Correlation between gene mutation status and molecular subtypes
Pheochromocytoma and Paraganglioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1H41QWT
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1H41QWT
Overview
Introduction

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

Summary

Testing the association between mutation status of 8 genes and 10 molecular subtypes across 179 patients, 24 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • EPAS1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  '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 8 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, 24 significant findings 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
HRAS 18 (10%) 161 8e-05
(0.000914) 		7e-05
(0.000914) 		0.155
(0.401) 		0.00133
(0.00811) 		1e-05
(0.000267) 		1e-05
(0.000267) 		1e-05
(0.000267) 		0.00024
(0.00213) 		0.00052
(0.00416) 		5e-05
(0.000914)
NF1 15 (8%) 164 0.574
(0.883) 		0.00564
(0.0237) 		0.00717
(0.0287) 		0.0884
(0.253) 		0.00974
(0.0354) 		0.00012
(0.0012) 		0.00071
(0.00516) 		0.00553
(0.0237) 		0.0176
(0.0613) 		0.00965
(0.0354)
EPAS1 8 (4%) 171 0.181
(0.453) 		0.00323
(0.0152) 		0.354
(0.712) 		0.356
(0.712) 		0.00203
(0.0108) 		0.00142
(0.00811) 		0.00096
(0.0064) 		0.0189
(0.063) 		0.00298
(0.0149) 		6e-05
(0.000914)
NUDT11 5 (3%) 174 0.907
(1.00) 		0.719
(0.975) 		0.788
(1.00) 		1
(1.00) 		0.341
(0.712) 		0.675
(0.965) 		0.37
(0.721) 		0.281
(0.643) 		0.836
(1.00) 		0.694
(0.97)
RET 6 (3%) 173 0.434
(0.79) 		0.424
(0.79) 		0.429
(0.79) 		0.324
(0.701) 		0.0873
(0.253) 		0.0982
(0.271) 		0.507
(0.845) 		0.062
(0.198) 		0.249
(0.587) 		0.468
(0.796)
SHROOM4 3 (2%) 176 1
(1.00) 		0.462
(0.796) 		0.543
(0.876) 		1
(1.00) 		0.676
(0.965) 		0.916
(1.00) 		0.859
(1.00)
AMMECR1 3 (2%) 176 0.458
(0.796) 		1
(1.00) 		0.548
(0.876) 		1
(1.00) 		0.241
(0.583) 		0.627
(0.929) 		0.79
(1.00) 		1
(1.00) 		0.605
(0.913) 		0.143
(0.381)
GPR128 4 (2%) 175 0.563
(0.883) 		0.0758
(0.233) 		0.889
(1.00) 		0.887
(1.00) 		0.295
(0.655) 		0.879
(1.00) 		0.703
(0.97) 		0.979
(1.00)
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00091

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 37 40 10 50 25
HRAS MUTATED 1 0 5 7 2
HRAS WILD-TYPE 36 40 5 43 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 = 7e-05 (Fisher's exact test), Q value = 0.00091

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 84 50
HRAS MUTATED 0 17 1
HRAS WILD-TYPE 45 67 49

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

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 21 23 18
HRAS MUTATED 3 2 5 0
HRAS WILD-TYPE 14 19 18 18
'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.0081

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 28
HRAS MUTATED 1 7 2
HRAS WILD-TYPE 32 11 26

Figure S3.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 70 50 21
HRAS MUTATED 0 18 0 0
HRAS WILD-TYPE 38 52 50 21

Figure S4.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 71 48 21
HRAS MUTATED 0 18 0 0
HRAS WILD-TYPE 39 53 48 21

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

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 44 63
HRAS MUTATED 0 2 16
HRAS WILD-TYPE 72 42 47

Figure S6.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0021

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 59 18 25
HRAS MUTATED 1 14 1 2
HRAS WILD-TYPE 76 45 17 23

