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, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

  • IDH1 mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • WT1 mutation correlated to 'METHLYATION_CNMF'.

  • U2AF1 mutation correlated to 'MIRSEQ_CNMF'.

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

  • CEBPA mutation correlated to 'METHLYATION_CNMF',  '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, 36 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
TP53 15 (8%) 178 0.0174
(0.0799) 		1e-05
(0.000197) 		0.00105
(0.00805) 		0.00237
(0.0149) 		1e-05
(0.000197) 		9e-05
(0.00113)
NPM1 33 (17%) 160 0.278
(0.547) 		1e-05
(0.000197) 		1e-05
(0.000197) 		1e-05
(0.000197) 		2e-05
(0.000307) 		1e-05
(0.000197)
FLT3 52 (27%) 141 0.681
(0.805) 		4e-05
(0.000552) 		1e-05
(0.000197) 		0.00082
(0.00742) 		0.0805
(0.258) 		0.00071
(0.007)
DNMT3A 48 (25%) 145 0.341
(0.601) 		2e-05
(0.000307) 		0.0507
(0.189) 		0.00218
(0.0147) 		0.00086
(0.00742) 		0.00203
(0.0147)
RUNX1 16 (8%) 177 0.459
(0.667) 		0.00871
(0.0462) 		0.00992
(0.0507) 		0.0003
(0.00318) 		0.0565
(0.195) 		0.00224
(0.0147)
CEBPA 13 (7%) 180 1
(1.00) 		0.0348
(0.145) 		0.226
(0.518) 		0.00021
(0.00241) 		0.0124
(0.0609) 		0.0133
(0.0631)
IDH1 18 (9%) 175 0.0234
(0.104) 		0.00096
(0.00779) 		0.0983
(0.302) 		0.262
(0.525) 		0.447
(0.667) 		0.804
(0.881)
STAG2 6 (3%) 187 1
(1.00) 		0.337
(0.601) 		0.13
(0.365) 		0.0273
(0.118) 		0.0788
(0.258) 		0.049
(0.188)
KIT 8 (4%) 185 0.744
(0.839) 		0.00361
(0.0208) 		0.325
(0.601) 		0.00604
(0.0333) 		0.676
(0.805) 		0.222
(0.518)
WT1 12 (6%) 181 0.822
(0.894) 		0.00275
(0.0165) 		0.0598
(0.201) 		0.372
(0.603) 		0.0553
(0.195) 		0.252
(0.525)
U2AF1 8 (4%) 185 0.242
(0.525) 		0.129
(0.365) 		0.262
(0.525) 		0.263
(0.525) 		0.0487
(0.188) 		0.471
(0.677)
PTPN11 9 (5%) 184 0.128
(0.365) 		0.164
(0.436) 		0.0477
(0.188) 		0.513
(0.699) 		0.459
(0.667) 		0.185
(0.46)
IDH2 20 (10%) 173 0.391
(0.627) 		0.215
(0.511) 		0.646
(0.783) 		0.344
(0.601) 		0.753
(0.839) 		0.182
(0.46)
TET2 17 (9%) 176 0.699
(0.817) 		0.513
(0.699) 		0.35
(0.601) 		0.582
(0.746) 		0.366
(0.601) 		0.753
(0.839)
NRAS 15 (8%) 178 0.149
(0.404) 		0.353
(0.601) 		0.515
(0.699) 		0.931
(0.953) 		0.928
(0.953) 		0.588
(0.746)
KRAS 8 (4%) 185 0.864
(0.91) 		0.576
(0.746) 		0.324
(0.601) 		0.637
(0.778) 		0.301
(0.584) 		0.683
(0.805)
PHF6 6 (3%) 187 0.517
(0.699) 		0.422
(0.648) 		0.727
(0.836) 		0.476
(0.677) 		0.897
(0.938) 		0.35
(0.601)
RAD21 5 (3%) 188 0.932
(0.953) 		0.437
(0.663) 		0.605
(0.746) 		0.182
(0.46) 		0.363
(0.601) 		0.603
(0.746)
EZH2 3 (2%) 190 0.0903
(0.283) 		0.256
(0.525) 		0.593
(0.746) 		0.19
(0.46) 		0.42
(0.648)
SMC3 7 (4%) 186 0.839
(0.899) 		0.418
(0.648) 		0.485
(0.683) 		0.453
(0.667) 		0.744
(0.839) 		0.362
(0.601)
ASXL1 5 (3%) 188 0.724
(0.836) 		0.187
(0.46) 		0.255
(0.525) 		0.593
(0.746) 		0.11
(0.331) 		0.416
(0.648)
SMC1A 6 (3%) 187 0.852
(0.904) 		0.0544
(0.195) 		0.568
(0.746) 		0.229
(0.518) 		0.335
(0.601) 		0.576
(0.746)
SUZ12 3 (2%) 190 0.791
(0.873) 		0.84
(0.899) 		0.257
(0.525) 		0.596
(0.746) 		0.326
(0.601) 		0.139
(0.385)
'FLT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
FLT3 MUTATED 12 11 18 9
FLT3 WILD-TYPE 37 31 36 30
'FLT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00055

