Correlation between gene mutation status and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1GT5M92
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1GT5M92
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 10 molecular subtypes across 57 patients, 8 significant findings detected with P value < 0.05 and Q value < 0.25.

  • PTEN mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • CHD4 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 13 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 0.0935
(0.539) 		6e-05
(0.0078) 		1
(1.00) 		0.0181
(0.262) 		0.00216
(0.14) 		0.0467
(0.506) 		0.0952
(0.539) 		0.0598
(0.539) 		0.00343
(0.149) 		0.0136
(0.241)
KRAS 7 (12%) 50 0.104
(0.539) 		0.0148
(0.241) 		1
(1.00) 		0.203
(0.645) 		0.033
(0.427) 		0.00677
(0.176) 		0.466
(0.89) 		0.0905
(0.539) 		0.308
(0.79) 		0.0585
(0.539)
CHD4 10 (18%) 47 0.346
(0.79) 		0.0102
(0.222) 		0.712
(0.98) 		0.161
(0.62) 		0.184
(0.627) 		0.00525
(0.171) 		0.478
(0.89) 		0.41
(0.82) 		0.0887
(0.539) 		0.217
(0.671)
TP53 51 (89%) 6 0.566
(0.953) 		0.629
(0.98) 		0.641
(0.98) 		0.138
(0.618) 		0.878
(1.00) 		0.51
(0.909) 		1
(1.00) 		0.912
(1.00) 		1
(1.00) 		1
(1.00)
FBXW7 22 (39%) 35 0.264
(0.762) 		0.724
(0.98) 		0.144
(0.618) 		0.168
(0.624) 		0.632
(0.98) 		0.103
(0.539) 		0.469
(0.89) 		0.931
(1.00) 		1
(1.00) 		0.773
(0.999)
PPP2R1A 16 (28%) 41 0.762
(0.999) 		0.709
(0.98) 		0.192
(0.627) 		0.501
(0.909) 		0.59
(0.972) 		0.673
(0.98) 		0.568
(0.953) 		0.319
(0.79) 		0.697
(0.98) 		0.234
(0.693)
ZBTB7B 6 (11%) 51 0.72
(0.98) 		0.939
(1.00) 		0.641
(0.98) 		0.377
(0.79) 		1
(1.00) 		0.914
(1.00) 		0.0963
(0.539) 		0.148
(0.618) 		0.479
(0.89) 		0.162
(0.62)
PIK3R1 6 (11%) 51 1
(1.00) 		0.939
(1.00) 		0.383
(0.79) 		0.776
(0.999) 		0.544
(0.953) 		0.706
(0.98) 		0.424
(0.835) 		0.506
(0.909) 		1
(1.00) 		0.307
(0.79)
ARHGAP35 6 (11%) 51 0.572
(0.953) 		0.333
(0.79) 		1
(1.00) 		0.343
(0.79) 		1
(1.00) 		0.4
(0.813) 		1
(1.00) 		0.191
(0.627) 		1
(1.00) 		0.176
(0.627)
PIK3CA 20 (35%) 37 0.638
(0.98) 		0.901
(1.00) 		0.133
(0.618) 		0.295
(0.79) 		0.362
(0.79) 		0.369
(0.79) 		0.112
(0.561) 		0.339
(0.79) 		0.193
(0.627) 		0.27
(0.763)
MAMLD1 4 (7%) 53 1
(1.00) 		0.903
(1.00) 		0.121
(0.582) 		0.0362
(0.427) 		0.688
(0.98) 		0.768
(0.999) 		0.0645
(0.539) 		0.678
(0.98) 		0.152
(0.618) 		0.354
(0.79)
RB1 6 (11%) 51 0.227
(0.686) 		0.0906
(0.539) 		0.369
(0.79) 		0.313
(0.79) 		0.0787
(0.539) 		0.0981
(0.539) 		0.837
(1.00) 		0.86
(1.00) 		0.866
(1.00) 		1
(1.00)
LYPLA2 3 (5%) 54 0.767
(0.999) 		0.617
(0.98) 		1
(1.00) 		0.838
(1.00) 		0.678
(0.98) 		0.348
(0.79) 		0.378
(0.79) 		0.564
(0.953) 		1
(1.00) 		0.693
(0.98)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 0.95

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 = 0.629 (Fisher's exact test), Q value = 0.98

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 'RPPA_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2
ALL 27 21
TP53 MUTATED 25 18
TP53 WILD-TYPE 2 3
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.62

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 = 0.878 (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 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 = 0.51 (Fisher's exact test), Q value = 0.91

