Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 7 genes and 6 molecular subtypes across 196 patients, 16 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • IDH2 mutation correlated to 'METHLYATION_CNMF'.

  • IDH1 mutation correlated to 'METHLYATION_CNMF'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 7 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, 16 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
NPM1 54 (28%) 142 4.59e-06
(0.000156) 		3.26e-20
(1.34e-18) 		3.08e-13
(1.2e-11) 		0.00649
(0.175) 		1.59e-13
(6.36e-12) 		3.26e-22
(1.37e-20)
FLT3 56 (29%) 140 0.000153
(0.00474) 		2.48e-05
(0.000819) 		2.2e-07
(8.36e-06) 		0.0209
(0.523) 		0.0005
(0.015) 		4.14e-05
(0.00132)
DNMT3A 51 (26%) 145 0.511
(1.00) 		4e-07
(1.48e-05) 		0.0118
(0.308) 		0.195
(1.00) 		0.000888
(0.0258) 		4.26e-06
(0.000149)
IDH2 20 (10%) 176 0.109
(1.00) 		1.59e-06
(5.74e-05) 		0.733
(1.00) 		1
(1.00) 		0.739
(1.00) 		0.61
(1.00)
IDH1 19 (10%) 177 0.321
(1.00) 		0.00563
(0.158) 		0.433
(1.00) 		0.268
(1.00) 		0.281
(1.00) 		0.436
(1.00)
U2AF1 8 (4%) 188 1
(1.00) 		0.128
(1.00) 		0.232
(1.00) 		0.426
(1.00) 		0.0716
(1.00) 		0.234
(1.00)
NRAS 15 (8%) 181 0.297
(1.00) 		0.892
(1.00) 		0.645
(1.00) 		0.539
(1.00) 		0.825
(1.00) 		0.756
(1.00)
'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 3
DNMT3A MUTATED 38 4 4 1
DNMT3A WILD-TYPE 105 10 23 2
'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-07 (Chi-square test), Q value = 1.5e-05

Table S2.  Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 44 65 14 20
DNMT3A MUTATED 25 1 19 1 3
DNMT3A WILD-TYPE 22 43 46 13 17

Figure S1.  Get High-res Image Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.31

Table S3.  Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 52 45
DNMT3A MUTATED 11 20 12
DNMT3A WILD-TYPE 62 32 33

Figure S2.  Get High-res Image Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 57 113
DNMT3A MUTATED 18 25
DNMT3A WILD-TYPE 39 88
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000888 (Fisher's exact test), Q value = 0.026

Table S5.  Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 38 42 46
DNMT3A MUTATED 24 4 5 13
DNMT3A WILD-TYPE 34 34 37 33

Figure S3.  Get High-res Image Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.26e-06 (Fisher's exact test), Q value = 0.00015

Table S6.  Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 80 68
DNMT3A MUTATED 2 34 10
DNMT3A WILD-TYPE 34 46 58

Figure S4.  Get High-res Image Gene #1: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'U2AF1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S7.  Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 3
U2AF1 MUTATED 5 0 1 0
U2AF1 WILD-TYPE 138 14 26 3
'U2AF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.128 (Chi-square test), Q value = 1

Table S8.  Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 44 65 14 20
U2AF1 MUTATED 1 0 6 0 1
U2AF1 WILD-TYPE 46 44 59 14 19
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S9.  Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 52 45
U2AF1 MUTATED 5 2 0
U2AF1 WILD-TYPE 68 50 45
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.426 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 57 113
U2AF1 MUTATED 1 6
U2AF1 WILD-TYPE 56 107
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0716 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 38 42 46
U2AF1 MUTATED 1 2 4 0
U2AF1 WILD-TYPE 57 36 38 46
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S12.  Gene #2: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 80 68
U2AF1 MUTATED 2 1 4
U2AF1 WILD-TYPE 34 79 64
'FLT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000153 (Fisher's exact test), Q value = 0.0047

Table S13.  Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 3
FLT3 MUTATED 51 3 0 0
FLT3 WILD-TYPE 92 11 27 3

Figure S5.  Get High-res Image Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FLT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.48e-05 (Chi-square test), Q value = 0.00082

Table S14.  Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 44 65 14 20
FLT3 MUTATED 26 12 8 2 7
FLT3 WILD-TYPE 21 32 57 12 13

Figure S6.  Get High-res Image Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2.2e-07 (Fisher's exact test), Q value = 8.4e-06

Table S15.  Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 52 45
FLT3 MUTATED 6 20 23
FLT3 WILD-TYPE 67 32 22

Figure S7.  Get High-res Image Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'FLT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0209 (Fisher's exact test), Q value = 0.52

