Correlation between gene mutation status and molecular subtypes
Lung Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1H70DQH
Overview
Introduction

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

Summary

Testing the association between mutation status of 20 genes and 12 molecular subtypes across 172 patients, 7 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • STK11 mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • KEAP1 mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 20 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, 7 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 86 (50%) 86 0.00161
(0.327)
0.0194
(1.00)
4e-05
(0.00824)
0.0329
(1.00)
0.0565
(1.00)
0.0201
(1.00)
1e-05
(0.0021)
3e-05
(0.00621)
0.00266
(0.537)
0.00743
(1.00)
0.286
(1.00)
0.368
(1.00)
STK11 20 (12%) 152 0.555
(1.00)
0.424
(1.00)
0.394
(1.00)
0.638
(1.00)
0.164
(1.00)
0.121
(1.00)
0.00024
(0.0492)
1e-05
(0.0021)
0.851
(1.00)
0.0303
(1.00)
1
(1.00)
0.189
(1.00)
KEAP1 31 (18%) 141 0.556
(1.00)
0.423
(1.00)
0.123
(1.00)
0.441
(1.00)
0.00531
(1.00)
0.00616
(1.00)
0.00027
(0.0551)
1e-05
(0.0021)
1
(1.00)
0.236
(1.00)
0.36
(1.00)
0.0194
(1.00)
KRAS 47 (27%) 125 0.816
(1.00)
1
(1.00)
0.0745
(1.00)
0.596
(1.00)
0.0279
(1.00)
0.597
(1.00)
0.64
(1.00)
0.00838
(1.00)
0.00448
(0.896)
0.452
(1.00)
0.95
(1.00)
0.502
(1.00)
SMARCA4 15 (9%) 157 0.12
(1.00)
0.146
(1.00)
0.132
(1.00)
0.0093
(1.00)
1
(1.00)
0.419
(1.00)
0.041
(1.00)
0.00655
(1.00)
0.14
(1.00)
0.126
(1.00)
0.19
(1.00)
0.0602
(1.00)
ARID1A 11 (6%) 161 0.0324
(1.00)
0.472
(1.00)
0.347
(1.00)
0.96
(1.00)
0.673
(1.00)
0.847
(1.00)
0.00326
(0.655)
0.0514
(1.00)
0.867
(1.00)
0.224
(1.00)
NF1 22 (13%) 150 0.911
(1.00)
0.826
(1.00)
0.0203
(1.00)
0.021
(1.00)
0.92
(1.00)
0.46
(1.00)
0.3
(1.00)
0.584
(1.00)
0.136
(1.00)
0.88
(1.00)
0.148
(1.00)
0.169
(1.00)
U2AF1 6 (3%) 166 1
(1.00)
0.0607
(1.00)
0.0824
(1.00)
0.662
(1.00)
0.536
(1.00)
0.473
(1.00)
0.06
(1.00)
0.39
(1.00)
0.708
(1.00)
1
(1.00)
EGFR 23 (13%) 149 0.279
(1.00)
0.22
(1.00)
0.15
(1.00)
0.646
(1.00)
0.325
(1.00)
0.245
(1.00)
0.017
(1.00)
0.018
(1.00)
0.766
(1.00)
0.953
(1.00)
0.273
(1.00)
0.0603
(1.00)
SETD2 15 (9%) 157 0.502
(1.00)
0.342
(1.00)
0.766
(1.00)
0.155
(1.00)
0.654
(1.00)
0.544
(1.00)
0.232
(1.00)
0.807
(1.00)
0.272
(1.00)
0.64
(1.00)
CDKN2A 8 (5%) 164 1
(1.00)
1
(1.00)
1
(1.00)
0.939
(1.00)
0.476
(1.00)
0.452
(1.00)
1
(1.00)
0.0645
(1.00)
1
(1.00)
0.0171
(1.00)
MET 11 (6%) 161 0.137
(1.00)
0.0229
(1.00)
0.897
(1.00)
0.451
(1.00)
0.696
(1.00)
0.0505
(1.00)
0.726
(1.00)
0.0721
(1.00)
0.765
(1.00)
0.444
(1.00)
ERBB2 8 (5%) 164 0.326
(1.00)
0.868
(1.00)
1
(1.00)
0.741
(1.00)
0.193
(1.00)
0.432
(1.00)
0.717
(1.00)
0.0132
(1.00)
0.771
(1.00)
0.61
(1.00)
CHRND 9 (5%) 163 0.454
(1.00)
0.126
(1.00)
0.503
(1.00)
0.0979
(1.00)
0.207
(1.00)
0.17
(1.00)
0.0295
(1.00)
0.299
(1.00)
0.519
(1.00)
0.324
(1.00)
BRAF 16 (9%) 156 0.249
(1.00)
0.244
(1.00)
1
(1.00)
0.587
(1.00)
0.658
(1.00)
0.768
(1.00)
0.803
(1.00)
0.762
(1.00)
0.191
(1.00)
0.834
(1.00)
0.718
(1.00)
0.139
(1.00)
GEN1 4 (2%) 168 1
(1.00)
0.433
(1.00)
0.607
(1.00)
0.0944
(1.00)
1
(1.00)
0.724
(1.00)
0.709
(1.00)
0.379
(1.00)
STX2 4 (2%) 168 0.535
(1.00)
0.619
(1.00)
0.523
(1.00)
0.305
(1.00)
0.265
(1.00)
0.883
(1.00)
0.371
(1.00)
0.38
(1.00)
MGA 15 (9%) 157 0.57
(1.00)
0.108
(1.00)
0.335
(1.00)
0.33
(1.00)
0.309
(1.00)
0.594
(1.00)
0.124
(1.00)
0.367
(1.00)
0.0155
(1.00)
1
(1.00)
GALC 5 (3%) 167 0.84
(1.00)
0.612
(1.00)
0.492
(1.00)
0.839
(1.00)
0.218
(1.00)
0.274
(1.00)
0.151
(1.00)
0.782
(1.00)
CTNNB1 9 (5%) 163 0.556
(1.00)
0.359
(1.00)
0.35
(1.00)
0.0107
(1.00)
0.216
(1.00)
0.3
(1.00)
0.906
(1.00)
0.699
(1.00)
0.45
(1.00)
0.107
(1.00)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
TP53 MUTATED 1 6 2 6
TP53 WILD-TYPE 4 3 10 0

