Correlation between gene mutation status and molecular subtypes
Pheochromocytoma and Paraganglioma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1NP236J
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1NP236J
Overview
Introduction

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

Summary

Testing the association between mutation status of 9 genes and 8 molecular subtypes across 178 patients, 18 significant findings detected with P value < 0.05 and Q value < 0.25.

  • HRAS mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • EPAS1 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • NF1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 9 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 18 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
HRAS 18 (10%) 160 1e-05
(0.00071) 		5e-05
(0.00325) 		1e-05
(0.00071) 		1e-05
(0.00071) 		0.00011
(0.00693) 		0.00029
(0.0174) 		2e-05
(0.00134) 		1e-05
(0.00071)
EPAS1 8 (4%) 170 0.0587
(1.00) 		0.00661
(0.33) 		0.00147
(0.0838) 		0.00167
(0.0935) 		0.002
(0.11) 		0.0169
(0.81) 		0.00025
(0.0152) 		0.00429
(0.232)
NF1 15 (8%) 163 0.348
(1.00) 		0.00051
(0.0296) 		0.00967
(0.474) 		0.0001
(0.0064) 		0.00018
(0.0112) 		0.0057
(0.293) 		2e-05
(0.00134) 		0.00042
(0.0248)
RET 6 (3%) 172 0.149
(1.00) 		0.482
(1.00) 		0.0904
(1.00) 		0.104
(1.00) 		0.433
(1.00) 		0.0684
(1.00) 		0.438
(1.00) 		0.0429
(1.00)
CSDE1 4 (2%) 174 0.107
(1.00) 		0.582
(1.00) 		0.489
(1.00) 		0.00511
(0.271) 		0.35
(1.00) 		0.00564
(0.293) 		0.363
(1.00) 		0.0458
(1.00)
GPR128 4 (2%) 174 0.145
(1.00) 		0.0986
(1.00) 		0.888
(1.00) 		0.887
(1.00) 		0.542
(1.00) 		0.774
(1.00) 		0.567
(1.00) 		0.551
(1.00)
AMMECR1 3 (2%) 175 0.738
(1.00) 		1
(1.00) 		0.242
(1.00) 		0.626
(1.00) 		0.795
(1.00) 		1
(1.00) 		0.261
(1.00) 		0.799
(1.00)
SHROOM4 3 (2%) 175 1
(1.00) 		0.467
(1.00) 		0.541
(1.00) 		1
(1.00) 		0.679
(1.00) 		1
(1.00) 		1
(1.00)
FAM83D 3 (2%) 175 0.261
(1.00) 		0.337
(1.00) 		0.405
(1.00) 		0.465
(1.00) 		0.0577
(1.00) 		0.819
(1.00) 		0.182
(1.00) 		0.0475
(1.00)
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
HRAS MUTATED 0 0 15 0 0
HRAS WILD-TYPE 15 24 40 42 23

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

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0032

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
HRAS MUTATED 0 17 1
HRAS WILD-TYPE 44 68 48

Figure S2.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
HRAS MUTATED 0 18 0 0
HRAS WILD-TYPE 39 51 49 21

Figure S3.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
HRAS MUTATED 0 18 0 0
HRAS WILD-TYPE 38 53 48 21

Figure S4.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0069

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
HRAS MUTATED 1 15 2
HRAS WILD-TYPE 73 50 37

Figure S5.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
HRAS MUTATED 1 14 1 2
HRAS WILD-TYPE 75 45 17 23

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

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0013

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
HRAS MUTATED 0 17 1
HRAS WILD-TYPE 44 58 58

Figure S7.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00071

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
HRAS MUTATED 0 16 2
HRAS WILD-TYPE 78 45 37

Figure S8.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0587 (Fisher's exact test), Q value = 1

Table S9.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
EPAS1 MUTATED 1 1 0 5 1
EPAS1 WILD-TYPE 14 23 55 37 22
'EPAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00661 (Fisher's exact test), Q value = 0.33

Table S10.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
EPAS1 MUTATED 4 0 4
EPAS1 WILD-TYPE 40 85 45

Figure S9.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.084

Table S11.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
EPAS1 MUTATED 1 0 7 0
EPAS1 WILD-TYPE 38 69 42 21

Figure S10.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.094

Table S12.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
EPAS1 MUTATED 1 0 7 0
EPAS1 WILD-TYPE 37 71 41 21

