Correlation between gene mutation status and molecular subtypes
Lung Squamous Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C11R6PRC
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C11R6PRC
Overview
Introduction

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

Summary

Testing the association between mutation status of 19 genes and 12 molecular subtypes across 178 patients, 28 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CDKN2A mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • NFE2L2 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • KEAP1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • NOTCH1 mutation correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CPS1 mutation correlated to 'MIRSEQ_CNMF'.

  • SLC28A1 mutation correlated to 'MRNA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 19 genes and 12 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 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		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 Fisher's exact test Fisher's exact test
TP53 145 (81%) 33 0.0622
(0.394) 		0.0224
(0.233) 		6e-05
(0.00342) 		0.00367
(0.0761) 		0.123
(0.586) 		0.713
(1.00) 		0.00096
(0.0274) 		0.00405
(0.0769) 		0.174
(0.686) 		0.367
(0.878) 		0.0303
(0.248) 		0.0114
(0.163)
NFE2L2 27 (15%) 151 0.00024
(0.00912) 		0.00018
(0.00821) 		0.0141
(0.178) 		0.047
(0.333) 		0.122
(0.586) 		0.348
(0.878) 		1e-05
(0.00114) 		1e-05
(0.00114) 		0.00584
(0.0951) 		5e-05
(0.00342) 		0.63
(1.00) 		0.863
(1.00)
CDKN2A 26 (15%) 152 0.00162
(0.0369) 		0.00572
(0.0951) 		0.0243
(0.241) 		0.54
(0.959) 		0.438
(0.938) 		0.344
(0.878) 		0.378
(0.878) 		0.0882
(0.491) 		0.666
(1.00) 		0.818
(1.00) 		0.844
(1.00) 		0.0305
(0.248)
KEAP1 22 (12%) 156 0.00147
(0.0369) 		0.0007
(0.0228) 		0.117
(0.582) 		0.0609
(0.394) 		0.0161
(0.193) 		0.359
(0.878) 		0.187
(0.691) 		0.0288
(0.248) 		0.18
(0.691) 		0.445
(0.938) 		0.483
(0.948) 		0.67
(1.00)
SLC28A1 9 (5%) 169 0.0136
(0.178) 		0.0503
(0.337) 		0.0806
(0.477) 		0.098
(0.523) 		0.415
(0.918) 		0.457
(0.938) 		0.0384
(0.302) 		0.0272
(0.248) 		0.188
(0.691) 		0.0174
(0.199) 		0.817
(1.00) 		0.182
(0.691)
NOTCH1 14 (8%) 164 0.817
(1.00) 		0.603
(0.982) 		0.471
(0.948) 		0.0479
(0.333) 		0.509
(0.953) 		0.587
(0.974) 		0.756
(1.00) 		0.392
(0.894) 		0.348
(0.878) 		0.318
(0.878) 		0.01
(0.152) 		0.0289
(0.248)
CPS1 24 (13%) 154 0.754
(1.00) 		0.208
(0.73) 		0.403
(0.91) 		1
(1.00) 		0.621
(1.00) 		0.857
(1.00) 		0.913
(1.00) 		0.847
(1.00) 		0.0213
(0.231) 		0.128
(0.588) 		1
(1.00) 		1
(1.00)
MLL2 36 (20%) 142 0.17
(0.68) 		0.465
(0.948) 		0.548
(0.959) 		0.307
(0.878) 		0.982
(1.00) 		0.938
(1.00) 		0.532
(0.959) 		0.741
(1.00) 		0.95
(1.00) 		0.921
(1.00) 		0.746
(1.00) 		1
(1.00)
PTEN 14 (8%) 164 0.381
(0.878) 		0.324
(0.878) 		0.414
(0.918) 		0.152
(0.62) 		1
(1.00) 		0.771
(1.00) 		0.594
(0.974) 		0.514
(0.953) 		0.57
(0.959) 		0.511
(0.953) 		0.197
(0.712) 		1
(1.00)
PIK3CA 27 (15%) 151 0.69
(1.00) 		0.755
(1.00) 		0.295
(0.878) 		0.918
(1.00) 		0.854
(1.00) 		0.763
(1.00) 		0.343
(0.878) 		0.59
(0.974) 		0.365
(0.878) 		0.373
(0.878) 		0.723
(1.00) 		0.757
(1.00)
RB1 12 (7%) 166 0.314
(0.878) 		0.645
(1.00) 		0.522
(0.959) 		0.129
(0.588) 		0.101
(0.523) 		0.571
(0.959) 		0.776
(1.00) 		0.242
(0.824) 		0.322
(0.878) 		0.752
(1.00)
CYP11B1 15 (8%) 163 0.652
(1.00) 		0.679
(1.00) 		0.663
(1.00) 		0.348
(0.878) 		0.67
(1.00) 		0.442
(0.938) 		0.572
(0.959) 		0.368
(0.878) 		0.56
(0.959) 		0.977
(1.00)
ASB5 9 (5%) 169 0.491
(0.948) 		0.549
(0.959) 		0.259
(0.849) 		0.454
(0.938) 		1
(1.00) 		0.482
(0.948) 		0.495
(0.949) 		0.254
(0.849) 		0.335
(0.878)
IRF6 6 (3%) 172 0.261
(0.849) 		0.447
(0.938) 		0.135
(0.603) 		0.33
(0.878) 		0.795
(1.00) 		0.146
(0.612) 		0.752
(1.00) 		0.747
(1.00) 		0.538
(0.959) 		0.822
(1.00)
EP300 8 (4%) 170 0.147
(0.612) 		0.117
(0.582) 		0.438
(0.938) 		1
(1.00) 		0.714
(1.00) 		0.0828
(0.477) 		0.0837
(0.477) 		0.569
(0.959) 		0.823
(1.00)
ARID1A 13 (7%) 165 0.305
(0.878) 		0.648
(1.00) 		0.481
(0.948) 		0.355
(0.878) 		0.142
(0.612) 		0.674
(1.00) 		0.101
(0.523) 		0.808
(1.00) 		0.344
(0.878) 		0.503
(0.953)
POLR2B 6 (3%) 172 1
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.238
(0.824) 		1
(1.00) 		0.201
(0.715) 		0.374
(0.878) 		0.311
(0.878) 		0.0482
(0.333) 		0.455
(0.938) 		1
(1.00) 		0.289
(0.878)
HRAS 5 (3%) 173 0.908
(1.00) 		0.68
(1.00) 		0.273
(0.876) 		0.93
(1.00) 		1
(1.00) 		0.533
(0.959) 		0.752
(1.00)
PI16 7 (4%) 171 0.148
(0.612) 		0.721
(1.00) 		0.559
(0.959) 		0.074
(0.456) 		0.0441
(0.333) 		0.286
(0.878) 		0.732
(1.00) 		0.882
(1.00) 		0.307
(0.878) 		0.487
(0.948)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0622 (Fisher's exact test), Q value = 0.39

