Correlation between gene mutation status and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1WQ02R2
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/C1WQ02R2
Overview
Introduction

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

Summary

Testing the association between mutation status of 13 genes and 8 molecular subtypes across 57 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 13 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 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 0.0948
(1.00) 		5e-05
(0.0052) 		0.0024
(0.247) 		0.0457
(1.00) 		0.0934
(1.00) 		0.0622
(1.00) 		0.00335
(0.342) 		0.0138
(1.00)
TP53 51 (89%) 6 0.57
(1.00) 		0.628
(1.00) 		0.878
(1.00) 		0.515
(1.00) 		1
(1.00) 		0.912
(1.00) 		1
(1.00) 		1
(1.00)
FBXW7 22 (39%) 35 0.262
(1.00) 		0.724
(1.00) 		0.633
(1.00) 		0.103
(1.00) 		0.467
(1.00) 		0.93
(1.00) 		1
(1.00) 		0.774
(1.00)
PPP2R1A 16 (28%) 41 0.759
(1.00) 		0.71
(1.00) 		0.591
(1.00) 		0.672
(1.00) 		0.564
(1.00) 		0.314
(1.00) 		0.698
(1.00) 		0.238
(1.00)
KRAS 7 (12%) 50 0.103
(1.00) 		0.0141
(1.00) 		0.0316
(1.00) 		0.00625
(0.625) 		0.461
(1.00) 		0.0905
(1.00) 		0.308
(1.00) 		0.0582
(1.00)
ZBTB7B 6 (11%) 51 0.724
(1.00) 		0.939
(1.00) 		1
(1.00) 		0.914
(1.00) 		0.099
(1.00) 		0.145
(1.00) 		0.48
(1.00) 		0.164
(1.00)
CHD4 10 (18%) 47 0.346
(1.00) 		0.0104
(1.00) 		0.184
(1.00) 		0.0059
(0.596) 		0.482
(1.00) 		0.412
(1.00) 		0.0897
(1.00) 		0.214
(1.00)
PIK3R1 6 (11%) 51 1
(1.00) 		0.94
(1.00) 		0.545
(1.00) 		0.702
(1.00) 		0.427
(1.00) 		0.508
(1.00) 		1
(1.00) 		0.305
(1.00)
ARHGAP35 6 (11%) 51 0.567
(1.00) 		0.332
(1.00) 		1
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.192
(1.00) 		1
(1.00) 		0.175
(1.00)
PIK3CA 20 (35%) 37 0.636
(1.00) 		0.902
(1.00) 		0.362
(1.00) 		0.371
(1.00) 		0.111
(1.00) 		0.341
(1.00) 		0.193
(1.00) 		0.269
(1.00)
MAMLD1 4 (7%) 53 1
(1.00) 		0.903
(1.00) 		0.687
(1.00) 		0.771
(1.00) 		0.0669
(1.00) 		0.677
(1.00) 		0.155
(1.00) 		0.358
(1.00)
RB1 6 (11%) 51 0.229
(1.00) 		0.0917
(1.00) 		0.0798
(1.00) 		0.0984
(1.00) 		0.834
(1.00) 		0.861
(1.00) 		0.865
(1.00) 		1
(1.00)
LYPLA2 3 (5%) 54 0.77
(1.00) 		0.617
(1.00) 		0.678
(1.00) 		0.346
(1.00) 		0.379
(1.00) 		0.564
(1.00) 		1
(1.00) 		0.694
(1.00)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
TP53 MUTATED 17 19 14
TP53 WILD-TYPE 1 2 3
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.628 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
TP53 MUTATED 12 8 8 12 11
TP53 WILD-TYPE 0 1 2 1 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
TP53 MUTATED 14 18 10 9
TP53 WILD-TYPE 1 2 2 1
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.515 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: '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 S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
TP53 MUTATED 10 20 4 17
TP53 WILD-TYPE 1 2 0 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S6.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: '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 = 1 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
TP53 MUTATED 12 21 18
TP53 WILD-TYPE 1 2 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.262 (Fisher's exact test), Q value = 1

Table S9.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
FBXW7 MUTATED 9 9 4
FBXW7 WILD-TYPE 9 12 13
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.633 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
FBXW7 MUTATED 7 8 5 2
FBXW7 WILD-TYPE 8 12 7 8
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 1

Table S12.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: '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 = 0.467 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
FBXW7 MUTATED 5 8 3 6
FBXW7 WILD-TYPE 6 14 1 13
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S14.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: '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 = 1 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
FBXW7 MUTATED 5 9 8
FBXW7 WILD-TYPE 8 14 12
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S16.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.759 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
PPP2R1A MUTATED 4 7 5
PPP2R1A WILD-TYPE 14 14 12
'PPP2R1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 1

Table S18.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

P value = 0.591 (Fisher's exact test), Q value = 1

Table S19.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
PPP2R1A MUTATED 6 5 2 3
PPP2R1A WILD-TYPE 9 15 10 7
'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.672 (Fisher's exact test), Q value = 1

