Correlation between gene mutation status and molecular subtypes
Cholangiocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C12806M0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C12806M0
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 16 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 16 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
BAP1 8 (23%) 27 0.424
(1.00) 		0.874
(1.00) 		0.622
(1.00) 		0.719
(1.00) 		0.347
(1.00) 		0.607
(1.00) 		0.714
(1.00) 		0.852
(1.00) 		0.7
(1.00) 		0.818
(1.00)
PBRM1 8 (23%) 27 0.105
(0.868) 		0.0126
(0.267) 		0.362
(1.00) 		0.232
(1.00) 		0.307
(1.00) 		0.319
(1.00) 		0.851
(1.00) 		0.226
(1.00) 		1
(1.00) 		0.358
(1.00)
MLL3 7 (20%) 28 0.207
(1.00) 		0.326
(1.00) 		0.362
(1.00) 		1
(1.00) 		0.871
(1.00) 		0.979
(1.00) 		0.243
(1.00) 		0.738
(1.00) 		0.43
(1.00) 		0.615
(1.00)
TP53 5 (14%) 30 0.642
(1.00) 		1
(1.00) 		0.268
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.984
(1.00) 		0.923
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.894
(1.00)
HLA-B 5 (14%) 30 1
(1.00) 		0.0188
(0.307) 		0.622
(1.00) 		0.437
(1.00) 		0.0133
(0.267) 		0.183
(1.00) 		0.00743
(0.267) 		0.0192
(0.307) 		0.631
(1.00) 		0.442
(1.00)
FTH1 3 (9%) 32 0.582
(1.00) 		0.1
(0.868) 		0.268
(1.00) 		0.59
(1.00) 		0.0996
(0.868) 		0.231
(1.00) 		0.849
(1.00) 		0.661
(1.00) 		0.565
(1.00) 		1
(1.00)
ARID1A 5 (14%) 30 0.642
(1.00) 		0.606
(1.00) 		0.268
(1.00) 		0.207
(1.00) 		0.223
(1.00) 		0.648
(1.00) 		1
(1.00) 		0.15
(1.00) 		0.631
(1.00) 		0.624
(1.00)
DDHD1 4 (11%) 31 0.312
(1.00) 		1
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.338
(1.00) 		0.915
(1.00) 		0.595
(1.00) 		0.204
(1.00) 		0.292
(1.00) 		0.642
(1.00)
IDH1 4 (11%) 31 1
(1.00) 		0.00249
(0.267) 		0.622
(1.00) 		0.586
(1.00) 		0.0722
(0.739) 		0.45
(1.00) 		0.0054
(0.267) 		0.039
(0.567) 		1
(1.00) 		0.392
(1.00)
MUC2 7 (20%) 28 0.415
(1.00) 		0.574
(1.00) 		0.622
(1.00) 		0.398
(1.00) 		0.275
(1.00) 		0.152
(1.00) 		0.684
(1.00) 		0.202
(1.00) 		0.43
(1.00) 		0.744
(1.00)
MUC21 3 (9%) 32 1
(1.00) 		0.767
(1.00) 		1
(1.00) 		0.602
(1.00) 		0.0442
(0.589) 		1
(1.00) 		0.737
(1.00) 		0.565
(1.00) 		1
(1.00)
PAXIP1 4 (11%) 31 0.608
(1.00) 		1
(1.00) 		0.539
(1.00) 		0.775
(1.00) 		0.653
(1.00) 		0.299
(1.00) 		0.598
(1.00) 		0.472
(1.00) 		0.619
(1.00) 		0.108
(0.868)
EPHA2 4 (11%) 31 1
(1.00) 		0.071
(0.739) 		0.622
(1.00) 		0.486
(1.00) 		0.653
(1.00) 		0.912
(1.00) 		0.00582
(0.267) 		0.329
(1.00) 		1
(1.00) 		0.975
(1.00)
OTOP1 4 (11%) 31 1
(1.00) 		1
(1.00) 		0.539
(1.00) 		0.0739
(0.739) 		1
(1.00) 		0.601
(1.00) 		0.81
(1.00) 		0.533
(1.00) 		0.619
(1.00) 		0.428
(1.00)
CDC27 5 (14%) 30 0.347
(1.00) 		0.831
(1.00) 		1
(1.00) 		0.0665
(0.739) 		0.833
(1.00) 		0.427
(1.00) 		0.349
(1.00) 		0.147
(1.00) 		0.00925
(0.267) 		0.232
(1.00)
FAM35A 3 (9%) 32 0.582
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.797
(1.00) 		0.68
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.0107
(0.267)
'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
BAP1 MUTATED 3 5
BAP1 WILD-TYPE 16 11
'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.874 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
BAP1 MUTATED 2 2 4
BAP1 WILD-TYPE 11 7 9
'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
BAP1 MUTATED 1 4
BAP1 WILD-TYPE 10 14
'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: '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 1 2 2
BAP1 WILD-TYPE 6 6 6 6
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 14 9
BAP1 MUTATED 1 4 3
BAP1 WILD-TYPE 11 10 6
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.607 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: '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 3 1 0 1
BAP1 WILD-TYPE 4 4 3 6 4 5 1
'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
BAP1 MUTATED 1 1 2 4
BAP1 WILD-TYPE 8 4 8 7
'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S8.  Gene #1: '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 1 1 1
BAP1 WILD-TYPE 7 8 2 3 4 3
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
BAP1 MUTATED 4 4
BAP1 WILD-TYPE 11 16
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S10.  Gene #1: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
BAP1 MUTATED 0 1 1 3 1 1 1
BAP1 WILD-TYPE 6 2 2 6 4 4 3
'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.87

