Correlation between gene mutation status and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1FB51FP
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/C1FB51FP
Overview
Introduction

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

Summary

Testing the association between mutation status of 9 genes and 8 molecular subtypes across 56 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 9 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 2 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
PTEN 10 (18%) 46 0.0264
(1.00) 		0.000529
(0.0381) 		0.00902
(0.632) 		0.000947
(0.0672) 		0.141
(1.00) 		0.0169
(1.00) 		0.038
(1.00) 		0.0442
(1.00)
FBXW7 21 (38%) 35 0.0476
(1.00) 		0.697
(1.00) 		0.725
(1.00) 		0.715
(1.00) 		0.347
(1.00) 		1
(1.00) 		0.9
(1.00) 		0.671
(1.00)
KRAS 7 (12%) 49 0.322
(1.00) 		0.0205
(1.00) 		0.151
(1.00) 		0.0976
(1.00) 		0.464
(1.00) 		0.496
(1.00) 		0.54
(1.00) 		0.327
(1.00)
TP53 50 (89%) 6 0.338
(1.00) 		0.54
(1.00) 		1
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.694
(1.00) 		1
(1.00) 		1
(1.00)
PPP2R1A 15 (27%) 41 1
(1.00) 		0.807
(1.00) 		0.728
(1.00) 		0.973
(1.00) 		0.503
(1.00) 		0.72
(1.00) 		0.185
(1.00) 		1
(1.00)
PIK3CA 19 (34%) 37 0.33
(1.00) 		0.967
(1.00) 		0.328
(1.00) 		0.547
(1.00) 		0.142
(1.00) 		0.0374
(1.00) 		0.226
(1.00) 		0.0369
(1.00)
PCDHAC2 11 (20%) 45 0.156
(1.00) 		0.126
(1.00) 		0.538
(1.00) 		0.896
(1.00) 		0.597
(1.00) 		0.586
(1.00) 		0.434
(1.00) 		0.435
(1.00)
PIK3R1 6 (11%) 50 0.859
(1.00) 		0.952
(1.00) 		0.574
(1.00) 		0.689
(1.00) 		0.425
(1.00) 		0.706
(1.00) 		0.804
(1.00) 		0.464
(1.00)
ZBTB7B 6 (11%) 50 0.49
(1.00) 		0.952
(1.00) 		1
(1.00) 		0.844
(1.00) 		0.104
(1.00) 		0.194
(1.00) 		0.152
(1.00) 		0.287
(1.00)
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
FBXW7 MUTATED 12 8 1
FBXW7 WILD-TYPE 10 15 9

Figure S1.  Get High-res Image Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.697 (Chi-square test), Q value = 1

Table S2.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 9 13 13
FBXW7 MUTATED 6 4 3 3 5
FBXW7 WILD-TYPE 6 5 6 10 8
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.725 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
FBXW7 MUTATED 8 7 6
FBXW7 WILD-TYPE 9 13 12
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.715 (Chi-square test), Q value = 1

Table S4.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
FBXW7 MUTATED 1 1 8 4 7
FBXW7 WILD-TYPE 3 2 7 8 14
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S5.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
FBXW7 MUTATED 5 8 3 5
FBXW7 WILD-TYPE 6 14 1 13
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S6.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
FBXW7 MUTATED 0 10 11
FBXW7 WILD-TYPE 1 16 17
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.9 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
FBXW7 MUTATED 5 9 2 5
FBXW7 WILD-TYPE 6 14 3 11
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.671 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
FBXW7 MUTATED 0 11 10
FBXW7 WILD-TYPE 1 14 19
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
KRAS MUTATED 2 5 0
KRAS WILD-TYPE 20 18 10
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0205 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 9 13 13
KRAS MUTATED 0 1 1 0 5
KRAS WILD-TYPE 12 8 8 13 8

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

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
KRAS MUTATED 0 3 4
KRAS WILD-TYPE 17 17 14
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0976 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
KRAS MUTATED 0 0 0 4 3
KRAS WILD-TYPE 4 3 15 8 18
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
KRAS MUTATED 1 4 1 1
KRAS WILD-TYPE 10 18 3 17
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.496 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
KRAS MUTATED 0 2 5
KRAS WILD-TYPE 1 24 23
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
KRAS MUTATED 1 5 0 1
KRAS WILD-TYPE 10 18 5 15
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.327 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
KRAS MUTATED 0 5 2
KRAS WILD-TYPE 1 20 27
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
TP53 MUTATED 21 20 8
TP53 WILD-TYPE 1 3 2
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.54 (Chi-square test), Q value = 1

