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 13 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 13 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 Fisher's exact 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 0.011
(1.00) 		0.00012
(0.0125) 		0.00231
(0.238) 		0.0452
(1.00) 		0.0964
(1.00) 		0.0612
(1.00) 		0.0223
(1.00) 		0.122
(1.00)
TP53 51 (89%) 6 0.331
(1.00) 		0.627
(1.00) 		0.877
(1.00) 		0.513
(1.00) 		1
(1.00) 		0.911
(1.00) 		1
(1.00) 		1
(1.00)
FBXW7 22 (39%) 35 0.0631
(1.00) 		0.723
(1.00) 		0.633
(1.00) 		0.102
(1.00) 		0.47
(1.00) 		0.931
(1.00) 		0.975
(1.00) 		0.712
(1.00)
PPP2R1A 16 (28%) 41 1
(1.00) 		0.709
(1.00) 		0.592
(1.00) 		0.673
(1.00) 		0.57
(1.00) 		0.318
(1.00) 		0.237
(1.00) 		0.49
(1.00)
KRAS 7 (12%) 50 0.321
(1.00) 		0.0148
(1.00) 		0.0325
(1.00) 		0.00609
(0.615) 		0.462
(1.00) 		0.0906
(1.00) 		0.513
(1.00) 		0.0479
(1.00)
ZBTB7B 6 (11%) 51 0.483
(1.00) 		0.94
(1.00) 		1
(1.00) 		0.913
(1.00) 		0.0995
(1.00) 		0.146
(1.00) 		0.15
(1.00) 		0.303
(1.00)
CHD4 10 (18%) 47 0.199
(1.00) 		0.0101
(1.00) 		0.187
(1.00) 		0.00576
(0.588) 		0.479
(1.00) 		0.412
(1.00) 		0.493
(1.00) 		0.479
(1.00)
PIK3R1 6 (11%) 51 0.855
(1.00) 		0.939
(1.00) 		0.546
(1.00) 		0.705
(1.00) 		0.426
(1.00) 		0.506
(1.00) 		0.743
(1.00) 		0.747
(1.00)
ARHGAP35 6 (11%) 51 1
(1.00) 		0.333
(1.00) 		1
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.253
(1.00)
PIK3CA 20 (35%) 37 0.256
(1.00) 		0.9
(1.00) 		0.365
(1.00) 		0.37
(1.00) 		0.111
(1.00) 		0.34
(1.00) 		0.165
(1.00) 		0.111
(1.00)
MAMLD1 4 (7%) 53 0.826
(1.00) 		0.9
(1.00) 		0.687
(1.00) 		0.769
(1.00) 		0.0638
(1.00) 		0.679
(1.00) 		0.163
(1.00) 		0.572
(1.00)
RB1 6 (11%) 51 0.544
(1.00) 		0.0894
(1.00) 		0.0783
(1.00) 		0.0981
(1.00) 		0.835
(1.00) 		0.862
(1.00) 		0.92
(1.00) 		0.688
(1.00)
LYPLA2 3 (5%) 54 1
(1.00) 		0.621
(1.00) 		0.673
(1.00) 		0.349
(1.00) 		0.381
(1.00) 		0.564
(1.00) 		0.478
(1.00) 		0.49
(1.00)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

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

Table S1.  Gene #1: '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 = 0.627 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: '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 S3.  Gene #1: '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 = 0.513 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
TP53 MUTATED 11 3 8 5 7 5 12
TP53 WILD-TYPE 0 1 0 1 1 1 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S5.  Gene #1: '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 = 0.911 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
TP53 MUTATED 21 8 16 6
TP53 WILD-TYPE 3 0 2 0
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S7.  Gene #1: '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 S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
TP53 MUTATED 9 7 13 9 8 5
TP53 WILD-TYPE 1 0 2 1 1 0
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0631 (Fisher's exact test), Q value = 1

Table S9.  Gene #2: '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 = 0.723 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: '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 = 0.633 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: '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 = 0.102 (Fisher's exact test), Q value = 1

Table S12.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
FBXW7 MUTATED 4 4 5 2 2 2 3
FBXW7 WILD-TYPE 7 0 3 4 6 4 11
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: '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 = 0.931 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
FBXW7 MUTATED 9 4 7 2
FBXW7 WILD-TYPE 15 4 11 4
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.975 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: '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 = 0.712 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
FBXW7 MUTATED 2 4 7 4 3 2
FBXW7 WILD-TYPE 8 3 8 6 6 3
'PPP2R1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S17.  Gene #3: '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 = 0.709 (Fisher's exact test), Q value = 1

Table S18.  Gene #3: '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 = 0.592 (Fisher's exact test), Q value = 1

Table S19.  Gene #3: '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 = 0.673 (Fisher's exact test), Q value = 1

Table S20.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
PPP2R1A MUTATED 4 1 4 1 2 2 2
PPP2R1A WILD-TYPE 7 3 4 5 6 4 12
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: '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 = 0.318 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
PPP2R1A MUTATED 8 4 3 1
PPP2R1A WILD-TYPE 16 4 15 5
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: '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 = 0.49 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
PPP2R1A MUTATED 3 4 5 2 1 1
PPP2R1A WILD-TYPE 7 3 10 8 8 4
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 1

