Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 20 genes and 12 molecular subtypes across 172 patients, 10 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_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, 10 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 0.0016
(0.33) 		0.0195
(1.00) 		2e-05
(0.00426) 		0.0162
(1.00) 		0.00043
(0.089) 		0.00019
(0.0399) 		1e-05
(0.00216) 		6e-05
(0.0127) 		0.00335
(0.683) 		0.00018
(0.038) 		0.384
(1.00) 		0.848
(1.00)
STK11 20 (12%) 152 0.554
(1.00) 		0.427
(1.00) 		0.521
(1.00) 		0.591
(1.00) 		0.405
(1.00) 		0.249
(1.00) 		0.00033
(0.069) 		1e-05
(0.00216) 		0.635
(1.00) 		0.108
(1.00) 		0.268
(1.00) 		0.636
(1.00)
KEAP1 31 (18%) 141 0.553
(1.00) 		0.426
(1.00) 		0.202
(1.00) 		0.361
(1.00) 		0.0905
(1.00) 		0.164
(1.00) 		0.00034
(0.0707) 		1e-05
(0.00216) 		1
(1.00) 		0.366
(1.00) 		0.686
(1.00) 		0.326
(1.00)
KRAS 47 (27%) 125 0.817
(1.00) 		1
(1.00) 		0.0572
(1.00) 		0.432
(1.00) 		0.188
(1.00) 		0.413
(1.00) 		0.639
(1.00) 		0.00882
(1.00) 		0.0148
(1.00) 		0.11
(1.00) 		0.182
(1.00) 		0.0188
(1.00)
SMARCA4 15 (9%) 157 0.118
(1.00) 		0.146
(1.00) 		0.273
(1.00) 		0.0138
(1.00) 		1
(1.00) 		0.432
(1.00) 		0.0414
(1.00) 		0.00646
(1.00) 		0.171
(1.00) 		0.335
(1.00) 		0.175
(1.00) 		0.256
(1.00)
ARID1A 11 (6%) 161 0.0353
(1.00) 		0.501
(1.00) 		0.0962
(1.00) 		0.0758
(1.00) 		0.673
(1.00) 		0.846
(1.00) 		0.00585
(1.00) 		0.0498
(1.00) 		0.256
(1.00) 		0.409
(1.00)
NF1 22 (13%) 150 0.909
(1.00) 		0.826
(1.00) 		0.00318
(0.652) 		0.0417
(1.00) 		0.886
(1.00) 		0.77
(1.00) 		0.298
(1.00) 		0.585
(1.00) 		0.0737
(1.00) 		0.906
(1.00) 		0.0857
(1.00) 		0.391
(1.00)
U2AF1 6 (3%) 166 1
(1.00) 		0.0608
(1.00) 		0.238
(1.00) 		0.821
(1.00) 		0.538
(1.00) 		0.479
(1.00) 		0.323
(1.00) 		0.236
(1.00) 		0.793
(1.00) 		0.705
(1.00)
EGFR 23 (13%) 149 0.279
(1.00) 		0.219
(1.00) 		0.159
(1.00) 		0.723
(1.00) 		0.292
(1.00) 		0.686
(1.00) 		0.0167
(1.00) 		0.0181
(1.00) 		0.395
(1.00) 		0.115
(1.00) 		0.0995
(1.00) 		0.00644
(1.00)
SETD2 15 (9%) 157 0.383
(1.00) 		0.345
(1.00) 		0.418
(1.00) 		0.0801
(1.00) 		0.65
(1.00) 		0.547
(1.00) 		0.252
(1.00) 		0.692
(1.00) 		0.283
(1.00) 		0.0922
(1.00)
CDKN2A 8 (5%) 164 0.898
(1.00) 		0.89
(1.00) 		0.768
(1.00) 		0.865
(1.00) 		0.471
(1.00) 		0.454
(1.00) 		1
(1.00) 		0.342
(1.00) 		0.457
(1.00) 		0.0783
(1.00)
MET 11 (6%) 161 0.16
(1.00) 		0.0349
(1.00) 		0.663
(1.00) 		0.309
(1.00) 		0.696
(1.00) 		0.052
(1.00) 		0.538
(1.00) 		0.0759
(1.00) 		0.712
(1.00) 		0.477
(1.00)
ERBB2 8 (5%) 164 0.282
(1.00) 		0.814
(1.00) 		0.884
(1.00) 		0.779
(1.00) 		0.193
(1.00) 		0.432
(1.00) 		0.713
(1.00) 		0.00771
(1.00) 		1
(1.00) 		1
(1.00)
CHRND 9 (5%) 163 0.824
(1.00) 		0.168
(1.00) 		0.428
(1.00) 		0.865
(1.00) 		0.201
(1.00) 		0.169
(1.00) 		0.06
(1.00) 		0.382
(1.00) 		0.116
(1.00) 		0.512
(1.00)
BRAF 16 (9%) 156 0.248
(1.00) 		0.242
(1.00) 		0.837
(1.00) 		0.466
(1.00) 		0.739
(1.00) 		0.306
(1.00) 		0.802
(1.00) 		0.763
(1.00) 		0.211
(1.00) 		0.586
(1.00) 		0.7
(1.00) 		0.0928
(1.00)
GEN1 4 (2%) 168 0.675
(1.00) 		0.55
(1.00) 		1
(1.00) 		1
(1.00) 		0.607
(1.00) 		0.0952
(1.00) 		1
(1.00) 		1
(1.00) 		0.322
(1.00) 		0.14
(1.00)
STX2 4 (2%) 168 1
(1.00) 		0.624
(1.00) 		0.641
(1.00) 		1
(1.00) 		0.523
(1.00) 		0.3
(1.00) 		0.307
(1.00) 		0.654
(1.00) 		1
(1.00) 		0.465
(1.00)
MGA 15 (9%) 157 0.639
(1.00) 		0.146
(1.00) 		0.232
(1.00) 		1
(1.00) 		0.31
(1.00) 		0.601
(1.00) 		0.14
(1.00) 		0.432
(1.00) 		0.263
(1.00) 		0.536
(1.00)
GALC 5 (3%) 167 0.514
(1.00) 		0.677
(1.00) 		1
(1.00) 		0.822
(1.00) 		0.493
(1.00) 		0.837
(1.00) 		0.197
(1.00) 		0.373
(1.00) 		0.819
(1.00) 		0.761
(1.00)
CTNNB1 9 (5%) 163 0.601
(1.00) 		0.312
(1.00) 		0.385
(1.00) 		0.188
(1.00) 		0.217
(1.00) 		0.299
(1.00) 		1
(1.00) 		0.776
(1.00) 		0.296
(1.00) 		0.225
(1.00)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0016 (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 = 0.0195 (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 = 2e-05 (Fisher's exact test), Q value = 0.0043