Table S11.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
PBRM1 MUTATED 2 6
PBRM1 WILD-TYPE 17 10
'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.27

Table S12.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
PBRM1 MUTATED 0 2 6
PBRM1 WILD-TYPE 13 7 7

Figure S1.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
PBRM1 MUTATED 1 5
PBRM1 WILD-TYPE 10 13
'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: '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 = 0.307 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 14 9
PBRM1 MUTATED 1 5 2
PBRM1 WILD-TYPE 11 9 7
'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: '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 = 0.851 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
PBRM1 MUTATED 1 1 3 3
PBRM1 WILD-TYPE 8 4 7 8
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S18.  Gene #2: '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 = 1 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
PBRM1 MUTATED 3 5
PBRM1 WILD-TYPE 12 15
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S20.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
PBRM1 MUTATED 0 1 0 2 3 1 1
PBRM1 WILD-TYPE 6 2 3 7 2 4 3
'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2
ALL 19 16
MLL3 MUTATED 2 5
MLL3 WILD-TYPE 17 11
'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
MLL3 MUTATED 1 3 3
MLL3 WILD-TYPE 12 6 10
'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2
ALL 11 18
MLL3 MUTATED 1 5
MLL3 WILD-TYPE 10 13
'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 = 0.871 (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
ALL 12 14 9
MLL3 MUTATED 3 3 1
MLL3 WILD-TYPE 9 11 8
'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 = 0.243 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
MLL3 MUTATED 3 1 0 3
MLL3 WILD-TYPE 6 4 10 8
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.738 (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 = 0.43 (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
ALL 15 20
MLL3 MUTATED 4 3
MLL3 WILD-TYPE 11 17
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.615 (Fisher's exact test), Q value = 1

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 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
MLL3 MUTATED 3 0 0 1 1 1 1
MLL3 WILD-TYPE 3 3 3 8 4 4 3
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
TP53 MUTATED 2 3
TP53 WILD-TYPE 17 13
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S32.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
TP53 MUTATED 2 1 2
TP53 WILD-TYPE 11 8 11
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
TP53 MUTATED 0 4
TP53 WILD-TYPE 11 14
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: '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 = 1 (Fisher's exact test), Q value = 1

Table S35.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

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

Table S36.  Gene #4: '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 = 0.923 (Fisher's exact test), Q value = 1

