Correlation between gene mutation status and molecular subtypes
Colorectal Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C10K26ZQ
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/C10K26ZQ
Overview
Introduction

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

Summary

Testing the association between mutation status of 24 genes and 10 molecular subtypes across 223 patients, 9 significant findings detected with P value < 0.05 and Q value < 0.25.

  • FBXW7 mutation correlated to 'CN_CNMF'.

  • BRAF mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL', and 'CN_CNMF'.

  • KRAS mutation correlated to 'MRNA_CNMF' and 'MRNA_CHIERARCHICAL'.

  • TP53 mutation correlated to 'MRNA_CHIERARCHICAL' and 'CN_CNMF'.

  • PIK3CA mutation correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 24 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 9 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
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
BRAF 22 (10%) 201 2.84e-06
(0.000594) 		1.41e-07
(2.97e-05) 		0.000332
(0.0678) 		0.482
(1.00) 		0.304
(1.00) 		0.473
(1.00) 		0.277
(1.00) 		1
(1.00) 		0.684
(1.00)
KRAS 96 (43%) 127 7.86e-05
(0.0162) 		4.23e-05
(0.00877) 		0.322
(1.00) 		0.107
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.00165
(0.331) 		0.716
(1.00) 		0.0218
(1.00) 		0.0431
(1.00)
TP53 119 (53%) 104 0.00206
(0.412) 		0.000493
(0.1) 		1.15e-10
(2.42e-08) 		0.562
(1.00) 		0.755
(1.00) 		0.0253
(1.00) 		0.736
(1.00) 		0.0307
(1.00) 		0.567
(1.00)
FBXW7 38 (17%) 185 0.0626
(1.00) 		0.0455
(1.00) 		2.6e-05
(0.00541) 		0.0122
(1.00) 		0.0362
(1.00) 		0.00143
(0.289) 		0.442
(1.00) 		0.416
(1.00) 		0.156
(1.00)
PIK3CA 33 (15%) 190 0.208
(1.00) 		0.569
(1.00) 		0.00032
(0.0655) 		0.0673
(1.00) 		0.129
(1.00) 		0.0826
(1.00) 		1
(1.00) 		0.165
(1.00) 		1
(1.00)
APC 160 (72%) 63 0.00773
(1.00) 		0.0271
(1.00) 		0.119
(1.00) 		0.466
(1.00) 		0.461
(1.00) 		0.381
(1.00) 		0.187
(1.00) 		0.34
(1.00) 		0.837
(1.00)
NRAS 20 (9%) 203 0.0478
(1.00) 		0.127
(1.00) 		0.199
(1.00) 		0.909
(1.00) 		0.474
(1.00) 		0.191
(1.00) 		1
(1.00) 		0.268
(1.00) 		1
(1.00)
SMAD4 26 (12%) 197 0.0322
(1.00) 		0.289
(1.00) 		0.0646
(1.00) 		0.827
(1.00) 		0.339
(1.00) 		0.589
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
FAM123B 25 (11%) 198 0.0787
(1.00) 		0.0924
(1.00) 		0.00912
(1.00) 		0.345
(1.00) 		0.588
(1.00) 		0.0494
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SMAD2 15 (7%) 208 0.134
(1.00) 		0.518
(1.00) 		0.161
(1.00) 		0.592
(1.00) 		0.133
(1.00) 		0.71
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
TCF7L2 18 (8%) 205 1
(1.00) 		0.416
(1.00) 		0.00239
(0.477) 		0.836
(1.00) 		0.896
(1.00) 		0.353
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ACVR2A 9 (4%) 214 0.00717
(1.00) 		0.184
(1.00) 		0.0236
(1.00) 		0.0952
(1.00) 		0.469
(1.00) 		1
(1.00) 		1
(1.00) 		0.173
(1.00) 		1
(1.00)
SOX9 10 (4%) 213 0.129
(1.00) 		0.123
(1.00) 		0.00856
(1.00) 		0.189
(1.00) 		0.694
(1.00) 		0.773
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ELF3 6 (3%) 217 0.363
(1.00) 		0.811
(1.00) 		0.273
(1.00) 		0.544
(1.00) 		0.436
(1.00) 		0.0496
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CRTC1 6 (3%) 217 0.123
(1.00) 		0.165
(1.00) 		0.273
(1.00) 		0.175
(1.00) 		0.482
(1.00) 		0.775
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
TNFRSF10C 6 (3%) 217 0.317
(1.00) 		0.287
(1.00) 		0.707
(1.00) 		0.278
(1.00) 		0.378
(1.00) 		0.223
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
KIAA1804 15 (7%) 208 0.271
(1.00) 		0.394
(1.00) 		0.028
(1.00) 		0.506
(1.00) 		0.474
(1.00) 		0.71
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
KRTAP5-5 4 (2%) 219 0.327
(1.00) 		0.482
(1.00) 		0.839
(1.00) 		0.385
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PTEN 7 (3%) 216 0.0276
(1.00) 		0.337
(1.00) 		0.07
(1.00) 		0.544
(1.00) 		0.436
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.347
(1.00) 		0.298
(1.00)
ACOT4 3 (1%) 220 0.255
(1.00) 		0.49
(1.00) 		0.792
(1.00) 		0.523
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
MYO1B 13 (6%) 210 0.00868
(1.00) 		0.00887
(1.00) 		0.00479
(0.949) 		0.0215
(1.00) 		0.469
(1.00) 		0.175
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PCBP1 6 (3%) 217 0.234
(1.00) 		0.811
(1.00) 		0.795
(1.00) 		0.648
(1.00) 		0.482
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
GGT1 3 (1%) 220 0.162
(1.00) 		0.523
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ACVR1B 14 (6%) 209 0.374
(1.00) 		0.316
(1.00) 		0.0986
(1.00) 		0.735
(1.00) 		0.376
(1.00) 		0.86
(1.00) 		1
(1.00) 		0.581
(1.00) 		1
(1.00)
'APC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00773 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
APC MUTATED 21 46 50 30
APC WILD-TYPE 21 11 17 9