Table S20.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: '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 = 0.564 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
PPP2R1A MUTATED 5 5 1 5
PPP2R1A WILD-TYPE 6 17 3 14
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.314 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.698 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
PPP2R1A MUTATED 5 6 5
PPP2R1A WILD-TYPE 8 17 15
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.238 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: '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
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0948 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
PTEN MUTATED 1 7 3
PTEN WILD-TYPE 17 14 14
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0052

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
PTEN MUTATED 0 0 6 5 0
PTEN WILD-TYPE 12 9 4 8 13

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

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
PTEN MUTATED 0 8 0 3
PTEN WILD-TYPE 15 12 12 7

Figure S2.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0457 (Fisher's exact test), Q value = 1

Table S28.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: '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 S3.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0934 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
PTEN MUTATED 2 1 1 6
PTEN WILD-TYPE 9 21 3 13
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0622 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.00335 (Fisher's exact test), Q value = 0.34

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
PTEN MUTATED 3 0 7
PTEN WILD-TYPE 10 23 13

Figure S4.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: '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 S5.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
KRAS MUTATED 2 5 0
KRAS WILD-TYPE 16 16 17
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
KRAS MUTATED 0 1 1 0 5
KRAS WILD-TYPE 12 8 9 13 8

Figure S6.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
KRAS MUTATED 0 3 4 0
KRAS WILD-TYPE 15 17 8 10

Figure S7.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00625 (Fisher's exact test), Q value = 0.62

Table S36.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: '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 S8.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.461 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
KRAS MUTATED 1 4 1 1
KRAS WILD-TYPE 10 18 3 18
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0905 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.308 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
KRAS MUTATED 1 5 1
KRAS WILD-TYPE 12 18 19
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0582 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: '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
'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S41.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
ZBTB7B MUTATED 2 1 2
ZBTB7B WILD-TYPE 16 20 15
'ZBTB7B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.939 (Fisher's exact test), Q value = 1

Table S42.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

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

Table S43.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
ZBTB7B MUTATED 2 2 1 1
ZBTB7B WILD-TYPE 13 18 11 9
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S44.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: '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 = 0.099 (Fisher's exact test), Q value = 1

Table S45.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
ZBTB7B MUTATED 1 1 2 2
ZBTB7B WILD-TYPE 10 21 2 17
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S46.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.48 (Fisher's exact test), Q value = 1

Table S47.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
ZBTB7B MUTATED 2 1 3
ZBTB7B WILD-TYPE 11 22 17
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 1

Table S48.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: '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
'CHD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S49.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
CHD4 MUTATED 2 6 2
CHD4 WILD-TYPE 16 15 15
'CHD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 1

Table S50.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
CHD4 MUTATED 0 4 4 1 1
CHD4 WILD-TYPE 12 5 6 12 12

Figure S9.  Get High-res Image Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CHD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 1

Table S51.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
CHD4 MUTATED 2 5 0 3
CHD4 WILD-TYPE 13 15 12 7
'CHD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0059 (Fisher's exact test), Q value = 0.6

Table S52.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: '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
CHD4 MUTATED 0 2 4 0 3 0 1
CHD4 WILD-TYPE 11 2 4 6 5 6 13

Figure S10.  Get High-res Image Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S53.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
CHD4 MUTATED 3 2 1 3
CHD4 WILD-TYPE 8 20 3 16
'CHD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 1

Table S54.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
CHD4 MUTATED 6 0 2 1
CHD4 WILD-TYPE 18 8 16 5
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0897 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
CHD4 MUTATED 4 1 4
CHD4 WILD-TYPE 9 22 16
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.214 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
CHD4 MUTATED 6 0 1 2
CHD4 WILD-TYPE 19 7 16 5
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (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 18 21 17
PIK3R1 MUTATED 2 2 2
PIK3R1 WILD-TYPE 16 19 15
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.94 (Fisher's exact 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 10 13 13
PIK3R1 MUTATED 2 1 1 1 1
PIK3R1 WILD-TYPE 10 8 9 12 12
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.545 (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 CLUS_4
ALL 15 20 12 10
PIK3R1 MUTATED 3 2 1 0
PIK3R1 WILD-TYPE 12 18 11 10
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.702 (Fisher's exact 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 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 = 0.427 (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 19
PIK3R1 MUTATED 2 2 1 1
PIK3R1 WILD-TYPE 9 20 3 18
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.508 (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 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 = 1 (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
ALL 13 23 20
PIK3R1 MUTATED 1 3 2
PIK3R1 WILD-TYPE 12 20 18
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.305 (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 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 = 0.567 (Fisher's exact test), Q value = 1

Table S65.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
ARHGAP35 MUTATED 1 2 3
ARHGAP35 WILD-TYPE 17 19 14
'ARHGAP35 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 1

