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 23 genes and 6 molecular subtypes across 193 patients, 39 significant findings detected with P value < 0.05 and Q value < 0.25.

  • FLT3 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • DNMT3A mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • NPM1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • IDH2 mutation correlated to 'METHLYATION_CNMF'.

  • IDH1 mutation correlated to 'METHLYATION_CNMF'.

  • WT1 mutation correlated to 'METHLYATION_CNMF'.

  • RUNX1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • CEBPA mutation correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • STAG2 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • KIT mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • PTPN11 mutation correlated to 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 23 genes and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 39 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
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
FLT3 52 (27%) 141 0.00033
(0.0035) 		0.00037
(0.00365) 		1e-05
(0.000197) 		0.00095
(0.00771) 		0.00197
(0.0129) 		0.00076
(0.00699)
NPM1 33 (17%) 160 0.0037
(0.0196) 		0.00013
(0.00224) 		1e-05
(0.000197) 		1e-05
(0.000197) 		1e-05
(0.000197) 		1e-05
(0.000197)
TP53 15 (8%) 178 1e-05
(0.000197) 		1e-05
(0.000197) 		0.0009
(0.00771) 		0.00235
(0.0142) 		0.00022
(0.00276) 		0.00016
(0.00245)
DNMT3A 48 (25%) 145 0.852
(0.898) 		0.038
(0.146) 		0.0212
(0.0861) 		0.00257
(0.0148) 		0.0016
(0.0123) 		0.00195
(0.0129)
RUNX1 16 (8%) 177 0.59
(0.737) 		0.0039
(0.0199) 		0.00869
(0.04) 		0.00025
(0.00287) 		0.00172
(0.0125) 		0.00236
(0.0142)
CEBPA 13 (7%) 180 0.598
(0.737) 		0.434
(0.644) 		0.212
(0.471) 		0.00019
(0.00262) 		0.0394
(0.147) 		0.0131
(0.0585)
STAG2 6 (3%) 187 0.566
(0.737) 		0.179
(0.433) 		0.129
(0.355) 		0.0272
(0.107) 		0.683
(0.786) 		0.0484
(0.171)
KIT 8 (4%) 185 0.104
(0.295) 		0.014
(0.0602) 		0.323
(0.559) 		0.00617
(0.0294) 		0.367
(0.589) 		0.221
(0.484)
IDH2 20 (10%) 173 0.102
(0.295) 		0.0171
(0.0716) 		0.684
(0.786) 		0.343
(0.585) 		0.758
(0.83) 		0.185
(0.433)
IDH1 18 (9%) 175 1
(1.00) 		0.00487
(0.024) 		0.274
(0.497) 		0.265
(0.487) 		0.239
(0.485) 		0.805
(0.855)
WT1 12 (6%) 181 0.423
(0.639) 		0.00329
(0.0182) 		0.0755
(0.237) 		0.372
(0.589) 		0.0716
(0.237) 		0.251
(0.487)
PTPN11 9 (5%) 184 0.683
(0.786) 		0.424
(0.639) 		0.0478
(0.171) 		0.506
(0.706) 		0.0838
(0.251) 		0.185
(0.433)
TET2 17 (9%) 176 0.358
(0.588) 		0.452
(0.663) 		0.311
(0.55) 		0.58
(0.737) 		0.642
(0.764) 		0.754
(0.83)
NRAS 15 (8%) 178 0.426
(0.639) 		0.948
(0.983) 		0.558
(0.737) 		0.926
(0.968) 		0.786
(0.842) 		0.584
(0.737)
U2AF1 8 (4%) 185 1
(1.00) 		0.061
(0.211) 		0.233
(0.485) 		0.262
(0.487) 		0.0759
(0.237) 		0.476
(0.679)
KRAS 8 (4%) 185 0.0774
(0.237) 		0.727
(0.819) 		0.324
(0.559) 		0.633
(0.76) 		0.255
(0.487) 		0.682
(0.786)
PHF6 6 (3%) 187 1
(1.00) 		0.631
(0.76) 		0.73
(0.819) 		0.477
(0.679) 		0.726
(0.819) 		0.349
(0.588)
RAD21 5 (3%) 188 0.484
(0.682) 		0.361
(0.588) 		0.602
(0.737) 		0.18
(0.433) 		0.198
(0.452) 		0.603
(0.737)
EZH2 3 (2%) 190 0.105
(0.295) 		0.261
(0.487) 		0.593
(0.737) 		0.159
(0.411) 		0.421
(0.639)
SMC3 7 (4%) 186 1
(1.00) 		0.2
(0.452) 		0.554
(0.737) 		0.456
(0.663) 		0.231
(0.485) 		0.362
(0.588)
ASXL1 5 (3%) 188 0.74
(0.824) 		0.0756
(0.237) 		0.259
(0.487) 		0.596
(0.737) 		0.161
(0.411) 		0.42
(0.639)
SMC1A 6 (3%) 187 0.763
(0.83) 		0.131
(0.355) 		0.571
(0.737) 		0.228
(0.485) 		0.164
(0.412) 		0.577
(0.737)
SUZ12 3 (2%) 190 0.293
(0.525) 		0.787
(0.842) 		0.258
(0.487) 		0.594
(0.737) 		0.239
(0.485) 		0.138
(0.366)
'FLT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0035