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

'APC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0271 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
APC MUTATED 32 35 35 45
APC WILD-TYPE 8 13 26 11

Figure S2.  Get High-res Image Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'APC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
APC MUTATED 54 53 47 3
APC WILD-TYPE 15 32 15 1
'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
APC MUTATED 32 44 17 18
APC WILD-TYPE 8 23 7 8
'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S5.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
APC MUTATED 16 75 15 5
APC WILD-TYPE 4 34 4 4
'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
APC MUTATED 5 20 7 124
APC WILD-TYPE 3 6 6 45
'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
APC MUTATED 155 1 0
APC WILD-TYPE 58 1 1
'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
APC MUTATED 3 5 141
APC WILD-TYPE 0 4 53
'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'APC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
APC MUTATED 6 1 142
APC WILD-TYPE 2 1 54
'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0626 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
FBXW7 MUTATED 11 6 7 9
FBXW7 WILD-TYPE 31 51 60 30
'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
FBXW7 MUTATED 4 5 17 7
FBXW7 WILD-TYPE 36 43 44 49

Figure S3.  Get High-res Image Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 2.6e-05 (Fisher's exact test), Q value = 0.0054

Table S12.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
FBXW7 MUTATED 2 26 9 1
FBXW7 WILD-TYPE 67 59 53 3

Figure S4.  Get High-res Image Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
FBXW7 MUTATED 7 9 2 11
FBXW7 WILD-TYPE 33 58 22 15

Figure S5.  Get High-res Image Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
FBXW7 MUTATED 3 18 8 0
FBXW7 WILD-TYPE 17 91 11 9

Figure S6.  Get High-res Image Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.29

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
FBXW7 MUTATED 0 12 1 25
FBXW7 WILD-TYPE 8 14 12 144

Figure S7.  Get High-res Image Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
FBXW7 MUTATED 37 1 0
FBXW7 WILD-TYPE 176 1 1
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.416 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
FBXW7 MUTATED 0 0 36
FBXW7 WILD-TYPE 3 9 158
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S18.  Gene #2: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
FBXW7 MUTATED 0 1 35
FBXW7 WILD-TYPE 8 1 161
'NRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0478 (Fisher's exact test), Q value = 1

Table S19.  Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
NRAS MUTATED 0 8 6 5
NRAS WILD-TYPE 42 49 61 34

Figure S8.  Get High-res Image Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'NRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S20.  Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
NRAS MUTATED 1 8 4 6
NRAS WILD-TYPE 39 40 57 50
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
NRAS MUTATED 9 9 2 0
NRAS WILD-TYPE 60 76 60 4
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.909 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
NRAS MUTATED 3 7 1 2
NRAS WILD-TYPE 37 60 23 24
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.474 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
NRAS MUTATED 0 10 2 1
NRAS WILD-TYPE 20 99 17 8
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
NRAS MUTATED 0 5 0 14
NRAS WILD-TYPE 8 21 13 155
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S25.  Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
NRAS MUTATED 19 0 0
NRAS WILD-TYPE 194 2 1
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
NRAS MUTATED 1 0 17
NRAS WILD-TYPE 2 9 177
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S27.  Gene #3: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
NRAS MUTATED 0 0 18
NRAS WILD-TYPE 8 2 178
'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 2.84e-06 (Fisher's exact test), Q value = 0.00059