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 72 33
TP53 MUTATED 47 22 17
TP53 WILD-TYPE 20 50 16

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 = 0.0162 (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 23 25 29 33
TP53 MUTATED 6 12 18 22
TP53 WILD-TYPE 17 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 = 0.00043 (Fisher's exact test), Q value = 0.089

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 23 39
TP53 MUTATED 37 5 28
TP53 WILD-TYPE 36 18 11

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.04

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 27 27
TP53 MUTATED 43 6 21
TP53 WILD-TYPE 38 21 6

Figure S6.  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 = 0.0022

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 S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.013

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 S8.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 80 29
TP53 MUTATED 19 48 17
TP53 WILD-TYPE 40 32 12

Figure S9.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.038

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
TP53 MUTATED 6 3 27 23 23 2
TP53 WILD-TYPE 12 14 17 21 9 11

Figure S10.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.384 (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 46 35 24
TP53 MUTATED 24 21 10
TP53 WILD-TYPE 22 14 14
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.848 (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 42 52 11
TP53 MUTATED 23 27 5
TP53 WILD-TYPE 19 25 6
'STK11 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.554 (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 = 0.427 (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 = 0.521 (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 67 72 33
STK11 MUTATED 6 11 3
STK11 WILD-TYPE 61 61 30
'STK11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.591 (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 23 25 29 33
STK11 MUTATED 3 3 1 3
STK11 WILD-TYPE 20 22 28 30
'STK11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.405 (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 73 23 39
STK11 MUTATED 6 4 4
STK11 WILD-TYPE 67 19 35
'STK11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.249 (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
ALL 81 27 27
STK11 MUTATED 6 5 3
STK11 WILD-TYPE 75 22 24
'STK11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.069

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 S11.  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 = 0.0022