Table S16.  Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 57 113
FLT3 MUTATED 23 26
FLT3 WILD-TYPE 34 87

Figure S8.  Get High-res Image Gene #3: '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 = 0.015

Table S17.  Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 38 42 46
FLT3 MUTATED 25 4 7 18
FLT3 WILD-TYPE 33 34 35 28

Figure S9.  Get High-res Image Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'FLT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4.14e-05 (Fisher's exact test), Q value = 0.0013

Table S18.  Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 80 68
FLT3 MUTATED 4 37 13
FLT3 WILD-TYPE 32 43 55

Figure S10.  Get High-res Image Gene #3: 'FLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'IDH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.109 (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 143 14 27 3
IDH2 MUTATED 14 4 1 0
IDH2 WILD-TYPE 129 10 26 3
'IDH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.59e-06 (Chi-square test), Q value = 5.7e-05

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 47 44 65 14 20
IDH2 MUTATED 0 0 11 6 1
IDH2 WILD-TYPE 47 44 54 8 19

Figure S11.  Get High-res Image Gene #4: 'IDH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.733 (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 52 45
IDH2 MUTATED 8 6 3
IDH2 WILD-TYPE 65 46 42
'IDH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (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
ALL 57 113
IDH2 MUTATED 6 11
IDH2 WILD-TYPE 51 102
'IDH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.739 (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 58 38 42 46
IDH2 MUTATED 5 2 5 5
IDH2 WILD-TYPE 53 36 37 41
'IDH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.61 (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 36 80 68
IDH2 MUTATED 2 7 8
IDH2 WILD-TYPE 34 73 60
'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 3
IDH1 MUTATED 15 1 1 1
IDH1 WILD-TYPE 128 13 26 2
'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00563 (Chi-square test), Q value = 0.16

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 47 44 65 14 20
IDH1 MUTATED 5 0 10 4 0
IDH1 WILD-TYPE 42 44 55 10 20

Figure S12.  Get High-res Image Gene #5: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.433 (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 52 45
IDH1 MUTATED 7 3 6
IDH1 WILD-TYPE 66 49 39
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.268 (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
ALL 57 113
IDH1 MUTATED 3 13
IDH1 WILD-TYPE 54 100
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.281 (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 58 38 42 46
IDH1 MUTATED 5 4 2 8
IDH1 WILD-TYPE 53 34 40 38
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.436 (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 36 80 68
IDH1 MUTATED 3 11 5
IDH1 WILD-TYPE 33 69 63
'NPM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 4.59e-06 (Fisher's exact test), Q value = 0.00016

Table S31.  Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 3
NPM1 MUTATED 52 0 0 0
NPM1 WILD-TYPE 91 14 27 3

Figure S13.  Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NPM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.26e-20 (Chi-square test), Q value = 1.3e-18

Table S32.  Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 44 65 14 20
NPM1 MUTATED 36 0 4 9 4
NPM1 WILD-TYPE 11 44 61 5 16

Figure S14.  Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.08e-13 (Fisher's exact test), Q value = 1.2e-11

Table S33.  Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 52 45
NPM1 MUTATED 1 22 25
NPM1 WILD-TYPE 72 30 20

Figure S15.  Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'NPM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00649 (Fisher's exact test), Q value = 0.18

Table S34.  Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 57 113
NPM1 MUTATED 24 24
NPM1 WILD-TYPE 33 89

Figure S16.  Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.59e-13 (Fisher's exact test), Q value = 6.4e-12

Table S35.  Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 38 42 46
NPM1 MUTATED 37 2 1 12
NPM1 WILD-TYPE 21 36 41 34

Figure S17.  Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NPM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3.26e-22 (Fisher's exact test), Q value = 1.4e-20

Table S36.  Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 80 68
NPM1 MUTATED 0 51 1
NPM1 WILD-TYPE 36 29 67

Figure S18.  Get High-res Image Gene #6: 'NPM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 143 14 27 3
NRAS MUTATED 10 1 3 1
NRAS WILD-TYPE 133 13 24 2
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.892 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 47 44 65 14 20
NRAS MUTATED 4 3 5 2 1
NRAS WILD-TYPE 43 41 60 12 19
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 52 45
NRAS MUTATED 5 5 2
NRAS WILD-TYPE 68 47 43
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.539 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2
ALL 57 113
NRAS MUTATED 5 7
NRAS WILD-TYPE 52 106
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 38 42 46
NRAS MUTATED 5 3 4 2
NRAS WILD-TYPE 53 35 38 44
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.756 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 80 68
NRAS MUTATED 3 7 4
NRAS WILD-TYPE 33 73 64
Methods & Data
Input

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

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

  • Number of patients = 196

  • Number of significantly mutated genes = 7

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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