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 15 genes and 10 molecular subtypes across 35 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

  • No gene mutations related to molecuar subtypes.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 15 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		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 Fisher's exact test Fisher's exact test
PBRM1 8 (23%) 27 0.553
(1.00) 		0.117
(0.88) 		0.852
(1.00) 		0.23
(0.886) 		0.138
(0.88) 		0.318
(0.908) 		0.807
(1.00) 		0.224
(0.886) 		0.563
(1.00) 		0.434
(0.996)
HLA-B 5 (14%) 30 0.361
(0.968) 		0.0128
(0.418) 		0.588
(1.00) 		0.436
(0.996) 		0.116
(0.88) 		0.184
(0.886) 		0.0071
(0.355) 		0.0178
(0.418) 		0.727
(1.00) 		0.0563
(0.768)
MLL3 7 (20%) 28 0.12
(0.88) 		0.314
(0.908) 		0.319
(0.908) 		1
(1.00) 		0.916
(1.00) 		0.979
(1.00) 		0.164
(0.88) 		0.74
(1.00) 		0.819
(1.00) 		0.223
(0.886)
FTH1 3 (9%) 32 0.124
(0.88) 		0.0466
(0.7) 		0.0924
(0.88) 		0.585
(1.00) 		0.327
(0.908) 		0.23
(0.886) 		1
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.933
(1.00)
TP53 5 (14%) 30 0.686
(1.00) 		1
(1.00) 		0.521
(1.00) 		0.756
(1.00) 		0.867
(1.00) 		0.984
(1.00) 		1
(1.00) 		0.854
(1.00) 		1
(1.00) 		0.733
(1.00)
ARID1A 5 (14%) 30 1
(1.00) 		0.592
(1.00) 		0.522
(1.00) 		0.209
(0.886) 		0.109
(0.88) 		0.649
(1.00) 		1
(1.00) 		0.151
(0.88) 		0.349
(0.952) 		0.29
(0.908)
DDHD1 4 (11%) 31 0.449
(0.996) 		0.656
(1.00) 		0.472
(0.996) 		0.468
(0.996) 		0.871
(1.00) 		0.913
(1.00) 		0.646
(1.00) 		0.206
(0.886) 		0.469
(0.996) 		0.214
(0.886)
MUC2 7 (20%) 28 0.105
(0.88) 		0.654
(1.00) 		0.279
(0.908) 		0.398
(0.996) 		0.437
(0.996) 		0.151
(0.88) 		0.932
(1.00) 		0.201
(0.886) 		0.568
(1.00) 		0.853
(1.00)
IDH1 4 (11%) 31 0.282
(0.908) 		0.00223
(0.334) 		1
(1.00) 		0.585
(1.00) 		0.296
(0.908) 		0.448
(0.996) 		0.00569
(0.355) 		0.0386
(0.7) 		0.184
(0.886) 		0.0195
(0.418)
MUC21 3 (9%) 32 0.666
(1.00) 		0.767
(1.00) 		0.262
(0.908) 		0.0443
(0.7) 		1
(1.00) 		0.737
(1.00) 		1
(1.00) 		0.933
(1.00)
CLIP4 4 (11%) 31 0.815
(1.00) 		0.538
(1.00) 		0.647
(1.00) 		0.887
(1.00) 		0.798
(1.00) 		0.914
(1.00) 		0.905
(1.00) 		0.153
(0.88) 		1
(1.00) 		0.747
(1.00)
BAP1 6 (17%) 29 0.6
(1.00) 		0.732
(1.00) 		0.759
(1.00) 		0.589
(1.00) 		0.507
(1.00) 		0.412
(0.996) 		0.647
(1.00) 		0.444
(0.996) 		0.242
(0.908) 		0.282
(0.908)
CDC27 5 (14%) 30 0.905
(1.00) 		0.834
(1.00) 		0.322
(0.908) 		0.0677
(0.847) 		0.705
(1.00) 		0.427
(0.996) 		0.371
(0.977) 		0.148
(0.88) 		0.251
(0.908) 		0.102
(0.88)
FAM35A 3 (9%) 32 0.279
(0.908) 		1
(1.00) 		1
(1.00) 		0.793
(1.00) 		0.618
(1.00) 		0.693
(1.00) 		0.197
(0.886) 		0.0163
(0.418)
PAXIP1 4 (11%) 31 0.164
(0.88) 		0.814
(1.00) 		1
(1.00) 		0.772
(1.00) 		0.478
(0.996) 		0.3
(0.908) 		0.645
(1.00) 		0.475
(0.996) 		0.0779
(0.88) 		0.398
(0.996)
'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
PBRM1 MUTATED 2 2 3 1
PBRM1 WILD-TYPE 12 6 4 5
'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.88