Table S28.  Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
BRAF MUTATED 13 1 1 5
BRAF WILD-TYPE 29 56 66 34

Figure S9.  Get High-res Image Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.41e-07 (Fisher's exact test), Q value = 3e-05

Table S29.  Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
BRAF MUTATED 1 0 18 1
BRAF WILD-TYPE 39 48 43 55

Figure S10.  Get High-res Image Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000332 (Fisher's exact test), Q value = 0.068

Table S30.  Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
BRAF MUTATED 1 18 3 0
BRAF WILD-TYPE 68 67 59 4

Figure S11.  Get High-res Image Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S31.  Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
BRAF MUTATED 3 4 4 2
BRAF WILD-TYPE 37 63 20 24
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
BRAF MUTATED 1 8 2 2
BRAF WILD-TYPE 19 101 17 7
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.473 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
BRAF MUTATED 1 4 0 17
BRAF WILD-TYPE 7 22 13 152
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
BRAF MUTATED 21 1 0
BRAF WILD-TYPE 192 1 1
'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S35.  Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
BRAF MUTATED 0 1 21
BRAF WILD-TYPE 3 8 173
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.684 (Fisher's exact test), Q value = 1

Table S36.  Gene #4: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
BRAF MUTATED 0 0 22
BRAF WILD-TYPE 8 2 174
'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 7.86e-05 (Fisher's exact test), Q value = 0.016

Table S37.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
KRAS MUTATED 13 14 31 27
KRAS WILD-TYPE 29 43 36 12

Figure S12.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 4.23e-05 (Fisher's exact test), Q value = 0.0088

Table S38.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
KRAS MUTATED 10 33 26 16
KRAS WILD-TYPE 30 15 35 40

Figure S13.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

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

Table S39.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
KRAS MUTATED 25 40 27 3
KRAS WILD-TYPE 44 45 35 1
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 2 1
KRAS MUTATED 1 2 0
KRAS WILD-TYPE 4 0 1
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S41.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
KRAS MUTATED 16 34 9 13
KRAS WILD-TYPE 24 33 15 13
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S42.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
KRAS MUTATED 9 50 9 4
KRAS WILD-TYPE 11 59 10 5
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.33

Table S43.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
KRAS MUTATED 4 19 2 66
KRAS WILD-TYPE 4 7 11 103

Figure S14.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.716 (Fisher's exact test), Q value = 1

Table S44.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
KRAS MUTATED 89 1 1
KRAS WILD-TYPE 124 1 0
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 1

Table S45.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
KRAS MUTATED 0 7 79
KRAS WILD-TYPE 3 2 115

Figure S15.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S46.  Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
KRAS MUTATED 1 2 83
KRAS WILD-TYPE 7 0 113

Figure S16.  Get High-res Image Gene #5: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.41

Table S47.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
TP53 MUTATED 17 40 39 14
TP53 WILD-TYPE 25 17 28 25

Figure S17.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000493 (Fisher's exact test), Q value = 0.1

Table S48.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
TP53 MUTATED 30 19 25 36
TP53 WILD-TYPE 10 29 36 20

Figure S18.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.15e-10 (Fisher's exact test), Q value = 2.4e-08

Table S49.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
TP53 MUTATED 55 23 38 1
TP53 WILD-TYPE 14 62 24 3

Figure S19.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S50.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
TP53 MUTATED 18 34 15 12
TP53 WILD-TYPE 22 33 9 14
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
TP53 MUTATED 8 57 9 5
TP53 WILD-TYPE 12 52 10 4
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 1

Table S52.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
TP53 MUTATED 3 7 8 96
TP53 WILD-TYPE 5 19 5 73

Figure S20.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.736 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
TP53 MUTATED 113 1 0
TP53 WILD-TYPE 100 1 1
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
TP53 MUTATED 3 2 106
TP53 WILD-TYPE 0 7 88

Figure S21.  Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S55.  Gene #6: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
TP53 MUTATED 6 1 104
TP53 WILD-TYPE 2 1 92
'SMAD4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
SMAD4 MUTATED 7 4 4 9
SMAD4 WILD-TYPE 35 53 63 30

Figure S22.  Get High-res Image Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'SMAD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 1

Table S57.  Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
SMAD4 MUTATED 5 6 10 3
SMAD4 WILD-TYPE 35 42 51 53
'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0646 (Fisher's exact test), Q value = 1

Table S58.  Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
SMAD4 MUTATED 3 15 8 0
SMAD4 WILD-TYPE 66 70 54 4
'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S59.  Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
SMAD4 MUTATED 4 10 4 3
SMAD4 WILD-TYPE 36 57 20 23
'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 1