Figure S11.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.11

Table S13.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
EPAS1 MUTATED 8 0 0
EPAS1 WILD-TYPE 66 65 39

Figure S12.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.81

Table S14.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
EPAS1 MUTATED 8 0 0 0
EPAS1 WILD-TYPE 68 59 18 25

Figure S13.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.015

Table S15.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
EPAS1 MUTATED 7 0 1
EPAS1 WILD-TYPE 37 75 58

Figure S14.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00429 (Fisher's exact test), Q value = 0.23

Table S16.  Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
EPAS1 MUTATED 8 0 0
EPAS1 WILD-TYPE 70 61 39

Figure S15.  Get High-res Image Gene #2: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
NF1 MUTATED 1 0 7 5 1
NF1 WILD-TYPE 14 24 48 37 22
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.03

Table S18.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
NF1 MUTATED 0 14 1
NF1 WILD-TYPE 44 71 48

Figure S16.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00967 (Fisher's exact test), Q value = 0.47

Table S19.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
NF1 MUTATED 3 11 0 1
NF1 WILD-TYPE 36 58 49 20

Figure S17.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0064

Table S20.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
NF1 MUTATED 0 14 0 1
NF1 WILD-TYPE 38 57 48 20

Figure S18.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.011

Table S21.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
NF1 MUTATED 1 13 1
NF1 WILD-TYPE 73 52 38

Figure S19.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0057 (Fisher's exact test), Q value = 0.29

Table S22.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
NF1 MUTATED 2 11 0 2
NF1 WILD-TYPE 74 48 18 23

Figure S20.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0013

Table S23.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
NF1 MUTATED 0 15 0
NF1 WILD-TYPE 44 60 59

Figure S21.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.025

Table S24.  Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
NF1 MUTATED 1 12 2
NF1 WILD-TYPE 77 49 37

Figure S22.  Get High-res Image Gene #3: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
RET MUTATED 0 0 5 0 1
RET WILD-TYPE 15 24 50 42 22
'RET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
RET MUTATED 0 4 2
RET WILD-TYPE 44 81 47
'RET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0904 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
RET MUTATED 0 5 0 1
RET WILD-TYPE 39 64 49 20
'RET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
RET MUTATED 0 5 0 1
RET WILD-TYPE 38 66 48 20
'RET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
RET MUTATED 1 3 2
RET WILD-TYPE 73 62 37
'RET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0684 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
RET MUTATED 0 4 1 1
RET WILD-TYPE 76 55 17 24
'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
RET MUTATED 0 3 3
RET WILD-TYPE 44 72 56
'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
RET MUTATED 0 4 2
RET WILD-TYPE 78 57 37

Figure S23.  Get High-res Image Gene #4: 'RET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 1

Table S33.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
CSDE1 MUTATED 0 0 0 2 2
CSDE1 WILD-TYPE 15 24 55 40 21
'CSDE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S34.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
CSDE1 MUTATED 1 3 0
CSDE1 WILD-TYPE 43 82 49
'CSDE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
CSDE1 MUTATED 1 3 0 0
CSDE1 WILD-TYPE 38 66 49 21
'CSDE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00511 (Fisher's exact test), Q value = 0.27

Table S36.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
CSDE1 MUTATED 4 0 0 0
CSDE1 WILD-TYPE 34 71 48 21

Figure S24.  Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
CSDE1 MUTATED 1 3 0
CSDE1 WILD-TYPE 73 62 39
'CSDE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00564 (Fisher's exact test), Q value = 0.29

Table S38.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
CSDE1 MUTATED 1 0 3 0
CSDE1 WILD-TYPE 75 59 15 25

Figure S25.  Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CSDE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
CSDE1 MUTATED 1 3 0
CSDE1 WILD-TYPE 43 72 59
'CSDE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0458 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
CSDE1 MUTATED 1 0 3
CSDE1 WILD-TYPE 77 61 36

Figure S26.  Get High-res Image Gene #5: 'CSDE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GPR128 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 1

Table S41.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
GPR128 MUTATED 1 0 0 2 0
GPR128 WILD-TYPE 14 24 55 40 23
'GPR128 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0986 (Fisher's exact test), Q value = 1