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

Table S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: '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 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 = 0.264 (Fisher's exact test), Q value = 0.76

Table S11.  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 = 0.98

Table S12.  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 'RPPA_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2
ALL 27 21
FBXW7 MUTATED 14 6
FBXW7 WILD-TYPE 13 15
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.62

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 = 0.632 (Fisher's exact test), Q value = 0.98

Table S15.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.54

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 = 0.469 (Fisher's exact test), Q value = 0.89

Table S17.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.931 (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 = 1 (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
ALL 13 23 20
FBXW7 MUTATED 5 9 8
FBXW7 WILD-TYPE 8 14 12
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.773 (Fisher's exact test), Q value = 1

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 = 0.762 (Fisher's exact test), Q value = 1

Table S21.  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 = 0.709 (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 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 'RPPA_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2
ALL 27 21
PPP2R1A MUTATED 5 8
PPP2R1A WILD-TYPE 22 13
'PPP2R1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.501 (Fisher's exact test), Q value = 0.91

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 = 0.59 (Fisher's exact test), Q value = 0.97

Table S25.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.673 (Fisher's exact test), Q value = 0.98

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 = 0.568 (Fisher's exact test), Q value = 0.95

Table S27.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.319 (Fisher's exact test), Q value = 0.79

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 = 0.697 (Fisher's exact test), Q value = 0.98

Table S29.  Gene #3: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.234 (Fisher's exact test), Q value = 0.69

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
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0935 (Fisher's exact test), Q value = 0.54

Table S31.  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 = 6e-05 (Fisher's exact test), Q value = 0.0078

Table S32.  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 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2
ALL 27 21
PTEN MUTATED 5 3
PTEN WILD-TYPE 22 18
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.26

Table S34.  Gene #4: '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 S2.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.14

Table S35.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: '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 S3.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 0.51

Table S36.  Gene #4: '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 S4.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0952 (Fisher's exact test), Q value = 0.54

Table S37.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0598 (Fisher's exact test), Q value = 0.54

Table S38.  Gene #4: '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 = 0.00343 (Fisher's exact test), Q value = 0.15

Table S39.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: '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 S5.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.24

Table S40.  Gene #4: '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 S6.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.54

Table S41.  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 = 0.0148 (Fisher's exact test), Q value = 0.24

Table S42.  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 S7.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2
ALL 27 21
KRAS MUTATED 3 2
KRAS WILD-TYPE 24 19
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 0.65

Table S44.  Gene #5: '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 = 0.033 (Fisher's exact test), Q value = 0.43

Table S45.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: '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 S8.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00677 (Fisher's exact test), Q value = 0.18

Table S46.  Gene #5: '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 S9.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 0.89

Table S47.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.54

Table S48.  Gene #5: '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 = 0.308 (Fisher's exact test), Q value = 0.79

Table S49.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.0585 (Fisher's exact test), Q value = 0.54

Table S50.  Gene #5: '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
'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.72 (Fisher's exact test), Q value = 0.98

Table S51.  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 S52.  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 'RPPA_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 0.98

Table S53.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 27 21
ZBTB7B MUTATED 2 3
ZBTB7B WILD-TYPE 25 18
'ZBTB7B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 0.79

Table S54.  Gene #6: '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 S55.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #5: '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 S56.  Gene #6: '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 = 0.0963 (Fisher's exact test), Q value = 0.54

Table S57.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.148 (Fisher's exact test), Q value = 0.62

Table S58.  Gene #6: '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 = 0.479 (Fisher's exact test), Q value = 0.89

Table S59.  Gene #6: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.162 (Fisher's exact test), Q value = 0.62

Table S60.  Gene #6: '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
'CHD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.79

Table S61.  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 = 0.0102 (Fisher's exact test), Q value = 0.22

Table S62.  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 S10.  Get High-res Image Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CHD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 0.98

Table S63.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 27 21
CHD4 MUTATED 6 3
CHD4 WILD-TYPE 21 18
'CHD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.62

Table S64.  Gene #7: 'CHD4 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
CHD4 MUTATED 0 2 0 3 1 2 1
CHD4 WILD-TYPE 9 6 7 4 6 3 4
'CHD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.63

Table S65.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.00525 (Fisher's exact test), Q value = 0.17

Table S66.  Gene #7: 'CHD4 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
CHD4 MUTATED 0 2 4 0 3 0 1
CHD4 WILD-TYPE 11 2 4 6 5 6 13

Figure S11.  Get High-res Image Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 0.89

Table S67.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.41 (Fisher's exact test), Q value = 0.82

Table S68.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.0887 (Fisher's exact test), Q value = 0.54

