Correlation between gene mutation status and molecular subtypes
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C13777FS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13777FS
Overview
Introduction

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

Summary

Testing the association between mutation status of 25 genes and 6 molecular subtypes across 195 patients, 27 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • DNMT3A mutation correlated to 'METHLYATION_CNMF'.

  • IDH2 mutation correlated to 'METHLYATION_CNMF'.

  • IDH1 mutation correlated to 'METHLYATION_CNMF'.

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

  • WT1 mutation correlated to 'METHLYATION_CNMF'.

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

  • CEBPA mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 25 genes and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 27 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
FLT3 53 (27%) 142 0.00034
(0.0425) 		7e-05
(0.00917) 		2e-05
(0.00268) 		0.00021
(0.0267) 		0.0005
(0.062) 		0.00058
(0.0713)
NPM1 52 (27%) 143 1e-05
(0.00144) 		1e-05
(0.00144) 		1e-05
(0.00144) 		1e-05
(0.00144) 		1e-05
(0.00144) 		1e-05
(0.00144)
RUNX1 18 (9%) 177 0.377
(1.00) 		0.00012
(0.0156) 		0.00191
(0.227) 		4e-05
(0.00528) 		0.0006
(0.0732) 		0.00118
(0.142)
TP53 15 (8%) 180 1e-05
(0.00144) 		2e-05
(0.00268) 		0.00089
(0.108) 		0.00214
(0.25) 		0.00024
(0.0302) 		0.00013
(0.0168)
DNMT3A 49 (25%) 146 0.533
(1.00) 		1e-05
(0.00144) 		0.0246
(1.00) 		0.00264
(0.306) 		0.00269
(0.307) 		0.00264
(0.306)
IDH2 20 (10%) 175 0.113
(1.00) 		1e-05
(0.00144) 		0.689
(1.00) 		0.344
(1.00) 		0.748
(1.00) 		0.185
(1.00)
IDH1 18 (9%) 177 0.372
(1.00) 		0.00193
(0.228) 		0.257
(1.00) 		0.257
(1.00) 		0.234
(1.00) 		0.805
(1.00)
WT1 12 (6%) 183 0.457
(1.00) 		1e-05
(0.00144) 		0.0811
(1.00) 		0.367
(1.00) 		0.0694
(1.00) 		0.273
(1.00)
CEBPA 13 (7%) 182 0.622
(1.00) 		0.00821
(0.92) 		0.199
(1.00) 		0.00016
(0.0205) 		0.0344
(1.00) 		0.0103
(1.00)
TET2 17 (9%) 178 0.387
(1.00) 		0.516
(1.00) 		0.293
(1.00) 		0.575
(1.00) 		0.661
(1.00) 		0.845
(1.00)
NRAS 15 (8%) 180 0.3
(1.00) 		0.888
(1.00) 		0.602
(1.00) 		0.939
(1.00) 		0.814
(1.00) 		0.669
(1.00)
U2AF1 8 (4%) 187 1
(1.00) 		0.149
(1.00) 		0.232
(1.00) 		0.26
(1.00) 		0.077
(1.00) 		0.471
(1.00)
PHF6 6 (3%) 189 1
(1.00) 		0.0841
(1.00) 		0.728
(1.00) 		0.473
(1.00) 		0.726
(1.00) 		0.347
(1.00)
KRAS 8 (4%) 187 0.0967
(1.00) 		0.365
(1.00) 		0.325
(1.00) 		0.645
(1.00) 		0.255
(1.00) 		0.68
(1.00)
SMC3 7 (4%) 188 1
(1.00) 		0.299
(1.00) 		0.549
(1.00) 		0.447
(1.00) 		0.218
(1.00) 		0.415
(1.00)
KIT 8 (4%) 187 0.128
(1.00) 		0.128
(1.00) 		0.325
(1.00) 		0.00556
(0.628) 		0.358
(1.00) 		0.192
(1.00)
RAD21 5 (3%) 190 0.493
(1.00) 		0.665
(1.00) 		0.606
(1.00) 		0.185
(1.00) 		0.216
(1.00) 		0.607
(1.00)
EZH2 3 (2%) 192 0.0296
(1.00) 		0.256
(1.00) 		0.594
(1.00) 		0.158
(1.00) 		0.416
(1.00)
STAG2 6 (3%) 189 0.58
(1.00) 		0.33
(1.00) 		0.13
(1.00) 		0.0261
(1.00) 		0.687
(1.00) 		0.0655
(1.00)
PTPN11 9 (5%) 186 0.697
(1.00) 		0.388
(1.00) 		0.0472
(1.00) 		0.506
(1.00) 		0.0987
(1.00) 		0.209
(1.00)
ASXL1 5 (3%) 190 0.747
(1.00) 		0.216
(1.00) 		0.258
(1.00) 		0.591
(1.00) 		0.161
(1.00) 		0.415
(1.00)
SUZ12 3 (2%) 192 0.298
(1.00) 		0.332
(1.00) 		0.26
(1.00) 		0.589
(1.00) 		0.197
(1.00) 		0.143
(1.00)
PHACTR1 3 (2%) 192 0.33
(1.00) 		0.891
(1.00) 		0.415
(1.00)
SMC1A 6 (3%) 189 0.77
(1.00) 		0.552
(1.00) 		0.575
(1.00) 		0.244
(1.00) 		0.172
(1.00) 		0.661
(1.00)
KDM6A 3 (2%) 192 0.556
(1.00) 		1
(1.00) 		0.891
(1.00) 		0.783
(1.00)
'FLT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.042