Table S25.  Gene #4: '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 S1.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.012

Table S26.  Gene #4: '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 S2.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.24

Table S27.  Gene #4: '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 S3.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
PTEN MUTATED 0 0 3 0 3 0 5
PTEN WILD-TYPE 11 4 5 6 5 6 9

Figure S4.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0964 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: '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 = 0.0612 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
PTEN MUTATED 8 0 1 1
PTEN WILD-TYPE 16 8 17 5
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: '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 S5.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.122 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
PTEN MUTATED 2 0 6 1 0 1
PTEN WILD-TYPE 8 7 9 9 9 4
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 1

Table S33.  Gene #5: '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 = 0.0148 (Fisher's exact test), Q value = 1

Table S34.  Gene #5: '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 S6.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: '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 S7.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00609 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
KRAS MUTATED 0 0 1 0 0 4 2
KRAS WILD-TYPE 11 4 7 6 8 2 12

Figure S8.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: '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 = 0.0906 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
KRAS MUTATED 1 0 5 1
KRAS WILD-TYPE 23 8 13 5
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S39.  Gene #5: '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 = 0.0479 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
KRAS MUTATED 0 0 1 1 4 1
KRAS WILD-TYPE 10 7 14 9 5 4

Figure S9.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

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

Table S41.  Gene #6: '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 = 0.94 (Fisher's exact test), Q value = 1

Table S42.  Gene #6: '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 S43.  Gene #6: '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 = 0.913 (Fisher's exact test), Q value = 1

Table S44.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
ZBTB7B MUTATED 2 0 0 0 1 1 2
ZBTB7B WILD-TYPE 9 4 8 6 7 5 12
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0995 (Fisher's exact test), Q value = 1

Table S45.  Gene #6: '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 = 0.146 (Fisher's exact test), Q value = 1

Table S46.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
ZBTB7B MUTATED 5 1 0 0
ZBTB7B WILD-TYPE 19 7 18 6
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S47.  Gene #6: '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 = 0.303 (Fisher's exact test), Q value = 1

Table S48.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
ZBTB7B MUTATED 1 1 4 0 0 0
ZBTB7B WILD-TYPE 9 6 11 10 9 5
'CHD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

Table S49.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
CHD4 MUTATED 2 7 1
CHD4 WILD-TYPE 20 17 9
'CHD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 1

Table S50.  Gene #7: 'CHD4 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
CHD4 MUTATED 0 4 4 1 1
CHD4 WILD-TYPE 12 5 6 12 12

Figure S10.  Get High-res Image Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 1

Table S51.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
CHD4 MUTATED 2 5 0 3
CHD4 WILD-TYPE 13 15 12 7
'CHD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00576 (Fisher's exact test), Q value = 0.59

Table S52.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
CHD4 MUTATED 0 2 4 0 3 0 1
CHD4 WILD-TYPE 11 2 4 6 5 6 13

Figure S11.  Get High-res Image Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
CHD4 MUTATED 3 2 1 3
CHD4 WILD-TYPE 8 20 3 16
'CHD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 1

Table S54.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
CHD4 MUTATED 6 0 2 1
CHD4 WILD-TYPE 18 8 16 5
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
CHD4 MUTATED 3 2 1 3
CHD4 WILD-TYPE 8 21 4 14
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
CHD4 MUTATED 2 0 4 2 0 1
CHD4 WILD-TYPE 8 7 11 8 9 4
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.855 (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 24 10
PIK3R1 MUTATED 3 2 1
PIK3R1 WILD-TYPE 19 22 9
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.939 (Fisher's exact 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 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 = 0.546 (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 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 = 0.705 (Fisher's exact 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 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
PIK3R1 MUTATED 2 1 1 0 0 1 1
PIK3R1 WILD-TYPE 9 3 7 6 8 5 13
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.426 (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 19
PIK3R1 MUTATED 2 2 1 1
PIK3R1 WILD-TYPE 9 20 3 18
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.506 (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 CLUS_4
ALL 24 8 18 6
PIK3R1 MUTATED 2 2 2 0
PIK3R1 WILD-TYPE 22 6 16 6
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.743 (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 17
PIK3R1 MUTATED 2 3 0 1
PIK3R1 WILD-TYPE 9 20 5 16
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.747 (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 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
PIK3R1 MUTATED 1 2 1 1 1 0
PIK3R1 WILD-TYPE 9 5 14 9 8 5
'ARHGAP35 MUTATION STATUS' versus 'CN_CNMF'

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

Table S65.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
ARHGAP35 MUTATED 2 3 1
ARHGAP35 WILD-TYPE 20 21 9
'ARHGAP35 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 1

