Correlation between gene mutation status and molecular subtypes
Thyroid Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1XG9PTQ
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/C1XG9PTQ
Overview
Introduction

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

Summary

Testing the association between mutation status of 6 genes and 10 molecular subtypes across 401 patients, 28 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'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 6 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, 28 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 0.000429
(0.0133) 		2.44e-41
(1.22e-39) 		1.54e-05
(0.00051) 		6.51e-10
(2.73e-08) 		6.71e-51
(3.69e-49) 		8.55e-53
(4.79e-51) 		1.33e-44
(6.93e-43) 		3.88e-49
(2.09e-47) 		8.54e-42
(4.36e-40) 		1.78e-47
(9.46e-46)
HRAS 14 (3%) 387 7.2e-06
(0.000245) 		9.42e-08
(3.58e-06) 		7.6e-05
(0.00243) 		0.00362
(0.105) 		2.76e-06
(9.65e-05) 		5.97e-08
(2.33e-06) 		3.4e-07
(1.26e-05) 		3.31e-08
(1.32e-06) 		1.03e-06
(3.71e-05) 		3.01e-08
(1.24e-06)
NRAS 34 (8%) 367 0.0109
(0.294) 		4.4e-18
(2.03e-16) 		1
(1.00) 		0.00046
(0.0138) 		5.94e-16
(2.67e-14) 		4.71e-19
(2.31e-17) 		6.24e-16
(2.75e-14) 		3.39e-18
(1.6e-16) 		1.85e-14
(7.94e-13) 		1.66e-18
(7.96e-17)
EIF1AX 6 (1%) 395 0.73
(1.00) 		0.13
(1.00) 		0.324
(1.00) 		0.13
(1.00) 		0.0594
(1.00) 		0.0097
(0.272) 		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) 		0.59
(1.00) 		0.619
(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) 		0.41
(1.00) 		0.286
(1.00) 		0.777
(1.00) 		0.0536
(1.00) 		0.533
(1.00) 		0.0614
(1.00)
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.29

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

'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.4e-18 (Fisher's exact test), Q value = 2e-16

Table S2.  Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #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 S2.  Get High-res Image Gene #1: '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 S3.  Gene #1: '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 = 0.00046 (Fisher's exact test), Q value = 0.014

Table S4.  Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #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 S3.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5.94e-16 (Fisher's exact test), Q value = 2.7e-14

Table S5.  Gene #1: '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 S4.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.71e-19 (Fisher's exact test), Q value = 2.3e-17

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 109 78 54
NRAS MUTATED 0 34 0 0
NRAS WILD-TYPE 158 75 78 54

Figure S5.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 6.24e-16 (Fisher's exact test), Q value = 2.7e-14

Table S7.  Gene #1: '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 S6.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.39e-18 (Fisher's exact test), Q value = 1.6e-16

Table S8.  Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #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 S7.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1.85e-14 (Fisher's exact test), Q value = 7.9e-13

Table S9.  Gene #1: '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 S8.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.66e-18 (Fisher's exact test), Q value = 8e-17

Table S10.  Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #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 S9.  Get High-res Image Gene #1: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000429 (Fisher's exact test), Q value = 0.013

Table S11.  Gene #2: '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 S10.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.44e-41 (Fisher's exact test), Q value = 1.2e-39

Table S12.  Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #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 S11.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1.54e-05 (Fisher's exact test), Q value = 0.00051

Table S13.  Gene #2: '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 S12.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 6.51e-10 (Fisher's exact test), Q value = 2.7e-08

Table S14.  Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #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 S13.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 6.71e-51 (Fisher's exact test), Q value = 3.7e-49

Table S15.  Gene #2: '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 S14.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.55e-53 (Fisher's exact test), Q value = 4.8e-51

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 109 78 54
BRAF MUTATED 143 4 60 33
BRAF WILD-TYPE 15 105 18 21

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

'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.33e-44 (Fisher's exact test), Q value = 6.9e-43