Table S37.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
TP53 MUTATED 1 1 2 1
TP53 WILD-TYPE 8 4 8 10
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.855 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: '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 S39.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
TP53 MUTATED 2 3
TP53 WILD-TYPE 13 17
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S40.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
TP53 MUTATED 1 1 0 1 0 1 1
TP53 WILD-TYPE 5 2 3 8 5 4 3
'HLA-B MUTATION STATUS' versus 'CN_CNMF'

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

Table S41.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
HLA-B MUTATED 3 2
HLA-B WILD-TYPE 16 14
'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.31

Table S42.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S2.  Get High-res Image Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S43.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
HLA-B MUTATED 1 4
HLA-B WILD-TYPE 10 14
'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S44.  Gene #5: '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 = 0.0133 (Fisher's exact test), Q value = 0.27

Table S45.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

Figure S3.  Get High-res Image Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 1

Table S46.  Gene #5: '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 = 0.00743 (Fisher's exact test), Q value = 0.27

Table S47.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
HLA-B MUTATED 0 3 0 2
HLA-B WILD-TYPE 9 2 10 9

Figure S4.  Get High-res Image Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.31

Table S48.  Gene #5: '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 S5.  Get High-res Image Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
HLA-B MUTATED 3 2
HLA-B WILD-TYPE 12 18
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
HLA-B MUTATED 0 0 0 2 0 2 1
HLA-B WILD-TYPE 6 3 3 7 5 3 3
'FTH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 1

Table S51.  Gene #6: 'FTH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
FTH1 MUTATED 1 2
FTH1 WILD-TYPE 18 14
'FTH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.1 (Fisher's exact test), Q value = 0.87

Table S52.  Gene #6: 'FTH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
FTH1 MUTATED 0 0 3
FTH1 WILD-TYPE 13 9 10
'FTH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'FTH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
FTH1 MUTATED 0 3
FTH1 WILD-TYPE 11 15
'FTH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: '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 = 0.0996 (Fisher's exact test), Q value = 0.87

Table S55.  Gene #6: 'FTH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 14 9
FTH1 MUTATED 0 3 0
FTH1 WILD-TYPE 12 11 9
'FTH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 1

Table S56.  Gene #6: '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 = 0.849 (Fisher's exact test), Q value = 1

Table S57.  Gene #6: 'FTH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
FTH1 MUTATED 0 0 1 2
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 S58.  Gene #6: '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 = 0.565 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'FTH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
FTH1 MUTATED 2 1
FTH1 WILD-TYPE 13 19
'FTH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S60.  Gene #6: 'FTH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
FTH1 MUTATED 1 0 0 1 1 0 0
FTH1 WILD-TYPE 5 3 3 8 4 5 4
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
ARID1A MUTATED 2 3
ARID1A WILD-TYPE 17 13
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S62.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
ARID1A MUTATED 1 1 3
ARID1A WILD-TYPE 12 8 10
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S63.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
ARID1A MUTATED 0 4
ARID1A WILD-TYPE 11 14
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 1

Table S64.  Gene #7: '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 = 0.223 (Fisher's exact test), Q value = 1

Table S65.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 14 9
ARID1A MUTATED 0 3 2
ARID1A WILD-TYPE 12 11 7
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S66.  Gene #7: '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 S67.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
ARID1A MUTATED 1 1 1 2
ARID1A WILD-TYPE 8 4 9 9
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S68.  Gene #7: '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 = 0.631 (Fisher's exact test), Q value = 1

Table S69.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
ARID1A MUTATED 3 2
ARID1A WILD-TYPE 12 18
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.624 (Fisher's exact test), Q value = 1

Table S70.  Gene #7: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
ARID1A MUTATED 0 0 0 3 1 1 0
ARID1A WILD-TYPE 6 3 3 6 4 4 4
'DDHD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 1

Table S71.  Gene #8: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
DDHD1 MUTATED 1 3
DDHD1 WILD-TYPE 18 13
'DDHD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S72.  Gene #8: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
DDHD1 MUTATED 1 1 2
DDHD1 WILD-TYPE 12 8 11
'DDHD1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S73.  Gene #8: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
DDHD1 MUTATED 1 2
DDHD1 WILD-TYPE 10 16
'DDHD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: '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 = 0.338 (Fisher's exact test), Q value = 1

