Correlation between gene mutation status and molecular subtypes
Prostate Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
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/C1VM49R4
Overview
Introduction

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

Summary

Testing the association between mutation status of 7 genes and 10 molecular subtypes across 249 patients, 9 significant findings detected with P value < 0.05 and Q value < 0.25.

  • SPOP mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • FOXA1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • TP53 mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 7 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, 9 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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
SPOP 24 (10%) 225 0.000575
(0.0379)
2.68e-08
(1.88e-06)
0.538
(1.00)
0.769
(1.00)
5.99e-05
(0.00401)
1.07e-07
(7.27e-06)
0.155
(1.00)
0.253
(1.00)
0.0173
(1.00)
0.0214
(1.00)
TP53 20 (8%) 229 3.88e-08
(2.68e-06)
0.355
(1.00)
0.0102
(0.625)
0.025
(1.00)
0.00267
(0.168)
0.00309
(0.192)
0.456
(1.00)
0.802
(1.00)
0.644
(1.00)
0.749
(1.00)
FOXA1 11 (4%) 238 0.156
(1.00)
0.000691
(0.0449)
1
(1.00)
0.68
(1.00)
0.0768
(1.00)
0.00255
(0.163)
0.299
(1.00)
0.0728
(1.00)
0.212
(1.00)
0.235
(1.00)
CTNNB1 9 (4%) 240 0.481
(1.00)
0.0431
(1.00)
0.0208
(1.00)
0.0357
(1.00)
0.0126
(0.756)
0.368
(1.00)
0.674
(1.00)
0.75
(1.00)
0.58
(1.00)
0.761
(1.00)
PTEN 13 (5%) 236 0.0581
(1.00)
0.291
(1.00)
0.196
(1.00)
0.658
(1.00)
0.025
(1.00)
0.0815
(1.00)
0.527
(1.00)
0.761
(1.00)
0.556
(1.00)
0.559
(1.00)
PCDHAC2 26 (10%) 223 0.547
(1.00)
0.105
(1.00)
0.93
(1.00)
0.546
(1.00)
0.212
(1.00)
0.158
(1.00)
0.683
(1.00)
0.527
(1.00)
0.584
(1.00)
0.651
(1.00)
TMEM216 4 (2%) 245 1
(1.00)
0.836
(1.00)
0.781
(1.00)
0.0272
(1.00)
1
(1.00)
1
(1.00)
0.792
(1.00)
1
(1.00)
0.839
(1.00)
0.832
(1.00)
'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 130 74
CTNNB1 MUTATED 2 3 4
CTNNB1 WILD-TYPE 40 127 70
'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 84 92
CTNNB1 MUTATED 3 0 6
CTNNB1 WILD-TYPE 70 84 86

Figure S1.  Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 57 56
CTNNB1 MUTATED 0 0 4
CTNNB1 WILD-TYPE 41 57 52

Figure S2.  Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 57 47
CTNNB1 MUTATED 0 4 0
CTNNB1 WILD-TYPE 50 53 47

Figure S3.  Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.76

Table S5.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 63 68 50
CTNNB1 MUTATED 3 0 6 0
CTNNB1 WILD-TYPE 63 63 62 50

Figure S4.  Get High-res Image Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 76 62 33
CTNNB1 MUTATED 1 5 2 1
CTNNB1 WILD-TYPE 75 71 60 32
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.674 (Chi-square test), Q value = 1

Table S7.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 23 15 70 77
CTNNB1 MUTATED 2 0 0 4 3
CTNNB1 WILD-TYPE 60 23 15 66 74
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.75 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 111 69
CTNNB1 MUTATED 3 3 3
CTNNB1 WILD-TYPE 64 108 66
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.58 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 89 78
CTNNB1 MUTATED 3 2 4
CTNNB1 WILD-TYPE 77 87 74
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.761 (Fisher's exact test), Q value = 1

Table S10.  Gene #1: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 93 77
CTNNB1 MUTATED 2 3 4
CTNNB1 WILD-TYPE 75 90 73
'SPOP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000575 (Fisher's exact test), Q value = 0.038

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 130 74
SPOP MUTATED 11 6 6
SPOP WILD-TYPE 31 124 68

Figure S5.  Get High-res Image Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SPOP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.68e-08 (Fisher's exact test), Q value = 1.9e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 84 92
SPOP MUTATED 20 3 1
SPOP WILD-TYPE 53 81 91