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
TP53 MUTATED 29 44 11 15
TP53 WILD-TYPE 8 4 6 4
'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.23

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
TP53 MUTATED 31 48 20
TP53 WILD-TYPE 10 4 8

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0034

Table S3.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
TP53 MUTATED 37 65 43
TP53 WILD-TYPE 21 4 8

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00367 (Fisher's exact test), Q value = 0.076

Table S4.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
TP53 MUTATED 17 29 15
TP53 WILD-TYPE 10 1 2

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.59

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
TP53 MUTATED 24 34 27 4
TP53 WILD-TYPE 8 11 2 2
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.713 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
TP53 MUTATED 17 16 19 23 10 4
TP53 WILD-TYPE 5 4 5 3 4 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.027

Table S7.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
TP53 MUTATED 31 56 44 14
TP53 WILD-TYPE 9 6 6 12

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00405 (Fisher's exact test), Q value = 0.077

Table S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
TP53 MUTATED 47 67 31
TP53 WILD-TYPE 21 7 5

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.69

Table S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
TP53 MUTATED 81 13 14 21 8
TP53 WILD-TYPE 12 1 7 3 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.88

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
TP53 MUTATED 32 41 47 17
TP53 WILD-TYPE 3 10 7 5
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.25

Table S11.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
TP53 MUTATED 10 18 12
TP53 WILD-TYPE 6 1 1

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.16

Table S12.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
TP53 MUTATED 4 19 17
TP53 WILD-TYPE 0 0 8

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.037

Table S13.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
CDKN2A MUTATED 0 13 3 2
CDKN2A WILD-TYPE 37 35 14 17

Figure S8.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CDKN2A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00572 (Fisher's exact test), Q value = 0.095

Table S14.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
CDKN2A MUTATED 1 13 4
CDKN2A WILD-TYPE 40 39 24

Figure S9.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.24

Table S15.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
CDKN2A MUTATED 3 15 8
CDKN2A WILD-TYPE 55 54 43

Figure S10.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.96

Table S16.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
CDKN2A MUTATED 2 4 3
CDKN2A WILD-TYPE 25 26 14
'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 0.94

Table S17.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
CDKN2A MUTATED 2 8 3 0
CDKN2A WILD-TYPE 30 37 26 6
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.88

Table S18.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
CDKN2A MUTATED 2 2 4 1 2 2
CDKN2A WILD-TYPE 20 18 20 25 12 4
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.88

Table S19.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
CDKN2A MUTATED 4 12 5 5
CDKN2A WILD-TYPE 36 50 45 21
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0882 (Fisher's exact test), Q value = 0.49

