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

  • PTEN mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 9 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
PTEN 10 (18%) 46 0.0264
(1.00) 		0.000529
(0.0381) 		0.00902
(0.632) 		0.000947
(0.0672) 		0.141
(1.00) 		0.0169
(1.00) 		0.038
(1.00) 		0.0442
(1.00)
FBXW7 21 (38%) 35 0.0476
(1.00) 		0.697
(1.00) 		0.725
(1.00) 		0.715
(1.00) 		0.347
(1.00) 		1
(1.00) 		0.9
(1.00) 		0.671
(1.00)
KRAS 7 (12%) 49 0.322
(1.00) 		0.0205
(1.00) 		0.151
(1.00) 		0.0976
(1.00) 		0.464
(1.00) 		0.496
(1.00) 		0.54
(1.00) 		0.327
(1.00)
TP53 50 (89%) 6 0.338
(1.00) 		0.54
(1.00) 		1
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.694
(1.00) 		1
(1.00) 		1
(1.00)
PPP2R1A 15 (27%) 41 1
(1.00) 		0.807
(1.00) 		0.728
(1.00) 		0.973
(1.00) 		0.503
(1.00) 		0.72
(1.00) 		0.185
(1.00) 		1
(1.00)
PIK3CA 19 (34%) 37 0.33
(1.00) 		0.967
(1.00) 		0.328
(1.00) 		0.547
(1.00) 		0.142
(1.00) 		0.0374
(1.00) 		0.226
(1.00) 		0.0369
(1.00)
PCDHAC2 11 (20%) 45 0.156
(1.00) 		0.126
(1.00) 		0.538
(1.00) 		0.896
(1.00) 		0.597
(1.00) 		0.586
(1.00) 		0.434
(1.00) 		0.435
(1.00)
PIK3R1 6 (11%) 50 0.859
(1.00) 		0.952
(1.00) 		0.574
(1.00) 		0.689
(1.00) 		0.425
(1.00) 		0.706
(1.00) 		0.804
(1.00) 		0.464
(1.00)
ZBTB7B 6 (11%) 50 0.49
(1.00) 		0.952
(1.00) 		1
(1.00) 		0.844
(1.00) 		0.104
(1.00) 		0.194
(1.00) 		0.152
(1.00) 		0.287
(1.00)
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0476 (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 23 10
FBXW7 MUTATED 12 8 1
FBXW7 WILD-TYPE 10 15 9

Figure S1.  Get High-res Image Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.697 (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 9 13 13
FBXW7 MUTATED 6 4 3 3 5
FBXW7 WILD-TYPE 6 5 6 10 8
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.725 (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
ALL 17 20 18
FBXW7 MUTATED 8 7 6
FBXW7 WILD-TYPE 9 13 12
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.715 (Chi-square 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 CLUS_5
ALL 4 3 15 12 21
FBXW7 MUTATED 1 1 8 4 7
FBXW7 WILD-TYPE 3 2 7 8 14
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.347 (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 18
FBXW7 MUTATED 5 8 3 5
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 26 28
FBXW7 MUTATED 0 10 11
FBXW7 WILD-TYPE 1 16 17
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.9 (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 16
FBXW7 MUTATED 5 9 2 5
FBXW7 WILD-TYPE 6 14 3 11
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.671 (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 29
FBXW7 MUTATED 0 11 10
FBXW7 WILD-TYPE 1 14 19
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.322 (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 23 10
KRAS MUTATED 2 5 0
KRAS WILD-TYPE 20 18 10
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0205 (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 9 13 13
KRAS MUTATED 0 1 1 0 5
KRAS WILD-TYPE 12 8 8 13 8

