)	387	7.2e-06 (0.000302)	1.13e-07 (5.32e-06)	7.6e-05 (0.00304)	0.00362 (0.134)	9.11e-07 (3.92e-05)	1.94e-07 (8.72e-06)	1.79e-07 (8.22e-06)	1.12e-08 (5.38e-07)	4.91e-07 (2.16e-05)	8.59e-09 (4.21e-07)
NRAS	34 (8%)	367	0.0106 (0.361)	8.51e-19 (4.6e-17)	1 (1.00)	0.000377 (0.0147)	1.44e-17 (7.65e-16)	2.64e-19 (1.48e-17)	1.04e-16 (5.41e-15)	4.4e-19 (2.42e-17)	3.09e-15 (1.57e-13)	2.21e-19 (1.26e-17)
OTUD4	5 (1%)	396	1 (1.00)	0.32 (1.00)			0.00555 (0.194)	0.0182 (0.601)	1 (1.00)	0.0707 (1.00)	0.168 (1.00)	0.384 (1.00)
EIF1AX	6 (1%)	395	0.73 (1.00)	0.13 (1.00)	0.324 (1.00)	0.13 (1.00)	0.137 (1.00)	0.00381 (0.137)	0.331 (1.00)	0.586 (1.00)	0.38 (1.00)	0.516 (1.00)
NUP93	4 (1%)	397	1 (1.00)	0.827 (1.00)			0.504 (1.00)	0.87 (1.00)	1 (1.00)	1 (1.00)	0.841 (1.00)	1 (1.00)
NLRP6	3 (1%)	398	0.518 (1.00)	0.295 (1.00)			0.37 (1.00)	0.686 (1.00)	0.777 (1.00)	0.0536 (1.00)	0.533 (1.00)	0.0614 (1.00)

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 8.51e-19 (Fisher's exact test), Q value = 4.6e-17

Table S1. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	70	204
NRAS MUTATED	34	0	0
NRAS WILD-TYPE	93	70	204

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

'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.000377 (Fisher's exact test), Q value = 0.015

Table S2. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	90	92
NRAS MUTATED	5	0	9
NRAS WILD-TYPE	26	90	83

Figure S2. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.44e-17 (Fisher's exact test), Q value = 7.7e-16

Table S3. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	46	91	128
NRAS MUTATED	34	0	0	0
NRAS WILD-TYPE	91	46	91	128

Figure S3. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.64e-19 (Fisher's exact test), Q value = 1.5e-17

Table S4. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	171	76	31
NRAS MUTATED	34	0	0	0
NRAS WILD-TYPE	78	171	76	31

Figure S4. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.04e-16 (Fisher's exact test), Q value = 5.4e-15

Table S5. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #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 S5. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.4e-19 (Fisher's exact test), Q value = 2.4e-17

Table S6. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	113	160
NRAS MUTATED	0	33	1
NRAS WILD-TYPE	127	80	159

Figure S6. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 3.09e-15 (Fisher's exact test), Q value = 1.6e-13

Table S7. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #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 S7. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2.21e-19 (Fisher's exact test), Q value = 1.3e-17

Table S8. Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	111	138
NRAS MUTATED	1	33	0
NRAS WILD-TYPE	150	78	138

Figure S8. Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000423 (Fisher's exact test), Q value = 0.016

Table S9. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S9. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.56e-41 (Fisher's exact test), Q value = 9e-40

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	70	204
BRAF MUTATED	19	42	179
BRAF WILD-TYPE	108	28	25

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

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1.51e-05 (Fisher's exact test), Q value = 0.00062

Table S11. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S11. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 6.5e-10 (Fisher's exact test), Q value = 3.3e-08

Table S12. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	90	92
BRAF MUTATED	16	73	32
BRAF WILD-TYPE	15	17	60

Figure S12. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8.11e-54 (Fisher's exact test), Q value = 5.2e-52

Table S13. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	46	91	128
BRAF MUTATED	10	29	76	119
BRAF WILD-TYPE	115	17	15	9

Figure S13. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.54e-51 (Fisher's exact test), Q value = 9.7e-50

Table S14. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	171	76	31
BRAF MUTATED	5	151	58	20
BRAF WILD-TYPE	107	20	18	11

Figure S14. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 9.16e-45 (Fisher's exact test), Q value = 5.5e-43

Table S15. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S15. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.33e-49 (Fisher's exact test), Q value = 1.4e-47

Table S16. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	113	160
BRAF MUTATED	107	5	127
BRAF WILD-TYPE	20	108	33

Figure S16. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.03e-42 (Fisher's exact test), Q value = 3.6e-40

Table S17. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #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 S17. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.72e-48 (Fisher's exact test), Q value = 5.9e-46

Table S18. Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	111	138
BRAF MUTATED	122	5	112
BRAF WILD-TYPE	29	106	26

Figure S18. Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 7.2e-06 (Fisher's exact test), Q value = 3e-04

Table S19. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S19. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.13e-07 (Fisher's exact test), Q value = 5.3e-06

Table S20. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	70	204
HRAS MUTATED	14	0	0
HRAS WILD-TYPE	113	70	204

Figure S20. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 7.6e-05 (Fisher's exact test), Q value = 0.003

Table S21. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S21. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00362 (Fisher's exact test), Q value = 0.13

Table S22. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	31	90	92
HRAS MUTATED	1	0	9
HRAS WILD-TYPE	30	90	83

Figure S22. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9.11e-07 (Fisher's exact test), Q value = 3.9e-05

Table S23. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	46	91	128
HRAS MUTATED	14	0	0	0
HRAS WILD-TYPE	111	46	91	128

Figure S23. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.94e-07 (Fisher's exact test), Q value = 8.7e-06

Table S24. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	171	76	31
HRAS MUTATED	14	0	0	0
HRAS WILD-TYPE	98	171	76	31

Figure S24. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.79e-07 (Fisher's exact test), Q value = 8.2e-06

Table S25. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S25. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.12e-08 (Fisher's exact test), Q value = 5.4e-07

Table S26. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	127	113	160
HRAS MUTATED	0	14	0
HRAS WILD-TYPE	127	99	160

Figure S26. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 4.91e-07 (Fisher's exact test), Q value = 2.2e-05

Table S27. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #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 S27. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.59e-09 (Fisher's exact test), Q value = 4.2e-07

Table S28. Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	111	138
HRAS MUTATED	0	14	0
HRAS WILD-TYPE	151	97	138

Figure S28. Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Clinical Feature #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'OTUD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00555 (Fisher's exact test), Q value = 0.19

Table S29. Gene #4: 'OTUD4 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	125	46	91	128
OTUD4 MUTATED	0	1	4	0
OTUD4 WILD-TYPE	125	45	87	128

Figure S29. Get High-res Image Gene #4: 'OTUD4 MUTATION STATUS' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00381 (Fisher's exact test), Q value = 0.14

Table S30. Gene #5: 'EIF1AX MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	112	171	76	31
EIF1AX MUTATED	4	0	0	2
EIF1AX WILD-TYPE	108	171	76	29

Figure S30. Get High-res Image Gene #5: 'EIF1AX MUTATION STATUS' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

Methods & Data

Input

Mutation data file = THCA-TP.mutsig.cluster.txt
Molecular subtypes file = THCA-TP.transferedmergedcluster.txt
Number of patients = 401
Number of significantly mutated genes = 7
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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