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
FLT3 MUTATED 48 3 0 0
FLT3 WILD-TYPE 94 11 27 3

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 = 7e-05 (Fisher's exact test), Q value = 0.0092

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 46 44 65 14 20
FLT3 MUTATED 24 11 8 2 7
FLT3 WILD-TYPE 22 33 57 12 13

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 = 2e-05 (Fisher's exact test), Q value = 0.0027

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

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

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

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
FLT3 MUTATED 5 2 2 6 14 17
FLT3 WILD-TYPE 11 11 13 51 12 24

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

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.062

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

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

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

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.071

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

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

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

'NPM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
NPM1 MUTATED 50 0 0 0
NPM1 WILD-TYPE 92 14 27 3

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

'NPM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
NPM1 MUTATED 34 0 4 9 4
NPM1 WILD-TYPE 12 44 61 5 16

Figure S8.  Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

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

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

Figure S9.  Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

Table S10.  Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
NPM1 MUTATED 0 0 0 1 23 22
NPM1 WILD-TYPE 16 13 15 56 3 19

Figure S10.  Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

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

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

Figure S11.  Get High-res Image Gene #2: 'NPM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

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

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

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

'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
DNMT3A MUTATED 36 4 4 1
DNMT3A WILD-TYPE 106 10 23 2
'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
DNMT3A MUTATED 23 1 19 1 3
DNMT3A WILD-TYPE 23 43 46 13 17

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

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 1

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

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

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

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00264 (Fisher's exact test), Q value = 0.31

Table S16.  Gene #3: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
DNMT3A MUTATED 0 3 0 14 11 13
DNMT3A WILD-TYPE 16 10 15 43 15 28

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

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.31

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

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

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

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00264 (Fisher's exact test), Q value = 0.31

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

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

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

'IDH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
IDH2 MUTATED 14 4 1 0
IDH2 WILD-TYPE 128 10 26 3
'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

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 46 44 65 14 20
IDH2 MUTATED 0 0 11 6 1
IDH2 WILD-TYPE 46 44 54 8 19

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 = 0.689 (Fisher's exact test), Q value = 1

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

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

P value = 0.344 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
IDH2 MUTATED 0 2 0 9 2 4
IDH2 WILD-TYPE 16 11 15 48 24 37
'IDH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.748 (Fisher's exact test), Q value = 1

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

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

P value = 0.185 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
IDH2 MUTATED 5 1 11
IDH2 WILD-TYPE 62 34 70
'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.372 (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 142 14 27 3
IDH1 MUTATED 14 1 1 1
IDH1 WILD-TYPE 128 13 26 2
'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00193 (Fisher's exact test), Q value = 0.23