Table S66.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
ARHGAP35 MUTATED 2 0 2 0 2
ARHGAP35 WILD-TYPE 10 9 8 13 11
'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S67.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
ARHGAP35 MUTATED 2 2 1 1
ARHGAP35 WILD-TYPE 13 18 11 9
'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 1

Table S68.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #4: '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 = 1 (Fisher's exact test), Q value = 1

Table S69.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
ARHGAP35 MUTATED 1 2 0 2
ARHGAP35 WILD-TYPE 10 20 4 17
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 1

Table S70.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #6: '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 = 1 (Fisher's exact test), Q value = 1

Table S71.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
ARHGAP35 MUTATED 1 2 2
ARHGAP35 WILD-TYPE 12 21 18
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.175 (Fisher's exact test), Q value = 1

Table S72.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.636 (Fisher's exact test), Q value = 1

Table S73.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
PIK3CA MUTATED 5 9 5
PIK3CA WILD-TYPE 13 12 12
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S74.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
PIK3CA MUTATED 4 3 5 4 4
PIK3CA WILD-TYPE 8 6 5 9 9
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 1

Table S75.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
PIK3CA MUTATED 5 10 3 2
PIK3CA WILD-TYPE 10 10 9 8
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.371 (Fisher's exact test), Q value = 1

Table S76.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: '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 = 0.111 (Fisher's exact test), Q value = 1

Table S77.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
PIK3CA MUTATED 4 4 2 10
PIK3CA WILD-TYPE 7 18 2 9
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 1

Table S78.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.193 (Fisher's exact test), Q value = 1

Table S79.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
PIK3CA MUTATED 6 5 9
PIK3CA WILD-TYPE 7 18 11
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 1

Table S80.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: '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 S81.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
MAMLD1 MUTATED 1 2 1
MAMLD1 WILD-TYPE 17 19 16
'MAMLD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S82.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
MAMLD1 MUTATED 0 1 1 1 1
MAMLD1 WILD-TYPE 12 8 9 12 12
'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S83.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
MAMLD1 MUTATED 0 2 1 1
MAMLD1 WILD-TYPE 15 18 11 9
'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S84.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #4: '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 = 0.0669 (Fisher's exact test), Q value = 1

Table S85.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
MAMLD1 MUTATED 0 0 1 3
MAMLD1 WILD-TYPE 11 22 3 16
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 1

Table S86.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.155 (Fisher's exact test), Q value = 1

Table S87.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
MAMLD1 MUTATED 2 0 2
MAMLD1 WILD-TYPE 11 23 18
'MAMLD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 1

Table S88.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #8: '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
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 1

Table S89.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
RB1 MUTATED 2 4 0
RB1 WILD-TYPE 16 17 17
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0917 (Fisher's exact test), Q value = 1

Table S90.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
RB1 MUTATED 0 1 3 2 0
RB1 WILD-TYPE 12 8 7 11 13
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0798 (Fisher's exact test), Q value = 1

Table S91.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
RB1 MUTATED 0 4 0 2
RB1 WILD-TYPE 15 16 12 8
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0984 (Fisher's exact test), Q value = 1

Table S92.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: '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 = 0.834 (Fisher's exact test), Q value = 1

Table S93.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
RB1 MUTATED 2 2 0 2
RB1 WILD-TYPE 9 20 4 17
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.861 (Fisher's exact test), Q value = 1

Table S94.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.865 (Fisher's exact test), Q value = 1

Table S95.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
RB1 MUTATED 2 2 2
RB1 WILD-TYPE 11 21 18
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S96.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: '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
'LYPLA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S97.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 21 17
LYPLA2 MUTATED 1 2 0
LYPLA2 WILD-TYPE 17 19 17
'LYPLA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S98.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
LYPLA2 MUTATED 0 1 1 0 1
LYPLA2 WILD-TYPE 12 8 9 13 12
'LYPLA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.678 (Fisher's exact test), Q value = 1

Table S99.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
LYPLA2 MUTATED 0 1 1 1
LYPLA2 WILD-TYPE 15 19 11 9
'LYPLA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S100.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #4: '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
LYPLA2 MUTATED 0 0 1 0 1 1 0
LYPLA2 WILD-TYPE 11 4 7 6 7 5 14
'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S101.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
LYPLA2 MUTATED 0 1 1 1
LYPLA2 WILD-TYPE 11 21 3 18
'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S102.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 8 18 6
LYPLA2 MUTATED 1 0 1 1
LYPLA2 WILD-TYPE 23 8 17 5
'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S103.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 13 23 20
LYPLA2 MUTATED 1 1 1
LYPLA2 WILD-TYPE 12 22 19
'LYPLA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S104.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 7 17 7
LYPLA2 MUTATED 1 0 1 1
LYPLA2 WILD-TYPE 24 7 16 6
Methods & Data
Input

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

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

  • Number of patients = 57

  • Number of significantly mutated genes = 13

  • Number of Molecular subtypes = 8

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

Fisher's exact test

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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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