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

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
TP53 MUTATED 3 6 6
TP53 WILD-TYPE 11 5 1

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0082

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
TP53 MUTATED 47 20 19
TP53 WILD-TYPE 21 48 17

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
TP53 MUTATED 8 11 17 22
TP53 WILD-TYPE 18 13 11 11

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0565 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
TP53 MUTATED 3 27 16
TP53 WILD-TYPE 12 29 12
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0201 (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
ALL 30 15 30 14 10
TP53 MUTATED 11 5 21 7 2
TP53 WILD-TYPE 19 10 9 7 8

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0021

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
TP53 MUTATED 40 6 11 22 6
TP53 WILD-TYPE 18 31 18 12 7

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0062

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
TP53 MUTATED 10 4 22 21 3 7 8 1 9
TP53 WILD-TYPE 16 16 6 6 11 8 12 3 8

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
TP53 MUTATED 19 46 19
TP53 WILD-TYPE 40 29 15

Figure S8.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00743 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
TP53 MUTATED 6 31 21 26
TP53 WILD-TYPE 13 39 23 9

Figure S9.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
TP53 MUTATED 32 5 18
TP53 WILD-TYPE 29 9 11
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
TP53 MUTATED 5 34 16
TP53 WILD-TYPE 9 25 15
'STK11 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.555 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
STK11 MUTATED 0 0 2 1
STK11 WILD-TYPE 5 9 10 5
'STK11 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.424 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
STK11 MUTATED 2 0 1
STK11 WILD-TYPE 12 11 6
'STK11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
STK11 MUTATED 6 11 3
STK11 WILD-TYPE 62 57 33
'STK11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
STK11 MUTATED 3 3 1 3
STK11 WILD-TYPE 23 21 27 30
'STK11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
STK11 MUTATED 3 4 5
STK11 WILD-TYPE 12 52 23
'STK11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
STK11 MUTATED 1 4 3 3 1
STK11 WILD-TYPE 29 11 27 11 9
'STK11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.049

Table S19.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
STK11 MUTATED 0 7 7 5 0
STK11 WILD-TYPE 58 30 22 29 13

Figure S10.  Get High-res Image Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'STK11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0021

Table S20.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
STK11 MUTATED 1 0 0 0 8 2 8 0 0
STK11 WILD-TYPE 25 20 28 27 6 13 12 4 17

Figure S11.  Get High-res Image Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'STK11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.851 (Fisher's exact test), Q value = 1

Table S21.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
STK11 MUTATED 7 7 4
STK11 WILD-TYPE 52 68 30
'STK11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 1

Table S22.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
STK11 MUTATED 5 5 2 6
STK11 WILD-TYPE 14 65 42 29

Figure S12.  Get High-res Image Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'STK11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S23.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
STK11 MUTATED 6 1 3
STK11 WILD-TYPE 55 13 26
'STK11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 1

Table S24.  Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
STK11 MUTATED 3 4 3
STK11 WILD-TYPE 11 55 28
'KEAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 1

