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 25 genes and 8 molecular subtypes across 220 patients, 26 significant findings detected with P value < 0.05 and Q value < 0.25.

  • PGM5 mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • CBWD1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • PIK3CA mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • ARID1A mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • RHOA mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • IRF2 mutation correlated to 'MIRSEQ_CNMF'.

  • APC mutation correlated to 'MIRSEQ_CNMF'.

  • BCOR mutation correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 25 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, 26 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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
CBWD1 28 (13%) 192 0.000149
(0.027) 		1.79e-06
(0.000348) 		0.000857
(0.15) 		7.48e-05
(0.0139) 		2.36e-05
(0.0045) 		0.000274
(0.049) 		0.078
(1.00) 		0.0267
(1.00)
TP53 99 (45%) 121 4.33e-09
(8.49e-07) 		3.18e-05
(0.00605) 		7.74e-05
(0.0143) 		0.00381
(0.641) 		6.4e-06
(0.00124) 		9.12e-06
(0.00175) 		0.0704
(1.00) 		9.4e-05
(0.0173)
PIK3CA 48 (22%) 172 0.000108
(0.0198) 		1.83e-09
(3.6e-07) 		0.00058
(0.103) 		1.37e-07
(2.68e-05) 		0.0245
(1.00) 		0.0119
(1.00) 		0.000367
(0.0654) 		0.00471
(0.777)
ARID1A 41 (19%) 179 0.000215
(0.0387) 		0.00656
(1.00) 		3.52e-05
(0.00665) 		0.000131
(0.0238) 		0.0198
(1.00) 		0.0128
(1.00) 		0.761
(1.00) 		0.312
(1.00)
PGM5 22 (10%) 198 0.00138
(0.237) 		4.28e-05
(0.00804) 		0.00635
(1.00) 		0.00164
(0.279) 		0.0126
(1.00) 		0.00398
(0.665) 		0.208
(1.00) 		0.168
(1.00)
RHOA 13 (6%) 207 0.142
(1.00) 		0.189
(1.00) 		0.829
(1.00) 		0.604
(1.00) 		0.106
(1.00) 		0.283
(1.00) 		0.000594
(0.105) 		0.297
(1.00)
IRF2 15 (7%) 205 0.0906
(1.00) 		0.233
(1.00) 		0.434
(1.00) 		0.0297
(1.00) 		0.00102
(0.176) 		0.0125
(1.00) 		0.135
(1.00) 		0.249
(1.00)
APC 33 (15%) 187 0.97
(1.00) 		0.0207
(1.00) 		0.102
(1.00) 		0.0318
(1.00) 		0.000956
(0.166) 		0.0129
(1.00) 		0.0272
(1.00) 		0.0049
(0.803)
BCOR 16 (7%) 204 0.0156
(1.00) 		6.67e-05
(0.0125) 		0.0045
(0.747) 		0.0561
(1.00) 		0.00821
(1.00) 		0.00336
(0.567) 		0.183
(1.00) 		0.0259
(1.00)
TRIM48 14 (6%) 206 0.252
(1.00) 		0.322
(1.00) 		0.41
(1.00) 		0.109
(1.00) 		0.126
(1.00) 		0.192
(1.00) 		0.0907
(1.00) 		1
(1.00)
KRAS 25 (11%) 195 0.00873
(1.00) 		0.127
(1.00) 		0.351
(1.00) 		0.128
(1.00) 		0.85
(1.00) 		0.96
(1.00) 		0.179
(1.00) 		0.674
(1.00)
SMAD4 19 (9%) 201 0.648
(1.00) 		0.963
(1.00) 		0.0524
(1.00) 		0.226
(1.00) 		0.258
(1.00) 		0.16
(1.00) 		0.94
(1.00) 		0.462
(1.00)
MXRA8 11 (5%) 209 0.118
(1.00) 		0.0232
(1.00) 		0.0909
(1.00) 		0.0394
(1.00) 		0.153
(1.00) 		0.00949
(1.00) 		0.428
(1.00) 		0.0635
(1.00)
CDH1 18 (8%) 202 0.252
(1.00) 		0.458
(1.00) 		0.0314
(1.00) 		0.00564
(0.92) 		0.11
(1.00) 		0.0876
(1.00) 		0.278
(1.00) 		0.114
(1.00)
PTEN 14 (6%) 206 0.0057
(0.924) 		0.0152
(1.00) 		0.00155
(0.265) 		0.0452
(1.00) 		0.027
(1.00) 		0.0397
(1.00) 		0.1
(1.00) 		0.0575
(1.00)
B2M 8 (4%) 212 0.0258
(1.00) 		0.0232
(1.00) 		0.0329
(1.00) 		0.0968
(1.00) 		0.108
(1.00) 		0.287
(1.00) 		0.428
(1.00) 		0.0635
(1.00)
FBXW7 19 (9%) 201 0.0833
(1.00) 		0.022
(1.00) 		0.0157
(1.00) 		0.292
(1.00) 		0.102
(1.00) 		0.0169
(1.00) 		0.0238
(1.00) 		0.0812
(1.00)
PTH2 4 (2%) 216 1
(1.00) 		0.687
(1.00) 		0.281
(1.00) 		0.472
(1.00) 		0.672
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
FAM46D 6 (3%) 214 1
(1.00) 		0.708
(1.00) 		0.222
(1.00) 		0.636
(1.00) 		0.56
(1.00) 		0.767
(1.00) 		1
(1.00) 		0.731
(1.00)
RNF43 9 (4%) 211 0.175
(1.00) 		0.596
(1.00) 		0.202
(1.00) 		0.525
(1.00) 		0.338
(1.00) 		0.167
(1.00) 		0.521
(1.00) 		0.45
(1.00)
MAP2K7 14 (6%) 206 0.00583
(0.938) 		0.0984
(1.00) 		0.41
(1.00) 		0.51
(1.00) 		0.133
(1.00) 		0.171
(1.00) 		0.33
(1.00) 		0.052
(1.00)
WSB2 7 (3%) 213 0.341
(1.00) 		0.131
(1.00) 		0.215
(1.00) 		0.0394
(1.00) 		0.103
(1.00) 		0.0913
(1.00) 		0.0244
(1.00) 		0.00941
(1.00)
C13ORF33 6 (3%) 214 0.364
(1.00) 		0.0165
(1.00) 		0.243
(1.00) 		0.407
(1.00) 		0.0768
(1.00) 		0.324
(1.00) 		0.274
(1.00) 		0.45
(1.00)
TRPS1 30 (14%) 190 0.64
(1.00) 		0.0397
(1.00) 		0.0233
(1.00) 		0.24
(1.00) 		0.0327
(1.00) 		0.866
(1.00) 		0.378
(1.00) 		0.583
(1.00)
IAPP 4 (2%) 216 0.84
(1.00) 		0.763
(1.00) 		0.257
(1.00) 		0.449
(1.00) 		0.816
(1.00)
'PGM5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.24