Table S60.  Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
SMAD4 MUTATED 2 14 2 3
SMAD4 WILD-TYPE 18 95 17 6
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
SMAD4 MUTATED 1 4 0 20
SMAD4 WILD-TYPE 7 22 13 149
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S62.  Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
SMAD4 MUTATED 25 0 0
SMAD4 WILD-TYPE 188 2 1
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S63.  Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
SMAD4 MUTATED 0 1 24
SMAD4 WILD-TYPE 3 8 170
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S64.  Gene #7: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
SMAD4 MUTATED 1 0 24
SMAD4 WILD-TYPE 7 2 172
'FAM123B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0787 (Fisher's exact test), Q value = 1

Table S65.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
FAM123B MUTATED 9 5 4 6
FAM123B WILD-TYPE 33 52 63 33
'FAM123B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0924 (Fisher's exact test), Q value = 1

Table S66.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
FAM123B MUTATED 2 3 12 7
FAM123B WILD-TYPE 38 45 49 49
'FAM123B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00912 (Fisher's exact test), Q value = 1

Table S67.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
FAM123B MUTATED 5 17 2 0
FAM123B WILD-TYPE 64 68 60 4

Figure S23.  Get High-res Image Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FAM123B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 1

Table S68.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
FAM123B MUTATED 2 7 2 5
FAM123B WILD-TYPE 38 60 22 21
'FAM123B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S69.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
FAM123B MUTATED 1 12 3 0
FAM123B WILD-TYPE 19 97 16 9
'FAM123B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 1

Table S70.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
FAM123B MUTATED 1 7 0 17
FAM123B WILD-TYPE 7 19 13 152

Figure S24.  Get High-res Image Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FAM123B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S71.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
FAM123B MUTATED 25 0 0
FAM123B WILD-TYPE 188 2 1
'FAM123B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S72.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
FAM123B MUTATED 0 1 23
FAM123B WILD-TYPE 3 8 171
'FAM123B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S73.  Gene #8: 'FAM123B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
FAM123B MUTATED 1 0 23
FAM123B WILD-TYPE 7 2 173
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S74.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PIK3CA MUTATED 8 4 7 7
PIK3CA WILD-TYPE 34 53 60 32
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.569 (Fisher's exact test), Q value = 1

Table S75.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
PIK3CA MUTATED 3 7 10 6
PIK3CA WILD-TYPE 37 41 51 50
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.066

Table S76.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
PIK3CA MUTATED 4 23 4 1
PIK3CA WILD-TYPE 65 62 58 3

Figure S25.  Get High-res Image Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 1

Table S77.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
PIK3CA MUTATED 11 9 1 6
PIK3CA WILD-TYPE 29 58 23 20
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 1

Table S78.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
PIK3CA MUTATED 6 16 5 0
PIK3CA WILD-TYPE 14 93 14 9
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0826 (Fisher's exact test), Q value = 1

Table S79.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
PIK3CA MUTATED 2 7 0 23
PIK3CA WILD-TYPE 6 19 13 146
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S80.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
PIK3CA MUTATED 32 0 0
PIK3CA WILD-TYPE 181 2 1
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 1

Table S81.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PIK3CA MUTATED 0 3 26
PIK3CA WILD-TYPE 3 6 168
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S82.  Gene #9: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
PIK3CA MUTATED 1 0 28
PIK3CA WILD-TYPE 7 2 168
'SMAD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S83.  Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
SMAD2 MUTATED 4 2 2 5
SMAD2 WILD-TYPE 38 55 65 34
'SMAD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S84.  Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
SMAD2 MUTATED 3 2 6 2
SMAD2 WILD-TYPE 37 46 55 54
'SMAD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 1

Table S85.  Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
SMAD2 MUTATED 2 10 3 0
SMAD2 WILD-TYPE 67 75 59 4
'SMAD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 1

Table S86.  Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
SMAD2 MUTATED 2 3 2 3
SMAD2 WILD-TYPE 38 64 22 23
'SMAD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 1

Table S87.  Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
SMAD2 MUTATED 0 6 3 1
SMAD2 WILD-TYPE 20 103 16 8
'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S88.  Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
SMAD2 MUTATED 0 3 0 12
SMAD2 WILD-TYPE 8 23 13 157
'SMAD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S89.  Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
SMAD2 MUTATED 15 0 0
SMAD2 WILD-TYPE 198 2 1
'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S90.  Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
SMAD2 MUTATED 0 0 14
SMAD2 WILD-TYPE 3 9 180
'SMAD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S91.  Gene #10: 'SMAD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
SMAD2 MUTATED 0 0 14
SMAD2 WILD-TYPE 8 2 182
'TCF7L2 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S92.  Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
TCF7L2 MUTATED 3 4 5 3
TCF7L2 WILD-TYPE 39 53 62 36
'TCF7L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.416 (Fisher's exact test), Q value = 1