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

'SPOP MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 57 56
SPOP MUTATED 4 3 6
SPOP WILD-TYPE 37 54 50
'SPOP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 57 47
SPOP MUTATED 4 6 3
SPOP WILD-TYPE 46 51 44
'SPOP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5.99e-05 (Fisher's exact test), Q value = 0.004

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 63 68 50
SPOP MUTATED 15 5 0 3
SPOP WILD-TYPE 51 58 68 47

Figure S7.  Get High-res Image Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SPOP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.07e-07 (Fisher's exact test), Q value = 7.3e-06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 76 62 33
SPOP MUTATED 3 0 18 2
SPOP WILD-TYPE 73 76 44 31

Figure S8.  Get High-res Image Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SPOP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.155 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 23 15 70 77
SPOP MUTATED 3 1 0 10 10
SPOP WILD-TYPE 59 22 15 60 67
'SPOP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 111 69
SPOP MUTATED 4 10 10
SPOP WILD-TYPE 63 101 59
'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 89 78
SPOP MUTATED 2 12 10
SPOP WILD-TYPE 78 77 68

Figure S9.  Get High-res Image Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 93 77
SPOP MUTATED 2 11 11
SPOP WILD-TYPE 75 82 66

Figure S10.  Get High-res Image Gene #2: 'SPOP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0581 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 130 74
PTEN MUTATED 4 3 6
PTEN WILD-TYPE 38 127 68
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 84 92
PTEN MUTATED 4 2 7
PTEN WILD-TYPE 69 82 85
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 57 56
PTEN MUTATED 4 1 3
PTEN WILD-TYPE 37 56 53
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.658 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 57 47
PTEN MUTATED 4 2 2
PTEN WILD-TYPE 46 55 45
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.025 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 63 68 50
PTEN MUTATED 5 1 7 0
PTEN WILD-TYPE 61 62 61 50

Figure S11.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0815 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 76 62 33
PTEN MUTATED 1 8 3 1
PTEN WILD-TYPE 75 68 59 32
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.527 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 23 15 70 77
PTEN MUTATED 3 0 1 6 3
PTEN WILD-TYPE 59 23 14 64 74
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.761 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 111 69
PTEN MUTATED 3 5 5
PTEN WILD-TYPE 64 106 64
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 89 78
PTEN MUTATED 3 4 6
PTEN WILD-TYPE 77 85 72
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 93 77
PTEN MUTATED 3 4 6
PTEN WILD-TYPE 74 89 71
'PCDHAC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.547 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 130 74
PCDHAC2 MUTATED 6 14 6
PCDHAC2 WILD-TYPE 36 116 68
'PCDHAC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 84 92
PCDHAC2 MUTATED 11 10 5
PCDHAC2 WILD-TYPE 62 74 87
'PCDHAC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 57 56
PCDHAC2 MUTATED 4 7 7
PCDHAC2 WILD-TYPE 37 50 49
'PCDHAC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.546 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 57 47
PCDHAC2 MUTATED 4 7 7
PCDHAC2 WILD-TYPE 46 50 40
'PCDHAC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S35.  Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 63 68 50
PCDHAC2 MUTATED 9 7 3 7
PCDHAC2 WILD-TYPE 57 56 65 43
'PCDHAC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 1

Table S36.  Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 76 62 33
PCDHAC2 MUTATED 11 4 9 2
PCDHAC2 WILD-TYPE 65 72 53 31
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.683 (Chi-square test), Q value = 1

Table S37.  Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 23 15 70 77
PCDHAC2 MUTATED 6 4 2 5 9
PCDHAC2 WILD-TYPE 56 19 13 65 68
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.527 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 111 69
PCDHAC2 MUTATED 7 14 5
PCDHAC2 WILD-TYPE 60 97 64
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 89 78
PCDHAC2 MUTATED 10 10 6
PCDHAC2 WILD-TYPE 70 79 72
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S40.  Gene #4: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 93 77
PCDHAC2 MUTATED 9 11 6
PCDHAC2 WILD-TYPE 68 82 71
'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 1

Table S41.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 130 74
FOXA1 MUTATED 3 3 5
FOXA1 WILD-TYPE 39 127 69
'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000691 (Fisher's exact test), Q value = 0.045

Table S42.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 84 92
FOXA1 MUTATED 9 1 1
FOXA1 WILD-TYPE 64 83 91

Figure S12.  Get High-res Image Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S43.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 57 56
FOXA1 MUTATED 2 2 2
FOXA1 WILD-TYPE 39 55 54
'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S44.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 57 47
FOXA1 MUTATED 3 2 1
FOXA1 WILD-TYPE 47 55 46
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0768 (Fisher's exact test), Q value = 1