Table S1.  Gene #2: 'PGM5 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 22 19 79
PGM5 MUTATED 13 4 4 1
PGM5 WILD-TYPE 86 18 15 78

Figure S1.  Get High-res Image Gene #2: 'PGM5 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'PGM5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4.28e-05 (Fisher's exact test), Q value = 0.008

Table S2.  Gene #2: 'PGM5 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 51 44 53
PGM5 MUTATED 3 12 1 0
PGM5 WILD-TYPE 24 39 43 53

Figure S2.  Get High-res Image Gene #2: 'PGM5 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'CBWD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000149 (Fisher's exact test), Q value = 0.027

Table S3.  Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 22 19 79
CBWD1 MUTATED 20 3 4 1
CBWD1 WILD-TYPE 79 19 15 78

Figure S3.  Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'CBWD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.00035

Table S4.  Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 51 44 53
CBWD1 MUTATED 4 16 2 0
CBWD1 WILD-TYPE 23 35 42 53

Figure S4.  Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000857 (Chi-square test), Q value = 0.15

Table S5.  Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 35 28 33 39
CBWD1 MUTATED 11 2 3 4 0
CBWD1 WILD-TYPE 25 33 25 29 39

Figure S5.  Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.48e-05 (Fisher's exact test), Q value = 0.014

Table S6.  Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 46 57
CBWD1 MUTATED 2 1 1 16
CBWD1 WILD-TYPE 33 32 45 41

Figure S6.  Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.36e-05 (Fisher's exact test), Q value = 0.0045

Table S7.  Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 50 61 43
CBWD1 MUTATED 14 1 11 0
CBWD1 WILD-TYPE 44 49 50 43

Figure S7.  Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000274 (Fisher's exact test), Q value = 0.049

Table S8.  Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 65 94
CBWD1 MUTATED 0 7 19
CBWD1 WILD-TYPE 53 58 75

Figure S8.  Get High-res Image Gene #4: 'CBWD1 MUTATION STATUS' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 4.33e-09 (Fisher's exact test), Q value = 8.5e-07

Table S9.  Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 22 19 79
TP53 MUTATED 22 15 9 52
TP53 WILD-TYPE 77 7 10 27

