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 57 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.

  • PTEN mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_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, 2 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 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
PTEN 11 (19%) 46 0.0123
(0.833) 		0.000216
(0.0156) 		0.00212
(0.151) 		0.00433
(0.303) 		0.096
(1.00) 		0.00872
(0.602) 		0.0237
(1.00) 		0.0241
(1.00)
FBXW7 22 (39%) 35 0.0511
(1.00) 		0.714
(1.00) 		0.595
(1.00) 		0.494
(1.00) 		0.441
(1.00) 		1
(1.00) 		0.938
(1.00) 		0.737
(1.00)
KRAS 7 (12%) 50 0.32
(1.00) 		0.0187
(1.00) 		0.0323
(1.00) 		0.0264
(1.00) 		0.463
(1.00) 		0.494
(1.00) 		0.513
(1.00) 		0.322
(1.00)
TP53 51 (89%) 6 0.331
(1.00) 		0.591
(1.00) 		0.877
(1.00) 		0.822
(1.00) 		1
(1.00) 		0.699
(1.00) 		1
(1.00) 		1
(1.00)
PIK3CA 20 (35%) 37 0.267
(1.00) 		0.875
(1.00) 		0.365
(1.00) 		0.303
(1.00) 		0.105
(1.00) 		0.0268
(1.00) 		0.162
(1.00) 		0.0274
(1.00)
PPP2R1A 16 (28%) 41 1
(1.00) 		0.701
(1.00) 		0.584
(1.00) 		0.852
(1.00) 		0.56
(1.00) 		0.635
(1.00) 		0.234
(1.00) 		1
(1.00)
PIK3R1 6 (11%) 51 0.856
(1.00) 		0.95
(1.00) 		0.544
(1.00) 		0.592
(1.00) 		0.425
(1.00) 		0.705
(1.00) 		0.744
(1.00) 		0.459
(1.00)
ZBTB7B 6 (11%) 51 0.483
(1.00) 		0.95
(1.00) 		1
(1.00) 		1
(1.00) 		0.0978
(1.00) 		0.197
(1.00) 		0.15
(1.00) 		0.29
(1.00)
RB1 6 (11%) 51 0.541
(1.00) 		0.121
(1.00) 		0.08
(1.00) 		0.0401
(1.00) 		0.835
(1.00) 		0.484
(1.00) 		0.918
(1.00) 		0.712
(1.00)
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0511 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
FBXW7 MUTATED 12 9 1
FBXW7 WILD-TYPE 10 15 9
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.714 (Chi-square test), Q value = 1

Table S2.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
FBXW7 MUTATED 6 4 4 3 5
FBXW7 WILD-TYPE 6 5 6 10 8
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.595 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
FBXW7 MUTATED 7 8 5 2
FBXW7 WILD-TYPE 8 12 7 8
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
FBXW7 MUTATED 8 4 8 2
FBXW7 WILD-TYPE 7 7 14 7
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
FBXW7 MUTATED 5 8 3 6
FBXW7 WILD-TYPE 6 14 1 13
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S6.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
FBXW7 MUTATED 0 11 11
FBXW7 WILD-TYPE 1 16 17
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
FBXW7 MUTATED 5 9 2 6
FBXW7 WILD-TYPE 6 14 3 11
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.737 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
FBXW7 MUTATED 0 11 11
FBXW7 WILD-TYPE 1 14 19
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
KRAS MUTATED 2 5 0
KRAS WILD-TYPE 20 19 10
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0187 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
KRAS MUTATED 0 1 1 0 5
KRAS WILD-TYPE 12 8 9 13 8

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

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
KRAS MUTATED 0 3 4 0
KRAS WILD-TYPE 15 17 8 10

Figure S2.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
KRAS MUTATED 0 4 3 0
KRAS WILD-TYPE 15 7 19 9

