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 25 genes and 6 molecular subtypes across 195 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'.

  • NPM1 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'.

  • IDH2 mutation correlated to 'METHLYATION_CNMF'.

  • IDH1 mutation correlated to 'METHLYATION_CNMF'.

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

  • WT1 mutation correlated to 'METHLYATION_CNMF'.

  • U2AF1 mutation correlated to 'METHLYATION_CNMF'.

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

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

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

  • STAG2 mutation correlated to '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 25 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 53 (27%) 142 0.00026
(0.00244) 		0.00016
(0.00171) 		1e-05
(0.000167) 		0.00011
(0.0015) 		0.00043
(0.00379) 		0.00078
(0.00585)
NPM1 52 (27%) 143 1e-05
(0.000167) 		1e-05
(0.000167) 		1e-05
(0.000167) 		1e-05
(0.000167) 		1e-05
(0.000167) 		1e-05
(0.000167)
TP53 15 (8%) 180 1e-05
(0.000167) 		1e-05
(0.000167) 		0.0009
(0.00627) 		0.0024
(0.0144) 		0.00018
(0.0018) 		0.00012
(0.0015)
DNMT3A 49 (25%) 146 0.854
(0.949) 		0.0305
(0.127) 		0.0242
(0.107) 		0.00249
(0.0144) 		0.00235
(0.0144) 		0.00263
(0.0146)
RUNX1 18 (9%) 177 0.36
(0.629) 		0.0005
(0.00417) 		0.00205
(0.0134) 		5e-05
(0.00075) 		0.00055
(0.00434) 		0.00092
(0.00627)
CEBPA 13 (7%) 182 0.59
(0.798) 		0.434
(0.693) 		0.198
(0.488) 		0.00013
(0.0015) 		0.0345
(0.14) 		0.00969
(0.0469)
KIT 8 (4%) 187 0.103
(0.315) 		0.0136
(0.0638) 		0.327
(0.613) 		0.00593
(0.0296) 		0.357
(0.629) 		0.189
(0.488)
IDH2 20 (10%) 175 0.0995
(0.315) 		0.0164
(0.0745) 		0.686
(0.839) 		0.342
(0.629) 		0.748
(0.877) 		0.185
(0.488)
IDH1 18 (9%) 177 1
(1.00) 		0.00585
(0.0296) 		0.256
(0.52) 		0.256
(0.52) 		0.235
(0.52) 		0.803
(0.913)
WT1 12 (6%) 183 0.421
(0.679) 		0.0046
(0.0246) 		0.0825
(0.275) 		0.365
(0.629) 		0.0678
(0.248) 		0.275
(0.543)
U2AF1 8 (4%) 187 1
(1.00) 		0.0481
(0.185) 		0.23
(0.52) 		0.259
(0.52) 		0.0756
(0.263) 		0.469
(0.713)
STAG2 6 (3%) 189 0.562
(0.798) 		0.198
(0.488) 		0.132
(0.395) 		0.0278
(0.119) 		0.688
(0.839) 		0.0649
(0.243)
PTPN11 9 (5%) 186 0.682
(0.839) 		0.46
(0.711) 		0.0474
(0.185) 		0.504
(0.741) 		0.0996
(0.315) 		0.208
(0.496)
TET2 17 (9%) 178 0.354
(0.629) 		0.44
(0.693) 		0.29
(0.558) 		0.572
(0.798) 		0.66
(0.839) 		0.845
(0.946)
NRAS 15 (8%) 180 0.421
(0.679) 		0.949
(1.00) 		0.601
(0.798) 		0.938
(1.00) 		0.813
(0.917) 		0.668
(0.839)
PHF6 6 (3%) 189 1
(1.00) 		0.632
(0.825) 		0.732
(0.871) 		0.473
(0.713) 		0.726
(0.871) 		0.344
(0.629)
KRAS 8 (4%) 187 0.074
(0.263) 		0.725
(0.871) 		0.324
(0.613) 		0.65
(0.839) 		0.255
(0.52) 		0.682
(0.839)
SMC3 7 (4%) 188 1
(1.00) 		0.205
(0.495) 		0.552
(0.796) 		0.444
(0.693) 		0.218
(0.503) 		0.416
(0.679)
RAD21 5 (3%) 190 0.48
(0.713) 		0.365
(0.629) 		0.606
(0.798) 		0.187
(0.488) 		0.213
(0.499) 		0.606
(0.798)
EZH2 3 (2%) 192 0.103
(0.315) 		0.258
(0.52) 		0.589
(0.798) 		0.158
(0.439) 		0.418
(0.679)
ASXL1 5 (3%) 190 0.737
(0.871) 		0.0773
(0.263) 		0.259
(0.52) 		0.592
(0.798) 		0.158
(0.439) 		0.416
(0.679)
SUZ12 3 (2%) 192 0.288
(0.558) 		0.788
(0.902) 		0.26
(0.52) 		0.592
(0.798) 		0.198
(0.488) 		0.14
(0.403)
PHACTR1 3 (2%) 192 1
(1.00) 		0.891
(0.975) 		0.416
(0.679)
SMC1A 6 (3%) 189 0.763
(0.888) 		0.134
(0.396) 		0.573
(0.798) 		0.246
(0.52) 		0.174
(0.475) 		0.661
(0.839)
KDM6A 3 (2%) 192 0.547
(0.796) 		0.475
(0.713) 		0.89
(0.975) 		0.783
(0.902)
'FLT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0024