Figure S9.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.18e-05 (Fisher's exact test), Q value = 0.006

Table S10.  Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 51 44 53
TP53 MUTATED 5 25 15 37
TP53 WILD-TYPE 22 26 29 16

Figure S10.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 7.74e-05 (Chi-square test), Q value = 0.014

Table S11.  Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 35 28 33 39
TP53 MUTATED 9 10 10 19 28
TP53 WILD-TYPE 27 25 18 14 11

Figure S11.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 6.4e-06 (Fisher's exact test), Q value = 0.0012

Table S12.  Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 50 61 43
TP53 MUTATED 20 16 26 34
TP53 WILD-TYPE 38 34 35 9

Figure S12.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9.12e-06 (Fisher's exact test), Q value = 0.0018

Table S13.  Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 53 65 94
TP53 MUTATED 39 22 35
TP53 WILD-TYPE 14 43 59

Figure S13.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9.4e-05 (Fisher's exact test), Q value = 0.017

Table S14.  Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 57 69
TP53 MUTATED 30 16 34
TP53 WILD-TYPE 12 41 35

Figure S14.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.02

Table S15.  Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 22 19 79
PIK3CA MUTATED 30 7 6 5
PIK3CA WILD-TYPE 69 15 13 74

Figure S15.  Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.83e-09 (Fisher's exact test), Q value = 3.6e-07

Table S16.  Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 51 44 53
PIK3CA MUTATED 19 15 4 4
PIK3CA WILD-TYPE 8 36 40 49

Figure S16.  Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Chi-square test), Q value = 0.1

Table S17.  Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 35 28 33 39
PIK3CA MUTATED 16 6 4 10 2
PIK3CA WILD-TYPE 20 29 24 23 37

Figure S17.  Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.37e-07 (Fisher's exact test), Q value = 2.7e-05

Table S18.  Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 46 57
PIK3CA MUTATED 1 14 2 21
PIK3CA WILD-TYPE 34 19 44 36

Figure S18.  Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000367 (Fisher's exact test), Q value = 0.065

Table S19.  Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 66
PIK3CA MUTATED 23 6 10
PIK3CA WILD-TYPE 31 42 56

Figure S19.  Get High-res Image Gene #6: 'PIK3CA MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_MATURE_CNMF'

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000215 (Fisher's exact test), Q value = 0.039

Table S20.  Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 99 22 19 79
ARID1A MUTATED 30 2 4 5
ARID1A WILD-TYPE 69 20 15 74

Figure S20.  Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #1: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3.52e-05 (Chi-square test), Q value = 0.0066

Table S21.  Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 36 35 28 33 39
ARID1A MUTATED 17 7 3 6 1
ARID1A WILD-TYPE 19 28 25 27 38

Figure S21.  Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000131 (Fisher's exact test), Q value = 0.024

Table S22.  Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 35 33 46 57
ARID1A MUTATED 3 9 2 20
ARID1A WILD-TYPE 32 24 44 37

Figure S22.  Get High-res Image Gene #7: 'ARID1A MUTATION STATUS' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.000594 (Fisher's exact test), Q value = 0.1

Table S23.  Gene #9: 'RHOA MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 66
RHOA MUTATED 3 8 0
RHOA WILD-TYPE 51 40 66

Figure S23.  Get High-res Image Gene #9: 'RHOA MUTATION STATUS' versus Clinical Feature #7: 'MIRSEQ_MATURE_CNMF'

'IRF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.18

Table S24.  Gene #11: 'IRF2 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 50 61 43
IRF2 MUTATED 9 0 5 0
IRF2 WILD-TYPE 49 50 56 43

Figure S24.  Get High-res Image Gene #11: 'IRF2 MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000956 (Fisher's exact test), Q value = 0.17

Table S25.  Gene #19: 'APC MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 50 61 43
APC MUTATED 16 1 10 4
APC WILD-TYPE 42 49 51 39

Figure S25.  Get High-res Image Gene #19: 'APC MUTATION STATUS' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'BCOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.67e-05 (Fisher's exact test), Q value = 0.012

Table S26.  Gene #22: 'BCOR MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 27 51 44 53
BCOR MUTATED 7 2 1 0
BCOR WILD-TYPE 20 49 43 53

Figure S26.  Get High-res Image Gene #22: 'BCOR MUTATION STATUS' versus Clinical Feature #2: 'METHLYATION_CNMF'

Methods & Data
Input

  • Mutation data file = STAD-TP.mutsig.cluster.txt

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

  • Number of patients = 220

  • Number of significantly mutated genes = 25

  • 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

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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