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
FLT3 MUTATED 11 5 7 7 21
FLT3 WILD-TYPE 11 20 55 30 20

Figure S1.  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 74 48 45
FLT3 MUTATED 6 17 22
FLT3 WILD-TYPE 68 31 23

Figure S2.  Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.0074

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 S3.  Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0805 (Fisher's exact test), Q value = 0.26

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
FLT3 MUTATED 21 4 14 7 4
FLT3 WILD-TYPE 34 27 28 25 17
'FLT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00071 (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 S4.  Get High-res Image Gene #1: 'FLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
DNMT3A MUTATED 13 6 16 9
DNMT3A WILD-TYPE 36 36 38 30
'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
DNMT3A MUTATED 16 2 13 6 9
DNMT3A WILD-TYPE 6 23 49 31 32

Figure S5.  Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0507 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
DNMT3A MUTATED 12 17 12
DNMT3A WILD-TYPE 62 31 33
'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00218 (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 S6.  Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
DNMT3A MUTATED 23 2 11 3 5
DNMT3A WILD-TYPE 32 29 31 29 16

Figure S7.  Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.015

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 S8.  Get High-res Image Gene #2: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NPM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
NPM1 MUTATED 12 8 7 4
NPM1 WILD-TYPE 37 34 47 35
'NPM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
NPM1 MUTATED 9 3 2 0 18
NPM1 WILD-TYPE 13 22 60 37 23

Figure S9.  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 74 48 45
NPM1 MUTATED 1 10 17
NPM1 WILD-TYPE 73 38 28

Figure S10.  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 S11.  Get High-res Image Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
NPM1 MUTATED 21 0 6 1 4
NPM1 WILD-TYPE 34 31 36 31 17

Figure S12.  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 S13.  Get High-res Image Gene #3: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
IDH2 MUTATED 6 2 8 3
IDH2 WILD-TYPE 43 40 46 36
'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.51

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
IDH2 MUTATED 0 2 10 2 4
IDH2 WILD-TYPE 22 23 52 35 37
'IDH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.646 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
IDH2 MUTATED 8 6 3
IDH2 WILD-TYPE 66 42 42
'IDH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.6

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 = 0.753 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
IDH2 MUTATED 6 1 4 4 2
IDH2 WILD-TYPE 49 30 38 28 19
'IDH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.46

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 = 0.0234 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
IDH1 MUTATED 7 1 2 7
IDH1 WILD-TYPE 42 41 52 32

Figure S14.  Get High-res Image Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0078

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
IDH1 MUTATED 3 5 10 0 0
IDH1 WILD-TYPE 19 20 52 37 41