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 S12.  Get High-res Image Gene #2: 'STK11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'STK11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.635 (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 80 29
STK11 MUTATED 7 7 4
STK11 WILD-TYPE 52 73 25
'STK11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.108 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
STK11 MUTATED 5 1 6 2 4 0
STK11 WILD-TYPE 13 16 38 42 28 13
'STK11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.268 (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 46 35 24
STK11 MUTATED 6 1 3
STK11 WILD-TYPE 40 34 21
'STK11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.636 (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 42 52 11
STK11 MUTATED 5 5 0
STK11 WILD-TYPE 37 47 11
'KEAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.553 (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 = 0.426 (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 = 0.202 (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 67 72 33
KEAP1 MUTATED 8 15 8
KEAP1 WILD-TYPE 59 57 25
'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.361 (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 23 25 29 33
KEAP1 MUTATED 2 6 3 7
KEAP1 WILD-TYPE 21 19 26 26
'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0905 (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 73 23 39
KEAP1 MUTATED 9 7 9
KEAP1 WILD-TYPE 64 16 30
'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.164 (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
ALL 81 27 27
KEAP1 MUTATED 11 7 7
KEAP1 WILD-TYPE 70 20 20
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.071

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 S13.  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 = 0.0022

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 S14.  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 80 29
KEAP1 MUTATED 10 13 5
KEAP1 WILD-TYPE 49 67 24
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.366 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
KEAP1 MUTATED 5 2 9 4 7 1
KEAP1 WILD-TYPE 13 15 35 40 25 12
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.686 (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 46 35 24
KEAP1 MUTATED 10 6 3
KEAP1 WILD-TYPE 36 29 21
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.326 (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 42 52 11
KEAP1 MUTATED 8 11 0
KEAP1 WILD-TYPE 34 41 11
'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.817 (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 = 0.0572 (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 67 72 33
KRAS MUTATED 13 20 14
KRAS WILD-TYPE 54 52 19
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.432 (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 23 25 29 33
KRAS MUTATED 4 8 9 6
KRAS WILD-TYPE 19 17 20 27
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.188 (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 73 23 39
KRAS MUTATED 15 9 9
KRAS WILD-TYPE 58 14 30
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.413 (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
ALL 81 27 27
KRAS MUTATED 17 9 7
KRAS WILD-TYPE 64 18 20
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.639 (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 = 0.00882 (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 S15.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 80 29
KRAS MUTATED 24 16 5
KRAS WILD-TYPE 35 64 24

Figure S16.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.11 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
KRAS MUTATED 6 8 7 15 7 2
KRAS WILD-TYPE 12 9 37 29 25 11
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.182 (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 46 35 24
KRAS MUTATED 16 6 5
KRAS WILD-TYPE 30 29 19
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0188 (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 42 52 11
KRAS MUTATED 16 11 0
KRAS WILD-TYPE 26 41 11

Figure S17.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SMARCA4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.118 (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 = 0.273 (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 67 72 33
SMARCA4 MUTATED 6 4 5
SMARCA4 WILD-TYPE 61 68 28
'SMARCA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0138 (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 23 25 29 33
SMARCA4 MUTATED 1 6 0 5
SMARCA4 WILD-TYPE 22 19 29 28

Figure S18.  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 73 23 39
SMARCA4 MUTATED 7 2 4
SMARCA4 WILD-TYPE 66 21 35
'SMARCA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.432 (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
ALL 81 27 27
SMARCA4 MUTATED 6 3 4
SMARCA4 WILD-TYPE 75 24 23
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0414 (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 S19.  Get High-res Image Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00646 (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 S20.  Get High-res Image Gene #5: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.171 (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 80 29
SMARCA4 MUTATED 2 10 3
SMARCA4 WILD-TYPE 57 70 26
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.335 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
SMARCA4 MUTATED 1 0 6 2 5 1
SMARCA4 WILD-TYPE 17 17 38 42 27 12
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.175 (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 46 35 24
SMARCA4 MUTATED 2 5 4
SMARCA4 WILD-TYPE 44 30 20
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.256 (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 42 52 11
SMARCA4 MUTATED 2 8 1
SMARCA4 WILD-TYPE 40 44 10
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0353 (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 67 72 33
ARID1A MUTATED 6 1 4
ARID1A WILD-TYPE 61 71 29