Table S42.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
GPR128 MUTATED 3 1 0
GPR128 WILD-TYPE 41 84 49
'GPR128 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S43.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
GPR128 MUTATED 1 1 2 0
GPR128 WILD-TYPE 38 68 47 21
'GPR128 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S44.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
GPR128 MUTATED 1 1 2 0
GPR128 WILD-TYPE 37 70 46 21
'GPR128 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 1

Table S45.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
GPR128 MUTATED 3 1 0
GPR128 WILD-TYPE 71 64 39
'GPR128 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S46.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
GPR128 MUTATED 3 1 0 0
GPR128 WILD-TYPE 73 58 18 25
'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S47.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
GPR128 MUTATED 2 1 1
GPR128 WILD-TYPE 42 74 58
'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.551 (Fisher's exact test), Q value = 1

Table S48.  Gene #6: 'GPR128 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
GPR128 MUTATED 3 1 0
GPR128 WILD-TYPE 75 60 39
'AMMECR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S49.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
AMMECR1 MUTATED 0 0 1 2 0
AMMECR1 WILD-TYPE 15 24 54 40 23
'AMMECR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S50.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
AMMECR1 MUTATED 1 1 1
AMMECR1 WILD-TYPE 43 84 48
'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 1

Table S51.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
AMMECR1 MUTATED 1 0 2 0
AMMECR1 WILD-TYPE 38 69 47 21
'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S52.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
AMMECR1 MUTATED 0 1 2 0
AMMECR1 WILD-TYPE 38 70 46 21
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
AMMECR1 MUTATED 2 1 0
AMMECR1 WILD-TYPE 72 64 39
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S54.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
AMMECR1 MUTATED 2 1 0 0
AMMECR1 WILD-TYPE 74 58 18 25
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
AMMECR1 MUTATED 2 1 0
AMMECR1 WILD-TYPE 42 74 59
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
AMMECR1 MUTATED 2 1 0
AMMECR1 WILD-TYPE 76 60 39
'SHROOM4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S57.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
SHROOM4 MUTATED 1 1 1
SHROOM4 WILD-TYPE 43 84 48
'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S58.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
SHROOM4 MUTATED 1 1 0 1
SHROOM4 WILD-TYPE 38 68 49 20
'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S59.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
SHROOM4 MUTATED 0 1 1 1
SHROOM4 WILD-TYPE 38 70 47 20
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S60.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
SHROOM4 MUTATED 1 1 1
SHROOM4 WILD-TYPE 73 64 38
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S61.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
SHROOM4 MUTATED 1 1 0 1
SHROOM4 WILD-TYPE 75 58 18 24
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S62.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
SHROOM4 MUTATED 1 1 1
SHROOM4 WILD-TYPE 43 74 58
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S63.  Gene #8: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
SHROOM4 MUTATED 1 1 1
SHROOM4 WILD-TYPE 77 60 38
'FAM83D MUTATION STATUS' versus 'CN_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 1

Table S64.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 15 24 55 42 23
FAM83D MUTATED 1 0 1 0 1
FAM83D WILD-TYPE 14 24 54 42 22
'FAM83D MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 1

Table S65.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 85 49
FAM83D MUTATED 0 3 0
FAM83D WILD-TYPE 44 82 49
'FAM83D MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 1

Table S66.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 69 49 21
FAM83D MUTATED 0 3 0 0
FAM83D WILD-TYPE 39 66 49 21
'FAM83D MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S67.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 71 48 21
FAM83D MUTATED 0 3 0 0
FAM83D WILD-TYPE 38 68 48 21
'FAM83D MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0577 (Fisher's exact test), Q value = 1

Table S68.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 65 39
FAM83D MUTATED 0 3 0
FAM83D WILD-TYPE 74 62 39
'FAM83D MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S69.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 59 18 25
FAM83D MUTATED 1 2 0 0
FAM83D WILD-TYPE 75 57 18 25
'FAM83D MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S70.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 75 59
FAM83D MUTATED 0 3 0
FAM83D WILD-TYPE 44 72 59
'FAM83D MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 1

Table S71.  Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 61 39
FAM83D MUTATED 0 3 0
FAM83D WILD-TYPE 78 58 39

Figure S27.  Get High-res Image Gene #9: 'FAM83D MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 178

  • Number of significantly mutated genes = 9

  • Number of Molecular subtypes = 8

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

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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