Table S20.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
CDKN2A MUTATED 6 16 4
CDKN2A WILD-TYPE 62 58 32
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.666 (Fisher's exact test), Q value = 1

Table S21.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
CDKN2A MUTATED 16 1 4 3 0
CDKN2A WILD-TYPE 77 13 17 21 10
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S22.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
CDKN2A MUTATED 5 6 10 3
CDKN2A WILD-TYPE 30 45 44 19
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.844 (Fisher's exact test), Q value = 1

Table S23.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
CDKN2A MUTATED 1 2 2
CDKN2A WILD-TYPE 15 17 11
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0305 (Fisher's exact test), Q value = 0.25

Table S24.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
CDKN2A MUTATED 1 4 0
CDKN2A WILD-TYPE 3 15 25

Figure S11.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0091

Table S25.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
NFE2L2 MUTATED 0 14 1 1
NFE2L2 WILD-TYPE 37 34 16 18

Figure S12.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0082

Table S26.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
NFE2L2 MUTATED 0 14 2
NFE2L2 WILD-TYPE 41 38 26

Figure S13.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.18

Table S27.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
NFE2L2 MUTATED 7 17 3
NFE2L2 WILD-TYPE 51 52 48

Figure S14.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.047 (Fisher's exact test), Q value = 0.33

Table S28.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
NFE2L2 MUTATED 4 8 0
NFE2L2 WILD-TYPE 23 22 17

Figure S15.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.59

Table S29.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
NFE2L2 MUTATED 8 4 7 0
NFE2L2 WILD-TYPE 24 41 22 6
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.348 (Fisher's exact test), Q value = 0.88

Table S30.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
NFE2L2 MUTATED 4 3 1 7 3 1
NFE2L2 WILD-TYPE 18 17 23 19 11 5
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S31.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
NFE2L2 MUTATED 2 22 1 2
NFE2L2 WILD-TYPE 38 40 49 24

Figure S16.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

Table S32.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
NFE2L2 MUTATED 2 24 1
NFE2L2 WILD-TYPE 66 50 35

Figure S17.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00584 (Fisher's exact test), Q value = 0.095

Table S33.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
NFE2L2 MUTATED 14 1 1 10 0
NFE2L2 WILD-TYPE 79 13 20 14 10

Figure S18.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0034

Table S34.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
NFE2L2 MUTATED 15 6 2 3
NFE2L2 WILD-TYPE 20 45 52 19

Figure S19.  Get High-res Image Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S35.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
NFE2L2 MUTATED 3 2 3
NFE2L2 WILD-TYPE 13 17 10
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S36.  Gene #3: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
NFE2L2 MUTATED 0 4 4
NFE2L2 WILD-TYPE 4 15 21
'MLL2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.68

Table S37.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
MLL2 MUTATED 4 10 6 5
MLL2 WILD-TYPE 33 38 11 14
'MLL2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 0.95

Table S38.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
MLL2 MUTATED 6 13 6
MLL2 WILD-TYPE 35 39 22
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 0.96

Table S39.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
MLL2 MUTATED 9 15 12
MLL2 WILD-TYPE 49 54 39
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.88

Table S40.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
MLL2 MUTATED 6 7 1
MLL2 WILD-TYPE 21 23 16
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.982 (Fisher's exact test), Q value = 1

Table S41.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
MLL2 MUTATED 7 9 7 1
MLL2 WILD-TYPE 25 36 22 5
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S42.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
MLL2 MUTATED 5 4 6 5 2 2
MLL2 WILD-TYPE 17 16 18 21 12 4
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.532 (Fisher's exact test), Q value = 0.96

Table S43.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
MLL2 MUTATED 5 15 11 5
MLL2 WILD-TYPE 35 47 39 21
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S44.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
MLL2 MUTATED 12 17 7
MLL2 WILD-TYPE 56 57 29
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.95 (Fisher's exact test), Q value = 1

Table S45.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
MLL2 MUTATED 17 2 5 4 2
MLL2 WILD-TYPE 76 12 16 20 8
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.921 (Fisher's exact test), Q value = 1

Table S46.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
MLL2 MUTATED 5 10 11 4
MLL2 WILD-TYPE 30 41 43 18
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S47.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
MLL2 MUTATED 4 3 3
MLL2 WILD-TYPE 12 16 10
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S48.  Gene #4: 'MLL2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
MLL2 MUTATED 1 4 5
MLL2 WILD-TYPE 3 15 20
'KEAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.037

Table S49.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
KEAP1 MUTATED 0 12 1 4
KEAP1 WILD-TYPE 37 36 16 15

Figure S20.  Get High-res Image Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'KEAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.023

Table S50.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
KEAP1 MUTATED 0 13 4
KEAP1 WILD-TYPE 41 39 24