Table S1.  Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
FLT3 MUTATED 47 3 0 0
FLT3 WILD-TYPE 94 11 27 2

Figure S1.  Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FLT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0036

Table S2.  Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
FLT3 MUTATED 9 7 14 21
FLT3 WILD-TYPE 23 56 34 23

Figure S2.  Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S3.  Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
FLT3 MUTATED 6 17 22
FLT3 WILD-TYPE 67 32 23

Figure S3.  Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0077

Table S4.  Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
FLT3 MUTATED 5 3 2 6 13 16
FLT3 WILD-TYPE 11 10 13 51 13 24

Figure S4.  Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.013

Table S5.  Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
FLT3 MUTATED 22 4 7 17
FLT3 WILD-TYPE 33 34 35 29

Figure S5.  Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.007

Table S6.  Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
FLT3 MUTATED 29 5 16
FLT3 WILD-TYPE 36 30 65

Figure S6.  Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 0.9

Table S7.  Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
DNMT3A MUTATED 35 4 5 0
DNMT3A WILD-TYPE 106 10 22 2
'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.15

Table S8.  Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
DNMT3A MUTATED 5 15 19 7
DNMT3A WILD-TYPE 27 48 29 37

Figure S7.  Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.086

Table S9.  Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
DNMT3A MUTATED 11 18 12
DNMT3A WILD-TYPE 62 31 33

Figure S8.  Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00257 (Fisher's exact test), Q value = 0.015

Table S10.  Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
DNMT3A MUTATED 0 3 0 14 11 13
DNMT3A WILD-TYPE 16 10 15 43 15 27

Figure S9.  Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.012

Table S11.  Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
DNMT3A MUTATED 22 4 5 13
DNMT3A WILD-TYPE 33 34 37 33

Figure S10.  Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.013

Table S12.  Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
DNMT3A MUTATED 25 3 16
DNMT3A WILD-TYPE 40 32 65

Figure S11.  Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NPM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.02

Table S13.  Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
NPM1 MUTATED 31 0 0 0
NPM1 WILD-TYPE 110 14 27 2

Figure S12.  Get High-res Image Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NPM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0022

Table S14.  Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
NPM1 MUTATED 5 3 7 17
NPM1 WILD-TYPE 27 60 41 27

Figure S13.  Get High-res Image Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S15.  Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
NPM1 MUTATED 1 10 17
NPM1 WILD-TYPE 72 39 28

Figure S14.  Get High-res Image Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S16.  Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
NPM1 MUTATED 0 0 0 1 15 12
NPM1 WILD-TYPE 16 13 15 56 11 28

Figure S15.  Get High-res Image Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S17.  Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
NPM1 MUTATED 21 2 1 8
NPM1 WILD-TYPE 34 36 41 38

Figure S16.  Get High-res Image Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S18.  Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
NPM1 MUTATED 30 1 1
NPM1 WILD-TYPE 35 34 80

Figure S17.  Get High-res Image Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.29

