Correlation between gene mutation status and molecular subtypes
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, 35 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 'CN_CNMF',  'METHLYATION_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'.

  • EIF1AX mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • TG mutation correlated to 'RPPA_CNMF',  'MRNASEQ_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, 35 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 0.0038
(0.0167) 		1e-05
(5e-05) 		1e-05
(5e-05) 		1e-05
(5e-05) 		1e-05
(5e-05) 		1e-05
(5e-05) 		1e-05
(5e-05) 		1e-05
(5e-05) 		1e-05
(5e-05) 		1e-05
(5e-05)
HRAS 14 (3%) 387 1e-05
(5e-05) 		1e-05
(5e-05) 		0.00659
(0.0268) 		0.00869
(0.0341) 		1e-05
(5e-05) 		1e-05
(5e-05) 		1e-05
(5e-05) 		1e-05
(5e-05) 		0.00029
(0.00133) 		1e-05
(5e-05)
NRAS 34 (8%) 367 0.0272
(0.0951) 		1e-05
(5e-05) 		0.106
(0.278) 		0.00957
(0.0363) 		1e-05
(5e-05) 		1e-05
(5e-05) 		1e-05
(5e-05) 		1e-05
(5e-05) 		4e-05
(0.000191) 		1e-05
(5e-05)
TG 11 (3%) 390 0.882
(1.00) 		0.0609
(0.181) 		0.0296
(0.0987) 		0.89
(1.00) 		0.0277
(0.0951) 		0.147
(0.327) 		0.0557
(0.17) 		0.00615
(0.026) 		0.0353
(0.114) 		0.018
(0.066)
EIF1AX 6 (1%) 395 0.79
(1.00) 		0.134
(0.313) 		0.511
(0.78) 		0.319
(0.573) 		0.149
(0.327) 		0.0478
(0.15) 		0.291
(0.545) 		0.394
(0.666) 		0.676
(0.932) 		0.137
(0.313)
NUP93 4 (1%) 397 0.453
(0.732) 		1
(1.00) 		0.506
(0.78) 		0.563
(0.808) 		0.845
(1.00) 		1
(1.00) 		0.684
(0.932) 		0.686
(0.932)
PPM1D 5 (1%) 396 0.762
(1.00) 		1
(1.00) 		0.118
(0.289) 		0.848
(1.00) 		0.808
(1.00) 		0.212
(0.424) 		0.21
(0.424) 		0.191
(0.403) 		0.743
(0.997) 		0.16
(0.345)
KRAS 4 (1%) 397 1
(1.00) 		0.211
(0.424) 		0.251
(0.493) 		0.292
(0.545) 		0.0791
(0.229) 		0.0978
(0.269) 		0.378
(0.651) 		0.105
(0.278)
DLC1 4 (1%) 397 1
(1.00) 		1
(1.00) 		0.504
(0.78) 		0.558
(0.808) 		0.846
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ITGAL 4 (1%) 397 0.0935
(0.264) 		0.379
(0.651) 		0.284
(0.545) 		0.323
(0.573) 		0.553
(0.808) 		0.564
(0.808) 		0.829
(1.00) 		0.565
(0.808)
NLRP6 3 (1%) 398 0.608
(0.857) 		0.414
(0.69) 		0.319
(0.573) 		0.127
(0.304) 		0.428
(0.703) 		0.114
(0.289) 		0.493
(0.78) 		0.117
(0.289)
'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0038 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 292 66
BRAF MUTATED 19 190 31
BRAF WILD-TYPE 22 102 35

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 = 5e-05

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 = 1e-05 (Fisher's exact test), Q value = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 49
BRAF MUTATED 24 43 10 44
BRAF WILD-TYPE 39 18 30 5

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 = 5e-05

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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 128 48 93
BRAF MUTATED 120 12 30 78
BRAF WILD-TYPE 10 116 18 15

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 = 5e-05

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 81 112 66 78 62
BRAF MUTATED 78 5 40 62 55
BRAF WILD-TYPE 3 107 26 16 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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 129 134
BRAF MUTATED 109 14 116
BRAF WILD-TYPE 28 115 18