Table S75.  Gene #8: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 14 9
DDHD1 MUTATED 0 2 2
DDHD1 WILD-TYPE 12 12 7
'DDHD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S76.  Gene #8: '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 = 0.595 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
DDHD1 MUTATED 1 1 0 2
DDHD1 WILD-TYPE 8 4 10 9
'DDHD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 1

Table S78.  Gene #8: '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 = 0.292 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
DDHD1 MUTATED 3 1
DDHD1 WILD-TYPE 12 19
'DDHD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S80.  Gene #8: 'DDHD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
DDHD1 MUTATED 1 0 0 1 0 2 0
DDHD1 WILD-TYPE 5 3 3 8 5 3 4
'IDH1 MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2
ALL 19 16
IDH1 MUTATED 2 2
IDH1 WILD-TYPE 17 14
'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00249 (Fisher's exact test), Q value = 0.27

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
IDH1 MUTATED 0 4 0
IDH1 WILD-TYPE 13 5 13

Figure S6.  Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.622 (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
ALL 11 18
IDH1 MUTATED 2 2
IDH1 WILD-TYPE 9 16
'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.586 (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 = 0.0722 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 14 9
IDH1 MUTATED 0 1 3
IDH1 WILD-TYPE 12 13 6
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.45 (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 = 0.0054 (Fisher's exact test), Q value = 0.27

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
IDH1 MUTATED 0 3 0 1
IDH1 WILD-TYPE 9 2 10 10

Figure S7.  Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.039 (Fisher's exact test), Q value = 0.57

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 S8.  Get High-res Image Gene #9: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2
ALL 15 20
IDH1 MUTATED 2 2
IDH1 WILD-TYPE 13 18
'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 1

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 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
IDH1 MUTATED 0 0 0 2 0 2 0
IDH1 WILD-TYPE 6 3 3 7 5 3 4
'MUC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.415 (Fisher's exact test), Q value = 1

Table S91.  Gene #10: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
MUC2 MUTATED 5 2
MUC2 WILD-TYPE 14 14
'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S92.  Gene #10: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
MUC2 MUTATED 4 1 2
MUC2 WILD-TYPE 9 8 11
'MUC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
MUC2 MUTATED 2 2
MUC2 WILD-TYPE 9 16
'MUC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S94.  Gene #10: '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 = 0.275 (Fisher's exact test), Q value = 1

Table S95.  Gene #10: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 14 9
MUC2 MUTATED 4 1 2
MUC2 WILD-TYPE 8 13 7
'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S96.  Gene #10: '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 = 0.684 (Fisher's exact test), Q value = 1

Table S97.  Gene #10: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
MUC2 MUTATED 3 1 1 2
MUC2 WILD-TYPE 6 4 9 9
'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 1

Table S98.  Gene #10: '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 = 0.43 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: 'MUC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
MUC2 MUTATED 4 3
MUC2 WILD-TYPE 11 17
'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S100.  Gene #10: 'MUC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
MUC2 MUTATED 2 1 1 2 0 1 0
MUC2 WILD-TYPE 4 2 2 7 5 4 4
'MUC21 MUTATION STATUS' versus 'CN_CNMF'

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

Table S101.  Gene #11: 'MUC21 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
MUC21 MUTATED 2 1
MUC21 WILD-TYPE 17 15
'MUC21 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S102.  Gene #11: 'MUC21 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
MUC21 MUTATED 2 0 1
MUC21 WILD-TYPE 11 9 12
'MUC21 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S103.  Gene #11: 'MUC21 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
MUC21 MUTATED 1 1
MUC21 WILD-TYPE 10 17
'MUC21 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S104.  Gene #11: 'MUC21 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 14 9
MUC21 MUTATED 2 1 0
MUC21 WILD-TYPE 10 13 9
'MUC21 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0442 (Fisher's exact test), Q value = 0.59