Figure S21.  Get High-res Image Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.58

Table S51.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
KEAP1 MUTATED 4 13 5
KEAP1 WILD-TYPE 54 56 46
'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0609 (Fisher's exact test), Q value = 0.39

Table S52.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
KEAP1 MUTATED 0 4 3
KEAP1 WILD-TYPE 27 26 14
'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.19

Table S53.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
KEAP1 MUTATED 1 2 7 1
KEAP1 WILD-TYPE 31 43 22 5

Figure S22.  Get High-res Image Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 0.88

Table S54.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
KEAP1 MUTATED 2 4 1 4 0 0
KEAP1 WILD-TYPE 20 16 23 22 14 6
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.69

Table S55.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
KEAP1 MUTATED 2 12 5 3
KEAP1 WILD-TYPE 38 50 45 23
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.25

Table S56.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
KEAP1 MUTATED 3 13 6
KEAP1 WILD-TYPE 65 61 30

Figure S23.  Get High-res Image Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.18 (Fisher's exact test), Q value = 0.69

Table S57.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
KEAP1 MUTATED 10 3 0 3 2
KEAP1 WILD-TYPE 83 11 21 21 8
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.445 (Fisher's exact test), Q value = 0.94

Table S58.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
KEAP1 MUTATED 5 3 8 2
KEAP1 WILD-TYPE 30 48 46 20
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.95

Table S59.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
KEAP1 MUTATED 0 2 1
KEAP1 WILD-TYPE 16 17 12
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S60.  Gene #5: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
KEAP1 MUTATED 0 2 1
KEAP1 WILD-TYPE 4 17 24
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 0.88

Table S61.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
PTEN MUTATED 4 2 0 2
PTEN WILD-TYPE 33 46 17 17
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 0.88

Table S62.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
PTEN MUTATED 5 2 1
PTEN WILD-TYPE 36 50 27
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 0.92

Table S63.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
PTEN MUTATED 7 4 3
PTEN WILD-TYPE 51 65 48
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 0.62

Table S64.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
PTEN MUTATED 5 3 0
PTEN WILD-TYPE 22 27 17
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S65.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
PTEN MUTATED 2 4 2 0
PTEN WILD-TYPE 30 41 27 6
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S66.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
PTEN MUTATED 1 1 1 3 2 0
PTEN WILD-TYPE 21 19 23 23 12 6
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.594 (Fisher's exact test), Q value = 0.97

Table S67.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
PTEN MUTATED 4 3 4 3
PTEN WILD-TYPE 36 59 46 23
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.514 (Fisher's exact test), Q value = 0.95

Table S68.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
PTEN MUTATED 6 4 4
PTEN WILD-TYPE 62 70 32
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.96

Table S69.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
PTEN MUTATED 7 0 3 1 1
PTEN WILD-TYPE 86 14 18 23 9
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.511 (Fisher's exact test), Q value = 0.95

Table S70.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
PTEN MUTATED 1 3 6 2
PTEN WILD-TYPE 34 48 48 20
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.71

Table S71.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
PTEN MUTATED 1 4 0
PTEN WILD-TYPE 15 15 13
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S72.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
PTEN MUTATED 0 2 3
PTEN WILD-TYPE 4 17 22
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S73.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
PIK3CA MUTATED 4 6 3 4
PIK3CA WILD-TYPE 33 42 14 15
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S74.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
PIK3CA MUTATED 7 6 4
PIK3CA WILD-TYPE 34 46 24
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 0.88

Table S75.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
PIK3CA MUTATED 10 7 10
PIK3CA WILD-TYPE 48 62 41
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S76.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
PIK3CA MUTATED 4 4 3
PIK3CA WILD-TYPE 23 26 14
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S77.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
PIK3CA MUTATED 6 7 4 0
PIK3CA WILD-TYPE 26 38 25 6
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.763 (Fisher's exact test), Q value = 1

Table S78.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
PIK3CA MUTATED 3 5 4 4 1 0
PIK3CA WILD-TYPE 19 15 20 22 13 6
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 0.88

Table S79.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
PIK3CA MUTATED 8 7 10 2
PIK3CA WILD-TYPE 32 55 40 24
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.59 (Fisher's exact test), Q value = 0.97

Table S80.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
PIK3CA MUTATED 11 9 7
PIK3CA WILD-TYPE 57 65 29
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.88

Table S81.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
PIK3CA MUTATED 15 4 3 2 0
PIK3CA WILD-TYPE 78 10 18 22 10
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test), Q value = 0.88

Table S82.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
PIK3CA MUTATED 3 11 8 2
PIK3CA WILD-TYPE 32 40 46 20
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.723 (Fisher's exact test), Q value = 1