Figure S3.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
KRAS MUTATED 1 4 1 1
KRAS WILD-TYPE 10 18 3 18
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
KRAS MUTATED 0 2 5
KRAS WILD-TYPE 1 25 23
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
KRAS MUTATED 1 5 0 1
KRAS WILD-TYPE 10 18 5 16
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
KRAS MUTATED 0 5 2
KRAS WILD-TYPE 1 20 28
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
TP53 MUTATED 21 21 8
TP53 WILD-TYPE 1 3 2
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.591 (Chi-square test), Q value = 1

Table S18.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
TP53 MUTATED 12 8 8 12 11
TP53 WILD-TYPE 0 1 2 1 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S19.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
TP53 MUTATED 14 18 10 9
TP53 WILD-TYPE 1 2 2 1
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S20.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
TP53 MUTATED 14 9 20 8
TP53 WILD-TYPE 1 2 2 1
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S21.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
TP53 MUTATED 10 20 4 17
TP53 WILD-TYPE 1 2 0 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
TP53 MUTATED 1 24 26
TP53 WILD-TYPE 0 3 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S23.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
TP53 MUTATED 10 21 5 15
TP53 WILD-TYPE 1 2 0 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S24.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
TP53 MUTATED 1 23 27
TP53 WILD-TYPE 0 2 3
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 1

Table S25.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
PIK3CA MUTATED 5 11 3
PIK3CA WILD-TYPE 17 13 7
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.875 (Chi-square test), Q value = 1

Table S26.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
PIK3CA MUTATED 4 3 5 4 4
PIK3CA WILD-TYPE 8 6 5 9 9
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 1

Table S27.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
PIK3CA MUTATED 5 10 3 2
PIK3CA WILD-TYPE 10 10 9 8
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 1

Table S28.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
PIK3CA MUTATED 6 3 10 1
PIK3CA WILD-TYPE 9 8 12 8
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
PIK3CA MUTATED 4 4 2 10
PIK3CA WILD-TYPE 7 18 2 9
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
PIK3CA MUTATED 1 13 6
PIK3CA WILD-TYPE 0 14 22

Figure S4.  Get High-res Image Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S31.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
PIK3CA MUTATED 5 5 1 9
PIK3CA WILD-TYPE 6 18 4 8
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
PIK3CA MUTATED 1 5 14
PIK3CA WILD-TYPE 0 20 16

Figure S5.  Get High-res Image Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PPP2R1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S33.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
PPP2R1A MUTATED 6 7 3
PPP2R1A WILD-TYPE 16 17 7
'PPP2R1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.701 (Chi-square test), Q value = 1

Table S34.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
PPP2R1A MUTATED 4 3 4 3 2
PPP2R1A WILD-TYPE 8 6 6 10 11
'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
PPP2R1A MUTATED 6 5 2 3
PPP2R1A WILD-TYPE 9 15 10 7
'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S36.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
PPP2R1A MUTATED 5 2 6 3
PPP2R1A WILD-TYPE 10 9 16 6
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
PPP2R1A MUTATED 5 5 1 5
PPP2R1A WILD-TYPE 6 17 3 14
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.635 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
PPP2R1A MUTATED 0 9 7
PPP2R1A WILD-TYPE 1 18 21
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S39.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
PPP2R1A MUTATED 6 5 1 4
PPP2R1A WILD-TYPE 5 18 4 13
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S40.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
PPP2R1A MUTATED 0 7 9
PPP2R1A WILD-TYPE 1 18 21
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.83

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
PTEN MUTATED 1 9 1
PTEN WILD-TYPE 21 15 9

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

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000216 (Chi-square test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
PTEN MUTATED 0 0 6 5 0
PTEN WILD-TYPE 12 9 4 8 13

Figure S7.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.15

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
PTEN MUTATED 0 8 0 3
PTEN WILD-TYPE 15 12 12 7

Figure S8.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00433 (Fisher's exact test), Q value = 0.3