Figure S15.  Get High-res Image Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0983 (Fisher's exact test), Q value = 0.3

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
IDH1 MUTATED 8 1 6
IDH1 WILD-TYPE 66 47 39
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.53

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 = 0.447 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
IDH1 MUTATED 5 3 7 1 2
IDH1 WILD-TYPE 50 28 35 31 19
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.804 (Fisher's exact test), Q value = 0.88

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 = 0.699 (Fisher's exact test), Q value = 0.82

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
TET2 MUTATED 3 4 4 5
TET2 WILD-TYPE 46 38 50 34
'TET2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
TET2 MUTATED 1 2 8 1 4
TET2 WILD-TYPE 21 23 54 36 37
'TET2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
TET2 MUTATED 9 2 4
TET2 WILD-TYPE 65 46 41
'TET2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.582 (Fisher's exact test), Q value = 0.75

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 = 0.366 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
TET2 MUTATED 5 2 5 1 4
TET2 WILD-TYPE 50 29 37 31 17
'TET2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.753 (Fisher's exact test), Q value = 0.84

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 = 0.149 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
NRAS MUTATED 3 2 3 7
NRAS WILD-TYPE 46 40 51 32
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
NRAS MUTATED 0 1 5 3 6
NRAS WILD-TYPE 22 24 57 34 35
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
NRAS MUTATED 5 5 2
NRAS WILD-TYPE 69 43 43
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.931 (Fisher's exact test), Q value = 0.95

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 = 0.928 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
NRAS MUTATED 5 2 2 3 2
NRAS WILD-TYPE 50 29 40 29 19
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 0.75

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 = 0.822 (Fisher's exact test), Q value = 0.89

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
WT1 MUTATED 3 2 3 4
WT1 WILD-TYPE 46 40 51 35
'WT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
WT1 MUTATED 0 2 0 2 7
WT1 WILD-TYPE 22 23 62 35 34

Figure S16.  Get High-res Image Gene #8: 'WT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'WT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0598 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
WT1 MUTATED 2 2 6
WT1 WILD-TYPE 72 46 39
'WT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.6

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 = 0.0553 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
WT1 MUTATED 2 0 6 3 0
WT1 WILD-TYPE 53 31 36 29 21
'WT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 0.53

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 = 0.242 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
U2AF1 MUTATED 2 0 1 3
U2AF1 WILD-TYPE 47 42 53 36
'U2AF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.37

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
U2AF1 MUTATED 1 0 6 1 0
U2AF1 WILD-TYPE 21 25 56 36 41
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
U2AF1 MUTATED 5 2 0
U2AF1 WILD-TYPE 69 46 45
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.53

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 = 0.0487 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
U2AF1 MUTATED 1 1 0 2 3
U2AF1 WILD-TYPE 54 30 42 30 18

Figure S17.  Get High-res Image Gene #9: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.471 (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 = 0.459 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
RUNX1 MUTATED 2 4 7 3
RUNX1 WILD-TYPE 47 38 47 36
'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00871 (Fisher's exact test), Q value = 0.046

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
RUNX1 MUTATED 0 0 11 2 1
RUNX1 WILD-TYPE 22 25 51 35 40

Figure S18.  Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00992 (Fisher's exact test), Q value = 0.051

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
RUNX1 MUTATED 11 3 0
RUNX1 WILD-TYPE 63 45 45

Figure S19.  Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.0032

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 S20.  Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0565 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
RUNX1 MUTATED 1 3 2 4 4
RUNX1 WILD-TYPE 54 28 40 28 17
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00224 (Fisher's exact test), Q value = 0.015

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 S21.  Get High-res Image Gene #10: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
CEBPA MUTATED 3 3 4 2
CEBPA WILD-TYPE 46 39 50 37
'CEBPA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.15

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
CEBPA MUTATED 0 2 2 7 2
CEBPA WILD-TYPE 22 23 60 30 39