Table S93.  Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
TCF7L2 MUTATED 4 5 2 4
TCF7L2 WILD-TYPE 36 43 59 52
'TCF7L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.48

Table S94.  Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
TCF7L2 MUTATED 7 6 2 3
TCF7L2 WILD-TYPE 62 79 60 1

Figure S26.  Get High-res Image Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TCF7L2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S95.  Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
TCF7L2 MUTATED 3 5 1 3
TCF7L2 WILD-TYPE 37 62 23 23
'TCF7L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.896 (Fisher's exact test), Q value = 1

Table S96.  Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
TCF7L2 MUTATED 1 9 2 0
TCF7L2 WILD-TYPE 19 100 17 9
'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 1

Table S97.  Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
TCF7L2 MUTATED 0 0 1 16
TCF7L2 WILD-TYPE 8 26 12 153
'TCF7L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S98.  Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
TCF7L2 MUTATED 17 0 0
TCF7L2 WILD-TYPE 196 2 1
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S99.  Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
TCF7L2 MUTATED 0 0 15
TCF7L2 WILD-TYPE 3 9 179
'TCF7L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S100.  Gene #11: 'TCF7L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
TCF7L2 MUTATED 0 0 15
TCF7L2 WILD-TYPE 8 2 181
'ACVR2A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00717 (Fisher's exact test), Q value = 1

Table S101.  Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ACVR2A MUTATED 5 1 0 2
ACVR2A WILD-TYPE 37 56 67 37

Figure S27.  Get High-res Image Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'ACVR2A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S102.  Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
ACVR2A MUTATED 1 0 5 2
ACVR2A WILD-TYPE 39 48 56 54
'ACVR2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 1

Table S103.  Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
ACVR2A MUTATED 1 8 0 0
ACVR2A WILD-TYPE 68 77 62 4

Figure S28.  Get High-res Image Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ACVR2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0952 (Fisher's exact test), Q value = 1

Table S104.  Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ACVR2A MUTATED 0 4 0 3
ACVR2A WILD-TYPE 40 63 24 23
'ACVR2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S105.  Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
ACVR2A MUTATED 0 5 2 0
ACVR2A WILD-TYPE 20 104 17 9
'ACVR2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S106.  Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
ACVR2A MUTATED 0 1 0 8
ACVR2A WILD-TYPE 8 25 13 161
'ACVR2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S107.  Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
ACVR2A MUTATED 9 0 0
ACVR2A WILD-TYPE 204 2 1
'ACVR2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 1

Table S108.  Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ACVR2A MUTATED 1 0 8
ACVR2A WILD-TYPE 2 9 186
'ACVR2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S109.  Gene #12: 'ACVR2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
ACVR2A MUTATED 0 0 9
ACVR2A WILD-TYPE 8 2 187
'SOX9 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 1

Table S110.  Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
SOX9 MUTATED 2 1 6 0
SOX9 WILD-TYPE 40 56 61 39
'SOX9 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 1

Table S111.  Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
SOX9 MUTATED 2 5 1 1
SOX9 WILD-TYPE 38 43 60 55
'SOX9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 1

Table S112.  Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
SOX9 MUTATED 0 9 1 0
SOX9 WILD-TYPE 69 76 61 4

Figure S29.  Get High-res Image Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SOX9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 1

Table S113.  Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
SOX9 MUTATED 0 3 0 2
SOX9 WILD-TYPE 40 64 24 24
'SOX9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S114.  Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
SOX9 MUTATED 0 4 1 0
SOX9 WILD-TYPE 20 105 18 9
'SOX9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S115.  Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
SOX9 MUTATED 0 2 0 8
SOX9 WILD-TYPE 8 24 13 161
'SOX9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S116.  Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
SOX9 MUTATED 10 0 0
SOX9 WILD-TYPE 203 2 1
'SOX9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S117.  Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
SOX9 MUTATED 0 0 10
SOX9 WILD-TYPE 3 9 184
'SOX9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118.  Gene #13: 'SOX9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
SOX9 MUTATED 0 0 10
SOX9 WILD-TYPE 8 2 186
'ELF3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 1

Table S119.  Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ELF3 MUTATED 1 0 3 2
ELF3 WILD-TYPE 41 57 64 37
'ELF3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S120.  Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
ELF3 MUTATED 2 1 2 1
ELF3 WILD-TYPE 38 47 59 55
'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 1