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
FLT3 MUTATED 48 3 0 0
FLT3 WILD-TYPE 95 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 = 0.00016 (Fisher's exact test), Q value = 0.0017

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
FLT3 MUTATED 9 7 13 23
FLT3 WILD-TYPE 24 56 35 22

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 = 0.00017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
FLT3 MUTATED 6 17 23
FLT3 WILD-TYPE 67 33 22

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 = 0.00011 (Fisher's exact test), Q value = 0.0015

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 41
FLT3 MUTATED 5 2 2 6 14 17
FLT3 WILD-TYPE 11 11 13 51 12 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 = 0.00043 (Fisher's exact test), Q value = 0.0038

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
FLT3 MUTATED 23 4 6 18
FLT3 WILD-TYPE 34 34 36 28

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 = 0.00078 (Fisher's exact test), Q value = 0.0058

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
FLT3 MUTATED 30 5 16
FLT3 WILD-TYPE 37 30 65

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

'NPM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S7.  Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
NPM1 MUTATED 50 0 0 0
NPM1 WILD-TYPE 93 14 27 2

Figure S7.  Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NPM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S8.  Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
NPM1 MUTATED 8 4 13 26
NPM1 WILD-TYPE 25 59 35 19

Figure S8.  Get High-res Image Gene #2: '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 = 0.00017

Table S9.  Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
NPM1 MUTATED 1 20 25
NPM1 WILD-TYPE 72 30 20

Figure S9.  Get High-res Image Gene #2: '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 = 0.00017

Table S10.  Gene #2: '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 41
NPM1 MUTATED 0 0 0 1 23 22
NPM1 WILD-TYPE 16 13 15 56 3 19

Figure S10.  Get High-res Image Gene #2: '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 = 0.00017

Table S11.  Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
NPM1 MUTATED 35 2 1 12
NPM1 WILD-TYPE 22 36 41 34

Figure S11.  Get High-res Image Gene #2: '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 = 0.00017

Table S12.  Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
NPM1 MUTATED 48 1 1
NPM1 WILD-TYPE 19 34 80

Figure S12.  Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 0.95

Table S13.  Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
DNMT3A MUTATED 36 4 5 0
DNMT3A WILD-TYPE 107 10 22 2
'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.13

Table S14.  Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
DNMT3A MUTATED 5 16 19 7
DNMT3A WILD-TYPE 28 47 29 38

Figure S13.  Get High-res Image Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.11

Table S15.  Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
DNMT3A MUTATED 11 18 12
DNMT3A WILD-TYPE 62 32 33