Figure S7.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0042

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 56 17 40 30
HRAS MUTATED 1 12 4 1 0
HRAS WILD-TYPE 34 44 13 39 30

Figure S8.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00091

Table S10.  Gene #1: 'HRAS 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 21 47 31 16 26 18 19
HRAS MUTATED 0 9 0 7 0 1 1
HRAS WILD-TYPE 21 38 31 9 26 17 18

Figure S9.  Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 0.88

Table S11.  Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
NF1 MUTATED 2 3 1 7 1
NF1 WILD-TYPE 35 37 9 43 24
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00564 (Fisher's exact test), Q value = 0.024

Table S12.  Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 84 50
NF1 MUTATED 1 13 1
NF1 WILD-TYPE 44 71 49

Figure S10.  Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00717 (Fisher's exact test), Q value = 0.029

Table S13.  Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 21 23 18
NF1 MUTATED 3 0 6 0
NF1 WILD-TYPE 14 21 17 18

Figure S11.  Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0884 (Fisher's exact test), Q value = 0.25

Table S14.  Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 28
NF1 MUTATED 1 4 4
NF1 WILD-TYPE 32 14 24
'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00974 (Fisher's exact test), Q value = 0.035

Table S15.  Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 70 50 21
NF1 MUTATED 3 11 0 1
NF1 WILD-TYPE 35 59 50 20

Figure S12.  Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0012

Table S16.  Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 71 48 21
NF1 MUTATED 0 14 0 1
NF1 WILD-TYPE 39 57 48 20

Figure S13.  Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0052

Table S17.  Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 44 63
NF1 MUTATED 1 2 12
NF1 WILD-TYPE 71 42 51

Figure S14.  Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00553 (Fisher's exact test), Q value = 0.024

Table S18.  Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 59 18 25
NF1 MUTATED 2 11 0 2
NF1 WILD-TYPE 75 48 18 23

Figure S15.  Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.061

Table S19.  Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 56 17 40 30
NF1 MUTATED 2 10 2 1 0
NF1 WILD-TYPE 33 46 15 39 30

Figure S16.  Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00965 (Fisher's exact test), Q value = 0.035

Table S20.  Gene #2: 'NF1 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 21 47 31 16 26 18 19
NF1 MUTATED 3 9 0 2 0 0 1
NF1 WILD-TYPE 18 38 31 14 26 18 18

Figure S17.  Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.45

Table S21.  Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
EPAS1 MUTATED 2 5 0 1 0
EPAS1 WILD-TYPE 35 35 10 49 25
'EPAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.015

Table S22.  Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 84 50
EPAS1 MUTATED 5 0 3
EPAS1 WILD-TYPE 40 84 47

Figure S18.  Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPAS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.71

Table S23.  Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 21 23 18
EPAS1 MUTATED 1 3 1 0
EPAS1 WILD-TYPE 16 18 22 18
'EPAS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.71

Table S24.  Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 28
EPAS1 MUTATED 2 0 3
EPAS1 WILD-TYPE 31 18 25
'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.011

Table S25.  Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 70 50 21
EPAS1 MUTATED 1 0 7 0
EPAS1 WILD-TYPE 37 70 43 21

Figure S19.  Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0081

Table S26.  Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 71 48 21
EPAS1 MUTATED 1 0 7 0
EPAS1 WILD-TYPE 38 71 41 21

Figure S20.  Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0064

Table S27.  Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 44 63
EPAS1 MUTATED 8 0 0
EPAS1 WILD-TYPE 64 44 63

Figure S21.  Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.063

Table S28.  Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 59 18 25
EPAS1 MUTATED 8 0 0 0
EPAS1 WILD-TYPE 69 59 18 25

Figure S22.  Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00298 (Fisher's exact test), Q value = 0.015

Table S29.  Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 56 17 40 30
EPAS1 MUTATED 0 0 1 6 1
EPAS1 WILD-TYPE 35 56 16 34 29