Table S18.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 9 13 13
TP53 MUTATED 12 8 7 12 11
TP53 WILD-TYPE 0 1 2 1 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S19.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
TP53 MUTATED 15 18 16
TP53 WILD-TYPE 2 2 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.752 (Chi-square test), Q value = 1

Table S20.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
TP53 MUTATED 3 3 14 10 19
TP53 WILD-TYPE 1 0 1 2 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S21.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
TP53 MUTATED 10 20 4 16
TP53 WILD-TYPE 1 2 0 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
TP53 MUTATED 1 23 26
TP53 WILD-TYPE 0 3 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S23.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
TP53 MUTATED 10 21 5 14
TP53 WILD-TYPE 1 2 0 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S24.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
TP53 MUTATED 1 23 26
TP53 WILD-TYPE 0 2 3
'PPP2R1A MUTATION STATUS' versus 'CN_CNMF'

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

Table S25.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
PPP2R1A MUTATED 6 6 3
PPP2R1A WILD-TYPE 16 17 7
'PPP2R1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.807 (Chi-square test), Q value = 1

Table S26.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 9 13 13
PPP2R1A MUTATED 4 3 3 3 2
PPP2R1A WILD-TYPE 8 6 6 10 11
'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.728 (Fisher's exact test), Q value = 1

Table S27.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
PPP2R1A MUTATED 6 5 4
PPP2R1A WILD-TYPE 11 15 14
'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.973 (Chi-square test), Q value = 1

Table S28.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
PPP2R1A MUTATED 1 1 5 3 5
PPP2R1A WILD-TYPE 3 2 10 9 16
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.503 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
PPP2R1A MUTATED 5 5 1 4
PPP2R1A WILD-TYPE 6 17 3 14
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.72 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
PPP2R1A MUTATED 0 8 7
PPP2R1A WILD-TYPE 1 18 21
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
PPP2R1A MUTATED 6 5 1 3
PPP2R1A WILD-TYPE 5 18 4 13
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S32.  Gene #4: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
PPP2R1A MUTATED 0 7 8
PPP2R1A WILD-TYPE 1 18 21
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 1

Table S33.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
PIK3CA MUTATED 5 10 3
PIK3CA WILD-TYPE 17 13 7
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.967 (Chi-square test), Q value = 1

Table S34.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 9 13 13
PIK3CA MUTATED 4 3 4 4 4
PIK3CA WILD-TYPE 8 6 5 9 9
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
PIK3CA MUTATED 6 9 4
PIK3CA WILD-TYPE 11 11 14
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.547 (Chi-square test), Q value = 1

Table S36.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
PIK3CA MUTATED 1 0 6 3 9
PIK3CA WILD-TYPE 3 3 9 9 12
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
PIK3CA MUTATED 4 4 2 9
PIK3CA WILD-TYPE 7 18 2 9
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0374 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
PIK3CA MUTATED 1 12 6
PIK3CA WILD-TYPE 0 14 22

Figure S3.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S39.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
PIK3CA MUTATED 5 5 1 8
PIK3CA WILD-TYPE 6 18 4 8
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
PIK3CA MUTATED 1 5 13
PIK3CA WILD-TYPE 0 20 16

Figure S4.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
PTEN MUTATED 1 8 1
PTEN WILD-TYPE 21 15 9

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

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000529 (Chi-square test), Q value = 0.038

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 9 13 13
PTEN MUTATED 0 0 5 5 0
PTEN WILD-TYPE 12 9 4 8 13

Figure S6.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00902 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
PTEN MUTATED 1 8 1
PTEN WILD-TYPE 16 12 17

Figure S7.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000947 (Chi-square test), Q value = 0.067

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
PTEN MUTATED 3 0 0 0 7
PTEN WILD-TYPE 1 3 15 12 14

Figure S8.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
PTEN MUTATED 2 1 1 5
PTEN WILD-TYPE 9 21 3 13
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
PTEN MUTATED 0 8 1
PTEN WILD-TYPE 1 18 27