Table S2.  Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
PBRM1 MUTATED 1 2 5
PBRM1 WILD-TYPE 13 7 7
'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S3.  Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
PBRM1 MUTATED 2 1 3
PBRM1 WILD-TYPE 8 7 8
'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 0.89

Table S4.  Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
PBRM1 MUTATED 2 1 3 0
PBRM1 WILD-TYPE 4 6 5 8
'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.88

Table S5.  Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
PBRM1 MUTATED 0 0 1 4 2 1
PBRM1 WILD-TYPE 6 3 4 2 7 5
'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 0.91

Table S6.  Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
PBRM1 MUTATED 0 0 3 2 2 1 0
PBRM1 WILD-TYPE 4 5 2 7 3 4 2
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
PBRM1 MUTATED 1 1 3 3
PBRM1 WILD-TYPE 9 4 7 7
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 0.89

Table S8.  Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
PBRM1 MUTATED 0 3 2 1 2 0
PBRM1 WILD-TYPE 8 7 2 3 3 4
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.563 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
PBRM1 MUTATED 1 0 3 2 2
PBRM1 WILD-TYPE 7 5 4 5 6
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S10.  Gene #1: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
PBRM1 MUTATED 0 3 3 1 1
PBRM1 WILD-TYPE 6 4 6 6 5
'HLA-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.97

Table S11.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
HLA-B MUTATED 2 0 1 2
HLA-B WILD-TYPE 12 8 6 4
'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.42

Table S12.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
HLA-B MUTATED 1 4 0
HLA-B WILD-TYPE 13 5 12

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

'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
HLA-B MUTATED 1 1 3
HLA-B WILD-TYPE 9 7 8
'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
HLA-B MUTATED 0 1 1 3
HLA-B WILD-TYPE 6 6 7 5
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.88

Table S15.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
HLA-B MUTATED 0 0 0 1 4 0
HLA-B WILD-TYPE 6 3 5 5 5 6
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.184 (Fisher's exact test), Q value = 0.89

Table S16.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
HLA-B MUTATED 0 0 0 4 1 0 0
HLA-B WILD-TYPE 4 5 5 5 4 5 2
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0071 (Fisher's exact test), Q value = 0.35

Table S17.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
HLA-B MUTATED 0 3 0 2
HLA-B WILD-TYPE 10 2 10 8

Figure S2.  Get High-res Image Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0178 (Fisher's exact test), Q value = 0.42

Table S18.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
HLA-B MUTATED 0 0 0 2 1 2
HLA-B WILD-TYPE 8 10 4 2 4 2

Figure S3.  Get High-res Image Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
HLA-B MUTATED 0 1 1 1 2
HLA-B WILD-TYPE 8 4 6 6 6
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0563 (Fisher's exact test), Q value = 0.77

Table S20.  Gene #2: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
HLA-B MUTATED 0 1 0 1 3
HLA-B WILD-TYPE 6 6 9 6 3
'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.88

Table S21.  Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
MLL3 MUTATED 1 1 2 3
MLL3 WILD-TYPE 13 7 5 3
'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 0.91