Figure S23.  Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00091

Table S30.  Gene #3: 'EPAS1 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 21 47 31 16 26 18 19
EPAS1 MUTATED 1 0 0 0 7 0 0
EPAS1 WILD-TYPE 20 47 31 16 19 18 19

Figure S24.  Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
NUDT11 MUTATED 1 2 0 2 0
NUDT11 WILD-TYPE 36 38 10 48 25
'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.719 (Fisher's exact test), Q value = 0.97

Table S32.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 84 50
NUDT11 MUTATED 2 2 1
NUDT11 WILD-TYPE 43 82 49
'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 21 23 18
NUDT11 MUTATED 1 0 1 1
NUDT11 WILD-TYPE 16 21 22 17
'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S34.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 28
NUDT11 MUTATED 1 1 1
NUDT11 WILD-TYPE 32 17 27
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.71

Table S35.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 70 50 21
NUDT11 MUTATED 2 3 0 0
NUDT11 WILD-TYPE 36 67 50 21
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.675 (Fisher's exact test), Q value = 0.97

Table S36.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 71 48 21
NUDT11 MUTATED 0 3 2 0
NUDT11 WILD-TYPE 39 68 46 21
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.37 (Fisher's exact test), Q value = 0.72

Table S37.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 44 63
NUDT11 MUTATED 2 0 3
NUDT11 WILD-TYPE 70 44 60
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.281 (Fisher's exact test), Q value = 0.64

Table S38.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 59 18 25
NUDT11 MUTATED 1 4 0 0
NUDT11 WILD-TYPE 76 55 18 25
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 56 17 40 30
NUDT11 MUTATED 1 3 0 1 0
NUDT11 WILD-TYPE 34 53 17 39 30
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 0.97

Table S40.  Gene #4: 'NUDT11 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 21 47 31 16 26 18 19
NUDT11 MUTATED 1 3 0 0 1 0 0
NUDT11 WILD-TYPE 20 44 31 16 25 18 19
'RET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
RET MUTATED 3 0 0 2 1
RET WILD-TYPE 34 40 10 48 24
'RET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 84 50
RET MUTATED 0 4 2
RET WILD-TYPE 45 80 48
'RET MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.429 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 21 23 18
RET MUTATED 1 0 2 0
RET WILD-TYPE 16 21 21 18
'RET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 28
RET MUTATED 0 1 2
RET WILD-TYPE 33 17 26
'RET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0873 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 70 50 21
RET MUTATED 0 5 0 1
RET WILD-TYPE 38 65 50 20
'RET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0982 (Fisher's exact test), Q value = 0.27

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 71 48 21
RET MUTATED 0 5 0 1
RET WILD-TYPE 39 66 48 20
'RET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 44 63
RET MUTATED 1 2 3
RET WILD-TYPE 71 42 60
'RET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.062 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 59 18 25
RET MUTATED 0 4 1 1
RET WILD-TYPE 77 55 17 24
'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 56 17 40 30
RET MUTATED 1 4 1 0 0
RET WILD-TYPE 34 52 16 40 30
'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 0.8

Table S50.  Gene #5: 'RET 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 21 47 31 16 26 18 19
RET MUTATED 0 3 0 1 0 1 1
RET WILD-TYPE 21 44 31 15 26 17 18
'SHROOM4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S51.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 84 50
SHROOM4 MUTATED 1 1 1
SHROOM4 WILD-TYPE 44 83 49
'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.8

Table S52.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 70 50 21
SHROOM4 MUTATED 1 1 0 1
SHROOM4 WILD-TYPE 37 69 50 20
'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.543 (Fisher's exact test), Q value = 0.88

Table S53.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 71 48 21
SHROOM4 MUTATED 0 1 1 1
SHROOM4 WILD-TYPE 39 70 47 20
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S54.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 44 63
SHROOM4 MUTATED 1 1 1
SHROOM4 WILD-TYPE 71 43 62
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.676 (Fisher's exact test), Q value = 0.97