Table S105.  Gene #11: '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 #11: '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 S106.  Gene #11: 'MUC21 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
MUC21 MUTATED 1 0 1 1
MUC21 WILD-TYPE 8 5 9 10
'MUC21 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S107.  Gene #11: '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 = 0.565 (Fisher's exact test), Q value = 1

Table S108.  Gene #11: 'MUC21 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
MUC21 MUTATED 2 1
MUC21 WILD-TYPE 13 19
'MUC21 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S109.  Gene #11: 'MUC21 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
MUC21 MUTATED 1 0 0 1 1 0 0
MUC21 WILD-TYPE 5 3 3 8 4 5 4
'PAXIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S110.  Gene #12: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
PAXIP1 MUTATED 3 1
PAXIP1 WILD-TYPE 16 15
'PAXIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S111.  Gene #12: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
PAXIP1 MUTATED 1 1 2
PAXIP1 WILD-TYPE 12 8 11
'PAXIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S112.  Gene #12: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
PAXIP1 MUTATED 2 1
PAXIP1 WILD-TYPE 9 17
'PAXIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S113.  Gene #12: '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 = 0.653 (Fisher's exact test), Q value = 1

Table S114.  Gene #12: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 14 9
PAXIP1 MUTATED 1 1 2
PAXIP1 WILD-TYPE 11 13 7
'PAXIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.299 (Fisher's exact test), Q value = 1

Table S115.  Gene #12: '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 = 0.598 (Fisher's exact test), Q value = 1

Table S116.  Gene #12: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
PAXIP1 MUTATED 0 1 2 1
PAXIP1 WILD-TYPE 9 4 8 10
'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S117.  Gene #12: '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 = 0.619 (Fisher's exact test), Q value = 1

Table S118.  Gene #12: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
PAXIP1 MUTATED 1 3
PAXIP1 WILD-TYPE 14 17
'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 0.87

Table S119.  Gene #12: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
PAXIP1 MUTATED 0 2 0 1 0 1 0
PAXIP1 WILD-TYPE 6 1 3 8 5 4 4
'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S120.  Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
EPHA2 MUTATED 2 2
EPHA2 WILD-TYPE 17 14
'EPHA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.071 (Fisher's exact test), Q value = 0.74

Table S121.  Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
EPHA2 MUTATED 0 3 1
EPHA2 WILD-TYPE 13 6 12
'EPHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S122.  Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
EPHA2 MUTATED 2 2
EPHA2 WILD-TYPE 9 16
'EPHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.486 (Fisher's exact test), Q value = 1

Table S123.  Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
EPHA2 MUTATED 1 2 0 1
EPHA2 WILD-TYPE 5 5 8 7
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 14 9
EPHA2 MUTATED 1 1 2
EPHA2 WILD-TYPE 11 13 7
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S125.  Gene #13: 'EPHA2 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
EPHA2 MUTATED 0 1 0 2 1 0 0
EPHA2 WILD-TYPE 4 4 5 7 4 5 2
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00582 (Fisher's exact test), Q value = 0.27

Table S126.  Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
EPHA2 MUTATED 0 3 0 1
EPHA2 WILD-TYPE 9 2 10 10

Figure S10.  Get High-res Image Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 1

Table S127.  Gene #13: 'EPHA2 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
EPHA2 MUTATED 1 0 1 1 0 1
EPHA2 WILD-TYPE 7 10 3 3 5 3
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S128.  Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
EPHA2 MUTATED 2 2
EPHA2 WILD-TYPE 13 18
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S129.  Gene #13: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
EPHA2 MUTATED 1 0 0 2 0 1 0
EPHA2 WILD-TYPE 5 3 3 7 5 4 4
'OTOP1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S130.  Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
OTOP1 MUTATED 2 2
OTOP1 WILD-TYPE 17 14
'OTOP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S131.  Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
OTOP1 MUTATED 1 1 2
OTOP1 WILD-TYPE 12 8 11
'OTOP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 1

Table S132.  Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
OTOP1 MUTATED 2 1
OTOP1 WILD-TYPE 9 17
'OTOP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0739 (Fisher's exact test), Q value = 0.74

