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 90 patients, 4 significant findings detected with P value < 0.05 and Q value < 0.25.

  • CTNNB1 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • KRTAP4-5 mutation correlated to 'METHLYATION_CNMF'.

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, 4 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 Chi-square test Chi-square 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
CTNNB1 13 (14%) 77 0.51
(1.00) 		0.0755
(1.00) 		0.000319
(0.0226) 		0.000102
(0.00737) 		0.000609
(0.0426) 		0.541
(1.00) 		0.00882
(0.582) 		0.456
(1.00)
KRTAP4-5 4 (4%) 86 0.538
(1.00) 		0.000785
(0.0541) 		1
(1.00) 		1
(1.00) 		0.781
(1.00) 		0.213
(1.00) 		0.797
(1.00) 		0.234
(1.00)
MUC5B 16 (18%) 74 0.134
(1.00) 		0.207
(1.00) 		0.218
(1.00) 		0.364
(1.00) 		0.167
(1.00) 		0.409
(1.00) 		0.393
(1.00) 		0.465
(1.00)
CRIPAK 11 (12%) 79 0.0539
(1.00) 		0.533
(1.00) 		0.257
(1.00) 		0.162
(1.00) 		0.588
(1.00) 		0.688
(1.00) 		0.655
(1.00) 		0.623
(1.00)
TP53 15 (17%) 75 0.00857
(0.574) 		0.444
(1.00) 		0.0122
(0.767) 		0.0784
(1.00) 		0.00968
(0.629) 		0.087
(1.00) 		0.0321
(1.00) 		0.0377
(1.00)
MEN1 7 (8%) 83 0.427
(1.00) 		0.0201
(1.00) 		0.352
(1.00) 		0.0698
(1.00) 		0.666
(1.00) 		0.514
(1.00) 		0.771
(1.00) 		0.536
(1.00)
PRKAR1A 6 (7%) 84 0.958
(1.00) 		0.702
(1.00) 		0.188
(1.00) 		0.878
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.3
(1.00) 		0.854
(1.00)
ATN1 4 (4%) 86 0.0602
(1.00) 		0.657
(1.00) 		0.877
(1.00) 		1
(1.00) 		0.781
(1.00) 		0.691
(1.00) 		0.797
(1.00) 		0.709
(1.00)
DMKN 3 (3%) 87 0.693
(1.00) 		0.344
(1.00) 		0.617
(1.00) 		0.262
(1.00) 		0.00736
(0.501) 		1
(1.00) 		0.0107
(0.686) 		1
(1.00)
'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.51 (Chi-square test), Q value = 1

Table S1.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 23 15 10 9
CTNNB1 MUTATED 6 2 3 2 0
CTNNB1 WILD-TYPE 25 21 12 8 9
'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0755 (Chi-square test), Q value = 1

Table S2.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 17 11 21 18 11
CTNNB1 MUTATED 4 4 2 0 2
CTNNB1 WILD-TYPE 13 7 19 18 9
'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000319 (Fisher's exact test), Q value = 0.023

Table S3.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 14 17 23
CTNNB1 MUTATED 7 5 0 0
CTNNB1 WILD-TYPE 16 9 17 23

Figure S1.  Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000102 (Fisher's exact test), Q value = 0.0074

Table S4.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 32 23
CTNNB1 MUTATED 9 0 3
CTNNB1 WILD-TYPE 13 32 20

Figure S2.  Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000609 (Fisher's exact test), Q value = 0.043

Table S5.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 16 25
CTNNB1 MUTATED 5 7 0
CTNNB1 WILD-TYPE 32 9 25

Figure S3.  Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S6.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 9 43
CTNNB1 MUTATED 4 0 8
CTNNB1 WILD-TYPE 22 9 35
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.58

Table S7.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 18 22
CTNNB1 MUTATED 6 6 0
CTNNB1 WILD-TYPE 32 12 22

Figure S4.  Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 10 27
CTNNB1 MUTATED 8 0 4
CTNNB1 WILD-TYPE 33 10 23
'MUC5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.134 (Chi-square test), Q value = 1