Figure S21.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.501 (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 23 25 29 33
ARID1A MUTATED 1 3 3 1
ARID1A WILD-TYPE 22 22 26 32
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0962 (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 73 23 39
ARID1A MUTATED 3 0 5
ARID1A WILD-TYPE 70 23 34
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0758 (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
ALL 81 27 27
ARID1A MUTATED 4 0 4
ARID1A WILD-TYPE 77 27 23
'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 = 0.846 (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 = 0.00585 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 80 29
ARID1A MUTATED 0 10 1
ARID1A WILD-TYPE 59 70 28

Figure S22.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0498 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
ARID1A MUTATED 0 2 2 1 6 0
ARID1A WILD-TYPE 18 15 42 43 26 13

Figure S23.  Get High-res Image Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.256 (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 46 35 24
ARID1A MUTATED 2 5 1
ARID1A WILD-TYPE 44 30 23
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.409 (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 42 52 11
ARID1A MUTATED 2 6 0
ARID1A WILD-TYPE 40 46 11
'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.909 (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 = 0.00318 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 72 33
NF1 MUTATED 16 4 2
NF1 WILD-TYPE 51 68 31

Figure S24.  Get High-res Image Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0417 (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 23 25 29 33
NF1 MUTATED 0 6 7 5
NF1 WILD-TYPE 23 19 22 28

Figure S25.  Get High-res Image Gene #7: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.886 (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 73 23 39
NF1 MUTATED 11 3 4
NF1 WILD-TYPE 62 20 35
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.77 (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
ALL 81 27 27
NF1 MUTATED 10 3 5
NF1 WILD-TYPE 71 24 22
'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.298 (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 = 0.585 (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 = 0.0737 (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 80 29
NF1 MUTATED 4 11 7
NF1 WILD-TYPE 55 69 22
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.906 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
NF1 MUTATED 2 1 6 6 6 1
NF1 WILD-TYPE 16 16 38 38 26 12
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0857 (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 46 35 24
NF1 MUTATED 4 5 7
NF1 WILD-TYPE 42 30 17
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.391 (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 42 52 11
NF1 MUTATED 4 10 2
NF1 WILD-TYPE 38 42 9
'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 67 72 33
U2AF1 MUTATED 2 3 1
U2AF1 WILD-TYPE 65 69 32
'U2AF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0608 (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 23 25 29 33
U2AF1 MUTATED 0 0 0 3
U2AF1 WILD-TYPE 23 25 29 30
'U2AF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.238 (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 73 23 39
U2AF1 MUTATED 3 2 0
U2AF1 WILD-TYPE 70 21 39
'U2AF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.821 (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
ALL 81 27 27
U2AF1 MUTATED 4 1 0
U2AF1 WILD-TYPE 77 26 27
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.538 (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 = 0.479 (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 = 0.323 (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 80 29
U2AF1 MUTATED 4 2 0
U2AF1 WILD-TYPE 55 78 29
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.236 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
U2AF1 MUTATED 0 1 0 4 1 0
U2AF1 WILD-TYPE 18 16 44 40 31 13
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.793 (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 46 35 24
U2AF1 MUTATED 2 1 0
U2AF1 WILD-TYPE 44 34 24
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.705 (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 42 52 11
U2AF1 MUTATED 2 1 0
U2AF1 WILD-TYPE 40 51 11
'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 = 0.219 (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 = 0.159 (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 67 72 33
EGFR MUTATED 13 8 2
EGFR WILD-TYPE 54 64 31
'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.723 (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 23 25 29 33
EGFR MUTATED 4 2 4 3
EGFR WILD-TYPE 19 23 25 30
'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.292 (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 73 23 39
EGFR MUTATED 13 2 3
EGFR WILD-TYPE 60 21 36
'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.686 (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
ALL 81 27 27
EGFR MUTATED 12 4 2
EGFR WILD-TYPE 69 23 25
'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0167 (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 S26.  Get High-res Image Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0181 (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 S27.  Get High-res Image Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.395 (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 80 29
EGFR MUTATED 6 11 6
EGFR WILD-TYPE 53 69 23
'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.115 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
EGFR MUTATED 2 4 2 7 4 4
EGFR WILD-TYPE 16 13 42 37 28 9
'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0995 (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 46 35 24
EGFR MUTATED 8 1 4
EGFR WILD-TYPE 38 34 20
'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00644 (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 42 52 11
EGFR MUTATED 7 2 4
EGFR WILD-TYPE 35 50 7