Table S19.  Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
IDH2 MUTATED 14 4 1 0
IDH2 WILD-TYPE 127 10 26 2
'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.072

Table S20.  Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
IDH2 MUTATED 0 11 2 5
IDH2 WILD-TYPE 32 52 46 39

Figure S18.  Get High-res Image Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.684 (Fisher's exact test), Q value = 0.79

Table S21.  Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
IDH2 MUTATED 8 6 3
IDH2 WILD-TYPE 65 43 42
'IDH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.343 (Fisher's exact test), Q value = 0.58

Table S22.  Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
IDH2 MUTATED 0 2 0 9 2 4
IDH2 WILD-TYPE 16 11 15 48 24 36
'IDH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.758 (Fisher's exact test), Q value = 0.83

Table S23.  Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
IDH2 MUTATED 5 2 5 5
IDH2 WILD-TYPE 50 36 37 41
'IDH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.43

Table S24.  Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
IDH2 MUTATED 5 1 11
IDH2 WILD-TYPE 60 34 70
'IDH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S25.  Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
IDH1 MUTATED 14 1 2 0
IDH1 WILD-TYPE 127 13 25 2
'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00487 (Fisher's exact test), Q value = 0.024

Table S26.  Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
IDH1 MUTATED 6 10 1 1
IDH1 WILD-TYPE 26 53 47 43

Figure S19.  Get High-res Image Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.5

Table S27.  Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
IDH1 MUTATED 7 2 6
IDH1 WILD-TYPE 66 47 39
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.265 (Fisher's exact test), Q value = 0.49

Table S28.  Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
IDH1 MUTATED 0 0 0 8 4 3
IDH1 WILD-TYPE 16 13 15 49 22 37
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.49

Table S29.  Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
IDH1 MUTATED 4 4 2 8
IDH1 WILD-TYPE 51 34 40 38
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.805 (Fisher's exact test), Q value = 0.85

Table S30.  Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
IDH1 MUTATED 8 3 7
IDH1 WILD-TYPE 57 32 74
'TET2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.358 (Fisher's exact test), Q value = 0.59

Table S31.  Gene #6: 'TET2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
TET2 MUTATED 11 3 2 0
TET2 WILD-TYPE 130 11 25 2
'TET2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.66

Table S32.  Gene #6: 'TET2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
TET2 MUTATED 2 8 2 4
TET2 WILD-TYPE 30 55 46 40
'TET2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.311 (Fisher's exact test), Q value = 0.55

Table S33.  Gene #6: 'TET2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
TET2 MUTATED 9 2 4
TET2 WILD-TYPE 64 47 41
'TET2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.58 (Fisher's exact test), Q value = 0.74

Table S34.  Gene #6: 'TET2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
TET2 MUTATED 0 0 2 7 3 3
TET2 WILD-TYPE 16 13 13 50 23 37
'TET2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 0.76

Table S35.  Gene #6: 'TET2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
TET2 MUTATED 6 2 3 6
TET2 WILD-TYPE 49 36 39 40
'TET2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 0.83

Table S36.  Gene #6: 'TET2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
TET2 MUTATED 7 2 8
TET2 WILD-TYPE 58 33 73
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.426 (Fisher's exact test), Q value = 0.64

Table S37.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
NRAS MUTATED 10 1 4 0
NRAS WILD-TYPE 131 13 23 2
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.948 (Fisher's exact test), Q value = 0.98

Table S38.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
NRAS MUTATED 3 5 3 4
NRAS WILD-TYPE 29 58 45 40
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 0.74

Table S39.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
NRAS MUTATED 5 5 2
NRAS WILD-TYPE 68 44 43
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.926 (Fisher's exact test), Q value = 0.97

Table S40.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
NRAS MUTATED 0 1 1 4 2 4
NRAS WILD-TYPE 16 12 14 53 24 36
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 0.84

Table S41.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
NRAS MUTATED 5 3 4 2
NRAS WILD-TYPE 50 35 38 44
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 0.74

Table S42.  Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
NRAS MUTATED 7 2 5
NRAS WILD-TYPE 58 33 76
'WT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.64

