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 8 molecular subtypes across 168 patients, 4 significant findings detected with P value < 0.05 and Q value < 0.25.

  • NEFH mutation correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ZNF598 mutation correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 7 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
NEFH 10 (6%) 158 0.423
(1.00) 		0.567
(1.00) 		0.0614
(1.00) 		0.426
(1.00) 		0.0235
(1.00) 		0.00043
(0.0232) 		0.0157
(0.802) 		0.003
(0.159)
ZNF598 13 (8%) 155 0.134
(1.00) 		0.379
(1.00) 		0.0978
(1.00) 		0.385
(1.00) 		0.675
(1.00) 		0.0004
(0.022) 		0.452
(1.00) 		0.000209
(0.0117)
SKI 6 (4%) 162 0.0954
(1.00) 		0.0833
(1.00) 		0.127
(1.00) 		0.674
(1.00) 		0.696
(1.00) 		0.38
(1.00) 		0.776
(1.00) 		0.858
(1.00)
HNRNPM 11 (7%) 157 0.309
(1.00) 		0.845
(1.00) 		0.828
(1.00) 		0.258
(1.00) 		0.544
(1.00) 		0.345
(1.00) 		0.682
(1.00) 		0.403
(1.00)
NF2 12 (7%) 156 0.0523
(1.00) 		0.0338
(1.00) 		0.0768
(1.00) 		0.932
(1.00) 		0.93
(1.00) 		0.609
(1.00) 		0.868
(1.00) 		1
(1.00)
BMS1 13 (8%) 155 0.906
(1.00) 		0.52
(1.00) 		0.324
(1.00) 		0.876
(1.00) 		0.59
(1.00) 		0.0991
(1.00) 		1
(1.00) 		0.323
(1.00)
MUC2 26 (15%) 142 0.164
(1.00) 		0.319
(1.00) 		0.00856
(0.445) 		0.0821
(1.00) 		0.712
(1.00) 		0.171
(1.00) 		0.34
(1.00) 		0.317
(1.00)
'SKI MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0954 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 59 34 37 16 22
SKI MUTATED 5 0 0 1 0
SKI WILD-TYPE 54 34 37 15 22
'SKI MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0833 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 23 30 38 29
SKI MUTATED 4 0 0 1 1
SKI WILD-TYPE 29 23 30 37 28
'SKI MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 64 47 25
SKI MUTATED 1 1 1 3
SKI WILD-TYPE 31 63 46 22
'SKI MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 63 48
SKI MUTATED 1 3 2
SKI WILD-TYPE 56 60 46
'SKI MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 58 55
SKI MUTATED 3 2 1
SKI WILD-TYPE 52 56 54
'SKI MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 70 73
SKI MUTATED 2 2 2
SKI WILD-TYPE 23 68 71
'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.776 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 61 55
SKI MUTATED 2 3 1
SKI WILD-TYPE 50 58 54
'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.858 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 82 20
SKI MUTATED 2 3 1
SKI WILD-TYPE 64 79 19
'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.423 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 59 34 37 16 22
NEFH MUTATED 2 1 3 1 3
NEFH WILD-TYPE 57 33 34 15 19
'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.567 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 23 30 38 29
NEFH MUTATED 2 0 3 3 1
NEFH WILD-TYPE 31 23 27 35 28
'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0614 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 64 47 25
NEFH MUTATED 5 2 3 0
NEFH WILD-TYPE 27 62 44 25
'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 63 48
NEFH MUTATED 4 5 1
NEFH WILD-TYPE 53 58 47
'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 58 55
NEFH MUTATED 6 0 4
NEFH WILD-TYPE 49 58 51

Figure S1.  Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 70 73
NEFH MUTATED 0 0 10
NEFH WILD-TYPE 25 70 63

Figure S2.  Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 61 55
NEFH MUTATED 4 0 6
NEFH WILD-TYPE 48 61 49

Figure S3.  Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.003 (Fisher's exact test), Q value = 0.16

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 82 20
NEFH MUTATED 0 10 0
NEFH WILD-TYPE 66 72 20

Figure S4.  Get High-res Image Gene #2: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HNRNPM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.309 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 59 34 37 16 22
HNRNPM MUTATED 6 0 2 2 1
HNRNPM WILD-TYPE 53 34 35 14 21
'HNRNPM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.845 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 23 30 38 29
HNRNPM MUTATED 2 2 2 4 1
HNRNPM WILD-TYPE 31 21 28 34 28
'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 64 47 25
HNRNPM MUTATED 1 4 4 2
HNRNPM WILD-TYPE 31 60 43 23
'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 63 48
HNRNPM MUTATED 6 2 3
HNRNPM WILD-TYPE 51 61 45
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 58 55
HNRNPM MUTATED 2 4 5
HNRNPM WILD-TYPE 53 54 50
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.345 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 70 73
HNRNPM MUTATED 1 7 3
HNRNPM WILD-TYPE 24 63 70
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 61 55
HNRNPM MUTATED 2 5 4
HNRNPM WILD-TYPE 50 56 51
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.403 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 82 20
HNRNPM MUTATED 6 5 0
HNRNPM WILD-TYPE 60 77 20
'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0523 (Chi-square test), Q value = 1