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
PTEN MUTATED 0 0 8 3
PTEN WILD-TYPE 15 11 14 6

Figure S9.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.096 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
PTEN MUTATED 2 1 1 6
PTEN WILD-TYPE 9 21 3 13
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00872 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
PTEN MUTATED 0 9 1
PTEN WILD-TYPE 1 18 27

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

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
PTEN MUTATED 1 1 2 6
PTEN WILD-TYPE 10 22 3 11

Figure S11.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
PTEN MUTATED 0 1 9
PTEN WILD-TYPE 1 24 21

Figure S12.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S49.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
PIK3R1 MUTATED 3 2 1
PIK3R1 WILD-TYPE 19 22 9
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.95 (Chi-square test), Q value = 1

Table S50.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
PIK3R1 MUTATED 2 1 1 1 1
PIK3R1 WILD-TYPE 10 8 9 12 12
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S51.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
PIK3R1 MUTATED 3 2 1 0
PIK3R1 WILD-TYPE 12 18 11 10
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 1

Table S52.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
PIK3R1 MUTATED 3 1 2 0
PIK3R1 WILD-TYPE 12 10 20 9
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
PIK3R1 MUTATED 2 2 1 1
PIK3R1 WILD-TYPE 9 20 3 18
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S54.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
PIK3R1 MUTATED 0 2 4
PIK3R1 WILD-TYPE 1 25 24
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
PIK3R1 MUTATED 2 3 0 1
PIK3R1 WILD-TYPE 9 20 5 16
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
PIK3R1 MUTATED 0 4 2
PIK3R1 WILD-TYPE 1 21 28
'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S57.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
ZBTB7B MUTATED 3 1 1
ZBTB7B WILD-TYPE 19 23 9
'ZBTB7B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.95 (Chi-square test), Q value = 1

Table S58.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
ZBTB7B MUTATED 2 1 1 1 1
ZBTB7B WILD-TYPE 10 8 9 12 12
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S59.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
ZBTB7B MUTATED 2 2 1 1
ZBTB7B WILD-TYPE 13 18 11 9
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S60.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
ZBTB7B MUTATED 2 1 2 1
ZBTB7B WILD-TYPE 13 10 20 8
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S61.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
ZBTB7B MUTATED 1 1 2 2
ZBTB7B WILD-TYPE 10 21 2 17
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 1

Table S62.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
ZBTB7B MUTATED 0 5 1
ZBTB7B WILD-TYPE 1 22 27
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 1

Table S63.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
ZBTB7B MUTATED 1 1 2 2
ZBTB7B WILD-TYPE 10 22 3 15
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 1

Table S64.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
ZBTB7B MUTATED 0 1 5
ZBTB7B WILD-TYPE 1 24 25
'RB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S65.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
RB1 MUTATED 2 4 0
RB1 WILD-TYPE 20 20 10
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.121 (Chi-square test), Q value = 1

Table S66.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
RB1 MUTATED 0 1 3 2 0
RB1 WILD-TYPE 12 8 7 11 13
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.08 (Fisher's exact test), Q value = 1

Table S67.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
RB1 MUTATED 0 4 0 2
RB1 WILD-TYPE 15 16 12 8
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0401 (Fisher's exact test), Q value = 1

Table S68.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
RB1 MUTATED 0 0 3 3
RB1 WILD-TYPE 15 11 19 6

Figure S13.  Get High-res Image Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S69.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
RB1 MUTATED 2 2 0 2
RB1 WILD-TYPE 9 20 4 17
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S70.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
RB1 MUTATED 0 4 2
RB1 WILD-TYPE 1 23 26
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S71.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
RB1 MUTATED 1 2 1 2
RB1 WILD-TYPE 10 21 4 15
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S72.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
RB1 MUTATED 0 2 4
RB1 WILD-TYPE 1 23 26
Methods & Data
Input

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

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

  • Number of patients = 57

  • 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

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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