Table S22.  Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
MLL3 MUTATED 1 3 3
MLL3 WILD-TYPE 13 6 9
'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.91

Table S23.  Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
MLL3 MUTATED 1 1 4
MLL3 WILD-TYPE 9 7 7
'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S24.  Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
MLL3 MUTATED 1 1 2 2
MLL3 WILD-TYPE 5 6 6 6
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S25.  Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
MLL3 MUTATED 1 1 1 2 1 1
MLL3 WILD-TYPE 5 2 4 4 8 5
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.979 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
MLL3 MUTATED 1 1 1 1 2 1 0
MLL3 WILD-TYPE 3 4 4 8 3 4 2
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.88

Table S27.  Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
MLL3 MUTATED 4 1 0 2
MLL3 WILD-TYPE 6 4 10 8
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
MLL3 MUTATED 2 1 1 1 2 0
MLL3 WILD-TYPE 6 9 3 3 3 4
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.819 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
MLL3 MUTATED 3 1 1 1 1
MLL3 WILD-TYPE 5 4 6 6 7
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 0.89

Table S30.  Gene #3: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
MLL3 MUTATED 3 2 1 0 1
MLL3 WILD-TYPE 3 5 8 7 5
'FTH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.88

Table S31.  Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
FTH1 MUTATED 0 1 2 0
FTH1 WILD-TYPE 14 7 5 6
'FTH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.7

Table S32.  Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
FTH1 MUTATED 0 0 3
FTH1 WILD-TYPE 14 9 9

Figure S4.  Get High-res Image Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FTH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0924 (Fisher's exact test), Q value = 0.88

Table S33.  Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
FTH1 MUTATED 0 0 3
FTH1 WILD-TYPE 10 8 8
'FTH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
FTH1 MUTATED 0 0 1 2
FTH1 WILD-TYPE 6 7 7 6
'FTH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.91

Table S35.  Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
FTH1 MUTATED 0 1 0 1 0 1
FTH1 WILD-TYPE 6 2 5 5 9 5
'FTH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 0.89

Table S36.  Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
FTH1 MUTATED 0 0 1 0 0 1 1
FTH1 WILD-TYPE 4 5 4 9 5 4 1
'FTH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S37.  Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
FTH1 MUTATED 1 0 1 1
FTH1 WILD-TYPE 9 5 9 9
'FTH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.661 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
FTH1 MUTATED 0 1 1 0 1 0
FTH1 WILD-TYPE 8 9 3 4 4 4
'FTH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S39.  Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
FTH1 MUTATED 1 0 0 1 1
FTH1 WILD-TYPE 7 5 7 6 7
'FTH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S40.  Gene #4: 'FTH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
FTH1 MUTATED 1 0 1 1 0
FTH1 WILD-TYPE 5 7 8 6 6
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S41.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
TP53 MUTATED 2 1 2 0
TP53 WILD-TYPE 12 7 5 6
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S42.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
TP53 MUTATED 2 1 2
TP53 WILD-TYPE 12 8 10
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.521 (Fisher's exact test), Q value = 1

Table S43.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
TP53 MUTATED 2 0 2
TP53 WILD-TYPE 8 8 9
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S44.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
TP53 MUTATED 1 0 1 2
TP53 WILD-TYPE 5 7 7 6
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S45.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
TP53 MUTATED 2 0 0 1 1 1
TP53 WILD-TYPE 4 3 5 5 8 5
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.984 (Fisher's exact test), Q value = 1

Table S46.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
TP53 MUTATED 1 0 1 1 1 1 0
TP53 WILD-TYPE 3 5 4 8 4 4 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S47.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
TP53 MUTATED 1 1 2 1
TP53 WILD-TYPE 9 4 8 9
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S48.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
TP53 MUTATED 1 2 1 1 0 0
TP53 WILD-TYPE 7 8 3 3 5 4
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S49.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
TP53 MUTATED 1 1 1 1 1
TP53 WILD-TYPE 7 4 6 6 7
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
TP53 MUTATED 1 2 1 0 1
TP53 WILD-TYPE 5 5 8 7 5
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S51.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
ARID1A MUTATED 2 1 1 1
ARID1A WILD-TYPE 12 7 6 5
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S52.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
ARID1A MUTATED 1 2 2
ARID1A WILD-TYPE 13 7 10
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
ARID1A MUTATED 2 0 2
ARID1A WILD-TYPE 8 8 9
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 0.89