Table S121.  Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
ELF3 MUTATED 0 3 3 0
ELF3 WILD-TYPE 69 82 59 4
'ELF3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S122.  Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ELF3 MUTATED 2 1 0 1
ELF3 WILD-TYPE 38 66 24 25
'ELF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S123.  Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
ELF3 MUTATED 1 2 1 0
ELF3 WILD-TYPE 19 107 18 9
'ELF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 1

Table S124.  Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
ELF3 MUTATED 1 2 0 2
ELF3 WILD-TYPE 7 24 13 167

Figure S30.  Get High-res Image Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S125.  Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
ELF3 MUTATED 5 0 0
ELF3 WILD-TYPE 208 2 1
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S126.  Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ELF3 MUTATED 0 0 6
ELF3 WILD-TYPE 3 9 188
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S127.  Gene #14: 'ELF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
ELF3 MUTATED 0 0 6
ELF3 WILD-TYPE 8 2 190
'CRTC1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 1

Table S128.  Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
CRTC1 MUTATED 2 0 4 0
CRTC1 WILD-TYPE 40 57 63 39
'CRTC1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.165 (Fisher's exact test), Q value = 1

Table S129.  Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
CRTC1 MUTATED 3 1 2 0
CRTC1 WILD-TYPE 37 47 59 56
'CRTC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 1

Table S130.  Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
CRTC1 MUTATED 0 3 3 0
CRTC1 WILD-TYPE 69 82 59 4
'CRTC1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S131.  Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
CRTC1 MUTATED 2 0 0 1
CRTC1 WILD-TYPE 38 67 24 25
'CRTC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S132.  Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
CRTC1 MUTATED 0 2 1 0
CRTC1 WILD-TYPE 20 107 18 9
'CRTC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S133.  Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
CRTC1 MUTATED 0 1 0 5
CRTC1 WILD-TYPE 8 25 13 164
'CRTC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S134.  Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
CRTC1 MUTATED 6 0 0
CRTC1 WILD-TYPE 207 2 1
'CRTC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S135.  Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
CRTC1 MUTATED 0 0 6
CRTC1 WILD-TYPE 3 9 188
'CRTC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S136.  Gene #15: 'CRTC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
CRTC1 MUTATED 0 0 6
CRTC1 WILD-TYPE 8 2 190
'TNFRSF10C MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S137.  Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
TNFRSF10C MUTATED 3 1 2 0
TNFRSF10C WILD-TYPE 39 56 65 39
'TNFRSF10C MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S138.  Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
TNFRSF10C MUTATED 1 3 2 0
TNFRSF10C WILD-TYPE 39 45 59 56
'TNFRSF10C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.707 (Fisher's exact test), Q value = 1

Table S139.  Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
TNFRSF10C MUTATED 3 2 1 0
TNFRSF10C WILD-TYPE 66 83 61 4
'TNFRSF10C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S140.  Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
TNFRSF10C MUTATED 3 1 0 1
TNFRSF10C WILD-TYPE 37 66 24 25
'TNFRSF10C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S141.  Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
TNFRSF10C MUTATED 2 3 0 0
TNFRSF10C WILD-TYPE 18 106 19 9
'TNFRSF10C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 1

Table S142.  Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
TNFRSF10C MUTATED 1 1 0 4
TNFRSF10C WILD-TYPE 7 25 13 165
'TNFRSF10C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S143.  Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
TNFRSF10C MUTATED 6 0 0
TNFRSF10C WILD-TYPE 207 2 1
'TNFRSF10C MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S144.  Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
TNFRSF10C MUTATED 0 0 6
TNFRSF10C WILD-TYPE 3 9 188
'TNFRSF10C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S145.  Gene #16: 'TNFRSF10C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
TNFRSF10C MUTATED 0 0 6
TNFRSF10C WILD-TYPE 8 2 190
'KIAA1804 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 1

Table S146.  Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
KIAA1804 MUTATED 3 1 6 4
KIAA1804 WILD-TYPE 39 56 61 35
'KIAA1804 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S147.  Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
KIAA1804 MUTATED 4 2 6 2
KIAA1804 WILD-TYPE 36 46 55 54
'KIAA1804 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 1

Table S148.  Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
KIAA1804 MUTATED 3 10 1 1
KIAA1804 WILD-TYPE 66 75 61 3

Figure S31.  Get High-res Image Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KIAA1804 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 1

Table S149.  Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
KIAA1804 MUTATED 2 6 1 4
KIAA1804 WILD-TYPE 38 61 23 22
'KIAA1804 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.474 (Fisher's exact test), Q value = 1