Table S55.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 59 18 25
SHROOM4 MUTATED 1 1 0 1
SHROOM4 WILD-TYPE 76 58 18 24
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S56.  Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 56 17 40 30
SHROOM4 MUTATED 0 1 0 1 1
SHROOM4 WILD-TYPE 35 55 17 39 29
'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S57.  Gene #6: 'SHROOM4 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 21 47 31 16 26 18 19
SHROOM4 MUTATED 0 1 1 0 0 0 1
SHROOM4 WILD-TYPE 21 46 30 16 26 18 18
'AMMECR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.8

Table S58.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
AMMECR1 MUTATED 0 0 0 2 1
AMMECR1 WILD-TYPE 37 40 10 48 24
'AMMECR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S59.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 84 50
AMMECR1 MUTATED 1 1 1
AMMECR1 WILD-TYPE 44 83 49
'AMMECR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 0.88

Table S60.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 21 23 18
AMMECR1 MUTATED 0 2 1 0
AMMECR1 WILD-TYPE 17 19 22 18
'AMMECR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S61.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 28
AMMECR1 MUTATED 1 1 1
AMMECR1 WILD-TYPE 32 17 27
'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.241 (Fisher's exact test), Q value = 0.58

Table S62.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 70 50 21
AMMECR1 MUTATED 1 0 2 0
AMMECR1 WILD-TYPE 37 70 48 21
'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 0.93

Table S63.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 71 48 21
AMMECR1 MUTATED 0 1 2 0
AMMECR1 WILD-TYPE 39 70 46 21
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S64.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 44 63
AMMECR1 MUTATED 2 0 1
AMMECR1 WILD-TYPE 70 44 62
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S65.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 59 18 25
AMMECR1 MUTATED 2 1 0 0
AMMECR1 WILD-TYPE 75 58 18 25
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 0.91

Table S66.  Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 56 17 40 30
AMMECR1 MUTATED 0 1 0 2 0
AMMECR1 WILD-TYPE 35 55 17 38 30
'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.38

Table S67.  Gene #7: 'AMMECR1 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 21 47 31 16 26 18 19
AMMECR1 MUTATED 1 0 0 0 2 0 0
AMMECR1 WILD-TYPE 20 47 31 16 24 18 19
'GPR128 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.563 (Fisher's exact test), Q value = 0.88

Table S68.  Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 40 10 50 25
GPR128 MUTATED 1 1 0 0 1
GPR128 WILD-TYPE 36 39 10 50 24
'GPR128 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0758 (Fisher's exact test), Q value = 0.23

Table S69.  Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 45 84 50
GPR128 MUTATED 3 1 0
GPR128 WILD-TYPE 42 83 50
'GPR128 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S70.  Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 70 50 21
GPR128 MUTATED 1 1 2 0
GPR128 WILD-TYPE 37 69 48 21
'GPR128 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S71.  Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 39 71 48 21
GPR128 MUTATED 1 1 2 0
GPR128 WILD-TYPE 38 70 46 21
'GPR128 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 0.66

Table S72.  Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 44 63
GPR128 MUTATED 3 1 0
GPR128 WILD-TYPE 69 43 63
'GPR128 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S73.  Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 59 18 25
GPR128 MUTATED 3 1 0 0
GPR128 WILD-TYPE 74 58 18 25
'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.703 (Fisher's exact test), Q value = 0.97

Table S74.  Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 56 17 40 30
GPR128 MUTATED 0 1 0 2 1
GPR128 WILD-TYPE 35 55 17 38 29
'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S75.  Gene #8: 'GPR128 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 21 47 31 16 26 18 19
GPR128 MUTATED 1 1 1 0 1 0 0
GPR128 WILD-TYPE 20 46 30 16 25 18 19
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/PCPG-TP/22569696/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/22542422/PCPG-TP.transferedmergedcluster.txt

  • Number of patients = 179

  • Number of significantly mutated genes = 8

  • 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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