Correlation between gene mutation status and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C12N51SV
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/C12N51SV
Overview
Introduction

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

Summary

Testing the association between mutation status of 11 genes and 10 molecular subtypes across 57 patients, 8 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • PTEN mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_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 11 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, 8 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
PTEN 11 (19%) 46 0.00877
(0.204) 		0.00121
(0.104) 		0.0515
(0.388) 		0.0182
(0.25) 		0.0111
(0.204) 		0.0447
(0.378) 		0.0653
(0.392) 		0.06
(0.388) 		0.0093
(0.204) 		0.0134
(0.211)
KRAS 7 (12%) 50 0.14
(0.532) 		0.00189
(0.104) 		0.611
(0.884) 		0.201
(0.583) 		0.0301
(0.331) 		0.00587
(0.204) 		0.875
(1.00) 		0.0928
(0.464) 		0.169
(0.532) 		0.0592
(0.388)
TP53 51 (89%) 6 0.631
(0.89) 		0.645
(0.892) 		0.418
(0.825) 		0.138
(0.532) 		1
(1.00) 		0.513
(0.841) 		1
(1.00) 		0.912
(1.00) 		0.801
(0.977) 		1
(1.00)
FBXW7 22 (39%) 35 0.0886
(0.464) 		0.775
(0.958) 		0.0703
(0.392) 		0.166
(0.532) 		0.54
(0.848) 		0.104
(0.475) 		0.508
(0.841) 		0.932
(1.00) 		0.914
(1.00) 		0.774
(0.958)
PPP2R1A 16 (28%) 41 0.649
(0.892) 		0.808
(0.977) 		0.583
(0.862) 		0.501
(0.841) 		0.775
(0.958) 		0.672
(0.911) 		0.364
(0.792) 		0.316
(0.772) 		0.588
(0.862) 		0.235
(0.662)
RB1 6 (11%) 51 1
(1.00) 		0.368
(0.792) 		0.471
(0.841) 		0.313
(0.772) 		0.0712
(0.392) 		0.0977
(0.467) 		0.871
(1.00) 		0.863
(1.00) 		0.522
(0.841) 		1
(1.00)
ZBTB7B 6 (11%) 51 0.527
(0.841) 		1
(1.00) 		0.144
(0.532) 		0.375
(0.792) 		1
(1.00) 		0.915
(1.00) 		0.157
(0.532) 		0.148
(0.532) 		0.427
(0.825) 		0.16
(0.532)
PIK3R1 6 (11%) 51 0.871
(1.00) 		1
(1.00) 		0.506
(0.841) 		0.773
(0.958) 		0.571
(0.862) 		0.706
(0.935) 		1
(1.00) 		0.501
(0.841) 		0.423
(0.825) 		0.305
(0.772)
ARHGAP35 6 (11%) 51 1
(1.00) 		0.458
(0.841) 		0.551
(0.853) 		0.344
(0.792) 		0.572
(0.862) 		0.398
(0.811) 		0.502
(0.841) 		0.192
(0.57) 		0.445
(0.841) 		0.174
(0.532)
PIK3CA 20 (35%) 37 0.389
(0.808) 		0.156
(0.532) 		0.715
(0.937) 		0.294
(0.771) 		0.275
(0.738) 		0.369
(0.792) 		0.0233
(0.284) 		0.339
(0.792) 		0.173
(0.532) 		0.269
(0.738)
MAMLD1 4 (7%) 53 1
(1.00) 		0.137
(0.532) 		0.0396
(0.363) 		0.036
(0.36) 		0.626
(0.89) 		0.769
(0.958) 		0.0593
(0.388) 		0.679
(0.911) 		0.493
(0.841) 		0.356
(0.792)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 0.89

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
TP53 MUTATED 20 19 11
TP53 WILD-TYPE 1 3 2
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 0.89

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 13 13 11
TP53 MUTATED 19 11 12 9
TP53 WILD-TYPE 1 2 1 2
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.418 (Fisher's exact test), Q value = 0.82

Table S3.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 12 6 9
TP53 MUTATED 12 8 10 6 7
TP53 WILD-TYPE 0 1 2 0 2
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.53

Table S4.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 9 8 7 7 7 5 5
TP53 MUTATED 9 8 7 6 6 4 3
TP53 WILD-TYPE 0 0 0 1 1 1 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 12 10
TP53 MUTATED 14 17 11 9
TP53 WILD-TYPE 2 2 1 1
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.513 (Fisher's exact test), Q value = 0.84