Table S83.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
PIK3CA MUTATED 2 4 3
PIK3CA WILD-TYPE 14 15 10
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S84.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
PIK3CA MUTATED 1 4 4
PIK3CA WILD-TYPE 3 15 21
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 0.88

Table S85.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
RB1 MUTATED 2 5 0 3
RB1 WILD-TYPE 35 43 17 16
'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S86.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
RB1 MUTATED 2 5 3
RB1 WILD-TYPE 39 47 25
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 0.96

Table S87.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
RB1 MUTATED 4 3 5
RB1 WILD-TYPE 54 66 46
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.59

Table S88.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
RB1 MUTATED 0 4 1
RB1 WILD-TYPE 27 26 16
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.52

Table S89.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
RB1 MUTATED 0 2 3 1
RB1 WILD-TYPE 32 43 26 5
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.571 (Fisher's exact test), Q value = 0.96

Table S90.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
RB1 MUTATED 0 1 2 3 0 0
RB1 WILD-TYPE 22 19 22 23 14 6
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S91.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
RB1 MUTATED 2 4 3 3
RB1 WILD-TYPE 38 58 47 23
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 0.82

Table S92.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
RB1 MUTATED 2 6 4
RB1 WILD-TYPE 66 68 32
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 0.88

Table S93.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
RB1 MUTATED 7 1 0 2 2
RB1 WILD-TYPE 86 13 21 22 8
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S94.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
RB1 MUTATED 2 3 6 1
RB1 WILD-TYPE 33 48 48 21
'CYP11B1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S95.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
CYP11B1 MUTATED 3 5 3 1
CYP11B1 WILD-TYPE 34 43 14 18
'CYP11B1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

Table S96.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
CYP11B1 MUTATED 3 5 4
CYP11B1 WILD-TYPE 38 47 24
'CYP11B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 1

Table S97.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
CYP11B1 MUTATED 4 5 6
CYP11B1 WILD-TYPE 54 64 45
'CYP11B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.88

Table S98.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
CYP11B1 MUTATED 3 1 0
CYP11B1 WILD-TYPE 24 29 17
'CYP11B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S99.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
CYP11B1 MUTATED 2 3 4 0
CYP11B1 WILD-TYPE 30 42 25 6
'CYP11B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.94

Table S100.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
CYP11B1 MUTATED 2 4 1 2 0 0
CYP11B1 WILD-TYPE 20 16 23 24 14 6
'CYP11B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 0.96

Table S101.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
CYP11B1 MUTATED 2 4 6 3
CYP11B1 WILD-TYPE 38 58 44 23
'CYP11B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 0.88

Table S102.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
CYP11B1 MUTATED 4 6 5
CYP11B1 WILD-TYPE 64 68 31
'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 0.96

Table S103.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
CYP11B1 MUTATED 6 2 1 3 1
CYP11B1 WILD-TYPE 87 12 20 21 9
'CYP11B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.977 (Fisher's exact test), Q value = 1

Table S104.  Gene #9: 'CYP11B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
CYP11B1 MUTATED 3 4 5 1
CYP11B1 WILD-TYPE 32 47 49 21
'NOTCH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S105.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
NOTCH1 MUTATED 1 4 1 1
NOTCH1 WILD-TYPE 36 44 16 18
'NOTCH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.603 (Fisher's exact test), Q value = 0.98

Table S106.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
NOTCH1 MUTATED 1 4 2
NOTCH1 WILD-TYPE 40 48 26
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 0.95

Table S107.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
NOTCH1 MUTATED 3 5 6
NOTCH1 WILD-TYPE 55 64 45
'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.33

Table S108.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
NOTCH1 MUTATED 0 5 3
NOTCH1 WILD-TYPE 27 25 14

Figure S24.  Get High-res Image Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 0.95

Table S109.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
NOTCH1 MUTATED 3 3 1 1
NOTCH1 WILD-TYPE 29 42 28 5
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 0.97

Table S110.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
NOTCH1 MUTATED 1 2 1 4 0 0
NOTCH1 WILD-TYPE 21 18 23 22 14 6
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S111.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
NOTCH1 MUTATED 2 6 5 1
NOTCH1 WILD-TYPE 38 56 45 25
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 0.89

Table S112.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
NOTCH1 MUTATED 3 8 3
NOTCH1 WILD-TYPE 65 66 33
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.88

Table S113.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
NOTCH1 MUTATED 7 2 0 3 1
NOTCH1 WILD-TYPE 86 12 21 21 9
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 0.88

Table S114.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
NOTCH1 MUTATED 4 3 6 0
NOTCH1 WILD-TYPE 31 48 48 22
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.01 (Fisher's exact test), Q value = 0.15

Table S115.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
NOTCH1 MUTATED 1 0 4
NOTCH1 WILD-TYPE 15 19 9

Figure S25.  Get High-res Image Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.25