Table S9.  Gene #2: 'MUC5B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 23 15 10 9
MUC5B MUTATED 4 4 1 3 4
MUC5B WILD-TYPE 27 19 14 7 5
'MUC5B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.207 (Chi-square test), Q value = 1

Table S10.  Gene #2: 'MUC5B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 17 11 21 18 11
MUC5B MUTATED 2 2 3 3 5
MUC5B WILD-TYPE 15 9 18 15 6
'MUC5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S11.  Gene #2: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 14 17 23
MUC5B MUTATED 3 1 6 5
MUC5B WILD-TYPE 20 13 11 18
'MUC5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.364 (Fisher's exact test), Q value = 1

Table S12.  Gene #2: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 32 23
MUC5B MUTATED 2 8 5
MUC5B WILD-TYPE 20 24 18
'MUC5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'MUC5B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 16 25
MUC5B MUTATED 5 2 8
MUC5B WILD-TYPE 32 14 17
'MUC5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 9 43
MUC5B MUTATED 7 2 6
MUC5B WILD-TYPE 19 7 37
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.393 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 18 22
MUC5B MUTATED 5 4 6
MUC5B WILD-TYPE 33 14 16
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S16.  Gene #2: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 10 27
MUC5B MUTATED 6 2 7
MUC5B WILD-TYPE 35 8 20
'CRIPAK MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0539 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 23 15 10 9
CRIPAK MUTATED 3 3 0 4 1
CRIPAK WILD-TYPE 28 20 15 6 8
'CRIPAK MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.533 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 17 11 21 18 11
CRIPAK MUTATED 3 2 1 1 2
CRIPAK WILD-TYPE 14 9 20 17 9
'CRIPAK MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 14 17 23
CRIPAK MUTATED 5 0 2 2
CRIPAK WILD-TYPE 18 14 15 21
'CRIPAK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 32 23
CRIPAK MUTATED 5 3 1
CRIPAK WILD-TYPE 17 29 22
'CRIPAK MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.588 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 16 25
CRIPAK MUTATED 6 1 2
CRIPAK WILD-TYPE 31 15 23
'CRIPAK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.688 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 9 43
CRIPAK MUTATED 3 0 6
CRIPAK WILD-TYPE 23 9 37
'CRIPAK MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 18 22
CRIPAK MUTATED 6 1 2
CRIPAK WILD-TYPE 32 17 20
'CRIPAK MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.623 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 10 27
CRIPAK MUTATED 6 0 3
CRIPAK WILD-TYPE 35 10 24
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00857 (Chi-square test), Q value = 0.57

Table S25.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 23 15 10 9
TP53 MUTATED 5 0 4 5 1
TP53 WILD-TYPE 26 23 11 5 8

Figure S5.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.444 (Chi-square test), Q value = 1

Table S26.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 17 11 21 18 11
TP53 MUTATED 3 3 5 1 1
TP53 WILD-TYPE 14 8 16 17 10
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.77

Table S27.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 14 17 23
TP53 MUTATED 4 3 6 0
TP53 WILD-TYPE 19 11 11 23

Figure S6.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0784 (Fisher's exact test), Q value = 1

Table S28.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 32 23
TP53 MUTATED 5 2 6
TP53 WILD-TYPE 17 30 17
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00968 (Fisher's exact test), Q value = 0.63

Table S29.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 16 25
TP53 MUTATED 9 4 0
TP53 WILD-TYPE 28 12 25

Figure S7.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.087 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 9 43
TP53 MUTATED 2 0 11
TP53 WILD-TYPE 24 9 32
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 18 22
TP53 MUTATED 9 4 0
TP53 WILD-TYPE 29 14 22

Figure S8.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 10 27
TP53 MUTATED 11 0 2
TP53 WILD-TYPE 30 10 25

Figure S9.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MEN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.427 (Chi-square test), Q value = 1

Table S33.  Gene #5: 'MEN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 23 15 10 9
MEN1 MUTATED 1 1 1 2 1
MEN1 WILD-TYPE 30 22 14 8 8
'MEN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0201 (Chi-square test), Q value = 1