Table S150.  Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
KIAA1804 MUTATED 0 11 2 0
KIAA1804 WILD-TYPE 20 98 17 9
'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S151.  Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
KIAA1804 MUTATED 0 3 0 12
KIAA1804 WILD-TYPE 8 23 13 157
'KIAA1804 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S152.  Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
KIAA1804 MUTATED 15 0 0
KIAA1804 WILD-TYPE 198 2 1
'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S153.  Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
KIAA1804 MUTATED 0 0 15
KIAA1804 WILD-TYPE 3 9 179
'KIAA1804 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S154.  Gene #17: 'KIAA1804 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
KIAA1804 MUTATED 0 0 15
KIAA1804 WILD-TYPE 8 2 181
'KRTAP5-5 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S155.  Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
KRTAP5-5 MUTATED 1 0 3 0
KRTAP5-5 WILD-TYPE 41 57 64 39
'KRTAP5-5 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S156.  Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
KRTAP5-5 MUTATED 1 2 1 0
KRTAP5-5 WILD-TYPE 39 46 60 56
'KRTAP5-5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S157.  Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
KRTAP5-5 MUTATED 2 1 1 0
KRTAP5-5 WILD-TYPE 67 84 61 4
'KRTAP5-5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S158.  Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
KRTAP5-5 MUTATED 0 3 1 0
KRTAP5-5 WILD-TYPE 40 64 23 26
'KRTAP5-5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S159.  Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
KRTAP5-5 MUTATED 0 4 0 0
KRTAP5-5 WILD-TYPE 20 105 19 9
'KRTAP5-5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S160.  Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
KRTAP5-5 MUTATED 0 0 0 4
KRTAP5-5 WILD-TYPE 8 26 13 165
'KRTAP5-5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S161.  Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
KRTAP5-5 MUTATED 4 0 0
KRTAP5-5 WILD-TYPE 209 2 1
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S162.  Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
KRTAP5-5 MUTATED 0 0 3
KRTAP5-5 WILD-TYPE 3 9 191
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S163.  Gene #18: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
KRTAP5-5 MUTATED 0 0 3
KRTAP5-5 WILD-TYPE 8 2 193
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 1

Table S164.  Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PTEN MUTATED 2 0 1 4
PTEN WILD-TYPE 40 57 66 35

Figure S32.  Get High-res Image Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 1

Table S165.  Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
PTEN MUTATED 1 0 4 2
PTEN WILD-TYPE 39 48 57 54
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.07 (Fisher's exact test), Q value = 1

Table S166.  Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
PTEN MUTATED 0 6 1 0
PTEN WILD-TYPE 69 79 61 4
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S167.  Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
PTEN MUTATED 2 1 0 1
PTEN WILD-TYPE 38 66 24 25
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S168.  Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
PTEN MUTATED 1 2 1 0
PTEN WILD-TYPE 19 107 18 9
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 1

Table S169.  Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
PTEN MUTATED 1 2 0 4
PTEN WILD-TYPE 7 24 13 165
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S170.  Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
PTEN MUTATED 7 0 0
PTEN WILD-TYPE 206 2 1
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S171.  Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PTEN MUTATED 0 1 6
PTEN WILD-TYPE 3 8 188
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 1

Table S172.  Gene #19: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
PTEN MUTATED 1 0 6
PTEN WILD-TYPE 7 2 190
'ACOT4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 1

Table S173.  Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ACOT4 MUTATED 2 0 1 0
ACOT4 WILD-TYPE 40 57 66 39
'ACOT4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S174.  Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
ACOT4 MUTATED 0 1 2 0
ACOT4 WILD-TYPE 40 47 59 56
'ACOT4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S175.  Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
ACOT4 MUTATED 1 2 0 0
ACOT4 WILD-TYPE 68 83 62 4
'ACOT4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 1

Table S176.  Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
ACOT4 MUTATED 0 1 0 2
ACOT4 WILD-TYPE 8 25 13 167
'ACOT4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S177.  Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
ACOT4 MUTATED 3 0 0
ACOT4 WILD-TYPE 210 2 1
'ACOT4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S178.  Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ACOT4 MUTATED 0 0 3
ACOT4 WILD-TYPE 3 9 191
'ACOT4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S179.  Gene #20: 'ACOT4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
ACOT4 MUTATED 0 0 3
ACOT4 WILD-TYPE 8 2 193
'MYO1B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00868 (Fisher's exact test), Q value = 1

Table S180.  Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
MYO1B MUTATED 6 1 1 4
MYO1B WILD-TYPE 36 56 66 35

Figure S33.  Get High-res Image Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'MYO1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00887 (Fisher's exact test), Q value = 1

Table S181.  Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
MYO1B MUTATED 3 0 8 1
MYO1B WILD-TYPE 37 48 53 55

Figure S34.  Get High-res Image Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'MYO1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00479 (Fisher's exact test), Q value = 0.95