Figure S14.  Get High-res Image Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00249 (Fisher's exact test), Q value = 0.014

Table S16.  Gene #3: '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 41
DNMT3A MUTATED 0 3 0 14 11 13
DNMT3A WILD-TYPE 16 10 15 43 15 28

Figure S15.  Get High-res Image Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S17.  Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
DNMT3A MUTATED 22 4 5 13
DNMT3A WILD-TYPE 35 34 37 33

Figure S16.  Get High-res Image Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00263 (Fisher's exact test), Q value = 0.015

Table S18.  Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
DNMT3A MUTATED 25 3 16
DNMT3A WILD-TYPE 42 32 65

Figure S17.  Get High-res Image Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0995 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
IDH2 MUTATED 14 4 1 0
IDH2 WILD-TYPE 129 10 26 2
'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
IDH2 MUTATED 0 11 2 5
IDH2 WILD-TYPE 33 52 46 40

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 = 0.686 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
IDH2 MUTATED 8 6 3
IDH2 WILD-TYPE 65 44 42
'IDH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 0.63

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 41
IDH2 MUTATED 0 2 0 9 2 4
IDH2 WILD-TYPE 16 11 15 48 24 37
'IDH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.748 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
IDH2 MUTATED 5 2 5 5
IDH2 WILD-TYPE 52 36 37 41
'IDH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
IDH2 MUTATED 5 1 11
IDH2 WILD-TYPE 62 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 143 14 27 2
IDH1 MUTATED 14 1 2 0
IDH1 WILD-TYPE 129 13 25 2
'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00585 (Fisher's exact test), Q value = 0.03

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
IDH1 MUTATED 6 10 1 1
IDH1 WILD-TYPE 27 53 47 44

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 = 0.256 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
IDH1 MUTATED 7 2 6
IDH1 WILD-TYPE 66 48 39
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 0.52

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 41
IDH1 MUTATED 0 0 0 8 4 3
IDH1 WILD-TYPE 16 13 15 49 22 38
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
IDH1 MUTATED 4 4 2 8
IDH1 WILD-TYPE 53 34 40 38
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.803 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
IDH1 MUTATED 8 3 7
IDH1 WILD-TYPE 59 32 74
'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.36 (Fisher's exact test), Q value = 0.63

Table S31.  Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
RUNX1 MUTATED 12 3 3 0
RUNX1 WILD-TYPE 131 11 24 2
'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0042

Table S32.  Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
RUNX1 MUTATED 0 13 2 1
RUNX1 WILD-TYPE 33 50 46 44

Figure S20.  Get High-res Image Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.013

Table S33.  Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
RUNX1 MUTATED 13 3 0
RUNX1 WILD-TYPE 60 47 45

Figure S21.  Get High-res Image Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00075

Table S34.  Gene #6: '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 41
RUNX1 MUTATED 0 1 0 15 0 0
RUNX1 WILD-TYPE 16 12 15 42 26 41

Figure S22.  Get High-res Image Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0043

Table S35.  Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
RUNX1 MUTATED 1 4 10 1
RUNX1 WILD-TYPE 56 34 32 45

Figure S23.  Get High-res Image Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0063

Table S36.  Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
RUNX1 MUTATED 0 4 12
RUNX1 WILD-TYPE 67 31 69

Figure S24.  Get High-res Image Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'TET2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.63

Table S37.  Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
TET2 MUTATED 11 3 2 0
TET2 WILD-TYPE 132 11 25 2
'TET2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.69

Table S38.  Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
TET2 MUTATED 2 8 2 4
TET2 WILD-TYPE 31 55 46 41
'TET2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.29 (Fisher's exact test), Q value = 0.56

Table S39.  Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
TET2 MUTATED 9 2 4
TET2 WILD-TYPE 64 48 41
'TET2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 0.8

Table S40.  Gene #7: '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 41
TET2 MUTATED 0 0 2 7 3 3
TET2 WILD-TYPE 16 13 13 50 23 38
'TET2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 0.84

Table S41.  Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
TET2 MUTATED 6 2 3 6
TET2 WILD-TYPE 51 36 39 40
'TET2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.845 (Fisher's exact test), Q value = 0.95