Table S43.  Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
WT1 MUTATED 11 1 0 0
WT1 WILD-TYPE 130 13 27 2
'WT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.018

Table S44.  Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
WT1 MUTATED 1 0 3 7
WT1 WILD-TYPE 31 63 45 37

Figure S20.  Get High-res Image Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'WT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0755 (Fisher's exact test), Q value = 0.24

Table S45.  Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
WT1 MUTATED 2 2 6
WT1 WILD-TYPE 71 47 39
'WT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.59

Table S46.  Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
WT1 MUTATED 0 1 0 3 4 2
WT1 WILD-TYPE 16 12 15 54 22 38
'WT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0716 (Fisher's exact test), Q value = 0.24

Table S47.  Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
WT1 MUTATED 2 0 3 6
WT1 WILD-TYPE 53 38 39 40
'WT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.49

Table S48.  Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
WT1 MUTATED 5 0 6
WT1 WILD-TYPE 60 35 75
'U2AF1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S49.  Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
U2AF1 MUTATED 5 0 1 0
U2AF1 WILD-TYPE 136 14 26 2
'U2AF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.061 (Fisher's exact test), Q value = 0.21

Table S50.  Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
U2AF1 MUTATED 0 6 2 0
U2AF1 WILD-TYPE 32 57 46 44
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 0.49

Table S51.  Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
U2AF1 MUTATED 5 2 0
U2AF1 WILD-TYPE 68 47 45
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.49

Table S52.  Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
U2AF1 MUTATED 0 0 0 6 0 1
U2AF1 WILD-TYPE 16 13 15 51 26 39
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0759 (Fisher's exact test), Q value = 0.24

Table S53.  Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
U2AF1 MUTATED 1 2 4 0
U2AF1 WILD-TYPE 54 36 38 46
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.476 (Fisher's exact test), Q value = 0.68

Table S54.  Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
U2AF1 MUTATED 1 2 4
U2AF1 WILD-TYPE 64 33 77
'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 0.74

Table S55.  Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
RUNX1 MUTATED 11 2 3 0
RUNX1 WILD-TYPE 130 12 24 2
'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.02

Table S56.  Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
RUNX1 MUTATED 0 11 2 1
RUNX1 WILD-TYPE 32 52 46 43

Figure S21.  Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00869 (Fisher's exact test), Q value = 0.04

Table S57.  Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
RUNX1 MUTATED 11 3 0
RUNX1 WILD-TYPE 62 46 45

Figure S22.  Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.0029

Table S58.  Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
RUNX1 MUTATED 0 1 0 13 0 0
RUNX1 WILD-TYPE 16 12 15 44 26 40

Figure S23.  Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.012

Table S59.  Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
RUNX1 MUTATED 1 3 9 1
RUNX1 WILD-TYPE 54 35 33 45

Figure S24.  Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.014

Table S60.  Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
RUNX1 MUTATED 0 3 11
RUNX1 WILD-TYPE 65 32 70

Figure S25.  Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 0.74

Table S61.  Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
CEBPA MUTATED 9 0 3 0
CEBPA WILD-TYPE 132 14 24 2
'CEBPA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.64

Table S62.  Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
CEBPA MUTATED 2 2 5 4
CEBPA WILD-TYPE 30 61 43 40
'CEBPA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.47

Table S63.  Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
CEBPA MUTATED 9 2 2
CEBPA WILD-TYPE 64 47 43
'CEBPA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0026

Table S64.  Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
CEBPA MUTATED 0 0 7 4 1 1
CEBPA WILD-TYPE 16 13 8 53 25 39

Figure S26.  Get High-res Image Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0394 (Fisher's exact test), Q value = 0.15

Table S65.  Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
CEBPA MUTATED 1 1 4 7
CEBPA WILD-TYPE 54 37 38 39

Figure S27.  Get High-res Image Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.059

Table S66.  Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
CEBPA MUTATED 2 0 11
CEBPA WILD-TYPE 63 35 70

Figure S28.  Get High-res Image Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S67.  Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
TP53 MUTATED 0 2 13 0
TP53 WILD-TYPE 141 12 14 2