Table S116.  Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
NOTCH1 MUTATED 1 4 0
NOTCH1 WILD-TYPE 3 15 25

Figure S26.  Get High-res Image Gene #10: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ASB5 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 0.95

Table S117.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
ASB5 MUTATED 1 4 2 2
ASB5 WILD-TYPE 36 44 15 17
'ASB5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.549 (Fisher's exact test), Q value = 0.96

Table S118.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
ASB5 MUTATED 2 4 3
ASB5 WILD-TYPE 39 48 25
'ASB5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.85

Table S119.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
ASB5 MUTATED 2 6 1
ASB5 WILD-TYPE 56 63 50
'ASB5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 0.94

Table S120.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
ASB5 MUTATED 0 1 2 0
ASB5 WILD-TYPE 32 44 27 6
'ASB5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S121.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
ASB5 MUTATED 1 0 1 1 0 0
ASB5 WILD-TYPE 21 20 23 25 14 6
'ASB5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 0.95

Table S122.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
ASB5 MUTATED 1 4 4 0
ASB5 WILD-TYPE 39 58 46 26
'ASB5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 0.95

Table S123.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
ASB5 MUTATED 2 4 3
ASB5 WILD-TYPE 66 70 33
'ASB5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.254 (Fisher's exact test), Q value = 0.85

Table S124.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
ASB5 MUTATED 5 2 0 0 0
ASB5 WILD-TYPE 88 12 21 24 10
'ASB5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.335 (Fisher's exact test), Q value = 0.88

Table S125.  Gene #11: 'ASB5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
ASB5 MUTATED 0 4 2 1
ASB5 WILD-TYPE 35 47 52 21
'IRF6 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 0.85

Table S126.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
IRF6 MUTATED 1 1 2 0
IRF6 WILD-TYPE 36 47 15 19
'IRF6 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.447 (Fisher's exact test), Q value = 0.94

Table S127.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
IRF6 MUTATED 1 1 2
IRF6 WILD-TYPE 40 51 26
'IRF6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.6

Table S128.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
IRF6 MUTATED 4 2 0
IRF6 WILD-TYPE 54 67 51
'IRF6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 0.88

Table S129.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
IRF6 MUTATED 2 0 1
IRF6 WILD-TYPE 25 30 16
'IRF6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S130.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
IRF6 MUTATED 1 2 2 0
IRF6 WILD-TYPE 31 43 27 6
'IRF6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.61

Table S131.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
IRF6 MUTATED 0 3 1 0 1 0
IRF6 WILD-TYPE 22 17 23 26 13 6
'IRF6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S132.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
IRF6 MUTATED 2 1 2 1
IRF6 WILD-TYPE 38 61 48 25
'IRF6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.747 (Fisher's exact test), Q value = 1

Table S133.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
IRF6 MUTATED 2 2 2
IRF6 WILD-TYPE 66 72 34
'IRF6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 0.96

Table S134.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
IRF6 MUTATED 2 1 0 1 0
IRF6 WILD-TYPE 91 13 21 23 10
'IRF6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S135.  Gene #12: 'IRF6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
IRF6 MUTATED 1 1 1 1
IRF6 WILD-TYPE 34 50 53 21
'EP300 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.61

Table S136.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
EP300 MUTATED 5 2 0 0
EP300 WILD-TYPE 32 46 17 19
'EP300 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 0.58

Table S137.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
EP300 MUTATED 5 2 0
EP300 WILD-TYPE 36 50 28
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 0.94

Table S138.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
EP300 MUTATED 2 2 4
EP300 WILD-TYPE 56 67 47
'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S139.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
EP300 MUTATED 1 1 1 0
EP300 WILD-TYPE 31 44 28 6
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S140.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
EP300 MUTATED 0 0 1 2 0 0
EP300 WILD-TYPE 22 20 23 24 14 6
'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0828 (Fisher's exact test), Q value = 0.48

Table S141.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
EP300 MUTATED 3 0 3 2
EP300 WILD-TYPE 37 62 47 24
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0837 (Fisher's exact test), Q value = 0.48

Table S142.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
EP300 MUTATED 6 1 1
EP300 WILD-TYPE 62 73 35
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.96

Table S143.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
EP300 MUTATED 6 1 0 0 0
EP300 WILD-TYPE 87 13 21 24 10
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.823 (Fisher's exact test), Q value = 1

Table S144.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
EP300 MUTATED 1 3 3 0
EP300 WILD-TYPE 34 48 51 22
'CPS1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.754 (Fisher's exact test), Q value = 1

Table S145.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
CPS1 MUTATED 5 7 4 2
CPS1 WILD-TYPE 32 41 13 17
'CPS1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 0.73

Table S146.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
CPS1 MUTATED 4 7 7
CPS1 WILD-TYPE 37 45 21
'CPS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.91