Figure S28.  Get High-res Image Gene #9: 'EGFR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.383 (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 67 72 33
SETD2 MUTATED 4 9 2
SETD2 WILD-TYPE 63 63 31
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.345 (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 23 25 29 33
SETD2 MUTATED 3 1 6 4
SETD2 WILD-TYPE 20 24 23 29
'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.418 (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 73 23 39
SETD2 MUTATED 4 3 2
SETD2 WILD-TYPE 69 20 37
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0801 (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
ALL 81 27 27
SETD2 MUTATED 5 4 0
SETD2 WILD-TYPE 76 23 27
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.65 (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 = 0.547 (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 = 0.252 (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 80 29
SETD2 MUTATED 8 5 1
SETD2 WILD-TYPE 51 75 28
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.692 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
SETD2 MUTATED 1 0 4 5 2 2
SETD2 WILD-TYPE 17 17 40 39 30 11
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.283 (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 46 35 24
SETD2 MUTATED 8 2 3
SETD2 WILD-TYPE 38 33 21
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0922 (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 42 52 11
SETD2 MUTATED 8 3 2
SETD2 WILD-TYPE 34 49 9
'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.898 (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 67 72 33
CDKN2A MUTATED 3 3 2
CDKN2A WILD-TYPE 64 69 31
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.89 (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 23 25 29 33
CDKN2A MUTATED 1 0 1 1
CDKN2A WILD-TYPE 22 25 28 32
'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.768 (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 73 23 39
CDKN2A MUTATED 3 1 3
CDKN2A WILD-TYPE 70 22 36
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.865 (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
ALL 81 27 27
CDKN2A MUTATED 4 1 2
CDKN2A WILD-TYPE 77 26 25
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.471 (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 = 0.454 (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 80 29
CDKN2A MUTATED 3 4 1
CDKN2A WILD-TYPE 56 76 28
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.342 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
CDKN2A MUTATED 0 0 1 5 2 0
CDKN2A WILD-TYPE 18 17 43 39 30 13
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.457 (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 46 35 24
CDKN2A MUTATED 2 0 1
CDKN2A WILD-TYPE 44 35 23
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0783 (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 42 52 11
CDKN2A MUTATED 2 0 1
CDKN2A WILD-TYPE 40 52 10
'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.16 (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 67 72 33
MET MUTATED 4 7 0
MET WILD-TYPE 63 65 33
'MET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0349 (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 23 25 29 33
MET MUTATED 0 0 5 3
MET WILD-TYPE 23 25 24 30

Figure S29.  Get High-res Image Gene #12: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MET MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.663 (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 73 23 39
MET MUTATED 7 1 2
MET WILD-TYPE 66 22 37
'MET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.309 (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
ALL 81 27 27
MET MUTATED 8 2 0
MET WILD-TYPE 73 25 27
'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 = 0.052 (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 = 0.538 (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 80 29
MET MUTATED 4 4 3
MET WILD-TYPE 55 76 26
'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0759 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
MET MUTATED 0 0 6 5 0 0
MET WILD-TYPE 18 17 38 39 32 13
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.712 (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 46 35 24
MET MUTATED 5 2 1
MET WILD-TYPE 41 33 23
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.477 (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 42 52 11
MET MUTATED 5 3 0
MET WILD-TYPE 37 49 11
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.282 (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 67 72 33
ERBB2 MUTATED 5 3 0
ERBB2 WILD-TYPE 62 69 33
'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.814 (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 23 25 29 33
ERBB2 MUTATED 2 1 1 1
ERBB2 WILD-TYPE 21 24 28 32
'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.884 (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 73 23 39
ERBB2 MUTATED 4 1 3
ERBB2 WILD-TYPE 69 22 36
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.779 (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
ALL 81 27 27
ERBB2 MUTATED 6 1 1
ERBB2 WILD-TYPE 75 26 26
'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 = 0.713 (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 80 29
ERBB2 MUTATED 4 3 1
ERBB2 WILD-TYPE 55 77 28
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00771 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
ERBB2 MUTATED 4 2 1 1 0 0
ERBB2 WILD-TYPE 14 15 43 43 32 13

Figure S30.  Get High-res Image Gene #13: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (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 46 35 24
ERBB2 MUTATED 2 1 1
ERBB2 WILD-TYPE 44 34 23
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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 42 52 11
ERBB2 MUTATED 2 2 0
ERBB2 WILD-TYPE 40 50 11
'CHRND MUTATION STATUS' versus 'CN_CNMF'