Figure S29.  Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2e-04

Table S68.  Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
TP53 MUTATED 0 15 0 0
TP53 WILD-TYPE 32 48 48 44

Figure S30.  Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0077

Table S69.  Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
TP53 MUTATED 12 1 0
TP53 WILD-TYPE 61 48 45

Figure S31.  Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.014

Table S70.  Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
TP53 MUTATED 0 0 0 12 0 1
TP53 WILD-TYPE 16 13 15 45 26 39

Figure S32.  Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0028

Table S71.  Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
TP53 MUTATED 0 9 3 2
TP53 WILD-TYPE 55 29 39 44

Figure S33.  Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.0025

Table S72.  Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
TP53 MUTATED 0 8 6
TP53 WILD-TYPE 65 27 75

Figure S34.  Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0774 (Fisher's exact test), Q value = 0.24

Table S73.  Gene #13: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
KRAS MUTATED 5 0 2 1
KRAS WILD-TYPE 136 14 25 1
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 0.82

Table S74.  Gene #13: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
KRAS MUTATED 0 3 2 1
KRAS WILD-TYPE 32 60 46 43
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.56

Table S75.  Gene #13: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
KRAS MUTATED 4 3 0
KRAS WILD-TYPE 69 46 45
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.633 (Fisher's exact test), Q value = 0.76

Table S76.  Gene #13: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
KRAS MUTATED 0 0 0 4 0 3
KRAS WILD-TYPE 16 13 15 53 26 37
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.49

Table S77.  Gene #13: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
KRAS MUTATED 3 3 0 1
KRAS WILD-TYPE 52 35 42 45
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.682 (Fisher's exact test), Q value = 0.79

Table S78.  Gene #13: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
KRAS MUTATED 3 2 2
KRAS WILD-TYPE 62 33 79
'PHF6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S79.  Gene #14: 'PHF6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
PHF6 MUTATED 5 0 1 0
PHF6 WILD-TYPE 136 14 26 2
'PHF6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 0.76

Table S80.  Gene #14: 'PHF6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
PHF6 MUTATED 1 1 3 1
PHF6 WILD-TYPE 31 62 45 43
'PHF6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.73 (Fisher's exact test), Q value = 0.82

Table S81.  Gene #14: 'PHF6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
PHF6 MUTATED 2 1 2
PHF6 WILD-TYPE 71 48 43
'PHF6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.477 (Fisher's exact test), Q value = 0.68

Table S82.  Gene #14: 'PHF6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
PHF6 MUTATED 0 0 0 4 1 0
PHF6 WILD-TYPE 16 13 15 53 25 40
'PHF6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 0.82

Table S83.  Gene #14: 'PHF6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
PHF6 MUTATED 2 0 2 1
PHF6 WILD-TYPE 53 38 40 45
'PHF6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 0.59

Table S84.  Gene #14: 'PHF6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
PHF6 MUTATED 1 0 4
PHF6 WILD-TYPE 64 35 77
'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 0.74

Table S85.  Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
STAG2 MUTATED 5 1 0 0
STAG2 WILD-TYPE 136 13 27 2
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 0.43

Table S86.  Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
STAG2 MUTATED 0 2 0 3
STAG2 WILD-TYPE 32 61 48 41
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.35

Table S87.  Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
STAG2 MUTATED 2 0 3
STAG2 WILD-TYPE 71 49 42
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 0.11

Table S88.  Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
STAG2 MUTATED 0 0 0 1 4 0
STAG2 WILD-TYPE 16 13 15 56 22 40

Figure S35.  Get High-res Image Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 0.79

Table S89.  Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
STAG2 MUTATED 2 1 0 2
STAG2 WILD-TYPE 53 37 42 44
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0484 (Fisher's exact test), Q value = 0.17

Table S90.  Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
STAG2 MUTATED 4 1 0
STAG2 WILD-TYPE 61 34 81

Figure S36.  Get High-res Image Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'CN_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.29

Table S91.  Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
KIT MUTATED 6 0 0 1
KIT WILD-TYPE 135 14 27 1
'KIT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.06

Table S92.  Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
KIT MUTATED 1 1 6 0
KIT WILD-TYPE 31 62 42 44