Table S147.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
CPS1 MUTATED 5 10 9
CPS1 WILD-TYPE 53 59 42
'CPS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S148.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
CPS1 MUTATED 3 3 1
CPS1 WILD-TYPE 24 27 16
'CPS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S149.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
CPS1 MUTATED 5 7 2 1
CPS1 WILD-TYPE 27 38 27 5
'CPS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S150.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
CPS1 MUTATED 2 3 5 3 2 0
CPS1 WILD-TYPE 20 17 19 23 12 6
'CPS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S151.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
CPS1 MUTATED 4 9 7 4
CPS1 WILD-TYPE 36 53 43 22
'CPS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S152.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
CPS1 MUTATED 8 11 5
CPS1 WILD-TYPE 60 63 31
'CPS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.23

Table S153.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
CPS1 MUTATED 6 0 5 5 2
CPS1 WILD-TYPE 87 14 16 19 8

Figure S27.  Get High-res Image Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CPS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 0.59

Table S154.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
CPS1 MUTATED 6 2 6 4
CPS1 WILD-TYPE 29 49 48 18
'CPS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S155.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
CPS1 MUTATED 2 2 1
CPS1 WILD-TYPE 14 17 12
'CPS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S156.  Gene #14: 'CPS1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
CPS1 MUTATED 0 2 3
CPS1 WILD-TYPE 4 17 22
'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 0.88

Table S157.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
ARID1A MUTATED 1 5 1 3
ARID1A WILD-TYPE 36 43 16 16
'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S158.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
ARID1A MUTATED 2 5 3
ARID1A WILD-TYPE 39 47 25
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 0.95

Table S159.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
ARID1A MUTATED 6 5 2
ARID1A WILD-TYPE 52 64 49
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 0.88

Table S160.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
ARID1A MUTATED 3 2 0
ARID1A WILD-TYPE 24 28 17
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.61

Table S161.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
ARID1A MUTATED 4 1 1 1
ARID1A WILD-TYPE 28 44 28 5
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S162.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
ARID1A MUTATED 1 3 1 2 0 0
ARID1A WILD-TYPE 21 17 23 24 14 6
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.52

Table S163.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
ARID1A MUTATED 0 6 6 1
ARID1A WILD-TYPE 40 56 44 25
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.808 (Fisher's exact test), Q value = 1

Table S164.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
ARID1A MUTATED 4 6 3
ARID1A WILD-TYPE 64 68 33
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 0.88

Table S165.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
ARID1A MUTATED 4 1 2 3 1
ARID1A WILD-TYPE 89 13 19 21 9
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.503 (Fisher's exact test), Q value = 0.95

Table S166.  Gene #15: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
ARID1A MUTATED 4 2 3 2
ARID1A WILD-TYPE 31 49 51 20
'SLC28A1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.18

Table S167.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
SLC28A1 MUTATED 0 1 3 0
SLC28A1 WILD-TYPE 37 47 14 19

Figure S28.  Get High-res Image Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SLC28A1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0503 (Fisher's exact test), Q value = 0.34

Table S168.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
SLC28A1 MUTATED 0 1 3
SLC28A1 WILD-TYPE 41 51 25
'SLC28A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0806 (Fisher's exact test), Q value = 0.48

Table S169.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
SLC28A1 MUTATED 6 1 2
SLC28A1 WILD-TYPE 52 68 49
'SLC28A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.098 (Fisher's exact test), Q value = 0.52

Table S170.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
SLC28A1 MUTATED 3 0 2
SLC28A1 WILD-TYPE 24 30 15
'SLC28A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.415 (Fisher's exact test), Q value = 0.92

Table S171.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
SLC28A1 MUTATED 2 4 0 0
SLC28A1 WILD-TYPE 30 41 29 6
'SLC28A1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.457 (Fisher's exact test), Q value = 0.94

Table S172.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
SLC28A1 MUTATED 1 1 2 0 2 0
SLC28A1 WILD-TYPE 21 19 22 26 12 6
'SLC28A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.3

Table S173.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
SLC28A1 MUTATED 3 0 5 1
SLC28A1 WILD-TYPE 37 62 45 25

Figure S29.  Get High-res Image Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SLC28A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 0.25

Table S174.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
SLC28A1 MUTATED 3 1 5
SLC28A1 WILD-TYPE 65 73 31

Figure S30.  Get High-res Image Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.188 (Fisher's exact test), Q value = 0.69

Table S175.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
SLC28A1 MUTATED 4 1 3 0 0
SLC28A1 WILD-TYPE 89 13 18 24 10
'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.2

Table S176.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
SLC28A1 MUTATED 0 1 3 4
SLC28A1 WILD-TYPE 35 50 51 18

Figure S31.  Get High-res Image Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S177.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
SLC28A1 MUTATED 2 1 1
SLC28A1 WILD-TYPE 14 18 12
'SLC28A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.69