Table S34.  Gene #5: 'MEN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 17 11 21 18 11
MEN1 MUTATED 0 3 4 0 0
MEN1 WILD-TYPE 17 8 17 18 11

Figure S10.  Get High-res Image Gene #5: 'MEN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MEN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: 'MEN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 14 17 23
MEN1 MUTATED 1 2 3 1
MEN1 WILD-TYPE 22 12 14 22
'MEN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0698 (Fisher's exact test), Q value = 1

Table S36.  Gene #5: 'MEN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 32 23
MEN1 MUTATED 1 1 5
MEN1 WILD-TYPE 21 31 18
'MEN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.666 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'MEN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 16 25
MEN1 MUTATED 4 2 1
MEN1 WILD-TYPE 33 14 24
'MEN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.514 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'MEN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 9 43
MEN1 MUTATED 1 1 5
MEN1 WILD-TYPE 25 8 38
'MEN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'MEN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 18 22
MEN1 MUTATED 4 2 1
MEN1 WILD-TYPE 34 16 21
'MEN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.536 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'MEN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 10 27
MEN1 MUTATED 5 1 1
MEN1 WILD-TYPE 36 9 26
'PRKAR1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.958 (Chi-square test), Q value = 1

Table S41.  Gene #6: 'PRKAR1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 23 15 10 9
PRKAR1A MUTATED 2 1 1 1 1
PRKAR1A WILD-TYPE 29 22 14 9 8
'PRKAR1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.702 (Chi-square test), Q value = 1

Table S42.  Gene #6: 'PRKAR1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 17 11 21 18 11
PRKAR1A MUTATED 1 1 1 1 2
PRKAR1A WILD-TYPE 16 10 20 17 9
'PRKAR1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.188 (Fisher's exact test), Q value = 1

Table S43.  Gene #6: 'PRKAR1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 14 17 23
PRKAR1A MUTATED 2 1 3 0
PRKAR1A WILD-TYPE 21 13 14 23
'PRKAR1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S44.  Gene #6: 'PRKAR1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 32 23
PRKAR1A MUTATED 1 3 2
PRKAR1A WILD-TYPE 21 29 21
'PRKAR1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.855 (Fisher's exact test), Q value = 1

Table S45.  Gene #6: 'PRKAR1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 16 25
PRKAR1A MUTATED 4 1 1
PRKAR1A WILD-TYPE 33 15 24
'PRKAR1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S46.  Gene #6: 'PRKAR1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 9 43
PRKAR1A MUTATED 2 0 4
PRKAR1A WILD-TYPE 24 9 39
'PRKAR1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S47.  Gene #6: 'PRKAR1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 18 22
PRKAR1A MUTATED 4 2 0
PRKAR1A WILD-TYPE 34 16 22
'PRKAR1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S48.  Gene #6: 'PRKAR1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 10 27
PRKAR1A MUTATED 4 0 2
PRKAR1A WILD-TYPE 37 10 25
'KRTAP4-5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.538 (Chi-square test), Q value = 1

Table S49.  Gene #7: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 23 15 10 9
KRTAP4-5 MUTATED 1 2 0 0 1
KRTAP4-5 WILD-TYPE 30 21 15 10 8
'KRTAP4-5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000785 (Chi-square test), Q value = 0.054

Table S50.  Gene #7: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 17 11 21 18 11
KRTAP4-5 MUTATED 0 3 0 0 0
KRTAP4-5 WILD-TYPE 17 8 21 18 11

Figure S11.  Get High-res Image Gene #7: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRTAP4-5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S51.  Gene #7: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 14 17 23
KRTAP4-5 MUTATED 1 0 1 1
KRTAP4-5 WILD-TYPE 22 14 16 22
'KRTAP4-5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S52.  Gene #7: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 32 23
KRTAP4-5 MUTATED 1 1 1
KRTAP4-5 WILD-TYPE 21 31 22
'KRTAP4-5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 16 25
KRTAP4-5 MUTATED 1 1 1
KRTAP4-5 WILD-TYPE 36 15 24
'KRTAP4-5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 1