Table S182.  Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
MYO1B MUTATED 2 11 0 0
MYO1B WILD-TYPE 67 74 62 4

Figure S35.  Get High-res Image Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MYO1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 1

Table S183.  Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
MYO1B MUTATED 3 0 1 3
MYO1B WILD-TYPE 37 67 23 23

Figure S36.  Get High-res Image Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MYO1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S184.  Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
MYO1B MUTATED 0 5 2 0
MYO1B WILD-TYPE 20 104 17 9
'MYO1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S185.  Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
MYO1B MUTATED 0 4 0 8
MYO1B WILD-TYPE 8 22 13 161
'MYO1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S186.  Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
MYO1B MUTATED 12 0 0
MYO1B WILD-TYPE 201 2 1
'MYO1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S187.  Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
MYO1B MUTATED 0 0 12
MYO1B WILD-TYPE 3 9 182
'MYO1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S188.  Gene #21: 'MYO1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
MYO1B MUTATED 0 0 12
MYO1B WILD-TYPE 8 2 184
'PCBP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 1

Table S189.  Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
PCBP1 MUTATED 0 1 2 3
PCBP1 WILD-TYPE 42 56 65 36
'PCBP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S190.  Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
PCBP1 MUTATED 2 1 2 1
PCBP1 WILD-TYPE 38 47 59 55
'PCBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S191.  Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
PCBP1 MUTATED 1 3 2 0
PCBP1 WILD-TYPE 68 82 60 4
'PCBP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S192.  Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
PCBP1 MUTATED 0 2 0 1
PCBP1 WILD-TYPE 40 65 24 25
'PCBP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S193.  Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
PCBP1 MUTATED 0 2 1 0
PCBP1 WILD-TYPE 20 107 18 9
'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S194.  Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
PCBP1 MUTATED 0 0 0 6
PCBP1 WILD-TYPE 8 26 13 163
'PCBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S195.  Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
PCBP1 MUTATED 6 0 0
PCBP1 WILD-TYPE 207 2 1
'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S196.  Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
PCBP1 MUTATED 0 0 5
PCBP1 WILD-TYPE 3 9 189
'PCBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S197.  Gene #22: 'PCBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
PCBP1 MUTATED 0 0 5
PCBP1 WILD-TYPE 8 2 191
'GGT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S198.  Gene #23: 'GGT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
GGT1 MUTATED 0 3 0 0
GGT1 WILD-TYPE 69 82 62 4
'GGT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 1

Table S199.  Gene #23: 'GGT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
GGT1 MUTATED 0 1 0 2
GGT1 WILD-TYPE 8 25 13 167
'GGT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S200.  Gene #23: 'GGT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
GGT1 MUTATED 3 0 0
GGT1 WILD-TYPE 210 2 1
'GGT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S201.  Gene #23: 'GGT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
GGT1 MUTATED 0 0 3
GGT1 WILD-TYPE 3 9 191
'GGT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S202.  Gene #23: 'GGT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
GGT1 MUTATED 0 0 3
GGT1 WILD-TYPE 8 2 193
'ACVR1B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 1

Table S203.  Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 57 67 39
ACVR1B MUTATED 3 2 2 4
ACVR1B WILD-TYPE 39 55 65 35
'ACVR1B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 1

Table S204.  Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 48 61 56
ACVR1B MUTATED 0 3 5 3
ACVR1B WILD-TYPE 40 45 56 53
'ACVR1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0986 (Fisher's exact test), Q value = 1

Table S205.  Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 85 62 4
ACVR1B MUTATED 2 10 2 0
ACVR1B WILD-TYPE 67 75 60 4
'ACVR1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.735 (Fisher's exact test), Q value = 1

Table S206.  Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 40 67 24 26
ACVR1B MUTATED 2 5 1 3
ACVR1B WILD-TYPE 38 62 23 23
'ACVR1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S207.  Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 20 109 19 9
ACVR1B MUTATED 1 7 3 0
ACVR1B WILD-TYPE 19 102 16 9
'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S208.  Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 8 26 13 169
ACVR1B MUTATED 0 2 1 11
ACVR1B WILD-TYPE 8 24 12 158
'ACVR1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S209.  Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 213 2 1
ACVR1B MUTATED 14 0 0
ACVR1B WILD-TYPE 199 2 1
'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S210.  Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 3 9 194
ACVR1B MUTATED 0 1 13
ACVR1B WILD-TYPE 3 8 181
'ACVR1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S211.  Gene #24: 'ACVR1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 8 2 196
ACVR1B MUTATED 0 0 14
ACVR1B WILD-TYPE 8 2 182
Methods & Data
Input

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

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

  • Number of patients = 223

  • Number of significantly mutated genes = 24

  • 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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