Table S42.  Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
TET2 MUTATED 7 2 8
TET2 WILD-TYPE 60 33 73
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
NRAS MUTATED 10 1 4 0
NRAS WILD-TYPE 133 13 23 2
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.949 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
NRAS MUTATED 3 5 3 4
NRAS WILD-TYPE 30 58 45 41
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
NRAS MUTATED 5 5 2
NRAS WILD-TYPE 68 45 43
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S46.  Gene #8: '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 41
NRAS MUTATED 0 1 1 4 2 4
NRAS WILD-TYPE 16 12 14 53 24 37
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
NRAS MUTATED 5 3 4 2
NRAS WILD-TYPE 52 35 38 44
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
NRAS MUTATED 7 2 5
NRAS WILD-TYPE 60 33 76
'WT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.68

Table S49.  Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
WT1 MUTATED 11 1 0 0
WT1 WILD-TYPE 132 13 27 2
'WT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0046 (Fisher's exact test), Q value = 0.025

Table S50.  Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
WT1 MUTATED 1 0 3 7
WT1 WILD-TYPE 32 63 45 38

Figure S25.  Get High-res Image Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'WT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0825 (Fisher's exact test), Q value = 0.28

Table S51.  Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
WT1 MUTATED 2 2 6
WT1 WILD-TYPE 71 48 39
'WT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 0.63

Table S52.  Gene #9: '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 41
WT1 MUTATED 0 1 0 3 4 2
WT1 WILD-TYPE 16 12 15 54 22 39
'WT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0678 (Fisher's exact test), Q value = 0.25

Table S53.  Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
WT1 MUTATED 2 0 3 6
WT1 WILD-TYPE 55 38 39 40
'WT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.54

Table S54.  Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
WT1 MUTATED 5 0 6
WT1 WILD-TYPE 62 35 75
'U2AF1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S55.  Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
U2AF1 MUTATED 5 0 1 0
U2AF1 WILD-TYPE 138 14 26 2
'U2AF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.18

Table S56.  Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
U2AF1 MUTATED 0 6 2 0
U2AF1 WILD-TYPE 33 57 46 45

Figure S26.  Get High-res Image Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.52

Table S57.  Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
U2AF1 MUTATED 5 2 0
U2AF1 WILD-TYPE 68 48 45
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.259 (Fisher's exact test), Q value = 0.52

Table S58.  Gene #10: '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 41
U2AF1 MUTATED 0 0 0 6 0 1
U2AF1 WILD-TYPE 16 13 15 51 26 40
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0756 (Fisher's exact test), Q value = 0.26

Table S59.  Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
U2AF1 MUTATED 1 2 4 0
U2AF1 WILD-TYPE 56 36 38 46
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 0.71

Table S60.  Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
U2AF1 MUTATED 1 2 4
U2AF1 WILD-TYPE 66 33 77
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00017

Table S61.  Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
TP53 MUTATED 0 2 13 0
TP53 WILD-TYPE 143 12 14 2

Figure S27.  Get High-res Image Gene #11: '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 = 0.00017

Table S62.  Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
TP53 MUTATED 0 15 0 0
TP53 WILD-TYPE 33 48 48 45

Figure S28.  Get High-res Image Gene #11: '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 = 0.0063

Table S63.  Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
TP53 MUTATED 12 1 0
TP53 WILD-TYPE 61 49 45

Figure S29.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0024 (Fisher's exact test), Q value = 0.014

Table S64.  Gene #11: '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 41
TP53 MUTATED 0 0 0 12 0 1
TP53 WILD-TYPE 16 13 15 45 26 40

Figure S30.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0018

Table S65.  Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
TP53 MUTATED 0 9 3 2
TP53 WILD-TYPE 57 29 39 44

Figure S31.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0015

Table S66.  Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
TP53 MUTATED 0 8 6
TP53 WILD-TYPE 67 27 75