Table S25.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
KEAP1 MUTATED 0 0 2 1
KEAP1 WILD-TYPE 5 9 10 5
'KEAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
KEAP1 MUTATED 2 0 1
KEAP1 WILD-TYPE 12 11 6
'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 1

Table S27.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
KEAP1 MUTATED 8 13 10
KEAP1 WILD-TYPE 60 55 26
'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
KEAP1 MUTATED 3 6 3 7
KEAP1 WILD-TYPE 23 18 25 26
'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00531 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
KEAP1 MUTATED 6 5 8
KEAP1 WILD-TYPE 9 51 20

Figure S13.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00616 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
KEAP1 MUTATED 2 6 3 6 2
KEAP1 WILD-TYPE 28 9 27 8 8

Figure S14.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.055

Table S31.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
KEAP1 MUTATED 3 7 13 7 1
KEAP1 WILD-TYPE 55 30 16 27 12

Figure S15.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0021

Table S32.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
KEAP1 MUTATED 1 0 2 6 7 2 12 0 1
KEAP1 WILD-TYPE 25 20 26 21 7 13 8 4 16

Figure S16.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S33.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
KEAP1 MUTATED 10 13 5
KEAP1 WILD-TYPE 49 62 29
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 1

Table S34.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
KEAP1 MUTATED 5 11 4 8
KEAP1 WILD-TYPE 14 59 40 27
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.36 (Fisher's exact test), Q value = 1

Table S35.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
KEAP1 MUTATED 14 1 4
KEAP1 WILD-TYPE 47 13 25
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 1

Table S36.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
KEAP1 MUTATED 3 15 1
KEAP1 WILD-TYPE 11 44 30

Figure S17.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.816 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
KRAS MUTATED 2 3 3 1
KRAS WILD-TYPE 3 6 9 5
'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
KRAS MUTATED 4 3 2
KRAS WILD-TYPE 10 8 5
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0745 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
KRAS MUTATED 14 18 15
KRAS WILD-TYPE 54 50 21
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.596 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
KRAS MUTATED 6 7 9 6
KRAS WILD-TYPE 20 17 19 27
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
KRAS MUTATED 8 11 5
KRAS WILD-TYPE 7 45 23

Figure S18.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.597 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
KRAS MUTATED 6 5 6 3 4
KRAS WILD-TYPE 24 10 24 11 6
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
KRAS MUTATED 14 12 10 8 2
KRAS WILD-TYPE 44 25 19 26 11
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00838 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
KRAS MUTATED 9 4 5 2 7 7 6 3 3
KRAS WILD-TYPE 17 16 23 25 7 8 14 1 14

Figure S19.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
KRAS MUTATED 25 13 7
KRAS WILD-TYPE 34 62 27

Figure S20.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
KRAS MUTATED 7 17 14 7
KRAS WILD-TYPE 12 53 30 28
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
KRAS MUTATED 15 4 7
KRAS WILD-TYPE 46 10 22
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.502 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
KRAS MUTATED 5 13 8
KRAS WILD-TYPE 9 46 23
'SMARCA4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
SMARCA4 MUTATED 0 1 0 2
SMARCA4 WILD-TYPE 5 8 12 4
'SMARCA4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
SMARCA4 MUTATED 1 0 2
SMARCA4 WILD-TYPE 13 11 5
'SMARCA4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 1

Table S51.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
SMARCA4 MUTATED 6 3 6
SMARCA4 WILD-TYPE 62 65 30
'SMARCA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0093 (Fisher's exact test), Q value = 1

Table S52.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
SMARCA4 MUTATED 1 6 0 5
SMARCA4 WILD-TYPE 25 18 28 28

Figure S21.  Get High-res Image Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SMARCA4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S53.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
SMARCA4 MUTATED 1 6 3
SMARCA4 WILD-TYPE 14 50 25
'SMARCA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.419 (Fisher's exact test), Q value = 1

Table S54.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
SMARCA4 MUTATED 1 2 4 1 2
SMARCA4 WILD-TYPE 29 13 26 13 8
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 1

Table S55.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
SMARCA4 MUTATED 3 1 6 5 0
SMARCA4 WILD-TYPE 55 36 23 29 13

Figure S22.  Get High-res Image Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00655 (Fisher's exact test), Q value = 1

Table S56.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
SMARCA4 MUTATED 2 0 1 4 0 1 7 0 0
SMARCA4 WILD-TYPE 24 20 27 23 14 14 13 4 17

Figure S23.  Get High-res Image Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 1

Table S57.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
SMARCA4 MUTATED 2 10 3
SMARCA4 WILD-TYPE 57 65 31
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 1