Figure S37.  Get High-res Image Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KIT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 0.56

Table S93.  Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
KIT MUTATED 4 3 0
KIT WILD-TYPE 69 46 45
'KIT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00617 (Fisher's exact test), Q value = 0.029

Table S94.  Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
KIT MUTATED 0 3 2 2 0 0
KIT WILD-TYPE 16 10 13 55 26 40

Figure S38.  Get High-res Image Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.59

Table S95.  Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
KIT MUTATED 1 3 3 1
KIT WILD-TYPE 54 35 39 45
'KIT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 0.48

Table S96.  Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
KIT MUTATED 1 3 4
KIT WILD-TYPE 64 32 77
'RAD21 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.68

Table S97.  Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
RAD21 MUTATED 4 1 0 0
RAD21 WILD-TYPE 137 13 27 2
'RAD21 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.59

Table S98.  Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
RAD21 MUTATED 0 1 1 3
RAD21 WILD-TYPE 32 62 47 41
'RAD21 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 0.74

Table S99.  Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
RAD21 MUTATED 1 2 2
RAD21 WILD-TYPE 72 47 43
'RAD21 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.43

Table S100.  Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
RAD21 MUTATED 0 0 1 0 2 2
RAD21 WILD-TYPE 16 13 14 57 24 38
'RAD21 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.45

Table S101.  Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
RAD21 MUTATED 2 0 0 3
RAD21 WILD-TYPE 53 38 42 43
'RAD21 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.603 (Fisher's exact test), Q value = 0.74

Table S102.  Gene #17: 'RAD21 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
RAD21 MUTATED 3 0 2
RAD21 WILD-TYPE 62 35 79
'EZH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.29

Table S103.  Gene #18: 'EZH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
EZH2 MUTATED 1 0 2 0
EZH2 WILD-TYPE 140 14 25 2
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 0.49

Table S104.  Gene #18: 'EZH2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
EZH2 MUTATED 3 0 0
EZH2 WILD-TYPE 70 49 45
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 0.74

Table S105.  Gene #18: 'EZH2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
EZH2 MUTATED 0 0 0 3 0 0
EZH2 WILD-TYPE 16 13 15 54 26 40
'EZH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.41

Table S106.  Gene #18: 'EZH2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
EZH2 MUTATED 0 1 2 0
EZH2 WILD-TYPE 55 37 40 46
'EZH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 0.64

Table S107.  Gene #18: 'EZH2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
EZH2 MUTATED 0 1 2
EZH2 WILD-TYPE 65 34 79
'SMC3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S108.  Gene #19: 'SMC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
SMC3 MUTATED 6 0 1 0
SMC3 WILD-TYPE 135 14 26 2
'SMC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.45

Table S109.  Gene #19: 'SMC3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
SMC3 MUTATED 0 1 4 2
SMC3 WILD-TYPE 32 62 44 42
'SMC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 0.74

Table S110.  Gene #19: 'SMC3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
SMC3 MUTATED 2 2 3
SMC3 WILD-TYPE 71 47 42
'SMC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.66

Table S111.  Gene #19: 'SMC3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
SMC3 MUTATED 0 0 1 2 3 1
SMC3 WILD-TYPE 16 13 14 55 23 39
'SMC3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.49

Table S112.  Gene #19: 'SMC3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
SMC3 MUTATED 1 0 3 3
SMC3 WILD-TYPE 54 38 39 43
'SMC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 0.59

Table S113.  Gene #19: 'SMC3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
SMC3 MUTATED 4 0 3
SMC3 WILD-TYPE 61 35 78
'ASXL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 0.82

Table S114.  Gene #20: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
ASXL1 MUTATED 4 0 1 0
ASXL1 WILD-TYPE 137 14 26 2
'ASXL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0756 (Fisher's exact test), Q value = 0.24

Table S115.  Gene #20: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
ASXL1 MUTATED 0 4 0 0
ASXL1 WILD-TYPE 32 59 48 44
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.49

Table S116.  Gene #20: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
ASXL1 MUTATED 3 0 0
ASXL1 WILD-TYPE 70 49 45
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 0.74