Figure S32.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
CEBPA MUTATED 9 0 3 0
CEBPA WILD-TYPE 134 14 24 2
'CEBPA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
CEBPA MUTATED 2 2 5 4
CEBPA WILD-TYPE 31 61 43 41
'CEBPA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
CEBPA MUTATED 9 2 2
CEBPA WILD-TYPE 64 48 43
'CEBPA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0015

Table S70.  Gene #12: '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 41
CEBPA MUTATED 0 0 7 4 1 1
CEBPA WILD-TYPE 16 13 8 53 25 40

Figure S33.  Get High-res Image Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
CEBPA MUTATED 1 1 4 7
CEBPA WILD-TYPE 56 37 38 39

Figure S34.  Get High-res Image Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00969 (Fisher's exact test), Q value = 0.047

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
CEBPA MUTATED 2 0 11
CEBPA WILD-TYPE 65 35 70

Figure S35.  Get High-res Image Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PHF6 MUTATION STATUS' versus 'CN_CNMF'

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

Table S73.  Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
PHF6 MUTATED 5 0 1 0
PHF6 WILD-TYPE 138 14 26 2
'PHF6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 0.82

Table S74.  Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
PHF6 MUTATED 1 1 3 1
PHF6 WILD-TYPE 32 62 45 44
'PHF6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 0.87

Table S75.  Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
PHF6 MUTATED 2 1 2
PHF6 WILD-TYPE 71 49 43
'PHF6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 0.71

Table S76.  Gene #13: '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 41
PHF6 MUTATED 0 0 0 4 1 0
PHF6 WILD-TYPE 16 13 15 53 25 41
'PHF6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 0.87

Table S77.  Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
PHF6 MUTATED 2 0 2 1
PHF6 WILD-TYPE 55 38 40 45
'PHF6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.63

Table S78.  Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
PHF6 MUTATED 1 0 4
PHF6 WILD-TYPE 66 35 77
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.074 (Fisher's exact test), Q value = 0.26

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
KRAS MUTATED 5 0 2 1
KRAS WILD-TYPE 138 14 25 1
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.725 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
KRAS MUTATED 0 3 2 1
KRAS WILD-TYPE 33 60 46 44
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
KRAS MUTATED 4 3 0
KRAS WILD-TYPE 69 47 45
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.65 (Fisher's exact test), Q value = 0.84

Table S82.  Gene #14: '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 41
KRAS MUTATED 0 0 0 4 0 3
KRAS WILD-TYPE 16 13 15 53 26 38
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
KRAS MUTATED 3 3 0 1
KRAS WILD-TYPE 54 35 42 45
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.682 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
KRAS MUTATED 3 2 2
KRAS WILD-TYPE 64 33 79
'SMC3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S85.  Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
SMC3 MUTATED 6 0 1 0
SMC3 WILD-TYPE 137 14 26 2
'SMC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.5

Table S86.  Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
SMC3 MUTATED 0 1 4 2
SMC3 WILD-TYPE 33 62 44 43
'SMC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.552 (Fisher's exact test), Q value = 0.8

Table S87.  Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
SMC3 MUTATED 2 2 3
SMC3 WILD-TYPE 71 48 42
'SMC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 0.69

Table S88.  Gene #15: '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 41
SMC3 MUTATED 0 0 1 2 3 1
SMC3 WILD-TYPE 16 13 14 55 23 40
'SMC3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 0.5

Table S89.  Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
SMC3 MUTATED 1 0 3 3
SMC3 WILD-TYPE 56 38 39 43
'SMC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 0.68

Table S90.  Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
SMC3 MUTATED 4 0 3
SMC3 WILD-TYPE 63 35 78
'KIT MUTATION STATUS' versus 'CN_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
KIT MUTATED 6 0 0 1
KIT WILD-TYPE 137 14 27 1
'KIT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.064

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
KIT MUTATED 1 1 6 0
KIT WILD-TYPE 32 62 42 45

Figure S36.  Get High-res Image Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KIT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
KIT MUTATED 4 3 0
KIT WILD-TYPE 69 47 45
'KIT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00593 (Fisher's exact test), Q value = 0.03