Table S54.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
ARID1A MUTATED 0 0 3 1
ARID1A WILD-TYPE 6 7 5 7
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.88

Table S55.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
ARID1A MUTATED 0 0 0 3 2 0
ARID1A WILD-TYPE 6 3 5 3 7 6
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.649 (Fisher's exact test), Q value = 1

Table S56.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
ARID1A MUTATED 0 0 2 2 1 0 0
ARID1A WILD-TYPE 4 5 3 7 4 5 2
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S57.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
ARID1A MUTATED 1 1 1 2
ARID1A WILD-TYPE 9 4 9 8
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 0.88

Table S58.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
ARID1A MUTATED 0 1 2 1 0 1
ARID1A WILD-TYPE 8 9 2 3 5 3
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.349 (Fisher's exact test), Q value = 0.95

Table S59.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
ARID1A MUTATED 1 0 0 1 3
ARID1A WILD-TYPE 7 5 7 6 5
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.91

Table S60.  Gene #6: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
ARID1A MUTATED 0 0 1 2 2
ARID1A WILD-TYPE 6 7 8 5 4
'DDHD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
DDHD1 MUTATED 1 1 2 0
DDHD1 WILD-TYPE 13 7 5 6
'DDHD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.656 (Fisher's exact test), Q value = 1

Table S62.  Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
DDHD1 MUTATED 1 2 1
DDHD1 WILD-TYPE 13 7 11
'DDHD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 1

Table S63.  Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
DDHD1 MUTATED 0 1 2
DDHD1 WILD-TYPE 10 7 9
'DDHD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 1

Table S64.  Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
DDHD1 MUTATED 0 1 0 2
DDHD1 WILD-TYPE 6 6 8 6
'DDHD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.871 (Fisher's exact test), Q value = 1

Table S65.  Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
DDHD1 MUTATED 0 0 0 1 2 1
DDHD1 WILD-TYPE 6 3 5 5 7 5
'DDHD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S66.  Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
DDHD1 MUTATED 0 0 1 2 0 1 0
DDHD1 WILD-TYPE 4 5 4 7 5 4 2
'DDHD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S67.  Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
DDHD1 MUTATED 2 1 0 1
DDHD1 WILD-TYPE 8 4 10 9
'DDHD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.89

Table S68.  Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
DDHD1 MUTATED 0 0 1 1 1 1
DDHD1 WILD-TYPE 8 10 3 3 4 3
'DDHD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S69.  Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
DDHD1 MUTATED 2 1 0 0 1
DDHD1 WILD-TYPE 6 4 7 7 7
'DDHD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.214 (Fisher's exact test), Q value = 0.89

Table S70.  Gene #7: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
DDHD1 MUTATED 1 0 0 1 2
DDHD1 WILD-TYPE 5 7 9 6 4
'MUC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.88

Table S71.  Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
MUC2 MUTATED 5 0 2 0
MUC2 WILD-TYPE 9 8 5 6
'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.654 (Fisher's exact test), Q value = 1

Table S72.  Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
MUC2 MUTATED 4 1 2
MUC2 WILD-TYPE 10 8 10
'MUC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.91

Table S73.  Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
MUC2 MUTATED 3 0 1
MUC2 WILD-TYPE 7 8 10
'MUC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
MUC2 MUTATED 2 0 1 1
MUC2 WILD-TYPE 4 7 7 7
'MUC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.437 (Fisher's exact test), Q value = 1

Table S75.  Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
MUC2 MUTATED 3 0 1 1 2 0
MUC2 WILD-TYPE 3 3 4 5 7 6
'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 0.88