P value = 0.824 (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 67 72 33
CHRND MUTATED 4 3 2
CHRND WILD-TYPE 63 69 31
'CHRND MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.168 (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 23 25 29 33
CHRND MUTATED 0 1 4 1
CHRND WILD-TYPE 23 24 25 32
'CHRND MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.428 (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 73 23 39
CHRND MUTATED 4 0 3
CHRND WILD-TYPE 69 23 36
'CHRND MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.865 (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
ALL 81 27 27
CHRND MUTATED 4 1 2
CHRND WILD-TYPE 77 26 25
'CHRND MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.201 (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 = 0.169 (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 = 0.06 (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 80 29
CHRND MUTATED 1 8 0
CHRND WILD-TYPE 58 72 29
'CHRND MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.382 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
CHRND MUTATED 0 1 3 1 4 0
CHRND WILD-TYPE 18 16 41 43 28 13
'CHRND MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.116 (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 46 35 24
CHRND MUTATED 1 4 0
CHRND WILD-TYPE 45 31 24
'CHRND MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.512 (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 42 52 11
CHRND MUTATED 1 4 0
CHRND WILD-TYPE 41 48 11
'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.248 (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 = 0.242 (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 = 0.837 (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 67 72 33
BRAF MUTATED 6 6 4
BRAF WILD-TYPE 61 66 29
'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.466 (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 23 25 29 33
BRAF MUTATED 4 1 4 3
BRAF WILD-TYPE 19 24 25 30
'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.739 (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 73 23 39
BRAF MUTATED 5 1 4
BRAF WILD-TYPE 68 22 35
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.306 (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
ALL 81 27 27
BRAF MUTATED 8 0 2
BRAF WILD-TYPE 73 27 25
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.802 (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 = 0.763 (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 = 0.211 (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 80 29
BRAF MUTATED 6 5 5
BRAF WILD-TYPE 53 75 24
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.586 (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 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
BRAF MUTATED 2 0 6 4 2 2
BRAF WILD-TYPE 16 17 38 40 30 11
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.7 (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 46 35 24
BRAF MUTATED 5 2 3
BRAF WILD-TYPE 41 33 21
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0928 (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 42 52 11
BRAF MUTATED 6 2 2
BRAF WILD-TYPE 36 50 9
'GEN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.675 (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 67 72 33
GEN1 MUTATED 2 1 1
GEN1 WILD-TYPE 65 71 32
'GEN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.55 (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 23 25 29 33
GEN1 MUTATED 0 0 2 1
GEN1 WILD-TYPE 23 25 27 32
'GEN1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S169.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 23 39
GEN1 MUTATED 2 0 1
GEN1 WILD-TYPE 71 23 38
'GEN1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S170.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 27 27
GEN1 MUTATED 2 1 0
GEN1 WILD-TYPE 79 26 27
'GEN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S171.  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 = 0.0952 (Fisher's exact test), Q value = 1

Table S172.  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 S173.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 80 29
GEN1 MUTATED 1 2 0
GEN1 WILD-TYPE 58 78 29
'GEN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S174.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
GEN1 MUTATED 0 0 1 1 1 0
GEN1 WILD-TYPE 18 17 43 43 31 13
'GEN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S175.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 35 24
GEN1 MUTATED 3 0 0
GEN1 WILD-TYPE 43 35 24
'GEN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S176.  Gene #16: 'GEN1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 11
GEN1 MUTATED 3 0 0
GEN1 WILD-TYPE 39 52 11
'STX2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S177.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 72 33
STX2 MUTATED 1 2 1
STX2 WILD-TYPE 66 70 32
'STX2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 1

Table S178.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 25 29 33
STX2 MUTATED 0 0 1 2
STX2 WILD-TYPE 23 25 28 31
'STX2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S179.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 23 39
STX2 MUTATED 2 0 2
STX2 WILD-TYPE 71 23 37
'STX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S180.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 27 27
STX2 MUTATED 2 1 1
STX2 WILD-TYPE 79 26 26
'STX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S181.  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 = 0.3 (Fisher's exact test), Q value = 1

Table S182.  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 = 0.307 (Fisher's exact test), Q value = 1