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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 109 155
BRAF MUTATED 108 4 127
BRAF WILD-TYPE 28 105 28

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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 150 101
BRAF MUTATED 102 81 47
BRAF WILD-TYPE 23 69 54

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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 106 146
BRAF MUTATED 94 9 127
BRAF WILD-TYPE 30 97 19

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 = 0.0272 (Fisher's exact test), Q value = 0.095

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 292 66
NRAS MUTATED 2 19 11
NRAS WILD-TYPE 39 273 55

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 = 5e-05

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 = 0.106 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 49
NRAS MUTATED 5 5 4 0
NRAS WILD-TYPE 58 56 36 49
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00957 (Fisher's exact test), Q value = 0.036

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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 128 48 93
NRAS MUTATED 0 34 0 0
NRAS WILD-TYPE 130 94 48 93

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 = 5e-05

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 81 112 66 78 62
NRAS MUTATED 0 34 0 0 0
NRAS WILD-TYPE 81 78 66 78 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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 129 134
NRAS MUTATED 1 33 0
NRAS WILD-TYPE 136 96 134

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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 109 155
NRAS MUTATED 1 33 0
NRAS WILD-TYPE 135 76 155

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 = 4e-05 (Fisher's exact test), Q value = 0.00019

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 150 101
NRAS MUTATED 2 11 18
NRAS WILD-TYPE 123 139 83

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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 106 146
NRAS MUTATED 1 30 0
NRAS WILD-TYPE 123 76 146

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 = 1e-05 (Fisher's exact test), Q value = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 292 66
HRAS MUTATED 0 4 10
HRAS WILD-TYPE 41 288 56

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 = 5e-05

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 = 0.00659 (Fisher's exact test), Q value = 0.027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 49
HRAS MUTATED 8 1 1 0
HRAS WILD-TYPE 55 60 39 49

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 = 0.00869 (Fisher's exact test), Q value = 0.034

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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 128 48 93
HRAS MUTATED 0 14 0 0
HRAS WILD-TYPE 130 114 48 93

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 = 5e-05

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 81 112 66 78 62
HRAS MUTATED 0 14 0 0 0
HRAS WILD-TYPE 81 98 66 78 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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 129 134
HRAS MUTATED 0 14 0
HRAS WILD-TYPE 137 115 134

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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 109 155
HRAS MUTATED 0 14 0
HRAS WILD-TYPE 136 95 155

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 = 0.00029 (Fisher's exact test), Q value = 0.0013

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 150 101
HRAS MUTATED 0 3 9
HRAS WILD-TYPE 125 147 92

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 = 5e-05

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 106 146
HRAS MUTATED 0 12 0
HRAS WILD-TYPE 124 94 146

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 = 0.79 (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 41 292 66
EIF1AX MUTATED 0 6 0
EIF1AX WILD-TYPE 41 286 66
'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.31

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 = 0.511 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 49
EIF1AX MUTATED 2 1 2 0
EIF1AX WILD-TYPE 61 60 38 49
'EIF1AX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.57

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 = 0.149 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 128 48 93
EIF1AX MUTATED 0 4 1 1
EIF1AX WILD-TYPE 130 124 47 92
'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.15

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 81 112 66 78 62
EIF1AX MUTATED 0 5 1 0 0
EIF1AX WILD-TYPE 81 107 65 78 62

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 = 0.291 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 129 134
EIF1AX MUTATED 1 4 1
EIF1AX WILD-TYPE 136 125 133
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 109 155
EIF1AX MUTATED 2 3 1
EIF1AX WILD-TYPE 134 106 154
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 150 101
EIF1AX MUTATED 1 3 2
EIF1AX WILD-TYPE 124 147 99
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 0.31

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 106 146
EIF1AX MUTATED 1 4 1
EIF1AX WILD-TYPE 123 102 145
'NUP93 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 292 66
NUP93 MUTATED 1 3 0
NUP93 WILD-TYPE 40 289 66
'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 = 0.506 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 128 48 93
NUP93 MUTATED 3 1 0 0
NUP93 WILD-TYPE 127 127 48 93
'NUP93 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.563 (Fisher's exact test), Q value = 0.81