Figure S22.  Get High-res Image Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CEBPA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
CEBPA MUTATED 9 2 2
CEBPA WILD-TYPE 65 46 43
'CEBPA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0024

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 S23.  Get High-res Image Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.061

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
CEBPA MUTATED 1 0 7 4 1
CEBPA WILD-TYPE 54 31 35 28 20

Figure S24.  Get High-res Image Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.063

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 S25.  Get High-res Image Gene #11: 'CEBPA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.08

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
TP53 MUTATED 0 7 5 3
TP53 WILD-TYPE 49 35 49 36

Figure S26.  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 CLUS_5
ALL 22 25 62 37 41
TP53 MUTATED 0 0 15 0 0
TP53 WILD-TYPE 22 25 47 37 41

Figure S27.  Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
TP53 MUTATED 12 1 0
TP53 WILD-TYPE 62 47 45

Figure S28.  Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.015

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 S29.  Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
TP53 MUTATED 0 6 0 2 6
TP53 WILD-TYPE 55 25 42 30 15

Figure S30.  Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0011

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 S31.  Get High-res Image Gene #12: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
KRAS MUTATED 3 1 2 2
KRAS WILD-TYPE 46 41 52 37
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.576 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
KRAS MUTATED 2 0 2 1 1
KRAS WILD-TYPE 20 25 60 36 40
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
KRAS MUTATED 4 3 0
KRAS WILD-TYPE 70 45 45
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 0.78

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 = 0.301 (Fisher's exact test), Q value = 0.58

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
KRAS MUTATED 3 3 1 0 0
KRAS WILD-TYPE 52 28 41 32 21
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.683 (Fisher's exact test), Q value = 0.81

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 = 0.517 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
PHF6 MUTATED 1 2 3 0
PHF6 WILD-TYPE 48 40 51 39
'PHF6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.422 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
PHF6 MUTATED 0 1 1 3 1
PHF6 WILD-TYPE 22 24 61 34 40
'PHF6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
PHF6 MUTATED 2 1 2
PHF6 WILD-TYPE 72 47 43
'PHF6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.476 (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 = 0.897 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
PHF6 MUTATED 2 0 1 1 1
PHF6 WILD-TYPE 53 31 41 31 20
'PHF6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.35 (Fisher's exact test), Q value = 0.6

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
STAG2 MUTATED 2 1 2 1
STAG2 WILD-TYPE 47 41 52 38
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
STAG2 MUTATED 0 0 2 0 3
STAG2 WILD-TYPE 22 25 60 37 38
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.37

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
STAG2 MUTATED 2 0 3
STAG2 WILD-TYPE 72 48 42
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.12

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 S32.  Get High-res Image Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0788 (Fisher's exact test), Q value = 0.26

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
STAG2 MUTATED 0 1 2 0 2
STAG2 WILD-TYPE 55 30 40 32 19
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.19

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 S33.  Get High-res Image Gene #15: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'CN_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
KIT MUTATED 1 1 3 2
KIT WILD-TYPE 48 41 51 37
'KIT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00361 (Fisher's exact test), Q value = 0.021

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
KIT MUTATED 1 0 1 6 0
KIT WILD-TYPE 21 25 61 31 41

Figure S34.  Get High-res Image Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KIT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
KIT MUTATED 4 3 0
KIT WILD-TYPE 70 45 45
'KIT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00604 (Fisher's exact test), Q value = 0.033

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 S35.  Get High-res Image Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
KIT MUTATED 1 2 3 1 1
KIT WILD-TYPE 54 29 39 31 20
'KIT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.52

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 = 0.932 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
RAD21 MUTATED 2 1 1 1
RAD21 WILD-TYPE 47 41 53 38
'RAD21 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.437 (Fisher's exact test), Q value = 0.66

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
RAD21 MUTATED 0 0 1 1 3
RAD21 WILD-TYPE 22 25 61 36 38
'RAD21 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
RAD21 MUTATED 1 2 2
RAD21 WILD-TYPE 73 46 43
'RAD21 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.46