Table S6.  Gene #1: '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 11 4 8 6 8 6 14
TP53 MUTATED 11 3 8 5 7 5 12
TP53 WILD-TYPE 0 1 0 1 1 1 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S7.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 24 17
TP53 MUTATED 14 22 15
TP53 WILD-TYPE 1 2 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
TP53 MUTATED 21 8 16 6
TP53 WILD-TYPE 3 0 2 0
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 0.98

Table S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 14 14 18
TP53 MUTATED 10 13 12 16
TP53 WILD-TYPE 0 1 2 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
TP53 MUTATED 22 7 15 7
TP53 WILD-TYPE 3 0 2 0
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0886 (Fisher's exact test), Q value = 0.46

Table S11.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
FBXW7 MUTATED 11 9 2
FBXW7 WILD-TYPE 10 13 11
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 0.96

Table S12.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 13 13 11
FBXW7 MUTATED 9 4 4 5
FBXW7 WILD-TYPE 11 9 9 6
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0703 (Fisher's exact test), Q value = 0.39

Table S13.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 12 6 9
FBXW7 MUTATED 5 6 7 1 1
FBXW7 WILD-TYPE 7 3 5 5 8
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 0.53

Table S14.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 9 8 7 7 7 5 5
FBXW7 MUTATED 4 4 1 3 5 3 0
FBXW7 WILD-TYPE 5 4 6 4 2 2 5
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.85

Table S15.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 12 10
FBXW7 MUTATED 7 7 6 2
FBXW7 WILD-TYPE 9 12 6 8
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 0.48

Table S16.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
FBXW7 MUTATED 4 4 5 2 2 2 3
FBXW7 WILD-TYPE 7 0 3 4 6 4 11
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 0.84

Table S17.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 24 17
FBXW7 MUTATED 4 10 8
FBXW7 WILD-TYPE 11 14 9
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S18.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
FBXW7 MUTATED 9 4 7 2
FBXW7 WILD-TYPE 15 4 11 4
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S19.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 14 14 18
FBXW7 MUTATED 5 5 5 7
FBXW7 WILD-TYPE 5 9 9 11
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.774 (Fisher's exact test), Q value = 0.96

Table S20.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
FBXW7 MUTATED 9 4 6 3
FBXW7 WILD-TYPE 16 3 11 4
'PPP2R1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.649 (Fisher's exact test), Q value = 0.89

Table S21.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
PPP2R1A MUTATED 5 8 3
PPP2R1A WILD-TYPE 16 14 10
'PPP2R1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 0.98

Table S22.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 13 13 11
PPP2R1A MUTATED 7 4 3 2
PPP2R1A WILD-TYPE 13 9 10 9
'PPP2R1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 0.86

Table S23.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 12 6 9
PPP2R1A MUTATED 5 2 4 1 1
PPP2R1A WILD-TYPE 7 7 8 5 8
'PPP2R1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.501 (Fisher's exact test), Q value = 0.84

Table S24.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 9 8 7 7 7 5 5
PPP2R1A MUTATED 3 1 3 3 1 2 0
PPP2R1A WILD-TYPE 6 7 4 4 6 3 5
'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 0.96

Table S25.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 12 10
PPP2R1A MUTATED 6 4 3 3
PPP2R1A WILD-TYPE 10 15 9 7
'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.672 (Fisher's exact test), Q value = 0.91

Table S26.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
PPP2R1A MUTATED 4 1 4 1 2 2 2
PPP2R1A WILD-TYPE 7 3 4 5 6 4 12
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 0.79

Table S27.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 24 17
PPP2R1A MUTATED 6 7 3
PPP2R1A WILD-TYPE 9 17 14
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 0.77

Table S28.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
PPP2R1A MUTATED 8 4 3 1
PPP2R1A WILD-TYPE 16 4 15 5
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.588 (Fisher's exact test), Q value = 0.86

Table S29.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 14 14 18
PPP2R1A MUTATED 3 6 3 4
PPP2R1A WILD-TYPE 7 8 11 14
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.66

Table S30.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
PPP2R1A MUTATED 8 4 3 1
PPP2R1A WILD-TYPE 17 3 14 6
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
KRAS MUTATED 2 5 0
KRAS WILD-TYPE 19 17 13
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 13 13 11
KRAS MUTATED 0 1 1 5
KRAS WILD-TYPE 20 12 12 6