Table S58.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
SMARCA4 MUTATED 1 7 1 6
SMARCA4 WILD-TYPE 18 63 43 29
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S59.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
SMARCA4 MUTATED 4 2 5
SMARCA4 WILD-TYPE 57 12 24
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0602 (Fisher's exact test), Q value = 1

Table S60.  Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
SMARCA4 MUTATED 0 10 1
SMARCA4 WILD-TYPE 14 49 30
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 1

Table S61.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
ARID1A MUTATED 5 1 5
ARID1A WILD-TYPE 63 67 31

Figure S24.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 1

Table S62.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
ARID1A MUTATED 1 3 3 1
ARID1A WILD-TYPE 25 21 25 32
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 1

Table S63.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
ARID1A MUTATED 0 2 3
ARID1A WILD-TYPE 15 54 25
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.96 (Fisher's exact test), Q value = 1

Table S64.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
ARID1A MUTATED 1 1 2 1 0
ARID1A WILD-TYPE 29 14 28 13 10
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 1

Table S65.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
ARID1A MUTATED 3 2 1 4 1
ARID1A WILD-TYPE 55 35 28 30 12
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S66.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
ARID1A MUTATED 1 2 1 3 0 2 1 0 1
ARID1A WILD-TYPE 25 18 27 24 14 13 19 4 16
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.66

Table S67.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
ARID1A MUTATED 0 10 1
ARID1A WILD-TYPE 59 65 33

Figure S25.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0514 (Fisher's exact test), Q value = 1

Table S68.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
ARID1A MUTATED 0 4 1 6
ARID1A WILD-TYPE 19 66 43 29
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S69.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
ARID1A MUTATED 4 1 3
ARID1A WILD-TYPE 57 13 26
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 1

Table S70.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
ARID1A MUTATED 0 7 1
ARID1A WILD-TYPE 14 52 30
'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S71.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
NF1 MUTATED 0 2 2 1
NF1 WILD-TYPE 5 7 10 5
'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S72.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
NF1 MUTATED 3 1 1
NF1 WILD-TYPE 11 10 6
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 1

Table S73.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
NF1 MUTATED 15 5 2
NF1 WILD-TYPE 53 63 34

Figure S26.  Get High-res Image Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 1

Table S74.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
NF1 MUTATED 0 6 7 5
NF1 WILD-TYPE 26 18 21 28

Figure S27.  Get High-res Image Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.92 (Fisher's exact test), Q value = 1

Table S75.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
NF1 MUTATED 2 8 3
NF1 WILD-TYPE 13 48 25
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.46 (Fisher's exact test), Q value = 1

Table S76.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
NF1 MUTATED 3 1 5 1 3
NF1 WILD-TYPE 27 14 25 13 7
'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 1

Table S77.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
NF1 MUTATED 11 2 2 4 2
NF1 WILD-TYPE 47 35 27 30 11
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S78.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
NF1 MUTATED 4 1 4 5 0 1 2 0 4
NF1 WILD-TYPE 22 19 24 22 14 14 18 4 13
'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 1

Table S79.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
NF1 MUTATED 4 11 7
NF1 WILD-TYPE 55 64 27
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S80.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
NF1 MUTATED 2 9 5 6
NF1 WILD-TYPE 17 61 39 29
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 1

Table S81.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
NF1 MUTATED 6 3 7
NF1 WILD-TYPE 55 11 22
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 1

Table S82.  Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
NF1 MUTATED 0 12 4
NF1 WILD-TYPE 14 47 27
'U2AF1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S83.  Gene #8: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
U2AF1 MUTATED 2 3 1
U2AF1 WILD-TYPE 66 65 35
'U2AF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0607 (Fisher's exact test), Q value = 1

Table S84.  Gene #8: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
U2AF1 MUTATED 0 0 0 3
U2AF1 WILD-TYPE 26 24 28 30
'U2AF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0824 (Fisher's exact test), Q value = 1

Table S85.  Gene #8: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
U2AF1 MUTATED 2 2 0
U2AF1 WILD-TYPE 13 54 28
'U2AF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S86.  Gene #8: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
U2AF1 MUTATED 2 0 1 0 1
U2AF1 WILD-TYPE 28 15 29 14 9
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.536 (Fisher's exact test), Q value = 1

Table S87.  Gene #8: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
U2AF1 MUTATED 3 1 1 0 1
U2AF1 WILD-TYPE 55 36 28 34 12
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 1

Table S88.  Gene #8: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
U2AF1 MUTATED 3 1 0 1 0 0 0 0 1
U2AF1 WILD-TYPE 23 19 28 26 14 15 20 4 16
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.06 (Fisher's exact test), Q value = 1

Table S89.  Gene #8: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
U2AF1 MUTATED 5 1 0
U2AF1 WILD-TYPE 54 74 34
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 1