Table S117.  Gene #20: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
ASXL1 MUTATED 0 0 0 3 0 0
ASXL1 WILD-TYPE 16 13 15 54 26 40
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 0.41

Table S118.  Gene #20: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
ASXL1 MUTATED 0 1 2 0
ASXL1 WILD-TYPE 55 37 40 46
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.42 (Fisher's exact test), Q value = 0.64

Table S119.  Gene #20: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
ASXL1 MUTATED 0 1 2
ASXL1 WILD-TYPE 65 34 79
'SMC1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.763 (Fisher's exact test), Q value = 0.83

Table S120.  Gene #21: 'SMC1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
SMC1A MUTATED 6 0 0 0
SMC1A WILD-TYPE 135 14 27 2
'SMC1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 0.35

Table S121.  Gene #21: 'SMC1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
SMC1A MUTATED 0 1 1 4
SMC1A WILD-TYPE 32 62 47 40
'SMC1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.571 (Fisher's exact test), Q value = 0.74

Table S122.  Gene #21: 'SMC1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
SMC1A MUTATED 2 3 1
SMC1A WILD-TYPE 71 46 44
'SMC1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.49

Table S123.  Gene #21: 'SMC1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
SMC1A MUTATED 0 0 1 1 0 4
SMC1A WILD-TYPE 16 13 14 56 26 36
'SMC1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.41

Table S124.  Gene #21: 'SMC1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
SMC1A MUTATED 3 0 0 3
SMC1A WILD-TYPE 52 38 42 43
'SMC1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.577 (Fisher's exact test), Q value = 0.74

Table S125.  Gene #21: 'SMC1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
SMC1A MUTATED 3 0 3
SMC1A WILD-TYPE 62 35 78
'PTPN11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 0.79

Table S126.  Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
PTPN11 MUTATED 6 0 2 0
PTPN11 WILD-TYPE 135 14 25 2
'PTPN11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.64

Table S127.  Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
PTPN11 MUTATED 2 1 3 3
PTPN11 WILD-TYPE 30 62 45 41
'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 0.17

Table S128.  Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
PTPN11 MUTATED 1 2 5
PTPN11 WILD-TYPE 72 47 40

Figure S39.  Get High-res Image Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 0.71

Table S129.  Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
PTPN11 MUTATED 0 1 0 2 3 2
PTPN11 WILD-TYPE 16 12 15 55 23 38
'PTPN11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0838 (Fisher's exact test), Q value = 0.25

Table S130.  Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
PTPN11 MUTATED 6 1 0 2
PTPN11 WILD-TYPE 49 37 42 44
'PTPN11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.43

Table S131.  Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
PTPN11 MUTATED 6 1 2
PTPN11 WILD-TYPE 59 34 79
'SUZ12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.52

Table S132.  Gene #23: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 141 14 27 2
SUZ12 MUTATED 2 1 0 0
SUZ12 WILD-TYPE 139 13 27 2
'SUZ12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.787 (Fisher's exact test), Q value = 0.84

Table S133.  Gene #23: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 63 48 44
SUZ12 MUTATED 0 2 1 0
SUZ12 WILD-TYPE 32 61 47 44
'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.49

Table S134.  Gene #23: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 49 45
SUZ12 MUTATED 3 0 0
SUZ12 WILD-TYPE 70 49 45
'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.594 (Fisher's exact test), Q value = 0.74

Table S135.  Gene #23: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 40
SUZ12 MUTATED 0 0 0 3 0 0
SUZ12 WILD-TYPE 16 13 15 54 26 40
'SUZ12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.49

Table S136.  Gene #23: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 38 42 46
SUZ12 MUTATED 0 1 0 2
SUZ12 WILD-TYPE 55 37 42 44
'SUZ12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.37

Table S137.  Gene #23: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 65 35 81
SUZ12 MUTATED 0 2 1
SUZ12 WILD-TYPE 65 33 80
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/20018555/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/19785823/LAML-TB.transferedmergedcluster.txt

  • Number of patients = 193

  • Number of significantly mutated genes = 23

  • Number of Molecular subtypes = 6

  • 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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