Table S17.  Gene #2: '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 S16.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.88e-49 (Fisher's exact test), Q value = 2.1e-47

Table S18.  Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #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 S17.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 8.54e-42 (Fisher's exact test), Q value = 4.4e-40

Table S19.  Gene #2: '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 S18.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.78e-47 (Fisher's exact test), Q value = 9.5e-46

Table S20.  Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #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 S19.  Get High-res Image Gene #2: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 7.2e-06 (Fisher's exact test), Q value = 0.00024

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 = 9.42e-08 (Fisher's exact test), Q value = 3.6e-06

Table S22.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #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 S21.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 7.6e-05 (Fisher's exact test), Q value = 0.0024

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 = 0.00362 (Fisher's exact test), Q value = 0.11

Table S24.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #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 S23.  Get High-res Image Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.76e-06 (Fisher's exact test), Q value = 9.7e-05

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 = 5.97e-08 (Fisher's exact test), Q value = 2.3e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 109 78 54
HRAS MUTATED 0 14 0 0
HRAS WILD-TYPE 158 95 78 54

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 = 3.4e-07 (Fisher's exact test), Q value = 1.3e-05

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 = 3.31e-08 (Fisher's exact test), Q value = 1.3e-06

Table S28.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #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 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 = 1.03e-06 (Fisher's exact test), Q value = 3.7e-05

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 = 3.01e-08 (Fisher's exact test), Q value = 1.2e-06

Table S30.  Gene #3: 'HRAS MUTATION STATUS' versus Molecular Subtype #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 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 = 0.73 (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 = 0.13 (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 127 70 204
EIF1AX MUTATED 4 1 1
EIF1AX WILD-TYPE 123 69 203
'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 = 0.13 (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
ALL 31 90 92
EIF1AX MUTATED 1 0 4
EIF1AX WILD-TYPE 30 90 88
'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0594 (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 = 0.0097 (Fisher's exact test), Q value = 0.27

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 109 78 54
EIF1AX MUTATED 0 4 0 2
EIF1AX WILD-TYPE 158 105 78 52

Figure S30.  Get High-res Image Gene #4: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.331 (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 = 0.586 (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 127 113 160
EIF1AX MUTATED 1 3 2
EIF1AX WILD-TYPE 126 110 158
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.38 (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 = 0.516 (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
ALL 151 111 138
EIF1AX MUTATED 2 3 1
EIF1AX WILD-TYPE 149 108 137
'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 = 0.827 (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 127 70 204
NUP93 MUTATED 1 0 3
NUP93 WILD-TYPE 126 70 201
'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 = 0.619 (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
ALL 158 109 78 54
NUP93 MUTATED 3 1 0 0
NUP93 WILD-TYPE 155 108 78 54
'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 127 113 160
NUP93 MUTATED 1 1 2
NUP93 WILD-TYPE 126 112 158
'NUP93 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.841 (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 = 1 (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
ALL 151 111 138
NUP93 MUTATED 2 1 1
NUP93 WILD-TYPE 149 110 137
'NLRP6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S49.  Gene #6: '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 = 0.295 (Fisher's exact test), Q value = 1

Table S50.  Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 70 204
NLRP6 MUTATED 0 0 3
NLRP6 WILD-TYPE 127 70 201
'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 1

Table S51.  Gene #6: '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 = 0.286 (Fisher's exact test), Q value = 1

Table S52.  Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 158 109 78 54
NLRP6 MUTATED 1 0 2 0
NLRP6 WILD-TYPE 157 109 76 54
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: '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 = 0.0536 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 127 113 160
NLRP6 MUTATED 3 0 0
NLRP6 WILD-TYPE 124 113 160
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S55.  Gene #6: '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 = 0.0614 (Fisher's exact test), Q value = 1

Table S56.  Gene #6: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 151 111 138
NLRP6 MUTATED 0 0 3
NLRP6 WILD-TYPE 151 111 135
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 = 6

  • 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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