Table S54.  Gene #7: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 9 43
KRTAP4-5 MUTATED 0 1 2
KRTAP4-5 WILD-TYPE 26 8 41
'KRTAP4-5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 18 22
KRTAP4-5 MUTATED 1 1 1
KRTAP4-5 WILD-TYPE 37 17 21
'KRTAP4-5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S56.  Gene #7: 'KRTAP4-5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 10 27
KRTAP4-5 MUTATED 2 1 0
KRTAP4-5 WILD-TYPE 39 9 27
'ATN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0602 (Chi-square test), Q value = 1

Table S57.  Gene #8: 'ATN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 23 15 10 9
ATN1 MUTATED 0 2 0 2 0
ATN1 WILD-TYPE 31 21 15 8 9
'ATN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.657 (Chi-square test), Q value = 1

Table S58.  Gene #8: 'ATN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 17 11 21 18 11
ATN1 MUTATED 1 1 0 1 0
ATN1 WILD-TYPE 16 10 21 17 11
'ATN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S59.  Gene #8: 'ATN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 14 17 23
ATN1 MUTATED 1 1 0 1
ATN1 WILD-TYPE 22 13 17 22
'ATN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S60.  Gene #8: 'ATN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 32 23
ATN1 MUTATED 1 1 1
ATN1 WILD-TYPE 21 31 22
'ATN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S61.  Gene #8: 'ATN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 16 25
ATN1 MUTATED 1 1 1
ATN1 WILD-TYPE 36 15 24
'ATN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.691 (Fisher's exact test), Q value = 1

Table S62.  Gene #8: 'ATN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 9 43
ATN1 MUTATED 2 0 1
ATN1 WILD-TYPE 24 9 42
'ATN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S63.  Gene #8: 'ATN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 18 22
ATN1 MUTATED 1 1 1
ATN1 WILD-TYPE 37 17 21
'ATN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.709 (Fisher's exact test), Q value = 1

Table S64.  Gene #8: 'ATN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 10 27
ATN1 MUTATED 1 0 2
ATN1 WILD-TYPE 40 10 25
'DMKN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.693 (Chi-square test), Q value = 1

Table S65.  Gene #9: 'DMKN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 31 23 15 10 9
DMKN MUTATED 1 1 0 1 0
DMKN WILD-TYPE 30 22 15 9 9
'DMKN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.344 (Chi-square test), Q value = 1

Table S66.  Gene #9: 'DMKN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 17 11 21 18 11
DMKN MUTATED 0 1 2 0 0
DMKN WILD-TYPE 17 10 19 18 11
'DMKN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S67.  Gene #9: 'DMKN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 14 17 23
DMKN MUTATED 1 1 1 0
DMKN WILD-TYPE 22 13 16 23
'DMKN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S68.  Gene #9: 'DMKN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 32 23
DMKN MUTATED 1 0 2
DMKN WILD-TYPE 21 32 21
'DMKN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00736 (Fisher's exact test), Q value = 0.5

Table S69.  Gene #9: 'DMKN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 37 16 25
DMKN MUTATED 0 3 0
DMKN WILD-TYPE 37 13 25

Figure S12.  Get High-res Image Gene #9: 'DMKN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'DMKN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S70.  Gene #9: 'DMKN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 9 43
DMKN MUTATED 1 0 2
DMKN WILD-TYPE 25 9 41
'DMKN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.69

Table S71.  Gene #9: 'DMKN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 38 18 22
DMKN MUTATED 0 3 0
DMKN WILD-TYPE 38 15 22

Figure S13.  Get High-res Image Gene #9: 'DMKN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'DMKN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S72.  Gene #9: 'DMKN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 10 27
DMKN MUTATED 2 0 1
DMKN WILD-TYPE 39 10 26
Methods & Data
Input

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

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

  • Number of patients = 90

  • Number of significantly mutated genes = 9

  • Number of Molecular subtypes = 8

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

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[2] 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)
[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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