Table S45.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 63 68 50
FOXA1 MUTATED 7 2 1 1
FOXA1 WILD-TYPE 59 61 67 49
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00255 (Fisher's exact test), Q value = 0.16

Table S46.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 76 62 33
FOXA1 MUTATED 2 0 4 5
FOXA1 WILD-TYPE 74 76 58 28

Figure S13.  Get High-res Image Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.299 (Chi-square test), Q value = 1

Table S47.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 23 15 70 77
FOXA1 MUTATED 1 0 0 5 5
FOXA1 WILD-TYPE 61 23 15 65 72
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0728 (Fisher's exact test), Q value = 1

Table S48.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 111 69
FOXA1 MUTATED 0 6 5
FOXA1 WILD-TYPE 67 105 64
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 89 78
FOXA1 MUTATED 1 5 5
FOXA1 WILD-TYPE 79 84 73
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 93 77
FOXA1 MUTATED 1 5 5
FOXA1 WILD-TYPE 76 88 72
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 3.88e-08 (Fisher's exact test), Q value = 2.7e-06

Table S51.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 130 74
TP53 MUTATED 0 2 18
TP53 WILD-TYPE 42 128 56

Figure S14.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 1

Table S52.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 84 92
TP53 MUTATED 6 4 10
TP53 WILD-TYPE 67 80 82
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.62

Table S53.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 57 56
TP53 MUTATED 0 3 9
TP53 WILD-TYPE 41 54 47

Figure S15.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 57 47
TP53 MUTATED 1 9 2
TP53 WILD-TYPE 49 48 45

Figure S16.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00267 (Fisher's exact test), Q value = 0.17

Table S55.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 63 68 50
TP53 MUTATED 2 4 13 1
TP53 WILD-TYPE 64 59 55 49

Figure S17.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00309 (Fisher's exact test), Q value = 0.19

Table S56.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 76 62 33
TP53 MUTATED 1 13 5 1
TP53 WILD-TYPE 75 63 57 32

Figure S18.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.456 (Chi-square test), Q value = 1

Table S57.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 23 15 70 77
TP53 MUTATED 4 0 1 6 9
TP53 WILD-TYPE 58 23 14 64 68
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S58.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 111 69
TP53 MUTATED 4 10 6
TP53 WILD-TYPE 63 101 63
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 89 78
TP53 MUTATED 5 9 6
TP53 WILD-TYPE 75 80 72
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.749 (Fisher's exact test), Q value = 1

Table S60.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 93 77
TP53 MUTATED 5 9 6
TP53 WILD-TYPE 72 84 71
'TMEM216 MUTATION STATUS' versus 'CN_CNMF'

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

Table S61.  Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 130 74
TMEM216 MUTATED 0 3 1
TMEM216 WILD-TYPE 42 127 73
'TMEM216 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S62.  Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 73 84 92
TMEM216 MUTATED 1 2 1
TMEM216 WILD-TYPE 72 82 91
'TMEM216 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S63.  Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 41 57 56
TMEM216 MUTATED 0 2 1
TMEM216 WILD-TYPE 41 55 55
'TMEM216 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0272 (Fisher's exact test), Q value = 1

Table S64.  Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 57 47
TMEM216 MUTATED 0 0 3
TMEM216 WILD-TYPE 50 57 44

Figure S19.  Get High-res Image Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TMEM216 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S65.  Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 66 63 68 50
TMEM216 MUTATED 1 1 1 1
TMEM216 WILD-TYPE 65 62 67 49
'TMEM216 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S66.  Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 76 62 33
TMEM216 MUTATED 1 2 1 0
TMEM216 WILD-TYPE 75 74 61 33
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.792 (Chi-square test), Q value = 1

Table S67.  Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 62 23 15 70 77
TMEM216 MUTATED 2 0 0 1 1
TMEM216 WILD-TYPE 60 23 15 69 76
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S68.  Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 111 69
TMEM216 MUTATED 1 2 1
TMEM216 WILD-TYPE 66 109 68
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S69.  Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 89 78
TMEM216 MUTATED 2 1 1
TMEM216 WILD-TYPE 78 88 77
'TMEM216 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S70.  Gene #7: 'TMEM216 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 77 93 77
TMEM216 MUTATED 2 1 1
TMEM216 WILD-TYPE 75 92 76
Methods & Data
Input
  • Mutation data file = transformed.cor.cli.txt

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

  • Number of patients = 249

  • Number of significantly mutated genes = 7

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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)