Table S90.  Gene #8: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
U2AF1 MUTATED 1 1 3 1
U2AF1 WILD-TYPE 18 69 41 34
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.708 (Fisher's exact test), Q value = 1

Table S91.  Gene #8: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
U2AF1 MUTATED 3 0 0
U2AF1 WILD-TYPE 58 14 29
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S92.  Gene #8: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
U2AF1 MUTATED 0 2 1
U2AF1 WILD-TYPE 14 57 30
'EGFR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 1

Table S93.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
EGFR MUTATED 0 0 3 0
EGFR WILD-TYPE 5 9 9 6
'EGFR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 1

Table S94.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
EGFR MUTATED 3 0 0
EGFR WILD-TYPE 11 11 7
'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 1

Table S95.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
EGFR MUTATED 13 8 2
EGFR WILD-TYPE 55 60 34
'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S96.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
EGFR MUTATED 5 2 3 3
EGFR WILD-TYPE 21 22 25 30
'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 1

Table S97.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
EGFR MUTATED 1 12 3
EGFR WILD-TYPE 14 44 25
'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.245 (Fisher's exact test), Q value = 1

Table S98.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
EGFR MUTATED 9 2 3 1 1
EGFR WILD-TYPE 21 13 27 13 9
'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 1

Table S99.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
EGFR MUTATED 10 8 0 2 3
EGFR WILD-TYPE 48 29 29 32 10

Figure S28.  Get High-res Image Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 1

Table S100.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
EGFR MUTATED 2 7 3 6 1 0 0 0 4
EGFR WILD-TYPE 24 13 25 21 13 15 20 4 13

Figure S29.  Get High-res Image Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 1

Table S101.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
EGFR MUTATED 7 10 6
EGFR WILD-TYPE 52 65 28
'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.953 (Fisher's exact test), Q value = 1

Table S102.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
EGFR MUTATED 2 11 6 4
EGFR WILD-TYPE 17 59 38 31
'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 1

Table S103.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
EGFR MUTATED 10 0 3
EGFR WILD-TYPE 51 14 26
'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0603 (Fisher's exact test), Q value = 1

Table S104.  Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
EGFR MUTATED 2 4 7
EGFR WILD-TYPE 12 55 24
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.502 (Fisher's exact test), Q value = 1

Table S105.  Gene #10: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
SETD2 MUTATED 4 8 3
SETD2 WILD-TYPE 64 60 33
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 1

Table S106.  Gene #10: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
SETD2 MUTATED 3 1 6 4
SETD2 WILD-TYPE 23 23 22 29
'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 1

Table S107.  Gene #10: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
SETD2 MUTATED 2 4 2
SETD2 WILD-TYPE 13 52 26
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 1

Table S108.  Gene #10: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
SETD2 MUTATED 2 1 2 0 3
SETD2 WILD-TYPE 28 14 28 14 7
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.654 (Fisher's exact test), Q value = 1

Table S109.  Gene #10: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
SETD2 MUTATED 6 5 1 2 1
SETD2 WILD-TYPE 52 32 28 32 12
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S110.  Gene #10: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
SETD2 MUTATED 4 4 3 1 1 0 1 0 1
SETD2 WILD-TYPE 22 16 25 26 13 15 19 4 16
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S111.  Gene #10: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
SETD2 MUTATED 8 4 2
SETD2 WILD-TYPE 51 71 32
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S112.  Gene #10: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
SETD2 MUTATED 1 6 5 2
SETD2 WILD-TYPE 18 64 39 33
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 1

Table S113.  Gene #10: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
SETD2 MUTATED 10 0 3
SETD2 WILD-TYPE 51 14 26
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S114.  Gene #10: 'SETD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
SETD2 MUTATED 2 6 5
SETD2 WILD-TYPE 12 53 26
'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

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

Table S115.  Gene #11: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
CDKN2A MUTATED 3 3 2
CDKN2A WILD-TYPE 65 65 34
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S116.  Gene #11: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
CDKN2A MUTATED 1 0 1 1
CDKN2A WILD-TYPE 25 24 27 32
'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S117.  Gene #11: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
CDKN2A MUTATED 1 3 2
CDKN2A WILD-TYPE 14 53 26
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.939 (Fisher's exact test), Q value = 1

Table S118.  Gene #11: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
CDKN2A MUTATED 2 1 1 1 1
CDKN2A WILD-TYPE 28 14 29 13 9
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 1