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 = 0.363 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
RAD21 MUTATED 2 0 3 0 0
RAD21 WILD-TYPE 53 31 39 32 21
'RAD21 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.603 (Fisher's exact test), Q value = 0.75

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 = 0.0903 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
EZH2 MUTATED 0 1 0 2
EZH2 WILD-TYPE 49 41 54 37
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
EZH2 MUTATED 3 0 0
EZH2 WILD-TYPE 71 48 45
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 0.75

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 = 0.19 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
EZH2 MUTATED 0 1 0 1 1
EZH2 WILD-TYPE 55 30 42 31 20
'EZH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.42 (Fisher's exact test), Q value = 0.65

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 = 0.839 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
SMC3 MUTATED 3 1 2 1
SMC3 WILD-TYPE 46 41 52 38
'SMC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.418 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
SMC3 MUTATED 1 0 1 2 3
SMC3 WILD-TYPE 21 25 61 35 38
'SMC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
SMC3 MUTATED 2 2 3
SMC3 WILD-TYPE 72 46 42
'SMC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 0.67

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 = 0.744 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
SMC3 MUTATED 2 0 2 2 1
SMC3 WILD-TYPE 53 31 40 30 20
'SMC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 0.6

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 = 0.724 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
ASXL1 MUTATED 2 0 2 1
ASXL1 WILD-TYPE 47 42 52 38
'ASXL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
ASXL1 MUTATED 0 0 4 0 0
ASXL1 WILD-TYPE 22 25 58 37 41
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
ASXL1 MUTATED 3 0 0
ASXL1 WILD-TYPE 71 48 45
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 0.75

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 = 0.11 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
ASXL1 MUTATED 0 1 0 2 0
ASXL1 WILD-TYPE 55 30 42 30 21
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 0.65

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
SMC1A MUTATED 2 2 1 1
SMC1A WILD-TYPE 47 40 53 38
'SMC1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0544 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
SMC1A MUTATED 0 1 0 1 4
SMC1A WILD-TYPE 22 24 62 36 37
'SMC1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
SMC1A MUTATED 2 3 1
SMC1A WILD-TYPE 72 45 44
'SMC1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 0.52

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 = 0.335 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
SMC1A MUTATED 3 0 3 0 0
SMC1A WILD-TYPE 52 31 39 32 21
'SMC1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.576 (Fisher's exact test), Q value = 0.75

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 = 0.128 (Fisher's exact test), Q value = 0.37

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
PTPN11 MUTATED 3 4 1 0
PTPN11 WILD-TYPE 46 38 53 39
'PTPN11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
PTPN11 MUTATED 2 0 1 2 4
PTPN11 WILD-TYPE 20 25 61 35 37
'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
PTPN11 MUTATED 1 2 5
PTPN11 WILD-TYPE 73 46 40

Figure S36.  Get High-res Image Gene #22: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.513 (Fisher's exact test), Q value = 0.7

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 = 0.459 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
PTPN11 MUTATED 4 1 2 0 2
PTPN11 WILD-TYPE 51 30 40 32 19
'PTPN11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.46

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 = 0.791 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 49 42 54 39
SUZ12 MUTATED 0 1 1 1
SUZ12 WILD-TYPE 49 41 53 38
'SUZ12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 22 25 62 37 41
SUZ12 MUTATED 0 0 2 1 0
SUZ12 WILD-TYPE 22 25 60 36 41
'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 48 45
SUZ12 MUTATED 3 0 0
SUZ12 WILD-TYPE 71 48 45
'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 0.75

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 = 0.326 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 55 31 42 32 21
SUZ12 MUTATED 0 1 1 0 1
SUZ12 WILD-TYPE 55 30 41 32 20
'SUZ12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 0.38

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/22570965/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/22541002/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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