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

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.151 (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
ALL 17 20 18
KRAS MUTATED 0 3 4
KRAS WILD-TYPE 17 17 14
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0976 (Chi-square 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 CLUS_5
ALL 4 3 15 12 21
KRAS MUTATED 0 0 0 4 3
KRAS WILD-TYPE 4 3 15 8 18
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.464 (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 18
KRAS MUTATED 1 4 1 1
KRAS WILD-TYPE 10 18 3 17
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.496 (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 26 28
KRAS MUTATED 0 2 5
KRAS WILD-TYPE 1 24 23
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.54 (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 16
KRAS MUTATED 1 5 0 1
KRAS WILD-TYPE 10 18 5 15
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.327 (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 29
KRAS MUTATED 0 5 2
KRAS WILD-TYPE 1 20 27
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.338 (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 23 10
TP53 MUTATED 21 20 8
TP53 WILD-TYPE 1 3 2
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.54 (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 9 13 13
TP53 MUTATED 12 8 7 12 11
TP53 WILD-TYPE 0 1 2 1 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (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
ALL 17 20 18
TP53 MUTATED 15 18 16
TP53 WILD-TYPE 2 2 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.752 (Chi-square 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 CLUS_5
ALL 4 3 15 12 21
TP53 MUTATED 3 3 14 10 19
TP53 WILD-TYPE 1 0 1 2 2
'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 18
TP53 MUTATED 10 20 4 16
TP53 WILD-TYPE 1 2 0 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.694 (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 26 28
TP53 MUTATED 1 23 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 16
TP53 MUTATED 10 21 5 14
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 29
TP53 MUTATED 1 23 26
TP53 WILD-TYPE 0 2 3
'PPP2R1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S25.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
PPP2R1A MUTATED 6 6 3
PPP2R1A WILD-TYPE 16 17 7
'PPP2R1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.807 (Chi-square test), Q value = 1

Table S26.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.728 (Fisher's exact test), Q value = 1

Table S27.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
PPP2R1A MUTATED 6 5 4
PPP2R1A WILD-TYPE 11 15 14
'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.973 (Chi-square test), Q value = 1

Table S28.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
PPP2R1A MUTATED 1 1 5 3 5
PPP2R1A WILD-TYPE 3 2 10 9 16
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.503 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
PPP2R1A MUTATED 5 5 1 4
PPP2R1A WILD-TYPE 6 17 3 14
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.72 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
PPP2R1A MUTATED 0 8 7
PPP2R1A WILD-TYPE 1 18 21
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
PPP2R1A MUTATED 6 5 1 3
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 S32.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
PPP2R1A MUTATED 0 7 8
PPP2R1A WILD-TYPE 1 18 21
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 1

Table S33.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
PIK3CA MUTATED 5 10 3
PIK3CA WILD-TYPE 17 13 7
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.967 (Chi-square test), Q value = 1

Table S34.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.328 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
PIK3CA MUTATED 6 9 4
PIK3CA WILD-TYPE 11 11 14
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.547 (Chi-square test), Q value = 1

Table S36.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
PIK3CA MUTATED 1 0 6 3 9
PIK3CA WILD-TYPE 3 3 9 9 12
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

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

P value = 0.0374 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
PIK3CA MUTATED 1 12 6
PIK3CA WILD-TYPE 0 14 22

Figure S3.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
PIK3CA MUTATED 5 5 1 8
PIK3CA WILD-TYPE 6 18 4 8
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
PIK3CA MUTATED 1 5 13
PIK3CA WILD-TYPE 0 20 16

Figure S4.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
PTEN MUTATED 1 8 1
PTEN WILD-TYPE 21 15 9

Figure S5.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000529 (Chi-square test), Q value = 0.038

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 9 13 13
PTEN MUTATED 0 0 5 5 0
PTEN WILD-TYPE 12 9 4 8 13

Figure S6.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00902 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
PTEN MUTATED 1 8 1
PTEN WILD-TYPE 16 12 17

Figure S7.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000947 (Chi-square test), Q value = 0.067

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
PTEN MUTATED 3 0 0 0 7
PTEN WILD-TYPE 1 3 15 12 14