Table S25.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 59 34 37 16 22
NF2 MUTATED 2 1 6 0 3
NF2 WILD-TYPE 57 33 31 16 19
'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0338 (Chi-square test), Q value = 1

Table S26.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 23 30 38 29
NF2 MUTATED 0 4 2 5 0
NF2 WILD-TYPE 33 19 28 33 29

Figure S5.  Get High-res Image Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0768 (Fisher's exact test), Q value = 1

Table S27.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 64 47 25
NF2 MUTATED 0 7 5 0
NF2 WILD-TYPE 32 57 42 25
'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 1

Table S28.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 63 48
NF2 MUTATED 4 4 4
NF2 WILD-TYPE 53 59 44
'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 58 55
NF2 MUTATED 4 5 3
NF2 WILD-TYPE 51 53 52
'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 70 73
NF2 MUTATED 1 4 7
NF2 WILD-TYPE 24 66 66
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 61 55
NF2 MUTATED 4 5 3
NF2 WILD-TYPE 48 56 52
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S32.  Gene #4: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 82 20
NF2 MUTATED 5 6 1
NF2 WILD-TYPE 61 76 19
'ZNF598 MUTATION STATUS' versus 'CN_CNMF'

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

Table S33.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 59 34 37 16 22
ZNF598 MUTATED 5 0 5 0 3
ZNF598 WILD-TYPE 54 34 32 16 19
'ZNF598 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.379 (Chi-square test), Q value = 1

Table S34.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 23 30 38 29
ZNF598 MUTATED 3 4 1 2 2
ZNF598 WILD-TYPE 30 19 29 36 27
'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0978 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 64 47 25
ZNF598 MUTATED 1 5 2 5
ZNF598 WILD-TYPE 31 59 45 20
'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S36.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 63 48
ZNF598 MUTATED 3 4 6
ZNF598 WILD-TYPE 54 59 42
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 58 55
ZNF598 MUTATED 3 6 4
ZNF598 WILD-TYPE 52 52 51
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.022

Table S38.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 70 73
ZNF598 MUTATED 5 8 0
ZNF598 WILD-TYPE 20 62 73

Figure S6.  Get High-res Image Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 61 55
ZNF598 MUTATED 3 7 3
ZNF598 WILD-TYPE 49 54 52
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000209 (Fisher's exact test), Q value = 0.012

Table S40.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 82 20
ZNF598 MUTATED 10 0 3
ZNF598 WILD-TYPE 56 82 17

Figure S7.  Get High-res Image Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BMS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.906 (Chi-square test), Q value = 1

Table S41.  Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 59 34 37 16 22
BMS1 MUTATED 6 2 3 1 1
BMS1 WILD-TYPE 53 32 34 15 21
'BMS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.52 (Chi-square test), Q value = 1

Table S42.  Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 23 30 38 29
BMS1 MUTATED 3 1 1 2 4
BMS1 WILD-TYPE 30 22 29 36 25
'BMS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S43.  Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 64 47 25
BMS1 MUTATED 3 3 3 4
BMS1 WILD-TYPE 29 61 44 21
'BMS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S44.  Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 63 48
BMS1 MUTATED 5 4 4
BMS1 WILD-TYPE 52 59 44
'BMS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S45.  Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 58 55
BMS1 MUTATED 6 4 3
BMS1 WILD-TYPE 49 54 52
'BMS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0991 (Fisher's exact test), Q value = 1

Table S46.  Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 70 73
BMS1 MUTATED 3 2 8
BMS1 WILD-TYPE 22 68 65
'BMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S47.  Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 61 55
BMS1 MUTATED 4 5 4
BMS1 WILD-TYPE 48 56 51
'BMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 1

Table S48.  Gene #6: 'BMS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 82 20
BMS1 MUTATED 3 9 1
BMS1 WILD-TYPE 63 73 19
'MUC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.164 (Chi-square test), Q value = 1

Table S49.  Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 59 34 37 16 22
MUC2 MUTATED 8 2 10 3 3
MUC2 WILD-TYPE 51 32 27 13 19
'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.319 (Chi-square test), Q value = 1

Table S50.  Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 33 23 30 38 29
MUC2 MUTATED 7 5 5 6 1
MUC2 WILD-TYPE 26 18 25 32 28
'MUC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 0.45

Table S51.  Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 32 64 47 25
MUC2 MUTATED 11 10 4 1
MUC2 WILD-TYPE 21 54 43 24

Figure S8.  Get High-res Image Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0821 (Fisher's exact test), Q value = 1

Table S52.  Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 63 48
MUC2 MUTATED 6 15 5
MUC2 WILD-TYPE 51 48 43
'MUC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 55 58 55
MUC2 MUTATED 10 9 7
MUC2 WILD-TYPE 45 49 48
'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 1

Table S54.  Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 25 70 73
MUC2 MUTATED 6 7 13
MUC2 WILD-TYPE 19 63 60
'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 52 61 55
MUC2 MUTATED 11 9 6
MUC2 WILD-TYPE 41 52 49
'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'MUC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 66 82 20
MUC2 MUTATED 7 15 4
MUC2 WILD-TYPE 59 67 16
Methods & Data
Input

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

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

  • Number of patients = 168

  • Number of significantly mutated genes = 7

  • 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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