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 9 genes and 8 molecular subtypes across 178 patients, 18 significant findings detected with P value < 0.05 and Q value < 0.25.

  • HRAS mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • EPAS1 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • NF1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 9 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 18 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
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 Fisher's exact test Fisher's exact test
HRAS 18 (10%) 160 1e-05
(0.00071) 		5e-05
(0.00325) 		1e-05
(0.00071) 		1e-05
(0.00071) 		0.00011
(0.00693) 		0.00029
(0.0174) 		2e-05
(0.00134) 		1e-05
(0.00071)
EPAS1 8 (4%) 170 0.0587
(1.00) 		0.00661
(0.33) 		0.00147
(0.0838) 		0.00167
(0.0935) 		0.002
(0.11) 		0.0169
(0.81) 		0.00025
(0.0152) 		0.00429
(0.232)
NF1 15 (8%) 163 0.348
(1.00) 		0.00051
(0.0296) 		0.00967
(0.474) 		0.0001
(0.0064) 		0.00018
(0.0112) 		0.0057
(0.293) 		2e-05
(0.00134) 		0.00042
(0.0248)
RET 6 (3%) 172 0.149
(1.00) 		0.482
(1.00) 		0.0904
(1.00) 		0.104
(1.00) 		0.433
(1.00) 		0.0684
(1.00) 		0.438
(1.00) 		0.0429
(1.00)
CSDE1 4 (2%) 174 0.107
(1.00) 		0.582
(1.00) 		0.489
(1.00) 		0.00511
(0.271) 		0.35
(1.00) 		0.00564
(0.293) 		0.363
(1.00) 		0.0458
(1.00)
GPR128 4 (2%) 174 0.145
(1.00) 		0.0986
(1.00) 		0.888
(1.00) 		0.887
(1.00) 		0.542
(1.00) 		0.774
(1.00) 		0.567
(1.00) 		0.551
(1.00)
AMMECR1 3 (2%) 175 0.738
(1.00) 		1
(1.00) 		0.242
(1.00) 		0.626
(1.00) 		0.795
(1.00) 		1
(1.00) 		0.261
(1.00) 		0.799
(1.00)
SHROOM4 3 (2%) 175 1
(1.00) 		0.467
(1.00) 		0.541
(1.00) 		1
(1.00) 		0.679
(1.00) 		1
(1.00) 		1
(1.00)
FAM83D 3 (2%) 175 0.261
(1.00) 		0.337
(1.00) 		0.405
(1.00) 		0.465
(1.00) 		0.0577
(1.00) 		0.819
(1.00) 		0.182
(1.00) 		0.0475
(1.00)
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
HRAS MUTATED 0 0 15 0 0
HRAS WILD-TYPE 15 24 40 42 23

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

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0032

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
HRAS MUTATED 0 17 1
HRAS WILD-TYPE 44 68 48

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

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
HRAS MUTATED 0 18 0 0
HRAS WILD-TYPE 39 51 49 21

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

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
HRAS MUTATED 0 18 0 0
HRAS WILD-TYPE 38 53 48 21

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

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0069

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
HRAS MUTATED 1 15 2
HRAS WILD-TYPE 73 50 37

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

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
HRAS MUTATED 1 14 1 2
HRAS WILD-TYPE 75 45 17 23

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

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0013

Table S7.  Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
HRAS MUTATED 0 17 1
HRAS WILD-TYPE 44 58 58

Figure S7.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

Table S8.  Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
HRAS MUTATED 0 16 2
HRAS WILD-TYPE 78 45 37

Figure S8.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0587 (Fisher's exact test), Q value = 1

Table S9.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
EPAS1 MUTATED 1 1 0 5 1
EPAS1 WILD-TYPE 14 23 55 37 22
'EPAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00661 (Fisher's exact test), Q value = 0.33

Table S10.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
EPAS1 MUTATED 4 0 4
EPAS1 WILD-TYPE 40 85 45

Figure S9.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.084

Table S11.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
EPAS1 MUTATED 1 0 7 0
EPAS1 WILD-TYPE 38 69 42 21

Figure S10.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.094

Table S12.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
EPAS1 MUTATED 1 0 7 0
EPAS1 WILD-TYPE 37 71 41 21