Figure S1.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 12 6 9
KRAS MUTATED 1 2 2 0 0
KRAS WILD-TYPE 11 7 10 6 9
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.58

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 9 8 7 7 7 5 5
KRAS MUTATED 0 0 2 1 2 0 0
KRAS WILD-TYPE 9 8 5 6 5 5 5
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 12 10
KRAS MUTATED 0 3 4 0
KRAS WILD-TYPE 16 16 8 10

Figure S2.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00587 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
KRAS MUTATED 0 0 1 0 0 4 2
KRAS WILD-TYPE 11 4 7 6 8 2 12

Figure S3.  Get High-res Image Gene #4: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.875 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 24 17
KRAS MUTATED 1 4 2
KRAS WILD-TYPE 14 20 15
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0928 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
KRAS MUTATED 1 0 5 1
KRAS WILD-TYPE 23 8 13 5
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 14 14 18
KRAS MUTATED 0 2 4 1
KRAS WILD-TYPE 10 12 10 17
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0592 (Fisher's exact test), Q value = 0.39

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
KRAS MUTATED 1 0 5 1
KRAS WILD-TYPE 24 7 12 6
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00877 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
PTEN MUTATED 1 9 1
PTEN WILD-TYPE 20 13 12

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

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 13 13 11
PTEN MUTATED 1 7 3 0
PTEN WILD-TYPE 19 6 10 11

Figure S5.  Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0515 (Fisher's exact test), Q value = 0.39

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 12 6 9
PTEN MUTATED 0 0 3 2 3
PTEN WILD-TYPE 12 9 9 4 6
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0182 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 9 8 7 7 7 5 5
PTEN MUTATED 0 2 0 1 0 3 2
PTEN WILD-TYPE 9 6 7 6 7 2 3

Figure S6.  Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 12 10
PTEN MUTATED 1 8 0 2
PTEN WILD-TYPE 15 11 12 8

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

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.38

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
PTEN MUTATED 0 0 3 0 3 0 5
PTEN WILD-TYPE 11 4 5 6 5 6 9

Figure S8.  Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0653 (Fisher's exact test), Q value = 0.39

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 24 17
PTEN MUTATED 4 1 5
PTEN WILD-TYPE 11 23 12
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.06 (Fisher's exact test), Q value = 0.39

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
PTEN MUTATED 8 0 1 1
PTEN WILD-TYPE 16 8 17 5
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0093 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 14 14 18
PTEN MUTATED 0 3 0 7
PTEN WILD-TYPE 10 11 14 11

Figure S9.  Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.21

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
PTEN MUTATED 8 0 0 2
PTEN WILD-TYPE 17 7 17 5

Figure S10.  Get High-res Image Gene #5: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S51.  Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
RB1 MUTATED 2 3 1
RB1 WILD-TYPE 19 19 12
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.79

Table S52.  Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 13 13 11
RB1 MUTATED 2 3 1 0
RB1 WILD-TYPE 18 10 12 11
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 0.84

Table S53.  Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 12 6 9
RB1 MUTATED 0 2 1 1 1
RB1 WILD-TYPE 12 7 11 5 8
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.77

Table S54.  Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 9 8 7 7 7 5 5
RB1 MUTATED 0 1 0 2 0 1 1
RB1 WILD-TYPE 9 7 7 5 7 4 4
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0712 (Fisher's exact test), Q value = 0.39

Table S55.  Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 12 10
RB1 MUTATED 0 4 0 2
RB1 WILD-TYPE 16 15 12 8
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0977 (Fisher's exact test), Q value = 0.47

Table S56.  Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
RB1 MUTATED 0 0 2 0 3 0 1
RB1 WILD-TYPE 11 4 6 6 5 6 13
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S57.  Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 24 17
RB1 MUTATED 2 2 2
RB1 WILD-TYPE 13 22 15
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S58.  Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
RB1 MUTATED 3 0 2 1
RB1 WILD-TYPE 21 8 16 5
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 0.84

Table S59.  Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 14 14 18
RB1 MUTATED 0 3 1 2
RB1 WILD-TYPE 10 11 13 16
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S60.  Gene #6: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
RB1 MUTATED 3 0 2 1
RB1 WILD-TYPE 22 7 15 6
'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 0.84

Table S61.  Gene #7: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
ZBTB7B MUTATED 2 1 2
ZBTB7B WILD-TYPE 19 21 11
'ZBTB7B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S62.  Gene #7: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 13 13 11
ZBTB7B MUTATED 2 1 2 1
ZBTB7B WILD-TYPE 18 12 11 10
'ZBTB7B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.53