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 46 44 65 14 20
IDH1 MUTATED 4 0 10 4 0
IDH1 WILD-TYPE 42 44 55 10 20

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 = 0.257 (Fisher's exact test), Q value = 1

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

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

P value = 0.257 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
IDH1 MUTATED 0 0 0 8 4 3
IDH1 WILD-TYPE 16 13 15 49 22 38
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 1

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

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

P value = 0.805 (Fisher's exact test), Q value = 1

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

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

P value = 0.377 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
RUNX1 MUTATED 12 3 3 0
RUNX1 WILD-TYPE 130 11 24 3
'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
RUNX1 MUTATED 0 0 13 0 3
RUNX1 WILD-TYPE 46 44 52 14 17

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

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.23

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

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

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

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0053

Table S34.  Gene #6: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
RUNX1 MUTATED 0 1 0 15 0 0
RUNX1 WILD-TYPE 16 12 15 42 26 41

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

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.073

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

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

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

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.14

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

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

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

'TET2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
TET2 MUTATED 11 3 2 0
TET2 WILD-TYPE 131 11 25 3
'TET2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.516 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
TET2 MUTATED 3 2 8 2 1
TET2 WILD-TYPE 43 42 57 12 19
'TET2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 1

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

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

P value = 0.575 (Fisher's exact test), Q value = 1

Table S40.  Gene #7: 'TET2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
TET2 MUTATED 0 0 2 7 3 3
TET2 WILD-TYPE 16 13 13 50 23 38
'TET2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.661 (Fisher's exact test), Q value = 1

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

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

P value = 0.845 (Fisher's exact test), Q value = 1

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

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

P value = 0.3 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
NRAS MUTATED 10 1 3 1
NRAS WILD-TYPE 132 13 24 2
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.888 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
NRAS MUTATED 4 3 5 2 1
NRAS WILD-TYPE 42 41 60 12 19
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 1

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

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

P value = 0.939 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
NRAS MUTATED 0 1 1 4 2 4
NRAS WILD-TYPE 16 12 14 53 24 37
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.814 (Fisher's exact test), Q value = 1

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

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

P value = 0.669 (Fisher's exact test), Q value = 1

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

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

P value = 0.457 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
WT1 MUTATED 11 1 0 0
WT1 WILD-TYPE 131 13 27 3
'WT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
WT1 MUTATED 1 1 0 2 7
WT1 WILD-TYPE 45 43 65 12 13

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

'WT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0811 (Fisher's exact test), Q value = 1

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

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

P value = 0.367 (Fisher's exact test), Q value = 1

Table S52.  Gene #9: 'WT1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
WT1 MUTATED 0 1 0 3 4 2
WT1 WILD-TYPE 16 12 15 54 22 39
'WT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0694 (Fisher's exact test), Q value = 1

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

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

P value = 0.273 (Fisher's exact test), Q value = 1

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

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

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
U2AF1 MUTATED 5 0 1 0
U2AF1 WILD-TYPE 137 14 26 3
'U2AF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
U2AF1 MUTATED 1 0 6 0 1
U2AF1 WILD-TYPE 45 44 59 14 19
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 1

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

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

P value = 0.26 (Fisher's exact test), Q value = 1

Table S58.  Gene #10: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
U2AF1 MUTATED 0 0 0 6 0 1
U2AF1 WILD-TYPE 16 13 15 51 26 40
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.077 (Fisher's exact test), Q value = 1

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

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

P value = 0.471 (Fisher's exact test), Q value = 1

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

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

P value = 1e-05 (Fisher's exact test), Q value = 0.0014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
TP53 MUTATED 0 2 13 0
TP53 WILD-TYPE 142 12 14 3

Figure S26.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
TP53 MUTATED 0 0 15 0 0
TP53 WILD-TYPE 46 44 50 14 20

Figure S27.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.11

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

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

Figure S28.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00214 (Fisher's exact test), Q value = 0.25

Table S64.  Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
TP53 MUTATED 0 0 0 12 0 1
TP53 WILD-TYPE 16 13 15 45 26 40