Figure S9.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
PTEN MUTATED 1 1 2 5
PTEN WILD-TYPE 10 22 3 11

Figure S10.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0442 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
PTEN MUTATED 0 1 8
PTEN WILD-TYPE 1 24 21

Figure S11.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PCDHAC2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S49.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
PCDHAC2 MUTATED 2 7 1
PCDHAC2 WILD-TYPE 20 16 9
'PCDHAC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.126 (Chi-square test), Q value = 1

Table S50.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 9 13 13
PCDHAC2 MUTATED 3 0 4 1 3
PCDHAC2 WILD-TYPE 9 9 5 12 10
'PCDHAC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S51.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
PCDHAC2 MUTATED 4 5 2
PCDHAC2 WILD-TYPE 13 15 16
'PCDHAC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.896 (Chi-square test), Q value = 1

Table S52.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
PCDHAC2 MUTATED 1 0 3 2 5
PCDHAC2 WILD-TYPE 3 3 12 10 16
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
PCDHAC2 MUTATED 2 3 0 5
PCDHAC2 WILD-TYPE 9 19 4 13
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 1

Table S54.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
PCDHAC2 MUTATED 0 6 4
PCDHAC2 WILD-TYPE 1 20 24
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
PCDHAC2 MUTATED 2 3 0 5
PCDHAC2 WILD-TYPE 9 20 5 11
'PCDHAC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'PCDHAC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
PCDHAC2 MUTATED 0 3 7
PCDHAC2 WILD-TYPE 1 22 22
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S57.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
PIK3R1 MUTATED 3 2 1
PIK3R1 WILD-TYPE 19 21 9
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.952 (Chi-square test), Q value = 1

Table S58.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 9 13 13
PIK3R1 MUTATED 2 1 1 1 1
PIK3R1 WILD-TYPE 10 8 8 12 12
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S59.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
PIK3R1 MUTATED 3 2 1
PIK3R1 WILD-TYPE 14 18 17
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.689 (Chi-square test), Q value = 1

Table S60.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
PIK3R1 MUTATED 0 0 3 1 2
PIK3R1 WILD-TYPE 4 3 12 11 19
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S61.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
PIK3R1 MUTATED 2 2 1 1
PIK3R1 WILD-TYPE 9 20 3 17
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.706 (Fisher's exact test), Q value = 1

Table S62.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
PIK3R1 MUTATED 0 2 4
PIK3R1 WILD-TYPE 1 24 24
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S63.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
PIK3R1 MUTATED 2 3 0 1
PIK3R1 WILD-TYPE 9 20 5 15
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S64.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
PIK3R1 MUTATED 0 4 2
PIK3R1 WILD-TYPE 1 21 27
'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S65.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 23 10
ZBTB7B MUTATED 3 1 1
ZBTB7B WILD-TYPE 19 22 9
'ZBTB7B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.952 (Chi-square test), Q value = 1

Table S66.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 9 13 13
ZBTB7B MUTATED 2 1 1 1 1
ZBTB7B WILD-TYPE 10 8 8 12 12
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S67.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 20 18
ZBTB7B MUTATED 2 2 2
ZBTB7B WILD-TYPE 15 18 16
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.844 (Chi-square test), Q value = 1

Table S68.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 4 3 15 12 21
ZBTB7B MUTATED 1 0 2 1 2
ZBTB7B WILD-TYPE 3 3 13 11 19
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S69.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 18
ZBTB7B MUTATED 1 1 2 2
ZBTB7B WILD-TYPE 10 21 2 16
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 1

Table S70.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 26 28
ZBTB7B MUTATED 0 5 1
ZBTB7B WILD-TYPE 1 21 27
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S71.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 16
ZBTB7B MUTATED 1 1 2 2
ZBTB7B WILD-TYPE 10 22 3 14
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 1

Table S72.  Gene #9: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 29
ZBTB7B MUTATED 0 1 5
ZBTB7B WILD-TYPE 1 24 24
Methods & Data
Input

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

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

  • Number of patients = 56

  • Number of significantly mutated genes = 9

  • Number of Molecular subtypes = 8

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

Fisher's exact test

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

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)
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