Table S63.  Gene #7: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 12 6 9
ZBTB7B MUTATED 2 0 0 2 1
ZBTB7B WILD-TYPE 10 9 12 4 8
'ZBTB7B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 0.79

Table S64.  Gene #7: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 9 8 7 7 7 5 5
ZBTB7B MUTATED 2 2 0 0 0 0 1
ZBTB7B WILD-TYPE 7 6 7 7 7 5 4
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S65.  Gene #7: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 12 10
ZBTB7B MUTATED 2 2 1 1
ZBTB7B WILD-TYPE 14 17 11 9
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S66.  Gene #7: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
ZBTB7B MUTATED 2 0 0 0 1 1 2
ZBTB7B WILD-TYPE 9 4 8 6 7 5 12
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.53

Table S67.  Gene #7: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 24 17
ZBTB7B MUTATED 1 1 4
ZBTB7B WILD-TYPE 14 23 13
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.53

Table S68.  Gene #7: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
ZBTB7B MUTATED 5 1 0 0
ZBTB7B WILD-TYPE 19 7 18 6
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.82

Table S69.  Gene #7: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 14 14 18
ZBTB7B MUTATED 2 2 0 2
ZBTB7B WILD-TYPE 8 12 14 16
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.53

Table S70.  Gene #7: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
ZBTB7B MUTATED 5 1 0 0
ZBTB7B WILD-TYPE 20 6 17 7
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S71.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
PIK3R1 MUTATED 3 2 1
PIK3R1 WILD-TYPE 18 20 12
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S72.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 13 13 11
PIK3R1 MUTATED 3 1 1 1
PIK3R1 WILD-TYPE 17 12 12 10
'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 0.84

Table S73.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 12 6 9
PIK3R1 MUTATED 2 2 0 1 1
PIK3R1 WILD-TYPE 10 7 12 5 8
'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.773 (Fisher's exact test), Q value = 0.96

Table S74.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 9 8 7 7 7 5 5
PIK3R1 MUTATED 2 2 0 1 1 0 0
PIK3R1 WILD-TYPE 7 6 7 6 6 5 5
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.571 (Fisher's exact test), Q value = 0.86

Table S75.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 12 10
PIK3R1 MUTATED 3 2 1 0
PIK3R1 WILD-TYPE 13 17 11 10
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.706 (Fisher's exact test), Q value = 0.94

Table S76.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
PIK3R1 MUTATED 2 1 1 0 0 1 1
PIK3R1 WILD-TYPE 9 3 7 6 8 5 13
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S77.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 24 17
PIK3R1 MUTATED 1 3 2
PIK3R1 WILD-TYPE 14 21 15
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.501 (Fisher's exact test), Q value = 0.84

Table S78.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
PIK3R1 MUTATED 2 2 2 0
PIK3R1 WILD-TYPE 22 6 16 6
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.82

Table S79.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 14 14 18
PIK3R1 MUTATED 2 0 2 2
PIK3R1 WILD-TYPE 8 14 12 16
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.305 (Fisher's exact test), Q value = 0.77

Table S80.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
PIK3R1 MUTATED 2 2 1 1
PIK3R1 WILD-TYPE 23 5 16 6
'ARHGAP35 MUTATION STATUS' versus 'CN_CNMF'

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

Table S81.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
ARHGAP35 MUTATED 2 3 1
ARHGAP35 WILD-TYPE 19 19 12
'ARHGAP35 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.84

Table S82.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 13 13 11
ARHGAP35 MUTATED 2 2 0 2
ARHGAP35 WILD-TYPE 18 11 13 9
'ARHGAP35 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 0.85

Table S83.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 12 6 9
ARHGAP35 MUTATED 2 0 3 0 1
ARHGAP35 WILD-TYPE 10 9 9 6 8
'ARHGAP35 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.79

Table S84.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 9 8 7 7 7 5 5
ARHGAP35 MUTATED 2 0 0 0 2 1 1
ARHGAP35 WILD-TYPE 7 8 7 7 5 4 4
'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 0.86

Table S85.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 12 10
ARHGAP35 MUTATED 3 2 1 0
ARHGAP35 WILD-TYPE 13 17 11 10
'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 0.81

Table S86.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
ARHGAP35 MUTATED 2 0 2 0 1 1 0
ARHGAP35 WILD-TYPE 9 4 6 6 7 5 14
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.502 (Fisher's exact test), Q value = 0.84