Table S119.  Gene #11: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
CDKN2A MUTATED 3 0 2 2 1
CDKN2A WILD-TYPE 55 37 27 32 12
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S120.  Gene #11: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
CDKN2A MUTATED 2 0 2 1 0 1 0 1 1
CDKN2A WILD-TYPE 24 20 26 26 14 14 20 3 16
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S121.  Gene #11: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
CDKN2A MUTATED 3 4 1
CDKN2A WILD-TYPE 56 71 33
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0645 (Fisher's exact test), Q value = 1

Table S122.  Gene #11: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
CDKN2A MUTATED 0 1 5 2
CDKN2A WILD-TYPE 19 69 39 33
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S123.  Gene #11: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
CDKN2A MUTATED 2 0 1
CDKN2A WILD-TYPE 59 14 28
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 1

Table S124.  Gene #11: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
CDKN2A MUTATED 2 0 1
CDKN2A WILD-TYPE 12 59 30

Figure S30.  Get High-res Image Gene #11: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S125.  Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
MET MUTATED 4 7 0
MET WILD-TYPE 64 61 36
'MET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 1

Table S126.  Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
MET MUTATED 0 0 5 3
MET WILD-TYPE 26 24 23 30

Figure S31.  Get High-res Image Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MET MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.897 (Fisher's exact test), Q value = 1

Table S127.  Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
MET MUTATED 1 7 2
MET WILD-TYPE 14 49 26
'MET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.451 (Fisher's exact test), Q value = 1

Table S128.  Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
MET MUTATED 1 1 5 2 1
MET WILD-TYPE 29 14 25 12 9
'MET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S129.  Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
MET MUTATED 5 2 3 1 0
MET WILD-TYPE 53 35 26 33 13
'MET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0505 (Fisher's exact test), Q value = 1

Table S130.  Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
MET MUTATED 0 1 5 0 1 0 2 1 1
MET WILD-TYPE 26 19 23 27 13 15 18 3 16
'MET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 1

Table S131.  Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
MET MUTATED 4 4 3
MET WILD-TYPE 55 71 31
'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0721 (Fisher's exact test), Q value = 1

Table S132.  Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
MET MUTATED 0 5 6 0
MET WILD-TYPE 19 65 38 35
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.765 (Fisher's exact test), Q value = 1

Table S133.  Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
MET MUTATED 6 0 2
MET WILD-TYPE 55 14 27
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S134.  Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
MET MUTATED 1 3 4
MET WILD-TYPE 13 56 27
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 1

Table S135.  Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
ERBB2 MUTATED 5 3 0
ERBB2 WILD-TYPE 63 65 36
'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S136.  Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
ERBB2 MUTATED 2 1 1 1
ERBB2 WILD-TYPE 24 23 27 32
'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S137.  Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
ERBB2 MUTATED 1 3 1
ERBB2 WILD-TYPE 14 53 27
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S138.  Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
ERBB2 MUTATED 3 1 1 0 0
ERBB2 WILD-TYPE 27 14 29 14 10
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 1

Table S139.  Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
ERBB2 MUTATED 5 2 0 0 1
ERBB2 WILD-TYPE 53 35 29 34 12
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.432 (Fisher's exact test), Q value = 1

Table S140.  Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
ERBB2 MUTATED 4 1 1 1 1 0 0 0 0
ERBB2 WILD-TYPE 22 19 27 26 13 15 20 4 17
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.717 (Fisher's exact test), Q value = 1

Table S141.  Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
ERBB2 MUTATED 4 3 1
ERBB2 WILD-TYPE 55 72 33
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 1

Table S142.  Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
ERBB2 MUTATED 4 3 1 0
ERBB2 WILD-TYPE 15 67 43 35

Figure S32.  Get High-res Image Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S143.  Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
ERBB2 MUTATED 2 1 1
ERBB2 WILD-TYPE 59 13 28
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S144.  Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
ERBB2 MUTATED 1 2 1
ERBB2 WILD-TYPE 13 57 30
'CHRND MUTATION STATUS' versus 'CN_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 1

Table S145.  Gene #14: 'CHRND MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
CHRND MUTATED 4 2 3
CHRND WILD-TYPE 64 66 33
'CHRND MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 1

Table S146.  Gene #14: 'CHRND MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
CHRND MUTATED 1 0 4 1
CHRND WILD-TYPE 25 24 24 32
'CHRND MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.503 (Fisher's exact test), Q value = 1

Table S147.  Gene #14: 'CHRND MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
CHRND MUTATED 0 3 3
CHRND WILD-TYPE 15 53 25
'CHRND MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0979 (Fisher's exact test), Q value = 1

Table S148.  Gene #14: 'CHRND MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
CHRND MUTATED 0 3 2 1 0
CHRND WILD-TYPE 30 12 28 13 10
'CHRND MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 1

Table S149.  Gene #14: 'CHRND MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
CHRND MUTATED 4 0 1 4 0
CHRND WILD-TYPE 54 37 28 30 13
'CHRND MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.17 (Fisher's exact test), Q value = 1