Figure S29.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.03

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

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

Figure S30.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.017

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

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

Figure S31.  Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CEBPA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
CEBPA MUTATED 9 0 3 0
CEBPA WILD-TYPE 133 14 24 3
'CEBPA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00821 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
CEBPA MUTATED 0 6 2 2 3
CEBPA WILD-TYPE 46 38 63 12 17

Figure S32.  Get High-res Image Gene #12: 'CEBPA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CEBPA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

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

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

P value = 0.00016 (Fisher's exact test), Q value = 0.02

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
CEBPA MUTATED 0 0 7 4 1 1
CEBPA WILD-TYPE 16 13 8 53 25 40

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

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 1

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

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

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

'CEBPA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 1

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

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

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

'PHF6 MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
PHF6 MUTATED 5 0 1 0
PHF6 WILD-TYPE 137 14 26 3
'PHF6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0841 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
PHF6 MUTATED 1 1 1 0 3
PHF6 WILD-TYPE 45 43 64 14 17
'PHF6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.728 (Fisher's exact test), Q value = 1

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

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

P value = 0.473 (Fisher's exact test), Q value = 1

Table S76.  Gene #13: 'PHF6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
PHF6 MUTATED 0 0 0 4 1 0
PHF6 WILD-TYPE 16 13 15 53 25 41
'PHF6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 1

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

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

P value = 0.347 (Fisher's exact test), Q value = 1

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

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

P value = 0.0967 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
KRAS MUTATED 5 0 2 1
KRAS WILD-TYPE 137 14 25 2
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
KRAS MUTATED 1 0 3 1 1
KRAS WILD-TYPE 45 44 62 13 19
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 1

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

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

P value = 0.645 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
KRAS MUTATED 0 0 0 4 0 3
KRAS WILD-TYPE 16 13 15 53 26 38
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 1

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

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

P value = 0.68 (Fisher's exact test), Q value = 1

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

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

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
SMC3 MUTATED 6 0 1 0
SMC3 WILD-TYPE 136 14 26 3
'SMC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
SMC3 MUTATED 3 1 1 0 2
SMC3 WILD-TYPE 43 43 64 14 18
'SMC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

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

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

P value = 0.447 (Fisher's exact test), Q value = 1

Table S88.  Gene #15: 'SMC3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
SMC3 MUTATED 0 0 1 2 3 1
SMC3 WILD-TYPE 16 13 14 55 23 40
'SMC3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 1

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

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

P value = 0.415 (Fisher's exact test), Q value = 1

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

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

P value = 0.128 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
KIT MUTATED 6 0 0 1
KIT WILD-TYPE 136 14 27 2
'KIT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 1

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 46 44 65 14 20
KIT MUTATED 1 5 1 0 1
KIT WILD-TYPE 45 39 64 14 19
'KIT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 1

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

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

P value = 0.00556 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
KIT MUTATED 0 3 2 2 0 0
KIT WILD-TYPE 16 10 13 55 26 41

Figure S36.  Get High-res Image Gene #16: 'KIT MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.358 (Fisher's exact test), Q value = 1

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

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

P value = 0.192 (Fisher's exact test), Q value = 1

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

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

P value = 0.493 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
RAD21 MUTATED 4 1 0 0
RAD21 WILD-TYPE 138 13 27 3
'RAD21 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.665 (Fisher's exact test), Q value = 1

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 46 44 65 14 20
RAD21 MUTATED 3 1 1 0 0
RAD21 WILD-TYPE 43 43 64 14 20
'RAD21 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 1

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

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

P value = 0.185 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
RAD21 MUTATED 0 0 1 0 2 2
RAD21 WILD-TYPE 16 13 14 57 24 39
'RAD21 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 1

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

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

P value = 0.607 (Fisher's exact test), Q value = 1

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

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

P value = 0.0296 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
EZH2 MUTATED 1 0 1 1
EZH2 WILD-TYPE 141 14 26 2

Figure S37.  Get High-res Image Gene #18: 'EZH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'EZH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 1

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

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

P value = 0.594 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
EZH2 MUTATED 0 0 0 3 0 0
EZH2 WILD-TYPE 16 13 15 54 26 41
'EZH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 1