Table S66.  Gene #9: 'ARHGAP35 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
ARHGAP35 MUTATED 2 0 2 0 2
ARHGAP35 WILD-TYPE 10 9 8 13 11
'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S67.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
ARHGAP35 MUTATED 2 2 1 1
ARHGAP35 WILD-TYPE 13 18 11 9
'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S68.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
ARHGAP35 MUTATED 2 0 2 0 1 1 0
ARHGAP35 WILD-TYPE 9 4 6 6 7 5 14
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S69.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
ARHGAP35 MUTATED 1 2 0 2
ARHGAP35 WILD-TYPE 10 20 4 17
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S70.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
ARHGAP35 MUTATED 1 2 1 1
ARHGAP35 WILD-TYPE 23 6 17 5
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S71.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
ARHGAP35 MUTATED 1 2 0 2
ARHGAP35 WILD-TYPE 10 21 5 15
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 1

Table S72.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
ARHGAP35 MUTATED 0 2 1 1 0 1
ARHGAP35 WILD-TYPE 10 5 14 9 9 4
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 1

Table S73.  Gene #10: '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 = 0.9 (Fisher's exact test), Q value = 1

Table S74.  Gene #10: '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 S75.  Gene #10: '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 = 0.37 (Fisher's exact test), Q value = 1

Table S76.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
PIK3CA MUTATED 3 3 4 2 1 1 6
PIK3CA WILD-TYPE 8 1 4 4 7 5 8
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 1

Table S77.  Gene #10: '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 = 0.34 (Fisher's exact test), Q value = 1

Table S78.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
PIK3CA MUTATED 11 2 4 3
PIK3CA WILD-TYPE 13 6 14 3
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 1

Table S79.  Gene #10: '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 = 0.111 (Fisher's exact test), Q value = 1

Table S80.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
PIK3CA MUTATED 3 1 9 3 1 3
PIK3CA WILD-TYPE 7 6 6 7 8 2
'MAMLD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S81.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
MAMLD1 MUTATED 1 2 1
MAMLD1 WILD-TYPE 21 22 9
'MAMLD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.9 (Fisher's exact test), Q value = 1

Table S82.  Gene #11: 'MAMLD1 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
MAMLD1 MUTATED 0 1 1 1 1
MAMLD1 WILD-TYPE 12 8 9 12 12
'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S83.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
MAMLD1 MUTATED 0 2 1 1
MAMLD1 WILD-TYPE 15 18 11 9
'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S84.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
MAMLD1 MUTATED 0 0 1 1 1 0 1
MAMLD1 WILD-TYPE 11 4 7 5 7 6 13
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0638 (Fisher's exact test), Q value = 1

Table S85.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
MAMLD1 MUTATED 0 0 1 3
MAMLD1 WILD-TYPE 11 22 3 16
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

Table S86.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
MAMLD1 MUTATED 2 0 1 1
MAMLD1 WILD-TYPE 22 8 17 5
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 1

Table S87.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
MAMLD1 MUTATED 1 0 1 2
MAMLD1 WILD-TYPE 10 23 4 15
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S88.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
MAMLD1 MUTATED 1 0 2 0 0 1
MAMLD1 WILD-TYPE 9 7 13 10 9 4
'RB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S89.  Gene #12: '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 = 0.0894 (Fisher's exact test), Q value = 1

Table S90.  Gene #12: '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 = 0.0783 (Fisher's exact test), Q value = 1

Table S91.  Gene #12: '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 = 0.0981 (Fisher's exact test), Q value = 1

Table S92.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
RB1 MUTATED 0 0 2 0 3 0 1
RB1 WILD-TYPE 11 4 6 6 5 6 13
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S93.  Gene #12: '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 = 0.862 (Fisher's exact test), Q value = 1

Table S94.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
RB1 MUTATED 3 0 2 1
RB1 WILD-TYPE 21 8 16 5
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.92 (Fisher's exact test), Q value = 1

Table S95.  Gene #12: '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 = 0.688 (Fisher's exact test), Q value = 1

Table S96.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
RB1 MUTATED 1 0 2 2 0 1
RB1 WILD-TYPE 9 7 13 8 9 4
'LYPLA2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S97.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
LYPLA2 MUTATED 1 2 0
LYPLA2 WILD-TYPE 21 22 10
'LYPLA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S98.  Gene #13: 'LYPLA2 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
LYPLA2 MUTATED 0 1 1 0 1
LYPLA2 WILD-TYPE 12 8 9 13 12
'LYPLA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 1

Table S99.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
LYPLA2 MUTATED 0 1 1 1
LYPLA2 WILD-TYPE 15 19 11 9
'LYPLA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 1

Table S100.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
LYPLA2 MUTATED 0 0 1 0 1 1 0
LYPLA2 WILD-TYPE 11 4 7 6 7 5 14
'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S101.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
LYPLA2 MUTATED 0 1 1 1
LYPLA2 WILD-TYPE 11 21 3 18
'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S102.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
LYPLA2 MUTATED 1 0 1 1
LYPLA2 WILD-TYPE 23 8 17 5
'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 1

Table S103.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
LYPLA2 MUTATED 0 1 1 1
LYPLA2 WILD-TYPE 11 22 4 16
'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S104.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 10 7 15 10 9 5
LYPLA2 MUTATED 0 0 1 0 1 1
LYPLA2 WILD-TYPE 10 7 14 10 8 4
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 = 13

  • 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

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] 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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