Table S150.  Gene #14: 'CHRND MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
CHRND MUTATED 1 0 1 0 1 3 1 0 2
CHRND WILD-TYPE 25 20 27 27 13 12 19 4 15
'CHRND MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 1

Table S151.  Gene #14: 'CHRND MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
CHRND MUTATED 1 8 0
CHRND WILD-TYPE 58 67 34

Figure S33.  Get High-res Image Gene #14: 'CHRND MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CHRND MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.299 (Fisher's exact test), Q value = 1

Table S152.  Gene #14: 'CHRND MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
CHRND MUTATED 0 4 1 4
CHRND WILD-TYPE 19 66 43 31
'CHRND MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 1

Table S153.  Gene #14: 'CHRND MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
CHRND MUTATED 2 1 2
CHRND WILD-TYPE 59 13 27
'CHRND MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S154.  Gene #14: 'CHRND MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
CHRND MUTATED 1 4 0
CHRND WILD-TYPE 13 55 31
'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 1

Table S155.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 9 12 6
BRAF MUTATED 0 3 1 0
BRAF WILD-TYPE 5 6 11 6
'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.244 (Fisher's exact test), Q value = 1

Table S156.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 11 7
BRAF MUTATED 1 3 0
BRAF WILD-TYPE 13 8 7
'BRAF MUTATION STATUS' versus 'CN_CNMF'

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

Table S157.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
BRAF MUTATED 6 7 3
BRAF WILD-TYPE 62 61 33
'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 1

Table S158.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
BRAF MUTATED 4 1 4 3
BRAF WILD-TYPE 22 23 24 30
'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S159.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
BRAF MUTATED 1 3 3
BRAF WILD-TYPE 14 53 25
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S160.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
BRAF MUTATED 3 0 3 1 0
BRAF WILD-TYPE 27 15 27 13 10
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.803 (Fisher's exact test), Q value = 1

Table S161.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
BRAF MUTATED 7 4 1 3 1
BRAF WILD-TYPE 51 33 28 31 12
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S162.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
BRAF MUTATED 2 2 5 3 1 1 0 0 2
BRAF WILD-TYPE 24 18 23 24 13 14 20 4 15
'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 1

Table S163.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
BRAF MUTATED 5 5 6
BRAF WILD-TYPE 54 70 28
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S164.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
BRAF MUTATED 2 8 4 2
BRAF WILD-TYPE 17 62 40 33
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S165.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
BRAF MUTATED 5 1 4
BRAF WILD-TYPE 56 13 25
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 1

Table S166.  Gene #15: 'BRAF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
BRAF MUTATED 2 3 5
BRAF WILD-TYPE 12 56 26
'GEN1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S167.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
GEN1 MUTATED 2 1 1
GEN1 WILD-TYPE 66 67 35
'GEN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 1

Table S168.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
GEN1 MUTATED 0 0 2 1
GEN1 WILD-TYPE 26 24 26 32
'GEN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.607 (Fisher's exact test), Q value = 1

Table S169.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
GEN1 MUTATED 3 0 0 1 0
GEN1 WILD-TYPE 55 37 29 33 13
'GEN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0944 (Fisher's exact test), Q value = 1

Table S170.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
GEN1 MUTATED 3 0 0 0 1 0 0 0 0
GEN1 WILD-TYPE 23 20 28 27 13 15 20 4 17
'GEN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S171.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
GEN1 MUTATED 1 2 0
GEN1 WILD-TYPE 58 73 34
'GEN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S172.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
GEN1 MUTATED 0 2 0 1
GEN1 WILD-TYPE 19 68 44 34
'GEN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.709 (Fisher's exact test), Q value = 1

Table S173.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
GEN1 MUTATED 3 0 0
GEN1 WILD-TYPE 58 14 29
'GEN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S174.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
GEN1 MUTATED 1 1 1
GEN1 WILD-TYPE 13 58 30
'STX2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S175.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
STX2 MUTATED 1 3 0
STX2 WILD-TYPE 67 65 36
'STX2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 1

Table S176.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
STX2 MUTATED 0 0 1 2
STX2 WILD-TYPE 26 24 27 31
'STX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 1

Table S177.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
STX2 MUTATED 2 0 0 2 0
STX2 WILD-TYPE 56 37 29 32 13
'STX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 1

Table S178.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
STX2 MUTATED 0 0 2 0 1 1 0 0 0
STX2 WILD-TYPE 26 20 26 27 13 14 20 4 17
'STX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 1

Table S179.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
STX2 MUTATED 0 3 1
STX2 WILD-TYPE 59 72 33
'STX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S180.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
STX2 MUTATED 0 3 1 0
STX2 WILD-TYPE 19 67 43 35
'STX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 1