Table S76.  Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
MUC2 MUTATED 3 1 0 2 1 0 0
MUC2 WILD-TYPE 1 4 5 7 4 5 2
'MUC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S77.  Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
MUC2 MUTATED 3 1 1 2
MUC2 WILD-TYPE 7 4 9 8
'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.89

Table S78.  Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
MUC2 MUTATED 4 1 1 1 0 0
MUC2 WILD-TYPE 4 9 3 3 5 4
'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
MUC2 MUTATED 3 1 1 0 2
MUC2 WILD-TYPE 5 4 6 7 6
'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S80.  Gene #8: 'MUC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
MUC2 MUTATED 2 1 1 2 1
MUC2 WILD-TYPE 4 6 8 5 5
'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.91

Table S81.  Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
IDH1 MUTATED 1 0 2 1
IDH1 WILD-TYPE 13 8 5 5
'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.33

Table S82.  Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
IDH1 MUTATED 0 4 0
IDH1 WILD-TYPE 14 5 12

Figure S5.  Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S83.  Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
IDH1 MUTATED 1 1 2
IDH1 WILD-TYPE 9 7 9
'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S84.  Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
IDH1 MUTATED 1 1 0 2
IDH1 WILD-TYPE 5 6 8 6
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.91

Table S85.  Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
IDH1 MUTATED 0 0 0 0 3 1
IDH1 WILD-TYPE 6 3 5 6 6 5
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.448 (Fisher's exact test), Q value = 1

Table S86.  Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
IDH1 MUTATED 0 0 0 3 0 1 0
IDH1 WILD-TYPE 4 5 5 6 5 4 2
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.35

Table S87.  Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
IDH1 MUTATED 0 3 0 1
IDH1 WILD-TYPE 10 2 10 9

Figure S6.  Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.7

Table S88.  Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
IDH1 MUTATED 0 0 0 2 1 1
IDH1 WILD-TYPE 8 10 4 2 4 3

Figure S7.  Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.89

Table S89.  Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
IDH1 MUTATED 0 2 1 0 1
IDH1 WILD-TYPE 8 3 6 7 7
'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.42

Table S90.  Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
IDH1 MUTATED 0 0 0 1 3
IDH1 WILD-TYPE 6 7 9 6 3

Figure S8.  Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MUC21 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.666 (Fisher's exact test), Q value = 1

Table S91.  Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
MUC21 MUTATED 2 0 1 0
MUC21 WILD-TYPE 12 8 6 6
'MUC21 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
MUC21 MUTATED 2 0 1
MUC21 WILD-TYPE 12 9 11
'MUC21 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.91

Table S93.  Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
MUC21 MUTATED 2 0 0 1 0 0
MUC21 WILD-TYPE 4 3 5 5 9 6
'MUC21 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0443 (Fisher's exact test), Q value = 0.7

Table S94.  Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
MUC21 MUTATED 2 0 1 0 0 0 0
MUC21 WILD-TYPE 2 5 4 9 5 5 2

Figure S9.  Get High-res Image Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MUC21 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S95.  Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
MUC21 MUTATED 1 0 1 1
MUC21 WILD-TYPE 9 5 9 9
'MUC21 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S96.  Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
MUC21 MUTATED 2 1 0 0 0 0
MUC21 WILD-TYPE 6 9 4 4 5 4
'MUC21 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S97.  Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
MUC21 MUTATED 1 0 0 1 1
MUC21 WILD-TYPE 7 5 7 6 7
'MUC21 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S98.  Gene #10: 'MUC21 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
MUC21 MUTATED 1 0 1 1 0
MUC21 WILD-TYPE 5 7 8 6 6
'CLIP4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.815 (Fisher's exact test), Q value = 1

Table S99.  Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
CLIP4 MUTATED 2 1 0 1
CLIP4 WILD-TYPE 12 7 7 5
'CLIP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S100.  Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
CLIP4 MUTATED 2 0 2
CLIP4 WILD-TYPE 12 9 10
'CLIP4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 1