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 41
KIT MUTATED 0 3 2 2 0 0
KIT WILD-TYPE 16 10 13 55 26 41

Figure S37.  Get High-res Image Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
KIT MUTATED 1 3 3 1
KIT WILD-TYPE 56 35 39 45
'KIT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
KIT MUTATED 1 3 4
KIT WILD-TYPE 66 32 77
'RAD21 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
RAD21 MUTATED 4 1 0 0
RAD21 WILD-TYPE 139 13 27 2
'RAD21 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
RAD21 MUTATED 0 1 1 3
RAD21 WILD-TYPE 33 62 47 42
'RAD21 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
RAD21 MUTATED 1 2 2
RAD21 WILD-TYPE 72 48 43
'RAD21 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 0.49

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 41
RAD21 MUTATED 0 0 1 0 2 2
RAD21 WILD-TYPE 16 13 14 57 24 39
'RAD21 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
RAD21 MUTATED 2 0 0 3
RAD21 WILD-TYPE 55 38 42 43
'RAD21 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
RAD21 MUTATED 3 0 2
RAD21 WILD-TYPE 64 35 79
'EZH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
EZH2 MUTATED 1 0 2 0
EZH2 WILD-TYPE 142 14 25 2
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
EZH2 MUTATED 3 0 0
EZH2 WILD-TYPE 70 50 45
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 0.8

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 41
EZH2 MUTATED 0 0 0 3 0 0
EZH2 WILD-TYPE 16 13 15 54 26 41
'EZH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
EZH2 MUTATED 0 1 2 0
EZH2 WILD-TYPE 57 37 40 46
'EZH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
EZH2 MUTATED 0 1 2
EZH2 WILD-TYPE 67 34 79
'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.8

Table S108.  Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
STAG2 MUTATED 5 1 0 0
STAG2 WILD-TYPE 138 13 27 2
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.49

Table S109.  Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
STAG2 MUTATED 0 2 0 3
STAG2 WILD-TYPE 33 61 48 42
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.39

Table S110.  Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
STAG2 MUTATED 2 0 3
STAG2 WILD-TYPE 71 50 42
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.12

Table S111.  Gene #19: '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 41
STAG2 MUTATED 0 0 0 1 4 0
STAG2 WILD-TYPE 16 13 15 56 22 41

Figure S38.  Get High-res Image Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.84

Table S112.  Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
STAG2 MUTATED 2 1 0 2
STAG2 WILD-TYPE 55 37 42 44
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0649 (Fisher's exact test), Q value = 0.24

Table S113.  Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
STAG2 MUTATED 4 1 0
STAG2 WILD-TYPE 63 34 81
'PTPN11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 0.84

Table S114.  Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
PTPN11 MUTATED 6 0 2 0
PTPN11 WILD-TYPE 137 14 25 2
'PTPN11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 0.71

Table S115.  Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
PTPN11 MUTATED 2 1 3 3
PTPN11 WILD-TYPE 31 62 45 42
'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.18

Table S116.  Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
PTPN11 MUTATED 1 2 5
PTPN11 WILD-TYPE 72 48 40

Figure S39.  Get High-res Image Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.504 (Fisher's exact test), Q value = 0.74

Table S117.  Gene #20: '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 41
PTPN11 MUTATED 0 1 0 2 3 2
PTPN11 WILD-TYPE 16 12 15 55 23 39
'PTPN11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0996 (Fisher's exact test), Q value = 0.32

Table S118.  Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
PTPN11 MUTATED 6 1 0 2
PTPN11 WILD-TYPE 51 37 42 44
'PTPN11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 0.5

Table S119.  Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
PTPN11 MUTATED 6 1 2
PTPN11 WILD-TYPE 61 34 79
'ASXL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 0.87

Table S120.  Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
ASXL1 MUTATED 4 0 1 0
ASXL1 WILD-TYPE 139 14 26 2
'ASXL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0773 (Fisher's exact test), Q value = 0.26

Table S121.  Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
ASXL1 MUTATED 0 4 0 0
ASXL1 WILD-TYPE 33 59 48 45
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.52