Table S87.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 24 17
ARHGAP35 MUTATED 0 3 2
ARHGAP35 WILD-TYPE 15 21 15
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 0.57

Table S88.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
ARHGAP35 MUTATED 1 2 1 1
ARHGAP35 WILD-TYPE 23 6 17 5
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 0.84

Table S89.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 14 14 18
ARHGAP35 MUTATED 2 0 1 2
ARHGAP35 WILD-TYPE 8 14 13 16
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.174 (Fisher's exact test), Q value = 0.53

Table S90.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
ARHGAP35 MUTATED 1 2 1 1
ARHGAP35 WILD-TYPE 24 5 16 6
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.81

Table S91.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
PIK3CA MUTATED 6 10 3
PIK3CA WILD-TYPE 15 12 10
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 0.53

Table S92.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 13 13 11
PIK3CA MUTATED 6 8 4 2
PIK3CA WILD-TYPE 14 5 9 9
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 0.94

Table S93.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 12 6 9
PIK3CA MUTATED 3 3 6 3 3
PIK3CA WILD-TYPE 9 6 6 3 6
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.294 (Fisher's exact test), Q value = 0.77

Table S94.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 9 8 7 7 7 5 5
PIK3CA MUTATED 2 3 2 1 3 4 3
PIK3CA WILD-TYPE 7 5 5 6 4 1 2
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.74

Table S95.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 12 10
PIK3CA MUTATED 5 10 3 2
PIK3CA WILD-TYPE 11 9 9 8
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 0.79

Table S96.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
PIK3CA MUTATED 3 3 4 2 1 1 6
PIK3CA WILD-TYPE 8 1 4 4 7 5 8
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.28

Table S97.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 24 17
PIK3CA MUTATED 6 4 10
PIK3CA WILD-TYPE 9 20 7

Figure S11.  Get High-res Image Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 0.79

Table S98.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
PIK3CA MUTATED 11 2 4 3
PIK3CA WILD-TYPE 13 6 14 3
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 0.53

Table S99.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 14 14 18
PIK3CA MUTATED 3 6 2 9
PIK3CA WILD-TYPE 7 8 12 9
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 0.74

Table S100.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
PIK3CA MUTATED 12 1 4 3
PIK3CA WILD-TYPE 13 6 13 4
'MAMLD1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S101.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 21 22 13
MAMLD1 MUTATED 1 2 1
MAMLD1 WILD-TYPE 20 20 12
'MAMLD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.53

Table S102.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 13 13 11
MAMLD1 MUTATED 0 2 2 0
MAMLD1 WILD-TYPE 20 11 11 11
'MAMLD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0396 (Fisher's exact test), Q value = 0.36

Table S103.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 12 6 9
MAMLD1 MUTATED 0 0 2 2 0
MAMLD1 WILD-TYPE 12 9 10 4 9

Figure S12.  Get High-res Image Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'MAMLD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.36

Table S104.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 9 8 7 7 7 5 5
MAMLD1 MUTATED 0 2 0 0 0 2 0
MAMLD1 WILD-TYPE 9 6 7 7 7 3 5

Figure S13.  Get High-res Image Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 0.89

Table S105.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 19 12 10
MAMLD1 MUTATED 0 2 1 1
MAMLD1 WILD-TYPE 16 17 11 9
'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.769 (Fisher's exact test), Q value = 0.96

Table S106.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 11 4 8 6 8 6 14
MAMLD1 MUTATED 0 0 1 1 1 0 1
MAMLD1 WILD-TYPE 11 4 7 5 7 6 13
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0593 (Fisher's exact test), Q value = 0.39

Table S107.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 15 24 17
MAMLD1 MUTATED 1 0 3
MAMLD1 WILD-TYPE 14 24 14
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 0.91

Table S108.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
MAMLD1 MUTATED 2 0 1 1
MAMLD1 WILD-TYPE 22 8 17 5
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 0.84

Table S109.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 10 14 14 18
MAMLD1 MUTATED 0 2 0 2
MAMLD1 WILD-TYPE 10 12 14 16
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.79

Table S110.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
MAMLD1 MUTATED 3 0 0 1
MAMLD1 WILD-TYPE 22 7 17 6
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/UCS-TP/22569431/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/22541488/UCS-TP.transferedmergedcluster.txt

  • Number of patients = 57

  • Number of significantly mutated genes = 11

  • 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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