Table S178.  Gene #16: 'SLC28A1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
SLC28A1 MUTATED 0 0 4
SLC28A1 WILD-TYPE 4 19 21
'POLR2B MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S179.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
POLR2B MUTATED 1 2 0 0
POLR2B WILD-TYPE 36 46 17 19
'POLR2B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S180.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
POLR2B MUTATED 1 2 0
POLR2B WILD-TYPE 40 50 28
'POLR2B MUTATION STATUS' versus 'CN_CNMF'

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

Table S181.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
POLR2B MUTATED 2 2 2
POLR2B WILD-TYPE 56 67 49
'POLR2B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.82

Table S182.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
POLR2B MUTATED 0 1 2
POLR2B WILD-TYPE 27 29 15
'POLR2B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S183.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
POLR2B MUTATED 1 2 1 0
POLR2B WILD-TYPE 31 43 28 6
'POLR2B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.72

Table S184.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
POLR2B MUTATED 0 0 2 1 0 1
POLR2B WILD-TYPE 22 20 22 25 14 5
'POLR2B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 0.88

Table S185.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
POLR2B MUTATED 0 2 2 2
POLR2B WILD-TYPE 40 60 48 24
'POLR2B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 0.88

Table S186.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
POLR2B MUTATED 4 2 0
POLR2B WILD-TYPE 64 72 36
'POLR2B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.33

Table S187.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
POLR2B MUTATED 2 1 0 0 2
POLR2B WILD-TYPE 91 13 21 24 8

Figure S32.  Get High-res Image Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'POLR2B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 0.94

Table S188.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
POLR2B MUTATED 0 1 3 1
POLR2B WILD-TYPE 35 50 51 21
'POLR2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S189.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 16 19 13
POLR2B MUTATED 1 1 1
POLR2B WILD-TYPE 15 18 12
'POLR2B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 0.88

Table S190.  Gene #17: 'POLR2B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 19 25
POLR2B MUTATED 1 1 1
POLR2B WILD-TYPE 3 18 24
'HRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S191.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
HRAS MUTATED 2 2 0 0
HRAS WILD-TYPE 35 46 17 19
'HRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S192.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
HRAS MUTATED 2 2 0
HRAS WILD-TYPE 39 50 28
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.88

Table S193.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
HRAS MUTATED 0 3 2
HRAS WILD-TYPE 58 66 49
'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S194.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
HRAS MUTATED 1 2 2 0
HRAS WILD-TYPE 39 60 48 26
'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S195.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
HRAS MUTATED 2 2 1
HRAS WILD-TYPE 66 72 35
'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 0.96

Table S196.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
HRAS MUTATED 3 0 0 1 1
HRAS WILD-TYPE 90 14 21 23 9
'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S197.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
HRAS MUTATED 2 1 2 0
HRAS WILD-TYPE 33 50 52 22
'PI16 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 0.61

Table S198.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 48 17 19
PI16 MUTATED 0 2 2 1
PI16 WILD-TYPE 37 46 15 18
'PI16 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S199.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 52 28
PI16 MUTATED 1 2 2
PI16 WILD-TYPE 40 50 26
'PI16 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.559 (Fisher's exact test), Q value = 0.96

Table S200.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 58 69 51
PI16 MUTATED 1 4 2
PI16 WILD-TYPE 57 65 49
'PI16 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.074 (Fisher's exact test), Q value = 0.46

Table S201.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 27 30 17
PI16 MUTATED 0 4 0
PI16 WILD-TYPE 27 26 17
'PI16 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.33

Table S202.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 45 29 6
PI16 MUTATED 3 0 1 1
PI16 WILD-TYPE 29 45 28 5

Figure S33.  Get High-res Image Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PI16 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.88

Table S203.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 20 24 26 14 6
PI16 MUTATED 1 2 0 1 0 1
PI16 WILD-TYPE 21 18 24 25 14 5
'PI16 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S204.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 62 50 26
PI16 MUTATED 1 4 1 1
PI16 WILD-TYPE 39 58 49 25
'PI16 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S205.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 74 36
PI16 MUTATED 2 4 1
PI16 WILD-TYPE 66 70 35
'PI16 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.88

Table S206.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 93 14 21 24 10
PI16 MUTATED 2 1 1 2 0
PI16 WILD-TYPE 91 13 20 22 10
'PI16 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.95

Table S207.  Gene #19: 'PI16 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 51 54 22
PI16 MUTATED 1 1 4 0
PI16 WILD-TYPE 34 50 50 22
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/LUSC-TP/19940360/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUSC-TP/20140646/LUSC-TP.transferedmergedcluster.txt

  • Number of patients = 178

  • Number of significantly mutated genes = 19

  • Number of Molecular subtypes = 12

  • 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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