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 81 112 66 78 62
NUP93 MUTATED 2 1 0 0 1
NUP93 WILD-TYPE 79 111 66 78 61
'NUP93 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.845 (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 137 129 134
NUP93 MUTATED 1 1 2
NUP93 WILD-TYPE 136 128 132
'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 136 109 155
NUP93 MUTATED 1 1 2
NUP93 WILD-TYPE 135 108 153
'NUP93 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.684 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 150 101
NUP93 MUTATED 1 1 2
NUP93 WILD-TYPE 124 149 99
'NUP93 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.686 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 106 146
NUP93 MUTATED 1 2 1
NUP93 WILD-TYPE 123 104 145
'PPM1D MUTATION STATUS' versus 'CN_CNMF'

P value = 0.762 (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 41 292 66
PPM1D MUTATED 0 5 0
PPM1D WILD-TYPE 41 287 66
'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 = 0.118 (Fisher's exact test), Q value = 0.29

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 49
PPM1D MUTATED 0 0 1 2
PPM1D WILD-TYPE 63 61 39 47
'PPM1D MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.848 (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 = 0.808 (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 130 128 48 93
PPM1D MUTATED 2 1 0 2
PPM1D WILD-TYPE 128 127 48 91
'PPM1D MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.42

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 81 112 66 78 62
PPM1D MUTATED 0 1 0 3 1
PPM1D WILD-TYPE 81 111 66 75 61
'PPM1D MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.42

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 129 134
PPM1D MUTATED 0 2 3
PPM1D WILD-TYPE 137 127 131
'PPM1D MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 109 155
PPM1D MUTATED 0 1 4
PPM1D WILD-TYPE 136 108 151
'PPM1D MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.743 (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 125 150 101
PPM1D MUTATED 1 3 1
PPM1D WILD-TYPE 124 147 100
'PPM1D MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.34

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 106 146
PPM1D MUTATED 0 1 4
PPM1D WILD-TYPE 124 105 142
'KRAS MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 292 66
KRAS MUTATED 0 4 0
KRAS WILD-TYPE 41 288 66
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 0.42

Table S60.  Gene #7: '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 = 0.251 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 128 48 93
KRAS MUTATED 0 3 0 1
KRAS WILD-TYPE 130 125 48 92
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 112 66 78 62
KRAS MUTATED 0 3 1 0 0
KRAS WILD-TYPE 81 109 65 78 62
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0791 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 129 134
KRAS MUTATED 0 3 1
KRAS WILD-TYPE 137 126 133
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0978 (Fisher's exact test), Q value = 0.27

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 109 155
KRAS MUTATED 0 3 1
KRAS WILD-TYPE 136 106 154
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 150 101
KRAS MUTATED 0 2 2
KRAS WILD-TYPE 125 148 99
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 106 146
KRAS MUTATED 0 3 1
KRAS WILD-TYPE 124 103 145
'DLC1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S67.  Gene #8: 'DLC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 292 66
DLC1 MUTATED 0 4 0
DLC1 WILD-TYPE 41 288 66
'DLC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S68.  Gene #8: '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 = 0.504 (Fisher's exact test), Q value = 0.78

Table S69.  Gene #8: 'DLC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 128 48 93
DLC1 MUTATED 3 1 0 0
DLC1 WILD-TYPE 127 127 48 93
'DLC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.558 (Fisher's exact test), Q value = 0.81

Table S70.  Gene #8: 'DLC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 112 66 78 62
DLC1 MUTATED 2 1 0 0 1
DLC1 WILD-TYPE 79 111 66 78 61
'DLC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.846 (Fisher's exact test), Q value = 1

Table S71.  Gene #8: 'DLC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 129 134
DLC1 MUTATED 1 1 2
DLC1 WILD-TYPE 136 128 132
'DLC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S72.  Gene #8: 'DLC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 109 155
DLC1 MUTATED 1 1 2
DLC1 WILD-TYPE 135 108 153
'DLC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S73.  Gene #8: 'DLC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 150 101
DLC1 MUTATED 1 2 1
DLC1 WILD-TYPE 124 148 100
'DLC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S74.  Gene #8: 'DLC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 106 146
DLC1 MUTATED 1 1 2
DLC1 WILD-TYPE 123 105 144
'ITGAL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0935 (Fisher's exact test), Q value = 0.26

