Correlation between gene mutation status and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1862FN8
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1862FN8
Overview
Introduction

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

Summary

Testing the association between mutation status of 23 genes and 6 molecular subtypes across 193 patients, 39 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

  • IDH2 mutation correlated to 'METHLYATION_CNMF'.

  • IDH1 mutation correlated to 'METHLYATION_CNMF'.

  • WT1 mutation correlated to 'METHLYATION_CNMF'.

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

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

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

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

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

  • PTPN11 mutation correlated to 'MRNASEQ_CNMF'.

Results
Overview of the results

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

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

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

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

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

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

'FLT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

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

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

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

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

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

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

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'NPM1 MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

'NPM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

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

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

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'IDH2 MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

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

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

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

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

'WT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'CEBPA MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

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

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

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

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

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

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

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

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

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

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'TP53 MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

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

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

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

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

'KRAS MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

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

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

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

'KIT MUTATION STATUS' versus 'CN_CNMF'

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

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

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

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

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

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

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

'KIT MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

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

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

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

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

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

'KIT MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

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

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

  • Number of patients = 193

  • Number of significantly mutated genes = 23

  • Number of Molecular subtypes = 6

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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