Table S122.  Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
ASXL1 MUTATED 3 0 0
ASXL1 WILD-TYPE 70 50 45
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 0.8

Table S123.  Gene #21: '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 41
ASXL1 MUTATED 0 0 0 3 0 0
ASXL1 WILD-TYPE 16 13 15 54 26 41
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.44

Table S124.  Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
ASXL1 MUTATED 0 1 2 0
ASXL1 WILD-TYPE 57 37 40 46
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 0.68

Table S125.  Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
ASXL1 MUTATED 0 1 2
ASXL1 WILD-TYPE 67 34 79
'SUZ12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.56

Table S126.  Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
SUZ12 MUTATED 2 1 0 0
SUZ12 WILD-TYPE 141 13 27 2
'SUZ12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.788 (Fisher's exact test), Q value = 0.9

Table S127.  Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
SUZ12 MUTATED 0 2 1 0
SUZ12 WILD-TYPE 33 61 47 45
'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 0.52

Table S128.  Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
SUZ12 MUTATED 3 0 0
SUZ12 WILD-TYPE 70 50 45
'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 0.8

Table S129.  Gene #22: '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 41
SUZ12 MUTATED 0 0 0 3 0 0
SUZ12 WILD-TYPE 16 13 15 54 26 41
'SUZ12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.49

Table S130.  Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
SUZ12 MUTATED 0 1 0 2
SUZ12 WILD-TYPE 57 37 42 44
'SUZ12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.14 (Fisher's exact test), Q value = 0.4

Table S131.  Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
SUZ12 MUTATED 0 2 1
SUZ12 WILD-TYPE 67 33 80
'PHACTR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S132.  Gene #23: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
PHACTR1 MUTATED 0 1 1 1
PHACTR1 WILD-TYPE 33 62 47 44
'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 0.98

Table S133.  Gene #23: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
PHACTR1 MUTATED 1 1 0 1
PHACTR1 WILD-TYPE 56 37 42 45
'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 0.68

Table S134.  Gene #23: 'PHACTR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
PHACTR1 MUTATED 0 1 2
PHACTR1 WILD-TYPE 67 34 79
'SMC1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.763 (Fisher's exact test), Q value = 0.89

Table S135.  Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
SMC1A MUTATED 6 0 0 0
SMC1A WILD-TYPE 137 14 27 2
'SMC1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.4

Table S136.  Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
SMC1A MUTATED 0 1 1 4
SMC1A WILD-TYPE 33 62 47 41
'SMC1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 0.8

Table S137.  Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 50 45
SMC1A MUTATED 2 3 1
SMC1A WILD-TYPE 71 47 44
'SMC1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.246 (Fisher's exact test), Q value = 0.52

Table S138.  Gene #24: '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 41
SMC1A MUTATED 0 0 1 1 0 4
SMC1A WILD-TYPE 16 13 14 56 26 37
'SMC1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.47

Table S139.  Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
SMC1A MUTATED 3 0 0 3
SMC1A WILD-TYPE 54 38 42 43
'SMC1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.661 (Fisher's exact test), Q value = 0.84

Table S140.  Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
SMC1A MUTATED 3 0 3
SMC1A WILD-TYPE 64 35 78
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.547 (Fisher's exact test), Q value = 0.8

Table S141.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 2
KDM6A MUTATED 2 0 1 0
KDM6A WILD-TYPE 141 14 26 2
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 0.71

Table S142.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 63 48 45
KDM6A MUTATED 0 1 2 0
KDM6A WILD-TYPE 33 62 46 45
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.89 (Fisher's exact test), Q value = 0.98

Table S143.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 38 42 46
KDM6A MUTATED 1 1 0 1
KDM6A WILD-TYPE 56 37 42 45
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.783 (Fisher's exact test), Q value = 0.9

Table S144.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
KDM6A MUTATED 1 1 1
KDM6A WILD-TYPE 66 34 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/15166008/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/15098833/LAML-TB.transferedmergedcluster.txt

  • Number of patients = 195

  • Number of significantly mutated genes = 25

  • 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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