Figure S8.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.141 (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 18
PTEN MUTATED 2 1 1 5
PTEN WILD-TYPE 9 21 3 13
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
PTEN MUTATED 0 8 1
PTEN WILD-TYPE 1 18 27

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

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.038 (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 16
PTEN MUTATED 1 1 2 5
PTEN WILD-TYPE 10 22 3 11

Figure S10.  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 = 0.0442 (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 29
PTEN MUTATED 0 1 8
PTEN WILD-TYPE 1 24 21

Figure S11.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PCDHAC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 1

Table S49.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
PCDHAC2 MUTATED 2 7 1
PCDHAC2 WILD-TYPE 20 16 9
'PCDHAC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.126 (Chi-square test), Q value = 1

Table S50.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 9 13 13
PCDHAC2 MUTATED 3 0 4 1 3
PCDHAC2 WILD-TYPE 9 9 5 12 10
'PCDHAC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S51.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
PCDHAC2 MUTATED 4 5 2
PCDHAC2 WILD-TYPE 13 15 16
'PCDHAC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.896 (Chi-square test), Q value = 1

Table S52.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
PCDHAC2 MUTATED 1 0 3 2 5
PCDHAC2 WILD-TYPE 3 3 12 10 16
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
PCDHAC2 MUTATED 2 3 0 5
PCDHAC2 WILD-TYPE 9 19 4 13
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 1

Table S54.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
PCDHAC2 MUTATED 0 6 4
PCDHAC2 WILD-TYPE 1 20 24
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
PCDHAC2 MUTATED 2 3 0 5
PCDHAC2 WILD-TYPE 9 20 5 11
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
PCDHAC2 MUTATED 0 3 7
PCDHAC2 WILD-TYPE 1 22 22
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.859 (Fisher's exact test), Q value = 1

Table S57.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
PIK3R1 MUTATED 3 2 1
PIK3R1 WILD-TYPE 19 21 9
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.952 (Chi-square test), Q value = 1

Table S58.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.574 (Fisher's exact test), Q value = 1

Table S59.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
PIK3R1 MUTATED 3 2 1
PIK3R1 WILD-TYPE 14 18 17
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.689 (Chi-square test), Q value = 1

Table S60.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
PIK3R1 MUTATED 0 0 3 1 2
PIK3R1 WILD-TYPE 4 3 12 11 19
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S61.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
PIK3R1 MUTATED 2 2 1 1
PIK3R1 WILD-TYPE 9 20 3 17
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.706 (Fisher's exact test), Q value = 1

Table S62.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
PIK3R1 MUTATED 0 2 4
PIK3R1 WILD-TYPE 1 24 24
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S63.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
PIK3R1 MUTATED 2 3 0 1
PIK3R1 WILD-TYPE 9 20 5 15
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S64.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
PIK3R1 MUTATED 0 4 2
PIK3R1 WILD-TYPE 1 21 27
'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S65.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.952 (Chi-square test), Q value = 1

Table S66.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

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

Table S67.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
ZBTB7B MUTATED 2 2 2
ZBTB7B WILD-TYPE 15 18 16
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.844 (Chi-square test), Q value = 1

Table S68.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
ZBTB7B MUTATED 1 0 2 1 2
ZBTB7B WILD-TYPE 3 3 13 11 19
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S69.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
ZBTB7B MUTATED 1 1 2 2
ZBTB7B WILD-TYPE 10 21 2 16
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 1

Table S70.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
ZBTB7B MUTATED 0 5 1
ZBTB7B WILD-TYPE 1 21 27
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 1

Table S71.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
ZBTB7B MUTATED 1 1 2 2
ZBTB7B WILD-TYPE 10 22 3 14
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 1

Table S72.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
ZBTB7B MUTATED 0 1 5
ZBTB7B WILD-TYPE 1 24 24
Methods & Data
Input

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

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

  • Number of patients = 56

  • 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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