Figure S11.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.11

Table S13.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
EPAS1 MUTATED 8 0 0
EPAS1 WILD-TYPE 66 65 39

Figure S12.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.81

Table S14.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
EPAS1 MUTATED 8 0 0 0
EPAS1 WILD-TYPE 68 59 18 25

Figure S13.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.015

Table S15.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
EPAS1 MUTATED 7 0 1
EPAS1 WILD-TYPE 37 75 58

Figure S14.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00429 (Fisher's exact test), Q value = 0.23

Table S16.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
EPAS1 MUTATED 8 0 0
EPAS1 WILD-TYPE 70 61 39

Figure S15.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
NF1 MUTATED 1 0 7 5 1
NF1 WILD-TYPE 14 24 48 37 22
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.03

Table S18.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
NF1 MUTATED 0 14 1
NF1 WILD-TYPE 44 71 48

Figure S16.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00967 (Fisher's exact test), Q value = 0.47

Table S19.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
NF1 MUTATED 3 11 0 1
NF1 WILD-TYPE 36 58 49 20

Figure S17.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0064

Table S20.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
NF1 MUTATED 0 14 0 1
NF1 WILD-TYPE 38 57 48 20

Figure S18.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.011

Table S21.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
NF1 MUTATED 1 13 1
NF1 WILD-TYPE 73 52 38

Figure S19.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0057 (Fisher's exact test), Q value = 0.29

Table S22.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
NF1 MUTATED 2 11 0 2
NF1 WILD-TYPE 74 48 18 23

Figure S20.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0013

Table S23.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
NF1 MUTATED 0 15 0
NF1 WILD-TYPE 44 60 59

Figure S21.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.025

Table S24.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
NF1 MUTATED 1 12 2
NF1 WILD-TYPE 77 49 37

Figure S22.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RET MUTATION STATUS' versus 'CN_CNMF'

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

Table S25.  Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
RET MUTATED 0 0 5 0 1
RET WILD-TYPE 15 24 50 42 22
'RET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 1

Table S26.  Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
RET MUTATED 0 4 2
RET WILD-TYPE 44 81 47
'RET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0904 (Fisher's exact test), Q value = 1

Table S27.  Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
RET MUTATED 0 5 0 1
RET WILD-TYPE 39 64 49 20
'RET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
RET MUTATED 0 5 0 1
RET WILD-TYPE 38 66 48 20
'RET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
RET MUTATED 1 3 2
RET WILD-TYPE 73 62 37
'RET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0684 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
RET MUTATED 0 4 1 1
RET WILD-TYPE 76 55 17 24
'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
RET MUTATED 0 3 3
RET WILD-TYPE 44 72 56
'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
RET MUTATED 0 4 2
RET WILD-TYPE 78 57 37

Figure S23.  Get High-res Image Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 1

Table S33.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
CSDE1 MUTATED 0 0 0 2 2
CSDE1 WILD-TYPE 15 24 55 40 21
'CSDE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 1

Table S34.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
CSDE1 MUTATED 1 3 0
CSDE1 WILD-TYPE 43 82 49
'CSDE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
CSDE1 MUTATED 1 3 0 0
CSDE1 WILD-TYPE 38 66 49 21
'CSDE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00511 (Fisher's exact test), Q value = 0.27

Table S36.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
CSDE1 MUTATED 4 0 0 0
CSDE1 WILD-TYPE 34 71 48 21

Figure S24.  Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
CSDE1 MUTATED 1 3 0
CSDE1 WILD-TYPE 73 62 39
'CSDE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00564 (Fisher's exact test), Q value = 0.29

Table S38.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
CSDE1 MUTATED 1 0 3 0
CSDE1 WILD-TYPE 75 59 15 25

Figure S25.  Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
CSDE1 MUTATED 1 3 0
CSDE1 WILD-TYPE 43 72 59
'CSDE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0458 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
CSDE1 MUTATED 1 0 3
CSDE1 WILD-TYPE 77 61 36

Figure S26.  Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GPR128 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 1

Table S41.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
GPR128 MUTATED 1 0 0 2 0
GPR128 WILD-TYPE 14 24 55 40 23
'GPR128 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0986 (Fisher's exact test), Q value = 1