Table S133.  Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 6 7 8 8
OTOP1 MUTATED 2 1 0 0
OTOP1 WILD-TYPE 4 6 8 8
'OTOP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S134.  Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 12 14 9
OTOP1 MUTATED 1 2 1
OTOP1 WILD-TYPE 11 12 8
'OTOP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S135.  Gene #14: 'OTOP1 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
OTOP1 MUTATED 0 1 0 1 0 2 0
OTOP1 WILD-TYPE 4 4 5 8 5 3 2
'OTOP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.81 (Fisher's exact test), Q value = 1

Table S136.  Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
OTOP1 MUTATED 1 0 2 1
OTOP1 WILD-TYPE 8 5 8 10
'OTOP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S137.  Gene #14: 'OTOP1 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
OTOP1 MUTATED 1 1 0 0 2 0
OTOP1 WILD-TYPE 7 9 4 4 3 4
'OTOP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 1

Table S138.  Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
OTOP1 MUTATED 1 3
OTOP1 WILD-TYPE 14 17
'OTOP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 1

Table S139.  Gene #14: 'OTOP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
OTOP1 MUTATED 0 1 1 1 1 0 0
OTOP1 WILD-TYPE 6 2 2 8 4 5 4
'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 1

Table S140.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
CDC27 MUTATED 4 1
CDC27 WILD-TYPE 15 15
'CDC27 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.831 (Fisher's exact test), Q value = 1

Table S141.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 9 13
CDC27 MUTATED 2 2 1
CDC27 WILD-TYPE 11 7 12
'CDC27 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S142.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
CDC27 MUTATED 2 3
CDC27 WILD-TYPE 9 15
'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0665 (Fisher's exact test), Q value = 0.74

Table S143.  Gene #15: '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 = 0.833 (Fisher's exact test), Q value = 1

Table S144.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

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

Table S145.  Gene #15: '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 = 0.349 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
CDC27 MUTATED 1 1 0 3
CDC27 WILD-TYPE 8 4 10 8
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.147 (Fisher's exact test), Q value = 1

Table S147.  Gene #15: '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 = 0.00925 (Fisher's exact test), Q value = 0.27

Table S148.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
CDC27 MUTATED 5 0
CDC27 WILD-TYPE 10 20

Figure S11.  Get High-res Image Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S149.  Gene #15: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
CDC27 MUTATED 1 0 0 4 0 0 0
CDC27 WILD-TYPE 5 3 3 5 5 5 4
'FAM35A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 1

Table S150.  Gene #16: 'FAM35A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 16
FAM35A MUTATED 1 2
FAM35A WILD-TYPE 18 14
'FAM35A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S151.  Gene #16: 'FAM35A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

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

Table S152.  Gene #16: 'FAM35A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 11 18
FAM35A MUTATED 1 1
FAM35A WILD-TYPE 10 17
'FAM35A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S153.  Gene #16: 'FAM35A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

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

P value = 0.797 (Fisher's exact test), Q value = 1

Table S154.  Gene #16: '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 = 0.68 (Fisher's exact test), Q value = 1

Table S155.  Gene #16: 'FAM35A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 9 5 10 11
FAM35A MUTATED 0 0 2 1
FAM35A WILD-TYPE 9 5 8 10
'FAM35A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.692 (Fisher's exact test), Q value = 1

Table S156.  Gene #16: '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 = 1 (Fisher's exact test), Q value = 1

Table S157.  Gene #16: 'FAM35A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 15 20
FAM35A MUTATED 1 2
FAM35A WILD-TYPE 14 18
'FAM35A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.27

Table S158.  Gene #16: 'FAM35A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 6 3 3 9 5 5 4
FAM35A MUTATED 0 2 0 0 0 0 1
FAM35A WILD-TYPE 6 1 3 9 5 5 3

Figure S12.  Get High-res Image Gene #16: 'FAM35A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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/15866307/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/15087707/CHOL-TP.transferedmergedcluster.txt

  • Number of patients = 35

  • Number of significantly mutated genes = 16

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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