Table S181.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
STX2 MUTATED 1 0 2
STX2 WILD-TYPE 60 14 27
'STX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S182.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
STX2 MUTATED 1 1 1
STX2 WILD-TYPE 13 58 30
'MGA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 1

Table S183.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
MGA MUTATED 7 4 4
MGA WILD-TYPE 61 64 32
'MGA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S184.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
MGA MUTATED 1 4 5 1
MGA WILD-TYPE 25 20 23 32
'MGA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 1

Table S185.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
MGA MUTATED 0 5 4
MGA WILD-TYPE 15 51 24
'MGA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 1

Table S186.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
MGA MUTATED 1 2 5 1 0
MGA WILD-TYPE 29 13 25 13 10
'MGA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 1

Table S187.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
MGA MUTATED 8 1 2 4 0
MGA WILD-TYPE 50 36 27 30 13
'MGA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.594 (Fisher's exact test), Q value = 1

Table S188.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
MGA MUTATED 5 1 2 4 1 1 1 0 0
MGA WILD-TYPE 21 19 26 23 13 14 19 4 17
'MGA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 1

Table S189.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
MGA MUTATED 2 10 2
MGA WILD-TYPE 57 65 32
'MGA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 1

Table S190.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
MGA MUTATED 0 6 3 5
MGA WILD-TYPE 19 64 41 30
'MGA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 1

Table S191.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
MGA MUTATED 7 4 0
MGA WILD-TYPE 54 10 29

Figure S34.  Get High-res Image Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MGA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S192.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
MGA MUTATED 1 7 3
MGA WILD-TYPE 13 52 28
'GALC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 1

Table S193.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
GALC MUTATED 3 1 1
GALC WILD-TYPE 65 67 35
'GALC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.612 (Fisher's exact test), Q value = 1

Table S194.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
GALC MUTATED 0 2 1 2
GALC WILD-TYPE 26 22 27 31
'GALC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 1

Table S195.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
GALC MUTATED 3 0 0 2 0
GALC WILD-TYPE 55 37 29 32 13
'GALC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S196.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
GALC MUTATED 2 0 1 1 0 1 0 0 0
GALC WILD-TYPE 24 20 27 26 14 14 20 4 17
'GALC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 1

Table S197.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
GALC MUTATED 0 4 1
GALC WILD-TYPE 59 71 33
'GALC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.274 (Fisher's exact test), Q value = 1

Table S198.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
GALC MUTATED 1 2 0 2
GALC WILD-TYPE 18 68 44 33
'GALC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 1

Table S199.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
GALC MUTATED 1 0 3
GALC WILD-TYPE 60 14 26
'GALC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S200.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
GALC MUTATED 0 2 2
GALC WILD-TYPE 14 57 29
'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 1

Table S201.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 68 36
CTNNB1 MUTATED 2 5 2
CTNNB1 WILD-TYPE 66 63 34
'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.359 (Fisher's exact test), Q value = 1

Table S202.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 24 28 33
CTNNB1 MUTATED 2 0 3 1
CTNNB1 WILD-TYPE 24 24 25 32
'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 1

Table S203.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 56 28
CTNNB1 MUTATED 1 2 3
CTNNB1 WILD-TYPE 14 54 25
'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 1

Table S204.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 30 15 30 14 10
CTNNB1 MUTATED 0 4 1 1 0
CTNNB1 WILD-TYPE 30 11 29 13 10

Figure S35.  Get High-res Image Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 1

Table S205.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 58 37 29 34 13
CTNNB1 MUTATED 1 3 1 4 0
CTNNB1 WILD-TYPE 57 34 28 30 13
'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.3 (Fisher's exact test), Q value = 1

Table S206.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 26 20 28 27 14 15 20 4 17
CTNNB1 MUTATED 1 1 0 2 3 0 1 0 1
CTNNB1 WILD-TYPE 25 19 28 25 11 15 19 4 16
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S207.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 75 34
CTNNB1 MUTATED 3 5 1
CTNNB1 WILD-TYPE 56 70 33
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S208.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 70 44 35
CTNNB1 MUTATED 2 3 2 2
CTNNB1 WILD-TYPE 17 67 42 33
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 1

Table S209.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 14 29
CTNNB1 MUTATED 4 0 0
CTNNB1 WILD-TYPE 57 14 29
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 1

Table S210.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 59 31
CTNNB1 MUTATED 2 1 1
CTNNB1 WILD-TYPE 12 58 30
Methods & Data
Input
  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = LUAD-TP.transferedmergedcluster.txt

  • Number of patients = 172

  • Number of significantly mutated genes = 20

  • 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)