Table S42.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
GPR128 MUTATED 3 1 0
GPR128 WILD-TYPE 41 84 49
'GPR128 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S43.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
GPR128 MUTATED 1 1 2 0
GPR128 WILD-TYPE 38 68 47 21
'GPR128 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S44.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
GPR128 MUTATED 1 1 2 0
GPR128 WILD-TYPE 37 70 46 21
'GPR128 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 1

Table S45.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
GPR128 MUTATED 3 1 0
GPR128 WILD-TYPE 71 64 39
'GPR128 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S46.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
GPR128 MUTATED 3 1 0 0
GPR128 WILD-TYPE 73 58 18 25
'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S47.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
GPR128 MUTATED 2 1 1
GPR128 WILD-TYPE 42 74 58
'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.551 (Fisher's exact test), Q value = 1

Table S48.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
GPR128 MUTATED 3 1 0
GPR128 WILD-TYPE 75 60 39
'AMMECR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S49.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
AMMECR1 MUTATED 0 0 1 2 0
AMMECR1 WILD-TYPE 15 24 54 40 23
'AMMECR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S50.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
AMMECR1 MUTATED 1 1 1
AMMECR1 WILD-TYPE 43 84 48
'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 1

Table S51.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
AMMECR1 MUTATED 1 0 2 0
AMMECR1 WILD-TYPE 38 69 47 21
'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S52.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
AMMECR1 MUTATED 0 1 2 0
AMMECR1 WILD-TYPE 38 70 46 21
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
AMMECR1 MUTATED 2 1 0
AMMECR1 WILD-TYPE 72 64 39
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S54.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
AMMECR1 MUTATED 2 1 0 0
AMMECR1 WILD-TYPE 74 58 18 25
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
AMMECR1 MUTATED 2 1 0
AMMECR1 WILD-TYPE 42 74 59
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
AMMECR1 MUTATED 2 1 0
AMMECR1 WILD-TYPE 76 60 39
'SHROOM4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S57.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
SHROOM4 MUTATED 1 1 1
SHROOM4 WILD-TYPE 43 84 48
'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S58.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
SHROOM4 MUTATED 1 1 0 1
SHROOM4 WILD-TYPE 38 68 49 20
'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S59.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
SHROOM4 MUTATED 0 1 1 1
SHROOM4 WILD-TYPE 38 70 47 20
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S60.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
SHROOM4 MUTATED 1 1 1
SHROOM4 WILD-TYPE 73 64 38
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

Table S61.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
SHROOM4 MUTATED 1 1 0 1
SHROOM4 WILD-TYPE 75 58 18 24
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S62.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
SHROOM4 MUTATED 1 1 1
SHROOM4 WILD-TYPE 43 74 58
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S63.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
SHROOM4 MUTATED 1 1 1
SHROOM4 WILD-TYPE 77 60 38
'FAM83D MUTATION STATUS' versus 'CN_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 1

Table S64.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
FAM83D MUTATED 1 0 1 0 1
FAM83D WILD-TYPE 14 24 54 42 22
'FAM83D MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 1

Table S65.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
FAM83D MUTATED 0 3 0
FAM83D WILD-TYPE 44 82 49
'FAM83D MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 1

Table S66.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
FAM83D MUTATED 0 3 0 0
FAM83D WILD-TYPE 39 66 49 21
'FAM83D MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 1

Table S67.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
FAM83D MUTATED 0 3 0 0
FAM83D WILD-TYPE 38 68 48 21
'FAM83D MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0577 (Fisher's exact test), Q value = 1

Table S68.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
FAM83D MUTATED 0 3 0
FAM83D WILD-TYPE 74 62 39
'FAM83D MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.819 (Fisher's exact test), Q value = 1

Table S69.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
FAM83D MUTATED 1 2 0 0
FAM83D WILD-TYPE 75 57 18 25
'FAM83D MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S70.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
FAM83D MUTATED 0 3 0
FAM83D WILD-TYPE 44 72 59
'FAM83D MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 1

Table S71.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
FAM83D MUTATED 0 3 0
FAM83D WILD-TYPE 78 58 39

Figure S27.  Get High-res Image Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

  • Molecular subtypes file = PCPG-TP.transferedmergedcluster.txt

  • Number of patients = 178

  • Number of significantly mutated genes = 9

  • Number of Molecular subtypes = 8

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

Fisher's exact test

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

Q value calculation

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

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