Correlation between gene mutation status and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1NG4Q1F
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1NG4Q1F
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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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