Table S183.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 80 29
STX2 MUTATED 0 3 1
STX2 WILD-TYPE 59 77 28
'STX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S184.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
STX2 MUTATED 0 0 3 1 0 0
STX2 WILD-TYPE 18 17 41 43 32 13
'STX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S185.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 35 24
STX2 MUTATED 1 1 1
STX2 WILD-TYPE 45 34 23
'STX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 1

Table S186.  Gene #17: 'STX2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 11
STX2 MUTATED 1 1 1
STX2 WILD-TYPE 41 51 10
'MGA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S187.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 72 33
MGA MUTATED 6 5 4
MGA WILD-TYPE 61 67 29
'MGA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S188.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 25 29 33
MGA MUTATED 1 4 5 1
MGA WILD-TYPE 22 21 24 32
'MGA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S189.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 23 39
MGA MUTATED 7 0 5
MGA WILD-TYPE 66 23 34
'MGA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S190.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 27 27
MGA MUTATED 8 2 2
MGA WILD-TYPE 73 25 25
'MGA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 1

Table S191.  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 = 0.601 (Fisher's exact test), Q value = 1

Table S192.  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 = 0.14 (Fisher's exact test), Q value = 1

Table S193.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 80 29
MGA MUTATED 2 10 2
MGA WILD-TYPE 57 70 27
'MGA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S194.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
MGA MUTATED 0 2 4 3 5 0
MGA WILD-TYPE 18 15 40 41 27 13
'MGA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 1

Table S195.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 35 24
MGA MUTATED 4 6 1
MGA WILD-TYPE 42 29 23
'MGA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S196.  Gene #18: 'MGA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 11
MGA MUTATED 4 7 0
MGA WILD-TYPE 38 45 11
'GALC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.514 (Fisher's exact test), Q value = 1

Table S197.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 72 33
GALC MUTATED 3 1 1
GALC WILD-TYPE 64 71 32
'GALC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 1

Table S198.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 25 29 33
GALC MUTATED 0 2 1 2
GALC WILD-TYPE 23 23 28 31
'GALC MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S199.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 23 39
GALC MUTATED 3 0 1
GALC WILD-TYPE 70 23 38
'GALC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S200.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 27 27
GALC MUTATED 3 0 1
GALC WILD-TYPE 78 27 26
'GALC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 1

Table S201.  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 = 0.837 (Fisher's exact test), Q value = 1

Table S202.  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 = 0.197 (Fisher's exact test), Q value = 1

Table S203.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 80 29
GALC MUTATED 0 4 1
GALC WILD-TYPE 59 76 28
'GALC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test), Q value = 1

Table S204.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
GALC MUTATED 1 1 1 0 2 0
GALC WILD-TYPE 17 16 43 44 30 13
'GALC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.819 (Fisher's exact test), Q value = 1

Table S205.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 35 24
GALC MUTATED 1 2 1
GALC WILD-TYPE 45 33 23
'GALC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.761 (Fisher's exact test), Q value = 1

Table S206.  Gene #19: 'GALC MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 11
GALC MUTATED 1 3 0
GALC WILD-TYPE 41 49 11
'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S207.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 72 33
CTNNB1 MUTATED 2 5 2
CTNNB1 WILD-TYPE 65 67 31
'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 1

Table S208.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 25 29 33
CTNNB1 MUTATED 2 0 3 1
CTNNB1 WILD-TYPE 21 25 26 32
'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S209.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 23 39
CTNNB1 MUTATED 2 1 3
CTNNB1 WILD-TYPE 71 22 36
'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.188 (Fisher's exact test), Q value = 1

Table S210.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 27 27
CTNNB1 MUTATED 2 3 1
CTNNB1 WILD-TYPE 79 24 26
'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 1

Table S211.  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 = 0.299 (Fisher's exact test), Q value = 1

Table S212.  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 = 1 (Fisher's exact test), Q value = 1

Table S213.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 59 80 29
CTNNB1 MUTATED 3 5 1
CTNNB1 WILD-TYPE 56 75 28
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S214.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 18 17 44 44 32 13
CTNNB1 MUTATED 2 0 3 2 2 0
CTNNB1 WILD-TYPE 16 17 41 42 30 13
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 1

Table S215.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 35 24
CTNNB1 MUTATED 4 1 0
CTNNB1 WILD-TYPE 42 34 24
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.225 (Fisher's exact test), Q value = 1

Table S216.  Gene #20: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 52 11
CTNNB1 MUTATED 4 1 0
CTNNB1 WILD-TYPE 38 51 11
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.

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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