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 292 66
ITGAL MUTATED 2 2 0
ITGAL WILD-TYPE 39 290 66
'ITGAL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 0.65

Table S76.  Gene #9: '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 = 0.284 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 128 48 93
ITGAL MUTATED 3 0 0 1
ITGAL WILD-TYPE 127 128 48 92
'ITGAL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 0.57

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 112 66 78 62
ITGAL MUTATED 2 0 0 1 1
ITGAL WILD-TYPE 79 112 66 77 61
'ITGAL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 129 134
ITGAL MUTATED 2 0 2
ITGAL WILD-TYPE 135 129 132
'ITGAL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 109 155
ITGAL MUTATED 2 0 2
ITGAL WILD-TYPE 134 109 153
'ITGAL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.829 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 150 101
ITGAL MUTATED 2 1 1
ITGAL WILD-TYPE 123 149 100
'ITGAL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.565 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 106 146
ITGAL MUTATED 2 0 2
ITGAL WILD-TYPE 122 106 144
'TG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.882 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 292 66
TG MUTATED 1 9 1
TG WILD-TYPE 40 283 65
'TG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0609 (Fisher's exact test), Q value = 0.18

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 127 61
TG MUTATED 4 7 0
TG WILD-TYPE 209 120 61
'TG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.099

Table S85.  Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 61 40 49
TG MUTATED 1 1 4 0
TG WILD-TYPE 62 60 36 49

Figure S31.  Get High-res Image Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.89 (Fisher's exact test), Q value = 1

Table S86.  Gene #10: 'TG 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
TG MUTATED 2 0 0 1 2 1 0
TG WILD-TYPE 44 27 31 25 45 26 9
'TG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.095

Table S87.  Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 128 48 93
TG MUTATED 0 7 1 3
TG WILD-TYPE 130 121 47 90

Figure S32.  Get High-res Image Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.147 (Fisher's exact test), Q value = 0.33

Table S88.  Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 112 66 78 62
TG MUTATED 1 7 1 2 0
TG WILD-TYPE 80 105 65 76 62
'TG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0557 (Fisher's exact test), Q value = 0.17

Table S89.  Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 129 134
TG MUTATED 1 7 3
TG WILD-TYPE 136 122 131
'TG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00615 (Fisher's exact test), Q value = 0.026

Table S90.  Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 109 155
TG MUTATED 0 7 4
TG WILD-TYPE 136 102 151

Figure S33.  Get High-res Image Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.11

Table S91.  Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 150 101
TG MUTATED 0 6 4
TG WILD-TYPE 125 144 97

Figure S34.  Get High-res Image Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.066

Table S92.  Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 106 146
TG MUTATED 0 6 4
TG WILD-TYPE 124 100 142

Figure S35.  Get High-res Image Gene #10: 'TG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NLRP6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 0.86

Table S93.  Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 292 66
NLRP6 MUTATED 0 2 1
NLRP6 WILD-TYPE 41 290 65
'NLRP6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 0.69

Table S94.  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 = 0.319 (Fisher's exact test), Q value = 0.57

Table S95.  Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 130 128 48 93
NLRP6 MUTATED 1 0 0 2
NLRP6 WILD-TYPE 129 128 48 91
'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.3

Table S96.  Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 81 112 66 78 62
NLRP6 MUTATED 0 0 0 2 1
NLRP6 WILD-TYPE 81 112 66 76 61
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.7

Table S97.  Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 137 129 134
NLRP6 MUTATED 0 1 2
NLRP6 WILD-TYPE 137 128 132
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 0.29

Table S98.  Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 136 109 155
NLRP6 MUTATED 0 0 3
NLRP6 WILD-TYPE 136 109 152
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 0.78

Table S99.  Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 125 150 101
NLRP6 MUTATED 0 2 1
NLRP6 WILD-TYPE 125 148 100
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 0.29

Table S100.  Gene #11: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 124 106 146
NLRP6 MUTATED 0 0 3
NLRP6 WILD-TYPE 124 106 143
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THCA-TP/19898941/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THCA-TP/20140899/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.

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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