Table S101.  Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
CLIP4 MUTATED 1 2 1
CLIP4 WILD-TYPE 9 6 10
'CLIP4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S102.  Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
CLIP4 MUTATED 0 1 1 2
CLIP4 WILD-TYPE 6 6 7 6
'CLIP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S103.  Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
CLIP4 MUTATED 0 0 1 0 2 1
CLIP4 WILD-TYPE 6 3 4 6 7 5
'CLIP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.914 (Fisher's exact test), Q value = 1

Table S104.  Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
CLIP4 MUTATED 0 0 1 2 0 1 0
CLIP4 WILD-TYPE 4 5 4 7 5 4 2
'CLIP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S105.  Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
CLIP4 MUTATED 1 0 2 1
CLIP4 WILD-TYPE 9 5 8 9
'CLIP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.153 (Fisher's exact test), Q value = 0.88

Table S106.  Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
CLIP4 MUTATED 0 2 0 0 0 2
CLIP4 WILD-TYPE 8 8 4 4 5 2
'CLIP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S107.  Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
CLIP4 MUTATED 1 0 1 1 1
CLIP4 WILD-TYPE 7 5 6 6 7
'CLIP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.747 (Fisher's exact test), Q value = 1

Table S108.  Gene #11: 'CLIP4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
CLIP4 MUTATED 0 0 2 1 1
CLIP4 WILD-TYPE 6 7 7 6 5
'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.6 (Fisher's exact test), Q value = 1

Table S109.  Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
BAP1 MUTATED 2 2 2 0
BAP1 WILD-TYPE 12 6 5 6
'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S110.  Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
BAP1 MUTATED 2 1 3
BAP1 WILD-TYPE 12 8 9
'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S111.  Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
BAP1 MUTATED 1 0 2
BAP1 WILD-TYPE 9 8 9
'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S112.  Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
BAP1 MUTATED 0 0 1 2
BAP1 WILD-TYPE 6 7 7 6
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 1

Table S113.  Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
BAP1 MUTATED 0 1 1 2 2 0
BAP1 WILD-TYPE 6 2 4 4 7 6
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S114.  Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
BAP1 MUTATED 0 1 2 2 0 0 1
BAP1 WILD-TYPE 4 4 3 7 5 5 1
'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 1

Table S115.  Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
BAP1 MUTATED 1 0 2 3
BAP1 WILD-TYPE 9 5 8 7
'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S116.  Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
BAP1 MUTATED 1 2 2 0 0 1
BAP1 WILD-TYPE 7 8 2 4 5 3
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.91

Table S117.  Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
BAP1 MUTATED 0 0 1 2 3
BAP1 WILD-TYPE 8 5 6 5 5
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 0.91

Table S118.  Gene #12: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
BAP1 MUTATED 0 1 2 3 0
BAP1 WILD-TYPE 6 6 7 4 6
'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S119.  Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
CDC27 MUTATED 3 1 1 0
CDC27 WILD-TYPE 11 7 6 6
'CDC27 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S120.  Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
CDC27 MUTATED 2 2 1
CDC27 WILD-TYPE 12 7 11
'CDC27 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 0.91

Table S121.  Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
CDC27 MUTATED 3 0 2
CDC27 WILD-TYPE 7 8 9
'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0677 (Fisher's exact test), Q value = 0.85

Table S122.  Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
CDC27 MUTATED 2 0 0 3
CDC27 WILD-TYPE 4 7 8 5
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S123.  Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
CDC27 MUTATED 1 1 0 0 2 1
CDC27 WILD-TYPE 5 2 5 6 7 5
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.427 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
CDC27 MUTATED 1 0 0 2 0 1 1
CDC27 WILD-TYPE 3 5 5 7 5 4 1
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.98

Table S125.  Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
CDC27 MUTATED 1 1 0 3
CDC27 WILD-TYPE 9 4 10 7
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.88