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

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

P value = 0.416 (Fisher's exact test), Q value = 1

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

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

P value = 0.58 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
STAG2 MUTATED 5 1 0 0
STAG2 WILD-TYPE 137 13 27 3
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
STAG2 MUTATED 1 0 2 1 1
STAG2 WILD-TYPE 45 44 63 13 19
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 1

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

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

P value = 0.0261 (Fisher's exact test), Q value = 1

Table S111.  Gene #19: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
STAG2 MUTATED 0 0 0 1 4 0
STAG2 WILD-TYPE 16 13 15 56 22 41

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

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

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

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

P value = 0.0655 (Fisher's exact test), Q value = 1

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

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

P value = 0.697 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
PTPN11 MUTATED 6 0 2 0
PTPN11 WILD-TYPE 136 14 25 3
'PTPN11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
PTPN11 MUTATED 4 1 2 0 2
PTPN11 WILD-TYPE 42 43 63 14 18
'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 1

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

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

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

'PTPN11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 1

Table S117.  Gene #20: 'PTPN11 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
PTPN11 MUTATED 0 1 0 2 3 2
PTPN11 WILD-TYPE 16 12 15 55 23 39
'PTPN11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0987 (Fisher's exact test), Q value = 1

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

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

P value = 0.209 (Fisher's exact test), Q value = 1

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

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

P value = 0.747 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
ASXL1 MUTATED 4 0 1 0
ASXL1 WILD-TYPE 138 14 26 3
'ASXL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
ASXL1 MUTATED 0 0 4 0 0
ASXL1 WILD-TYPE 46 44 61 14 20
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 1

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

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

P value = 0.591 (Fisher's exact test), Q value = 1

Table S123.  Gene #21: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
ASXL1 MUTATED 0 0 0 3 0 0
ASXL1 WILD-TYPE 16 13 15 54 26 41
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 1

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

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

P value = 0.415 (Fisher's exact test), Q value = 1

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

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

P value = 0.298 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
SUZ12 MUTATED 2 1 0 0
SUZ12 WILD-TYPE 140 13 27 3
'SUZ12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
SUZ12 MUTATED 0 0 2 0 1
SUZ12 WILD-TYPE 46 44 63 14 19
'SUZ12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 1

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

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

P value = 0.589 (Fisher's exact test), Q value = 1

Table S129.  Gene #22: 'SUZ12 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
SUZ12 MUTATED 0 0 0 3 0 0
SUZ12 WILD-TYPE 16 13 15 54 26 41
'SUZ12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 1

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

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

P value = 0.143 (Fisher's exact test), Q value = 1

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

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

P value = 0.33 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
PHACTR1 MUTATED 0 0 2 0 1
PHACTR1 WILD-TYPE 46 44 63 14 19
'PHACTR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 1

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

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

P value = 0.415 (Fisher's exact test), Q value = 1

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

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

P value = 0.77 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
SMC1A MUTATED 6 0 0 0
SMC1A WILD-TYPE 136 14 27 3
'SMC1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.552 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
SMC1A MUTATED 2 1 1 1 1
SMC1A WILD-TYPE 44 43 64 13 19
'SMC1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 1

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

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

P value = 0.244 (Fisher's exact test), Q value = 1

Table S138.  Gene #24: 'SMC1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 16 13 15 57 26 41
SMC1A MUTATED 0 0 1 1 0 4
SMC1A WILD-TYPE 16 13 14 56 26 37
'SMC1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 1

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

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

P value = 0.661 (Fisher's exact test), Q value = 1

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

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

P value = 0.556 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 142 14 27 3
KDM6A MUTATED 2 0 1 0
KDM6A WILD-TYPE 140 14 26 3
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 46 44 65 14 20
KDM6A MUTATED 1 1 1 0 0
KDM6A WILD-TYPE 45 43 64 14 20
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 1

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

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

P value = 0.783 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 35 81
KDM6A MUTATED 1 1 1
KDM6A WILD-TYPE 66 34 80
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = LAML-TB.transferedmergedcluster.txt

  • Number of patients = 195

  • Number of significantly mutated genes = 25

  • Number of Molecular subtypes = 6

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

Fisher's exact test

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

Q value calculation

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

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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