Table S69.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.217 (Fisher's exact test), Q value = 0.67

Table S70.  Gene #7: 'CHD4 MUTATION STATUS' versus Molecular Subtype #10: '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 S71.  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 = 0.939 (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 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 'RPPA_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2
ALL 27 21
PIK3R1 MUTATED 2 4
PIK3R1 WILD-TYPE 25 17
'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.776 (Fisher's exact test), Q value = 1

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 = 0.544 (Fisher's exact test), Q value = 0.95

Table S75.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.706 (Fisher's exact test), Q value = 0.98

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 = 0.424 (Fisher's exact test), Q value = 0.84

Table S77.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.506 (Fisher's exact test), Q value = 0.91

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

Table S79.  Gene #8: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.307 (Fisher's exact test), Q value = 0.79

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 = 0.572 (Fisher's exact test), Q value = 0.95

Table S81.  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 = 0.333 (Fisher's exact test), Q value = 0.79

Table S82.  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 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2
ALL 27 21
ARHGAP35 MUTATED 3 3
ARHGAP35 WILD-TYPE 24 18
'ARHGAP35 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.343 (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 = 1 (Fisher's exact test), Q value = 1

Table S85.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.4 (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 = 1 (Fisher's exact test), Q value = 1

Table S87.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.191 (Fisher's exact test), Q value = 0.63

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

Table S89.  Gene #9: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.176 (Fisher's exact test), Q value = 0.63

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 = 0.638 (Fisher's exact test), Q value = 0.98

Table S91.  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 = 0.901 (Fisher's exact test), Q value = 1

Table S92.  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 'RPPA_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2
ALL 27 21
PIK3CA MUTATED 13 5
PIK3CA WILD-TYPE 14 16
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 0.79

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 = 0.362 (Fisher's exact test), Q value = 0.79

Table S95.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.369 (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 = 0.112 (Fisher's exact test), Q value = 0.56

Table S97.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.339 (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 = 0.193 (Fisher's exact test), Q value = 0.63

Table S99.  Gene #10: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.27 (Fisher's exact test), Q value = 0.76

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 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 S102.  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 'RPPA_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.58

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

nPatients CLUS_1 CLUS_2
ALL 27 21
MAMLD1 MUTATED 4 0
MAMLD1 WILD-TYPE 23 21
'MAMLD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 0.43

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 S12.  Get High-res Image Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'MAMLD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.98

Table S105.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.768 (Fisher's exact test), Q value = 1

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 = 0.0645 (Fisher's exact test), Q value = 0.54

Table S107.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.678 (Fisher's exact test), Q value = 0.98

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 = 0.152 (Fisher's exact test), Q value = 0.62

Table S109.  Gene #11: 'MAMLD1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.354 (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
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 0.69

Table S111.  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 = 0.0906 (Fisher's exact test), Q value = 0.54

Table S112.  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 'RPPA_CNMF'

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

Table S113.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 27 21
RB1 MUTATED 4 1
RB1 WILD-TYPE 23 20
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.79

Table S114.  Gene #12: '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 = 0.0787 (Fisher's exact test), Q value = 0.54

Table S115.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.0981 (Fisher's exact test), Q value = 0.54

Table S116.  Gene #12: '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 = 0.837 (Fisher's exact test), Q value = 1

Table S117.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.86 (Fisher's exact test), Q value = 1

Table S118.  Gene #12: '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 = 0.866 (Fisher's exact test), Q value = 1

Table S119.  Gene #12: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: '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 S120.  Gene #12: '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
'LYPLA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S121.  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 = 0.98

Table S122.  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 'RPPA_CNMF'

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

Table S123.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2
ALL 27 21
LYPLA2 MUTATED 2 1
LYPLA2 WILD-TYPE 25 20
'LYPLA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: 'LYPLA2 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
LYPLA2 MUTATED 0 1 1 1 0 0 0
LYPLA2 WILD-TYPE 9 7 6 6 7 5 5
'LYPLA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.678 (Fisher's exact test), Q value = 0.98

Table S125.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.348 (Fisher's exact test), Q value = 0.79

Table S126.  Gene #13: 'LYPLA2 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
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 = 0.378 (Fisher's exact test), Q value = 0.79

Table S127.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.95

Table S128.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #8: '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 S129.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.693 (Fisher's exact test), Q value = 0.98

Table S130.  Gene #13: 'LYPLA2 MUTATION STATUS' versus Molecular Subtype #10: '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 = 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/15165005/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCS-TP/15115115/UCS-TP.transferedmergedcluster.txt

  • Number of patients = 57

  • Number of significantly mutated genes = 13

  • 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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