Table S126.  Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
CDC27 MUTATED 1 0 1 0 1 2
CDC27 WILD-TYPE 7 10 3 4 4 2
'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.251 (Fisher's exact test), Q value = 0.91

Table S127.  Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
CDC27 MUTATED 1 1 0 0 3
CDC27 WILD-TYPE 7 4 7 7 5
'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.102 (Fisher's exact test), Q value = 0.88

Table S128.  Gene #13: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
CDC27 MUTATED 1 0 0 3 1
CDC27 WILD-TYPE 5 7 9 4 5
'FAM35A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.91

Table S129.  Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
FAM35A MUTATED 0 1 1 1
FAM35A WILD-TYPE 14 7 6 5
'FAM35A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S130.  Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
FAM35A MUTATED 1 1 1
FAM35A WILD-TYPE 13 8 11
'FAM35A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S131.  Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
FAM35A MUTATED 1 0 0 1 1 0
FAM35A WILD-TYPE 5 3 5 5 8 6
'FAM35A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S132.  Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
FAM35A MUTATED 1 0 0 1 1 0 0
FAM35A WILD-TYPE 3 5 5 8 4 5 2
'FAM35A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 1

Table S133.  Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
FAM35A MUTATED 0 0 2 1
FAM35A WILD-TYPE 10 5 8 9
'FAM35A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S134.  Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
FAM35A MUTATED 0 2 0 0 1 0
FAM35A WILD-TYPE 8 8 4 4 4 4
'FAM35A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.89

Table S135.  Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
FAM35A MUTATED 0 0 2 1 0
FAM35A WILD-TYPE 8 5 5 6 8
'FAM35A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.42

Table S136.  Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
FAM35A MUTATED 0 3 0 0 0
FAM35A WILD-TYPE 6 4 9 7 6

Figure S10.  Get High-res Image Gene #14: 'FAM35A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PAXIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.88

Table S137.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 14 8 7 6
PAXIP1 MUTATED 0 2 1 1
PAXIP1 WILD-TYPE 14 6 6 5
'PAXIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.814 (Fisher's exact test), Q value = 1

Table S138.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 9 12
PAXIP1 MUTATED 1 1 2
PAXIP1 WILD-TYPE 13 8 10
'PAXIP1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S139.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 10 8 11
PAXIP1 MUTATED 1 1 1
PAXIP1 WILD-TYPE 9 7 10
'PAXIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S140.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
PAXIP1 MUTATED 1 1 0 1
PAXIP1 WILD-TYPE 5 6 8 7
'PAXIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S141.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 6 3 5 6 9 6
PAXIP1 MUTATED 1 1 0 0 2 0
PAXIP1 WILD-TYPE 5 2 5 6 7 6
'PAXIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.3 (Fisher's exact test), Q value = 0.91

Table S142.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 4 5 5 9 5 5 2
PAXIP1 MUTATED 1 0 0 2 0 0 1
PAXIP1 WILD-TYPE 3 5 5 7 5 5 1
'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S143.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 5 10 10
PAXIP1 MUTATED 0 1 2 1
PAXIP1 WILD-TYPE 10 4 8 9
'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.475 (Fisher's exact test), Q value = 1

Table S144.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 10 4 4 5 4
PAXIP1 MUTATED 0 2 1 1 0 0
PAXIP1 WILD-TYPE 8 8 3 3 5 4
'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0779 (Fisher's exact test), Q value = 0.88

Table S145.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 8 5 7 7 8
PAXIP1 MUTATED 0 0 3 0 1
PAXIP1 WILD-TYPE 8 5 4 7 7
'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 6 7 9 7 6
PAXIP1 MUTATED 0 2 0 1 1
PAXIP1 WILD-TYPE 6 5 9 6 5
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CHOL-TP/22563790/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/22541054/CHOL-TP.transferedmergedcluster.txt

  • Number of patients = 35

  • Number of significantly mutated genes = 15

  • Number of Molecular subtypes = 10

  • 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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